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Sample records for access microbial diversity

  1. Environmental Whole-Genome Amplification to Access Microbial Diversity in Contaminated Sediments

    Abulencia, C.B.; Wyborski, D.L.; Garcia, J.; Podar, M.; Chen, W.; Chang, S.H.; Chang, H.W.; Watson, D.; Brodie,E.I.; Hazen, T.C.; Keller, M.

    2005-12-10

    Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using ?29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2 percent genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9 percent of the sequences had significant similarities to known proteins, and ''clusters of orthologous groups'' (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible.

  2. Microbial diversity of marine sponges.

    Hentschel, U; Fieseler, L; Wehrl, M; Gernert, C; Steinert, M; Hacker, J; Horn, M

    2003-01-01

    The recent application of molecular microbial ecology tools to sponge-microbe associations has revealed a glimpse into the biodiversity of these microbial communities, that is considered just 'the tip of the iceberg'. This chapter provides an overview over these new findings with regard to identity, diversity and distribution patterns of sponge-associated microbial consortia. The sponges Aplysina aerophoba (Verongida), Rhopaloeides odorabile (Dicytoceratida) and Theonella swinhoei (Lithistida) were chosen as model systems for this review because they have been subject to both, cultivation-dependent and cultivation-independent approaches. A discussion of the microbial assemblages of Halichondriapanicea is presented in the accompanying chapter by Imhoff and Stöhr. Considering that a large fraction of sponge-associated microbes is not yet amenable to cultivation, an emphasis has been placed on the techniques centering around the 16S rRNA gene. A section has been included that covers the potential of sponge microbial communities for drug discovery. Finally, a 'sponge-microbe interaction model' is presented that summarizes our current understanding of the processes that might have shaped the community structure of the microbial assemblages within sponges. PMID:15825640

  3. Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

    Hurt, Jr., Richard Ashley [ORNL; Moberly, James G [ORNL; Shakya, Migun [ORNL; Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Elias, Dwayne A [ORNL

    2014-01-01

    Despite more than three decades of progress, efficient nucleic acid extraction from microbial communities has remained difficult, particularly from clay environments. Lysis with concentrated guanidine followed by concentrated sodium phosphate extraction supported DNA and RNA recovery from high iron, low humus content clay. Alterating the extraction pH or using other ionic solutions (Na2SO4 and NH4H2PO4) yielded no detectable nucleic acid. DNA recovered using a lysis solution with 500 mM phosphate buffer (PB) followed by a 1 M PB wash was 15.22 2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46 0.25 g DNA/g clay with the Powerlyzer soil DNA system (MoBio). Increasing [PB] in the lysis reagent coincided with increasing DNA fragment length. Rarefaction plots based on16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more bacterial species recovered using this system. Additionally, some OTU s having more than 100 sequences in these libraries were absent in samples extracted using the PowerLyzer reagents or the previous lysis method.

  4. Exploring the Diversity of the Microbial World

    Fischer, Caleb N.

    2011-01-01

    Yale’s Microbial Diversity Institute (MDI) comprises scientists who seek to understand the largely unknown microbial world. In the first MDI symposium at Yale’s West Campus in October 2010, four speakers discussed their research in diverse fields within the microbial sciences. The highlights of the symposium are presented here along with an outlook on the future of the MDI.

  5. Microbial diversity of marine sponges

    Hentschel, Ute

    2004-01-01

    16S rDNA library construction revealed a uniform microbial community in sponges that were collected from different oceans. Altogether 14 monophyletic, sponge-specific sequence clusters were identified that belong to at least seven different bacterial divisions. By definition, the sequences of each cluster are more closely related to each other than to a sequence from non-sponge sources. These monophyletic clusters comprise 70 % of all publicly available, sponge-derived 16S rDNA sequences refl...

  6. Molecular Technique to Understand Deep Microbial Diversity

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  7. The microbial diversity of water kefir.

    Gulitz, Anna; Stadie, Jasmin; Wenning, Mareike; Ehrmann, Matthias A; Vogel, Rudi F

    2011-12-15

    The microbial diversity of water kefir, made from a mixture of water, dried figs, a slice of lemon and sucrose was studied. The microbial consortia residing in the granules of three water kefirs of different origins were analyzed. A collection of 453 bacterial isolates was obtained on different selective/differential media. Bacterial isolates were grouped with randomly amplified polymorphic DNA (RAPD)-PCR analyses. One representative of each RAPD genotype was identified by comparative 16S rDNA gene sequencing. The predominant genus in water kefirs I and II was Lactobacillus, which accounted for 82.1% in water kefir I and 72.1% in water kefir II of the bacterial isolates. The most abundant species in water kefirs I and II were Lactobacillus hordei and Lb. nagelii followed by considerably lower numbers of Lb. casei. Other lactic acid bacteria (LAB) were identified as Leuconostoc mesenteroides and Lc. citreum in all three water kefirs. The most abundant species in water kefir III was Lc. mesenteroides (28%) and Lc. citreum (24.3%). A total of 57 LAB belonging to the species of Lb. casei, Lb. hordei, Lb. nagelii, Lb. hilgardii and Lc. mesenteroides were able to produce exopolysacchrides from sucrose. Non LABs were identified as Acetobacter fabarum and Ac. orientalis. The Acetobacter species were more prevalent in consortium III. Cluster analyses of RAPD-PCR patterns revealed an interspecies diversity among the Lactobacillus and Acetobacter strains. Aditionally, Saccharomyces cerevisiae, Lachancea fermentati, Hanseniaospora valbyensis and Zygotorulaspora florentina were isolated and identified by comparison of partial 26S rDNA sequences and FTIR spectroscopy. PMID:22000549

  8. A Review of Methods for Studying Microbial Diversity in Soils

    LIU Bing-Ru; JIA Guo-Mei; CHEN Jian; WANG Gang

    2006-01-01

    Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients,and in nutrient cycling. Recently, extensive studies have focused on soil microbial diversity. However, understanding the diversity of this complex microbial community in the soil environment is a challenging task. Thus, it is important to master and comprehend appropriate methods for studying soil microbial diversity. Concepts of soil microbial diversity and major methods of study are briefly introduced in this paper. Then, the application of biochemical-based and molecularbased techniques in this area, and their advantages and disadvantages are evaluated. Based on recent related research,perspectives for studying microbial diversity in soils are presented.

  9. AXIOME: automated exploration of microbial diversity

    Lynch, Michael DJ; Andre P Masella; Hall, Michael W; Bartram, Andrea K.; Neufeld, Josh D.

    2013-01-01

    Background Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research. Findings AXIOME streamlin...

  10. Microbial diversity observed during hemp retting.

    Ribeiro, Alexandra; Pochart, Philippe; Day, Arnaud; Mennuni, Sarah; Bono, Pierre; Baret, Jean-Luc; Spadoni, Jean-Louis; Mangin, Irène

    2015-05-01

    Historically used in textile and paper industry, hemp fibres have started to find new applications in composite materials with important economic and ecological advantages. However, their applications are limited since manufacturers have some difficulties to standardise fabrication processes. This study is a first step before selection and isolation of strains that could later be used to optimise microbial retting efficiency and hence fibre quality. We studied six samples harvested on different ground types, at different dates and with different retting durations on field to obtain an exhaustive representation of the process. After DNA extraction, total bacteria and fungi associated with stems during retting were specifically quantified using real-time PCR. Then, using sequence analysis of randomly cloned 16S and 18S ribosomal RNA (rRNA) genes, a phylogenetic characterisation of the dominant microorganisms was carried out. Quantitatively, we showed that there were 8.1-9.5 log₁₀ 16S rRNA gene copies per gram of hemp straw for bacteria and 8.6-9.6 log₁₀ 18S rRNA gene copies per gram for fungi. Qualitatively, we noticed a higher bacterial diversity in comparison to fungi. This work showed that in the different samples, the same species were present but in significantly different proportions according to ground type, harvest dates and retting durations on field. The most frequent bacterial sequences were affiliated to species Escherichia coli, Pantoea agglomerans, Pseudomonas rhizosphaerae, Rhodobacter sp., Pseudomonas fulva, Rhizobium huautlense and Massilia timonae, whereas fungal sequences were principally related to the genera Cladosporium and Cryptococcus. PMID:25575888

  11. Progress of microbial species diversity research in China

    Liangdong Guo

    2012-09-01

    Full Text Available Microbes with rich species and genetic diversity are widely distributed throughout various habitats in the world. China possesses a variety of climate zones, geographic environments, and complex ecosystems, which play a large role shaping the complex biodiversity of this country. Microbial diversity has been widely studied and well documented by Chinese scientists. For example, a total of ca. 14,700 eukaryotic microbe species have been recorded, including ca. 14,060 fungi, ca. 300 oomycetes, and ca. 340 slime molds. Within the Fungi, there have been 473 medicinal fungal species and 966 edible fungal taxa recorded. However, recent studies have documented much high species diversity of prokaryotic microbes using molecular techniques,which have greatly promoted the study level of microbial diversity in China. This review paper summarizes recent research progress of microbial (i.e., archaea, bacteria, fungi, oomycetes, and slime molds diversity in China based on traditional and molecular techniques.

  12. Functional metagenomic screen reveals new and diverse microbial rhodopsins

    Pushkarev, Alina; Béjà, Oded

    2016-01-01

    Ion-translocating retinylidene rhodopsins are widely distributed among marine and freshwater microbes. The translocation is light-driven, contributing to the production of biochemical energy in diverse microbes. Until today, most microbial rhodopsins had been detected using bioinformatics based on homology to other rhodopsins. In the past decade, there has been increased interest in microbial rhodopsins in the field of optogenetics since microbial rhodopsins were found to be most useful in vertebrate neuronal systems. Here we report on a functional metagenomic assay for detecting microbial rhodopsins. Using an array of narrow pH electrodes and light-emitting diode illumination, we were able to screen a metagenomic fosmid library to detect diverse marine proteorhodopsins and an actinorhodopsin based solely on proton-pumping activity. Our assay therefore provides a rather simple phenotypic means to enrich our understanding of microbial rhodopsins without any prior knowledge of the genomic content of the environmental entities screened. PMID:26894445

  13. Integrating microbial diversity in soil carbon dynamic models parameters

    Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

    2015-04-01

    Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

  14. Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

    Andrew, David R.; Fitak, Robert R.; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G.; Dontsova, Katerina

    2012-01-01

    High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our...

  15. Microbial Diversity Aboard Spacecraft: Evaluation of the International Space Station

    Castro, Victoria A.; Thrasher, Adrianna N.; Healy, Mimi; Ott, C. Mark; Pierson, Duane L.

    2003-01-01

    An evaluation of the microbial flora from air, water, and surface samples provided a baseline of microbial diversity onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PeR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and require continued surveillance.

  16. Diversity of wheat anti-microbial peptides.

    Egorov, Tsezi A; Odintsova, Tatyana I; Pukhalsky, Vitaliy A; Grishin, Eugene V

    2005-11-01

    From seeds of Triticum kiharae Dorof. et Migusch., 24 novel anti-microbial peptides were isolated and characterized by a combination of three-step HPLC (affinity, size-exclusion and reversed-phase) with matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and Edman degradation. Based on sequence similarity and cysteine motifs, partially sequenced peptides were assigned to 7 families: defensins, thionins, lipid-transfer proteins, hevein-like peptides, knottin-like peptides, glycine-rich peptides, and MBP-1 homologs. A novel subfamily of defensins consisting of 6 peptides and a new family of glycine-rich (8 peptides with different repeat motifs) were identified. Three 6-cysteine knottin-like peptides represented by N- and C-terminally truncated variants revealed no sequence homology to any known plant anti-microbial peptides. A new 8-cysteine hevein-like peptide and three 4-cysteine peptides homologous to MBP-1 from maize were isolated. This is the first communication on the occurrence of nearly all families of plant anti-microbial peptides in a single species. PMID:16269343

  17. Diversity Generation in Evolving Microbial Populations

    Markussen, Trine

    Organisms have evolved and diversified since the beginning of life. Although, generation and maintenance of diversity within ecosystems has been a central concern in ecology and evolutionary biology, little is known of the evolutionary processes driving diversification. Especially, diversification...... in relation to chronic infection is a major concern as high population diversity has been predicted to result in survival and persistence of the infecting microbe. Therefore, understanding within-host dynamics and population diversification is necessary for optimal diagnosis and therapeutic treatment....... aeruginosa diversity has been documented in contemporary respiratory specimens, it is less clear to what extent within-patient diversity contributes to the overall population structure and whether the population is geographically or homogeneously distributed throughout the airways. The focus of this thesis...

  18. GeoChip as a metagenomics tool to analyze the microbial gene diversity along an elevation gradient

    Ying Gao

    2014-12-01

    Full Text Available To examine microbial responses to climate change, we used a microarray-based metagenomics tool named GeoChip 4.0 to profile soil microbial functional genes along four sites/elevations of a Tibetan mountainous grassland. We found that microbial communities differed among four elevations. Soil pH, temperature, NH4+–N and vegetation diversity were four major attributes affecting soil microbial communities. Here we describe in details the experiment design, the data normalization process, soil and vegetation analyses associated with the study published on ISME Journal in 2014 [1], whose raw data have been uploaded to Gene Expression Omnibus (accession number GSM1185243.

  19. Abundance and diversity of marine microbial eukaryotes

    Pernice, Massimo Ciro

    2014-01-01

    [EN]Microeukaryotes are important ecological players in any kind of ecosystem, most notably in the ocean, and it is therefore essential to collect information about their abundance and diversity. To achieve this general goal this thesis was structured in two parts. The first part represents an effort to define our “diversity unit” from studies based on the well-known cloning and Sanger sequencing approach. Basically, we wanted to establish a solid baseline for the second part of the thesis. W...

  20. Scaling laws predict global microbial diversity.

    Locey, Kenneth J; Lennon, Jay T

    2016-05-24

    Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ∼35,000 sites and ∼5.6⋅10(6) species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we show similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upward of 1 trillion (10(12)) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome. PMID:27140646

  1. Microbial diversity of biological filters in recirculating aquaculture systems.

    Schreier, Harold J; Mirzoyan, Natella; Saito, Keiko

    2010-06-01

    Development of environmentally sustainable farming of marine and freshwater species using recirculating aquaculture systems (RASs) requires a complete understanding of the biological component involved in wastewater treatment. This component integrates biofilters composed of microbial communities whose structure, dynamics, and activities are responsible for system success. Engineering highly efficient, environmentally sound, disease-free, and economically viable systems necessitates a thorough knowledge of microbial processes involved in all facets of RAS biofilters and has only recently been the focus of comprehensive studies. These studies have included the application of molecular tools to characterize community diversity and have identified key processes useful for improving system performance. In this paper we summarize the current understanding of the microbial diversity and physiology of RAS biofilters and discuss directions for future studies. PMID:20371171

  2. Microbial diversity of a high salinity oil field

    Neria, I.; Gales, G.; Alazard, D.; Ollivier, B.; Borgomano, J.; Joulian, C.

    2009-07-01

    This work is a preliminary study to investigate the microbial diversity of an onshore oil field. It aim to compare results obtained from molecular methods, physicochemical analyses and cultivation. A core of 1150 m depth sediments ( in situ T=45 degree centigrade) was collected and immediately frozen with liquid nitrogen prior to further investigation. Macroscopic and Scanning Electron Microscopy analyses were performed. (Author)

  3. Microbial diversity of a high salinity oil field

    This work is a preliminary study to investigate the microbial diversity of an onshore oil field. It aim to compare results obtained from molecular methods, physicochemical analyses and cultivation. A core of 1150 m depth sediments ( in situ T=45 degree centigrade) was collected and immediately frozen with liquid nitrogen prior to further investigation. Macroscopic and Scanning Electron Microscopy analyses were performed. (Author)

  4. Analyses of the microbial diversity across the human microbiome.

    Kelvin Li

    Full Text Available Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ", based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for

  5. Comparison of multivariate microbial datasets with the Shannon index: An example using enzyme activity from diverse marine environments

    Steen, Andrew; Ziervogel, K.; Arnosti, C.

    2010-01-01

    Heterotrophic microbial communities contain substantial functional diversity, so studies of community function often generate multivariate data sets. Techniques for data reduction and analysis can help elucidate qualitative differences among sites from multivariate data sets that may be difficult...... that, in three of four cases, surface water communities accessed substrates at a more even rate than in deeper waters. The technique could usefully be applied to other types of data obtained in studies of microbial activity and the geochemical effects....

  6. Microbial diversity in Brazilian mangrove sediments – a mini review

    Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

    2012-01-01

    The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949

  7. Reaction Progress and the Changing Diversity of Chemolithotrophic Microbial Communities

    Shock, E.; Boyd, E.

    2012-12-01

    Is there a correlation between the abundance and diversity of geochemical energy sources and the diversity of chemolithotrophic microbial communities? The available data are suggestive, but not yet conclusive owing to a general lack of models and sampling strategies that integrate microbial, molecular, and geochemical data from microbially dominated ecosystems. While improvements are being made in sampling and analytical strategies, there is an opportunity to examine the underlying thermodynamic framework and generate hypotheses that can lead to quantitate tests of how reaction progress drives microbial diversity. Such quantitative approaches would allow accurate forecasts of the response of microbial communities, the base of all food webs, to environmental change, and development of strategies to deal with shifts in ecosystem function. As a first order consideration, chemolithotrophs require sources of chemical energy, which are provided by oxidation-reduction (redox) reactions that are far from equilibrium. Larger energy supplies can be expected to support larger populations of microbes unless nutrient supply (e.g., phosphate limitation) or other physiological limitations (e.g., thermal limits) are encountered. In geochemical systems, the magnitudes of disequilibria can be evaluated by quantifying how far from equilibrium individual reactions are. As reactions progress, fluctuations in disequilibria can be monitored by explicitly assessing values of reaction-progress variables. Such approaches are commonly used to develop dynamic models of weathering, diagenesis, hydrothermal alteration, and other geochemical processes involving mass transfer. The same framework applied to overall reactions capable of supporting chemolithotrophic populations enables dynamic predictions of changes in the predominant metabolic strategies capable of supporting microbial communities during geochemical processes. These predictions are not limited to changes in microbial biomass and

  8. Microbial diversity in restored wetlands of San Francisco Bay

    Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

    2013-12-09

    Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils, we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.

  9. Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity

    Tripathi, Binu M.; Song, Woojin; Slik, J.W.F.; Sukri, Rahayu S.; Jaafar, Salwana; Dong, Ke; Adams, Jonathan M

    2016-01-01

    There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland h...

  10. Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity.

    Tripathi, Binu M; Song, Woojin; Slik, J W F; Sukri, Rahayu S; Jaafar, Salwana; Dong, Ke; Adams, Jonathan M

    2016-01-01

    There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests) due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM) fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity. PMID:27092105

  11. Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

    Binu M Tripathi

    2016-04-01

    Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

  12. Diverse microbial species survive high ammonia concentrations

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  13. Highly specialized microbial diversity in hyper-arid polar desert

    Pointing, Stephen B.; Chan, Yuki; Lacap, Donnabella C.; Lau, Maggie C. Y.; Jurgens, Joel A.; Farrell, Roberta L.

    2009-01-01

    The McMurdo Dry Valleys in Antarctica are a cold hyperarid polar desert that present extreme challenges to life. Here, we report a culture-independent survey of multidomain microbial biodiversity in McKelvey Valley, a pristine example of the coldest desert on Earth. We demonstrate that life has adapted to form highly-specialized communities in distinct lithic niches occurring concomitantly within this terrain. Endoliths and chasmoliths in sandstone displayed greatest diversity, whereas soil w...

  14. Approaches to microbial diversity analysis in contaminated environments

    Uhlík, O.; Leewis, M. C.; Kurzawová, V.; Lovecká, P.; Štursa, P.; Demnerová, K.; Macková, M.; Macek, Tomáš

    Kerala: Research Signpost, 2010 - (Plaza, G.), s. 55-71 ISBN 978-81-308-0424-8 Grant ostatní: GA MŠk(CZ) ME09024; GA ČR(CZ) GA525/09/1058; GA MŠk(CZ) 2B08031 Institutional research plan: CEZ:AV0Z40550506 Keywords : microbial diversity * contaminated soil * rhizoremediation * phytoremediation Subject RIV: EI - Biotechnology ; Bionics

  15. Microbial community diversity associated with moonmilk deposits in a karstic cave system in Ireland

    Rooney, D.; Hutchens, E.; Clipson, Nick; McDermott, Frank

    2009-04-01

    Microbial ecology in subterranean systems has yet to be fully studied. Cave systems present highly unusual and extreme habitats, where microbial activity can potentially play a major role in nutrient cycling and possibly contribute to the formation of characteristic subaerial structures. How microorganisms actually function in cave systems, and what ecological roles they may perform, has yet to be widely addressed, although recent studies using molecular techniques combined with analytical geochemistry have begun to answer some questions surrounding subterranean microbial ecology (Northup et al., 2003). Moonmilk has a ‘cottage-cheese' like consistency, comprised of fine crystal aggregates of carbonate minerals, commonly calcite, hydromagnesite and gypsum, and is believed to be at least partially precipitated by microbial activity (Baskar et al., 2006). Microbial metabolic processes have been implicated in the formation of moonmilk, probably a result of biochemical corrosion of bedrock under high moisture conditions. Mineral weathering via bacterial activity has become accepted as a major influence on subsurface geochemistry and formation of belowground structures (Summers-Engel et al., 2004). While many studies focus on bacterial communities in subterranean systems, fungal community structure is also likely to be important in cave systems, given the important role fungi play in the transformations of organic and inorganic substrates (Gadd, 2004) and the significant role of fungi in mineral dissolution and secondary mineral formation (Burford et al., 2003). In general, it is agreed that both biotic and abiotic processes influence moonmilk formation, yet the diversity of the microbial community associated with moonmilk formations has not been characterised to date. Ballinamintra Cave (Waterford County, Ireland) is largely protected from human influence due to accessibility difficulties and thereby offers an opportunity to study microbial community structure that

  16. Contribution of microbial carbon to soil fractions: significance of diverse microbial group biochemistry

    Throckmorton, H.; Bird, J. A.; Dane, L.; Firestone, M. K.; Horwath, W. R.

    2011-12-01

    The importance of diverse microbial groups to soil C maintenance is still a matter of debate. This study follows the turnover of 13C labeled nonliving residues from diverse microbial groups into soil physical fractions in situ in a temperate forest in California (CA) and a tropical forest in Puerto Rico (PR), during 5 sampling points per site- over a 3 and 2 year period, respectively. Microbial groups include fungi, actinomycetes, Gm(+) bacteria, and Gm(-) bacteria, isolated from CA and PR soils to obtain temperate and tropical isolates composited of 3-4 species per group. The selected density fractionation approach isolated: a "light fraction" (LF), non-mineral aggregate "occluded fraction" (OF), and a "mineral bound fraction" (MF). Pyrolysis gas chromatography mass spectrometry (Py-GC-MS) was employed to characterize microbial group isolates, whole soils, and fractions. Microbial isolates contained unique biochemical fingerprints: temperate and tropical fungi and tropical Gm(-) were characterized by a low abundance of phenol, benzene, and N-compounds compared with other microbial group isolates. Py-GC-MS revealed compositional differences among soil fractions at both sites, likely attributed to differences in the decomposition stage and C source material (ie. plant vs. microbial). For both sites, benzene and N-compounds were greatest in the MF; lignin and phenol compounds were greatest in the LF; and lipids were greatest in the OF. The trend for polysaccharides differed between sites, with the greatest concentration in the CA OF; and for PR with the lowest concentration in the OF, and similar concentrations in the LF and MF. SOM chemistry was most similar between sites in the LF, compared with the OF and MF, suggesting that differences in SOM chemistry between sites may be more attributed to differential decomposition processes than unique litter quality inputs. A substantial portion of microbial C moved from the LF into the OF, and the MF by the first sampling

  17. Mineralogical Control on Microbial Diversity in a Weathered Granite?

    Gleeson, D.; Clipson, N.; McDermott, F.

    2003-12-01

    Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

  18. Ecological parameters influencing microbial diversity and stability of traditional sourdough.

    Minervini, Fabio; De Angelis, Maria; Di Cagno, Raffaella; Gobbetti, Marco

    2014-02-01

    The quality of some leavened, sourdough baked goods is not always consistent, unless a well propagated sourdough starter culture is used for the dough fermentation. Among the different types of sourdough used, the traditional sourdough has attracted the interest of researchers, mainly because of its large microbial diversity, especially with respect to lactic acid bacteria. Variation in this diversity and the factors that cause it will impact on quality and is the subject of this review. Sourdough microbial diversity is mainly caused by the following factors: (i) sourdough is obtained through spontaneous, multi-step fermentation; (ii) it is propagated using flour, whose nutrient content may vary according to the batch and to the crop, and which is naturally contaminated by microorganisms; and (iii) it is propagated under peculiar technological parameters, which vary depending on the historical and cultural background and type of baked good. In the population dynamics leading from flour to mature sourdough, lactic acid bacteria (several species of Lactobacillus sp., Leuconostoc sp., and Weissella sp.) and yeasts (mainly Saccharomyces cerevisiae and Candida sp.) outcompete other microbial groups contaminating flour, and interact with each other at different levels. Ecological parameters qualitatively and quantitatively affecting the dominant sourdough microbiota may be classified into specific technological parameters (e.g., percentage of sourdough used as inoculum, time and temperature of fermentation) and parameters that are not fully controlled by those who manage the propagation of sourdough (e.g., chemical, enzyme and microbial composition of flour). Although some sourdoughs have been reported to harbour a persistent dominant microbiota, the stability of sourdough ecosystem during time is debated. Indeed, several factors may interfere with the persistence of species and strains associations that are typical of a given sourdough: metabolic adaptability to the

  19. Microbial diversity and carbon cycling in San Francisco Bay wetlands

    Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

    2014-03-21

    Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled the diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.

  20. Microbial diversity in European alpine permafrost and active layers.

    Frey, Beat; Rime, Thomas; Phillips, Marcia; Stierli, Beat; Hajdas, Irka; Widmer, Franco; Hartmann, Martin

    2016-03-01

    Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world. PMID:26832204

  1. A review of microbial diversity in polar terrestrial environments

    Weidong Kong

    2013-07-01

    Full Text Available Polar regions refer to the areas at high latitudes and altitudes, that are characterized by low temperature and limited nutrients, and are very vulnerable and sensitive to global climate change. They include the Antarctic, the Arctic and the Tibetan Plateau, which is recognized as “the third pole”. The harsh polar environments are inhabited by abundant microbes that shape and maintain ecosystems by driving biogeochemical cycles. This article herein reviews microbial diversity in these polar terrestrial environments, including soils, lakes and glaciers in the Antarctic, the Arctic and the Tibetan Plateau. In the three poles, five major groups of microbes have been detected, e.g. Acidobacteria, Actinobacteria, Bacteroidetes, Cynobacteria, and Firmicutes. These microbes are salt- and cold-tolerant. Research in polar microbial ecology in China is currently lagging behind developed countries. Priorities should be given to long-term observations on theTibetan Plateau, which is easily approached. This will facilitate microbial ecology research and expand our understanding of microbial processes and their ecological roles in extreme environments.

  2. Access to what? Access, diversity and participation in India's schools

    Juneja, Nalini

    2010-01-01

    India has witnessed substantial diversification of provision to basic education. Policy changes from 1980s onwards, has seen the creation of para-formal delivery systems and the inclusion in the system of non state providers. The Education Guarantee Scheme and the Alternate Initiatives in Education programmes have generated new pathways to access. The paper examines the different educational providers and looks at the spread of provision, the enrolment shares, the different structure, costs a...

  3. PRELIMINARY INVESTIGATION ON SOIL MICROBIAL DIVERSITY : EFFECT OF PEDOGENIC SUBSTRATE

    Armando Pignataro

    2011-07-01

    Full Text Available Soil biological functions, in particular linked to the activities of microbial communities, are influenced by the interaction between the species (canopy, quantity and quality of litter, roots and rhizodepositions and the type of soil. The present study focused on the influence of different pedogenic substrates on the composition and the activities of microbial soil communities. Three systems with the same plant cover (Quercus cerris spp. and same topographic conditions but with different pedogenic material (Andosol, Entisol, Inceptisol were chosen. The soils were sampled in June 2009 in three Natural Reserves in the Centre of Italy (Selva di Meana/Monte Peglia, Monte Rufeno, Lago di Vico at 0-20cm in horizon A. Functional diversity was calculated by estimating eight enzyme activities and the Community Level Physiological Profile (CLPP, together with soil chemical characterization.

  4. Abiotic factors shape microbial diversity in Sonoran Desert soils.

    Andrew, David R; Fitak, Robert R; Munguia-Vega, Adrian; Racolta, Adriana; Martinson, Vincent G; Dontsova, Katerina

    2012-11-01

    High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments. PMID:22885757

  5. Diversity Enhances NPP, N Retention, and Soil Microbial Diversity in Experimental Urban Grassland Assemblages

    Thompson, Grant L.; Kao-Kniffin, Jenny

    2016-01-01

    Urban grasslands, landscapes dominated by turfgrasses for aesthetic or recreational groundcovers, are rapidly expanding in the United States and globally. These managed ecosystems are often less diverse than the natural or agricultural lands they replace, leading to potential losses in ecosystem functioning. Research in non-urban systems has provided evidence for increases in multiple ecosystem functions associated with greater plant diversity. To test if biodiversity-ecosystem function findings are applicable to urban grasslands, we examined the effect of plant species and genotypic diversity on three ecosystem functions, using grassland assemblages of increasing diversity that were grown within a controlled environment facility. We found positive effects of plant diversity on reduced nitrate leaching and plant productivity. Soil microbial diversity (Mean Shannon Diversity, H’) of bacteria and fungi were also enhanced in multi-species plantings, suggesting that moderate increments in plant diversity influence the composition of soil biota. The results from this study indicate that plant diversity impacts multiple functions that are important in urban ecosystems; therefore, further tests of urban grassland biodiversity should be examined in situ to determine the feasibility of manipulating plant diversity as an explicit landscape design and function trait. PMID:27243768

  6. Boom clay pore water, home of a diverse microbial community

    Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

  7. Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia

    Karla B Heidelberg

    2013-05-01

    Full Text Available This study describes the community structure of the microbial eukaryotic community from hypersaline Lake Tyrrell, Australia, using near full length 18S rRNA sequences. Water samples were taken in both summer and winter over a four year period. The extent of eukaryotic diversity detected was low, with only 35 unique phylotypes using a 97% sequence similarity threshold. The water samples were dominated (91% by a novel cluster of the Alveolate, Apicomplexa Colpodella spp., most closely related to C. edax. The Chlorophyte, Dunaliella spp. accounted for less than 35% of water column samples. However, the eukaryotic community entrained in a salt crust sample was vastly different and was dominated (83% by the Dunaliella spp. The patterns described here represent the first observation of microbial eukaryotic dynamics in this system and provide a multiyear comparison of community composition by season. The lack of expected seasonal distribution in eukaryotic communities paired with abundant nanoflagellates suggests that grazing may significantly structure microbial eukaryotic communities in this system.

  8. Microbial communities in salt lakes: Phylogenetic diversity, metabolic diversity, and in situ activities

    Oren, Aharon; Baxter, Bonnie K; Bart C Weimer

    2009-01-01

    A roundtable discussion was held on Monday, 12 May 2008, following the sessions on 'Microorganisms in Hypersaline Environments' at the 10th Conference on Salt Lake Research & 2008 FRIENDS of Great Salt Lake Issues Forum, University of Utah, Salt Lake City. Among the aspects discussed were: 1. The gap between our knowledge of the microorganisms isolated in culture and the true microbial diversity as apparent when using culture-independent techniques, in most cases based on the characterization...

  9. Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors.

    Thakur, Madhav Prakash; Milcu, Alexandru; Manning, Pete; Niklaus, Pascal A; Roscher, Christiane; Power, Sally; Reich, Peter B; Scheu, Stefan; Tilman, David; Ai, Fuxun; Guo, Hongyan; Ji, Rong; Pierce, Sarah; Ramirez, Nathaly Guerrero; Richter, Annabell Nicola; Steinauer, Katja; Strecker, Tanja; Vogel, Anja; Eisenhauer, Nico

    2015-11-01

    Soil microbial biomass is a key determinant of carbon dynamics in the soil. Several studies have shown that soil microbial biomass significantly increases with plant species diversity, but it remains unclear whether plant species diversity can also stabilize soil microbial biomass in a changing environment. This question is particularly relevant as many global environmental change (GEC) factors, such as drought and nutrient enrichment, have been shown to reduce soil microbial biomass. Experiments with orthogonal manipulations of plant diversity and GEC factors can provide insights whether plant diversity can attenuate such detrimental effects on soil microbial biomass. Here, we present the analysis of 12 different studies with 14 unique orthogonal plant diversity × GEC manipulations in grasslands, where plant diversity and at least one GEC factor (elevated CO2 , nutrient enrichment, drought, earthworm presence, or warming) were manipulated. Our results show that higher plant diversity significantly enhances soil microbial biomass with the strongest effects in long-term field experiments. In contrast, GEC factors had inconsistent effects with only drought having a significant negative effect. Importantly, we report consistent non-significant effects for all 14 interactions between plant diversity and GEC factors, which indicates a limited potential of plant diversity to attenuate the effects of GEC factors on soil microbial biomass. We highlight that plant diversity is a major determinant of soil microbial biomass in experimental grasslands that can influence soil carbon dynamics irrespective of GEC. PMID:26118993

  10. Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity

    Johan Habig

    2015-07-01

    Full Text Available Soil microbial communities perform critical functions in ecosystem processes. These functions can be used to assess the impact of agricultural practices on sustainable crop production. In this five-year study, the effect of various agricultural practices on soil microbial diversity and activity was investigated in a summer rainfall area under South African dryland conditions. Microbial diversity and activity were measured in the 0–15 cm layer of a field trial consisting of two fertilizer levels, three cropping systems, and two tillage systems. Using the Shannon–Weaver and Evenness diversity indices, soil microbial species richness and abundance were measured. Microbial enzymatic activities: β-glucosidase, phosphatase and urease, were used to evaluate ecosystem functioning. Cluster analysis revealed a shift in soil microbial community diversity and activity over time. Microbial diversity and activity were higher under no-till than conventional tillage. Fertilizer levels seemed to play a minor role in determining microbial diversity and activity, whereas the cropping systems played a more important role in determining the activity of soil microbial communities. Conservation agriculture yielded the highest soil microbial diversity and activity in diversified cropping systems under no-till.

  11. Microbial Diversity in KURT Groundwater and Biomineralization Characteristics

    The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxides, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

  12. Microbial Diversity and Characteristics in Anaerobic Environments in KURT Groundwater

    The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxide, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

  13. Microbial diversity on Icelandic glaciers and ice caps

    Stefanie eLutz

    2015-04-01

    Full Text Available Algae are important primary colonizers of snow and glacial ice, but hitherto little is known about their ecology on Iceland’s glaciers and ice caps. Due do the close proximity of active volcanoes delivering large amounts of ash and dust, they are special ecosystems. This study provides the first investigation of the presence and diversity of microbial communities on all major Icelandic glaciers and ice caps over a three year period. Using high-throughput sequencing of the small subunit ribosomal RNA genes (16S and 18S, we assessed the snow community structure and complemented these analyses with a comprehensive suite of physical-, geo- and biochemical characterizations of the aqueous and solid components contained in snow and ice samples. Our data reveal that a limited number of snow algal taxa (Chloromonas polyptera, Raphidonema sempervirens and two uncultured Chlamydomonadaceae support a rich community comprising of other micro-eukaryotes, bacteria and archaea. Proteobacteria and Bacteroidetes were the dominant bacterial phyla. Archaea were also detected in sites where snow algae dominated and they mainly belong to the Nitrososphaerales, which are known as important ammonia oxidizers. Multivariate analyses indicated no relationships between nutrient data and microbial community structure. However, the aqueous geochemical simulations suggest that the microbial communities were not nutrient limited because of the equilibrium of snow with the nutrient-rich and fast dissolving volcanic ash. Increasing algal secondary carotenoid contents in the last stages of the melt seasons have previously been associated with a decrease in surface albedo, which in turn could potentially have an impact on the melt rates of Icelandic glaciers.

  14. Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity

    Johan Habig; Corrie Swanepoel

    2015-01-01

    Soil microbial communities perform critical functions in ecosystem processes. These functions can be used to assess the impact of agricultural practices on sustainable crop production. In this five-year study, the effect of various agricultural practices on soil microbial diversity and activity was investigated in a summer rainfall area under South African dryland conditions. Microbial diversity and activity were measured in the 0–15 cm layer of a field trial consisting of two fertilizer leve...

  15. Functional Diversity of Microbial Communities in Soils in the Vicinity of Wanda Glacier, Antarctic Peninsula

    Pessi, Igor Stelmach; de Oliveira Elias, Susana; Simões, Felipe Lorenz; Simões, Jefferson Cardia; Macedo, Alexandre José

    2011-01-01

    Microbial functional diversity in four soils sampled in the vicinity of Wanda Glacier, Antarctic Peninsula, was determined using Biolog EcoPlates at 5°C and 25°C. Comparisons of the patterns of substrate utilization and the diversity index showed differences in community composition, reflecting the heterogeneous distribution of microorganisms in this environment. Differences in microbial diversity may be related to soil chemical properties. Higher incubation temperature influenced the overall...

  16. Microbial diversity in subseafloor fluids from Explorer Ridge, Northeast Pacific

    Bolton, S.; Huber, J. A.; Embley, R.; Butterfield, D. A.; Baross, J. A.

    2003-12-01

    The Gorda, Juan de Fuca and Explorer Ridges are first order spreading centers located in the northeast Pacific. While the Gorda and Juan de Fuca Ridges have been extensively sampled for chemical and microbiological analyses, what little is known about the Explorer Ridge is from preliminary observations made in the mid-1980's. A cruise in 2002 revisited the area and discovered vigorous hydrothermal activity at Magic Mountain, a site located outside the primary rift valley. Explorer Ridge is an important site to compare with other well-described vent sites on the Juan de Fuca Ridge. Our research has focused on describing the phylogenetic and physiological diversity of bacteria and archaea in low temperature hydrothermal fluids in an effort to identify subseafloor indicator organisms and to use the physiological characteristics of these organisms to help constrain subseafloor habitat characteristics. We have previously established that there are microbial taxa that are unique to subseafloor habitats associated with diffuse flow fluids at Axial Seamount and at Endeavour both located on the Juan de Fuca Ridge. These included cultured anaerobic, thermophilic and hyperthermophilic heterotrophs, methanogens and sulfur metabolizers. Moreover, results from molecular phylogeny analyses using the 16S rRNA sequences identified a phylogenetically diverse group of bacteria belonging to the epsilon-proteobacteria. While anaerobic hyperthermophiles were cultured from some diffuse-flow vent sites at Explorer, they were less abundant than at Axial Volcano and Endeavour, and curiously, no methanogens were cultured or detected in 16S rRNA clonal libraries. Like Axial, a diverse group of epsilon-proteobacterial clones were found with many similar to those identified from Axial Seamount and other hydrothermal vent sites, although there appears to be some unique species. The overall bacterial diversity at Explorer appears different than at Axial, possibly linked to temperature or chemical

  17. Functional Microbial Diversity Explains Groundwater Chemistry in a Pristine Aquifer

    Microbial communities inhabiting anoxic aquifers catalyze critical biogeochemical reactions in the subsurface, yet little is known about how their community structure correlates with groundwater chemistry. In this study, we described the composition of microbial communities in th...

  18. Unpasteurised commercial boza as a source of microbial diversity.

    Osimani, Andrea; Garofalo, Cristiana; Aquilanti, Lucia; Milanović, Vesna; Clementi, Francesca

    2015-02-01

    Boza is a cereal-based fermented beverage widely consumed in many countries of the Balkans. The aim of this study was to investigate the microbiota of three Bulgarian boza samples through a combination of culture-dependent and -independent methods with the long-term objective of formulating a multi-strain starter culture specifically destined for the manufacture of new cereal-based drinks. The isolation campaign for lactic acid bacteria (LAB) allowed the identification of Lactobacillus parabuchneri, Lactobacillus fermentum, Lactobacillus coryniformis, Lactobacillus buchneri, Pediococcus parvulus and members of the Lactobacillus casei group. Concerning yeasts, the following isolates were identified: Pichia fermentans, Pichia norvegensis, Pichia guilliermondii (synonym Meyerozyma guilliermondii) and Torulaspora spp. A high intra-species diversity was revealed by Randomly Amplified Polymorphic DNA (RAPD) analysis. In parallel, microbial DNA was directly extracted from the three boza samples, and portions of the rrn operons were analysed through Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The molecular fingerprinting partially confirmed the results of culturing. Among LAB, the species Weissella confusa, Weissella oryzae, Leuconostoc citreum, Lactococcus lactis, Pediococcus parvulus and Pediococcus ethanolidurans were detected together with members of the Lb. casei group. Among the yeasts, the species P. fermentans, M. guilliermondii, Galactomyces geotrichum and Geotrichum fragrans were found. The overall results confirmed boza as having a rich and heterogeneous biodiversity both in terms of species and genetically diverse strains, thus encouraging its exploitation for the isolation and future technological characterisation of cultures to be selected for the manufacture of innovative cereal-based drinks. PMID:25437059

  19. Standard filtration practices may significantly distort planktonic microbial diversity estimates

    Cory Cruz Padilla

    2015-06-01

    Full Text Available Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40-60% of prefilter datasets at low volumes (0.05-0.5 L to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold. Taxon richness (97% similarity clusters also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

  20. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-01-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. It

  1. Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

    Winding, Anne; Rutgers, Michiel; Creamer, Rachel;

    of estimating soil microbial activity. However, today several techniques are in use for determining microbial functional diversity and assessing soil biodiversity: Methods based on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development...

  2. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture

    Wood, Stephen A.; Almaraz, Maya; Bradford, Mark A.; McGuire, Krista L.; Naeem, Shahid; Neill, Christopher; Palm, Cheryl A.; Tully, Katherine L.; Zhou, Jizhong

    2015-01-01

    Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence process...

  3. Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

    Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

    2015-02-01

    Colonization of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focused on the settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associated vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soil types on the surface of the island. Total viable bacterial counts were performed with the plate count method at 22, 30 and 37 °C for all soil samples, and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms and aerobic and anaerobic bacteria. The subsurface biosphere was investigated by collecting liquid subsurface samples from a 181 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between nutrient deficits and the number of microorganisms in surface soil samples. The lowest number of bacteria (1 × 104-1 × 105 cells g-1) was detected in almost pure pumice but the count was significantly higher (1 × 106-1 × 109 cells g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated samples and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 and 172 m depth at 80 and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

  4. Microbial colonisation in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

    Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

    2014-09-01

    Colonisation of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focusing on settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associate vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soils types on the surface of the island. Total viable bacterial counts were performed with plate count at 22, 30 and 37 °C for all soils samples and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms aerobic and anaerobic bacteria. The deep subsurface biosphere was investigated by collecting liquid subsurface samples from a 182 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between N deficits and the number of microorganisms in surface soils samples. The lowest number of bacteria (1 × 104-1 × 105 g-1) was detected in almost pure pumice but the count was significant higher (1 × 106-1 × 109 g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 m and 172 m depth at 80 °C and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

  5. The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

    Xiao, Yunhua; Xu, YongDong; Dong, Weiling; Liang, Yili; Fan, Fenliang; Zhang, Xiaoxia; Zhang, Xian; Niu, Jiaojiao; Ma, Liyuan; She, Siyuan; He, Zhili; Liu, Xueduan; Yin, Huaqun

    2015-12-01

    This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function. PMID:26266752

  6. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

    Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys; Mele, Pauline M.; Reith, Frank der; Dennis, Paul G; Martin F Breed; Brown, Belinda; Brown, Mark V; Brugger, Joel; Byrne, Margaret; Caddy-Retalic, Stefan; Carmody, Bernie; Coates, David J; Correa, Carolina

    2016-01-01

    Background Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integratin...

  7. Effect of Pulp mill sludge on soil characteristics, microbial diversity and vegetal production of Lollium perene

    Gallardo, F.; Cea, M.; Diez, M. C.

    2009-07-01

    The Chemical properties of the sludge (High organic matter content, pH, buffer capacity, nitrogen and phosphorous level, and low concentration of trace heavy metals and organic pollutants) suggest that this material may represent a valuable resource as soil amendment, improving soil characteristics, microbial diversity and vegetal production of mill sludge addition to volcanic soil (Andisol) on soil characteristics, microbial diversity and vegetal production of Lollium perenne, in field assays. (Author)

  8. Effect of Pulp mill sludge on soil characteristics, microbial diversity and vegetal production of Lollium perene

    The Chemical properties of the sludge (High organic matter content, pH, buffer capacity, nitrogen and phosphorous level, and low concentration of trace heavy metals and organic pollutants) suggest that this material may represent a valuable resource as soil amendment, improving soil characteristics, microbial diversity and vegetal production of mill sludge addition to volcanic soil (Andisol) on soil characteristics, microbial diversity and vegetal production of Lollium perenne, in field assays. (Author)

  9. Microbial diversity in failed endodontic root-filled teeth

    ZHANG Chen; HOU Ben-xiang; ZHAO Huan-ying; SUN Zheng

    2012-01-01

    Background Persistent/secondary infections of human root canals play an important role in the failure of endodontic treatment.This study used 16S rRNA sequencing to assess microbial diversity in root-filled teeth associated with failed endodontic treatment.Methods DNA was extracted from 15 teeth with persistent intraradicular infections,and the 16S rRNA of all present bacteria were amplified by PCR,followed by cloning and sequencing of the 16S rRNA amplicons.Results All sample extracts were positive for PCR amplification using the universal 16S rRNA gene primers.Negative control reactions yielded no amplicons.Sixty-five phylotypes belonging to seven phyla were identified from 760 clones; a mean of 9.4 phylotypes were detected in each sample (range 3-15).Twenty-eight phylotypes were detected in more than one sample,revealing a high inter-sample variability.Parvimonas micra (60%,9/15),Solobacterium moore (47%,7/15),Dialister invisus (33%,5/15),Enterococcus faecalis (33%,5/15),Filifactor alocis (27%,4/15),and Fusobacterium nucleatum (27%,4/15) were the prevalent species.Nineteen as-yet-uncultivated phylotypes were identified,comprising a substantial proportion of the bacteria in many cases.Conclusions Persistent intraradicular infections were present in all root-filled teeth associated with failed endodontic treatment.The current observations reveal new candidate endodontic pathogens,including as-yet-uncultivated bacteria and phylotypes that may participate in the mixed infections associated with post-treatment apical periodontitis.

  10. Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity.

    Gaikwad, Swapnil; Shouche, Yogesh S; Gade, Wasudev N

    2016-12-01

    Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities. PMID:27299740

  11. Phylogenetic diversity of fungal communities in areas accessible and not accessible to tourists in Naracoorte Caves.

    Adetutu, Eric M; Thorpe, Krystal; Bourne, Steven; Cao, Xiangsheng; Shahsavari, Esmaeil; Kirby, Greg; Ball, Andrew S

    2011-01-01

    The fungal diversity in areas accessible and not accessible to tourists at UNESCO World Heritage-listed Naracoorte Caves was investigated with culture-dependent and culture-independent techniques for assistance in cave management protocol development. The caves were selected based on tourist numbers and configurations: Stick Tomato (open, high numbers), Alexandra (lockable openings, high numbers) and Strawhaven (control; no access). Culture-based survey revealed Ascomycota dominance irrespective of sampling area with Microascales (Trichurus sp.) being most frequently isolated. Some Hypocreales-like sequences belonging to Fusarium sp., Trichoderma sp. and Neonectria sp. (Stick Tomato) were cultured only from areas not accessible to tourists. These orders also were detected by DGGE assay irrespective of sampling area. The predominance of Ascomycota (especially Microascales) suggested their important ecological roles in these caves. Culture-independent analysis showed higher Shannon fungal diversity values (from ITS-based DGGE profiles) in tourist-accessible areas of these caves than in inaccessible areas with the fungal community banding patterns being substantially different in Stick Tomato Cave. Further investigations are needed to determine the cause of the differences in the fungal communities of Stick Tomato Cave, although cave-related factors such as use, configuration and sediment heterogeneity might have contributed to these differences. PMID:21642344

  12. Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0

    Jing Cong

    2015-09-01

    Full Text Available To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171.

  13. The effect of soil habitat connectivity on microbial interactions, community structure and diversity: a microcosm-based approach

    Wolf, A.B.

    2014-01-01

    Soils contain tremendous microbial phylogenetic and functional diversity. Recent advances in the application of molecular methods into microbial ecology have provided a new appreciation of the extent of soil-borne microbial diversity, but our understanding of the forces that shape and maintain this

  14. Assessment of soil microbial diversity with functional multi-endpoint methods

    Winding, Anne; Creamer, R. E.; Rutgers, M.;

    Soil microbial diversity provides the cornerstone for support of soil ecosystem services by key roles in soil organic matter turnover, carbon sequestration and water infiltration. However, standardized methods to quantify the multitude of microbial functions in soils are lacking. Methods based on...... three techniques of assessing soil microbial functional diversity in a European transect consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses and compare with the vast amount of data delivered in other projects (BISQ, RMQS-bioindicateur). Based on experimental results...... with these methods, microbiological reasoning and ecological theory, we will perform a qualitative comparison between the multi endpoint methods of determining soil microbial communities functional diversity, and will suggest standardized classification and assessment options for practical application...

  15. Determination of genetic diversity among some almond accessions

    Pinar Hasan

    2015-01-01

    Full Text Available More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD and 4 inter-simple sequence repeat (ISSR markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections. The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88% compared to RAPD (74%. RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

  16. Extensive Microbial and Functional Diversity within the Chicken Cecal Microbiome

    Sergeant, Martin J.; Chrystala Constantinidou; Tristan A Cogan; Bedford, Michael R.; Penn, Charles W.; Pallen, Mark J.

    2014-01-01

    Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown speci...

  17. Mangrove microbial diversity and the impact of trophic contamination

    Bouchez, Agnès; Pascault, Noémie; Chardon, Cècile; Bouvy, Marc; Cecchi, Philippe; Lambs, Luc; Herteman, Mélanie; Fromard, François; Got, Patrice; Leboulanger, Christophe

    2013-01-01

    Mangroves are threatened ecosystems that provide numerous ecosystem services, especially through their wide biodiversity, and their bioremediation capacity is a challenging question in tropical areas. In a mangrove in Mayotte, we studied the potential role of microbial biofilm communities in removing nutrient loads from pre-treated wastewater. Microbial community samples were collected from tree roots, sediments, water, and from a colonization device, and their structure and dynamics were com...

  18. Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain

    Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Chu, Haiyan

    2016-01-01

    The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change. PMID:27524983

  19. The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

    Kim, Hyeun Bum; Isaacson, Richard E

    2015-06-12

    The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. PMID:25843944

  20. Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

    Fernandez, Ana B.; Rasuk, Maria C.; Visscher, Pieter T.; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G.; Patterson, Molly M.; Ventosa, Antonio; Farias, Maria E.

    2016-01-01

    We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity. PMID:27597845

  1. Microbial diversity in opalinus clay and interaction of dominant microbial strains with actinides

    Moll, Henry; Luetke, Laura; Bachvarova, Velina; Steudtner, Robin; Geissler, Andrea; Krawczyk-Baersch, Evelyn; Selenska-Pobell, Sonja; Bernhardt, Gert

    2013-07-01

    For the first time microbial tDNA could be isolated from 50 g unperturbed Mont Terri Opalinus Clay. Based on the analysis of the tDNA the bacterial diversity of the unperturbed clay is dominated by representatives of Firmicutes, Betaproteobacteria, and Bacteriodetes. Firmicutes also dominate after treatment of the clay with R2A medium. Bacteria isolated from Mont Terri Opalinus Clay on R2A medium were related to Sporomusa spp., Paenibacillus spp., and Clostridium spp. All further investigations are concentrated on the unique isolates Sporomusa sp. MT-2 and Paenibacillus sp. MT-2. Cells of the type Sporomusa sp. MT-2 and Paenibacillus sp. MT-2 were comprehensively analyzed in terms of growing, morphology, functional groups of the cell envelope, and cell membrane structure. Strong actinide(An)/lanthanide(Ln)-interactions with the Opalinus Clay isolates and the Aespoe-strain Pseudomonas fluorescens (CCUG 32456) could be determined within a broad pH range (2-8). The metals bind as a function of pH on protonated phosphoryl, carboxyl and deprotonated phosphoryl sites of the respective cell membrane. The thermodynamic surface complexation constants of bacterial An/Ln-species were determined and can be used in modeling programs. Depending on the used An different interaction mechanisms were found (U(VI): biosorption, partly biomineralisation; Cm(III): biosorption, indications for embedded Cm(III); Pu: biosorption, bioreduction and indications for embedded Pu). Different strategies of coping with U(VI) were observed comparing P. fluorescens planktonic cells and biofilms under the chosen experimental conditions. An enhanced capability of the biofilm to form meta-autunite in comparison to the planktonic cells was proven. Conclusively, the P. fluorescens biofilm is more efficient in U(VI) detoxification. In conclusion, Mont Terri Opalinus Clay contains bacterial communities, that may influence the speciation and hence the migration behavior of selected An/Ln under

  2. Microbial diversity in opalinus clay and interaction of dominant microbial strains with actinides

    For the first time microbial tDNA could be isolated from 50 g unperturbed Mont Terri Opalinus Clay. Based on the analysis of the tDNA the bacterial diversity of the unperturbed clay is dominated by representatives of Firmicutes, Betaproteobacteria, and Bacteriodetes. Firmicutes also dominate after treatment of the clay with R2A medium. Bacteria isolated from Mont Terri Opalinus Clay on R2A medium were related to Sporomusa spp., Paenibacillus spp., and Clostridium spp. All further investigations are concentrated on the unique isolates Sporomusa sp. MT-2 and Paenibacillus sp. MT-2. Cells of the type Sporomusa sp. MT-2 and Paenibacillus sp. MT-2 were comprehensively analyzed in terms of growing, morphology, functional groups of the cell envelope, and cell membrane structure. Strong actinide(An)/lanthanide(Ln)-interactions with the Opalinus Clay isolates and the Aespoe-strain Pseudomonas fluorescens (CCUG 32456) could be determined within a broad pH range (2-8). The metals bind as a function of pH on protonated phosphoryl, carboxyl and deprotonated phosphoryl sites of the respective cell membrane. The thermodynamic surface complexation constants of bacterial An/Ln-species were determined and can be used in modeling programs. Depending on the used An different interaction mechanisms were found (U(VI): biosorption, partly biomineralisation; Cm(III): biosorption, indications for embedded Cm(III); Pu: biosorption, bioreduction and indications for embedded Pu). Different strategies of coping with U(VI) were observed comparing P. fluorescens planktonic cells and biofilms under the chosen experimental conditions. An enhanced capability of the biofilm to form meta-autunite in comparison to the planktonic cells was proven. Conclusively, the P. fluorescens biofilm is more efficient in U(VI) detoxification. In conclusion, Mont Terri Opalinus Clay contains bacterial communities, that may influence the speciation and hence the migration behavior of selected An/Ln under

  3. Assessment of the impact of textile effluents on microbial diversity in Tirupur district, Tamil Nadu

    Prabha, Shashi; Gogoi, Anindita; Mazumder, Payal; Ramanathan, AL.; Kumar, Manish

    2016-03-01

    The expedited advent of urbanization and industrialization for economic growth has adversely affected the biological diversity, which is one of the major concerns of the developing countries. Microbes play a crucial role in decontaminating polluted sites and degrades pollution load of textile effluent. The present study was based on identification of microbial diversity along the Noyaal river of Tirupur area. River water samples from industrial and non-industrial sites and effluent samples of before and after treatment were tested and it was found that microbial diversity was higher in the river water at the industrial site (Kasipalayam) as compared to the non-industrial site (Perur). Similarly, the microbial populations were found to be high in the untreated effluent as compared to the treated one by conventional treatment systems. Similar trends were observed for MBR treatment systems as well. Pseudomonas sp., Achromobacter sp. (bacterial species) and Aspergillus fumigates (fungal species), found exclusively at the industrial site have been reported to possess decolorization potential of dye effluent, thus can be used for treatment of dye effluent. The comparison of different microbial communities from different dye wastewater sources and textile effluents was done, which showed that the microbes degrade dyestuffs, reduce toxicity of wastewaters, etc. From the study, it can be concluded that the microbial community helps to check on the pollutants and minimize their affect. Therefore, there is a need to understand the systematic variation in microbial diversity with the accumulation of pollution load through monitoring.

  4. Bacterial diversity assessment of pristine mangrove microbial community from Dhulibhashani, Sundarbans using 16S rRNA gene tag sequencing.

    Basak, Pijush; Pramanik, Arnab; Sengupta, Sohan; Nag, Sudip; Bhattacharyya, Anish; Roy, Debojyoti; Pattanayak, Rudradip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

    2016-03-01

    The global knowledge of microbial diversity and function in Sundarbans ecosystem is still scarce, despite global advancement in understanding the microbial diversity. In the present study, we have analyzed the diversity and distribution of bacteria in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. Metagenome is comprised of 1,53,926 sequences with 108.8 Mbp data and with 55 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA245459. Bacterial community metagenome sequences were analyzed by MG-RAST software representing the presence of 56,547 species belonging to 44 different phyla. The taxonomic analysis revealed the dominance of phyla Proteobacteria within our dataset. Further taxonomic analysis revealed abundance of Bacteroidetes, Acidobactreia, Firmicutes, Actinobacteria, Nitrospirae, Cyanobacteria, Planctomycetes and Fusobacteria group as the predominant bacterial assemblages in this largely pristine mangrove habitat. The distribution of different community datasets obtained from four sediment samples originated from one sampling station at two different depths providing better understanding of the sediment bacterial diversity and its relationship to the ecosystem dynamics of this pristine mangrove sediment of Dhulibhashani in, Sundarbans. PMID:26981367

  5. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture

    Stephen A Wood

    2015-03-01

    Full Text Available Tropical smallholder agriculture supports the livelihoods of over 900 million of the world’s poorest people. This form of agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.

  6. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture.

    Wood, Stephen A; Almaraz, Maya; Bradford, Mark A; McGuire, Krista L; Naeem, Shahid; Neill, Christopher; Palm, Cheryl A; Tully, Katherine L; Zhou, Jizhong

    2015-01-01

    Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture. PMID:25926815

  7. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

    Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-01-01

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions. PMID:27113678

  8. Mississippi River Plume Enriches Microbial Diversity in the Northern Gulf of Mexico

    Mason, Olivia U.; Canter, Erin J.; Gillies, Lauren E.; Paisie, Taylor K.; Roberts, Brian J.

    2016-01-01

    The Mississippi River (MR) serves as the primary source of freshwater and nutrients to the northern Gulf of Mexico (nGOM). Whether this input of freshwater also enriches microbial diversity as the MR plume migrates and mixes with the nGOM serves as the central question addressed herein. Specifically, in this study physicochemical properties and planktonic microbial community composition and diversity was determined using iTag sequencing of 16S rRNA genes in 23 samples collected along a salinity (and nutrient) gradient from the mouth of the MR, in the MR plume, in the canyon, at the Deepwater Horizon wellhead and out to the loop current. Analysis of these datasets revealed that the MR influenced microbial diversity as far offshore as the Deepwater Horizon wellhead. The MR had the highest microbial diversity, which decreased with increasing salinity. MR bacterioplankton communities were distinct compared to the nGOM, particularly in the surface where Actinobacteria and Proteobacteria dominated, while the deeper MR was also enriched in Thaumarchaeota. Statistical analyses revealed that nutrients input by the MR, along with salinity and depth, were the primary drivers in structuring the microbial communities. These results suggested that the reduced salinity, nutrient enriched MR plume could act as a seed bank for microbial diversity as it mixes with the nGOM. Whether introduced microorganisms are active at higher salinities than freshwater would determine if this seed bank for microbial diversity is ecologically significant. Alternatively, microorganisms that are physiologically restricted to freshwater habitats that are entrained in the plume could be used as tracers for freshwater input to the marine environment. PMID:27458442

  9. [Seasonal variation of functional diversity of aquatic microbial community in Apostichopus japonicus cultural pond].

    Yan, Fa-Jun; Tian, Xiang-Li; Dong, Shuang-Lin; Yang, Gang

    2014-05-01

    The functional diversity of aquatic microbial communities in sea cucumber (Apostichopus japonicus) cultural ponds was examined in this paper. The Biolog plate technique and redundancy analysis (RDA) method were used to evaluate seasonal changes and their relationships with environmental factors. The results showed that both total amount and types of carbon sources utilized by microbes in the sea cucumber cultural ponds varied seasonally, and were the highest in summer and lowest in winter, with polymers being the main type of carbon sources. Principal component analysis revealed that the carbon utilization diversity of the microbial communities varied significantly over the seasonal courses. A total of 10 categories of carbon sources were significantly related to the principal component 1, among which were polymers, carbohydrates, carboxylic acids, amino acids, and amines. Significant seasonal changes were detected for all carbon utilization diversity indices of the microbial communities, including Shannon, McIntosh, Simpson, and S-E. However, seasonal variations were different among the microbial diversity indices. RDA analysis revealed that TP, NO(3-)-N, TN, and PO4(3-)-P were the critical environmental factors influencing the seasonal changes in functional diversity of aquatic microbial community in sea cucumber cultural ponds. PMID:25129954

  10. In vitro anticancer activity of microbial isolates from diverse habitats

    Angel Treasa Thomas

    2011-06-01

    Full Text Available Extracts from natural products, especially microorganisms, have served as a valuable source of diverse molecules in many drug discovery efforts and led to the discovery of several important drugs. Identification of microbial strains having promising biological activities and purifying the bio-molecules responsible for the activities, have led to the discovery of many bioactive molecules. Extracellular, as well as intracellular, extracts of the metabolites of thirty-six bacterial and twenty-four fungal isolates, grown under unusual conditions such as high temperature, high salt and low sugar concentrations, were in vitro tested for their cytotoxic potential on various cancer cell lines. The extracts were screened on HeLa and MCF-7 cell lines to study the cytotoxic potential. Nuclear staining and flow cytometric studies were carried out to assess the potential of the extracts in arresting the cell cycle. The crude ethylacetate extract of isolate F-21 showed promising results by MTT assay with IC50 as low as 20.37±0.36 µg/mL on HeLa, and 44.75±0.81 µg/mL on MCF-7 cells, comparable with Cisplatin. The isolate F-21 was identified as Aspergillus sp. Promising results were also obtained with B-2C and B-4E strains. Morphological studies, biochemical tests and preliminary chemical investigation of the extracts were also carried out.Extratos de produtos naturais, especialmente de microrganismos, constituíram-se em fonte valiosa de diversas moléculas em muitas descobertas de fármacos e levaram à descoberta de fármacos importantes. A identificação de espécies microbianas que apresentam atividade biológica e a purificação de biomoléculas responsáveis pelas atividades levou à descoberta de muitas moléculas bioativas. Extratos extracelulares tanto quanto intracelulares de metabólitos de 36 isolados de bactérias e 24 isolados de fungos, que cresceram sob condições não usuais, como alta temperatura, alta concentração de sal e baixa

  11. Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of

  12. Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation

    Xie, Yan; Fan, Jibiao; Zhu, Weixi; Amombo, Erick; Lou, Yanhong; Chen, Liang; Fu, Jinmin

    2016-01-01

    Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices. PMID:27303431

  13. Variations in AOC and microbial diversity in an advanced water treatment plant

    Yang, B. M.; Liu, J. K.; Chien, C. C.; Surampalli, R. Y.; Kao, C. M.

    2011-10-01

    SummaryThe objective of this study was to evaluate the variations in assimilable organic carbon (AOC) and microbial diversities in an advanced water treatment plant. The efficiency of biofiltration on AOC removal using anthracite and granular activated carbon (GAC) as the media was also evaluated through a pilot-scale column experiment. Effects of hydrological factors (seasonal effects and river flow) on AOC concentrations in raw water samples and hydraulic retention time (HRT) of biofiltration on AOC treatment were also evaluated. Results show that AOC concentrations in raw water and clear water of the plant were about 138 and 27 μg acetate-C/L, respectively. Higher AOC concentrations were observed in wet seasons probably due to the resuspension of organic-contained sediments and discharges of non-point source (NPS) pollutants from the upper catchment. This reveals that seasonal effect played an important role in the variations in influent AOC concentrations. Approximately 82% and 70% of AOC removal efficiencies were observed in GAC and anthracite columns, respectively. Results from column experiment reveal that the applied treatment processes in the plant and biofiltration system were able to remove AOC effectively. Microbial colonization on GAC and anthracite were detected via the observation of scanning electron microscopic (SEM) images. Results of polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and nucleotide sequence analysis reveal significant decrease in microbial diversities after the ozonation process. Higher HRT caused higher microbial contact time, and thus, more microbial colonies and higher microbial diversity were observed in the latter part of the biofilters. Some of the dominant microbial species in the biofiltration columns belonged to the beta- proteobacterium, which might contribute to the AOC degradation. Results of this study provide us insight into the variations in AOC and microbial diversity in the advanced

  14. Continuous exposure of pesticides in an aquifer changes microbial biomass, diversity and degradation potential

    de Lipthay, J. R.; Johnsen, K.; Aamand, J.; Tuxen, Nina; Albrechtsen, Hans-Jørgen; Bjerg, Poul Løgstrup

    We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential...... towards phenoxyalcanoic acid herbicides as well as impact on microbial diversity was observed. Furthermore, bacterial biomass was changed, e.g. increased numbers of phenoxyalcanoic acid degraders in pesticide exposed sediment....

  15. Effect of wildfires on the genetic microbial diversity in forest soils from Canary Islands (Spain

    J. Rodríguez

    2013-05-01

    Full Text Available Wildfires produce several ecological and environmental impacts on the physical and chemical soil characteristics, as well as on the properties and dynamics of soil microbial populations. Microorganisms are good indicators of ecosystem function and sustainability and therefore the studies about the impact of fire on microbial communities is relevant to understand the role of fire in ecosystem functioning. Although several authors have provided data about total microbial biomass and activity in soils affected by fires, there is little information about the composition and evolution of soil microbial populations after the passage of fire. In this work the effect of wildfires on the genetic diversity of microbial populations in soils from the island of Tenerife (Canary Islands, Spain is studied. The final objective was to get information about the recovery of soil functionality after wildfires.

  16. Invasive Acacia longifolia induce changes in the microbial catabolic diversity of sand dunes

    Marchante, Elizabete; Kjøller, Annelise; Struwe, Sten;

    2008-01-01

    Acacia longifolia is one of the main plant species invading Portuguese dune ecosystems. Areas invaded by this exotic tree have reduced plant diversity and altered soil microbial processes and nutrient pools, but the impacts on microbial functional diversity in the soil have been little explored...... of invasion, carbon (C) content, nitrogen (N) content, C/N ratio, pH, and litter quantity explained 39.6% of the variance of catabolic responses. It is concluded that invasion by A. longifolia has substantial effects on the catabolic diversity of the soil microbial communities. These effects may have wider...... implications for nutrient cycling and ecosystem-level processes and for the invasibility of the system....

  17. Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

    Radhakrishnan, Srinivasan; Varadharajan, Mohan

    2016-06-01

    Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. PMID:26924716

  18. Spatial variation in microbial community structure, richness, and diversity in an alluvial aquifer.

    Medihala, P G; Lawrence, J R; Swerhone, G D W; Korber, D R

    2012-09-01

    Relatively little is known regarding the spatial variability of microbial communities in aquifers where well fouling is an issue. In this study 2 water wells were installed in an alluvial aquifer located adjacent to the North Saskatchewan River and an associated piezometer network developed to facilitate the study of microbial community structure, richness, and diversity. Carbon utilization data analysis revealed reduced microbial activity in waters collected close to the wells. Functional PCR and quantitative PCR analysis indicated spatial variability in the potential for iron-, sulphate-, and nitrate-reducing activity at all locations in the aquifer. Denaturing gradient gel electrophoresis analysis of aquifer water samples using principal components analyses indicated that the microbial community composition was spatially variable, and denaturing gradient gel electrophoresis sequence analysis revealed that bacteria belonging to the genera Acidovorax , Rhodobacter , and Sulfuricurvum were common throughout the aquifer. Shannon's richness (H') and Pielou's evenness (J') indices revealed a varied microbial diversity (H' = 1.488-2.274) and an even distribution of microbial communities within the aquifer (J' = 0.811-0.917). Overall, these analyses revealed that the aquifer's microbial community varied spatially in terms of composition, richness, and metabolic activity. Such information may facilitate the diagnosis, prevention, and management of fouling. PMID:22913282

  19. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

    Alinne Pereira de Castro; Maria Regina Silveira Sartori da Silva; Betania Ferraz Quirino; Mercedes Maria da Cunha Bustamante; Ricardo Henrique Krüger

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiogno...

  20. Coastal microbial mat diversity along a natural salinity gradient.

    Henk Bolhuis

    Full Text Available The North Sea coast of the Dutch barrier island of Schiermonnikoog is covered by microbial mats that initiate a succession of plant communities that eventually results in the development of a densely vegetated salt marsh. The North Sea beach has a natural elevation running from the low water mark to the dunes resulting in gradients of environmental factors perpendicular to the beach. These gradients are due to the input of seawater at the low water mark and of freshwater from upwelling groundwater at the dunes and rainfall. The result is a natural and dynamic salinity gradient depending on the tide, rainfall and wind. We studied the microbial community composition in thirty three samples taken every ten meters along this natural salinity gradient by using denaturing gradient gel electrophoresis (DGGE of rRNA gene fragments. We looked at representatives from each Domain of life (Bacteria, Archaea and Eukarya and with a particular emphasis on Cyanobacteria. Analysis of the DGGE fingerprints together with pigment composition revealed three distinct microbial mat communities, a marine community dominated by diatoms as primary producers, an intermediate brackish community dominated by Cyanobacteria as primary producers and a freshwater community with Cyanobacteria and freshwater green algae.

  1. Extensive microbial and functional diversity within the chicken cecal microbiome.

    Martin J Sergeant

    Full Text Available Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs, the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.

  2. High functional diversity stimulates diversification in experimental microbial communities.

    Jousset, Alexandre; Eisenhauer, Nico; Merker, Monika; Mouquet, Nicolas; Scheu, Stefan

    2016-06-01

    There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available. PMID:27386573

  3. Microbial community diversity in the profile of an agricultural soil in Northern China

    ZHOU Juan; GUO Weihua; WANG Renqing; HAN Xuemei; WANG Qiang

    2008-01-01

    The soil microorganisms at different depths play an important role in soil formation, ecosystem biogeochemistry, recycling of nutrients, and degradation of waste products. The aims of this study were to observe the microbial diversity in the profile of an agricultural soil in Northern China, and to research the correlation between soil microbes and geochemistry. First, the soil geochemistry of the profile was investigated through 25 chemical elements. Secondly, the various physiological groups of microorganisms were studied by traditional culture methods. Thirdly, the functional diversity on sole carbon source utilization (SCSU) was evaluated by the BIOLOG(r) system. Finally, the correlation between the soil microbial diversity and geochemistry was analyzed statistically. The results showed that the amounts and proportions of various physiological groups of microorganisms changed with depth. The bacterial functional diversity on SCSU decreased with increasing depth, but evenness of the substrate utilization increased. Although the microbial metabolic diversity was different at every depth, it could be classified into three main grous by principal component analysis and cluster analysis. The various physiological groups of microorganisms showed remarkable correlation with relevant soil chemical elements. The sensitive microbial indicators of soil health were expected to be screened out from actinomyces or ammonifying bacteria.

  4. Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre.

    Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

    2016-06-01

    Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces. PMID:26645474

  5. Functionally stable and phylogenetically diverse microbial enrichments from microbial fuel cells during wastewater treatment.

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

    2012-01-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8-13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m(2), the maximum power density was 13 mW/m(2), and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application

  6. Functionally stable and phylogenetically diverse microbial enrichments from microbial fuel cells during wastewater treatment.

    Shun'ichi Ishii

    Full Text Available Microbial fuel cells (MFCs are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD was removed after an 8-13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m(2, the maximum power density was 13 mW/m(2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s and regular introduction of microbial competitors. These results contribute significantly toward the

  7. Use of Geographical Information Systems to influence the selection of sampling site locations for the evaluation of microbial diversity

    Soil microbial population densities can easily reach one billion cells per gram of soil; and soil microbial diversity has been estimated to reach ten thousand individual species per gram of soil. Soil type and underlying soil structure are considered primary determinants of microbial community struc...

  8. 16S/18S ribosomal DNA clone library analysis of rumen microbial diversity

    The rumen contains a complex ecosystem where billions of bacteria, archaea, protozoa and fungi reside. This diverse microbiota is well adapted to live in the rumen and play an important role in the digestion of feed and nutrient supply to the host in the form of microbial protein and volatile fatty acids. It is estimated that the rumen microbial population consists of about 106 protozoa/ml, 103-107 fungi/ml, 1010 bacteria/ml, and 109 methanogens/ml. To better understand the complex relationships in the rumen, it is necessary to gain an insight into the diversity of the rumen microbes and how the quantity and composition of rumen micro-organisms are altered by a number of different host factors such as age, genetics and diet. In the past, the diversity of micro-organisms from the digestive tracts of domesticated ruminants has been identified by classical microbiological techniques. However, given the fastidious growth requirements of rumen micro-organisms, it is reasonable to concede that the culture-dependent methods may select against some species, or taxonomic groups, leading researchers to underestimate the microbial diversity that is actually present in the rumen. In fact, it has been speculated that 90% of micro-organisms in nature have escaped traditional cultivation methods. Therefore, a major challenge in microbial ecology has been to assess the diversity and structure of natural microbial communities. The field of molecular biology has advanced with many innovative technological breakthroughs. The ability to extract and to isolate high-molecular weight DNA from rumen digesta, PCR amplify genes from specific microbial groups and obtain gene sequence data is now a routine event. The small subunit ribosomal RNA (SSU-rRNA) gene, called 16S in prokaryotes and 18S in eukaryotes, is the most widely used molecular marker to presumptively identify morphologically indistinguishable species, to infer their phylogenetic relationships, and to elucidate microbial

  9. Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-Diversity

    Ramirez, Gustavo A; Vaishampayan, Parag A.

    2011-01-01

    Alpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.

  10. A theoretical analysis of how strain-specific viruses can control microbial species diversity

    Thingstad, T. F.; Vage, S.; Storesund, J. E.; Sandaa, R.-A.; Giske, J.

    2014-01-01

    This work presents the first detailed analysis to the authors’ knowledge of how species-level diversity is a property emerging from competitive and defensive abilities at the organism level in a microbial system where the diversity-generating mechanism is strain-specific viral lysis. The theoretical analysis constitutes a general case treatment of the important special case question of what properties may make SAR11, a subphylum within the Alphaproteobacteria, so dominant in the pelagic envir...

  11. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

    Nyyssönen, Mari; Hultman, Jenni; Ahonen, Lasse; Kukkonen, Ilmo; Paulin, Lars; Laine, Pia; Itävaara, Merja; Auvinen, Petri

    2013-01-01

    Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metageno...

  12. Accessing diverse data comprehensively - CODM, the COSYNA data portal

    Breitbach, Gisbert; Krasemann, Hajo; Behr, Daniel; Beringer, Steffen; Lange, Uwe; Vo, Nhan; Schroeder, Friedhelm

    2016-07-01

    The coastal observation system COSYNA aims to describe the physical and biogeochemical state of a regional coastal system. The COSYNA data management is the link between observations, model results and data usage. The challenge for the COSYNA data management CODM1 COSYNA Data and Metadata, http://codm.hzg.de/codm or doi:10.17616/R3K02T is the integration of diverse data sources in terms of parameters, dimensionality and observation methods to gain a comprehensive view of the observations. This is achieved by describing the data using metadata in a generic way and by making all gathered data available for different analyses and visualisations in an interrelated way, independent of data dimensionality. Different parameter names for the same observed property are mapped to the corresponding CF2 climate and forecast standard name leading to standardised and comparable metadata. These metadata together with standardised web services are the base for the data portal. The URLs of these web services are also stored within the metadata as direct data access URLs, e.g. a map such as a GetMap request.

  13. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

    Kawakatsu, Taiji; Huang, Shao-Shan Carol; Jupe, Florian; Sasaki, Eriko; Schmitz, Robert J; Urich, Mark A; Castanon, Rosa; Nery, Joseph R; Barragan, Cesar; He, Yupeng; Chen, Huaming; Dubin, Manu; Lee, Cheng-Ruei; Wang, Congmao; Bemm, Felix; Becker, Claude; O'Neil, Ryan; O'Malley, Ronan C; Quarless, Danjuma X; Schork, Nicholas J; Weigel, Detlef; Nordborg, Magnus; Ecker, Joseph R

    2016-07-14

    The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant. PMID:27419873

  14. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M.; Ramón, Daniel; Porcar, Manuel

    2016-01-01

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

  15. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

    2016-01-01

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

  16. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

  17. Microbial diversity and potential pathogens in ornamental fish aquarium water.

    Katherine F Smith

    Full Text Available Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.. The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus and Chinese algae eaters (Gyrinocheilus aymonieri purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%, Bacteroidetes (18% and Planctomycetes (6%, with the top four phyla representing >80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species.

  18. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils.

    de Castro, Alinne Pereira; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  19. Microbial Diversity in Cerrado Biome (Neotropical Savanna Soils.

    Alinne Pereira de Castro

    Full Text Available The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture.

  20. Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils

    Pereira de Castro, Alinne; Sartori da Silva, Maria Regina Silveira; Quirino, Betania Ferraz; da Cunha Bustamante, Mercedes Maria; Krüger, Ricardo Henrique

    2016-01-01

    The Cerrado, the largest savanna region in South America, is located in central Brazil. Cerrado physiognomies, which range from savanna grasslands to forest formations, combined with the highly weathered, acidic clay Cerrado soils form a unique ecoregion. In this study, high-throughput sequencing of ribosomal RNA genes was combined with shotgun metagenomic analysis to explore the taxonomic composition and potential functions of soil microbial communities in four different vegetation physiognomies during both dry and rainy seasons. Our results showed that changes in bacterial, archaeal, and fungal community structures in cerrado denso, cerrado sensu stricto, campo sujo, and gallery forest soils strongly correlated with seasonal patterns of soil water uptake. The relative abundance of AD3, WPS-2, Planctomycetes, Thermoprotei, and Glomeromycota typically decreased in the rainy season, whereas the relative abundance of Proteobacteria and Ascomycota increased. In addition, analysis of shotgun metagenomic data revealed a significant increase in the relative abundance of genes associated with iron acquisition and metabolism, dormancy, and sporulation during the dry season, and an increase in the relative abundance of genes related to respiration and DNA and protein metabolism during the rainy season. These gene functional categories are associated with adaptation to water stress. Our results further the understanding of how tropical savanna soil microbial communities may be influenced by vegetation covering and temporal variations in soil moisture. PMID:26849674

  1. The effect of soil habitat connectivity on microbial interactions, community structure and diversity: a microcosm-based approach

    Wolf, A.B.

    2014-01-01

    Soils contain tremendous microbial phylogenetic and functional diversity. Recent advances in the application of molecular methods into microbial ecology have provided a new appreciation of the extent of soil-borne microbial diversity, but our understanding of the forces that shape and maintain this tremendous source of biodiversity still remain rudimentary. The overall aim of the work presented in this thesis was to increase our understanding of the forces that allow for the tremendous amount...

  2. Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures.

    Vázquez-Nion, D; Rodríguez-Castro, J; López-Rodríguez, M C; Fernández-Silva, I; Prieto, B

    2016-07-01

    Microbial communities of natural subaerial biofilms developed on granitic historic buildings of a World Heritage Site (Santiago de Compostela, NW Spain) were characterized and cultured in liquid BG11 medium. Environmental barcoding through next-generation sequencing (Pacific Biosciences) revealed that the biofilms were mainly composed of species of Chlorophyta (green algae) and Ascomycota (fungi) commonly associated with rock substrata. Richness and diversity were higher for the fungal than for the algal assemblages and fungi showed higher heterogeneity among samples. Cultures derived from natural biofilms showed the establishment of stable microbial communities mainly composed of Chlorophyta and Cyanobacteria. Although most taxa found in these cultures were not common in the original biofilms, they are likely common pioneer colonizers of building stone surfaces, including granite. Stable phototrophic multi-species cultures of known microbial diversity were thus obtained and their reliability to emulate natural colonization on granite should be confirmed in further experiments. PMID:27192622

  3. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity.

    Eloe-Fadrosh, Emiley A; Ivanova, Natalia N; Woyke, Tanja; Kyrpides, Nikos C

    2016-01-01

    Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. These results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages. PMID:27572438

  4. Microbial diversity in fecal samples depends on DNA extraction method

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten;

    2014-01-01

    was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). FINDINGS: In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France...

  5. Rhizoremediation for decontamination of long-term PCB contaminated soil with focus on microbial diversity

    Beranová, K.; Kochánková, L.; Macek, Tomáš; Macková, M.

    Elsevier. Roč. 131, 2S (2007), S243. ISSN 0168-1656. [European Congress on Biotechnology /13./. 16.09.2007-19.09.2007, Barcelona] R&D Projects: GA MŠk(CZ) 1P05ME745 Institutional research plan: CEZ:AV0Z40550506 Keywords : rhizoremediation * microbial diversity * PCB degradation Subject RIV: EI - Biotechnology ; Bionics

  6. The diversity of anti-microbial secondary metabolites produced by fungal endophytes: An interdisciplinary perspective

    Walaa Kamel Mousa; Raizada, Manish N

    2013-01-01

    Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human...

  7. The Diversity of Anti-Microbial Secondary Metabolites Produced by Fungal Endophytes: An Interdisciplinary Perspective

    Mousa, Walaa Kamel; Raizada, Manish N

    2013-01-01

    Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, huma...

  8. Diversity and dynamics of Antarctic marine microbial eukaryotes under manipulated environmental UV radiation

    Piquet, Anouk M. -T.; Bolhuis, Henk; Davidson, Andrew T.; Thomson, Paul G.; Buma, Anita G. J.

    2008-01-01

    In the light of the predicted global climate change, it is essential that the status and diversity of polar microbial communities is described and understood. In the present study, molecular tools were used to investigate the marine eukaryotic communities of Prydz Bay, Eastern Antarctica, from Novem

  9. Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition

    De Francisci, Davide; Kougias, Panagiotis; Treu, Laura; Campanaro, Stefano; Angelidaki, Irini

    2015-01-01

    The anaerobic digestion process is often inhibited by alteration of substrates and/or organic overload. This study aimed to elucidate changes of microbial ecology in biogas reactors upon radical changes of substrates and to determine their importance to process imbalance. For this reason......, continuously fed reactors were disturbed with pulses of proteins, lipids and carbohydrates and the microbial ecology of the reactors were characterized by 16S rRNA gene sequencing before and after the imposed changes. The microbial composition of the three reactors, initially similar, diverged greatly after...... substrate change. The greatest increase in diversity was observed in the reactor supplemented with carbohydrates and the microbial community became dominated by lactobacilli, while the lowest corresponded to the reactor overfed with proteins, where only Desulfotomaculum showed significant increase. The...

  10. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  11. Microbial diversity of a Brazilian coastal region influenced by an upwelling system and anthropogenic activity.

    Juliano C Cury

    Full Text Available BACKGROUND: Upwelling systems are characterised by an intense primary biomass production in the surface (warmest water after the outcrop of the bottom (coldest water, which is rich in nutrients. Although it is known that the microbial assemblage plays an important role in the food chain of marine systems and that the upwelling systems that occur in southwest Brazil drive the complex dynamics of the food chain, little is known about the microbial composition present in this region. METHODOLOGY/PRINCIPAL FINDINGS: We carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil. The aim was to analyse the horizontal and vertical variations of the microbial composition in two geographically close areas influenced by anthropogenic activity (sewage disposal/port activity and upwelling phenomena, respectively. A lower estimated diversity of microorganisms of the three domains of the phylogenetic tree of life was found in the water of the area influenced by anthropogenic activity compared to the area influenced by upwelling phenomena. We observed a heterogenic distribution of the relative abundance of taxonomic groups, especially in the Archaea and Eukarya domains. The bacterial community was dominated by Proteobacteria, Cyanobacteria and Bacteroidetes phyla, whereas the microeukaryotic community was dominated by Metazoa, Fungi, Alveolata and Stramenopile. The estimated archaeal diversity was the lowest of the three domains and was dominated by uncharacterised marine Crenarchaeota that were most closely related to Marine Group I. CONCLUSIONS/SIGNIFICANCE: The variety of conditions and the presence of different microbial assemblages indicated that the area of Arraial do Cabo can be used as a model for detailed studies that contemplate the correlation between pollution-indicating parameters and the depletion of microbial

  12. Abundance and functional diversity of riboswitches in microbial communities

    Gelfand Mikhail S

    2007-10-01

    Full Text Available Abstract Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes' which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes. Results Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932 and malate synthase glcB (COG2225 to be regulated by the glycine (GCVT riboswitch; fatty acid desaturase ole1 (COG1398, by the cobalamin (B12 riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182, by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP, cobalamine (B12, and glycine (GCVT, upstream of genes from COG4198. Conclusion This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes.

  13. Microbial Diversity in Soil Treatment Systems for Wastewater

    Van Cuyk, S.; Spear, J.; Siegrist, R.; Pace, N.

    2002-05-01

    There is an increasing awareness and concern over land based wastewater system performance with respect to the removal of bacteria and virus. The goal of this work is to describe and identify the organismal composition of the microbiota in the applied wastewater effluent, the rich biomat that develops at the infiltrative surface, and in the soil percolate in order to aid in the understanding of bacterial and virus purification in soil treatment systems. The traditional reliance on pure culture techniques to describe microbiota is circumvented by the employment of a molecular approach. Microbial community characterization is underway based on cloning and sequencing of 16S rRNA genes for phylogenetic analyses, to determine the nature and quantity of microbiota that constitute these ecosystems. Knowledge of the organisms naturally present can influence the design and treatment capacity of these widely used land based systems. Laboratory, intermediate and field scale systems are currently under study. Since human pathogens are known to exist in sewage effluents, their removal in wastewater infiltration systems and within the underlying soil are in need of a more fundamental understanding. The relationship between design parameters and environmental conditions, including a microbial characterization, is essential for the prevention of contamination in groundwater sources. Preliminary results indicate the presence of uncultured organisms and phylogenetic kinds that had not been detected in these systems using other methods. Acinetobacter johnsonii and Acrobacter cryaerophilus were the two dominant species found in septic tank effluent, comprising 20% and 11% of the library respectively. In soil samples collected from the infiltrative surface of a column dosed with STE, there was no dominant bacterial species present. Percolate samples collected from the outflow of the column showed that a tuber borchii symbiont, a common soil microorganism, dominated the bacterial

  14. Molecular microbial diversity of a spacecraft assembly facility

    Venkateswaran, K.; Satomi, M.; Chung, S.; Kern, R.; Koukol, R.; Basic, C.; White, D.

    2001-01-01

    In ongoing investigations to map and archive the microbial footprints in various components of the spacecraft and its accessories, we have examined the microbial populations of the Jet Propulsion Laboratory's Spacecraft Assembly Facility (JPL-SAF). Witness plates made up of spacecraft materials, some painted with spacecraft qualified paints, were exposed for approximately 7 to 9 months at JPL-SAF and examined the particulate materials collected for the incidence of total cultivable aerobic heterotrophs and heat-tolerant (80 degrees C for 15-min.) spore-formers. The results showed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non-coated stainless steel witness plates. Among the four paints tested, witness plates coated with NS43G accumulated the highest number of particles, and hence attracted more cultivable microbes. The conventional microbiological examination revealed that the JPL-SAF harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. Most of the isolated microbes were heat resistant to 80 degrees C and proliferate at 60 degrees C. The phylogenetic relationships among 23 cultivable heat-tolerant microbes were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. By 16S rDNA sequence analysis, the isolates fell into seven clades: Bacillus licheniformis, B. pumilus, B. cereus, B. circulans, Staphylococcus capitis, Planococcus sp. and Micrococcus lylae. In contrast to the cultivable approach, direct DNA isolation, cloning and 16S rDNA sequencing analysis revealed equal representation of both Gram-positive and Gram-negative microorganisms.

  15. Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water.

    Wouters, Katinka; Moors, Hugo; Boven, Patrick; Leys, Natalie

    2013-12-01

    The Boom Clay in Belgium is investigated in the context of geological nuclear waste disposal, making use of the High Activity Disposal Experimental Site (HADES) underground research facility. This facility, located in the Boom Clay at a depth of 225 m below the surface, offers a unique access to a microbial community in an environment, of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a microbial community in water samples retrieved from a Boom Clay piezometer (borehole water). Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community are disclosed. Despite the presumed low-energy environment, microscopy and molecular analyses show a large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among 10 borehole water samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, a corresponding large fraction of this community is found cultivable and active. In conclusion, this study shows the possibility of a microbial community of relative complexity to persist in subsurface Boom Clay borehole water. PMID:23802615

  16. Stress response, gut microbial diversity and sexual signals correlate with social interactions.

    Levin, Iris I; Zonana, David M; Fosdick, Bailey K; Song, Se Jin; Knight, Rob; Safran, Rebecca J

    2016-06-01

    Theory predicts that social interactions are dynamically linked to phenotype. Yet because social interactions are difficult to quantify, little is known about the precise details on how interactivity is linked to phenotype. Here, we deployed proximity loggers on North American barn swallows (Hirundo rustica erythrogaster) to examine intercorrelations among social interactions, morphology and features of the phenotype that are sensitive to the social context: stress-induced corticosterone (CORT) and gut microbial diversity. We analysed relationships at two spatial scales of interaction: (i) body contact and (ii) social interactions occurring between 0.1 and 5 m. Network analysis revealed that relationships between social interactions, morphology, CORT and gut microbial diversity varied depending on the sexes of the individuals interacting and the spatial scale of interaction proximity. We found evidence that body contact interactions were related to diversity of socially transmitted microbes and that looser social interactions were related to signalling traits and CORT. PMID:27354713

  17. ERDDAP - An Easier Way for Diverse Clients to Access Scientific Data From Diverse Sources

    Mendelssohn, R.; Simons, R. A.

    2008-12-01

    ERDDAP is a new open-source, web-based service that aggregates data from other web services: OPeNDAP grid servers (THREDDS), OPeNDAP sequence servers (Dapper), NOS SOAP service, SOS (IOOS, OOStethys), microWFS, DiGIR (OBIS, BMDE). Regardless of the data source, ERDDAP makes all datasets available to clients via standard (and enhanced) DAP requests and makes some datasets accessible via WMS. A client's request also specifies the desired format for the results, e.g., .asc, .csv, .das, .dds, .dods, htmlTable, XHTML, .mat, netCDF, .kml, .png, or .pdf (formats more directly useful to clients). ERDDAP interprets a client request, requests the data from the data source (in the appropriate way), reformats the data source's response, and sends the result to the client. Thus ERDDAP makes data from diverse sources available to diverse clients via standardized interfaces. Clients don't have to install libraries to get data from ERDDAP because ERDDAP is RESTful and resource-oriented: a URL completely defines a data request and the URL can be used in any application that can send a URL and receive a file. This also makes it easy to use ERDDAP in mashups with other web services. ERDDAP could be extended to support other protocols. ERDDAP's hub and spoke architecture simplifies adding support for new types of data sources and new types of clients. ERDDAP includes metadata management support, catalog services, and services to make graphs and maps.

  18. Comparison of three clustering approaches for detecting novel environmental microbial diversity.

    Forster, Dominik; Dunthorn, Micah; Stoeck, Thorsten; Mahé, Frédéric

    2016-01-01

    Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR(2)) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR(2). Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity. PMID:26966652

  19. Pattern of genetic diversity among Fusarium wilt resistant castor germplasm accessions (Ricinus communis L.

    K. Anjani

    2010-03-01

    Full Text Available Wilt caused by Fusarium oxysporum f.sp. ricini (Wr Gordon is one of the major yield losing diseases in castor.Cultivating wilt resistant cultivars is an effective strategy to control the disease. Utilization of diverse sources ofstable resistance is a prerequisite for durable resistance breeding. The experiment was conducted to identifygenetically diverse resistant sources in castor germplasm. Genetic diversity among 20 identified wilt resistantgermplasm was assessed using multivariate classificatory methods. Wide genetic diversity was demonstratedamong these accessions. These accessions are valuable in wilt resistance breeding programme. They wouldserve as base diverse material for wilt resistance breeding, wilt resistant genepool construction and moleculartagging of resistant genes.

  20. Characterization of the microbial diversity in yacon spontaneous fermentation

    Reina, L. D.; Pérez-Díaz, I. M.; Breidt, F.; Azcarate-Peril, M. A.; Medina, E.; Butz, N.V.

    2015-01-01

    The prebiotic fructooligosaccharides (FOS) content of yacon makes this root an attractive alternative for the supplementation of a variety of food products. The preservation of yacon by fermentation has been proposed as an alternative to increase the probiotic content of the root concomitantly with its shelf life. Thus the fermented yacon could have significant functional content. The objective of this research was to characterize the biochemistry and microbiology of spontaneous yacon fermentation and define the viability of the proposed process. The biochemical analysis of spontaneous heterolactic fermentation of yacon showed a progressive drop in pH with increased lactic and acetic acids, and the production of mannitol during fermentation. The microbial ecology of yacon fermentation was investigated using culture-dependent and culture-independent methods. Bacterial cell counts revealed a dominance of lactic acid bacteria (LAB) over yeasts, which were also present during fermentation. Results showed that the heterofermentative LAB were primarily Leuconostoc species, which dominated the fermentation. The fermentation of yacon by Leuconostoc spp. is thus presented as a viable method to achieve long term preservation of this root. PMID:25777679

  1. The veterinary antibiotic oxytetracycline and Cu influence functional diversity of the soil microbial community

    Kong, W.-D. [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China); Zhu, Y.-G. [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China)]. E-mail: ygzhu@mail.rcees.ac.cn; Fu, B.-J. [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China); Marschner, P. [Soil and Land Systems, School of Earth and Environmental Sciences, University of Adelaide, DP 636, 5005 (Australia); He, J.-Z. [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China)

    2006-09-15

    There are increasing concerns over the effects of veterinary antibiotics and heavy metals in agricultural soils. The widely used veterinary antibiotic oxytetracycline (OTC), Cu and their combination on soil microbial community function were assessed with the Biolog method. The microbial community was extracted from the soil and exposed to a 0.85% sodium chloride solution containing OTC (0, 1, 5, 11, 43, 109 and 217 {mu}M), or Cu (0, 10, 20, 100 and 300 {mu}M), or combination of the two pollutants (OTC 0, 5, 11 {mu}M and Cu 0, 20 {mu}M). Functional diversity, evenness, average well color development (AWCD) and substrate utilization decreased significantly with increasing concentrations of OTC or Cu (p < 0.005). The critical concentrations were 11 {mu}M for OTC and 20 {mu}M for Cu. The combination of OTC and Cu significantly decreased Shannon's diversity, evenness and utilization of carbohydrates and carboxylic acids compared to individual one of the contaminants. The antibiotic OTC and Cu had significant negative effects on soil microbial community function, particularly when both pollutants were present. - Oxytetracycline reduces the functional diversity of soil microbial community, and the combination of Cu and oxytetracycline leads to a further reduction.

  2. Microbial diversity in European and South American spacecraft assembly clean rooms

    Moissl-Eichinger, Christine; Stieglmeier, Michaela; Schwendner, Petra

    Spacecraft assembly clean rooms are unique environments for microbes: Due to low nutri-ent levels, desiccated, clean conditions, constant control of humidity and temperature, these environments are quite inhospitable to microbial life and even considered "extreme". Many procedures keep the contamination as low as possible, but these conditions are also highly se-lective for indigenous microbial communities. For space missions under planetary protection requirements, it is crucial to control the contaminating bioburden as much as possible; but for the development of novel cleaning/sterilization methods it is also important to identify and characterize (understand) the present microbial community of spacecraft clean rooms. In prepa-ration for the recently approved ESA ExoMars mission, two European and one South American spacecraft assembly clean rooms were analyzed with respect to their microbial diversity, using standard procedures, new cultivation approaches and molecular methods, that should shed light onto the presence of planetary protection relevant microorganisms. For this study, the Her-schel Space Observatory (launched in May 2009) and its housing clean rooms in Friedrichshafen (Germany), at ESTEC (The Netherlands) and CSG, Kourou (French Guyana) were sampled during assembly, test and launch operations. Although Herschel does not demand planetary protection requirements, all clean rooms were in a fully operating state during sampling. This gave us the opportunity to sample the microbial diversity under strict particulate and molecular contamination-control. Samples were collected from spacecraft and selected clean room surface areas and were subjected to cultivation assays (32 different media), molecular studies (based on 16S rRNA gene sequence analysis) and quantitative PCR. The results from different strategies will be compared and critically discussed, showing the advantages and limits of the selected methodologies. This talk will sum up the lessons

  3. Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

    Jiang, Hongchen; DONG, HAILIANG; Zhang, Gengxin; Yu, Bingsong; Chapman, Leah R.; Matthew W Fields

    2006-01-01

    We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10...

  4. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. PMID:24118303

  5. Carbon Turnover and Dynamics from Biochemically Diverse Microbial Groups in Temperate and Tropical Forest Soils

    Throckmorton, H.; Bird, J. A.; Firestone, M.; Horwath, W. R.

    2009-12-01

    Microorganisms represent an important source of actively cycling carbon (C) in terrestrial ecosystems, yet little is known of the fate or stability of microbial C in soils or the relative importance of microbial biochemistry as a factor influencing C stabilization. This project utilized uniformly 13C-labeled, biochemically diverse, non-living microbial residues including fungi, actinomycetes, bacteria Gm+, and bacteria Gm- as substrates in a reciprocal transplant experiment in a temperate forest in the Sierra Nevada and a tropical forest in Puerto Rico. Microbes were isolated from each site, grown with 13C media, autoclaved and lypholyzed, and non-living residues were added back to soils at each site. The temperate and tropical soils were analyzed over a 3 and 2 year period, respectively. Microbial C turnover differed substantially between the two sites, with microbial C levels stabilizing at 35% of initial input C after 12 months in the temperate site, while in Puerto Rico microbial C does not to begin to stabilize until about 16 months at less than 10% of initial input C. Physical fractionation of soils indicate that, despite the substantial difference in microbial C turnover between the two sites, microbial C turnover in the fraction occluded within aggregates and in the fraction associated with mineral surfaces did not differ between the two sites; the only physical fraction where microbial C turnover differed between the two sites was the light fraction, which is unassociated with the mineral matrix. These results underline the importance of the soil mineral matrix for protecting soil organic matter from mineralization. Although microbial groups did not differ in their relative partitioning among soil physical fractions, there was some evidence for slower overall decomposition of bacteria Gm+ and fungi relative to bacteria Gm- and actinomycetes; however, the observed effect was not substantial. Pyrolysis-GC-MS-IRMS results suggest there are some differences in

  6. The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity

    Timothy M. Vogel

    2013-02-01

    Full Text Available The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems.

  7. New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia.

    Watts, Mathew P; Moreau, John W

    2016-02-01

    Thiocyanate is a common contaminant of the gold mining and coal coking industries for which biological degradation generally represents the most viable approach to remediation. Recent studies of thiocyanate-degrading bioreactor systems have revealed new information on the structure and metabolic activity of thiocyanate-degrading microbial consortia. Previous knowledge was limited primarily to pure-culture or co-culture studies in which the effects of linked carbon, sulfur and nitrogen cycling could not be fully understood. High throughput sequencing, DNA fingerprinting and targeted gene amplification have now elucidated the genetic and metabolic diversity of these complex microbial consortia. Specifically, this has highlighted the roles of key consortium members involved in sulfur oxidation and nitrification. New insights into the biogeochemical cycling of sulfur and nitrogen in bioreactor systems allow tailoring of the microbial metabolism towards meeting effluent composition requirements. Here we review these rapidly advancing studies and synthesize a conceptual model to inform new biotechnologies for thiocyanate remediation. PMID:26596573

  8. Modeling spatial accessibility of immigrants to culturally diverse family physicians.

    Wanga, Lu; Roisman, Deborah

    2011-01-01

    This article uses accessibility as an analytical tool to examine health care access among immigrants in a multicultural urban setting. It applies and improves on two widely used accessibility models—the gravity model and the two-step floating catchment area model—in measuring spatial accessibility by Mainland Chinese immigrants in the Toronto Census Metropolitan Area. Empirical data on physician-seeking behaviors are collected through two rounds of questionnaire surveys. Attention is focused on journey to physician location and utilization of linguistically matched family physicians. Based on the survey data, a two-zone accessibility model is developed by relaxing the travel threshold and distance impedance parameters that are traditionally treated as a constant in the accessibility models. General linear models are used to identify relationships among spatial accessibility, geography, and socioeconomic characteristics of Mainland Chinese immigrants. The results suggest a spatial mismatch in the supply of and demand for culturally sensitive care, and residential location is the primary factor that determines spatial accessibility to family physicians. The article yields important policy implications. PMID:21488318

  9. Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

    Li, D.

    2012-07-13

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  10. Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield.

    Nyyssönen, Mari; Hultman, Jenni; Ahonen, Lasse; Kukkonen, Ilmo; Paulin, Lars; Laine, Pia; Itävaara, Merja; Auvinen, Petri

    2014-01-01

    Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metagenomic sequencing revealed variable carbon and nutrient utilization strategies as well as specific functional and physiological adaptations uniquely associated with specific environmental conditions. Altogether, our results show that predominant geological and hydrogeochemical conditions, including the existence and connectivity of fracture systems and the low amounts of available energy, have a key role in controlling microbial ecology and evolution in the nutrient and energy-poor deep crustal biosphere. PMID:23949662

  11. Solid and Aqueous Geochemical Controls on Phylogenetic Diversity and Abundance of Microbial Biofilms

    Jones, A. A.; Bennett, P. C.

    2015-12-01

    In the subsurface, the vast majority of microorganisms are found in biofilms attached to mineral surfaces. The fickle nature of these environments (chemically and physically) likely causes dynamic ecological shifts in these microbial communities. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the role of mineralogy as part of a microbe-mineral-water ecosystem under variable pressures (mineralogy, pH, carbon, phosphate). Following multivariate analyses, pH was identified as the key physicochemical property associated with variation in both phylogenetic and taxonomic diversity as well as overall community structure (Pbiofilm accumulation (Pbiofilm accumulation (Pbiofilm accumulation (Pbiofilms. All reactors harbored structurally, taxonomically, and phylogenetically distinct microbial communities.

  12. Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method.

    Costa, Ohana Yonara Assis; Souto, Betulia Morais; Tupinambá, Daiva Domenech; Bergmann, Jessica Carvalho; Kyaw, Cynthia Maria; Kruger, Ricardo Henrique; Barreto, Cristine Chaves; Quirino, Betania Ferraz

    2015-01-01

    Sugarcane ethanol production occurs in non-sterile conditions, and microbial contamination can decrease productivity. In this study, we assessed the microbial diversity of contaminants of ethanol production in an industrial facility in Brazil. Samples obtained at different stages were analyzed by pyrosequencing-based profiling of bacterial and archaeal 16S rRNA genes and the fungal internal transcribed spacer region. A total of 355 bacterial groups, 22 archaeal groups, and 203 fungal groups were identified, and community changes were related to temperature changes at certain stages. After fermentation, Lactobacillus and unclassified Lactobacillaceae accounted for nearly 100 % of the bacterial sequences. Predominant Fungi groups were "unclassified Fungi," Meyerozyma, and Candida. The predominant Archaea group was unclassified Thaumarchaeota. This is the first work to assess the diversity of Bacteria, and Archaea and Fungi associated with the industrial process of sugarcane-ethanol production using culture-independent techniques. PMID:25404204

  13. Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

    Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

    2011-04-01

    Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples. PMID:21563009

  14. Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance.

    Wertz, Sophie; Degrange, Valérie; Prosser, James I; Poly, Franck; Commeaux, Claire; Guillaumaud, Nadine; Le Roux, Xavier

    2007-09-01

    Analysing the consequences of the decrease in biodiversity for ecosystem functioning and stability has been a major concern in ecology. However, the impact of decline in soil microbial diversity on ecosystem sustainability remains largely unknown. This has been assessed for decomposition, which is insured by a large proportion of the soil microbial community, but not for more specialized and less diverse microbial groups. We determined the impact of a decrease in soil microbial diversity on the stability (i.e. resistance and resilience following disturbance) of two more specialized bacterial functional groups: denitrifiers and nitrite oxidizers. Soil microbial diversity was reduced using serial dilutions of a suspension obtained from a non-sterile soil that led to loss of species with low cell abundance, inoculation of microcosms of the same sterile soil with these serial dilutions, and subsequent incubation to enable establishment of similar cell abundances between treatments. The structure, cell abundance and activity of denitrifying and nitrite-oxidizing communities were characterized after incubation. Increasing dilution led to a progressive decrease in community diversity as assessed by the number of denaturating gradient gel electrophoresis (DGGE) bands, while community functioning was not impaired when cell abundance recovered after incubation. The microcosms were then subjected to a model disturbance: heating to 42 degrees C for 24 h. Abundance, structure and activity of each community were measured 3 h after completion of the disturbance to assess resistance, and after incubation of microcosms for 1 month to assess resilience. Resistance and resilience to the disturbance differed between the two communities, nitrite oxidizers being more affected. However, reducing the diversity of the two microbial functional groups did not impair either their resistance or their resilience following the disturbance. These results demonstrate the low sensitivity of the

  15. Characterization of microbial diversity and community in water flooding oil reservoirs in China.

    Zhao, Lingxia; Ma, Ting; Gao, Mengli; Gao, Peike; Cao, Meina; Zhu, Xudong; Li, Guoqiang

    2012-10-01

    The diversity and distribution of bacterial and archaeal communities in four different water flooding oil reservoirs with different geological properties were investigated using 16S rDNA clone library construction method. Canonical correspondence analysis was used to analyze microbial community clustering and the correlation with environmental factors. The results indicated that the diversity and abundance in the bacterial communities were significantly higher than the archaeal communities, while both of them had high similarity within the communities respectively. Phylogenetic analysis showed that of compositions of bacterial communities were distinctly different both at phylum and genus level. Proteobacteria dominated in each bacterial community, ranging from 61.35 to 75.83 %, in which α-proteobacteria and γ-proteobacteria were the main groups. In comparison to bacterial communities, the compositions of archaeal communities were similar at phylum level, while varied at genus level, and the dominant population was Methanomicrobia, ranging from 65.91 to 92.74 % in the single oil reservoir. The factor that most significantly influenced the microbial communities in these reservoirs was found to be temperature. Other environmental factors also influenced the microbial communities but not significantly. It is therefore assumed that microbial communities are formed by an accumulated effect of several factors. These results are essential for understanding ecological environment of the water flooding oil reservoirs and providing scientific guidance to the performance of MEOR technology. PMID:22806743

  16. Diversity of key players in the microbial ecosystems of the human body

    Ferenc Jordán; Mario Lauria; Marco Scotti; Thanh-Phuong Nguyen; Paurush Praveen; Melissa Morine; Corrado Priami

    2015-01-01

    Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem...

  17. Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities

    Dopheide, Andrew; Lear, Gavin; He, Zhili; Zhou, Jizhong; Lewis, Gillian D.

    2015-01-01

    We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream). Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphor...

  18. Convergence of soil microbial properties after plant colonization of an experimental plant diversity gradient

    Steinauer, Katja; Jensen, Britta; Strecker, Tanja; de Luca, Enrica; Scheu, Stefan; Eisenhauer, Nico

    2016-01-01

    Background: Several studies have examined the effects of plant colonization on aboveground communities and processes. However, the effects of plant colonization on soil microbial communities are less known. We addressed this gap by studying effects of plant colonization within an experimental plant diversity gradient in subplots that had not been weeded for 2 and 5 years. This study was part of a long-term grassland biodiversity experiment (Jena Experiment) with a gradient in plant species ri...

  19. Insights into microbial diversity in wastewater treatment systems: How far have we come?

    Ferrera, Isabel; Sánchez, Olga

    2016-01-01

    Abstract Biological wastewater treatment processes are based on the exploitation of the concerted activity of microorganisms. Knowledge on the microbial community structure and the links to the changing environmental conditions is therefore crucial for the development and optimization of biological systems by engineers. The advent of molecular techniques occurred in the last decades quickly showed the inadequacy of culture-dependent methodologies to unveil the great level of diversity pre...

  20. Microbial diversity in rhizoremediation of long-term PCB contaminated soil

    Beranová, K.; Kochánková, L.; Macek, Tomáš; Macková, Martina

    Praha: VŠCHT Praha, 2007 - (Macková, M.; Macek, T.; Demnerová, K.; Pazlar, V.). s. 39 ISBN 978-80-7080-025-6. [Symposium on Biosorption and Bioremediation /4./. 26.08.2007-30.08.2007, Praha] R&D Projects: GA ČR GA203/06/0563; GA MŠk(CZ) 1P05ME745 Institutional research plan: CEZ:AV0Z40550506 Keywords : microbial diversity * polychlorinated biphenyls Subject RIV: EI - Biotechnology ; Bionics

  1. Microbial diversity in the human intestine and novel insights from metagenomics

    Ventura, Marco; Turroni, Francesca; Canchaya, Carlos; Vaughan, Elaine E.; O'Toole, Paul W.; Van Sinderen, Douwe

    2009-01-01

    Bacterial communities reside in very different ecological niches on and within the human host, such as those associated with the alimentary tract. The human gastrointestinal tract is populated with as many as 100 trillion bacterial cells, whose collective genome likely reflects the co-evolution between the microbial community and its host. Recent progress has highlighted the intriguing diversity of these bacterial populations and their important contributions to human physiology. Thus, a thor...

  2. Tricholoma matsutake Dominates Diverse Microbial Communities in Different Forest Soils▿†

    Vaario, Lu-Min; Fritze, Hannu; Spetz, Peter; Heinonsalo, Jussi; Hanajík, Peter; Pennanen, Taina

    2011-01-01

    Fungal and actinobacterial communities were analyzed together with soil chemistry and enzyme activities in order to profile the microbial diversity associated with the economically important mushroom Tricholoma matsutake. Samples of mycelium-soil aggregation (shiro) were collected from three experimental sites where sporocarps naturally formed. PCR was used to confirm the presence and absence of matsutake in soil samples. PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and d...

  3. Microbial Diversity Similarities in Periodontal Pockets and Atheromatous Plaques of Cardiovascular Disease Patients

    Serra e Silva Filho, Wagner; Casarin, Renato C. V.; Nicolela Junior, Eduardo L.; Passos, Humberto M.; Antônio W Sallum; Gonçalves, Reginaldo B.

    2014-01-01

    Background and Objective The immune and infectious alterations occurring in periodontitis have been shown to alter the development and severity of cardiovascular disease. One of these relationships is the translocation of oral bacteria to atheroma plaques, thereby promoting plaque development. Thus, the aim of this study was to assess, by 16s cloning and sequencing, the microbial diversity of the subgingival environment and atheroma plaques of patients concomitantly suffering from periodontit...

  4. Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae).

    Kelley, Scott T; Dobler, Susanne

    2011-05-01

    Herbivorous beetles comprise a significant fraction of eukaryotic biodiversity and their plant-feeding adaptations make them notorious agricultural pests. Despite more than a century of research on their ecology and evolution, we know little about the diversity and function of their symbiotic microbial communities. Recent culture-independent molecular studies have shown that insects possess diverse gut microbial communities that appear critical for their survival. In this study, we combined culture-independent methods and high-throughput sequencing strategies to perform a comparative analysis of Longitarsus flea-beetles microbial community diversity (MCD). This genus of beetle herbivores contains host plant specialists and generalists that feed on a diverse array of toxic plants. Using a deep-sequencing approach, we characterized the MCD of eleven Longitarsus species across the genus, several of which represented independent shifts to the same host plant families. Database comparisons found that Longitarsus-associated microbes came from two habitat types: insect guts and the soil rhizosphere. Statistical clustering of the Longitarsus microbial communities found little correlation with the beetle phylogeny, and uncovered discrepancies between bacterial communities extracted directly from beetles and those from frass. A Principal Coordinates Analysis also found some correspondence between beetle MCD and host plant family. Collectively, our data suggest that environmental factors play a dominant role in shaping Longitarsus MCD and that the root-feeding beetle larvae of these insects are inoculated by soil rhizosphere microbes. Future studies will investigate MCD of select Longitarsus species across their geographic ranges and explore the connection between the soil rhizosphere and the beetle MCD. PMID:20844936

  5. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

    Trivedi, Pankaj; He, Zhili; Joy D Van Nostrand; Albrigo, Gene; Zhou, Jizhong; Wang, Nian

    2011-01-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘Ca. L. asiaticus'...

  6. Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

    Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

    2014-01-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

  7. Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells

    Wuchter, Cornelia; Banning, Erin; Mincer, Tracy J.; Drenzek, Nicholas J; Coolen, Marco J. L.

    2013-01-01

    The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S., but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina MiSeq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producin...

  8. Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells.

    Cornelia eWuchter; Erin eBanning; Tracy eMincer; Drenzek, Nicholas J; Marco JL Coolen

    2013-01-01

    The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S, but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina Miseq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing...

  9. Relationship between microbial diversity and chemical contamination along a 50-year-old sediment core

    Berthe, T.; Petit, F.; Boust, D.; Lesueur, P.; Roose-Amsaleg, C.; Cécillon, S.; Kaci-Benaicha, A.

    2013-12-01

    The purpose of this study was to evaluate the potential use of sediment microbial diversity (community structure) as an indicator of the impact of anthropogenic activities within an estuarine ecosystem. The diversity of microbial communities was investigated along a 5-m-long sediment core collected in an anthropized European estuary (Seine, France), giving an evolution of trace metal, polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls (PCBs) concentrations over the last 50 years. An increase of trace metal and PCB concentrations are observed with depth, with an enrichment of these contaminants in the 1970s. The concentration profiles of light, intermediate and heavy PAHs showed distinct peaks, but the highest total PAH concentration was also detected in the sediment from the 1970s. We first investigated the bacterial community resistant to cobalt, zinc and cadmium by analyzing the diversity of the czcA gene encoding an RND efflux pump (Heavy Metal Efflux-RND) in 5-year and 33-year-old sediment samples displaying contrasted concentrations in these trace metals. The diversity of the czcA gene was reduced in the 33-year-old and more contaminated sediments suggesting a selection of resistant bacterial species. A molecular fingerprinting method (DGGE) was used to study the evolution of total microbial (Bacteria and Archaea) community structures for samples selected along the sediment core. A correlation is observed between the bacterial community structures, the sediment age, the trace metal and PAH concentrations. The metabolically active and total microbial communities were further characterized by a microarray approach (Phylochips) in sediment samples selected according to the DGGE results. Bacterial diversity was found dominated by Proteobacteria, Actinobacteria, and Firmicutes in all analyzed samples. Diversity of phylotypes corresponds to changes in PAH and trace metal concentrations in sediment, suggesting that chemical contaminants have

  10. Mechanisms Controlling Carbon Turnover from Diverse Microbial Groups in Temperate and Tropical Forest Soils

    Throckmorton, H.; Dane, L.; Bird, J. A.; Firestone, M. K.; Horwath, W. R.

    2010-12-01

    Microorganisms represent an important intermediate along the pathway of plant litter decomposition to the formation of soil organic matter (SOM); yet little is known of the fate and stability of microbial C in soils and the importance of microbial biochemistry as a factor influencing SOM dynamics. This research investigates mechanisms controlling microbial C stabilization in a temperate forest in the Sierra Nevada of California (CA) and a tropical forest in Puerto Rico (PR). Biochemically diverse microbial groups (fungi, actinomycetes, bacteria gram (+), and bacteria gram (-)) were isolated from both sites, grown in the laboratory with C13 media, killed, and nonliving residues were added back to soils as a reciprocal transplant of microbial groups. The native microbial community in CA is dominated by fungi and in PR is dominated by bacteria, which provides an opportunity to asses the metabolic response of distinct microbial communities to the diverse microbial additions. CA and PR soils were sampled five times over a 3 and 2 year period, respectively. In CA there was no significant difference in the mean residence time (MRT) of diverse C13 microbial treatments; whereas in PR there were significant differences, whereby temperate fungi, temperate Gram (+) bacteria, and tropical actinomycetes exhibited a significantly longer MRT as compared with tropical fungi and temperate Gram (-). These results suggest that a bacterial dominated microbial community discriminates more amongst diverse substrates than a fungal-dominated community. MRT for labeled-C in CA was 5.21 ± 1.11 years, and in PR was 2.22 ± 0.45. Despite substantial differences in MRT between sites, physical fractionation of soils into light (LF), aggregated-occluded (OF), and mineral-associated (MF) fractions provided evidence that accelerated decomposition in PR (presumably due to climate) operated primarily on labeled-C unassociated with the mineral matrix (LF); labeled-C occluded within aggregates (OF) or

  11. Effects of sulphamethazine and zinc on the functional diversity of microbial communities during composting.

    Duan, Manli; Yang, Jiu; Gu, Jie; Qian, Xun; Sun, Wei; Gao, Hua; Wang, Xiaojuan

    2016-06-01

    The changes in the functional diversity of the microbial community in a compost matrix with a single or compound addition of zinc (Zn; 0, 600, and 1800 mg/kg) and sulphamethazine (SM2; 0, 1, and 25 mg/kg) were studied with the Biolog method during composting. The microbial community was extracted from the compost matrix comprising swine manure and wheat straw at day 6 (themophilic period) and day 25 (mature period) of composting. Results proved that the Shannon index, average well-colour development, and substrate utilization significantly decreased as the concentrations of SM2 and Zn increased on day 6. The negative effect of the combined addition of SM2 and Zn was lower than that of the individual addition of SM2 and Zn. On day 25, the inhibition effect disappeared, and microbial metabolic activities were higher than those on day 6. The effects of SM2 and Zn could be further differentiated via the principal component analysis (PCA) and cluster analysis. On day 6, the treatments were divided into three groups by PC1 and PC2. The separation of the different treatments in the PCA plots became increasingly apparent on day 25. In conclusion, the effects of SM2 and Zn on the microbial community during composting became evident in the themophilic period and that the microbial activity recovered in the mature period. The combination of SM2 and Zn decreased the inhibition with the addition of individual additive. PMID:26540188

  12. Microbial diversity similarities in periodontal pockets and atheromatous plaques of cardiovascular disease patients.

    Wagner Serra e Silva Filho

    Full Text Available BACKGROUND AND OBJECTIVE: The immune and infectious alterations occurring in periodontitis have been shown to alter the development and severity of cardiovascular disease. One of these relationships is the translocation of oral bacteria to atheroma plaques, thereby promoting plaque development. Thus, the aim of this study was to assess, by 16s cloning and sequencing, the microbial diversity of the subgingival environment and atheroma plaques of patients concomitantly suffering from periodontitis and obstructive coronary artery atherosclerosis (OCAA. METHODS: Subgingival biofilm and coronary balloons used in percutaneous transluminal coronary angioplasty were collected from 18 subjects presenting with generalized moderate to severe periodontitis and OCAA. DNA was extracted and the gene 16S was amplified, cloned and sequenced. RESULTS: Significant differences in microbial diversity were observed between both environments. While subgingival samples mostly contained the phylum Firmicutes, in coronary balloons, Proteobacteria (p<0.05 was predominant. In addition, the most commonly detected genera in coronary balloons were Acinetobacter, Alloprevotella, Pseudomonas, Enterobacter, Sphingomonas and Moraxella, while in subgingival samples Porphyromonas, Filifactor, Veillonella, Aggregatibacter and Treponema (p<0.05 were found. Interestingly, 17 identical phylotypes were found in atheroma and subgingival samples, indicating possible bacterial translocation between periodontal pockets and coronary arteries. CONCLUSION: Periodontal pockets and atheromatous plaques of cardiovascular disease patients can present similarities in the microbial diversity.

  13. Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert.

    Rasuk, Maria Cecilia; Fernández, Ana Beatriz; Kurth, Daniel; Contreras, Manuel; Novoa, Fernando; Poiré, Daniel; Farías, María Eugenia

    2016-01-01

    The Atacama Desert has extreme environmental conditions that allow the development of unique microbial communities. The present paper reports the bacterial diversity of microbial mats and sediments and its mineralogical components. Some physicochemical conditions of the water surrounding these ecosystems have also been studied trying to determine their influence on the diversity of these communities. In that way, mats and sediments distributed among different hypersaline lakes located in salt flats of the Atacama Desert were subjected to massive parallel sequencing of the V4 region of the 16S rRNA genes of Bacteria. A higher diversity in sediment than in mat samples have been found. Lakes that harbor microbial mats have higher salinity than lakes where mats are absent. Proteobacteria and/or Bacteroidetes are the major phyla represented in all samples. An interesting item is the finding of a low proportion or absence of Cyanobacteria sequences in the ecosystems studied, suggesting the possibility that other groups may be playing an essential role as primary producers in these extreme environments. Additionally, the large proportion of 16S rRNA gene sequences that could not be classified at the level of phylum indicates potential new phyla present in these ecosystems. PMID:26224164

  14. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems.

    Lallias, Delphine; Hiddink, Jan G; Fonseca, Vera G; Gaspar, John M; Sung, Way; Neill, Simon P; Barnes, Natalie; Ferrero, Tim; Hall, Neil; Lambshead, P John D; Packer, Margaret; Thomas, W Kelley; Creer, Simon

    2015-05-01

    Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a 'melting pot' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype-environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both. PMID:25423027

  15. Microbial diversity of the 180 million-year-old Toarcian argillite from Tournemire, France

    Even though the microbiology of various subsurface environments has been investigated for more than 30 a, the microbial diversity of deep argillaceous media is still poorly known. In the context of radioactive waste disposal in clayey formations, the consequence of microbial activity is of concern regarding e.g. the corrosion of metallic components. The purpose of the present work was to characterise the cultivable microbial diversity of different zones of the Toarcian argillite of Tournemire (France) as a preliminary indication regarding the potential of development of microbes in such subterrestrial environments. Cores were drilled in the Excavation Damaged Zone (EDZ) and in the deeper undisturbed zone of the argillite layer, as well as in a zone intersected by a geological fault. Samples from the wall of the drift were also collected. Microorganisms were cultivated from all samples, but the biodiversity differed depending mainly on the O2 and moisture content. Aerobic bacteria were identified on the wall, in the EDZ and in the wet faulted area, whereas SO4-reducing bacteria were isolated from the wet faulted area only. Anaerobic heterotrophs were cultivated from all zones. One hundred and twelve isolates were identified. Small ribosomal subunit gene sequences showed that bacteria of the undisturbed zone were affiliated to three genera only, whereas the three other sampled zones harbour more diverse microflora, including isolates closely related to taxons characterized from subsurface, deep marine and polar environments.

  16. Insights into microbial diversity in wastewater treatment systems: How far have we come?

    Ferrera, Isabel; Sánchez, Olga

    2016-01-01

    Biological wastewater treatment processes are based on the exploitation of the concerted activity of microorganisms. Knowledge on the microbial community structure and the links to the changing environmental conditions is therefore crucial for the development and optimization of biological systems by engineers. The advent of molecular techniques occurred in the last decades quickly showed the inadequacy of culture-dependent methodologies to unveil the great level of diversity present in sludge samples. Initially, culture-independent technologies and more recently the application of -omics in wastewater microbiology, have drawn a new view of microbial diversity and function of wastewater treatment systems. This article reviews the current knowledge on the topic placing emphasis on crucial microbial processes carried out in biological wastewater treatment systems driven by specific groups of microbes, such as nitrogen and phosphorus removal bacteria, filamentous and electrogenic microorganisms, as well as Archaea. Despite the recent -omics has offered substantial insights into the diversity and ecophysiology of these bacteria never envisioned before by providing millions of sequence reads at an unprecedented scale, studies based on high-throughput sequencing are still scarce. In order to obtain significant gains in the analysis of structure-function relationships, a greater sequencing investment is needed, particularly to uncover gene expression patterns of functionally relevant genes. PMID:27071535

  17. Ocean microbial metagenomics

    Kerkhof, Lee J.; Goodman, Robert M.

    2009-09-01

    Technology for accessing the genomic DNA of microorganisms, directly from environmental samples without prior cultivation, has opened new vistas to understanding microbial diversity and functions. Especially as applied to soils and the oceans, environments on Earth where microbial diversity is vast, metagenomics and its emergent approaches have the power to transform rapidly our understanding of environmental microbiology. Here we explore select recent applications of the metagenomic suite to ocean microbiology.

  18. 76 FR 60651 - Leased Commercial Access; Development of Competition and Diversity in Video Programming...

    2011-09-29

    ... Access; Development of Competition and Diversity in Video Programming Distribution and Carriage; Revision... Video Programming Distribution and Carriage AGENCY: Federal Communications Commission. ACTION: Final... carriage of video programming vendors by multichannel video programming distributors (``MVPDs''), known...

  19. GeoChip-based Analysis of Groundwater Microbial Diversity in Norman Landfill

    Lu, Zhenmei; He, Zhili; Parisi, Victoria; Kang, Sanghoon; Deng, Ye; Nostrand, Joy Van; Masoner, Jason; Cozzarelli, Isabelle; Suflita, Joseph; Zhou, Jizhong

    2010-05-17

    The Norman Landfill is a closed municipal solid waste landfill located on an alluvium associated with the Canadian River in Norman, Oklahoma. It has operated as a research site since 1994 because it is typical of many closed landfill sites across the U.S. Leachate from the unlined landfill forms a groundwater plume that extends downgradient approximately 250 m from the landfill toward the Canadian River. To investigate the impact of the landfill leachate on the diversity and functional structure of microbial communities, groundwater samples were taken from eight monitoring wells at a depth of 5m, and analyzed using a comprehensive functional gene array covering about 50,000 genes involved in key microbial processes, such as biogeochemical cycling of C, N, P, and S, and bioremediation of organic contaminants and metals. Wells are located within a transect along a presumed flow path with different distances to the center of the leachate plume. Our analyses showed that microbial communities were obviously impacted by the leachate-component from the landfill. The number of genes detected and microbial diversity indices in the center (LF2B) and its closest (MLS35) wells were significantly less than those detected in other more downgradient wells, while no significant changes were observed in the relative abundance (i.e., percentage of each gene category) for most gene categories. However, the microbial community composition or structure of the landfill groundwater did not clearly show a significant correlation with the distance from well LF2B. Burkholderia sp. and Pseudomonas sp. were found to be the dominant microbial populations detected in all wells, while Bradyrhizobium sp. and Ralstonia sp. were dominant populations for seven wells except LF2B. In addition, Mantel test and canonical correspondence analysis (CCA) indicate that pH, sulfate, ammonia nitrogen and dissolved organic carbon (DOC) have significant effects on the microbial community structure. The results

  20. A review of diversity-stability relationship of soil microbial community:What do we not know?

    Huan Deng

    2012-01-01

    The impact of decreased biodiversity on ecosystem stability,or the diversity-stability (D-S) relationship,is one of the major concerns of modern ecological studies.Studies on the D-S relationship for soil microbial communities began in 2000 when the fumigation method was developed to generate different levels of soil microbial biodiversity.The studies used various measures and levels of biodiversity,and covered several functional parameters.Due to the lack of general concepts and reliable approaches to define microbial species,studies on the D-S relationship of soil microbial communities concentrate on genetic diversity and functional diversity more than species diversity.Contradictory results were observed in various studies on D-S relationship with possible factors affecting or even changing the directions of the D-S relationship including:(1) the methods of stability measurement,(2) the techniques in microbial diversity measurement,(3) the measures and levels of diversity,(4) the type and strength of disturbance,(5) the traits of functions,and (6) the hidden treatments stemming from diversity manipulation.We argue that future studies should take diversity,species composition and interaction,and soil environmental conditions holistically into account in D-S studies to develop modeling to predict soil functional stability.We also suggest that studies should be carried out on a wider range of disturbance types and functional parameters,and efforts be shifted towards long-term field studies.

  1. Effect of distance and depth on soil microbial biomass, N mineralization and genetic diversity of Rhizobia under Acacia senegal Tree

    The relations between plants and soil biota involve positive and negative feedbacks between soil organisms, their chemical environment, and plants. Then, the characterization of microbial community functioning and their diversity are important to understand these linkages. An experiment was conducted in a field system for two years (2005 and 2006) to investigate the effect of distance from tree stem on soil microbial biomass, N mineral content and the diversity of rhizobia associated to Acacia senegal. (Author)

  2. Effect of distance and depth on soil microbial biomass, N mineralization and genetic diversity of Rhizobia under Acacia senegal Tree

    Fall, D.; Faye, A.; Sall, S. N.; Diouf, D.

    2009-07-01

    The relations between plants and soil biota involve positive and negative feedbacks between soil organisms, their chemical environment, and plants. Then, the characterization of microbial community functioning and their diversity are important to understand these linkages. An experiment was conducted in a field system for two years (2005 and 2006) to investigate the effect of distance from tree stem on soil microbial biomass, N mineral content and the diversity of rhizobia associated to Acacia senegal. (Author)

  3. Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food

    Zhang, Jiachao; Wang, Xiaoru; Huo, Dongxue; Li, Wu; Hu, Qisong; Xu, Chuanbiao; Liu, Sixin; Li, Congfa

    2016-01-01

    Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample. PMID:27578483

  4. Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food.

    Zhang, Jiachao; Wang, Xiaoru; Huo, Dongxue; Li, Wu; Hu, Qisong; Xu, Chuanbiao; Liu, Sixin; Li, Congfa

    2016-01-01

    Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample. PMID:27578483

  5. Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

    Pluske John R

    2009-11-01

    Full Text Available Abstract Background Early microbial colonization of the gut reduces the incidence of infectious, inflammatory and autoimmune diseases. Recent population studies reveal that childhood hygiene is a significant risk factor for development of inflammatory bowel disease, thereby reinforcing the hygiene hypothesis and the potential importance of microbial colonization during early life. The extent to which early-life environment impacts on microbial diversity of the adult gut and subsequent immune processes has not been comprehensively investigated thus far. We addressed this important question using the pig as a model to evaluate the impact of early-life environment on microbe/host gut interactions during development. Results Genetically-related piglets were housed in either indoor or outdoor environments or in experimental isolators. Analysis of over 3,000 16S rRNA sequences revealed major differences in mucosa-adherent microbial diversity in the ileum of adult pigs attributable to differences in early-life environment. Pigs housed in a natural outdoor environment showed a dominance of Firmicutes, in particular Lactobacillus, whereas animals housed in a hygienic indoor environment had reduced Lactobacillus and higher numbers of potentially pathogenic phylotypes. Our analysis revealed a strong negative correlation between the abundance of Firmicutes and pathogenic bacterial populations in the gut. These differences were exaggerated in animals housed in experimental isolators. Affymetrix microarray technology and Real-time Polymerase Chain Reaction revealed significant gut-specific gene responses also related to early-life environment. Significantly, indoor-housed pigs displayed increased expression of Type 1 interferon genes, Major Histocompatibility Complex class I and several chemokines. Gene Ontology and pathway analysis further confirmed these results. Conclusion Early-life environment significantly affects both microbial composition of the adult

  6. Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors

    Bassin, J.P.; Kleerebezem, R.; Muyzer, G.; Rosado, A.S.; Van Loosdrecht, M.C.M.; Dezotti, M.

    2011-01-01

    The effect of salinity on the activity of nitrifying bacteria, floc characteristics, and microbial community structure accessed by fluorescent in situ hybridization and polymerase chain reaction–denaturing gradient gel electrophoresis techniques was investigated. Two sequencing batch reactors (SRB1

  7. Determination of Microbial Diversity and Nitrogen Cycling from Kizildere Geothermal Field with Next Generation Sequencing

    Gulecal, Y.; Dilek, Y.

    2012-12-01

    The deep terrestrial subsurface biosphere represents an emerging frontier for studies of biodiversity, the physiological limits to life, microbial mechanisms of adaptation, and potentially analogous environments for extraterrestrial life (1). Last decade, researches of deep boreholes in the United States, Finland, Sweden, Japan and South Africa, using molecular tools, have shown an an active biosphere composed of diverse groups of microorganisms. The microbial communities reported from different subsurface communities vary widely; such differences are due to different host rock types and varied water origins and chemistry, as well as geography. Furthermore, nitrogen cycling is studied intensely in hot springs for instance in situ nifH expression in Yellowstone National Park, is a new upper temperature limit for nitrogen fixation in alkaline, terrestrial hydrothermal environments (2). This study explores the genetic diversity of microbial communities and genes of nitrogen cycling in Kizildere Geothermal Field, Turkey. The Kizildere thermal waters are located in the northern part of the Büyük Menderes rift zone. The hydrothermal alteration includes phyllic, argillic, silicic,hematitized, and carbonatized alteration zones. The surface temperatures of Kizildere thermal waters in drill holes range from 95 to100°C and pH 9.0-9.5. Microbial communities were examined using culture independent methods, next generation sequencing. Nitrogen fixation, the diversity of nifH, ammonia oxidation (amoA), narG, nosZ genes are investigated in deeply-sourced fluids. We present field observations and interpret new data, establishing a geobiological baseline for previously undescribed sitres of subsurface ecosystems. (1)Fredrickson et al. 2006. Geomicrobial processes and biodiversity in the deep terrestrial subsurface. Geomicrobiology J. 23:345-356. (2) Loiacono et al. 2012. Evidence for high-temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin

  8. Microbial Diversity of Chromium-Contaminated Soils and Characterization of Six Chromium-Removing Bacteria

    He, Zhiguo; Hu, Yuting; Yin, Zhen; Hu, Yuehua; Zhong, Hui

    2016-06-01

    Three soil samples obtained from different sites adjacent to a chromium slag heap in a steel alloy factory were taken to examine the effect of chromium contamination on soil bacterial diversity as determined by construction of 16S rDNA clone libraries and sequencing of selected clones based on restriction fragment length polymorphism (RFLP) analysis. Results revealed that Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Alphaproteobacteria occurred in all three soil samples, although the three samples differed in their total diversity. Sample 1 had the highest microbial diversity covering 12 different classes, while Sample 3 had the lowest microbial diversity. Strains of six different species were successfully isolated, one of which was identified as Zobellella denitrificans. To our knowledge, this is the first report of a strain belonging to the genus Zobellella able to resist and reduce chromium. Among all isolates studied, Bacillus odysseyi YH2 exhibited the highest Cr(VI)-reducing capability, with a total removal of 23.5 % of an initial Cr(VI) concentration of 350 mg L-1.

  9. Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

    Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

    2012-12-01

    Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

  10. Language Diversity and Language Policy in Educational Access and Equity

    Tollefson, James W.; Tsui, Amy B. M.

    2014-01-01

    This article examines the role of language policies in mediating access and equity in education. By examining a range of research and case studies on language policies, the authors explore how educational language policies serve as a central gatekeeper to education itself, as well as to quality education that may fundamentally depend on language…

  11. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland.

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  12. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  13. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland.

    Yufang Shen

    Full Text Available Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L. field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer, GMC (gravel mulching with inorganic N fertilizer, FMC (plastic-film mulching with inorganic N fertilizer and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition. The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological

  14. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Cody S Sheik

    Full Text Available Extensive use of chromium (Cr and arsenic (As based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI. Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.

  15. Exposure of soil microbial communities to chromium and arsenic alters their diversity and structure.

    Sheik, Cody S; Mitchell, Tyler W; Rizvi, Fariha Z; Rehman, Yasir; Faisal, Muhammad; Hasnain, Shahida; McInerney, Michael J; Krumholz, Lee R

    2012-01-01

    Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways. PMID:22768219

  16. Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment.

    José A Siles

    Full Text Available The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR, a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR and C. floccosa-transformed DOR (CORDOR on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.

  17. Microbial diversity and metabolite composition of Belgian red-brown acidic ales.

    Snauwaert, Isabel; Roels, Sanne P; Van Nieuwerburg, Filip; Van Landschoot, Anita; De Vuyst, Luc; Vandamme, Peter

    2016-03-16

    Belgian red-brown acidic ales are sour and alcoholic fermented beers, which are produced by mixed-culture fermentation and blending. The brews are aged in oak barrels for about two years, after which mature beer is blended with young, non-aged beer to obtain the end-products. The present study evaluated the microbial community diversity of Belgian red-brown acidic ales at the end of the maturation phase of three subsequent brews of three different breweries. The microbial diversity was compared with the metabolite composition of the brews at the end of the maturation phase. Therefore, mature brew samples were subjected to 454 pyrosequencing of the 16S rRNA gene (bacteria) and the internal transcribed spacer region (yeasts) and a broad range of metabolites was quantified. The most important microbial species present in the Belgian red-brown acidic ales investigated were Pediococcus damnosus, Dekkera bruxellensis, and Acetobacter pasteurianus. In addition, this culture-independent analysis revealed operational taxonomic units that were assigned to an unclassified fungal community member, Candida, and Lactobacillus. The main metabolites present in the brew samples were L-lactic acid, D-lactic acid, and ethanol, whereas acetic acid was produced in lower quantities. The most prevailing aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, and ethyl octanoate, which might be of impact on the aroma of the end-products. PMID:26802571

  18. Organic amendments enhance microbial diversity and abundance of functional genes in Australian Soils

    Aldorri, Sind; McMillan, Mary; Pereg, Lily

    2016-04-01

    Food and cash crops play important roles in Australia's economy with black, grey and red clay soil, widely use for growing cotton, wheat, corn and other crops in rotation. While the majority of cotton growers use nitrogen and phosphate fertilizers only in the form of agrochemicals, a few experiment with the addition of manure or composted plant material before planting. We hypothesized that the use of such organic amendments would enhance the soil microbial function through increased microbial diversity and abundance, thus contribute to improved soil sustainability. To test the hypothesis we collected soil samples from two cotton-growing farms in close geographical proximity and with mostly similar production practices other than one grower has been using composted plants as organic amendment and the second farmer uses only agrochemicals. We applied the Biolog Ecoplate system to study the metabolic signature of microbial communities and used qPCR to estimate the abundance of functional genes in the soil. The soil treated with organic amendments clearly showed higher metabolic activity of a more diverse range of carbon sources as well as higher abundance of genes involved in the nitrogen and phosphorous cycles. Since microbes undertake a large number of soil functions, the use of organic amendments can contribute to the sustainability of agricultural soils.

  19. Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland.

    Bai, Yaohui; Liang, Jinsong; Liu, Ruiping; Hu, Chengzhi; Qu, Jiuhui

    2014-01-01

    Microbial communities play a critical role in the degradation of effluent contaminants in constructed wetlands. Many questions remain, however, regarding the role ofmicrobial communities in rhizospheric soil. In this study, we used metagenomic analysis to assess microbial community composition and function in a constructed wetland receiving surface water. The diversity of the microbial community of rhizosphere soil was found to be significantly greater than that of the wetland influent water. This enhancement is likely due to the availability of diverse habitats and nutrients provided by the wetland plants. From function annotation of metagenomic data, a number of biodegradation pathways associated with 14 xenobiotic compounds were identified in soil. Nitrogen fixation, nitrification and denitrification genes were semi-quantitatively analysed. By screening of manganese transformation genes, we found that the biological oxidation of Mn2+ (mainly catalysed by multicopper oxidase) in the influent water yielded insoluble Mn4+, which subsequently precipitated and were incorporated into the wetland soil. These data show that the use of metagenomic analysis can provide important new insights for the study of wetland ecosystems and, in particular, how biologically mediated transformation or degradation can be used to reduce contamination of point and non-point source wastewater. PMID:25145207

  20. Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity.

    Velmourougane, Kulandaivelu

    2016-01-01

    A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system. PMID:27042378

  1. Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity

    2016-01-01

    A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system. PMID:27042378

  2. Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits.

    Reith, Frank; Zammit, Carla M; Pohrib, Rebecca; Gregg, Adrienne L; Wakelin, Steven A

    2015-11-01

    This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P land use (P 0.2 m) differed significantly with lithology and mineral deposit (P land use in determining soil microbial community diversity. PMID:26341204

  3. Microbial diversity differences within aerobic granular sludge and activated sludge flocs.

    Winkler, M-K H; Kleerebezem, R; de Bruin, L M M; Verheijen, P J T; Abbas, B; Habermacher, J; van Loosdrecht, M C M

    2013-08-01

    In this study, we investigated during 400 days the microbial community variations as observed from 16S DNA gene DGGE banding patterns from an aerobic granular sludge pilot plant as well as the from a full-scale activated sludge treatment plant in Epe, the Netherlands. Both plants obtained the same wastewater and had the same relative hydraulic variations and run stable over time. For the total bacterial population, a similarity analysis was conducted showing that the community composition of both sludge types was very dissimilar. Despite this difference, general bacterial population of both systems had on average comparable species richness, entropy, and evenness, suggesting that different bacteria were sharing the same functionality. Moreover, multi-dimensional scaling analysis revealed that the microbial populations of the flocculent sludge system moved closely around the initial population, whereas the bacterial population in the aerobic granular sludge moved away from its initial population representing a permanent change. In addition, the ammonium-oxidizing community of both sludge systems was studied in detail showing more unevenness than the general bacterial community. Nitrosomonas was the dominant AOB in flocculent sludge, whereas in granular sludge, Nitrosomonas and Nitrosospira were present in equal amounts. A correlation analysis of process data and microbial data from DGGE gels showed that the microbial diversity shift in ammonium-oxidizing bacteria clearly correlated with fluctuations in temperature. PMID:23064482

  4. The diversity of anti-microbial secondary metabolites produced by fungal endophytes: An interdisciplinary perspective

    ManishNRaizada

    2013-03-01

    Full Text Available Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g. Chinese herbs. However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens.

  5. The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil

    Enhanced rhizosphere degradation uses plants to stimulate the rhizosphere microbial community to degrade organic contaminants. We measured changes in microbial communities caused by the addition of two species of plants in a soil contaminated with 31,000 ppm of total petroleum hydrocarbons. Perennial ryegrass and/or alfalfa increased the number of rhizosphere bacteria in the hydrocarbon-contaminated soil. These plants also increased the number of bacteria capable of petroleum degradation as estimated by the most probable number (MPN) method. Eco-Biolog plates did not detect changes in metabolic diversity between bulk and rhizosphere samples but denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified partial 16S rDNA sequences indicated a shift in the bacterial community in the rhizosphere samples. Dice coefficient matrices derived from DGGE profiles showed similarities between the rhizospheres of alfalfa and perennial ryegrass/alfalfa mixture in the contaminated soil at week seven. Perennial ryegrass and perennial ryegrass/alfalfa mixture caused the greatest change in the rhizosphere bacterial community as determined by DGGE analysis. We concluded that plants altered the microbial population; these changes were plant-specific and could contribute to degradation of petroleum hydrocarbons in contaminated soil. - Plant-specific changes in microbial populations on roots affect degradation of petroleum hydrocarbons in contaminated soil

  6. Microbial diversity in oiled and un-oiled shoreline sediments in the Norwegian Arctic

    Field trials were conducted at an oiled shoreline on the island of Spitsbergen to examine the effect of nutrient addition on the metabolic status, potential for aromatic hydrocarbon degradation, and the phylogenetic diversity of the microbial community in oiled Arctic shoreline sediments. IF-30 intermediate fuel grade oil was applied to the shoreline which was then divided into four plots. One was left untreated and two were tilled. Four applications of fertilizer were applied over a two-month period. Phospholipid fatty acid (PLFA), gene probe and 16S microbial community analysis suggested that bioremediation stimulated the metabolic activity, increased microbial biomass and genetic potential for aromatic hydrocarbon degradation, and increased the population of hydrocarbon degradation of an oiled Arctic shoreline microbial community. The results of this study are in agreement with the results from stimulation of oil biodegradation in temperate marine environments. It was concluded that biodegradation and fertilizer addition are feasible treatment methods for oil spills in Arctic regions. 31 refs., 3 tabs., 3 figs

  7. Effects of vegetation type on soil microbial community structure and catabolic diversity assessed by polyphasic methods in North China

    2007-01-01

    Soil microbes play a major role in ecological processes and are closely associated with the aboveground plant community. In order to understand the effects of vegetation type on the characteristics of soil microbial communities, the soil microbial communities were assessed by plate counts, phospholipid fatty acid (PLFA) and Biolog microplate techniques in five plant communities, i.e., soybean field (SF), artificial turf (AT), artificial shrub (AS), natural shrub (NS), and maize field (MF) in Jinan, Shandong Province, North China. The results showed that plant diversity had little discernible effect on microbial biomass but a positive impact on the evennessof utilized substrates in Biolog microplate. Legumes could significantly enhance the number of cultural microorganisms, microbial biomass, and community catabolic diversity. Except for SF dominated by legumes, the biomass of fungi and the catabolic diversity of microbial community were higher in less disturbed soil beneath NS than in frequently disturbed soils beneath the other vegetation types. These results confirmed that high number of plant species, legumes, and natural vegetation types tend to support soil microbial communities with higher function. The present study also found a significant correlation between the number of cultured bacteria and catabolic diversity of the bacterial community. Different research methods led to varied results in this study. The combination of several approaches is recommended for accurately describing the characteristics of microbial communities in many respects.

  8. Plant diversity reduces the effect of multiple heavy metal pollution on soil enzyme activities and microbial community structure

    Yang GAO; Chiyuan MIAO; Jun XIA; Liang MAO; Yafeng WANG; Pei ZHOU

    2012-01-01

    It is unclear whether certain plant species and plant diversity could reduce the impacts of multiple heavy metal pollution on soil microbial structure and soil enzyme activities. Random amplified polymorphic DNA (RAPD) was used to analyze the genetic diversity and microbial similarity in planted and unplanted soil under combined cadmium (Cd) and lead (Pb) pollution. A metal hyper- accumulator, Brassica juncea, and a common plant, Festuca arundinacea Schreb, were used in this research. The results showed that microorganism quantity in planted soil significantly increased, compared with that in unplanted soil with Cd and Pb pollution. The order of microbial community sensitivity in response to Cd and Pb stress was as follows: actinomycetes 〉 bacteria 〉 fungi. Respiration, phosphatase, urease and dehydrogenase activity were significantly inhibited due to Cd and Pb stress. Compared with unplanted soil, planted soils have frequently been reported to have higher rates of microbial activity due to the presence of additional surfaces for microbial colonization and organic compounds released by the plant roots. Two coexisting plants could increase microbe population and the activity of phosphatases, dehydrogenases and, in particular, ureases. Soil enzyme activity was higher in B. juncea phytoremediated soil than in F. arundinacea planted soil in this study. Heavy metal pollution decreased the richness of the soil microbial community, but plant diversity increased DNA sequence diversity and maintained DNA sequence diversity at highlevels. The genetic polymorphism under heavy metal stress was higher in B. juncea phytoremediated soil than in F. arundinacea planted soil.

  9. Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

    Wang, Qiufeng; Tian, Jing; Yu, Guirui

    2014-05-01

    Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

  10. Diversity and similarity of microbial communities in petroleum crude oils produced in Asia.

    Yamane, Kunio; Maki, Hideaki; Nakayama, Tsuyoshi; Nakajima, Toshiaki; Nomura, Nobuhiko; Uchiyama, Hiroo; Kitaoka, Motomitsu

    2008-11-01

    To understand microbial communities in petroleum crude oils, we precipitated DNA using high concentrations of 2,2,4-trimethylpentane (isooctane) and purified. Samples of DNA from five crude oils, (Middle East, 3; China, 1; and Japan, 1) were characterized based upon their 16S rRNA gene sequences after PCR amplification and the construction of clone libraries. We detected 48 eubacterial species, one cyanobacterium, and one archaeon in total. The microbial constituents were diverse in the DNA samples. Most of the bacteria affiliated with the sequences of the three oils from the Middle East comprised similar mesophilic species. Acinetobacter, Propionibacterium, Sphingobium and a Bacillales were common. In contrast, the bacterial communities in Japanese and Chinese samples were unique. Thermophilic Petrotoga-like bacteria (11%) and several anaerobic-thermophilic Clostridia- and Synergistetes-like bacteria (20%) were detected in the Chinese sample. Different thermophiles (12%) and Clostridia (2%) were detected in the Japanese sample. PMID:18997416

  11. Diversity and distribution in hypersaline microbial mats of bacteria related to Chloroflexus spp

    Nübel, Ulrich; Bateson, Mary M.; Madigan, Michael T.; Kühl, Michael; Ward, David M.

    2001-01-01

    primers for the specific amplification of 16S rRNA genes from filamentous phototrophic bacteria within the kingdom of "green nonsulfur bacteria." PCR products recovered from microbial mats in a saltern in Guerrero Negro, Mexico, were subjected to cloning or denaturing gradient gel electrophoresis and then......Filamentous bacteria containing bacteriochlorophylls c and a were enriched from hypersaline microbial mats. Based on phylogenetic analyses of 16S rRNA gene sequences, these organisms form a previously undescribed lineage distantly related to Chloroflexus spp. We developed and tested a set of PCR...... sequenced. We found evidence of a high diversity of bacteria related to Chloroflexus which exhibit different distributions along a gradient of salinity from 5.5 to 16%....

  12. Extracellular enzyme activity assay as indicator of soil microbial functional diversity and activity

    Hendriksen, Niels Bohse; Winding, Anne

    2012-01-01

    Extracellular enzyme activity assay as indicator of soil microbial functional diversity and activity Niels Bohse Hendriksen, Anne Winding. Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark Soils provide numerous essential ecosystem services such as carbon cycling......, recycling of nutrients and waste, soil remediation, plant growth support and regulation of above ground biodiversity, resilience, and soil suppressiveness. As such, soil ecosystem services are beneficial and vital for human life and at the same time threatened by anthropogenic activities. Increasing...... of soil microbial functions is still needed. In soil, enzymes originate from a variety of organisms, notably fungi and bacteria and especially hydrolytic extracellular enzymes are of pivotal importance for decomposition of organic substrates and biogeochemical cycling. Their activity will reflect the...

  13. Degradation of chlorpyrifos in laboratory soil and its impact on soil microbial functional diversity

    FANG Hua; YU Yunlong; CHU Xiaoqiang; WANG Xiuguo; YANG Xiaoe; YU Jingquan

    2009-01-01

    Degradation of chlorpyrifos at different concentrations in soil and its impact on soil microbial functional diversity were investigated under laboratory conditions. The degradation half-lives of chlorpyrifos at levels of 4, 8, and 12 mg/kg in soil were calculated to be 14.3, 16.7, and 18.0 d, respectively. The Biolog study showed that average well color development (AWCD) in soils was significantly (P < 0.05) inhibited by chlorpyrifos within the first two weeks and thereafter recovered to the similar level as the control. A similar variation in the diversity indices (Simpson index 1/D and McIntosh index U) in chlorpyrifos-treated soils was observed, no significant difference in the Shannon-Wiener index H' was found in these soils. With increasing chlorpyrifos concentration, the half-lives of chlorpyrifos were significantly (P ≤ 0.05) extended and its inhibitory effects on soil microorganisms were aggravated. It is concluded that chlorpyrifos residues in soil had a temporary or short-term inhibitory effect on soil microbial functional diversity.

  14. Assessment of microbial biomarkers with environmental genomics: a comparison of biochemical and phylogenetic indicators of microbial diversity in Yellowstone National Park

    Kopf, S.; Gomes, M. L.; McAnena, A.; Vuillemin, A.; Sessions, A. L.; Spear, J. R.; International Geobiology Course 2010

    2010-12-01

    Hot spring microbial communities in Yellowstone National Park utilize diverse biochemical pathways to produce energy and survive in “simple” to “complex” systems. It has been hypothesized that these hydrothermal environments share several key attributes with environments of the Early Earth. Therefore, the characterization of microbial diversity in Yellowstone microbial mats is relevant to both modern and ancient microbial ecosystem studies. For decades, lipid biomarkers have been used to infer what microorganisms are present in microbial ecosystems. More recently, 16S ribosomal RNA gene sequencing has been utilized as the primary method to characterize microbial diversity in any environment. However, lipid biomolecules may be preserved through advanced stages of diagenesis when phylogenetic indicators are long gone. In order to better use lipid biomarkers as indicators of ancient microbial communities, it is important to understand how these biomarkers reflect modern microbial diversity as characterized by 16S rRNA gene sequences. In this study, we assessed the validity and scope of established lipid biomarkers by analyzing lipid extracts and 16S ribosomal RNA gene sequences from microbial mats at Imperial Geyser (Yellowstone National Park, Wyoming). Phyla detected in both 16S rRNA sequences and lipid biomarkers are Cholorobi, Deinococcus-Thermus, Chloroflexi, Aquificae, and Cyanobacteria. In many cases 16S rRNA data revealed the presence of a phylum without any of its diagnostic lipids being found in the respective biomarker dataset. Conversely, Cyanobacteria lipids were occasionally identified where no 16S rRNA sequences related to Cyanobacteria were detected. Most of the identified lipid biomarkers were indicative of organisms capable of autotrophy, and only few diagnostic of heterotrophic organisms, even though 16S rRNA data indicated the presence of numerous heterotrophs. Biomarkers of higher plants were also detected, indicating that allochthonous

  15. Microbial Community Diversity in Fault-Associated and Ophiolite-Hosted Springs

    Meyer-Dombard, D. R.; Cardace, D.; Uzunlar, N.; Gulecal, Y.; Yargicoglu, E. N.; Carbone, J. N.

    2010-12-01

    Deep biosphere habitats and hydrothermal systems are ideal candidates for analog ecosystems to life on Early Earth and Astrobiological targets. They also likely harbor vast repositories of novel biological and genetic diversity. This study compares the biological and genetic diversity of microbial communities in terrestrial hydrothermal and cool fluid seeps and springs, occuring in both ophiolite-hosted and non-ophiolite sequences. Fluids and solids (biofilms and sediment) with variable fractions of ultramafic-sourced and serpentinizing reaction fluids and mineral fragments were collected from surface seeps and deeply-sourced springs associated with the Northern Anatolian Fault Zone (NAFZ, Turkey) and the Anita Shear Zone (ASZ, New Zealand). Comparisons are drawn between three regimes: 1) cool fluid systems in ophiolite-hosted sequences in NAFZ vs. ASZ, 2) cool fluid vs. hydrothermal fluid systems in the NAFZ, and 3) hydrothermal systems in NAFZ ophiolite-hosted vs. non-ophiolite sequences. These comparisons help differentiate microbial community structure and metabolic strategies between hydrothermal and serpentinizing input to these ecosystems. The integration of geobiological data from these sites clarifies how microbial systems respond to even subtle shifts in geochemistry of the water-rock system, and our consideration of mafic/ultramafic rocks as habitable formations brings new astrobiological relevance to this work. Microbial communities were examined using a suite of culture-dependant and independent methods, co-registered with a network of geochemical contextual samples. Geochemical datasets allow prediction of available sources of energy in these nutrient-limited ecosystems. Sample locations varied in temperature 30-90C and pH 6.5-9.0 Potential sources of energy and carbon include dissolved organic carbon, CO2, sulfide, sulfate, and ferrous iron, depending on the sample location. Enrichments were obtained using a variety of carbon and energy sources, in

  16. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

    Susan M Huse

    2008-11-01

    Full Text Available Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the "rare biosphere" than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.

  17. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters.

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-09-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29-30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75-87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy-diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  18. Correlation between microbial diversity and toxicity of sludge treating synthetic wastewater containing 4-chlorophenol in sequencing batch reactors.

    Zhao, Jianguo; Chen, Xiurong; Bao, Linlin; Bao, Zheng; He, Yixuan; Zhang, Yuying; Li, Jiahui

    2016-06-01

    The relationship between microbial diversity and sludge toxicity in the biotreatment of refractory wastewater was investigated. Synthetic wastewater containing 4-chlorophenol (4-CP) was treated by an activated sludge using a sequencing batch bioreactor (SBR). At the end of a single SBR cycle, a stable operation stage was reached when the 4-CP was not detected both in aqueous and sludge phases and the effluent COD was maintained at approximately 70 mg L(-1) for the blank and control sludge groups. Then, the diversity of the microorganisms and the sludge toxicity were measured. The results showed that the Microtox acute toxicity of the control sludge was higher than those of the blank sludge. The difference analysis of the microbial diversity between the blank and control sludge indicated that the sludge toxicity was closely related to microbial diversity. PMID:27016808

  19. Microbial diversity in rhizoremediation of long-term PCB contaminated soil

    Beranová, K.; Kochánková, L.; Macek, Tomáš; Macková, Martina

    Praha: VŠCHT, 2007 - (Macková, M.; Macek, T.; Demnerová, K.; Pazlar, V.; Nováková, M.), s. 45-48 ISBN 978-80-7080-026-3. [Symposium on Biosorption and Bioremediation /4./. Praha (CZ), 26.08.2007-30.08.2007] R&D Projects: GA ČR GA203/06/0563 Grant ostatní: GA MŠk(CZ) 1P05ME745 Institutional research plan: CEZ:AV0Z40550506 Keywords : microbial diversity * PCB degradation * rhizoremediation Subject RIV: EI - Biotechnology ; Bionics

  20. Microbial Diversity: Relevance and Relationship Between Environmental Conservation And Human Health

    Jeremias Pakulski Panizzon

    2015-02-01

    Full Text Available This work presents bibliographic data on the role and function of microbial diversity. The increasing use of probiotics and prebiotics foods has led to the studies on their actual functions in the human body. It is known that in the environment, microorganisms are extremely important in recycling of nutrients, balance of trophic chains, vital physiological activities in the plants and animals, as well as the conservation of natural habitats. In human food, these microscopic organisms contribute from flavoring products to the synthesis of antimicrobial substances and vitamins essential to living beings.

  1. SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation.

    Tanhuanpää, P; Erkkilä, M; Tenhola-Roininen, T; Tanskanen, J; Manninen, O

    2016-01-01

    Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies. PMID:26694015

  2. Genetic diversity of soybean accessions using seed storage proteins

    Soybean, Glycine max (L) Merrill, is the most important grain legume in the world that has a fairly wide range of adaptations to different climatic conditions. The present study was conducted to assess genetic variations on 139 Soybean genotypes collected from different countries including Australia, Brazil, India, Japan, Pakistan, Tiwan, USA, Yugoslavia and China. A total of 17 bands have been identified for 139 Soybean genotypes which include 9 monomorphic bands and 8 polymorphic bands. Total number of bands was found highest for India (215) while these were lowest for Yugoslavia (33). Cluster analysis, clustered these accessions into 10 clusters without having any indication of grouping on the basis of their relationships to their regions. Pairwise comparisons based on Nei and Li similarities for inter-population genetic distances of soybean accessions ranged from 0.14 to 1.12. Genetic distances for soybean germplasm from different countries were found highest for Brazil (0.97+-0.03) while it was lowest for Taiwan (0.91+-0.02). Clustering for Soybean groups was clustered into three clusters including Korea, Taiwan in the first group while Yugoslavia and Japan were clustered in the second group. The third cluster was comprised of Soybean genotypes from China, Pakistan, USA, India Brazil and Australia. Total seed storage protein variation was partitioned by AMOVA on the basis of their origins into within-population and among-population components which revealed 10.00% of the total variation resided among countries and 90.0% within countries. Genetic patterns obtained from this study can help soybean breeders to make better plan for selecting germplasm from wide sources for a specific purposes. (author)

  3. Stabilization of diverse microbial residues in California and Puerto Rico Forest Soils

    Throckmorton, H.; Bird, J.; Dane, L.; Firestone, M.; Horwath, W.

    2012-04-01

    The contribution of C from the turnover of diverse microorganisms to stable C pools remains poorly understood. This study follows the turnover of 13C labeled nonliving residues from diverse microbial groups in situ in a temperate forest in California (CA) and a tropical forest in Puerto Rico (PR), during 5 sampling points per site- over a 3 and 2 year period, respectively. Microbial groups include fungi, actinomycetes, Gm(+) bacteria, and Gm(-) bacteria, isolated from CA and PR soils to obtain temperate and tropical isolates. Results indicated that, despite unique biochemical makeup among groups as determined by Py-GC-MS, microbial residues exhibited similar mean residence times (MRTs) within each site. A density fractionation approach isolated: a "light fraction" (LF), non-mineral aggregate "occluded fraction" (OF), and a "mineral bound fraction" (MF). Microbial C inputs were more stable in the OF and MF than the LF throughout the course of the study at both sites. There were no significant differences in 13C recovery among microbes in any PR fractions, despite minor differences in overall MRTs. In CA, there were some significant differences in 13C recovery among microbial inputs in the LF and OF, which related to 13C recoveries in whole soils. In the CA MF, microbial recoveries did not differ, and low variability among treatments was observed. Results support increased protection of microbial C via association with the mineral matrix; however, differential sorption of some microbial isolates over others was not observed. Overall results suggest that inherent recalcitrance of microbial residues may be more important to determining its stability in CA soils when it is 1) unassociated with the mineral matrix (LF); or 2) occluded within aggregates; compared with that strongly associated with mineral surfaces (MF). The overall composition of SOM in fractions also differed, with a greater concentration of benzene and N compounds in the MF; lignin and phenol compounds

  4. Spatial and Temporal Patterns in the Microbial Diversity of a Meromictic Soda Lake in Washington State▿ †

    Dimitriu, Pedro A; Pinkart, Holly C.; Peyton, Brent M.; Mormile, Melanie R.

    2008-01-01

    The microbial community diversity and composition of meromictic Soap Lake were studied using culture-dependent and culture-independent approaches. The water column and sediments were sampled monthly for a year. Denaturing gradient gel electrophoresis of bacterial and archaeal 16S rRNA genes showed an increase in diversity with depth for both groups. Late-summer samples harbored the highest prokaryotic diversity, and the bacteria exhibited less seasonal variability than the archaea. Most-proba...

  5. Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and microbial physiology.

    Wagai, Rota; Kishimoto-Mo, Ayaka W; Yonemura, Seiichiro; Shirato, Yasuhito; Hiradate, Syuntaro; Yagasaki, Yasumi

    2013-04-01

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by microbial physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure microbial respiration and quantified easily soluble C as well as microbial biomass C pools before and after the incubations. Carbon structure of LFs (<1.6 and 1.6-1.8 g cm(-3) ) and bulk soil was measured by solid-state (13) C-NMR. Decomposition Q10 was significantly correlated with the abundance of aromatic plus alkyl-C relative to O-alkyl-C groups in LFs but not in bulk soil fraction or with the indirect C quality indices based on microbial respiration or biomass. The warming did not significantly change the concentration of biomass C or the three types of soluble C despite two- to three-fold increase in respiration. Thus, enhanced microbial maintenance respiration (reduced C-use efficiency) especially in the soils rich in recalcitrant LF might lead to the apparent equilibrium between SOM solubilization and microbial C uptake. Our results showed physical fractionation coupled with direct assessment of molecular structure as an effective approach and supported the enzyme-kinetic interpretation of widely observed C quality-temperature relationship for

  6. Extracellular Enzyme Activity assay as indicator of soil microbial functional diversity and activity

    Hendriksen, Niels Bohse; Winding, Anne

    2012-01-01

    Extracellular Enzyme Activity assay as indicator of soil microbial functional diversity and activity Niels Bohse Hendriksen, Anne Winding. Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark Soil enzymes originate from a variety of organisms, notably fungi and bacteria...... and especially hydrolytic extracellular enzymes are of pivotal importance for decomposition of organic substrates and biogeochemical cycling. Their activity reflects the functional diversity and activity of the microorganisms involved in decomposition processes which are essential processes for soil...... functioning and soil ecosystem services. The soil enzyme activity has been measured by the use of fluorogenic model substrates e.g. methylumbelliferyl (MUF) substrates for a number of enzymes involved in the degradation of polysaccharides as cellulose, hemicellulose and chitin, while degradation of proteins...

  7. Spatial and temporal patterns in the microbial diversity of a meromictic soda lake in Washington State.

    Dimitriu, Pedro A; Pinkart, Holly C; Peyton, Brent M; Mormile, Melanie R

    2008-08-01

    The microbial community diversity and composition of meromictic Soap Lake were studied using culture-dependent and culture-independent approaches. The water column and sediments were sampled monthly for a year. Denaturing gradient gel electrophoresis of bacterial and archaeal 16S rRNA genes showed an increase in diversity with depth for both groups. Late-summer samples harbored the highest prokaryotic diversity, and the bacteria exhibited less seasonal variability than the archaea. Most-probable-number assays targeting anaerobic microbial guilds were performed to compare summer and fall samples. In both seasons, the anoxic samples appeared to be dominated by lactate-oxidizing sulfate-reducing prokaryotes. High numbers of lactate- and acetate-oxidizing iron-reducing bacteria, as well as fermentative microorganisms, were also found, whereas the numbers of methanogens were low or methanogens were undetectable. The bacterial community composition of summer and fall samples was also assessed by constructing 16S rRNA gene clone libraries. A total of 508 sequences represented an estimated >1,100 unique operational taxonomic units, most of which were from the monimolimnion, and the summer samples were more diverse than the fall samples (Chao1 = 530 and Chao1 = 295, respectively). For both seasons, the mixolimnion sequences were dominated by Gammaproteobacteria, and the chemocline and monimolimnion libraries were dominated by members of the low-G+C-content group, followed by the Cytophaga-Flexibacter-Bacteroides (CFB) group; the mixolimnion sediments contained sequences related to uncultured members of the Chloroflexi and the CFB group. Community overlap and phylogenetic analyses, however, not only demonstrated that there was a high degree of spatial turnover but also suggested that there was a degree of temporal variability due to differences in the members and structures of the communities. PMID:18552187

  8. Distinct soil microbial diversity under long-term organic and conventional farming.

    Hartmann, Martin; Frey, Beat; Mayer, Jochen; Mäder, Paul; Widmer, Franco

    2015-05-01

    Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms. PMID:25350160

  9. Chemical, physical and microbial properties and microbial diversity in manufactured soils produced from co-composting green waste and biosolids.

    Belyaeva, O N; Haynes, R J; Sturm, E C

    2012-12-01

    The effects of adding biosolids to a green waste feedstock (100% green waste, 25% v/v biosolids or 50% biosolids) on the properties of composted products were investigated. Following initial composting, 20% soil or 20% fly ash/river sand mix was added to the composts as would be carried out commercially to produce manufactured soil. Temperatures during composting reached 50 °C, or above, for 23 days when biosolids were included as a composting feedstock but temperatures barely reached 40 °C when green waste alone was composted. Addition of biosolids to the feedstock increased total N, EC, extractable NH(4), NO(3) and P but lowered pH, macroporosity, water holding capacity, microbial biomass C and basal respiration in composts. Additions of soil or ash/sand to the composts greatly increased the available water holding capacity of the materials. Principal component analysis (PCA) of PCR-DGGE 16S rDNA amplicons separated bacterial communities according to addition of soil to the compost. For fungal ITS-RNA amplicons, PCA separated communities based on the addition of biosolids. Bacterial species richness and Shannon's diversity index were greatest for composts where soil had been added but for fungal communities these parameters were greatest in the treatments where 50% biosolids had been included. These results were interpreted in relation to soil having an inoculation effect and biosolids having an acidifying effect thereby favouring a fungal community. PMID:22770779

  10. Novel Microbial Diversity Retrieved by Autonomous Robotic Exploration of the World's Deepest Vertical Phreatic Sinkhole

    Sahl, Jason W.; Fairfield, Nathaniel; Harris, J. Kirk; Wettergreen, David; Stone, William C.; Spear, John R.

    2010-03-01

    The deep phreatic thermal explorer (DEPTHX) is an autonomous underwater vehicle designed to navigate an unexplored environment, generate high-resolution three-dimensional (3-D) maps, collect biological samples based on an autonomous sampling decision, and return to its origin. In the spring of 2007, DEPTHX was deployed in Zacatón, a deep (˜318 m), limestone, phreatic sinkhole (cenote) in northeastern Mexico. As DEPTHX descended, it generated a 3-D map based on the processing of range data from 54 onboard sonars. The vehicle collected water column samples and wall biomat samples throughout the depth profile of the cenote. Post-expedition sample analysis via comparative analysis of 16S rRNA gene sequences revealed a wealth of microbial diversity. Traditional Sanger gene sequencing combined with a barcoded-amplicon pyrosequencing approach revealed novel, phylum-level lineages from the domains Bacteria and Archaea; in addition, several novel subphylum lineages were also identified. Overall, DEPTHX successfully navigated and mapped Zacatón, and collected biological samples based on an autonomous decision, which revealed novel microbial diversity in a previously unexplored environment.

  11. Soil microbial community profiles and functional diversity in limestone cedar glades

    Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

    2016-01-01

    Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

  12. Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments.

    Berg, Maureen; Stenuit, Ben; Ho, Joshua; Wang, Andrew; Parke, Caitlin; Knight, Matthew; Alvarez-Cohen, Lisa; Shapira, Michael

    2016-08-01

    It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota. PMID:26800234

  13. Microbial density and diversity in constructed wetland systems and the relation to pollutant removal efficiency.

    Zhang, Yang; Carvalho, Pedro N; Lv, Tao; Arias, Carlos; Brix, Hans; Chen, Zhanghe

    2016-01-01

    Microbes are believed to be at the core of the wastewater treatment processes in constructed wetlands (CWs). The aim of this study was to assess the microbial biomass carbon (MBC) and Shannon's diversity index (SDI) in the substrate of CWs planted with Phragmites australis, Hymenocallis littoralis, Canna indica and Cyperus flabelliformis, and to relate MBC and SDI to the pollutant removal in the systems. Significant higher MBC was observed in CWs with H. littoralis and C. indica than in CWs with P. australis, and the MBC differed with season and substrate depth. The microbial community in the wetlands included four phyla: Cyanobacteria, Proteobacteria, Chloroflexi, and Acidobacteria, with a more diverse community structure in wetlands with C. flabelliformis. The MBC in the substrate and the SDI of the 15-20 cm depth correlated with the removal of biochemical oxygen demand, NH4-N and NO3-N. Our results indicate that substrate SDI and MBC can both be regarded as bioindicators of the pollutant removal ability in CWs. PMID:26877053

  14. Diversity and dynamics of microbial communities at each step of treatment plant for potable water generation.

    Lin, Wenfang; Yu, Zhisheng; Zhang, Hongxun; Thompson, Ian P

    2014-04-01

    The dynamics of bacterial and eukaryotic community associated with each step of a water purification plant in China was investigated using 454 pyrosequencing and qPCR based approaches. Analysis of pyrosequencing revealed that a high degree diversity of bacterial and eukaryotic communities is present in the drinking water treatment process before sand filtration. In addition, the microbial compositions of the biofilm in the sand filters and those of the water of the putatively clear tanks were distinct, suggesting that sand filtration and chlorination treatments played primary roles in removing exposed microbial communities. Potential pathogens including Acinetobacter, Clostridium, Legionella, and Mycobacterium, co-occurred with protozoa such as Rhizopoda (Hartmannellidae), and fungi such as Penicillium and Aspergillus. Furthermore, this study supported the ideas based on molecular level that biofilm communities were different from those in corresponding water samples, and that the concentrations of Mycobacterium spp., Legionella spp., and Naegleria spp. in the water samples declined with each step of the water treatment process by qPCR. Overall, this study provides the first detailed evaluation of bacterial and eukaryotic diversity at each step of an individual potable water treatment process located in China. PMID:24268295

  15. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

    Laureys, David; De Vuyst, Luc

    2014-04-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  16. Genetic diversity analysis in a set of Caricaceae accessions using resistance gene analogues

    Sengupta, Samik; Das, Basabdatta; Acharyya, Pinaki; Prasad, Manoj; Ghose, Tapas Kumar

    2014-01-01

    Background In order to assess genetic diversity of a set of 41 Caricaceae accessions, this study used 34 primer pairs designed from the conserved domains of bacterial leaf blight resistance genes from rice, in a PCR based approach, to identify and analyse resistance gene analogues from various accessions of Carica papaya, Vasconcellea goudotiana, V. microcarpa, V. parviflora, V. pubescens, V. stipulata and, V. quercifolia and Jacaratia spinosa. Results Of the 34 primer pairs fourteen gave amp...

  17. Microbial functional diversity in a mediterranean forest soil: impact of soil nitrogen availability

    Dalmonech, D.; Lagomarsino, A.; Moscatelli, M. C.

    2009-04-01

    Beneficial or negative effects of N deposition on forest soil are strongly linked to the activity of microbial biomass and enzyme activities because they regulate soil quality and functioning due to their involvement in organic matter dynamics, nutrient cycling and decomposition processes. Moreover, because the ability of an ecosystem to withstand serious disturbances may depend in part on the microbial component of the system, by characterizing microbial functional diversity we may be able to better understand and manipulate ecosystem processes. Changes in the biodiversity of the soil microbial community are likely to be important in relation to maintenance of soil ecosystem function because the microbial communities influence the potential of soils for enzyme-mediated substrate catalysis. Objective of this study was to evaluate how soil N availability affected microbial functional diversity in a 4 months laboratory experiment. The incubation experiment was carried out with an organo-mineral soil collected in a Quercus cerris forest at the Roccarespampani site (Central Italy, Viterbo). All samples were incubated at 28°C and were kept to a water content between 55 and 65% of the water holding capacity. Different amount of N (NH4NO3) were added as solution once a week in order to mimic the N wet deposition and to let microbial community deal with a slow increase in time of inorganic N content. The amount of nutrient solutions was chosen depending on the average soil-water loss due to evaporation in one week. The total amount of N-NH4NO3 was chosen to be comparable with the range of N depositions currently reported in European forests, i.e. between 1 and 75 kg N ha-1 y-1. The total amount added at the end of incubation varied from 0, 10, 25, 50 and 75 kg N ha-1. Distilled water was added in the control soil in order to provide the same amount of solution as the treated soils. In order to discriminate the effect of N, the NH4NO3 solutions were adjusted to soil pH and

  18. Access to What? Access, Diversity and Participation in India's Schools. Research Monograph No. 32

    Juneja, Nalini

    2010-01-01

    India has witnessed substantial diversification of provision to basic education. Policy changes from 1980s onwards, has seen the creation of para-formal delivery systems and the inclusion in the system of non state providers. The Education Guarantee Scheme and the Alternate Initiatives in Education programmes have generated new pathways to access.…

  19. Effect of heavy metals on soil microbial activity and diversity in a reclaimed mining wasteland of red soil area

    LIAO Min; CHEN Cheng-li; HUANG Chang-yong

    2005-01-01

    The microbial biomass, basal respiration and substrate utilization pattern in copper mining wasteland of red soil area, southern China, were investigated. The results indicated that soil microflora were obviously different compared with that of the non-mine soil.Microbial biomass and basal respiration were negatively affected by the elevated heavy metal levels. Two important microbial ecophysiological parameters, namely, the ratio of microbial biomass C( Cmic )/organic C( Corg ) and metabolic quotient(qCO2 ) were closely correlated to heavy metal stress. There was a significant decrease in the Cmic/Corg ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters had great potential to become the early sensitive, effective and liable indicators of the stresses or perturbations in soils of mining ecosystems.

  20. Effect of Long-Term Application of Chemical Fertilizers on microbial biomass and Functional Diversity of a Black Soil

    KONG Wei-Dong; ZHU Yong-Guan; FU Bo-Jie; HAN Xiao-Zeng; ZHANG Lei; HE Ji-Zheng

    2008-01-01

    An experiment with seven N, P, K-fertilizer treatments, i.e., control (no fertilizer), NP, NK, PK, NPK, NP2K, and NPK2 where P2 and K2 indicate double amounts of P and K fertilizers respectively, was conducted to examine the effect of long-term continuous application of chemical fertilizers on microbial biomass and functional diversity of a black soil (Udoll in the USDA Soil Taxonomy) in Northeast China. The soil microbial biomass C ranged between 94 and 145 mg kg-1, with the NK treatment showing a lower biomass; the functional diversity of soil microbial community ranged from 4.13 to 4.25, with an increasing tendency from control to double-fertilizer treatments, and to triple-fertilizer treatments. The soil microbial biomass, and the microbial functional diversity and evenness did not show any significant differences among the different fertilizer treatments including control, suggesting that the long-term application of chemical fertilization would not result in significant changes in the microbial characteristics of the black soil.

  1. Geochemistry driven trends in microbial diversity and function across a temperature transect of a shallow water hydrothermal system off Milos (Greece)

    Bühring, Solveig I.; Amend, Jan P.; Gómez Sáez, Gonzalo V.; Häusler, Stefan; Hinrichs, Kai-Uwe; Pichler, Thomas; Pop Ristova, Petra; Price, Roy E.; Santi, Ioulia; Sollich, Miriam

    2014-05-01

    The shallow water hydrothermal vents off Milos Island, Greece, discharge hot, slightly acidic, reduced fluids into colder, slightly alkaline, oxygenated seawater. Gradients in temperature, pH, and geochemistry are established as the two fluids mix, leading to the formation of various microbial microniches. In contrast to deep-sea hydrothermal systems, the availability of sun light allows for a combination of photo- and chemotrophic carbon fixation. Despite the comparably easy accessibility of shallow water hydrothermal systems, little is known about their microbial diversity and functioning. We present data from a shallow hydrothermal system off Milos Island, one of the most hydrothermally active regions in the Mediterranean Sea. The physico-chemical changes from ambient seafloor to hydrothermal area were investigated and documented by in situ microsensor profiling of temperature, pH, total reduced sulfur and dissolved oxygen alongside porewater geochemistry. The spatial microbial diversity was determined using a combination of gene- and lipid-based approaches, whereas microbial functioning was assessed by stable isotope probing experiments targeting lipid biomarkers. In situ microprofiles indicated an extreme environment with steep gradients, offering a variety of microniches for metabolically diverse microbial communities. We sampled a transect along a hydrothermal patch, following an increase in sediment surface temperature from background to 90°C, including five sampling points up to 20 cm sediment depth. Investigation of the bacterial diversity using ARISA revealed differences in the community structure along the geochemical gradients, with the least similarity between the ambient and highly hydrothermally impacted sites. Furthermore, using multivariate statistical analyses it was shown that variations in the community structure could be attributed to differences in the sediment geochemistry and especially the sulfide content, and only indirectly to shifts in

  2. Linking Microbial Enzymatic Activities and Functional Diversity of Soil around Earthworm Burrows and Casts.

    Lipiec, Jerzy; Frąc, Magdalena; Brzezińska, Małgorzata; Turski, Marcin; Oszust, Karolina

    2016-01-01

    The aim of this work was to evaluate the effect of earthworms (Lumbricidae) on the enzymatic activity and microbial functional diversity in the burrow system [burrow wall (BW) 0-3 mm, transitional zone (TZ) 3-7 mm, bulk soil (BS) > 20 mm from the BW] and cast aggregates of a loess soil under a pear orchard. The dehydrogenase, β-glucosidase, protease, alkaline phosphomonoesterase, and acid phosphomonoesterase enzymes were assessed using standard methods. The functional diversity (catabolic potential) was assessed using the Average Well Color Development and Richness Index following the community level physiological profiling from Biolog Eco Plates. All measurements were done using soil from each compartment immediately after in situ sampling in spring. The enzymatic activites including dehydrogenase, protease, β-glucosidase and alkaline phosphomonoesterase were appreciably greater in the BW or casts than in BS and TZ. Conversely, acid phosphomonoesterase had the largest value in the BS. Average Well Color Development in both the TZ and the BS (0.98-0.94 A590 nm) were more than eight times higher than in the BWs and casts. The lowest richness index in the BS (15 utilized substrates) increased by 86-113% in all the other compartments. The PC1 in principal component analysis mainly differentiated the BWs and the TZ. Utilization of all substrate categories was the lowest in the BS. The PC2 differentiated the casts from the other compartments. The enhanced activity of a majority of the enzymes and increased microbial functional diversity in most earthworm-influenced compartments make the soils less vulnerable to degradation and thus increases the stability of ecologically relevant processes in the orchard ecosystem. PMID:27625645

  3. Developing Planetary Protection Technology: Microbial Diversity and Radiation Resistance of Microorganisms in a Spacecraft Assembly Facility.

    Chen, F.; La Duc, M. T.; Baker, A.; Koukol, R.; Barengoltz, J.; Kern, R.; Venkateswaran, K.

    2001-12-01

    Europa has attracted much attention as evidence suggests the presence of a liquid ocean beneath this Jupiter moon's frozen crust. Such an environment might be conducive to the origins of life. Since robotic exploration of Europa is being planned, it becomes crucial to prepare for bio-burden reduction of hardware assembled for Europa missions to avoid contamination of Europa's pristine environment. In this study, we examined the microbial diversity of samples collected from two flight-ready circuit boards and their assembly facility. Also, because Jupiter's strong radiation environment may be able to reduce the viable microbial contamination on flight components, we have also studied the effects of radiation on microbial communities found to be associated with the space-flight hardware and/or present in the assembly facility. Surface samples thought to be representative of considerable human contact were collected from two circuit boards and various locations within the assembly facility using polyester swabs (swab samples). Likewise, sterile wipes were used to sample a shelf above the workstation where the circuit boards were assembled and the floor of the facility (wipe samples). The swab and wipe samples were pooled separately and divided into two halves, one of which was irradiated with 1Mrad gamma radiation for 5.5 hours, the other was not irradiated. About 1.2x104 and 6x104 CFUs/m2 cultivable microbes were detected in the swab and wipe samples, respectively. Radiation proved effective in inhibiting the growth of most microbes. Further characterization of the bacterial colonies observed in the irradiated swab and wipe samples is necessary to determine the degree of the radiation resistance. The16S rDNA sequence analysis of the cultivable microbes indicated that the assembly facility consists mostly of the members of actinobacteria, corynebacteria and pseudomonads. However, the swab samples that include the circuit boards were predominantly populated with

  4. Microbial Ecosystems, Protection of

    Bodelier, P.L.E.; Nelson, K.E.

    2014-01-01

    Synonyms Conservation of microbial diversity and ecosystem functions provided by microbes; Preservation of microbial diversity and ecosystem functions provided by microbes Definition The use, management, and conservation of ecosystems in order to preserve microbial diversity and functioning. Introdu

  5. Genetic diversity and population structure of Korean and Chinese soybean [Glycine max (L.) Merr.] accessions

    Korean and Chinese cultivated soybean [Glycine max (L.) Merr.] populations are major soybean gene pools. Information has been reported comparing genetic diversity between soybeans from the two countries using an unequal number of accessions and only 6 to 35 genetic markers. This study compares diffe...

  6. Open Access in Higher Education--Strategies for Engaging Diverse Student Cohorts

    Signor, Luisa; Moore, Catherine

    2014-01-01

    With growth in online education, students gain tertiary qualifications through a mode more suited to their demographics such as work and life balance, learning styles and geographical accessibility. Inevitably this has led to a growth in diversity within student cohorts. The case study described in this paper illustrates strategies based on…

  7. Microbial Life in a Winogradsky Column: From Lab Course to Diverse Research Experience

    Samantha T. Parks

    2015-02-01

    Full Text Available Many traditional lab courses include both standard and inquiry-based experiments, yet lack cooperative and authentic lab experiences.  Such experiences are important for microbiology students and burgeoning researchers.  In a novel lab environment, students constructed Winogradsky columns using common soil and water sources.  During initial column incubation, students learned methods for identification of microbial isolates including staining, microscopy, biochemistry and 16S-rRNA sequencing.  Concurrently, students challenged their columns via varied substrates and contaminants including enrichment with nitro-compounds, hydrocarbons, acids and other environmental stressors.  Students were encouraged to use both basic and more advanced identification methods to study the effect of such challenges within their columns.  The students were required to maintain lab notebooks and attend weekly lab meetings, which were designed to share progress and facilitate experimentation among their lab-mates.  At the end of the semester, students gathered to present their data and conclusions.  By engaging in weekly meetings and a final conference, students were able to construct a snapshot of the microbial diversity, including phylogeny and metabolism, in the soil and water used to construct the Winogradsky columns.  By using a common source, students were able to observe an array of diversity within individual columns and extrapolate towards the tremendous microbial diversity in the initial soil and water samples.  Equally important to the data obtained, the students engaged in a collaborative effort through discussion, trouble-shooting, weekly meetings and the summative conference.  Such efforts enabled students to participate in an authentic research experience within a traditional undergraduate laboratory course. Editor's Note:The ASM advocates that students must successfully demonstrate the ability to explain and practice safe laboratory

  8. Microbial Diversity in Soil Cores From the Yukon River Basin, Alaska

    Baedecker, M.; Kirshtein, J. D.; Wickland, K. P.; Metge, D. W.; Schuster, P. F.; Voytek, M. A.

    2006-12-01

    Understanding the microbial environment in permafrost areas is important for understanding processes that release carbon and other nutrients from soils as a result of permafrost melting. Soils were collected in August 2005 from two sites in the Yukon River Basin, Alaska, and examined for microbial diversity as part of a larger project to investigate carbon cycling within the river basin. One site was located at the Bonanza Creek Long- Term Ecological Research Site near Fairbanks in an area of discontinuous permafrost and the other site was collected 400 kilometers to the north near Coldfoot in an area of continuous permafrost within the Arctic Circle. Both sites are characterized as black spruce forest and permafrost is 42-55 cm below land surface. Soil pore waters in the active layer at the Bonanza Creek site had a higher pH (5.06 versus 4.35), lower SO4 and DOC, and higher dissolved CH4 compared to the Coldfoot site. Dissolved oxygen was measured at >1.0 mg/L in water pumped from piezometers at both sites. Soil samples were collected from a range of depths above and below the permafrost and analyzed for total bacteria, for most probable number (MPN) of nine metabolic types of microorganisms, and for five metabolic types of microorganisms by quantitative polyermase chain reaction (QPCR). Soil geochemistry and climatic conditions affected the microbial abundances and distributions found at these two sites. The total number of bacteria by direct count ranged from 105 to 107 cells per gram dry weight (gdw) sediment with living cells comprising 1.4 to 98% of the total enumerated bacteria. In near-surface samples (top 40 cm), the MPN results indicate that aerobes, fermenters, humic acid reducers, and iron reducers account for most of the total bacteria. Nitrifiers and denitrifiers were found in a few samples, whereas sulfate reducers and methanogens were below our detection limit using the MPN method. The QPCR results indicated the presence of methanogens in 9 of 14

  9. Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

    Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

    2016-01-01

    Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

  10. A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

    Acácio A. Navarrete

    2010-05-01

    Full Text Available The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production.The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I—“Slash-and-Burn” the community structures detected by automated ribosomal intergenic spacer analysis (ARISA revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II—“Anthropogenic Soil”, the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP differed among an Amazonian Dark Earth (ADE, black carbon (BC and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria—24% ADE, 15% BC; Acidobacteria—10% ADE, 21% BC; Actinobacteria—7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes—3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the

  11. Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter

    Matyugina, Evgeniya; Belkova, Natalia

    2015-11-01

    Meromictic soda and saline lakes are unique ecosystems characterized by the stability of physical, chemical and biological parameters, and they are distributed all over the world. Lakes located in regions with average annual negative air temperature are of particular interest because of the presence of two periods with intensive and dynamic processes: the so-called biological summer and the long ice season with the biological spring. Soda Lake Doroninskoe is located in Eastern Transbaikalia (51°14'N, 112°14'E) in the permafrost zone in an extreme continental climate, and is covered by ice for seven months per year. The structure and diversity of the microbial communities throughout the water column of the lake was studied by 16S rRNA gene amplicon metasequencing. Different species with specific functions were found to dominate at different depths. Metabolically flexible bacteria with a capacity to switch between anoxygenic photosynthesis and aerobic chemotrophic metabolism dominate in soda Lake Doroninskoe.

  12. Optimisation of automated ribosomal intergenic spacer analysis for the estimation of microbial diversity in fynbos soil

    Karin Jacobs

    2010-07-01

    Full Text Available Automated ribosomal intergenic spacer analysis (ARISA has become a commonly used molecular technique for the study of microbial populations in environmental samples. The reproducibility and accuracy of ARISA, with and without the polymerase chain reaction (PCR are important aspects that influence the results and effectiveness of these techniques. We used the primer set ITS4/ITS5 for ARISA to assess the fungal community composition of two sites situated in the Sand Fynbos. The primer set proved to deliver reproducible ARISA profiles of the fungal community composition with little variation observed between ARISA-PCRs. Variation that occurred in a sample due to repeated DNA extraction is expected for ecological studies. This reproducibility made ARISA a useful tool for the assessment and comparison of diversity in ecological samples. In this paper, we also offered particular suggestions concerning the binning strategy for the analysis of ARISA profiles.

  13. Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion.

    Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

    2014-07-01

    The microbial communities associated with deteriorating concrete corrosion fronts were characterized in 35 samples taken from wastewater collection and treatment systems in ten utilities. Bacterial communities were described using Illumina MiSeq sequencing of the V1V2 region of the small subunit ribosomal ribonucleic acid (SSU-rRNA) gene recovered from fresh corrosion products. Headspace gas concentrations (hydrogen sulfide, carbon dioxide, and methane), pore water pH, moisture content, and select mineralogy were tested for correlation to community outcomes and corrosion extent using pairwise linear regressions and canonical correspondence analysis. Corroding concrete was most commonly characterized by moisture contents greater than 10%, pore water pH below one, and limited richness (100 ppm) and carbon dioxide (>1%) gases, conditions which also were associated with low diversity biofilms dominated by members of the acidophilic sulfur-oxidizer genus Acidithiobacillus. PMID:24842376

  14. Chemical diversity of microbial volatiles and their potential for plant growth and productivity

    CHIDANANDA NAGAMANGALA KANCHISWAMY

    2015-03-01

    Full Text Available Microbial volatile organic compounds (MVOCs are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs and their potential physiological effects on crops and analyze potential and actual limitations for MVOC use as a sustainable strategy for improving productivity and reducing pesticide use.

  15. New Tools For Understanding Microbial Diversity Using High-throughput Sequence Data

    Knight, R.; Hamady, M.; Liu, Z.; Lozupone, C.

    2007-12-01

    High-throughput sequencing techniques such as 454 are straining the limits of tools traditionally used to build trees, choose OTUs, and perform other essential sequencing tasks. We have developed a workflow for phylogenetic analysis of large-scale sequence data sets that combines existing tools, such as the Arb phylogeny package and the NAST multiple sequence alignment tool, with new methods for choosing and clustering OTUs and for performing phylogenetic community analysis with UniFrac. This talk discusses the cyberinfrastructure we are developing to support the human microbiome project, and the application of these workflows to analyze very large data sets that contrast the gut microbiota with a range of physical environments. These tools will ultimately help to define core and peripheral microbiomes in a range of environments, and will allow us to understand the physical and biotic factors that contribute most to differences in microbial diversity.

  16. Spatial and seasonal variation in microbial diversity in marine subtidal sediments in relation to sediment geochemistry and heavy metal pollution

    Pede, A.; Gillan, D.; Gao, Y.; Billon, G.; Lesven, L.; Leermakers, M; Baeyens, W.; Vyverman, W.; Sabbe, K

    2009-01-01

    Very little information is available on the diversity and structure of microbial communities in marine subtidal sediments, especially for micro-eukaryotes. In the framework of the Belgian MICROMET project, we investigated spatial and seasonal (February vs July) variation patterns in the molecular diversity of archaeal, bacterial and eukaryotic communities in 9 subtidal stations in the Belgian Continental Plate (BCP) in relation to sediment granulometry, geochemistry and metal contamination. M...

  17. Microbial diversity on spacecraft and in spacecraft assembly and testing facilities

    Rettberg, P.; Nellen, J.; Fritze, D.; Verbarg, S.; Stackebrandt, E.; Kminek, G.

    Planetary protection measures are necessary for all space flight missions involved with life detection and or sample return procedures to avoid the contamination of critical spacecraft hardware components with terrestrial organisms Spacecraft are assembled in clean rooms under defined and controlled environmental conditions These conditions might be considered as extreme with respect to controlled air circulation low relative humidity moderately high constant temperature and low nutrient conditions and represent a special artificial environment for microorganisms In the ESA-Project MiDiv the bioburden and the microbial diversity of three different spacecraft assembly and testing facilities has been investigated in periods where the facilities have been in full operation with the assembly and test of European satellites For the selected satellite missions SMART-1 and ROSETTA however no strict planetary protection measures like those required for a landing mission on Mars COSPAR Planetary Protection Category IV have been necessary and taken into consideration The result of this investigation therefore reflects the normal microbial conditions in standard class 100 000 clean rooms used by employees without any special training in planetary protection The investigation in the MiDiv project was restricted to so-called cultivable microorganisms in particular to those microorganisms that are able to grow under the selected conditions The analysis of the samples included cultivation on different media at different pH values and

  18. Dynamic changes of microbial community diversity in a photohydrogen producing reactor monitored by PCR-DGGE

    YING Yanling; LV Zhenmei; MIN Hang; CHENG Jun

    2008-01-01

    A PCR-DGGE (denaturing gradient gel electrophoresis of polymerase chain reaction) protocol was used for monitoring the dynamic changes in the microbial population during photohydrogen production. Total DNA was extracted directly from the mixed bacterial community in the reactor and subjected to PCR with V3-16S rDNA and pufM gene primers, and the amplifications were then analyzed by DGGE. The DGGE patterns demonstrated the dynamics of community structure and the shift of microbial diversity, which corresponded to different running periods of the reactor. The optimal hydrogen producing community formed on day 10. Using DGGE analysis with the pufM gene fragments was superior to V3-16S rDNA region genes for detecting the dynamic variations of the photosynthetic bacteria population during hydrogen production. The comparative sequence analysis of excised DGGE bands showed the relationship between specific population structures and system performance. Rhodopseudomonas palustris was presumed as one of the dominant community members for hydrogen production in the reactor. The PCR-DGGE protocol was proven to be a good tool for monitoring the photohydrogen production in real time and offered the available information to improve the photohydrogen producing system.

  19. Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca).

    Peng, Zhirong; Zeng, Dong; Wang, Qiang; Niu, Lili; Ni, Xueqin; Zou, Fuqin; Yang, Mingyue; Sun, Hao; Zhou, Yi; Liu, Qian; Yin, Zhongqiong; Pan, Kangcheng; Jing, Bo

    2016-05-01

    It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics (p  0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults (p  0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition. PMID:27038949

  20. Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments.

    Mora-Ruiz, Merit Del R; Font-Verdera, Francisca; Orfila, Alejandro; Rita, Joan; Rosselló-Móra, Ramon

    2016-09-01

    In this study, the microbial community structures of the endosphere of the halophyte Arthrocnemum macrostachyum were evaluated from two locations in Mallorca, Spain, focusing on three plant compartments (roots, green and red stems) compared to the rhizospheric soil where the plants grew. The physicochemical parameters of the rhizospheric soils differed between locations, and the soils were characterized by different microbial community structures. Accordingly, the endophytic community composition, mainly composed of putatively halophilic organisms, was highly influenced by the rhizospheric soil microbiota, as revealed by the co-occurrence of the major endophytic taxa in the endosphere and the rizospheric soils. Moreover, the reduction of diversity from the endorhizosphere towards the red leaves may support the fact that part of colonization of the plant by bacteria could have an origin in the rhizospheric soils through the roots and subsequent migration to the aerial parts of the plant. Finally, there were certain relevant ubiquitous taxa, such as Chromohalobacter canadensis, Rudaea cellulosilytica (never reported before as endophytic), Psychrobacter sp., Bradyrhizobium sp. and Halomonas sp., that, due their moderate halophilic nature, seemed to find an optimal environment inside the plants. Some of these relevant endophytes were not always detectable in their respective soils, and were probably part of the soils' rare biosphere, which would gain preponderance in a favorable endophytic environment. PMID:27353659

  1. Microbial diversity in a permanently cold and alkaline environment in Greenland

    Glaring, Mikkel Andreas; Vester, Jan Kjølhede; Lylloff, Jeanette Eva;

    2015-01-01

    The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting the i...... with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California.......The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting...... the ikaite columns and surrounding fjord was characterised by high-throughput pyrosequencing of 16S rRNA genes. Analysis of the ikaite community structure revealed the presence of a diverse bacterial community, both in the column interior and at the surface, and very few archaea. A clear difference...

  2. Microbial diversity inside pumpkins: microhabitat-specific communities display a high antagonistic potential against phytopathogens.

    Fürnkranz, Michael; Lukesch, Birgit; Müller, Henry; Huss, Herbert; Grube, Martin; Berg, Gabriele

    2012-02-01

    Recent and substantial yield losses of Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) are primarily caused by the ascomycetous fungus Didymella bryoniae but bacterial pathogens are frequently involved as well. The diversity of endophytic microbial communities from seeds (spermosphere), roots (endorhiza), flowers (anthosphere), and fruits (carposphere) of three different pumpkin cultivars was studied to develop a biocontrol strategy. A multiphasic approach combining molecular, microscopic, and cultivation techniques was applied to select a consortium of endophytes for biocontrol. Specific community structures for Pseudomonas and Bacillus, two important plant-associated genera, were found for each microenvironment by fingerprinting of 16S ribosomal RNA genes. All microenvironments were dominated by bacteria; fungi were less abundant. Of the 2,320 microbial isolates analyzed in dual culture assays, 165 (7%) were tested positively for in vitro antagonism against D. bryoniae. Out of these, 43 isolates inhibited the growth of bacterial pumpkin pathogens (Pectobacterium carotovorum, Pseudomonas viridiflava, Xanthomonas cucurbitae); here only bacteria were selected. Microenvironment-specific antagonists were found, and the spermosphere and anthosphere were revealed as underexplored reservoirs for antagonists. In the latter, a potential role of pollen grains as bacterial vectors between flowers was recognized. Six broad spectrum antagonists selected according to their activity, genotypic diversity, and occurrence were evaluated under greenhouse conditions. Disease severity on pumpkins of D. bryoniae was significantly reduced by Pseudomonas chlororaphis treatment and by a combined treatment of strains (Lysobacter gummosus, P. chlororaphis, Paenibacillus polymyxa, and Serratia plymuthica). This result provides a promising prospect to biologically control pumpkin diseases. PMID:21947430

  3. Diversity of microbial communities in ocean crust below ancient hotspot seamounts along the Louisville Seamount Chain

    Sylvan, J. B.; Edwards, K. J.

    2012-12-01

    The goal of Integrated Ocean Drilling Expedition 330, Louisville Seamount Trail, was to understand the motion of the Louisville hotspot during 50-80 Ma. As such, >1 km of volcanic basement was collected from five sites on four seamounts, providing an excellent chance to study how microbial populations are effected by different lithologies, different seamounts and age of basement rock along the Louisville Seamount Chain (LSC). Analysis of bacteria growing in enrichment incubations that targeted oligotrophs (with 1% or 10% Marine Broth 2216 diluted with 3% NaCl) and sulfur oxidizers reveals the presence of a diverse array of bacteria, including ɛ-proteobacteria closely related to Sulfurimonas autotrophica, β-proteobacterial methylotrophs, ζ-proteobacteria and Bacteroidetes most closely related to organisms cultured from sediments. Many of these sequences are Halomonas sulfidaeris str. Esulfude1, a bacterium originally isolated from a hydrothermal sulfide chimney. A second isolate may be a new species of Bacillus. Initial molecular analysis of bacterial communities by pyrosequencing of the 16S rRNA gene as part of the Census of Deep Life (CoDL) supports the data from the culturing work; in one sample collected 174 meters below seafloor, the most abundant bacteria detected include species from the genera Pseudomonas, Sulfurimonas, Methyloversatilis and Desulfocapsa. More CoDL samples will be analyzed in the near future. We will describe results to date on subsurface microbial diversity along the Louisville Seamount Chain from the culturing work and CoDL project and draw comparisons to data derived from younger crustal sites to try to understand how the LSC ecosystem fits into our global picture of life in ocean crust.

  4. Geochip-based analysis of microbial functional genes diversity in rutile bio-desilication reactor

    宋翔宇; 邱冠周; 王海东; 谢建平; 徐靖; 王娟

    2015-01-01

    Biological desilication process is an effective way to remove silicate from rutile so that high purity rutile could be obtained. However, little is known about the molecular mechanism of this process. In this work, a newly developed rutile bio-desilication reactor was applied to enrich rutile from rough rutile concentrate obtained from Nanzhao rutile mine and a comprehensive high through-put functional gene array (GeoChip 4.0) was used to analyze the functional gene diversity, structure and metabolic potential of microbial communities in the biological desilication reactor. The results show that TiO2grade of the rutile concentrate could increase from 78.21% to above 90% and the recovery rate could reach to 96% or more in 8−12 d. The results also show that almost all the key functional genes involved in the geochemical cycling process, totally 4324 and 4983 functional microorganism genes, are detected in the liquid and ore surface, respectively. There are totally 712 and 831 functional genes involved in nitrogen cycling for liquid and ore surface samples, respectively. The relative abundance of functional genes involved in the phosphorus and sulfur cycling is higher in the ore surface than liquid. These results indicate that nitrogen, phosphorus and sulfur cycling are also present in the desiliconization process of rutile. Acetogenesis genes are detected in the liquid and ore surface, which indicates that the desiliconizing process mainly depends on the function of acetic acid and other organic acids. Four silicon transporting genes are also detected in the sample, which proves that the bacteria have the potential to transfer silicon in the molecule level. It is shown that bio-desilication is an effective and environmental-friendly way for enrichment of rough rutile concentrate and presents an overview of functional diversity and structure of desilication microbial communities, which also provides insights into our understanding of metabolic potential in

  5. Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea.

    Koo, Ok-Kyung; Baker, Christopher A; Kim, Hyun-Jung; Park, Si Hong; Ricke, Steven C

    2016-09-01

    The purpose of this study was to characterize the microbial community in ground pork using molecular approaches. Forty six ground pork products were purchased from local stores in the north central area of South Korea. Aerobic plate counts varied 4.23 ± 5.14 × 10(5) CFU/g with the range between 5.00 × 10(3) and 1.85 × 10(6) CFU/g for ground pork samples. Four ground meat samples were further processed for metagenomic analysis. Pseudomonas species was the most relative abundant with a wide range occurring (1.72 to 77.7%) as part of the microbial genera in ground pork. Bacteria such as Carnobacterium, Yersinia, Photobacterium were also identified in ground pork. Despite the prominence of certain genera across all samples there was still extensive microbial diversity among ground pork products that originated from different slaughter houses and were processed in different markets. Such diversity indicates that designing interventions to extend shelf life may be hampered by the extensive variability in the microbial consortia associated with pork products. However, this diversity may be useful for developing microbial traceability signatures unique to a slaughter house or a particular market. PMID:27192496

  6. Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens

    Elsas, van J.D.; Garbeva, P.; Salles, J.

    2002-01-01

    The diversity of soil microbial communities can be key to the capacity of soils to suppress soil-borne plant diseases. As agricultural practice, as well as directed agronomical measures, are known to be able to affect soil microbial diversity, it is plausible that the soil microflora can be geared t

  7. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

    Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.; Dharne, Mahesh S.

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

  8. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico

    Arturo A. Massol-Deyá

    2006-09-01

    Full Text Available Hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. Our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. Under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic retention time. Over 25 different cultures were isolated from the treatment unit (96% which utilized diesel constituents as sole carbon source. Approximately 20% of the isolates were also capable of complete denitrification to nitrogen gas. Sequence analysis of 16S rDNA demonstrated ample diversity with most belonging to the ∝, β and γ subdivision of the Proteobacteria, Bacilli, and Actinobacteria groups. Moreover, the genetic constitution of the microbial community was examined at multiple time points with a Functional Gene Array (FGA containing over 12,000 probes for genes involved in organic degradation and major biogeochemical cycles. Total community DNA was extracted and amplified using an isothermal φ29 polymerase-based technique, labeled with Cy5 dye, and hybridized to the arrays in 50% formimide overnight at 50°C. Cluster analysis revealed comparable profiles over the course of treatment suggesting the early selection of a very stable microbial community. A total of 270 genes for organic contaminant degradation (including naphthalene, toluene [aerobic and anaerobic], octane, biphenyl, pyrene, xylene, phenanthrene, and benzene; and 333 genes involved in metabolic activities (nitrite and nitrous oxide reductases [nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB], potential metal reducing C-type cytochromes, and methane monooxygenase [pmoA] were repeatedly detected. Genes for degradation of MTBE

  9. Radionuclides distribution, properties, and microbial diversity of soils in uranium mill tailings from southeastern China

    Objective: To collect the radioactive contamination data for environmental rehabilitation in uranium mill tailings in southeastern China. Method: The sample areas were divided into high, moderate and low concentration areas, according to the uranium concentration. For every area, 3 soil samples were collected at 0–15 cm, 15–30 cm and 30–45 cm depth respectively, with 5 repetitions for each. Total 45 (3 × 5 × 3) soil samples were collected. Physicochemical properties and enzyme activities of soils were determined as described by references. The concentrations of the radionuclides 238U, 232Th, 226Ra and 40K in soils were determined by using HPGe gamma-ray spectrometer. Soil microbial diversity was analyzed via denaturing gradient gel electrophoresis (DGGE). Results: Soil samples were all acidic. Physicochemical properties, like pH, content of total/available N, P and K, as well as enzyme activities were all increased along with decreased uranium concentration. The 232Th concentration was increased with the decreased uranium concentration and was not influenced by the depth of sample sites. However, uranium concentration and depth of sample showed no significant influence on the concentrations of 226Ra and 40K. The concentration of 232Th was significantly correlated with that of 226Ra and 40K, while the concentrations of 226Ra and 40K were significantly correlated. However, Pearson correlation coefficients between 238U and other radionuclides were not significant. The microbial population in different concentration areas was different with four domain strains in low area, and two for both moderate and high areas. Furthermore, in each sample site, Proteobacteria was the most dominant flora, while environmental samples were the second according to GenBank database. Moreover, Serratia sp. of Proteobacteria was the dominant strain. Conclusion: Radionuclides distribution in the uranium mill tailing showed a profound influence on soil properties and microbial

  10. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

    Lu, Zhenmei; He, Zhili; Parisi, Victoria A.; Kang, Sanghoon; Deng, Ye; Van Nostrand, Joy D.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Suflita, Joseph M.; Zhou, Jizhong

    2012-01-01

    The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

  11. Fine-scale distribution patterns of Synechococcus ecological diversity in the microbial mats of Mushroom Spring, Yellowstone National Park

    Becraft, E.; Cohan, F.; Kühl, Michael;

    2011-01-01

    Past analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genus Synechococcus, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only...

  12. Phenotypic and RAPD diversity among 80 germplasm accessions of the medicinal plant isabgol (Plantago ovata, Plantaginaceae).

    Singh, N; Lal, R K; Shasany, A K

    2009-01-01

    Plantago ovata, popularly known as isabgol, has great commercial and medicinal importance due to thin rosy white membranous seed husk. Isabgol seeds and husks have emollient, demulcent and laxative properties. We used both biometric and molecular techniques to assess the genetic variability and relatedness of 80 germplasm accessions of Plantago spp (P. ovata, P. lanceolata, and P. major) collected both from India and abroad. The range of D2 values (2.01-4890.73) indicated a very high degree of divergence among the accessions. Based on the degree of divergence, 80 accessions/genotypes were grouped into seven clusters. Thirty-six accessions were analyzed through RAPD profiling for similarity and genetic distances, using 20 random primers. Intraspecific differences in all three species were smaller [range for P. ovata (2-17%), P. lanceolata (3-15%), P. major (2-11%)] than interspecific diversity. These highly divergent lines could be used to produce superior hybrids. PMID:19876869

  13. Microbial population, activity, and phylogenetic diversity in the subseafloor core sediment from the Sea of Okhotsk

    Inagaki, F.; Suzuki, M.; Takai, K.; Nealson, K. H.; Horikoshi, K.

    2002-12-01

    Subseafloor environments has already been recognized as the largest biosphere on the planet Earth, however, the microbial diversity and activity has been still poorly understood, even in their impacts on biogeochemical processes, tectonic settings, and paleoenvironmental events. We demonstrate here the evaluation of microbial community structure and active habitats in deeply buried cold marine sediments collected from the Sea of Okhotsk by a combined use of molecular ecological surveys and culturing assays. The piston core sediment (MD01-2412) was collected by IMAGES (International Marine Global Change Study) Project from the southeastern Okhotsk Sea, June 2001. The total recovered length was about 58m. The lithology of the core sediment was mainly constructed from pelagic clay (PC) and volcanic ash layers (Ash). We collected aseptically the most inside core parts from 16 sections at different depths for microbiological study. The direct count of DAPI-stained cells revealed that the cells in Ash samples were present 1.2 to 2.2 times higher than in PC samples. The quantitative-PCR of 16S rDNA between bacterial and archaeal rDNA suggested that the increased population density in Ash layers was caused by the bacterial components. We studied approximately 650 and 550 sequences from bacterial and archaeal rDNA clone libraries, respectively. The similarity and phylogenetic analyses revealed that the microbial community structures were apparently different between in Ash layers and PC samples. From bacterial rDNA clone libraries, the members within gamma-Proteobacteria such as genera Halomonas, Shewanella, Psychromonas and Methylosinus were predominantly detected in Ash layers whereas the Dehalococcoides group and delta-Proteobacteria were major bacterial components in PC samples. From archaeal libraries, the sequences from Ash and PC samples were affiliated into the clusters represented by the environmental sequences obtained from terrestrial and deep-sea environments

  14. Microbial Diversity of Planctomycetes and Related Bacteria in Wetlands with Different Anthropogenic Disturbances

    Yu Wang; Guibing Zhu; Erwin van der Biezen; Mike S M Jetten; Chengqing Yin

    2013-01-01

    The diversity of Planctomycetes and related bacteria in 3 types of freshwater wetlands with different anthropogenic disturbances were investigated by cloning and sequencing PCR-amplified partial 16S rRNA genes.Three clone libraries were constructed using 16S rRNA-targeted forward PCR primer specific for Planctomycetales and general bacterial reverse primer.Phylogenetic analysis of the 16S rRNA gene sequences defined 95 operational taxonomic units (OTUs) with 163 sequences.The clone libraries covered a wide microbial diversity of Proteobacteria and the Planctomycetes-Verrucomicrobia-Chlamydiales (PVC) superphylum.The majority of the OTUs were related to the phylum of Planctomycetes (33 OTUs),Proteobacteria (22 OTUs) and Verrucomicrobia (22 OTUs).Four known genera from the Planctomycetes phylum were all detected.The genus Pirellula (18 OTUs) dominated the Planetomycetes community,but different patterns of distribution were observed in the wetlands.The littoral wetlands of Baiyangdian Lake with the least anthropogenic disturbances covered more species and showed the highest biodiversity.However,the Jiaxing paddy fields with the highest anthropogenic disturbances showed a higher biodiversity than that in the riparian wetlands of the North Canal.Bacteria distantly related to anammox bacteria were also detected with a small proportion (4 OTUs).It showed that wetlands hold a great biodiversity of phyla Planctomycetes and related bacteria; furthermore,there is ample opportunity to discover novel phylotypes of Planctomycctes in the wctland ecosystems.

  15. Microbial diversity and methodological diversity: When standardized methods may or may not be beneficial in deep subseafloor biosphere research

    Darch, P. T.

    2015-12-01

    Scientists are often encouraged, and sometimes required, to standardize methods for collecting, analyzing, managing, and reporting data. Methods standardization within and between scientific domains is often considered beneficial for collaboration, developing scientific tools, and curation and sharing of data. However, efforts to standardize are often resisted for a range of social and technical reasons. Here we present findings from a case study of a domain characterized by high methodological diversity. This domain, the deep subseafloor biosphere, studies interactions between subseafloor microbial communities and the physical environment they inhabit. We have conducted 49 interviews and observed practice over a period of 18 months; the study is still ongoing. Domain scientists depend on core samples and data obtained from International Ocean Discovery Program (IODP) cruises. During cruises, basic data are produced about the physical composition of cores, using standard methods. However, no comparable microbiological data is produced on cruises. Many leading deep subseafloor biosphere scientists are concerned that this lack of standardized microbiological data limits their domain's scientific progress. They have identified heterogeneity of methods for microbiological analyses of cores as the major barrier to including such analyses on cruises. Among the actions these scientists have taken to promote methods standardization are journal articles and an international workshop. Despite these efforts, the community is not fully embracing standardization. One of the tensions is between perceived benefits for the community vs. a lack of incentives for individuals to perform necessary standardization work. This work includes meta-analyses to compare methods. However, the community lacks infrastructure and reward structures to support individuals to conduct such work. Another tension is concern amongst some scientists that standardizing methods now will foreclose

  16. Microbial community structure and functional metabolic diversity are associated with organic carbon availability in an agricultural soil

    LI Juan; LI Yan-ting; YANG Xiang-dong; ZHANG Jian-jun; LIN Zhi-an; ZHAO Bing-qiang

    2015-01-01

    Exploration of soil environmental characteristics governing soil microbial community structure and activity may improve our understanding of biogeochemical processes and soil quality. The impact of soil environmental characteristics especialy organic carbon availability after 15-yr different organic and inorganic fertilizer inputs on soil bacterial community structure and functional metabolic diversity of soil microbial communities were evaluated in a 15-yr fertilizer experiment in Chang-ping County, Beijing, China. The experiment was a wheat-maize rotation system which was established in 1991 including four different fertilizer treatments. These treatments included: a non-amended control (CK), a commonly used application rate of inorganic fertilizer treatment (NPK); a commonly used application rate of inorganic fertilizer with swine manure in-corporated treatment (NPKM), and a commonly used application rate of inorganic fertilizer with maize straw incorporated treatment (NPKS). Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene was used to determine the bacterial community structure and single carbon source utilization proifles were determined to characterize the microbial community functional metabolic diversity of different fertilizer treatments using Biolog Eco plates. The results indicated that long-term fertilized treatments signiifcantly increased soil bacterial community structure compared to CK. The use of inorganic fertilizer with organic amendments incorporated for long term (NPKM, NPKS) signiifcantly promoted soil bacterial structure than the application of inorganic fertilizer only (NPK), and NPKM treatment was the most important driver for in-creases in the soil microbial community richness (S) and structural diversity (H). Overal utilization of carbon sources by soil microbial communities (average wel color development, AWCD) and microbial substrate utilization diversity and evenness indices (H’ and E) indicated that long

  17. Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity

    Mulder, Imke; Schmidt, Bettina; Lewis, Marie; Delday, Margaret; Stokes, Christopher; Bailey, Mick; Aminov, Rustam; Gill, Bhupinder; Pluske, John; Mayer, Claus-Dieter; Kelly, Denise

    2011-01-01

    Background: Acquisition of the intestinal microbiota in early life corresponds with the development of the mucosal immune system. Recent work on caesarean-delivered infants revealed that early microbial composition is influenced by birthing method and environment. Furthermore, we have confirmed that early-life environment strongly influences both the adult gut microbiota and development of the gut immune system. Here, we address the impact of limiting microbial exposure after initial coloniza...

  18. Far from superficial: microbial diversity associated with the skin and mucus of fish

    Cipriano, Rocco C.; Dove, Alistair

    2011-01-01

    During horizontal or water-borne infection involving an obligate pathogen (e.g. – Aeromonas salmonicida, cause of furunculosis), the pathogen interacted with and influenced the microbial diversity of the dermal mucus of fish. Prior to infection, the prevalent bacterial flora cultured from juvenile Atlantic salmon (Salmo salar) included Pseudomonas fluorescens, Comomonas terrigenia, Acinetobacter sp., Moraxella sp., Pseudomonas dimunita, Alcaligenes denitrificans, Pseudomonas pseudoalcaligenes, and Pseudomonas alcaligenes, Serratia liquefaciens, Aeromonas hydrophila, other motile Aeromonas spp., and Corynebacterium aquaticum. After A. salmonicida was initially detected in this population as an external mucus infection, Acinetobacter sp., Moraxella sp., C. terrigenia, P. fluorescens, and P. dimunita, Staphylococcus sp., and A. hydrophila, were also present in appreciable numbers. Within several weeks, however, the A. salmonicida infection amplified and composed 78% of the total flora in the mucus. Only P. dimunita (4%). P. fluorescens (2%), and C. terrigenia (1%) were cultured at that time and more than a third of these fish showed evidence of a systemic A. salmonicida infection within their kidneys. Eight weeks after oral oxytetracycline treatments, A. salmonicida was no longer isolated from the mucus or kidneys of any fish and glucose inert or other oxidative microbes (e.g., P. fluorescens, C. terrigenia, Acinetobacter sp., Moraxella sp.) were beginning to repopulate the external surface of the salmon in increasing frequency. Still present and composing fairly large percentages of the total flora were A. hydrophila, as well as Enterobacter sp., and P. putrefaciens. A normal microbial diversity was re-established as the fish recovered. In another investigation, reduced biological diversity was noted in the dermal mucus among smallmouth bass that were sampled from the Jackson River (Covington, VA). In these fish, A. hydrophila and P. putrefaciens were the two

  19. Assessment of Genetic Diversity in Bamboo Accessions of India Using Molecular Markers

    Bharat Gami

    2015-06-01

    Full Text Available Bamboo is an important grass with wide scale applications in paper industries, medicines, constructions industries. It is potential feedstock for advanced biofuel production due to its favourable characteristics, natural abundance, rapid growth, perennial nature and higher CO2 sequestration. The objective of this study is to understand genetic diversity between the bamboo accessions with respect to geographical origin to correlate molecular information with feedstock characterization and adaptation to abiotic stress. In this study, genomic DNA was extracted from twenty bamboo accessions collected from different regions of India and genetic variations were assessed by inter simple sequence repeat (ISSR based molecular marker approach using 8 primers. Maximum genetic distance was observed between Bambusa wamin-Itanagar & B. ventricosa-Durg (0.48221 & minimum genetic distance between Bambusa balcooa-Modasa & Bambusa balcooa-Tripura (0.00787. Bambusa balcooa and Bambusa vulgaris were genetically similar as compared to other accessions. The genetic distance is independent of geographical distance for the bamboo accessions considered in this study. The findings of this study will help to understand the degree of differences between bamboo accessions under the same environmental conditions and to identify the representative accessions that can be used for abiotic stress resistance studies. The information can be explored for screening of closely related bamboo accessions for abiotic stress resistance screening trials.

  20. DIVERSITY ANALYSIS OF DIFFERENT ACCESSIONS OF ALOE BARBADENSIS MILL. (SYN. ALOE VERA .L) COLLECTED FROM RAJASTHAN USING RAPD MARKER SYSTEM

    DINESH CHANDRA; PREETI CHOUDHARY

    2014-01-01

    Under a survey and collection programme of National Agricultural Technology Project (NATP), various accessions of Aloe vera were collected from Rajasthan and Gujarat. In this study 10 Accessions from Rajasthan were characterized through RAPD. RAPD revealed 32.08 per cent polymorphic bands detecting 11.9% average diversity among the accessions studied. The diversity ranged from 4.3% to 20.4%. The primers like OPG-15 having high PIC value (0.346) are considered important for diversi...

  1. Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity.

    Jia Yin

    Full Text Available The adverse impact of antibiotics on the gut microbiota has attracted extensive interest, particularly due to the development of microbiome research techniques in recent years. However, a direct comparison of the dynamic effects of various types of antibiotics using the same animal model has not been available. In the present study, we selected six antibiotics from four categories with the broadest clinical usage, namely, β-lactams (Ceftriaxone Sodium, Cefoperazone/Sulbactam and meropenem, quinolones (ofloxacin, glycopeptides (vancomycin, and macrolides (azithromycin, to treat BALB/c mice. Stool samples were collected during and after the administration of antibiotics, and microbial diversity was analyzed through Illumina sequencing and bioinformatics analyses using QIIME. Both α and β diversity analyses showed that ceftriaxone sodium, cefoperazone/sulbactam, meropenem and vancomycin changed the gut microbiota dramatically by the second day of antibiotic administration whereas the influence of ofloxacin was trivial. Azithromycin clearly changed the gut microbiota but much less than vancomycin and the β-lactams. In general, the community changes induced by the three β-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium. The low diversity and high Clostridium level might be an important cause of Clostridium difficile infection after usage of β-lactams. Vancomycin was unique in that it inhibited Firmicutes, mainly the genus Clostridium. On the other hand, it induced the growth of Escherichia and effect lasted for months afterward. Azithromycin and meropenem induced the growth of Enterococcus. These findings will be useful for understanding the potential adverse effects of antibiotics on the gut microbiome and ensuring their better usage.

  2. Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity.

    Yin, Jia; M, Prabhakar; Wang, Shan; Liao, Shuo-Xi; Peng, Xin; He, Yan; Chen, Yi-Ran; Shen, Hua-Fang; Su, Jin; Chen, Ye; Jiang, Yun-Xia; Zhang, Guo-Xia; Zhou, Hong-Wei

    2015-01-01

    The adverse impact of antibiotics on the gut microbiota has attracted extensive interest, particularly due to the development of microbiome research techniques in recent years. However, a direct comparison of the dynamic effects of various types of antibiotics using the same animal model has not been available. In the present study, we selected six antibiotics from four categories with the broadest clinical usage, namely, β-lactams (Ceftriaxone Sodium, Cefoperazone/Sulbactam and meropenem), quinolones (ofloxacin), glycopeptides (vancomycin), and macrolides (azithromycin), to treat BALB/c mice. Stool samples were collected during and after the administration of antibiotics, and microbial diversity was analyzed through Illumina sequencing and bioinformatics analyses using QIIME. Both α and β diversity analyses showed that ceftriaxone sodium, cefoperazone/sulbactam, meropenem and vancomycin changed the gut microbiota dramatically by the second day of antibiotic administration whereas the influence of ofloxacin was trivial. Azithromycin clearly changed the gut microbiota but much less than vancomycin and the β-lactams. In general, the community changes induced by the three β-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium. The low diversity and high Clostridium level might be an important cause of Clostridium difficile infection after usage of β-lactams. Vancomycin was unique in that it inhibited Firmicutes, mainly the genus Clostridium. On the other hand, it induced the growth of Escherichia and effect lasted for months afterward. Azithromycin and meropenem induced the growth of Enterococcus. These findings will be useful for understanding the potential adverse effects of antibiotics on the gut microbiome and ensuring their better usage. PMID:25970622

  3. Impact of lfuxapyroxad on the microbial community structure and functional diversity in the silty-loam soil

    WU Xiao-hu; XU Jun; LIU Yong-zhuo; DONG Feng-shou; LIU Xin-gang; ZHANG Wen-wen; ZHENG Yong-quan

    2015-01-01

    The aim of this work was to assess the effect of applying three different doses of lfuxapyroxad on microbial activity, com-munity structure and functional diversity as measured by respiration, microbial biomass C, phospholipid fatty acid (PLFA) and community-level physiological proifles (CLPPs). Our results demonstrated that substrate-induced respiration (on day 15) and microbial biomass C (on days 7 and 15) were inhibited by lfuxapyroxad, but stimulation was observed thereafter. In contrast, lfuxapyroxad addition increased the basal respiration and metabolic quotients (qCO2) and respiratory quotients (QR). Analysis of the PLFA proifles revealed that the total and bacterial biomass (both Gram-positive bacteria (GP) and Gram-negative bacteria (GN)) were decreased within the initial 15 days, whereas those as wel as the GN/GP ratio were increased at days 30 and 60. Fluxapyroxad input decreased the fungi biomass but increased the bacteria/fungi ratio at al incubation time. Moreover, high lfuxapyroxad input (75 mg lfuxapyroxad kg–1 soil dry weight) increased the microbial stress level. A principal component analysis (PCA) of the PLFAs revealed that lfuxapyroxad treatment signiifcantly shifted the microbial community structure, but al of the observed effects were transient. Biolog results showed that average wel color development (AWCD) and functional diversity index (H´) were increased only on day 60. In addition, the dissipation of lfuxa-pyroxad was slow in soil, and the degradation half-lives varied from 158 to 385 days depending on the concentration tested.

  4. Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

    Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

    2016-08-01

    This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. PMID:27521934

  5. Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

    Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

    2016-06-01

    Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha‑1•yr‑1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

  6. Comparative analysis of intestinal microbial community diversity between healthy and orally infected ducklings with Salmonella enteritidis by ERIC-PCR

    Sheng-Yan Cao; De-Kang Zhu; Qi-Hui Luo; Xiao-Yue Chen; Ming-Shu Wang; An-Chun Cheng; Xue-Feng Qi; Xiao-Yan Yang; Shu-Xuan Deng; Nian-Chun Yin; Zhen-Hua Zhang; Deng-Chun Zhou

    2008-01-01

    AIM:To analyze the difference of intestinal microbial community diversity between healthy and (S.enteritidis)orally infected ducklings.METHODS:Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR was applied to analyze the intestinal microbial community diversity and dynamic change including duodenum,jejunum,ileum,cecum and rectum from healthy ducklings and 7-dayoold ducklings after oral infection with S.enteritidis at different time points.RESULTS:The intestinal microbial community of the control healthy ducklings was steady and the ERIC-PCR band numbers of the control healthy ducklings were the least with rectum and were the most with caecum.ER[C-PCR bands of orally inoculated ducklings did not obviously change until 24 h after inoculation (p.i.).The numbers of the ERIC-PCR bands gradually decreased from 24 h to 72 h p.i.,and then,with the development of disease,the band numbers gradually increased until 6 d p.i.The prominent bacteria changed because of S.enteritidis infection and the DNAstar of staple of ERIC-PCR showed that aerobe and facultative aerobe (Escherichia coli,Shigella,Salmonella) became preponderant bacilli in the intestine of orally infected ducklings with SE.CONCLUSION:This study has provided significant data to clarify the intestinal microbial community diversity and dynamic change of healthy and S.enterltidis orally infected ducklings,and valuable insight into the pathogenesis of S.enteritidis infection in both human and animals.

  7. Microbial Diversity in the Early In Vivo-Formed Dental Biofilm.

    Heller, D; Helmerhorst, E J; Gower, A C; Siqueira, W L; Paster, B J; Oppenheim, F G

    2016-03-01

    Although the mature dental biofilm composition is well studied, there is very little information on the earliest phase of in vivo tooth colonization. Progress in dental biofilm collection methodologies and techniques of large-scale microbial identification have made new studies in this field of oral biology feasible. The aim of this study was to characterize the temporal changes and diversity of the cultivable and noncultivable microbes in the early dental biofilm. Samples of early dental biofilm were collected from 11 healthy subjects at 0, 2, 4, and 6 h after removal of plaque and pellicle from tooth surfaces. With the semiquantitative Human Oral Microbiome Identification Microarray (HOMIM) technique, which is based on 16S rRNA sequence hybridizations, plaque samples were analyzed with the currently available 407 HOMIM microbial probes. This led to the identification of at least 92 species, with streptococci being the most abundant bacteria across all time points in all subjects. High-frequency detection was also made with Haemophilus parainfluenzae, Gemella haemolysans, Slackia exigua, and Rothia species. Abundance changes over time were noted for Streptococcus anginosus and Streptococcus intermedius (P = 0.02), Streptococcus mitis bv. 2 (P = 0.0002), Streptococcus oralis (P = 0.0002), Streptococcus cluster I (P = 0.003), G. haemolysans (P = 0.0005), and Stenotrophomonas maltophilia (P = 0.02). Among the currently uncultivable microbiota, eight phylotypes were detected in the early stages of biofilm formation, one belonging to the candidate bacterial division TM7, which has attracted attention due to its potential association with periodontal disease. PMID:26746720

  8. Investigating microbial diversity and UV radiation impact at the high-altitude Lake Aguas Calientes, Chile

    Escudero, Lorena; Chong, Guillermo; Demergasso, Cecilia; Farías, María Eugenia; Cabrol, Nathalie A.; Grin, Edmond; Minkley, Edwin, Jr.; Yu, Yeoungeob

    2007-09-01

    The High-Lakes Project is funded by the NAI and explores the highest perennial volcanic lakes on Earth in the Bolivian and Chilean Andes, including several lakes ~6,000 m elevation. These lakes represent an opportunity to study the evolution of microbial organisms in relatively shallow waters not providing substantial protection against UV radiation. Aguas Calientes (5,870 m) was investigated (November 2006) and samples of water and sediment collected at 1, 3, 5, and 10 cm depth. An Eldonet UV dosimeter positioned on the shore records UV radiation and temperature, and is logging data year round. A UV SolarLight sensor allowed acquisition of point measurements in all channels at the time of the sampling. UVA, UVB, and PAR peaks between 11:00 am and 1:00 pm reached 7.7 mW/cm2, 48.5 μW/cm2, and 511 W/m2, respectively. The chemical composition of the water sample was analyzed. DNA was extracted and DGGE analyses with bacterial and archaeal 16S fragments were performed to describe microbial diversity. Antibiotic resistances were established previously in similar environments in Argentine Andean wetlands. In order to determine these resistances in our samples, they were inoculated onto LB and R2A media and onto R2A medium containing either chloramphenicol, ampicillin or tetracycline. Bacterial was higher than archeal cell number determined by RT-PCR in all the samples, reaching maximum total values of 5x10 5 cell mL-1. DGGE results from these samples and Licancabur summit lake (5,916 m) samples were also compared. Eight antibiotic-resistant Gram negative strains have been isolated with distinct resistance patterns.

  9. Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells.

    Cornelia eWuchter

    2013-12-01

    Full Text Available The Antrim Shale in the Michigan Basin is one of the most productive shale gas formations in the U.S, but optimal resource recovery strategies must rely on a thorough understanding of the complex biogeochemical, microbial, and physical interdependencies in this and similar systems. We used Illumina Miseq 16S rDNA sequencing to analyze the diversity and relative abundance of prokaryotic communities present in Antrim shale formation water of three closely spaced recently fractured gas-producing wells. In addition, the well waters were incubated with a suite of fermentative and methanogenic substrates in an effort to stimulate microbial methane generation. The three wells exhibited substantial differences in their community structure that may arise from their different drilling and fracturing histories. Bacterial sequences greatly outnumbered those of archaea and shared highest similarity to previously described cultures of mesophiles and moderately halophiles within the Firmicutes, Bacteroidetes, and δ- and ε-Proteobacteria. The majority of archaeal sequences shared highest sequence similarity to uncultured euryarchaeotal environmental clones. Some sequences closely related to cultured methylotrophic and hydrogenotrophic methanogens were also present in the initial well water. Incubation with methanol and trimethylamine stimulated methylotrophic methanogens and resulted in the largest increase in methane production in the formation waters, while fermentation triggered by the addition of yeast extract and formate indirectly stimulated hydrogenotrophic methanogens. The addition of sterile powdered shale as a complex natural substrate stimulated the rate of methane production without affecting total methane yields. Depletion of methane indicative of anaerobic methane oxidation was observed over the course of incubation with some substrates. This process could constitute a substantial loss of methane in the shale formation.

  10. Evaluation of the Genetic Diversity of several Corylus avellana Accessions from the Romanian National Hazelnut Collection

    Iulia Francesca POP

    2010-09-01

    Full Text Available Romanian hazelnut (Corylus avellana germplasm is held in a national collection at SCDP Valcea. A clear situation of the held accessions is necessary for an efficient management of the germplasm collection. In order to achieve this, the genetic variability of 43 accessions was assessed using 23 RAPD primers. The RAPD analysis was carried out as a screening test to confirm the genetic identity of some accessions. Based on the screening results, 12 accessions were selected for analysis using nine SSR primers. A high level of genetic diversity was observed (He=0.75, Ho=0.81, F=-0.061 among the analyzed samples. A genetic similarity matrix was constructed and the resulting UPGMA dendrogram revealed three major groups, corresponding to the geographical origin of the accessions. In order to increase the effectiveness of genebank management, the identification of duplicate and mislabeled accessions with the aid of molecular markers is of high interest, especially being the first one of this kind in a Romanian hazelnut germplasm collection.

  11. A Comparison of Microbial Water Quality and Diversity for Ballast and Tropical Harbor Waters.

    Charmaine Ng

    broad-brush description of difference in microbial composition and diversity between open oceans and tropical coastal environments through the use of next generation sequencing technology.

  12. [Carbon source metabolic diversity of soil microbial community under different climate types in the area affected by Wenchuan earthquake].

    Zhang, Guang-Shuai; Lin, Yong-Ming; Ma, Rui-Feng; Deng, Hao-Jun; Du, Kun; Wu, Cheng-Zhen; Hong, Wei

    2015-02-01

    The MS8.0 Wenchuan earthquake in 2008 led to huge damage to land covers in northwest Sichuan, one of the critical fragile eco-regions in China which can be divided into Semi-arid dry hot climate zone (SDHC) and Subtropical humid monsoon climate zone (SHMC). Using the method of Bilog-ECO-microplate technique, this paper aimed to determine the functional diversity of soil microbial community in the earthquake-affected areas which can be divided into undamaged area (U), recover area (R) and damaged area without recovery (D) under different climate types, in order to provide scientific basis for ecological recovery. The results indicated that the average-well-color-development (AWCD) in undamaged area and recovery area showed SDHC > SHMC, which was contrary to the AWCD in the damaged area without recovery. The AWCD of damaged area without recovery was the lowest in both climate zones. The number of carbon source utilization types of soil microbial in SHMC zone was significantly higher than that in SDHC zone. The carbon source utilization types in both climate zones presented a trend of recover area > undamaged area > damaged area without recovery. The carbon source metabolic diversity characteristic of soil microbial community was significantly different in different climate zones. The diversity index and evenness index both showed a ranking of undamaged area > recover area > damaged area without recovery. In addition, the recovery area had the highest richness index. The soil microbial carbon sources metabolism characteristic was affected by soil nutrient, aboveground vegetation biomass and vegetation coverage to some extent. In conclusion, earthquake and its secondary disasters influenced the carbon source metabolic diversity characteristic of soil microbial community mainly through the change of aboveground vegetation and soil environmental factors. PMID:26031097

  13. DIVERSITY ANALYSIS OF DIFFERENT ACCESSIONS OF ALOE BARBADENSIS MILL. (SYN. ALOE VERA .L COLLECTED FROM RAJASTHAN USING RAPD MARKER SYSTEM

    DINESH CHANDRA

    2014-03-01

    Full Text Available Under a survey and collection programme of National Agricultural Technology Project (NATP, various accessions of Aloe vera were collected from Rajasthan and Gujarat. In this study 10 Accessions from Rajasthan were characterized through RAPD. RAPD revealed 32.08 per cent polymorphic bands detecting 11.9% average diversity among the accessions studied. The diversity ranged from 4.3% to 20.4%. The primers like OPG-15 having high PIC value (0.346 are considered important for diversity studies, whereas, OPG-14 have highest Discrimination index (0.911 and may be used for identification of different accessions. The clustering analysis resulted in the formation of one group, only consisting of eight accessions while Nagour collections remained out of cluster. The diversity pattern did not show any correlation with the site of collection indicating that original introduction consisted of small sample size its spread was random.

  14. Genetic diversity analysis of Capsicum spp germplasm bank accessions based on α/β-esterase polymorphism.

    Monteiro, E R; Bronzato, A R; Orasmo, G R; Lopes, A C A; Gomes, R L F; Mangolin, C A; Machado, M F P S

    2013-01-01

    Genetic diversity and structure were analyzed in 10 accessions belonging to Banco Ativo de Germoplasma de Capsicum located at Federal University of Piauí in northwestern Brazil that receives pepper samples grown in community gardens in various regions and Brazilian states. Selections were made from seeds of C. chinense (4 accessions), C. annuum (5 accessions), and C. baccatum (1 accession). Samples consisting of leaves were collected from 4-10 plants of each accession (a total of 85 plants). Native polyacrylamide gel electrophoresis was used to identify α- and β-esterase polymorphisms. Polymorphism was clearly detected in 5 loci. Sixteen alleles were found at 5 α/β-esterase loci of the three Capsicum species. In the C. chinense samples, the highest HO and HE values were 0.3625 and 0.4395, respectively, whereas in C. annuum samples, HO and HE values were 0.2980 and 0.3310, respectively; the estimated HO and HE values in C. chinense samples were higher than those detected in C. annuum samples. A deficit of homozygous individuals was found in C. chinense (FIS = -0.6978) and C. annuum (FIS = 0.7750). Genetic differentiation between C. chinense and C. annuum at these loci was high (FST = 0.1867) indicating that C. chinense and C. annuum are genetically structured species for α/β- esterase isozymes. The esterase analysis showed high genetic diversity among the C. chinense and C. annuum samples and very high genetic differentiation (FST = 0.6321) among the C. chinense and C. annuum samples and the C. baccatum accession. PMID:23661440

  15. Exploration of microbial diversity and function in Red Sea sponges by deep sequencing

    Moitinho e Silva, Lucas

    2014-01-01

    Marine sponges (phylum Porifera) are simple, sessile, filter-feeder animals. Microbial symbionts are commonly found in the sponge internal tissue, termed the mesohyl. With respect to the microbial content, sponges are classified as either low-microbial abundance sponges (LMA), or high-microbial abundance sponges (HMA). The HMA/LMA dichotomy was explored in this Thesis using the Red Sea sponges as experimental models. A range of methods encompassing transmission electron microscopy, 16S rRNA g...

  16. Microbial diversity of soil bacteria in agricultural field contaminated with heavy metals

    CHIEN Chihching; KUO Yumei; CHEN Changchieh; HUNG Chunwei; YEH Chihwei; YEH Weijen

    2008-01-01

    In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals.Analysis of 16S rDNA sequences amplified from DNA directly extracted from the soil revealed 17 different bacterial types (genera and/or species).They included Polyangium spp.,Sphingomonas spp.,Variovorax spp.,Hafina spp.,Clostridia,Acidobacteria,the enterics and some uncultured strains.Microbes able to tolerate high concentrations of cadmium (500 μmol/L and above) were also isolated from the soil.These isolates included strains of Acinetobacter (strain CD06),Enterobacter sp.(strains CD01,CD03,CD04 and CD08) (similar strains also identified inculture-independent approach) and a strain of Stenotrophomonas sp.The results indicated that the species identified from direct analysis of 16S rDNA of the soil can be quite different from those strains obtained from enrichment eultttres and the microbial activities for heavy metal resistance might be more appropriately addressed by the actual isolates.

  17. Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine.

    Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Finegold, Milton J; Petrosino, Joseph F; Conner, Margaret E; Versalovic, James

    2012-05-01

    Beneficial microbes and probiotics show promise for the treatment of pediatric gastrointestinal diseases. However, basic mechanisms of probiosis are not well understood, and most investigations have been performed in germ-free or microbiome-depleted animals. We sought to functionally characterize probiotic-host interactions in the context of normal early development. Outbred CD1 neonatal mice were orally gavaged with one of two strains of human-derived Lactobacillus reuteri or an equal volume of vehicle. Transcriptome analysis was performed on enterocyte RNA isolated by laser-capture microdissection. Enterocyte migration and proliferation were assessed by labeling cells with 5-bromo-2'-deoxyuridine, and fecal microbial community composition was determined by 16S metagenomic sequencing. Probiotic ingestion altered gene expression in multiple canonical pathways involving cell motility. L. reuteri strain DSM 17938 dramatically increased enterocyte migration (3-fold), proliferation (34%), and crypt height (29%) compared to vehicle-treated mice, whereas strain ATCC PTA 6475 increased cell migration (2-fold) without affecting crypt proliferative activity. In addition, both probiotic strains increased the phylogenetic diversity and evenness between taxa of the fecal microbiome 24 h after a single probiotic gavage. These experiments identify two targets of probiosis in early development, the intestinal epithelium and the gut microbiome, and suggest novel mechanisms for probiotic strain-specific effects. PMID:22267340

  18. Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula

    Bernd Wemheuer

    2013-01-01

    Full Text Available Volcanic regions contain a variety of environments suitable for extremophiles. This study was focused on assessing and exploiting the prokaryotic diversity of two microbial communities derived from different Kamchatkian thermal springs by metagenomic approaches. Samples were taken from a thermoacidophilic spring near the Mutnovsky Volcano and from a thermophilic spring in the Uzon Caldera. Environmental DNA for metagenomic analysis was isolated from collected sediment samples by direct cell lysis. The prokaryotic community composition was examined by analysis of archaeal and bacterial 16S rRNA genes. A total number of 1235 16S rRNA gene sequences were obtained and used for taxonomic classification. Most abundant in the samples were members of Thaumarchaeota, Thermotogae, and Proteobacteria. The Mutnovsky hot spring was dominated by the Terrestrial Hot Spring Group, Kosmotoga, and Acidithiobacillus. The Uzon Caldera was dominated by uncultured members of the Miscellaneous Crenarchaeotic Group and Enterobacteriaceae. The remaining 16S rRNA gene sequences belonged to the Aquificae, Dictyoglomi, Euryarchaeota, Korarchaeota, Thermodesulfobacteria, Firmicutes, and some potential new phyla. In addition, the recovered DNA was used for generation of metagenomic libraries, which were subsequently mined for genes encoding lipolytic and proteolytic enzymes. Three novel genes conferring lipolytic and one gene conferring proteolytic activity were identified.

  19. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing.

    Naveed, Muhammad; Mubeen, Samavia; Khan, SamiUllah; Ahmed, Iftikhar; Khalid, Nauman; Suleria, Hafiz Ansar Rasul; Bano, Asghari; Mumtaz, Abdul Samad

    2014-01-01

    In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization. PMID:25477935

  20. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

    Muhammad Naveed

    2014-09-01

    Full Text Available In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ. Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

  1. The source of the river as a nursery for microbial diversity.

    de Oliveira, Luiz Felipe Valter; Margis, Rogério

    2015-01-01

    Bacteria are highly diverse and ubiquitous organisms that play a key role as drivers for ecosystem processes. The application of NGS (next-generation sequencing technologies) for 16S analysis has been broadly used for understanding bacterioplankton composition and structure. Most of studies conducted on aquatic ecosystems with 16S NGS have been in seawater and lakes. A few studies using NGS have been conducted in river environments and have suggested the presence of a bacterial seed-bank. We performed 16S highly variable V4 region high-throughput analysis in the Sinos River, which is located in one of most important Brazilian industrial centers. This region has several contrasts in its environmental characteristics, presenting a longitudinal gradient of eutrophication and making it a remarkable study site for observing the dynamics of bacterioplankton. We demonstrated consistent evidence for the existence of a bacterial seed-bank and its longitudinal persistence. Seasonal shifts reinforce the importance of the source of the river in maintaining the bacterial seed-bank that spreads throughout the river. Therefore, the preservation of the source of the river is important not only for hydrologic reasons but also to maintain the microbial composition and the ecological integrity of the river. PMID:25803426

  2. Microbial aggregates within tissues infect a diversity of corals throughout the Indo-Pacific

    Work, Thierry M.; Aeby, Greta S.

    2014-01-01

    Coral reefs are highly diverse ecosystems where symbioses play a pivotal role. Corals contain cell-associated microbial aggregates (CAMA), yet little is known about how widespread they are among coral species or the nature of the symbiotic relationship. Using histology, we found CAMA within 24 species of corals from 6 genera from Hawaii, American Samoa, Palmyra, Johnston Atoll, Guam, and Australia. Prevalence (%) of infection varied among coral genera: Acropora, Porites, and Pocillopora were commonly infected whereas Montipora were not. Acropora from the Western Pacific were significantly more likely to be infected with CAMA than those from the Central Pacific, whereas the reverse was true for Porites. Compared with apparently healthy colonies, tissues from diseased colonies were significantly more likely to have both surface and basal body walls infected. The close association of CAMA with host cells in numerous species of apparently healthy corals and lack of associated cell pathology reveals an intimate agent-host association. Furthermore, CAMA are Gram negative and in some corals may be related to chlamydia or rickettsia. We propose that CAMA in adult corals are facultative secondary symbionts that could play an important ecological role in some dominant coral genera in the Indo-Pacific. CAMA are important in the life histories of other animals, and more work is needed to understand their role in the distribution, evolution, physiology, and immunology of reef corals.

  3. Physico-chemical Profile and Microbial Diversity During Bioconversion of Sugarcane Press Mud Using Bacterial Suspension

    Tushar Chandra SARKER

    2013-08-01

    Full Text Available This study was aimed at investigating the physico-chemical and microbial diversity for rapid composting of sugarcane press mud (PM leading to organic manure. Five bacterial strains (Cellulomonas sp., Klebsiella sp., Proteus sp., Enterobacter sp., Salmonella sp. were tested under in vivo conditions for bioconversion of PM using pile method. Results revealed that combined inoculation of bacterial consortia was found to be the best decomposer of PM resulting reduction of organic carbon content (26.75%, C:N ratio (12.44%. In parallel, it increased the nitrogen (2.34%, phosphorous (1.15% and potassium (1.37% content along with the population of microorganisms i.e. bacteria, fungi and actinomycetes. However, the population of tested bacteria was gradually depleted after completion of PM decomposition together with pathogenic bacteria and fungi due to full conversion of carbon component into other minerals, i.e. N, P, K etc. Taken together, these findings certainly pinpoints the effective role of bacterial suspension for composting sugarcane press mud which the eventually be used as organic manure.

  4. Prebiotics Modulate the Effects of Antibiotics on Gut Microbial Diversity and Functioning in Vitro

    Laura P. Johnson

    2015-06-01

    Full Text Available Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs, which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation—another method used to modulate gut composition and function—could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre, inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.

  5. Analysis of raw goat milk microbiota: impact of stage of lactation and lysozyme on microbial diversity.

    McInnis, Elizabeth A; Kalanetra, Karen M; Mills, David A; Maga, Elizabeth A

    2015-04-01

    To protect infants from infection, human milk contains high levels of the enzyme lysozyme, unlike the milk of dairy animals. We have genetically engineered goats to express human lysozyme (hLZ milk) in their milk at 68% the amount found in human milk to help extend this protection. This study looked at the effect of hLZ on bacteria in raw milk over time. As the microbial diversity of goats' milk has yet to be investigated in depth using next-generation sequencing (NGS) technologies, we applied NGS and clone library sequencing (CLS) to determine the microbiota of raw goat milk (WT milk) and hLZ milk at early, mid and late lactation. Overall, in WT milk, the bacterial populations in milk at early and mid lactation were similar to each other with a shift occurring at late lactation. Both methods found Proteobacteria as the dominant bacteria at early and mid lactation, while Actinobacteria surged at late lactation. These changes were related to decreases in Pseudomonas and increases in Micrococcus. The bacterial populations in hLZ milk were similar to WT milk at early and mid lactation with the only significant differences occurring at late lactation with the elevation of Bacillaceae, Alicyclobacillaceae, Clostridiaceae and Halomonadaceae. PMID:25475275

  6. Changes in microbial diversity of brined green asparagus upon treatment with high hydrostatic pressure.

    Toledo Del Árbol, Julia; Pérez Pulido, Rubén; La Storia, Antonietta; Grande Burgos, Maria José; Lucas, Rosario; Ercolini, Danilo; Gálvez, Antonio

    2016-01-01

    The application of high hydrostatic pressure (HHP, 600MPa, 8 min) on brined green asparagus and the changes in bacterial diversity after treatments and during storage at 4 °C (30 days) or 22 °C (10 days) were studied. HHP treatments reduced viable cell counts by 3.6 log cycles. The residual surviving population did not increase during storage at 4 °C. However, bacterial counts significantly increased at 22 °C by day 3, leading to rapid spoilage. The microbiota of green asparagus was composed mainly by Proteobacteria (mainly Pantoea and Pseudomonas), followed by Firmicutes (mainly Lactococcus and Enterococcus) and to a less extent Bacteroidetes and Actinobacteria. During chill storage of untreated asparagus, the relative abundance of Proteobacteria as well as Enterococcus and Lactococcus decreased while Lactobacillus increased. During storage of untreated asparagus at 22 °C, the abundance of Bacteroidetes decreased while Proteobacteria increased during late storage. The HHP treatment determined a reduction of the Proteobacteria both early after treatment and during chill storage. In the HHP treated samples stored at 22 °C, the relative abundance of Pseudomonas rapidly decreased at day 1, with an increase of Bacteroidetes. This was followed by a marked increase in Enterobacteriaceae (Escherichia) simultaneously with increase in viable counts and spoilage. Results from the study indicate that the effect of HHP treatments on the viability ofmicrobial populations in foods also has an impact on the dynamics of microbial populations during the storage of the treated foods. PMID:26372734

  7. Investigations on microbial diversity of Jakrem hot spring, Meghalaya, India using cultivation-independent approach

    Panda, Amrita Kumari; Bisht, Satpal Singh; Kumar, Nachimuthu Senthil; De Mandal, Surajit

    2015-01-01

    Jakrem hot water spring is located in the West Khasi Hill District of the state of Meghalaya, and is one of the most popular hot springs of the state. There is a populist belief among the inhabitants and people that the hot spring water has got curative properties against various skin ailments. This is the first report on V3 hyper-variable region of 16S rDNA metagenome sequence employing Illumina platform to profile the microbial community of this less known hot spring from Meghalaya, India. Metagenome comprised of 10, 74,120 raw sequences with a sequence length of 151 bp and 56.35% G + C content. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP056897. A total of 8, 77, 364 pre-processed reads were clustered into 694 OTUs (operational taxonomical units) comprising of 14 bacterial phyla including unknown phylum demonstrating 49 families. Hot spring bacterial community is dominated by Firmicutes (61.60%), Chloroflexi (21.37%), Cyanobacteria (12.96%) and unclassified bacteria (1.2%) respectively. PMID:26484205

  8. Investigations on microbial diversity of Jakrem hot spring, Meghalaya, India using cultivation-independent approach

    Amrita Kumari Panda

    2015-06-01

    Full Text Available Jakrem hot water spring is located in the West Khasi Hill District of the state of Meghalaya, and is one of the most popular hot springs of the state. There is a populist belief among the inhabitants and people that the hot spring water has got curative properties against various skin ailments. This is the first report on V3 hyper-variable region of 16S rDNA metagenome sequence employing Illumina platform to profile the microbial community of this less known hot spring from Meghalaya, India. Metagenome comprised of 10, 74,120 raw sequences with a sequence length of 151 bp and 56.35% G + C content. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP056897. A total of 8, 77, 364 pre-processed reads were clustered into 694 OTUs (operational taxonomical units comprising of 14 bacterial phyla including unknown phylum demonstrating 49 families. Hot spring bacterial community is dominated by Firmicutes (61.60%, Chloroflexi (21.37%, Cyanobacteria (12.96% and unclassified bacteria (1.2% respectively.

  9. Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock

    Dhiraj ePaul

    2016-01-01

    Full Text Available Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world created in the basalt rocks. Although culture-dependent studies have been reported, the comprehensive understanding of microbial community composition and structure of Lonar Lake remain obscure. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet near consistent community composition. The predominance of bacterial phyla Proteobacteria (30% followed by Actinobacteria (24%, Firmicutes (11% and Cyanobacteria (5% was observed. Bacterial phylum Bacteroidetes (1.12%, BD1-5 (0.5%, Nitrospirae (0.41% and Verrucomicrobia (0.28% were detected as relatively minor populations in Lonar Lake ecosystem. Within Proteobacteria, Gammaproteobacteria represented the most abundant population (21-47% among all the sediments and as a minor population in water samples. Bacterial members Proteobacteria and Firmicutes were present significantly higher (p≥0.05 in sediment samples, whereas members of Actinobacteria, Candidate_division_TM7 and Cyanobacteria (p≥0.05 were significantly abundant in water samples. It was noted that compared to other hypersaline soda lakes, Lonar Lake samples formed one distinct cluster, suggesting a different microbial community composition and structure. The present study reports for the first time the different composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. Having better insight of community structure of this Lake ecosystem could be useful in understanding the microbial role in the geochemical cycle for future functional exploration of the unique hypersaline Lonar Lake.

  10. Genetic diversity studies in twenty accessions of hot pepper (Capsicum spp L.) in Ghana

    Twenty (20) accessions of hot pepper (Capsicum spp L.) were collected from eight geographical regions of Ghana for genetic diversity studies. The objective was to assess genetic relationship among them using phenotypic and molecular traits and to evaluate their elemental composition. A replicated field experiment was conducted to assess their genetic diversity based on 13 quantitative traits and 22 qualitative traits using the IBPGR descriptor list for Capsicum. Confirmation of their identities was done using 10 SSR markers. The accessions were also evaluated for macro, micro and trace elements in their fresh fruits using the Instrumental Neutron Activation Analysis (INAA). Five essential macro elements (Ca, Cl, K, Mg and Na), two micro elements (Al and Mn) and one trace element (Br) were detected by INAA. Results from the agromorphological study revealed that accession Wes 01 had the widest stem width, matured leaf width, high fruit set but late maturing. Nor 03 was early maturing and had high fruit set, but also possessed the highest number of seeds per fruit. Fruit weight, fruit width, fruit length and plant canopy width, recorded the highest variabilities with 66.191; 53.24; 49.32; and 32.42 coefficients of variation (CVs), respectively. Few traits such as plant canopy width, plant height, fruit length, mature leaf length and number of seeds per fruit contributed substantially to total genetic variance as revealed by the principal component analysis (PCA). A dendrogram generated using morphological traits grouped accessions into cultivated and wild genotypes of pepper and all the accessions were identified as separate entities with no duplications. Strong correlation was recorded between plant canopy width and plant height, mature leaf length and mature leaf width, and also fruit weight and fruit width and fruit length. Negative correlation was however, observed between fruit length and days to 50% fruiting and flowering. All three accessions from the Northern

  11. Open Access in Higher Education–Strategies for Engaging Diverse Student Cohorts

    Luisa Signor

    2014-07-01

    Full Text Available With growth in online education, students gain tertiary qualifications through a mode more suited to their demographics such as work and life balance, learning styles and geographical accessibility. Inevitably this has led to a growth in diversity within student cohorts.The case study described in this paper illustrates strategies based on informed learning design for educating diverse student cohorts in an online program offered by Swinburne University of Technology. The case, an open-access, undergraduate information systems program, attracts mature age students studying while balancing employment and family commitments. The program’s open-access facet is the ‘no entry requirements’ such as prerequisite studies. Hence, many students enter the program via non-traditional pathways bringing significant differences in experience and consequent skill bases. The program’s innovative pedagogy encourages students to engage via active learning with tailored assessments, interactive communication via discussion boards and facilitated real-time sessions and formative feedback which include audio components.

  12. Effects of cultivation of Osr HSA transgenic rice on functional diversity of microbial communities in the soil rhizosphere

    Xiaobing; Zhang; Xujing; Wang; Qiaoling; Tang; Ning; Li; Peilei; Liu; Yufeng; Dong; Weimin; Pang; Jiangtao; Yang; Zhixing; Wang

    2015-01-01

    With the widespread cultivation of transgenic crops, there is increasing concern about unintended effects of these crops on soil environmental quality. In this study, we used the Biolog method and ELISA to evaluate the possible effects of Osr HSA transgenic rice on soil microbial utilization of carbon substrates under field conditions. There were no significant differences in average well-color development(AWCD) values, Shannon–Wiener diversity index(H), Simpson dominance indices(D) and Shannon–Wiener evenness indices(E) of microbial communities in rhizosphere soils at eight samplings between Osr HSA transgenic rice and its non-transgenic counterpart. The main carbon sources utilized by soil microbes were carbohydrates, carboxylic acids, amino acids and polymers. The types,capacities and patterns of carbon source utilization by microbial communities in rhizosphere soils were similar throughout the detection period. We detected no Osr HSA protein in the roots of Osr HSA transgenic rice. We concluded that Osr HSA transgenic rice and the r HSA protein it produced did not alter the functional diversity of microbial communities in the rhizosphere.

  13. Microbial Abundance and Diversity Patterns Associated with Sediments and Carbonates from the Methane Seep Environments of Hydrate Ridge, OR

    Jeffrey James Marlow

    2014-10-01

    Full Text Available Methane seeps are among the most productive habitats along continental margins, as anaerobic methane-oxidizing euryarchaeaota and sulfur-metabolizing deltaproteobacteria form the biological base of a dynamic deep-sea ecosystem. The degree of methane seepage therefore represents one important variable in ecosystem dynamics, and the recent discovery of carbonate-hosted endolithic methanotrophy exposes another potentially discriminating factor: physical substrate type. Methanotrophic microbial communities have been detected within diverse seep-associated habitats, including unlithified sediments, protolithic carbonate nodules, and lithified carbonate slabs and chemoherms of distinct mineralogies. However, a systematic assessment of the diversity and community structure associated with these different habitats has been lacking. In this study, microbial aggregate analysis, microbial abundance quantification, mineralogical identification, and archaeal and bacterial 16S rRNA gene clone libraries were used to deconvolve the relationships between seepage activity, substrate type, and microbial community structure. We report prevalent methane-oxidizing archaeal lineages in both active and low-activity seep settings, and a strong community dependence on both seepage activity and substrate type. Statistical treatments of relative taxa abundances indicate that archaeal community structure is more dependent on the degree of methane seepage than physical substrate type; bacterial assemblages appear to be more strongly influenced by the type of colonization substrate than seepage activity. These findings provide a window into the determinants of community structure and function, improving our understanding of potential elemental cycling at seep sites.

  14. Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats

    Nübel, Ulrich; Bateson, Mary M; Vandieken, Verona;

    2002-01-01

    We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park). By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S...... rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected. Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives...

  15. Microscopic Examination of Distribution and Phenotypic Properties of Phylogenetically Diverse Chloroflexaceae-Related Bacteria in Hot Spring Microbial Mats

    Nübel, U.; Bateson, Mary M.; Vandieken, V.;

    2002-01-01

    We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park). By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S...... rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected. Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives...

  16. Priming effect and microbial diversity in ecosystem functioning and response to global change : a modeling approach using the SYMPHONY model

    Perveen, N.; Barot, Sébastien; Alvarez, G; Klumpp, K.; R. Martin; Rapaport, A.; Herfurth, D.; Louault, F; Fontaine, S.

    2014-01-01

    Integration of the priming effect (PE) in ecosystem models is crucial to better predict the consequences of global change on ecosystem carbon (C) dynamics and its feedbacks on climate. Over the last decade, many attempts have been made to model PE in soil. However, PE has not yet been incorporated into any ecosystem models. Here, we build plant/soil models to explore how PE and microbial diversity influence soil/plant interactions and ecosystem C and nitrogen (N) dynamics in respo...

  17. Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

    Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

    2014-11-01

    In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

  18. Effects of different bulking agents on the maturity, enzymatic activity, and microbial community functional diversity of kitchen waste compost.

    Wang, Xiaojuan; Zhang, Wenwei; Gu, Jie; Gao, Hua; Qin, Qingjun

    2016-10-01

    Aerobic composting is an effective method for the disposal and utilization of kitchen waste. However, the addition of a bulking agent is necessary during kitchen waste composting because of its high moisture content and low C/N ratio. In order to select a suitable bulking agent, we investigated the influence of leaf litter (LL), sawdust (SD), and wheat straw (WS) on the enzymatic activity, microbial community functional diversity, and maturity indices during the kitchen waste composting process. The results showed that the addition of WS yielded the highest maturity (the C/N ratio decreased from 25 to 13, T value = 0.5, and germination index (GI) = 114.7%), whereas the compost containing SD as a bulking agent had the lowest maturity (GI = 32.4%). The maximum cellulase and urease activities were observed with the WS treatment on day 8, whereas the SD treatment had the lowest cellulase activity and the LL treatment had the lowest urease activity. The compost temperature and microbial activity (as the average well color development) showed that bulking the composts with SD prolonged the composting process. The diversity index based on the community-level physiological profile showed that the composts bulked with LL and WS had greater microbial community functional diversity compared with those bulked with SD. Thus, the maturity indexes and enzymatic activities suggest that WS is a suitable bulking agent for use in kitchen waste composting systems. PMID:26895274

  19. Diversity and dynamics of active microbial eukaryotes in the anoxic zone of a freshwater meromictic lake (Pavin, France

    CECILE eLEPERE

    2016-02-01

    Full Text Available Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene in conjunction with quantitative PCR (DNA and RNA and fluorescent in situ hybridization analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin. This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. 42 % of the OTUs (Operational taxonomic Units are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae and Fungi (Dikarya and Chytrids are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae are also present and active in this zone, which opens up questions regarding their metabolism.

  20. Soil microbial community structure in diverse land use systems:A comparative study using Biolog,DGGE,and PLFA analyses

    XUE Dong; YAO Huai-Ying; GE De-Yong; HUANG Chang-Yong

    2008-01-01

    Biolog,16S rRNA gene denaturing gradient gel electrophoresis (DGGE),and phospholipid fatty acid (PLFA) analyses were used to assess soil microbial community characteristics in a chronosequence of tea garden systems (8-,50-,and 90year-old tea gardens),an adjacent wasteland,and a 90-year-old forest.Biolog analysis showed that the average well color development (AWCD) of all carbon sources and the functional diversity based on the Shannon index decreased (P<0.05)in the following order:wasteland>forest>tea garden.For the DGGE analysis,the genetic diversity based on the Shannon index was significantly lower in the tea garden soils than in the wasteland.However,compared to the 90-year-old forest,the tea garden soils showed significantly higher genetic diversity.PLFA analysis showed that the ratio of Gram positive bacteria to Gram negative bacteria was significantly higher in the tea garden soils than in the wasteland,and the highest value was found in the 90-year-old forest.Both the fungal PLFA and the ratio of fungi to bacteria were significantly higher in the three tea garden soils than in the wasteland and forest,indicating that fungal PLFA was significantly affected by land-use change.Based on cluster analysis of the soil microbial community structure,all three analytical methods showed that land-use change had a greater effect on soil microbial community structure than tea garden age.

  1. Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France)

    Lepère, Cécile; Domaizon, Isabelle; Hugoni, Mylène; Vellet, Agnès; Debroas, Didier

    2016-01-01

    Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene) in conjunction with quantitative PCR (DNA and RNA) and fluorescent in situ hybridization (FISH) analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin). This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. Forty-two percent of the OTUs (Operational Taxonomic Units) are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae) and Fungi (Dikarya and Chytrids) are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae) are also present and active in this zone, which opens up questions regarding their metabolism. PMID:26904006

  2. Cooperative Medium Access Control Protocol for Mobile Ad-hoc Networks using Spatial Diversity

    Tazeem Ahmad Khan

    2013-10-01

    Full Text Available Enhancement the Performance of MANET (Mobile Ad-hoc Network using spatial diversity. Spatial diversity implemented using cooperative transmission technique in Medium access control (MAC layer level protocol. In noisy environment limit the network performance like coverage area, limit number of node, degrade packet transmission rate, increase packet loss rate etc. In this paper enhance the source to destination transmission range, minimize the packet loss, improve packet transmission rate and appropriate end to end delay. When direct link is fail to transmit packet then Cooperative scheme help to transmit packet. Cooperative scheme is to help the packet transmission with five handshakes instead of four. This scheme implemented in MANET network on MAC layer protocol. Cooperative scheme improve the performance with help of intermediate node between sources to destination. We are performance analysis using discrete simulator NS-2 in MANET. Our performance based on MAC layer level with cooperative scheme in IEEE WLAN standard CSMA/CA protocol.

  3. Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

    Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

    2014-12-01

    Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

  4. Diversity among Cynodon accessions and taxa based on DNA amplification fingerprinting.

    Assefa, S; Taliaferro, C M; Anderson, M P; de los Reyes, B G; Edwards, R M

    1999-06-01

    The genus Cynodon (Gramineae), comprised of 9 species, is geographically widely distributed and genetically diverse. Information on the amounts of molecular genetic variation among and within Cynodon taxa is needed to enhance understanding of phylogenetic relations and facilitate germplasm management and breeding improvement efforts. Genetic relatedness among 62 Cynodon accessions, representing eight species, was assessed using DNA amplification fingerprinting (DAF). Ten 8-mer oligonucleotides were used to amplify specific Cynodon genomic sequences. The DNA amplification products of individual accessions were scored for presence (1) or absence (0) of bands. Similarity matrices were developed and the accessions were grouped by cluster (UPGMA) and principal coordinate analysis. Analyses were conducted within ploidy level (2x = 18 and 4x = 36) and over ploidy levels. Each primer revealed polymorphic loci among accessions within species. Of 539 loci (bands) scored, 496 (92%) were polymorphic. Cynodon arcuatus was clearly separated from other species by numerous monomorphic bands. The strongest species similarities were between C. aethiopicus and C. arcuatus, C. transvaalensis and C. plectostachyus, and C. incompletus and C. nlemfuensis. Intraspecific variation was least for C. aethiopicus, C. arcuatus, and C. transvaalensis, and greatest for C. dactylon. Accessions of like taxonomic classification were generally clustered, except the cosmopolitan C. dactylon var. dactylon and C. dactylon var. afganicus. Within taxa, accessions differing in chromosome number clustered in all instances indicating the 2x and 4x forms to be closely related. Little, if any, relationship was found between relatedness as indicated by the DAF profiles and previous estimates of hybridization potential between the different taxa. PMID:10382294

  5. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

    Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; Handelsman, Jo; Knight, Rob; Fierer, Noah; Gilbert, Jack A.

    2014-01-01

    ABSTRACT Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare ...

  6. Effect of wildfires on the genetic microbial diversity in forest soils from Canary Islands (Spain)

    Rodríguez, J.; A. Turmero; J. A. González-Pérez; F.J. González-Vila; C. Arbelo; Rodríguez-Rodríguez, A.; M.I Pérez-Leblic; M.E. Arias

    2013-01-01

    Wildfires produce several ecological and environmental impacts on the physical and chemical soil characteristics, as well as on the properties and dynamics of soil microbial populations. Microorganisms are good indicators of ecosystem function and sustainability and therefore the studies about the impact of fire on microbial communities is relevant to understand the role of fire in ecosystem functioning. Although several authors have provided data about total microbial biomass and activity in...

  7. Long-Term Effects of Irrigation with Waste Water on Soil AM Fungi Diversity and Microbial Activities: The Implications for Agro-Ecosystem Resilience

    del Mar Alguacil, Maria; Torrecillas, Emma; Torres, Pilar; García-Orenes, Fuensanta; Roldán, Antonio

    2012-01-01

    The effects of irrigation with treated urban wastewater (WW) on the arbuscular mycorrhizal fungi (AMF) diversity and soil microbial activities were assayed on a long-term basis in a semiarid orange-tree orchard. After 43 years, the soil irrigated with fresh water (FW) had higher AMF diversity than soils irrigated with WW. Microbial activities were significantly higher in the soils irrigated with WW than in those irrigated with FW. Therefore, as no negative effects were observed on crop vitali...

  8. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

    Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

  9. Diversity and health status specific fluctuations of intrauterine microbial communities in postpartum dairy cows.

    Wagener, K; Prunner, I; Pothmann, H; Drillich, M; Ehling-Schulz, M

    2015-02-25

    For the interpretation of clinical findings of endometritis and the development of disease prevention and intervention strategies a better understanding of the dynamics and interactions within intrauterine bacterial communities in healthy and diseased cows is required. To gain deeper insights into fluctuations within the uterine microbiota, intrauterine samples were collected from 122 cows at the day of calving, days 3, 9, 15, 21 and 28 postpartum. A total of 2052 bacterial isolates were identified by Fourier-transform-infrared spectroscopy. This culturomics-based approach showed that the aerobic uterine microflora comprised a huge diversity of bacteria belonging to 202 different species, representing 76 genera, with members of the genus Staphylococcus (24.2%) being predominant. On species level the uterine microflora was dominated by Trueperella pyogenes (13.2%), Escherichia coli (11.2%), Staphylococcus xylosus (5.4%), Bacillus pumilus (5.2%) and Streptococcus uberis (4.9%). Comparative analysis of uterine bacteria from cows with different vaginal discharge scores (VDS) revealed health status specific temporal microbial diversifications. Although the intrauterine flora of all VDS groups was dominated by T. pyogenes, E. coli and Staphylococcus spp., the relative number of bacteria differed between VDS groups. The presence of T. pyogenes on days 15 and 21 significantly increased the risk of VDS 2 and 3 at day 21, whereas Staphylococci at day 9 reduced the likelihood of VDS 3 (P<0.05). This study demonstrates that intrauterine bacterial infections are highly dynamic processes and that bacterial species follow specific patterns of progression, which require further research to decipher their potential role in uterine disease development. PMID:25497238

  10. Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data.

    Thiago Bruce

    Full Text Available The health of the coral reefs of the Abrolhos Bank (Southwestern Atlantic was characterized with a holistic approach using measurements of four ecosystem components: (i inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California were compared with two unprotected coastal reefs (Sebastião Gomes and Pedra de Leste and one legally protected but poorly enforced coastal reef (the "paper park" of Timbebas Reef. The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebastião Gomes showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic

  11. Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data.

    Bruce, Thiago; Meirelles, Pedro M; Garcia, Gizele; Paranhos, Rodolfo; Rezende, Carlos E; de Moura, Rodrigo L; Filho, Ronaldo-Francini; Coni, Ericka O C; Vasconcelos, Ana Tereza; Amado Filho, Gilberto; Hatay, Mark; Schmieder, Robert; Edwards, Robert; Dinsdale, Elizabeth; Thompson, Fabiano L

    2012-01-01

    The health of the coral reefs of the Abrolhos Bank (Southwestern Atlantic) was characterized with a holistic approach using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv) microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California) were compared with two unprotected coastal reefs (Sebastião Gomes and Pedra de Leste) and one legally protected but poorly enforced coastal reef (the "paper park" of Timbebas Reef). The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebastião Gomes) showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic microbial pathogens

  12. Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif.

    Teresia Hallström

    Full Text Available Pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. Here we show that different human pathogens including Gram-negative and Gram-positive bacteria, as well as the fungal pathogen Candida albicans, acquire the human terminal complement regulator vitronectin to their surface. By using truncated vitronectin fragments we found that all analyzed microbial pathogens (n = 13 bound human vitronectin via the same C-terminal heparin-binding domain (amino acids 352-374. This specific interaction leaves the terminal complement complex (TCC regulatory region of vitronectin accessible, allowing inhibition of C5b-7 membrane insertion and C9 polymerization. Vitronectin complexed with the various microbes and corresponding proteins was thus functionally active and inhibited complement-mediated C5b-9 deposition. Taken together, diverse microbial pathogens expressing different structurally unrelated vitronectin-binding molecules interact with host vitronectin via the same conserved region to allow versatile control of the host innate immune response.

  13. Conserved Patterns of Microbial Immune Escape: Pathogenic Microbes of Diverse Origin Target the Human Terminal Complement Inhibitor Vitronectin via a Single Common Motif.

    Hallström, Teresia; Singh, Birendra; Kraiczy, Peter; Hammerschmidt, Sven; Skerka, Christine; Zipfel, Peter F; Riesbeck, Kristian

    2016-01-01

    Pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. Here we show that different human pathogens including Gram-negative and Gram-positive bacteria, as well as the fungal pathogen Candida albicans, acquire the human terminal complement regulator vitronectin to their surface. By using truncated vitronectin fragments we found that all analyzed microbial pathogens (n = 13) bound human vitronectin via the same C-terminal heparin-binding domain (amino acids 352-374). This specific interaction leaves the terminal complement complex (TCC) regulatory region of vitronectin accessible, allowing inhibition of C5b-7 membrane insertion and C9 polymerization. Vitronectin complexed with the various microbes and corresponding proteins was thus functionally active and inhibited complement-mediated C5b-9 deposition. Taken together, diverse microbial pathogens expressing different structurally unrelated vitronectin-binding molecules interact with host vitronectin via the same conserved region to allow versatile control of the host innate immune response. PMID:26808444

  14. Diversity, Abundance, and Potential Activity of Nitrifying and Nitrate-Reducing Microbial Assemblages in a Subglacial Ecosystem

    Skidmore, M. L.; Boyd, E. S.; Lange, R. K.; Mitchell, A. C.; Havig, J. R.; Hamilton, T. L.; Lafreniere, M. J.; Shock, E.; Peters, J.

    2011-12-01

    Ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of the planet during Earth's history. Significant microbial populations have been documented in all subglacial settings sampled to date. Recent research has demonstrated sizable volumes of subglacial sediment beneath the Antarctic Ice Sheet that are greater than 1km thick in places and where sampled active microbial populations have been documented. Collectively this suggests subglacial microbial populations may impact global biogeochemical cycles on glacial-interglacial timescales, however, nitrogen cycling in subglacial systems is poorly understood. Subglacial sediments sampled from beneath Robertson Glacier, Alberta, Canada harbor a diverse assemblage of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Archaeal amoA genes were less abundant and less diverse than bacterial amoA. Nitrification and nitrate reduction were measured in microcosms incubated at 4 degrees Celsius indicating the potential for these processes to occur in situ. Subglacial sediment porewaters and bulk meltwaters have low concentrations of dissolved inorganic and organic nitrogen compounds and a high C/N ratio of dissolved organic matter in sediment porewaters, indicating that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence for N limitation and detection of nifH, biological nitrogen fixation was not detected in subglacial sediment microcosm experiments at 4 degrees Celsius. Collectively, our results suggest a role for nitrification and nitrate reduction in sustaining microbial communities in subglacial environments.

  15. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Wuttichai Mhuantong

    Full Text Available The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

  16. Anaerobic carbon monoxide dehydrogenase diversity in the homoacetogenic hindgut microbial communities of lower termites and the wood roach.

    Eric G Matson

    Full Text Available Anaerobic carbon monoxide dehydrogenase (CODH is a key enzyme in the Wood-Ljungdahl (acetyl-CoA pathway for acetogenesis performed by homoacetogenic bacteria. Acetate generated by gut bacteria via the acetyl-CoA pathway provides considerable nutrition to wood-feeding dictyopteran insects making CODH important to the obligate mutualism occurring between termites and their hindgut microbiota. To investigate CODH diversity in insect gut communities, we developed the first degenerate primers designed to amplify cooS genes, which encode the catalytic (β subunit of anaerobic CODH enzyme complexes. These primers target over 68 million combinations of potential forward and reverse cooS primer-binding sequences. We used the primers to identify cooS genes in bacterial isolates from the hindgut of a phylogenetically lower termite and to sample cooS diversity present in a variety of insect hindgut microbial communities including those of three phylogenetically-lower termites, Zootermopsis nevadensis, Reticulitermes hesperus, and Incisitermes minor, a wood-feeding cockroach, Cryptocercus punctulatus, and an omnivorous cockroach, Periplaneta americana. In total, we sequenced and analyzed 151 different cooS genes. These genes encode proteins that group within one of three highly divergent CODH phylogenetic clades. Each insect gut community contained CODH variants from all three of these clades. The patterns of CODH diversity in these communities likely reflect differences in enzyme or physiological function, and suggest that a diversity of microbial species participate in homoacetogenesis in these communities.

  17. Chemical and genetic diversity of Zataria multiflora Boiss. accessions growing wild in Iran.

    Hadian, Javad; Ebrahimi, Samad Nejad; Mirjalili, Mohammad Hossein; Azizi, Ali; Ranjbar, Hamid; Friedt, Wolfgang

    2011-01-01

    Zataria multiflora Boiss. is an aromatic shrub belonging to the Lamiaceae family. Its aerial parts are used in the traditional medicine and in the pharmaceutical and food industries. The terpenoid and genetic profiles of 18 accessions of Z. multiflora, collected in different locations in Iran, have been analyzed by GC/FID and GC/MS or by AFLP (amplified fragment length polymorphism) analyses, respectively. Altogether, 56 compounds were identified in the essential oils, with the major constituents being thymol (6.0-54.9%), carvacrol (0.7-50.6%), linalool (1.2-46.8%), and p-cymene (1.6-14.8%). On the basis of the essential-oil composition, the 18 accessions were divided into four groups. The first group was characterized by a high content of carvacrol, thymol, and linalool, the second group was dominated by carvacrol, thymol, and p-cymene, the third group was characterized by a high concentration of thymol and a low content of carvacrol and p-cymene, and the forth group contained linalool and carvacrol as the main components. The AFLP results revealed that the average genetic similarity (GS) between the accessions was 0.61, ranging from 0.40 to 0.77. The UPGMA (unweighted pair-group method with arithmetic mean) cluster analysis divided all accessions into five groups at a similarity level of 0.60. The two clusters generated, the first based on the essential-oil compositions and the second on the AFLP data, showed a different pattern of relationships among the accessions. The knowledge of the Z. multiflora chemotype diversity, illustrated in this study, will allow an improvement of the homogeneity of the plant material for the production of different types of essential oils, depending on the demands of the pharmaceutical and food industries for specific uses. PMID:21259428

  18. Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field

    Naveed, Muhammad; Herath, Lasantha; Møldrup, Per;

    2016-01-01

    Silstrup Denmark, extends over 1.69 ha, and slopes 1–2° to the north. Soil samples for 454-pyrosequencing were extracted by pushing 50-mL sterilized plastic vials into the soil. Bulk soil samples were used for the measurement of pH, organic carbon, and soil texture. Intact 100 cm3 soil cores, collected in...... organic carbon nor clay content was significantly correlated with fungal richness and diversity indices. For soil structural parameters, soil water retention in the pF range 5–6.8 (parameter B) was significantly correlated with both bacterial and fungal Shannon diversities. Amount of macropores (> 30 μm......) and total porosity (ϕ) were only significantly correlated with fungal Shannon diversity. These results suggest that variation in microbial communities is not random but strongly related with variations in organic carbon, clay content, and soil water characteristics at the field scale....

  19. The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

    Sunderam, Vaidy S.

    2012-03-20

    The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept of a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.

  20. Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils.

    Jin-Hyeob Kwak

    Full Text Available Forest floor mineral soil mix (FMM and peat mineral soil mix (PMM are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM × 2 (near CWD vs away from CWD factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05 in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05 near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01 according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05 but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates in both cover soils (p<0.05 in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05 regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining.

  1. Impact of transgenic wheat with wheat yellow mosaic virus resistance on microbial community diversity and enzyme activity in rhizosphere soil.

    Jirong Wu

    Full Text Available The transgenic wheat line N12-1 containing the WYMV-Nib8 gene was obtained previously through particle bombardment, and it can effectively control the wheat yellow mosaic virus (WYMV disease transmitted by Polymyxa graminis at turngreen stage. Due to insertion of an exogenous gene, the transcriptome of wheat may be altered and affect root exudates. Thus, it is important to investigate the potential environmental risk of transgenic wheat before commercial release because of potential undesirable ecological side effects. Our 2-year study at two different experimental locations was performed to analyze the impact of transgenic wheat N12-1 on bacterial and fungal community diversity in rhizosphere soil using polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE at four growth stages (seeding stage, turngreen stage, grain-filling stage, and maturing stage. We also explored the activities of urease, sucrase and dehydrogenase in rhizosphere soil. The results showed that there was little difference in bacterial and fungal community diversity in rhizosphere soil between N12-1 and its recipient Y158 by comparing Shannon's, Simpson's diversity index and evenness (except at one or two growth stages. Regarding enzyme activity, only one significant difference was found during the maturing stage at Xinxiang in 2011 for dehydrogenase. Significant growth stage variation was observed during 2 years at two experimental locations for both soil microbial community diversity and enzyme activity. Analysis of bands from the gel for fungal community diversity showed that the majority of fungi were uncultured. The results of this study suggested that virus-resistant transgenic wheat had no adverse impact on microbial community diversity and enzyme activity in rhizosphere soil during 2 continuous years at two different experimental locations. This study provides a theoretical basis for environmental impact monitoring of transgenic wheat when the

  2. PHYLOPLANE ASSESSMENT OF LEAF AND STALK FOR CONSUMPTION AND MICROBIAL DIVERSITY OF SWEET POTATO (IPOMOEA BATATAS (L LAM., CONVOLVULACEAE

    C.M. Ahana

    2013-06-01

    Full Text Available The nutrient and microbial contents of the leaves and stalks of two varieties of sweet potato (Ipomoea batatas (L. Lam., Convolvulaceae were determined using standard analytical methods in order to ascertain its quality as a food material. The samples were found to contain a diverse array of carbohydrates, proteins, dietary fats, crude fiber and ash containing mineral deposits with potential nutritional benefits. However, the quick perishability of the food material is a major constraint to its wider utilization for consumption and this was attributed to the microbial load in it. The leaves and stalks contained strains of bacteria and fungi whose analyses were determined using pour plate method. The purple variety samples had lesser numbers of microbial loads in it while the white variety samples had more microbial load in it on the pour plate method. The pour plate method is a microbiological procedure used for isolating and growing individual colonies of micro organisms in pure culture. Pure cultures of the isolated organisms were identified through their colony appearance and microscopic observation of the stained samples. Some biochemical tests were conducted for the characterization of bacteria isolates. The shelf life of sweet potato leaves and stalks can be ascertained knowing the particular microorganisms present. It is important that consumers of this food material always harvest cultivars that have no sign of deterioration and food safety precautions should be adhered to in order to avoid consuming the toxic anti-nutrients.

  3. Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens.

    van Elsas, Jan Dirk; Garbeva, Paolina; Salles, Joana

    2002-01-01

    The diversity of soil microbial communities can be key to the capacity of soils to suppress soil-borne plant diseases. As agricultural practice, as well as directed agronomical measures, are known to be able to affect soil microbial diversity, it is plausible that the soil microflora can be geared towards a greater suppressivity of soil-borne diseases as a result of the selection of suitable soil management regimes. In the context of a programme aimed at investigating the microbial diversity of soils under different agricultural regimes, including permanent grassland versus arable land under agricultural rotation, we assessed how soil microbial diversity is affected in relation to the suppression of the soil-borne potato pathogen Rhizoctonia solani AG3. The diversity in the microbial communities over about a growing season was described by using cultivation-based--plating on different media--and cultivation-independent--soil DNA-based PCR followed by denaturing gradient gel electrophoresis (DGGE) community fingerprinting--methods. The results showed great diversity in the soil microbiota at both the culturable and cultivation-independent detection levels. Using cultivation methods, various differences between treatments with respect to sizes of bacterial and fungal populations were detected, with highest population sizes generally found in rhizospheres. In addition, the evenness of eco-physiologically differing bacterial types was higher in grassland than in arable land under rotation. At the cultivation-independent level, clear differences in the diversities of several microbial groups between permanent grassland and arable land under rotation were apparent. Bio-assays that assessed the growth of R. solani AG3 hyphae through soil indicated a greater growth suppression in grassland than in arable land soils. Similarly, an experiment performed in the glasshouse showed clear differences in both microbial diversities and suppressiveness of R. solani growth in soil

  4. Molecular analyses of microbial abundance and diversity in the water column of anchialine caves in Mallorca, Spain

    Damian Menning

    2014-05-01

    Full Text Available Water column samples from the island of Mallorca, Spain were collected from one site in Cova des Pas de Vallgornera (Vallgornera and three sites (Llac Martel, Llac Negre, and Llac de les Delícies in Coves del Drac (Drac. Vallgornera is located on the southern coast of Mallorca approximately 57 km southwest of Coves del Drac. Drac is Europe's most visited tourist cave, whereas Vallgornera is closed to the public. Water samples were analyzed for water chemistry using spectrophotometric methods, by quantitative PCR for estimated total abundance of microbial communities, and by length heterogeneity PCR for species richness and relative species abundance of Archaea, Bacteria, and microbial eukaryotes. Estimated total abundance was multiplied by relative species abundance to determine the absolute species abundance. All sites were compared to determine spatial distributions of the microbial communities and to determine water column physical and chemical gradients. Water quality and community structure data indicate that both Drac Delícies and Drac Negre have distinct biogeochemical gradients. These sites have communities that are similar to Vallgornera but distinct from Drac Martel, only a few hundred meters away. Drac Martel is accessible to the general public and had the most dissimilar microbial community of all the sites. Similarities among communities at sites in Drac and Vallgornera suggest that these two spatially separated systems are operating under similar ecological constraints.

  5. Changes in Transformation of Soil Organic C and Functional Diversity of Soil Microbial Community Under Different Land Uses

    LI Zhong-pei; WU Xiao-chen; CHEN Bi-yun

    2007-01-01

    Changes in soil biological and biochemical properties under different land uses in the subtropical region of China were investigated in order to develop rational cultivation and fertilization management. A small watershed of subtropical region of China was selected for this study. Land uses covered paddy fields, vegetable farming, fruit trees, upland crops, bamboo stands, and forestry. Soil biological and biochemical properties included soil organic C and nutrient contents, mineralization of soil organic C, and soil microbial biomass and community functional diversity. Soil organic C and total N contents, microbial biomass C and N, and respiration intensity under different land uses were changed in the following order: paddy fields (and vegetable farming) > bamboo stands > fruit trees (and upland). The top surface (0-15 cra) paddy fields (and vegetable farming) were 76.4 and 80.8% higher in soil organic C and total N contents than fruit trees (and upland) soils, respectively. Subsurface paddy soils (15-30 cm) were 59.8 and 67.3% higher in organic C and total N than upland soils, respectively. Soil microbial C, N and respiration intensity in paddy soils (0-15 cm) were 6.36, 3.63 and 3.20 times those in fruit tree (and upland) soils respectively. Soil microbial metabolic quotient was in the order: fruit trees (and upland) > forestry > paddy fields. Metabolic quotient in paddy soils was only 47.7% of that in fruit tree (and upland) soils.Rates of soil organic C mineralization during incubation changed in the order: paddy fields > bamboo stands > fruit trees (and upland) and soil bacteria population: paddy fields > fruit trees (and upland) > forestry. No significant difference was found for fungi and actinomycetes populations. BIOLOG analysis indicated a changing order of paddy fields > fruit trees (and upland) > forestry in values of the average well cell development (AWCD) and functional diversity indexes of microbial community. Results also

  6. Microbial Diversity in a Venezuelan Orthoquartzite Cave is Dominated by the Chloroflexi (Class Ktedonobacterales and Thaumarchaeota Group I.1c.

    Hazel A Barton

    2014-11-01

    Full Text Available The majority of caves are formed within limestone rock and hence our understanding of cave microbiology comes from carbonate-buffered systems. In this paper, we describe the microbial diversity of Roraima Sur Cave, an orthoquartzite (SiO4 cave within Roraima Tepui, Venezuela. The cave contains a high level of microbial activity when compared with other cave systems, as determined by an ATP-based luminescence assay and cell counting. Molecular phylogenetic analysis of microbial diversity within the cave demonstrate the dominance of Actinomycetales and Alphaproteobacteria in endolithic bacterial communities close to the entrance, while communities from deeper in the cave are dominated (82-84% by a unique clade of Ktedonobacterales within the Chloroflexi. While members of this phylum are commonly found in caves, this is the first identification of members of the Class Ktedonobacterales. An assessment of archaeal species demonstrates the dominance of phylotypes from the Thaumarchaeota Group I.1c (100%, which have previously been associated with acidic environments. While the Thaumarchaeota have been seen in numerous cave systems, the dominance of Group I.1c in Roraima Sur Cave is unique and a departure from the traditional archaeal community structure. Geochemical analysis of the cave environment suggests that water entering the cave, rather than the nutrient-limited orthoquartzite rock, provides the carbon and energy necessary for microbial community growth and subsistence, while the poor buffering capacity of quartzite or the low pH of the environment may be selecting for this unusual community structure. Together these data suggest that pH, imparted by the geochemistry of the host rock, can play as important a role in niche-differentiation in caves as in other environmental systems.

  7. Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c.

    Barton, Hazel A; Giarrizzo, Juan G; Suarez, Paula; Robertson, Charles E; Broering, Mark J; Banks, Eric D; Vaishampayan, Parag A; Venkateswaran, Kasthisuri

    2014-01-01

    The majority of caves are formed within limestone rock and hence our understanding of cave microbiology comes from carbonate-buffered systems. In this paper, we describe the microbial diversity of Roraima Sur Cave (RSC), an orthoquartzite (SiO4) cave within Roraima Tepui, Venezuela. The cave contains a high level of microbial activity when compared with other cave systems, as determined by an ATP-based luminescence assay and cell counting. Molecular phylogenetic analysis of microbial diversity within the cave demonstrates the dominance of Actinomycetales and Alphaproteobacteria in endolithic bacterial communities close to the entrance, while communities from deeper in the cave are dominated (82-84%) by a unique clade of Ktedonobacterales within the Chloroflexi. While members of this phylum are commonly found in caves, this is the first identification of members of the Class Ktedonobacterales. An assessment of archaeal species demonstrates the dominance of phylotypes from the Thaumarchaeota Group I.1c (100%), which have previously been associated with acidic environments. While the Thaumarchaeota have been seen in numerous cave systems, the dominance of Group I.1c in RSC is unique and a departure from the traditional archaeal community structure. Geochemical analysis of the cave environment suggests that water entering the cave, rather than the nutrient-limited orthoquartzite rock, provides the carbon and energy necessary for microbial community growth and subsistence, while the poor buffering capacity of quartzite or the low pH of the environment may be selecting for this unusual community structure. Together these data suggest that pH, imparted by the geochemistry of the host rock, can play as important a role in niche-differentiation in caves as in other environmental systems. PMID:25505450

  8. Life in Oligotropic Desert Environments: Contrasting Taxonomic and Functional Diversity of Two Microbial Mats with Metagenomics

    Bonilla-Rosso, G.; Peimbert, M.; Olmedo, G.; Alcaraz, L. D.; Eguiarte, L. E.; Souza, V.

    2010-04-01

    The metagenomic analysis of two microbial mats from the oligotrophic waters in the Cuatrociéngas basin reveals large differences both at taxonomic and functional level. These are explained in terms of environmental stability and nutrient availability.

  9. Microbial diversity and community structure in an antimony-rich tailings dump.

    Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

    2016-09-01

    To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities. PMID:27188777

  10. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation

    Komivi Dossa

    2016-04-01

    Full Text Available Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs, Eastern Asia (EAs, and Western Africa (WAf were highly diversified, while those from Western Asia (WAs, Northern Africa (NAf, and Southeastern Africa (SAf had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

  11. Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir

    Gao, Peike; Tian, Huimei; Li, Guoqiang; Sun, Hongwen; Ma, Ting

    2015-01-01

    Microbial populations associated with microbial enhanced oil recovery (MEOR) and their abundance in the Xinjiang Luliang water-flooding petroleum reservoir were investigated using 16S rRNA, nitrate reductases, dissimilatory sulfate reductase, and methyl coenzyme-M reductase-encoded genes to provide ecological information for the potential application of MEOR. 16S rRNA gene miseq sequencing revealed that this reservoir harbored large amounts of taxa, including 155 bacterial and 7 archeal gener...

  12. Up Against The Wall: The Effects of Climate Warming on Soil Microbial Diversity and The Potential for Feedbacks to The Carbon Cycle

    Kristen M. DeAngelis

    2013-06-01

    Full Text Available Earth’s climate is warming, and there is evidence that increased temperature alters soil C cycling, which may result in a self-reinforcing (positive, microbial mediated feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an understanding of how temperature affects SOM decomposition. Numerous studies have explored, to differing degrees, the extent to which climate change may affect biodiversity. While there is ample evidence that community diversity begets ecosystem stability and resilience, we know of keystone species that perform functions whose effects far outweigh their relative abundance. In this paper, we first review the meaning of microbial diversity and how it relates to ecosystem function, then conduct a literature review of field-based climate warming studies that have made some measure of microbial diversity. Finally, we explore how measures of diversity may yield a larger, more complete picture of climate warming effects on microbial communities, and how this may translate to altered carbon cycling and greenhouse gas emissions. While warming effects seem to be ecosystem-specific, the lack of observable consistency between measures is due in some part to the diversity in measures of microbial diversity.

  13. Spatial and temporal diversity of microbial mats in the shallow-water hydrothermal system of Milos Island (Greece)

    Giovannelli, D.; Foustoukos, D.; Le Bris, N.; Sievert, S. M.; Yucel, M.; Vetriani, C.

    2014-12-01

    Shallow-water hydrothermal vents are ubiquitous but poorly studied geothermal environments. The shallow-water hydrothermal system of Milos Island is a unique study site with vents exhibiting steep geothermal gradients in the presence of light that allows the co-occurrence of photosynthesis and chemosynthesis. The active hydrothermal emissions of the Milos hydrothermal system support complex microbial mats, which are fundamental in engineering the environmental niche in which extremophiles thrive. Because of the shallow depth, the mat community is wiped out during every major storm, when swell and wave action increase, and then it reconstitutes itself over a brief period of time (days). While most studies are focused on the diversity of the community residing in the underlying sediments, little information is available on the diversity and functioning of the mat community, and how it responds to abrupt geodynamic events. Here we report the results of a joint geochemical and microbiological survey of the microbial mats of Milos island, and analyze the spatial and temporal evolution of the mat community following a major storm. Our results show that the community is dominated by Epsilonproteobacteria, although significant variability is present within the systemm. The observed variability correlates with spatial profiles and in situ measurement of temperature and sulfide carried out over a 6 days periods, showing that tides, winds, and abrupt geodynamic events generate intermittent mixing conditions lasting for several hours to days. Diversity and metagenomic analyses of the mature mat provide further information on the metabolic potential of the community and on the influence of environmental factors on ecosystem functioning. Our work lays the basis for studies aimed at resolving the spatial and temporal dynamics of chemoautotrophic microbial communities in shallow-water hydrothermal systems.

  14. Winter road access to projected works in the diversion of the Little Whale River

    The Great Whale hydroelectric complex in northern Quebec will require diversion of the Little Whale River, involving construction of dams 40 m and 30 m high and a canal 600 m long. The main mode of access to the construction sites will be a winter road, supplemented by an airfield designed for large-capacity aircraft. The method used by Hydro-Quebec in its environmental assessment of the winter road project is described. This method comprises five steps: delimitation of the study zone; establishment of a road corridor of choice by successively eliminating territory according to given constraints; description of the physical and biological environment; determination and optimization of the road route; and evaluation of potential impacts, along with establishment of measures to mitigate those impacts. The optimal routing is determined on the basis of criteria such as the presence of permafrost, the nature of the soils, avoidance of slopes steeper than 10%, and the depth and width of ice crossings

  15. [Prokaryotic microbial diversity of the ancient salt deposits in the Kunming Salt Mine, P.R. China].

    Xiao, Wei; Peng, Qian; Liu, Hong-wei; Wen, Meng-liang; Cui, Xiao-long; Yang, Ya-ling; Duan, Dong-cheng; Chen, Wei; Deng, Lan; Li, Qin-yuan; Chen, Yi-guang; Wang, Zhi-gang; Ren, Zhen; Liu, Ji-hui

    2007-04-01

    The prokaryotic microbial diversity of the ancient salt deposits in the Kunming Salt Mine, PR China was investigated using PCR-DGGE and rRNA approaches. Total community DNA was extracted and purified by a direct method, which yielded amplified DNA of high molecular weight for samples. A variable region of 16S rRNA gene was then amplified by PCR with bacterial and archaeal primers and analyzed by denaturing gradient gel electrophoresis (DGGE). Twenty-seven major bands were detected in the bacterial DGGE profile of the sample, but only one band of pure culture strains of bacteria isolated from the Kunming Salt Mine matched with one band of sample. No band of pure culture strains of archaea isolated from the Kunming Salt Mine matched with 18 major bands of sample. The results indicated that most of microbes in this environment are likely uncultivable. Clones on the plate were not the predominant species in the community. Two 16S rRNA gene clone libraries (bacteria and archaea) were also constructed, and 36 and 20 clones were selected for amplified ribosomal DNA restriction analysis (ARDRA). ARDRA with enzymes Afa I, Hha I, Hae III revealed 10 bacterial operational taxonomic units (OTUs), with three most abundant OTUs accounting for 38.9%, 25.0%, 16.7% of all the bacterial 16S rDNA clones, respectively. The remaining 7 OTUs presented at low levels, were represented by a single clone. Eight archaeal OTUs were obtained but no predominant OTUs. Some clones were sequenced and each sequence was compared with all nucleotide sequences in GenBank database. Examination of 16S rDNA clones showed that the ancient salt deposits in the Kunming Salt Mine contained a phylogenetically diverse population of organisms from the Bacteria domain with members of three major lineages represented: alpha-proteobacteria, gamma-Proteobacteria and Actinobacteria, especially Pseudomonas. Surprisingly, we recovered a variety of sequence closely related to Actinobacteria which was not found in other

  16. Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India

    Dhasarathan, P.; Theriappan, P.; Ashokraja, C.

    2009-01-01

    Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 104 CFU/g and 5.6 × 104 CFU/ml respectively), compared to the THB of cultivable ar...

  17. Priming effect and microbial diversity in ecosystem functioning and response to global change: a modeling approach using the Symphony model

    Perveen, Nazia; Barot, Sébastien; ALVAREZ, Gaël; Klumpp, Katja; Martin, Raphaël; Herfurth, Damien; Louault, Frédérique; Fontaine, Sébastien

    2014-01-01

    Integration of the priming effect (PE) in ecosystem models is crucial to better predict the consequences of global change on ecosystem carbon (C) dynamics and its feedbacks on climate. Over the last decade, many attempts have been made to model PE in soil. However, PE has not yet been incorporated into any ecosystem models. Here we build plant-soil models to explore how PE and microbial diversity influence soil-plant interactions and ecosystem C and nitrogen (N) dynamics in response to global...

  18. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers

    Xu, Chaoqun; Gao, Jiao; Du, Zengfeng; Li, Dengke; Wang, Zhe; Li, Yingyue; Pang, Xiaoming

    2016-01-01

    Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources. PMID:27531220

  19. Polarization diversity scheme on spectral polarization coding optical code-division multiple-access network

    Yen, Chih-Ta; Huang, Jen-Fa; Chang, Yao-Tang; Chen, Bo-Hau

    2010-12-01

    We present an experiment demonstrating the spectral-polarization coding optical code-division multiple-access system introduced with a nonideal state of polarization (SOP) matching conditions. In the proposed system, the encoding and double balanced-detection processes are implemented using a polarization-diversity scheme. Because of the quasiorthogonality of Hadamard codes combining with array waveguide grating routers and a polarization beam splitter, the proposed codec pair can encode-decode multiple code words of Hadamard code while retaining the ability for multiple-access interference cancellation. The experimental results demonstrate that when the system is maintained with an orthogonal SOP for each user, an effective reduction in the phase-induced intensity noise is obtained. The analytical SNR values are found to overstate the experimental results by around 2 dB when the received effective power is large. This is mainly limited by insertion losses of components and a nonflattened optical light source. Furthermore, the matching conditions can be improved by decreasing nonideal influences.

  20. A Frequency—Diversity Spread—Spectrum Multiple Access System with Random Signature Sequences

    CaoYewen; XiangHaige

    1995-01-01

    A new scheme for the spread-spectrum multiple access system named Frequency-Diver-sity Spread-Spectrum Multiple Access(FD-DDMA)system,is proposed.In this FD-SSMA sys-tem,the same information will be modulated on a group of mutually orthogonal frequency compo-nents(carriers)with a random signature sequence at the same time,and it will be demodulated by a coherent receiver for every component and then incorporated (ad if using frequency diversity)on the basis of this random sequence.The spectrum of the modulated signal is very close to that of a white-noise in a wider frequency band due to orthogonality for all frequency components and prop-erty of the random sequence,the system becomes a spread-spectrum one.The (Inverse)Fast Froier Transform(IFFT,FFT)can be applied in the system ,which provides additional flexibility.The performance in an asynchronous mode,such as ability of multiusers,anti-interferences ,is an-alyzed.

  1. Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-Locked Lakes of Schirmacher Oasis and the Perennially Ice-Covered Lake Untersee in East Antarctica

    Huang, Jonathan; Hoover, Richard B.; Swain, Ashit; Murdock, Chris; Bej, Asim K.

    2010-01-01

    Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

  2. Phylogenetic Diversity of Nitrogen Fixation Genes in the Symbiotic Microbial Community in the Gut of Diverse Termites

    Ohkuma, Moriya; Noda, Satoko; Kudo, Toshiaki

    1999-01-01

    Nitrogen fixation by the microorganisms in the gut of termites is one of the crucial aspects of symbiosis, since termites usually thrive on a nitrogen-poor diet. The phylogenetic diversity of the nitrogen-fixing organisms within the symbiotic community in the guts of various termite species was investigated without culturing the resident microorganisms. A portion of the dinitrogenase reductase gene (nifH) was directly amplified from DNA extracted from the mixed population in the termite gut. ...

  3. Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core

    Vanya Miteva

    2015-02-01

    Full Text Available The 2537-m-deep North Greenland Eemian Ice Drilling (NEEM core provided a first-time opportunity to perform extensive microbiological analyses on selected, recently drilled ice core samples representing different depths, ages, ice structures, deposition climates and ionic compositions. Here, we applied cultivation, small subunit (SSU rRNA gene clone library construction and Illumina next-generation sequencing (NGS targeting the V4–V5 region, to examine the microbial abundance, viability and diversity in five decontaminated NEEM samples from selected depths (101.2, 633.05, 643.5, 1729.75 and 2051.5 m deposited 300–80 000 years ago. These comparisons of the indigenous glacial microbial populations in the ice samples detected significant spatial and temporal variations. Major findings include: (a different phylogenetic diversity of isolates, dominated by Actinobacteria and fungi, compared to the culture-independent diversity, in which Proteobacteria and Firmicutes were more frequent; (b cultivation of a novel alphaproteobacterium; (c dominance of Cyanobacteria among the SSU rRNA gene clones from the 1729.75-m ice; (d identification of Archaea by NGS that are rarely detected in glacial ice; (e detection of one or two dominant but different genera among the NGS sequences from each sample; (f finding dominance of Planococcaceae over Bacillaceae among Firmicutes in the brittle and the 2051.5-m ice. The overall beta diversity between the studied ice core samples examined at the phylum/class level for each approach showed that the population structure of the brittle ice was significantly different from the two deep clathrated ice samples and the shallow ice core.

  4. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.

    Uroz, S; Oger, P; Tisserand, E; Cébron, A; Turpault, M-P; Buée, M; De Boer, W; Leveau, J H J; Frey-Klett, P

    2016-01-01

    The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity. PMID:27302652

  5. Developing Planetary Protection Technology: Microbial Diversity of the Mars Orbiter "Odyssey" and the Spacecraft Assembly and Encapsulation Facility II

    La Duc, M. T.; Chen, F.; Baker, A.; Koukol, R. C.; Kern, R. G.; Venkateswaran, K. J.

    2001-12-01

    Sampling the surfaces of both spacecraft and their clean-room assembly facilities is crucial in monitoring the microbial burden associated with these pseudo-sterile, oligotrophic environments. Here, we present the results of a study in which several surface samples, retrieved from both the Mars Odyssey Spacecraft and the Kennedy Space Center (KSC) Spacecraft Assembly and Encapsulation Facility II (SAEF-II), were processed and evaluated by both molecular and traditional culture-based methods for microbial diversity. The findings of this study improve our current understanding of the microbial community structure, diversity, and dispersal in a spacecraft assembly facility, as well as physically associated with co-located spacecraft. Surfaces of 25 cm2 (spacecraft) or 0.4 m2 (SAEF-II) were swabbed or wiped, respectively, and were examined for total heterotrophic aerobes and spore-formers. Samples were further subjected to nucleic acid extraction, and 16S rDNA fragments were PCR amplified with eubacterial biased universal primers and cloned. Approximately 30 isolates grown by traditional culture-based techniques were included for 16S rDNA sequencing. For the most part, the population dynamics remained consistent when compared between the spacecraft and assembly facility libraries. Predominant microbes, as indicated by molecular methods, included members of the genera Variovorax and Aquaspirillum. Members of the Mesorhizobium, Bradyrhizobium, Enterococcus, Ralstonia, and Bacillus genera were also found to span the various libraries but in less abundance. Traditional culture-based techniques validated the presence of Bacillus and Ralstonia, while illuminating a larger diversity in revealing the presence of Staphylococcus, Comamonas, Microbacterium, and Actinomycetales. The bulk of these findings make sense, since species of Ralstonia, Rhizobium, Variovorax, and Bacillus are known to frequently inhabit rhizospheric environments, like that surrounding the KSC facility, and

  6. Analysis of microbial diversity on deli slicers using polymerase chain reaction and denaturing gradient gel electrophoresis technologies.

    Koo, O K; Mertz, A W; Akins, E L; Sirsat, S A; Neal, J A; Morawicki, R; Crandall, P G; Ricke, S C

    2013-02-01

    Cross-contamination of pathogenic and spoilage bacteria from food-contact surfaces to food products is a serious public health issue. Bacteria may survive and attach to food-contact surfaces by residual food components and/or background bacteria which may subsequently transfer to other food products. Deli slicers, generally used for slicing ready-to-eat products, can serve as potential sources for considerable bacterial transfer. The objective of this study was to assess the extent and distribution of microbial diversity of deli slicers by identification of pathogenic and background bacteria. Slicer-swab samples were collected from restaurants in Arkansas and Texas in the United States. Ten surface areas for each slicer were swabbed using sterile sponges. Denaturing gradient gel electrophoresis (DGGE) was applied to investigate the fingerprint of samples, and each band was further identified by sequence analysis. Pseudomonads were identified as the dominant bacteria followed by Enterobacteriaceae family, and lactic acid bacteria such as Lactococcus lactis and Streptococcus thermophilus were also found. Bacterial distribution was similar for all surface areas, while the blade guard exhibited the greatest diversity. This study provides a profile of the microbial ecology of slicers using DGGE to develop more specific sanitation practices and to reduce cross-contamination during slicing. PMID:23121623

  7. Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis.

    Barott, Katie L; Rodriguez-Brito, Beltran; Janouškovec, Jan; Marhaver, Kristen L; Smith, Jennifer E; Keeling, Patrick; Rohwer, Forest L

    2011-05-01

    The coral reef benthos is primarily colonized by corals and algae, which are often in direct competition with one another for space. Numerous studies have shown that coral-associated Bacteria are different from the surrounding seawater and are at least partially species specific (i.e. the same bacterial species on the same coral species). Here we extend these microbial studies to four of the major ecological functional groups of algae found on coral reefs: upright and encrusting calcifying algae, fleshy algae, and turf algae, and compare the results to the communities found on the reef-building coral Montastraea annularis. It was found using 16S rDNA tag pyrosequencing that the different algal genera harbour characteristic bacterial communities, and these communities were generally more diverse than those found on corals. While the majority of coral-associated Bacteria were related to known heterotrophs, primarily consuming carbon-rich coral mucus, algal-associated communities harboured a high percentage of autotrophs. The majority of algal-associated autotrophic Bacteria were Cyanobacteria and may be important for nitrogen cycling on the algae. There was also a rich diversity of photosynthetic eukaryotes associated with the algae, including protists, diatoms, and other groups of microalgae. Together, these observations support the hypothesis that coral reefs are a vast landscape of distinctive microbial communities and extend the holobiont concept to benthic algae. PMID:21272183

  8. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-04-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

  9. Microbial respiration with chlorine oxyanions: diversity and physiological and biochemical properties of chlorate- and perchlorate-reducing microorganisms.

    Liebensteiner, Martin G; Oosterkamp, Margreet J; Stams, Alfons J M

    2016-02-01

    Chlorine oxyanions are valuable electron acceptors for microorganisms. Recent findings have shed light on the natural formation of chlorine oxyanions in the environment. These suggest a permanent introduction of respective compounds on Earth, long before their anthropogenic manufacture. Microorganisms that are able to grow by the reduction of chlorate and perchlorate are affiliated with phylogenetically diverse lineages, spanning from the Proteobacteria to the Firmicutes and archaeal microorganisms. Microbial reduction of chlorine oxyanions can be found in diverse environments and different environmental conditions (temperature, salinities, pH). It commonly involves the enzymes perchlorate reductase (Pcr) or chlorate reductase (Clr) and chlorite dismutase (Cld). Horizontal gene transfer seems to play an important role for the acquisition of functional genes. Novel and efficient Clds were isolated from microorganisms incapable of growing on chlorine oxyanions. Archaea seem to use a periplasmic Nar-type reductase (pNar) for perchlorate reduction and lack a functional Cld. Chlorite is possibly eliminated by alternative (abiotic) reactions. This was already demonstrated for Archaeoglobus fulgidus, which uses reduced sulfur compounds to detoxify chlorite. A broad biochemical diversity of the trait, its environmental dispersal, and the occurrence of relevant enzymes in diverse lineages may indicate early adaptations of life toward chlorine oxyanions on Earth. PMID:26104311

  10. Biofilm removal technique using sands as a research tool for accessing microbial attachment on surface

    Nathanon Trachoo

    2004-01-01

    Biofilms have profound impacts on improved survival of the constituent microorganisms in nature. Biofilms were believed to protect constituent microorganisms from sanitizer treatment, provide a more suitable habitat for microorganisms, and become a site for genetic material exchanges between microorganisms. As we realize more about the significance of biofilm, methods used for biofilm study should be consistently developed and evaluated. To determine microbial attachment on surfaces, usually ...

  11. Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

    Coman, Cristian; Chiriac, Cecilia M.; Robeson, Michael S.; Ionescu, Corina; Dragos, Nicolae; Barbu-Tudoran, Lucian; Andrei, Adrian-Ştefan; Banciu, Horia L.; Sicora, Cosmin; Podar, Mircea

    2015-01-01

    Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients. PMID:25870594

  12. Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

    Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

    2015-04-01

    Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (psoil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (psoil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

  13. Noncompetitive microbial diversity patterns in soils: their causes and implications for bioremediation

    James M. Tiedje; Jizhong Zhou; Anthony Palumbo; Nathaniel Ostrom; Terence L. Marsh

    2007-07-05

    This funding provided support for over nine years of research on the structure and function of microbial communities in subsurface environments. The overarching goal during these years was to understand the impact of mixed contaminants, particularly heavy metals like uranium, on the structure and function of microbial communities. In addition we sought to identify microbial populations that were actively involved in the reduction of metals because these species of bacteria hold the potential for immobilizing soluble metals moving in subsurface water. Bacterial mediated biochemical reduction of metals like uranium, technetium and chromium, greatly reduces their mobility through complexation and precipitation. Hence, by taking advantage of natural metabolic capabilities of subsurface microbial populations it is possible to bioremediate contaminated subsurface environments with a cost-effective in situ approach. Towards this end we have i.) identified bacterial populations that have thrived under the adverse conditions at the contaminated FRC site, ii.) phylogenetically identified populations that respond to imposed remediation conditions at the FRC, iii.) used metagenomics to begin a reconstruction of the metabolic web in a contaminated subsurface zone, iv.) investigated the metal reducing attributes of a Gram-positive spore forming rod also capable of dechlorination.

  14. Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean

    Alves Junior, Nelson; Meirelles, Pedro Milet; de Oliveira Santos, Eidy; Dutilh, Bas; Silva, Genivaldo G Z; Paranhos, Rodolfo; Cabral, Anderson S; Rezende, Carlos; Iida, Tetsuya; de Moura, Rodrigo L; Kruger, Ricardo Henrique; Pereira, Renato C; Valle, Rogério; Sawabe, Tomoo; Thompson, Cristiane; Thompson, Fabiano

    2014-01-01

    Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This i

  15. Microbial diversity associated with copepods in the North Atlantic subtropical gyre.

    Shoemaker, Katyanne M; Moisander, Pia H

    2015-07-01

    Patchiness of marine microbial communities has an important influence on microbial activities in the ocean, particularly in the oligotrophic open ocean where bioavailable nutrients are otherwise scarce. Such spatial heterogeneity is present in associations with dead and living particles, including zooplankton. The microbial community composition of mesozooplankton was investigated from the Sargasso Sea using 16S rRNA amplicon pyrosequencing. Zooplankton microbiomes were studied on the copepods Undinula vulgaris, Pleuromamma spp., Sapphirina metalina, Pseudocalanus spp. and Tigriopus sp., and an amphipod, Phrosina semilunata. The overall richness was lower in the zooplankton than in the seawater, and zooplankton-specific bacterial communities were distinct from the communities in seawater. Gammaproteobacteria dominated in all zooplankton studied, with Vibrio spp. highly represented. Firmicutes were detected in all copepods, providing evidence for anaerobic conditions present on the copepods. Bacterial groups known to grow on concentrated organic substrates or to prevent biofouling were highly represented in association with copepods, suggesting they benefit from copepod-derived nutrients or carbon. The described copepod microbiome has similarities to communities previously described in coastal copepods, suggesting some aspects of the copepod microbiome are not habitat specific. The communities are distinct of that in seawater, demonstrating significant microbial patchiness in association with marine zooplankton in the oligotrophic open ocean. PMID:26077986

  16. Functional and structural diversity of soil microbial communities on colliery spoil heaps

    Malý, S.; Elhottová, Dana; Frouz, Jan; Chroňáková, Alica; Krištůfek, Václav; Kalčík, Jiří; Picek, T.

    Zaragoza : Society for Ecological Restoration International, 2005. s. 219. [The World Conference on Ecological Restoration . 12.09.2005-18.09.2005, Zaragoza] Institutional research plan: CEZ:AV0Z60660521 Keywords : soil microbial community * Czech Republic * environmental factors Subject RIV: EH - Ecology, Behaviour

  17. Approaches applied in study of soil microbial diversity in brown coal post-mining chronosequences

    Chroňáková, Alica; Elhottová, Dana; Malý, S.; Krištůfek, Václav

    2004-01-01

    Roč. 3, č. 1 (2004), s. 35-39. ISSN 1336-1120 R&D Projects: GA ČR GA526/03/1259 Institutional research plan: CEZ:AV0Z6066911 Keywords : ARDRA * colliery heaps * microbial community Subject RIV: EH - Ecology, Behaviour

  18. Microbial Terroir in Chilean Valleys: Diversity of Non-conventional Yeast

    Jara, Carla; Laurie, V. Felipe; Mas, Albert; Romero, Jaime

    2016-01-01

    In this study, the presence of non-conventional yeast associated with vineyards located between latitudes 30°S and 36°S was examined, including the valleys of Limarí, Casablanca, Maipo, Colchagua, Maule, and Itata. The microbial fingerprinting in each valley was examined based on the specific quantification of yeast of enological interest. Grape–berries were sampled to evaluate the presence and load of non-conventional yeast with enological potential, such as Metschnikowia, Hanseniaspora, Torulaspora, Debaryomyces, Meyerozyma, and Rhodotorula. These yeasts were present in all vineyards studied but with varying loads depending on the valley sampled. No identical fingerprints were observed; however, similarities and differences could be observed among the microbial profiles of each valley. A co-variation in the loads of Metschnikowia and Hanseniaspora with latitude was observed, showing high loads in the Casablanca and Itata valleys, which was coincident with the higher relative humidity or rainfall of those areas. Non-conventional yeasts were also isolated and identified after sequencing molecular markers. Potentially good aromatic properties were also screened among the isolates, resulting in the selection of mostly Metschnikowia and Hanseniaspora isolates. Finally, our results suggest that microbial terroir might be affected by climatic conditions such as relative humidity and rainfall, especially impacting the load of non-conventional yeast. In this study, the microbial fingerprint for yeast in Chilean vineyards is reported for the first time revealing an opportunity to study the contribution of this assembly of microorganisms to the final product. PMID:27242693

  19. Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.

    Richard R Rodrigues

    Full Text Available The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum, another by a shrub (Rhamnus davurica, and the third by a tree (Ailanthus altissima. The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME. Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that

  20. New insight into microbial diversity and functions in traditional Vietnamese alcoholic fermentation.

    Thanh, Vu Nguyen; Thuy, Nguyen Thanh; Chi, Nguyen Thuy; Hien, Dinh Duc; Ha, Bui Thi Viet; Luong, Dao Thi; Ngoc, Pham Duc; Ty, Pham Van

    2016-09-01

    The roles of microorganisms in traditional alcoholic fermentation are often assumed based on abundance in the starter and activity in pure culture. There is a serious lack of hard evidence on the behavior and activity of individual microbial species during the actual fermentation process. In this study, microbial succession and metabolite changes during 7days of traditional Vietnamese alcoholic fermentation were monitored. Special attention was devoted to starch degradation. In total, 22 microbial species, including 6 species of filamentous fungi (Rhizopus microsporus, Rhizopus arrhizus, Mucor indicus, Mucor circinelloides, Cunninghamella elegans, Aspergillus niger), 1 yeast-like fungus (Saccharomycopsis fibuligera), 7 yeasts (Saccharomyces cerevisiae, Clavispora lusitaniae, Wickerhamomyces anomalus, Lindnera fabianii, Pichia kudriavzevii, Candida rugosa, Candida tropicalis), and 8 bacteria (Stenotrophomonas maltophilia, Lactobacillus brevis, Lactobacillus helveticus, Acinetobacter baumannii, Staphylococcus hominis, Bacillus megaterium, Enterobacter asburiae, Pediococcus pentosaceus) were identified. Despite the presence of a complex microbiota in the starter, the fermentation process is consistent and involves a limited number of functional species. Rapid change in microbial composition of fermentation mash was observed and it was correlated with ethanol content. Microbial biomass reached maximum during first 2days of solid state fermentation. Acidification of the medium took place in day 1, starch degradation in days 2, 3, 4, and alcohol accumulation from day 3. Although Sm. fibuligera dominated by cell count amongst potential starch degraders, zymography indicated that it did not produce amylase in the fermentation mash. In mixed culture with Rhizopus, amylase production by Sm. fibuligera is regulated by the moisture content of the substrate. Rhizopus was identified as the main starch degrader and S. cerevisiae as the main ethanol producer. Bacterial load was

  1. Variation in honey bee gut microbial diversity affected by ontogenetic stage, age and geographic location.

    Zuzana Hroncova

    Full Text Available Social honey bees, Apis mellifera, host a set of distinct microbiota, which is similar across the continents and various honey bee species. Some of these bacteria, such as lactobacilli, have been linked to immunity and defence against pathogens. Pathogen defence is crucial, particularly in larval stages, as many pathogens affect the brood. However, information on larval microbiota is conflicting. Seven developmental stages and drones were sampled from 3 colonies at each of the 4 geographic locations of A. mellifera carnica, and the samples were maintained separately for analysis. We analysed the variation and abundance of important bacterial groups and taxa in the collected bees. Major bacterial groups were evaluated over the entire life of honey bee individuals, where digestive tracts of same aged bees were sampled in the course of time. The results showed that the microbial tract of 6-day-old 5th instar larvae were nearly equally rich in total microbial counts per total digestive tract weight as foraging bees, showing a high percentage of various lactobacilli (Firmicutes and Gilliamella apicola (Gammaproteobacteria 1. However, during pupation, microbial counts were significantly reduced but recovered quickly by 6 days post-emergence. Between emergence and day 6, imago reached the highest counts of Firmicutes and Gammaproteobacteria, which then gradually declined with bee age. Redundancy analysis conducted using denaturing gradient gel electrophoresis identified bacterial species that were characteristic of each developmental stage. The results suggest that 3-day 4th instar larvae contain low microbial counts that increase 2-fold by day 6 and then decrease during pupation. Microbial succession of the imago begins soon after emergence. We found that bacterial counts do not show only yearly cycles within a colony, but vary on the individual level. Sampling and pooling adult bees or 6th day larvae may lead to high errors and variability, as both

  2. Study of the diversity of microbial communities in a sequencing batch reactor oxic-settling-anaerobic process and its modified process.

    Sun, Lianpeng; Chen, Jianfan; Wei, Xiange; Guo, Wuzhen; Lin, Meishan; Yu, Xiaoyu

    2016-05-01

    To further reveal the mechanism of sludge reduction in the oxic-settling-anaerobic (OSA) process, the polymerase chain reaction - denaturing gradient gel electrophoresis protocol was used to study the possible difference in the microbial communities between a sequencing batch reactor (SBR)-OSA process and its modified process, by analyzing the change in the diversity of the microbial communities in each reactor of both systems. The results indicated that the structure of the microbial communities in aerobic reactors of the 2 processes was very different, but the predominant microbial populations in anaerobic reactors were similar. The predominant microbial population in the aerobic reactor of the SBR-OSA belonged to Burkholderia cepacia, class Betaproteobacteria, while those of the modified process belonged to the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. These 3 types of microbes had a cryptic growth characteristic, which was the main cause of a greater sludge reduction efficiency achieved by the modified process. PMID:27021584

  3. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen;

    2016-01-01

    second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with...... community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome....

  4. The giant cold-water coral mound as a nested microbial/metazoan system: physical, chemical, biological and geological picture (ESF EuroDiversity MiCROSYSTEMS)

    Henriet, J.-P.; The MICROSYSTEMS Team

    2009-01-01

    The MiCROSYSTEMS project under the ESF EUROCORES EuroDiversity scheme is a holistic and multi-scale approach in studying microbial diversity and functionality in a nested microbial/metazoan system, which thrives in deep waters: the giant cold-water coral mound. Studies on prolific cold-water coral sites have been carried out from the canyons of the Bay of Biscay to the fjords of the Norwegian margin, while the Pen Duick carbonate mound province off Morocco developed into a joint natural lab f...

  5. A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil.

    Treves, D S; Xia, B; Zhou, J; Tiedje, J M

    2003-01-01

    The hypothesis that spatial isolation is a key determinant of microbial community structure in soils was evaluated by examining the competitive dynamics of two species growing on a single resource in a uniform sand matrix under varied moisture content. One species dominated the community under highly connected, saturated treatments, suggesting that these conditions allow competitive interactions to structure the community. As moisture content decreased, however, the less competitive species became established in the community. This effect was most pronounced at a matric water potential of -0.14 MPa where estimates of final population density and species fitness were equal. A second but more closely related species pair exhibited a similar response to decreasing moisture, suggesting that the effects of spatial isolation we observed are not simply a species-pair-specific phenomenon. These findings indicate that spatial isolation, created by low moisture content, plays an important role in structuring soil microbial communities. PMID:12415419

  6. Microbial diversity of landslide soils assessed by RFLP and SSCP fingerprints.

    Guida, Marco; Cannavacciuolo, Paolo Losanno; Cesarano, Mara; Borra, Marco; Biffali, Elio; D'Alessandro, Raffaella; De Felice, Bruna

    2014-08-01

    Landslides are a significant component of natural disasters in most countries around the world. Understanding these destructive phenomena through the analysis of possible correlations between microbial communities and the alteration of the soil responsible for landslides is important in order to reduce their negative consequences. To address this issue, bacterial and fungal communities in soils triggering landslides in Termini-Nerano and Massa Lubrense-Nerano (Naples, Italy) were analysed by genetic profiling techniques. Fingerprints were generated by single-strand conformation polymorphisms (SSCP) and random amplified polymorphic DNA (RAPD). The microbial community in both soil types was enriched in species which could contribute to the degradation process occurring during landslides, forming biofilms and leading to the transformation or the formation of minerals. Indeed, some of the identified bacteria were found to favour the transformation of clay minerals. These findings suggest a possible relationship between bacterial and fungal community-colonising soils and the occurrence of landslides. PMID:24722859

  7. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

    Handelsman Jo; Schloss Patrick D

    2008-01-01

    Abstract Background The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes. Massive datasets of metagenomic sequences have been accumulated, but analysis of these sequences has focused primarily on the descriptive comparison of the relative abundance of proteins that belong to specific functional categories. More robust statistical methods are needed to ...

  8. Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

    Ute Hentschel; Sheila Marie Pimentel-Elardo; Sebastian Proksch; Lubomir Grozdanov

    2012-01-01

    Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows ...

  9. Relation of aggregate stability and microbial diversity in an incubated sandy soil

    Büks, Frederick; Rebensburg, Philip; Lentzsch, Peter; Kaupenjohann, Martin

    2016-01-01

    Beside physico-chemical interactions between particulate organic matter (POM), mineral particles and dissolved molecules, microbial biofilms are an important factor of aggregate stability as a proxy of soil quality. Soil primary particles are linked by the highly viscous extracellular biofilm matrix known as extracellular polymeric substance (EPS). Matrix composition depends on the community of biofilm producing species and environmental conditions affecting gene expression. This work ...

  10. Subsurface microbial diversity in deep-granitic-fracture water in Colorado.

    Sahl, Jason W; Schmidt, Raleigh; Swanner, Elizabeth D; Mandernack, Kevin W; Templeton, Alexis S; Kieft, Thomas L; Smith, Richard L; Sanford, William E; Callaghan, Robert L; Mitton, Jeffry B; Spear, John R

    2008-01-01

    A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. PMID:17981950

  11. No-till and cover crops shift soil microbial abundance and diversity in Laos tropical grasslands

    Lienhard, pascal; Tivet, Florent; Chabanne, Andre; Dequiedt, Samuel; Lelievre, Mélanie; Sayphoummie, Sengphanh; Leudphanane, Bounma; Chemidlin Prévost-Bouré, Nicolas; Seguy, Lucien; Maron, Pierre-Alain; Ranjard, Lionel

    2013-01-01

    Agricultural practices affect the physical and chemical characteristics of the soil, which in turn may influence soil microorganisms with consequences on soil biological functioning. However, there is little knowledge on the interactions between agricultural management, soil physicochemical properties, and soil microbial communities, notably in tropical ecosystems with few studies conducted in strongly weathered and acid soils. Here, we investigated the early effect of tillage and crop residu...

  12. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea)

    Wegener, G.; Shovitri, M.; Knittel, K.; Niemann, H.; Hovland, M.; Boetius, A.

    2008-02-01

    Fluid-flow related seafloor structures and gas seeps were detected in the North Sea in the 1970s and 1980s by acoustic sub-bottom profiling and oil rig surveys. A variety of features like pockmarks, gas vents and authigenic carbonate cements were found to be associated with sites of oil and gas exploration, indicating a link between these surface structures and underlying deep hydrocarbon reservoirs. In this study we performed acoustic surveys and videographic observation at Gullfaks, Holene Trench, Tommeliten, Witch's Hole and the giant pockmarks of the UK Block 15/25, to investigate the occurrence and distribution of cold seep ecosystems in the Northern North Sea. The most active gas seep sites, i.e. Gullfaks and Tommeliten, were investigated in detail: at both sites gas bubbles escaped continuously from small holes in the seabed to the water column, reaching the upper mixed surface layer as indicated by acoustic images of the gas flares. At Gullfaks a 0.1 km2 large gas emission site was detected on a flat sandy seabed, covered by filamentous sulfide-oxidizing bacteria. At Tommeliten we found a patchy distribution of small bacterial mats indicating sites of gas seepage. Here the seafloor consists of layers of sand and stiff clay, and gas emission was observed from small cracks in the seafloor. At both sites the anaerobic oxidation of methane (AOM) coupled to sulfate reduction is the major source of sulfide. Molecular analyses targeting specific lipid biomarkers and 16 S rRNA gene sequences identified an active microbial community dominated by sulfide-oxidizing and sulfate-reducing bacteria (SRB) as well as methanotrophic bacteria and archaea. Carbon isotope values of specific microbial fatty acids and alcohols were highly depleted, indicating that the microbial community at both gas seeps incorporates methane or its metabolites. The microbial community composition of both shallow seeps show high similarities to the deep water seeps associated with gas hydrates

  13. Effect of reduced nitrogen deposition on microbial activity, abundance and diversity in forest soils

    Enowashu, Esther Eneckeh

    2012-01-01

    The deposition of nitrogen has increased many-fold due to anthropogenic activities. Since forest ecosystems are often limited by N availability, elevated N inputs from the atmosphere can have a fertilization effect but in the long-term, excess N can influence above- and below-ground production. One of the consequences of N deposition and increased N inputs is a shift in microbial community structure and function as ecosystems move towards N saturation. Soil microorganisms through the action o...

  14. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments

    Klatt, Christian G.; Inskeep, William P.; Herrgard, Markus;

    2013-01-01

    Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across...... the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average 53Mbp/site) were...

  15. Microbial diversity in an anaerobic digester with biogeographical proximity to geothermally active region.

    Mahajan, Rishi; Nikitina, Anna; Nozhevnikova, Alla; Goel, Gunjan

    2016-11-01

    Anaerobic digestion of agricultural biomass or wastes can offer renewable energy, to help meet the rise in energy demands. The performance of an anaerobic digester considerably depends upon the complex interactions between bacterial and archaeal microbiome, which is greatly influenced by environmental factors. In the present study, we evaluate a microbial community of digester located at two different geographical locations, to understand whether the biogeographical proximity of a digester to a geothermally active region has any influence on microbial composition. The comparative microbial community profiling, highlights coexistence of specific bacterial and archaeal representatives (especially, Prosthecochloris sp., Conexibacter sp., Crenarchaeota isolate (Caldivirga sp.), Metallosphaera sp., Pyrobaculum sp. and Acidianus sp.) in a digester with close proximity to geothermally active region (Site I) and their absence in a digester located far-off from geothermally active region (Site II). A Sörensen's index of similarity of 83.33% and 66.66% for bacterial and archaeal community was observed in both the reactors, respectively. PMID:26934210

  16. Further exploration of the heterocyclic diversity accessible from the allylation chemistry of indigo

    Alireza Shakoori

    2015-04-01

    Full Text Available Diversity-directed synthesis based on the cascade allylation chemistry of indigo, with its embedded 2,2’-diindolic core, has resulted in rapid access to new examples of the hydroxy-8a,13-dihydroazepino[1,2-a:3,4-b']diindol-14(8H-one skeleton in up to 51% yield. Additionally a derivative of the novel bridged heterocycle 7,8-dihydro-6H-6,8a-epoxyazepino[1,2-a:3,4-b']diindol-14(13H-one was produced when the olefin of the allylic substrate was terminally disubstituted. Further optimisation also produced viable one-pot syntheses of derivatives of the spiro(indoline-2,9'-pyrido[1,2-a]indol-3-one (65% and pyrido[1,2,3-s,t]indolo[1,2-a]azepino[3,4-b]indol-17-one (72% heterocyclic systems. Ring-closing metathesis of the N,O-diallylic spiro structure and subsequent Claisen rearrangement gave rise to the new (1R,8aS,17aS-rel-1,2-dihydro-1-vinyl-8H,17H,9H-benz[2',3']pyrrolizino[1',7a':2,3]pyrido[1,2-a]indole-8,17-(2H,9H-dione heterocyclic system.

  17. High Genetic Diversity of Microbial Cellulase and Hemicellulase Genes in the Hindgut of Holotrichia parallela Larvae

    Ping Sheng; Yushan Li; Sean D. G. Marshall; Hongyu Zhang

    2015-01-01

    In this study, we used a culture-independent method based on library construction and sequencing to analyze the genetic diversity of the cellulase and hemicellulase genes of the bacterial community resident in the hindgut of Holotrichia parallela larvae. The results indicate that there is a large, diverse set of bacterial genes encoding lignocellulose hydrolysis enzymes in the hindgut of H. parallela. The total of 101 distinct gene fragments (similarity <95%) of glycosyl hydrolase families...

  18. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

    Thomas J Sharpton

    Full Text Available Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA sequences into operational taxonomic units (OTUs. Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?

  19. Genetic and functional diversity of soil microbial communities associated to grapevine plants and wine quality

    Mocali, Stefano; Fabiano, Arturo; Kuramae, Eiko; de Hollander, Matias; Kowalchuck, George; Vignozzi, Nadia; Valboa, Giuseppe; Pastorelli, Roberta; Fornasier, Flavio; Priori, Simone; Costantini, Edoardo

    2014-05-01

    Introduction Despite the economic importance of vineyards in Italy, the wine sector is facing severe challenges from increased global competition and climate changes. The quality of the grape at harvest has a strong direct impact on final wine quality and the strong relationship between wine composition, aroma, taste and soil properties has been outlined in the "Terroir concept". However, information on the impact of soil microbial communities on soil functions, grapevine plants and wine quality is still lacking. Objectives The aim of this study was to explore the composition and the potential functions of soil microbial communities associated to grapevine plants grown in two soils which showed similar physical, chemical and hydrological properties but which provided a different wine quality. Materials and Methods Soils from two sites of the Chianti region in Tuscany (BRO11 and BRO12) cultivated with the grapevine cultivar Sangiovese with contrasting wine quality were examined by means of a structural and functional approach: specifically, GeoChip microarrays, pyrosequencing of 16S rRNA and 18S rRNA genes, enzyme assays and measurements of some soil biological properties, such as microbial biomass C and soil respiration, were carried out. Results Enzyme assays and soil biological analyses revealed a higher biological activity in BRO11 as compared to BRO12. The structure of soil microbial communities, assessed using 16S and 18S rRNA gene-targeted pyrosequencing, revealed a higher presence of Actinobacteria in the BRO12 than in the BRO11 soil where, in contrast, the alfa-Proteobacteria are more abundant. GeoChip microarray analyses revealed a consistent difference in genes involved in S cycling, with a significant overrepresentation of sulfur-oxidation genes in BRO11 and increased levels of sulfate reduction genes BRO12. These results are consistent with the high content of sulfates and the abundance of Firmicutes such as Sulfobacillus thermosulfidooxidans in the BRO

  20. A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

    Lisle, John T.; Stellick, Sarah H.

    2011-01-01

    Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

  1. Out of the dark: Transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines

    Kristin eWoycheese

    2015-02-01

    Full Text Available In the Zambales ophiolite range terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca2+-OH--type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (<0.5 ppm. Influx of atmospheric carbon dioxide affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads and Firmicutes (19.1% of total reads. Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep’s source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes.

  2. Increasing microbial diversity and nitrogen cycling potential of burnt forest soil in Spain through post-fire management

    Pereg, Lily; Mataix-Solera, Jorge; McMillan, Mary; García-Orenes, Fuensanta

    2016-04-01

    Microbial diversity and function in soils are increasingly assessed by the application of molecular methods such as sequencing and PCR technology. We applied these techniques to study microbial recovery in post-fire forest soils. The recovery of forest ecosystems following severe fire is influenced by post-fire management. The removal of burnt tree stumps (salvage logging) is a common practice in Spain following fire. In some cases, the use of heavy machinery in addition to the vulnerability of soils to erosion and degradation make this management potentially damaging to soil, and therefore to the ecosystem. We hypothesized that tree removal slows down the recovery of soil biological communities including microbial and plant communities and contributes to soil degradation in the burnt affected area. The study area is located in "Sierra de Mariola Natural Park" in Alcoi, Alicante (E Spain). A big forest fire (>500 has) occurred in July 2012. The forest is composed mainly of Pinus halepensis trees with an understory of typical Mediterranean shrubs species such as Quercus coccifera, Rosmarinus officinalis, Thymus vulgaris, Brachypodium retusum, etc. Soil is classified as a Typic Xerorthent (Soil Survey Staff, 2014) developed over marls. In February 2013, salvage logging (SL) treatment, with a complete extraction of the burned wood using heavy machinery, was applied to a part of the affected forest. Plots for monitoring the effects of SL were installed in this area and in a similar nearby control (C) area, where no SL treatment was done. The recovery of soil bacterial and fungal communities post-fire with and without tree removal was analysed by using Next-Generation sequencing and the abundance of functional genes, related to nitrogen cycling, in the soil was estimated using quantitative PCR (qPCR). We will present the methods used and the results of our study in this PICO presentation.

  3. Microbial diversity and dynamics during methane production from municipal solid waste

    Highlights: ► Similar bacterial communities developed following different start-up operation. ► Total methanogens in leachate during the decelerated methane phase reflected overall methane yield. ► Created correlations between methanogens, methane yield, and available substrate. ► Predominant bacteria identified with syntrophic polysaccharide degraders. ► Hydrogenotrophic methanogens were dominant in the methane generation process. - Abstract: The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and

  4. Microbial diversity and dynamics during methane production from municipal solid waste

    Bareither, Christopher A., E-mail: christopher.bareither@colostate.edu [Civil and Environmental Engineering, Colorado State University, Ft. Collins, CO 80532 (United States); Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706 (United States); Wolfe, Georgia L., E-mail: gwolfe@wisc.edu [Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 (United States); McMahon, Katherine D., E-mail: tmcmahon@engr.wisc.edu [Bacteriology, Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706 (United States); Benson, Craig H., E-mail: chbenson@wisc.edu [Civil and Environmental Engineering, Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-10-15

    Highlights: ► Similar bacterial communities developed following different start-up operation. ► Total methanogens in leachate during the decelerated methane phase reflected overall methane yield. ► Created correlations between methanogens, methane yield, and available substrate. ► Predominant bacteria identified with syntrophic polysaccharide degraders. ► Hydrogenotrophic methanogens were dominant in the methane generation process. - Abstract: The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and

  5. Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches

    Taiga Asakura

    2014-10-01

    Full Text Available An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.

  6. Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch

    Xia, Yu; Hu, Man; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong

    2016-01-01

    The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.

  7. Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

    Zarsky, Jakub D.; Stibal, Marek; Hodson, Andy; Sattler, Birgit; Schostag, Morten; Hansen, Lars H.; Jacobsen, Carsten S.; Psenner, Roland

    2013-09-01

    The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier.

  8. [Microbial diversity in rhizosphere soil of transgenic Bt rice based on the characterization of phospholipids fatty acids].

    Liu, Wei; Wang, Shu-tao; Chen, Ying-xu; Wu, Wei-xiang; Wang, Jing

    2011-03-01

    Taking non-transgenic parental rice as the control, and by using 13C pulse-chase labeling method coupled with phospholipid fatty acid (PLFA) analysis, this paper studied the effects of transgenic Bt rice on the microbial diversity in rhizosphere soil. The results showed that in the rhizosphere soils of transgenic Bt rice and its non-transgenic parent, saturated PLFAs and branched PLFAs were the main, followed by monounsaturated PLFAs, and polyunsaturated PLFAs. A significantly lower amount of Gram-positive bacterial PLFAs and a higher amount of Gram-negative bacterial PLFAs were observed in the rhizosphere soil of transgenic Bt rice at its seedling, booting, and heading stages, as compared with the control. In the whole growth period of rice, transgenic Bt gene had no significant effects on the fungal and actinomycete PLFAs in rhizosphere soil, and no significant difference was observed in the rhizosphere soil 13C-PLFA content between transgenic Bt rice and its non-transgenic parent. These findings indicated that the insertion of exogenous cry1Ab gene into rice only had temporary effects on the microbial community composition in the rhizosphere soil of rice. PMID:21657031

  9. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea

    G. Wegener

    2008-02-01

    Full Text Available Fluid-flow related seafloor structures and gas seeps were detected in the North Sea in the 1970s and 1980s by acoustic sub-bottom profiling and oil rig surveys. A variety of features like pockmarks, gas vents and authigenic carbonate cements were found to be associated with sites of oil and gas exploration, indicating a link between these surface structures and underlying deep hydrocarbon reservoirs. In this study we performed acoustic surveys and videographic observation at Gullfaks, Holene Trench, Tommeliten, Witch's Hole and the giant pockmarks of the UK Block 15/25, to investigate the occurrence and distribution of cold seep ecosystems in the Northern North Sea. The most active gas seep sites, i.e. Gullfaks and Tommeliten, were investigated in detail: at both sites gas bubbles escaped continuously from small holes in the seabed to the water column, reaching the upper mixed surface layer as indicated by acoustic images of the gas flares. At Gullfaks a 0.1 km2 large gas emission site was detected on a flat sandy seabed, covered by filamentous sulfide-oxidizing bacteria. At Tommeliten we found a patchy distribution of small bacterial mats indicating sites of gas seepage. Here the seafloor consists of layers of sand and stiff clay, and gas emission was observed from small cracks in the seafloor. At both sites the anaerobic oxidation of methane (AOM coupled to sulfate reduction is the major source of sulfide. Molecular analyses targeting specific lipid biomarkers and 16 S rRNA gene sequences identified an active microbial community dominated by sulfide-oxidizing and sulfate-reducing bacteria (SRB as well as methanotrophic bacteria and archaea. Carbon isotope values of specific microbial fatty acids and alcohols were highly depleted, indicating that the microbial community at both gas seeps incorporates methane or its metabolites. The microbial community composition of both shallow seeps show high similarities to the deep water

  10. Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea

    G. Wegener

    2008-08-01

    Full Text Available Fluid flow related seafloor structures and gas seeps were detected in the North Sea in the 1970s and 1980s by acoustic sub-bottom profiling and oil rig surveys. A variety of features like pockmarks, gas vents and authigenic carbonate cements were found to be associated with sites of oil and gas exploration, indicating a link between these surface structures and the underlying, deep hydrocarbon reservoirs. In this study we performed acoustic surveys and videographic observation at Gullfaks, Holene Trench, Tommeliten, Witch's Hole and the giant pockmarks of the UK Block 15/25, to investigate the occurrence and distribution of cold seep ecosystems in the Northern North Sea. The most active gas seep sites, i.e. Gullfaks and Tommeliten, were investigated in detail. At both sites, gas bubbles escaped continuously from small holes in the seabed to the water column, reaching the upper mixed surface layer. At Gullfaks a gas emitting, flat area of 0.1 km2 of sandy seabed covered by filamentous sulfur-oxidizing bacteria was detected. At Tommeliten, we found a patchy distribution of small bacterial mats indicating sites of gas seepage. Below the patches the seafloor consisted of sand from which gas emissions were observed. At both sites, the anaerobic oxidation of methane (AOM coupled to sulfate reduction (SR was the major source of sulfide. Molecular analyses targeting specific lipid biomarkers and 16S rRNA gene sequences identified an active microbial community dominated by sulfur-oxidizing and sulfate-reducing bacteria (SRB as well as methanotrophic bacteria and archaea. Stable carbon isotope values of specific, microbial fatty acids and alcohols from both sites were highly depleted in the heavy isotope 13C, indicating that the microbial community incorporates methane or its metabolites. The microbial community composition of both shallow seeps shows high similarities to the deep water seeps associated with gas hydrates such as

  11. Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

    Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

    2016-08-15

    Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. PMID:27100015

  12. Making interdisciplinary solid Earth modeling and analysis tools accessible in a diverse undergraduate and graduate classroom

    Becker, T. W.

    2011-12-01

    I present results from ongoing, NSF-CAREER funded educational and research efforts that center around making numerical tools in seismology and geodynamics more accessible to a broader audience. The goal is not only to train students in quantitative, interdisciplinary research, but also to make methods more easily accessible to practitioners across disciplines. I describe the two main efforts that were funded, the Solid Earth Research and Teaching Environment (SEATREE, geosys.usc.edu/projects/seatree/), and a new Numerical Methods class. SEATREE is a modular and user-friendly software framework to facilitate using solid Earth research tools in the undergraduate and graduate classroom and for interdisciplinary, scientific collaboration. We use only open-source software, and most programming is done in the Python computer language. We strive to make use of modern software design and development concepts while remaining compatible with traditional scientific coding and existing, legacy software. Our goals are to provide a fully contained, yet transparent package that lets users operate in an easy, graphically supported "black box" mode, while also allowing to look under the hood, for example to conduct numerous forward models to explore parameter space. SEATREE currently has several implemented modules, including on global mantle flow, 2D phase velocity tomography, and 2D mantle convection and was used at the University of Southern California, Los Angeles, and at a 2010 CIDER summer school tutorial. SEATREE was developed in collaboration with engineering and computer science undergraduate students, some of which have gone on to work in Earth Science projects. In the long run, we envision SEATREE to contribute to new ways of sharing scientific research, and making (numerical) experiments truly reproducible again. The other project is a set of lecture notes and Matlab exercises on Numerical Methods in solid Earth, focusing on finite difference and element methods. The

  13. The Gut as Reservoir of Antibiotic Resistance: Microbial Diversity of Tetracycline Resistance in Mother and Infant

    de Vries, Lisbeth Elvira; Valles, Yvonne; Agersø, Yvonne;

    2011-01-01

    study using a metagenomic approach to determine the diversity of microorganisms conferring tetracycline resistance (Tc-r) in the guts of a healthy mother-infant pair one month after childbirth, and to investigate the potential for horizontal transfer and maternal transmission of Tc-r genes. Fecal fosmid...... the infant's gut. In addition, although not found in the infant metagenomic library, tet(O) and tet(W) could be detected in the uncloned DNA purified from the infant fecal sample. This is the first study to reveal the diversity of Tc-r bacteria in the human gut, to detect a likely transmission of antibiotic...

  14. The Gut as Reservoir of Antibiotic Resistance: Microbial Diversity of Tetracycline Resistance in Mother and Infant

    de Vries, Lisbeth Elvira; Valles, Yvonne; Agersø, Yvonne;

    2011-01-01

    study using a metagenomic approach to determine the diversity of microorganisms conferring tetracycline resistance (Tc-r) in the guts of a healthy mother-infant pair one month after childbirth, and to investigate the potential for horizontal transfer and maternal transmission of Tc-r genes. Fecal fosmid...... the infant's gut. In addition, although not found in the infant metagenomic library, tet(O) and tet(W) could be detected in the uncloned DNA purified from the infant fecal sample. This is the first study to reveal the diversity of Tc-r bacteria in the human gut, to detect a likely transmission of...

  15. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

    Handelsman Jo

    2008-01-01

    Full Text Available Abstract Background The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes. Massive datasets of metagenomic sequences have been accumulated, but analysis of these sequences has focused primarily on the descriptive comparison of the relative abundance of proteins that belong to specific functional categories. More robust statistical methods are needed to make inferences from metagenomic data. In this study, we developed and applied a suite of tools to describe and compare the richness, membership, and structure of microbial communities using peptide fragment sequences extracted from metagenomic sequence data. Results Application of these tools to acid mine drainage, soil, and whale fall metagenomic sequence collections revealed groups of peptide fragments with a relatively high abundance and no known function. When combined with analysis of 16S rRNA gene fragments from the same communities these tools enabled us to demonstrate that although there was no overlap in the types of 16S rRNA gene sequence observed, there was a core collection of operational protein families that was shared among the three environments. Conclusion The results of comparisons between the three habitats were surprising considering the relatively low overlap of membership and the distinctively different characteristics of the three habitats. These tools will facilitate the use of metagenomics to pursue statistically sound genome-based ecological analyses.

  16. The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants.

    Mustafa, Ghada A; Abd-Elgawad, Amr; Ouf, Amged; Siam, Rania

    2016-07-01

    The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported "Egyptian Red Sea Coastal Microbiome," sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants. PMID:27179234

  17. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Sajjad; Ahmad; Simerjeet; Kaur; Neil; Dylan; Lamb-Palmer; Mark; Lefsrud; Jaswinder; Singh

    2015-01-01

    Field pea(Pisum sativum L.) is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model(MLM) taking population structure(Q) and relative kinship(K) into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  18. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  19. Long-term effects of irrigation with waste water on soil AM fungi diversity and microbial activities: the implications for agro-ecosystem resilience.

    Maria del Mar Alguacil

    Full Text Available The effects of irrigation with treated urban wastewater (WW on the arbuscular mycorrhizal fungi (AMF diversity and soil microbial activities were assayed on a long-term basis in a semiarid orange-tree orchard. After 43 years, the soil irrigated with fresh water (FW had higher AMF diversity than soils irrigated with WW. Microbial activities were significantly higher in the soils irrigated with WW than in those irrigated with FW. Therefore, as no negative effects were observed on crop vitality and productivity, it seems that the ecosystem resilience gave rise to the selection of AMF species better able to thrive in soils with higher microbial activity and, thus, to higher soil fertility.

  20. Chemistry and microbial functional diversity differences in biofuel crop and grassland soils in multiple geographies

    As crop and non-crop lands are increasingly converted to biofuel feedstock production, it is of interest to identify potential impacts of annual and perennial feedstocks on soil ecosystem services. Soil samples were obtained from diverse regionally distributed biofuel cropping si...

  1. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

    Lallias, Delphine; Hiddink, Jan G.; Fonseca, Vera G.; Gaspar, John M; Sung, Way; Neill, Simon P.; Barnes, Natalie; Ferrero, Tim; Hall, Neil; Lambshead, P John D; Packer, Margaret; Thomas, W. Kelley; Creer, Simon

    2014-01-01

    Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a ‘melting pot' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model mic...

  2. Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems.

    Gong, Jun; Shi, Fei; Ma, Bin; Dong, Jun; Pachiadaki, Maria; Zhang, Xiaoli; Edgcomb, Virginia P

    2015-10-01

    Little is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single-celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on multiple environmental factors, we investigated the diversity of microeukaryotes in surficial sediments of three basins of the Yellow Sea Large Marine Ecosystem. A considerable proportion (about 20%) of reads was affiliated with known parasitoid protists. Dinophyta and Ciliophora appeared dominant in terms of relative proportion of reads and operational taxonomic unit (OTU) richness. Overall, OTU richness of benthic microeukaryotes decreased with increasing water depth and decreasing pH. While community composition was significantly different among basins, partial Mantel tests indicated a depth-decay pattern of community similarity, whereby water depth, rather than geographic distance or environment, shaped β-diversity of benthic microeukaryotes (including both the abundant and the rare biosphere) on a regional scale. Similar hydrographic and mineralogical factors contributed to the biogeography of both the abundant and the rare OTUs. The trace metal vanadium had a significant effect on the biogeography of the rare biosphere. Our study sheds new light on the composition, diversity patterns and underlying mechanisms of single-celled eukaryote distribution in surficial sediments of coastal oceans. PMID:25581721

  3. Microbial diversity determines the invasion of soil by a bacterial pathogen

    van Elsas, Jan Dirk; Chiurazzi, Mario; Mallon, Cyrus A.; Elhottova, Dana; Kristufek, Vaclav; Salles, Joana Falcao

    2012-01-01

    Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long be

  4. Characterizing Microbial Diversity and Function in Natural Subsurface CO2 Reservoir Systems for Applied Use in Geologic Carbon Sequestration Environments

    Freedman, A.; Thompson, J. R.

    2013-12-01

    The injection of CO2 into geological formations at quantities necessary to significantly reduce CO2 emissions will represent an environmental perturbation on a continental scale. The extent to which biological processes may play a role in the fate and transport of CO2 injected into geological formations has remained an open question due to the fact that at temperatures and pressures associated with reservoirs targeted for sequestration CO2 exists as a supercritical fluid (scCO2), which has generally been regarded as a sterilizing agent. Natural subsurface accumulations of CO2 serve as an excellent analogue for studying the long-term effects, implications and benefits of CO2 capture and storage (CCS). While several geologic formations bearing significant volumes of nearly pure scCO2 phases have been identified in the western United States, no study has attempted to characterize the microbial community present in these systems. Because the CO2 in the region is thought to have first accumulated millions of years ago, it is reasonable to assume that native microbial populations have undergone extensive and unique physiological and behavioral adaptations to adjust to the exceedingly high scCO2 content. Our study focuses on the microbial communities associated with the dolomite limestone McElmo Dome scCO2 Field in the Colorado Plateau region, approximately 1,000 m below the surface. Fluid samples were collected from 10 wells at an industrial CO2 production facility outside Cortez, CO. Subsamples preserved on site in 3.7% formaldehyde were treated in the lab with Syto 9 green-fluorescent nucleic acid stain, revealing 3.2E6 to 1.4E8 microbial cells per liter of produced fluid and 8.0E9 cells per liter of local pond water used in well drilling fluids. Extracted DNAs from sterivex 0.22 um filters containing 20 L of sample biomass were used as templates for PCR targeting the 16S rRNA gene. 16S rRNA amplicons from these samples were cloned, sequenced and subjected to microbial

  5. Biofilm removal technique using sands as a research tool for accessing microbial attachment on surface

    Nathanon Trachoo

    2004-01-01

    Full Text Available Biofilms have profound impacts on improved survival of the constituent microorganisms in nature. Biofilms were believed to protect constituent microorganisms from sanitizer treatment, provide a more suitable habitat for microorganisms, and become a site for genetic material exchanges between microorganisms. As we realize more about the significance of biofilm, methods used for biofilm study should be consistently developed and evaluated. To determine microbial attachment on surfaces, usually biofilms are grown on substratum surfaces and removed by vortexing with glass beads or scraping. However, scraping is not as effective as vortexing with glass beads. Another approach is direct-agar overlaying which cannot be used with high density biofilm. In this experiment, we compared effectiveness of glass beads (298±28 μm in diameter and sands (width: 221±55 μm and length: 329±118 μm in removing biofilm of Pseudomonas aeruginosa by vortexing method. The results suggested that acid-washed sands, which are significantly less inexpensive than glass beads, were as effective as (P>0.05 analytical grade glass beads in Pseudomonas aeruginosa biofilm removal without inhibiting growth of the organism.

  6. Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges.

    Pimentel-Elardo, Sheila Marie; Grozdanov, Lubomir; Proksch, Sebastian; Hentschel, Ute

    2012-06-01

    Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis. PMID:22822366

  7. Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

    Ute Hentschel

    2012-05-01

    Full Text Available Genomic mining revealed one major nonribosomal peptide synthetase (NRPS phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis.

  8. Exploring Western Ghats microbial diversity for antagonistic microorganisms against fungal phytopathogens of pepper and chickpea

    B.N. RAMKUMAR

    2015-08-01

    Full Text Available Newly isolated microbial cultures from Western Ghat soil samples of Kerala region in India were screened for antagonistic activity by well diffusion and dual culture plating against Phytophthora capsici and Rhizoctonia solani, infecting pepper and chickpea, respectively. Bioactive samples were made by varying solvent extraction of the culture broths of the potent isolates belongs to Actinomycetes, Pseudomonas, Bacillus and Trichoderma. The efficacy of the isolates to produce other potent antifungal metabolites such as cell wall degrading enzymes, HCN and volatile compounds were also checked. Treatment with antagonistic isolates in vivo under greenhouse conditions revealed significant reduction of the disease intensity of foot rot disease of black pepper and collar rot of chick pea.

  9. The Philippine National Collection of Microorganisms (PNCM):Repository of Microbial Diversity of the Country

    Monsalud R.G.; Magbanua F.O.; Parungao M.P.; Banaay C.G.B.; Bayer M.H.D.; Yap J.K.; Tapay L.M.

    2002-01-01

    The prime function of the Philippine National Collection of Microorganisms (PNCM), being the national repository of microbial strains, is to collect and preserve strains for their continued viability and availability for future use. To date, a total of 2144 strains of bacteria (1357), yeasts (250), filamentous fungi (377), algae (14), and strains still to be identified (146) are maintained at the PNCM. These are preserved and maintained using various methods which include modified liquid drying (lyophilization), ultra-low temperature ( -70℃ ) storage in 10% glycerol, storage in sterile soil, distilled water and overlaying with mineral oil. Periodic viability testing is done to assess the stability of these preserved cultures under storage. Aside from preservation and maintenance of cultures, the PNCM is also involved in several research activities.One of these is the isolation, characterization and identification of some Vibrio isolates from the Philippines. Details on this particular study is presented in this report.

  10. Diversity, abundance, and spatial distribution of riverine microbial communities response to effluents from swine farm versus farmhouse restaurant.

    Lu, Xiao-Ming; Lu, Peng-Zhen

    2014-09-01

    The 454 pyrosequencing technique was applied to evaluate microbial community composition in sediment and water samples collected from the river receiving effluents from a swine farm and a farmhouse restaurant, respectively. For each sample, 4,600 effective sequences were selected and used to do the bacterial diversity and abundance analysis, respectively. Bacterial phylotype richness in the river sediment sample without effluent input was higher than the other samples, and the river water sample with addition of effluent from the swine farm had the least richness. Effluents from both the swine farm and the farmhouse restaurant have the potential to decrease the bacterial diversity and abundance in the river sediment and water, especially it is more significant in the river sediment. Effect of effluent from the swine farm on riverine bacterial communities was more significant than that from the farmhouse restaurant. Characterization of bacterial community composition in sediments from two tributaries of the downstream river showed that various effluents from the swine farm and the farmhouse restaurant have the similar potential to reduce the natural variability in riverine ecosystems, and contribute to the biotic homogenization in the river sediment. PMID:24818690

  11. A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia.

    Sugitani, K; Mimura, K; Takeuchi, M; Yamaguchi, T; Suzuki, K; Senda, R; Asahara, Y; Wallis, S; Van Kranendonk, M J

    2015-11-01

    The 3.4-Ga Strelley Pool Formation (SPF) at the informally named 'Waterfall Locality' in the Goldsworthy greenstone belt of the Pilbara Craton, Western Australia, provides deeper insights into ancient, shallow subaqueous to possibly subaerial ecosystems. Outcrops at this locality contain a thin (metals represented by Zn. The massive black cherts were likely deposited by mixing of hydrothermal and non-hydrothermal fluids. Coniform structures in the cherts are characterized by diffuse laminae composed of sulfide particles, suggesting that unlike stromatolites, they were formed dominantly through physico-chemical processes related to hydrothermal activity. The cherts yield microfossils identical to previously described carbonaceous films, small and large spheres, and lenticular microfossils. In addition, new morphological types such as clusters composed of large carbonaceous spheroids (20-40 μm across each) with fluffy or foam-like envelope are identified. Finely laminated carbonaceous cherts are devoid of heavy metals and characterized by the enrichment of LREE. This chert locally contains conical to domal structures characterized by truncation of laminae and trapping of detrital grains and is interpreted as siliceous stromatolite formed by very early or contemporaneous silicification of biomats with the contribution of silica-rich hydrothermal fluids. Biological affinities of described microfossils and microbes constructing siliceous stromatolites are under investigation. However, this study emphasizes how diverse the microbial community in Paleoarchean coastal hydrothermal environment was. We propose the diversity is at least partially due to the availability of various energy sources in this depositional environment including reducing chemicals and sunlight. PMID:26189535

  12. Microbial Diversity Associated with High Temperature Sulfide Deposits Along the East Pacific Rise Deep-Sea Hydrothermal Vents

    Brooks, D.; Hoek, J.; Banta, A. B.; von Damm, K.; Reysenbach, A.

    2002-12-01

    In January 2002, hydrothermal chimneys were collected using DSV Alvin from active vents from 9° 17N to 9° 50N and 20° 49N to 20° 50N. Hydrothermal fluids were collected for end member chemistry prior to collecting the sulfide deposits. Chimney samples were sub-sectioned, separating surface and associated biofilm samples from inner chimney samples. Microbial diversity of sub-samples was assessed using culture-dependent and culturing-independent small subunit (16S) ribosomal RNA-based techniques. Initial bacterial diversity assessments using denaturing gradient gel electrophoresis (DGGE) support the global prevalence of epsilon Proteobacteria associated with deep-sea sulfide structures. These are closely related to the sulfur-reducing isolate Nautilia lithotrophica. The biofilm communities varied in complexity with one sample containing several 16S rRNA sequences (phylotypes, OTU's) of alpha, epsilon, and gamma Proteobacteria while others contained a single phylotype of epsilon Proteobacteria. One proteobacterial phylotype was present in all but one of the surface samples, and this sample contained unique alpha and epsilon proteobacterial sequences. The inner chimney samples lacked the most common epsilon proteobacterial 16S rRNA sequences. Enrichment culturing was restricted to selecting for thermophilic chemolithoautotrophic hydrogen-oxidizing Bacteria. The widespread distribution of Persephonella spp. was confirmed, and novel enrichments of a sheathed and as yet unidentified chemolithotroph were obtained.

  13. Dissolved Organic Matter Composition and Microbial Diversity In The Lake Tahoe Basin, Sierra Nevada, California.

    Aluwihare, L.; Goldberg, S. J.; Ball, G. I.; Mendoza, W. G.; Simpson, A.; Kharbush, J.; Nelson, C. E.

    2014-12-01

    Dissolved organic matter (DOM) inputs into high elevation lakes of the Sierra Nevada, California are seasonally segregated, and this enables an examination of the dominant compositional features and microbial responses associated with allochthonous versus autochthonous DOM inputs. Furthermore, because lakes within this watershed have very different hydraulic residence times, extending from days (e.g., Upper Angora Lake) to centuries (Lake Tahoe), the Tahoe Basin represents an ideal experimental system in which to characterize long-lived DOM. We used a variety of analytical tools, including elemental, stable isotope and radiocarbon measurements, nuclear magnetic resonance (NMR) spectroscopy, comprehensive 2D gas chromatography coupled to time of flight (TOF) mass spectrometry and fluorescence measurements, to characterize solid phase extracted (SPE) DOM, and in some cases, whole DOM. Our data show that DOM with typical terrestrial characteristics is quickly removed in lakes with >annual water residence time, leaving behind SPE DOM that is extremely N-rich, with a functional group distribution that is consistent with protein. Furthermore, our radiocarbon measurements estimate a 100-200 year residence time for the N-rich DOM accumulating in Lake Tahoe. All of the analytical techniques distinguish samples based on lake water residence time, which indicates that the lacustrine reactor plays an important role in determining the composition of DOM that accumulates on long timescales. We also examined temporal variations in the microbial community of Lake Tahoe to identify taxa that may be involved in processing DOM from distinct sources. Our results confirm the importance of DOM as a currency for carbon and nitrogen exchange between different compartments of the terrestrial ecosystem and argue for its inclusion in models that examine the response of lake ecosystems to global change.

  14. Bioremediation of 1,2-dichloroethane contaminated groundwater: Microcosm and microbial diversity studies

    In this study, the effectiveness of bioremediating 1,2-dichloroethane (DCA)-contaminated groundwater under different oxidation–reduction processes was evaluated. Microcosms were constructed using indigenous bacteria and activated sludge as the inocula and cane molasses and a slow polycolloid-releasing substrate (SPRS) as the primary substrates. Complete DCA removal was obtained within 30 days under aerobic and reductive dechlorinating conditions. In anaerobic microcosms with sludge and substrate addition, chloroethane, vinyl chloride, and ethene were produced. The microbial communities and DCA-degrading bacteria in microcosms were characterized by 16S rRNA-based denatured-gradient-gel electrophoresis profiling and nucleotide sequence analyses. Real-time polymerase chain reaction was applied to evaluate the variations in Dehalococcoides spp. and Desulfitobacterium spp. Increase in Desulfitobacterium spp. indicates that the growth of Desulfitobacterium might be induced by DCA. Results indicate that DCA could be used as the primary substrate under aerobic conditions. The increased ethene concentrations imply that dihaloelimination was the dominate mechanism for DCA biodegradation. - Highlights: • DCA can be used as the primary substrate and degraded by the indigenous microbial consortia. • Reductive dechlorination of DCA can be enhanced by the supplement of substrates and sludge. • Dihaloelimination is the dominant mechanism for DCA dechlorination and ethene is the end product. • SPRS can serve as the primary substrate and creates anaerobic conditions for DCA dechlorination. • Reductive dechlorination is a feasible option for DCA-contaminated groundwater remediation. - DCA can serve as the primary substrate and degraded by indigenous bacteria aerobically. Dihaloelimination is the dominant mechanism and ethene is the end product via dechlorination

  15. Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome.

    Quinn, Robert A; Phelan, Vanessa V; Whiteson, Katrine L; Garg, Neha; Bailey, Barbara A; Lim, Yan Wei; Conrad, Douglas J; Dorrestein, Pieter C; Rohwer, Forest L

    2016-06-01

    Cystic fibrosis (CF) lungs are filled with thick mucus that obstructs airways and facilitates chronic infections. Pseudomonas aeruginosa is a significant pathogen of this disease that produces a variety of toxic small molecules. We used molecular networking-based metabolomics to investigate the chemistry of CF sputa and assess how the microbial molecules detected reflect the microbiome and clinical culture history of the patients. Metabolites detected included xenobiotics, P. aeruginosa specialized metabolites and host sphingolipids. The clinical culture and microbiome profiles did not correspond to the detection of P. aeruginosa metabolites in the same samples. The P. aeruginosa molecules that were detected in sputum did not match those from laboratory cultures. The pseudomonas quinolone signal (PQS) was readily detectable from cultured strains, but absent from sputum, even when its precursor molecules were present. The lack of PQS production in vivo is potentially due to the chemical nature of the CF lung environment, indicating that culture-based studies of this pathogen may not explain its behavior in the lung. The most differentially abundant molecules between CF and non-CF sputum were sphingolipids, including sphingomyelins, ceramides and lactosylceramide. As these highly abundant molecules contain the inflammatory mediator ceramide, they may have a significant role in CF hyperinflammation. This study demonstrates that the chemical makeup of CF sputum is a complex milieu of microbial, host and xenobiotic molecules. Detection of a bacterium by clinical culturing and 16S rRNA gene profiling do not necessarily reflect the active production of metabolites from that bacterium in a sputum sample. PMID:26623545

  16. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-01-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities,...

  17. GeoChip-based Analysis of Groundwater Microbial Diversity in Norman Landfill

    Lu, Zhenmei

    2010-01-01

    The Norman Landfill is a closed municipal solid waste landfill located on an alluvium associated with the Canadian River in Norman, Oklahoma. It has operated as a research site since 1994 because it is typical of many closed landfill sites across the U.S. Leachate from the unlined landfill forms a groundwater plume that extends downgradient approximately 250 m from the landfill toward the Canadian River. To investigate the impact of the landfill leachate on the diversity and functional struct...

  18. Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

    Laureys, David; De Vuyst, Luc

    2014-01-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the...

  19. Microbial diversity in contaminated soils along the T22 trench of the Chernobyl experimental platform

    The diversity of bacterial communities exposed to radioactive contamination in Chernobyl soils was examined by a combination of molecular and culture-based approaches. A set of six radioactive soil samples, exhibiting high levels of 137Cs contamination, were collected from the T22 trench. Three samples were also collected in nearby soils with low contamination. Complex bacterial community structures were observed in both highly and weakly contaminated samples, using a molecular approach targeting the 16S rRNA gene. However, the presence of specific populations within samples from highly contaminated soils could not be revealed by statistical analysis of the DGGE profiles. More than 200 culturable isolates, representative of dominant morphotypes, were grouped into 83 Operational Taxonomic Units (OTUs) and affiliated to Firmicutes, Actinobacteria, Alpha-, Beta-, Gamma-Proteobacteria and Bacteroïdetes. No specific pattern linked to contamination was observed for these culturable bacteria. The results show that both highly and weakly contaminated soils host a wide diversity of bacteria, suggesting that long term exposure to radionuclides does not lead to the extinction of bacterial diversity.

  20. Decreases in soil microbial function and functional diversity in response to depleted uranium

    A soil microcosm experiment was used to analyze effects of depleted uranium (DU) on soil function, and the concomitant changes in bacterial functional diversity. Uranium treatment levels were 0, 50, 500, 5000, 10,000 and 25,000 mg DU kg-1 soil. Three measures of soil function were made. Overall soil biological activity was assessed via measurement of soil respiration. Decomposition was assessed by measurement of mass loss of four different plant litter types: wood sticks, cellulose paper, high-N grass, and low-N grass. Mineral N availability in the microcosms was estimated using ion-exchange resin bags. Functional diversity of the microcosms was analyzed through the use of the Biolog-system of sole-C-utilization patterns. Soil respiration was the most sensitive measure of functional changes, with significant decreases observed starting at the 500 mg kg-1 treatment. No differences in N availability were observed across the U treatments. Litter decomposition was significantly decreased at the 25,000 mg kg-1 level relative to the control for all litter types except the high-N grass. Wood decomposition was reduced by 84% at the 25,000 mg kg- treatment, cellulose paper by 68%, and low-N grass by 15%. Decreases in the functional diversity of the bacterial community were related to the observed decrease in soil respiration, and to the greater effect on decomposition of the lower-quality litter types

  1. Aquatic microbial habitats within a neotropical rainforest: bromeliads and pH-associated trends in bacterial diversity and composition.

    Goffredi, Shana K; Kantor, Adam H; Woodside, Walter T

    2011-04-01

    Tank-forming bromeliads, suspended in the rainforest canopy, possess foliage arranged in compact rosettes capable of long-term retention of rainwater. This large and unique aquatic habitat is inhabited by microorganisms involved in the important decomposition of impounded material. Moreover, these communities are likely influenced by environmental factors such as pH, oxygen, and light. Bacterial community composition and diversity was determined for the tanks of several bromeliad species (Aechmea and Werauhia) from northern Costa Rica, which span a range of parameters, including tank morphology and pH. These were compared with a nearby forest soil sample, an artificial tank (amber bottle), and a commercially available species (Aechmea). Bacterial community diversity, as measured by 16S rRNA analysis and tRFLP, showed a significant positive correlation with tank pH. A majority of 16S rRNA bacterial phylotypes found in association with acidic bromeliad tanks of pH  5.3, including the commercial bromeliad with the highest pH (6.7), were dominated by Betaproteobacteria, Firmicutes, and Bacteroidetes. To empirically determine the effect of pH on bacterial community, the tank pH of a specimen of Aechmea was depressed, in the field, from 6.5 to 4.5, for 62 days. The resulting community changed predictably with decreased abundance of Betaproteobacteria and Firmicutes and a concomitant increase in Alphaproteobacteria and Acidobacteria. Collectively, these results suggest that bromeliad tanks provide important habitats for a diverse microbial community, distinct from the surrounding environment, which are influenced greatly by acid-base conditions. Additionally, total organic carbon (∼46%) and nitrogen (∼2%) of bromeliad-impounded sediment was elevated relative to soil and gene surveys confirmed the presence of both chitinases and nitrogenases, suggesting that bromeliad tanks may provide important habitats for microbes involved in the biological cycling of carbon and

  2. Potential of Start Codon Targeted (SCoT Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions

    Junchao Zhang

    2015-04-01

    Full Text Available Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA. The molecular variance analysis (AMOVA showed that genetic variation was greater within geographical regions (50.99% than between them (49.01%. Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions.

  3. Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment

    Andrade Luiza L

    2012-08-01

    Full Text Available Abstract Background Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Results Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil, which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Conclusions Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm being greater than in both deeper sediment layers (15–20 and 35–40 cm, which were similar to each other.

  4. Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers.

    Egbadzor, Kenneth F; Ofori, Kwadwo; Yeboah, Martin; Aboagye, Lawrence M; Opoku-Agyeman, Michael O; Danquah, Eric Y; Offei, Samuel K

    2014-01-01

    Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection. PMID:25332852

  5. Evaluation of the microbial diversity of denitrifying bacteria in batch reactor

    S. I. Maintinguer

    2013-09-01

    Full Text Available Microbial communities in an industrial activated sludge plant may contribute to the denitrification process, but the information on the microorganisms present in denitrifying reactors is still scarce. Removal of inorganic nitrogen compounds can be accomplished by the addition of carbon sources to the biological process of denitrification. Ethanol is an economically viable alternative as a carbon source in tropical countries like Brazil, with large-scale production from sugarcane. This paper reports the successful aplication of activated sludge with nitrate and ethanol in a batch anaerobic reactor. The operation lasted 61.5 h with total consumption of nitrate in 42.5 h, nitrite generation (2.0 mg/L and ethanol consumption (830.0 mg/L in 23.5 h. Denitrifying cell counts by the most probable number at the start of the operation were lower than at the end, confirming the ability of the inoculum from activated sludge for the denitrification process. The samples from cell counts were identified as Acidovorax sp., Acinetobacter sp., Comamonas sp. and uncultured bacteria. Therefore, these species may be involved in nitrate reduction and ethanol consumption in the batch reactor.

  6. Characterization of the microbial diversity in yacon spontaneous fermentation at 20 °C.

    Reina, L D; Pérez-Díaz, I M; Breidt, F; Azcarate-Peril, M A; Medina, E; Butz, N

    2015-06-16

    The prebiotic fructooligosaccharide content of yacon makes this root an attractive alternative for the supplementation of a variety of food products. The preservation of yacon by fermentation has been proposed as an alternative to increase the probiotic content of the root concomitantly with its shelf life. Thus the fermented yacon could have significant functional content. The objective of this research was to characterize the biochemistry and microbiology of spontaneous yacon fermentation with 2% NaCl and define the viability of the proposed process. The biochemical analysis of spontaneous heterolactic fermentation of yacon showed a progressive drop in pH with increased lactic and acetic acids, and the production of mannitol during fermentation. The microbial ecology of yacon fermentation was investigated using culture-dependent and culture-independent methods. Bacterial cell counts revealed a dominance of lactic acid bacteria (LAB) over yeasts, which were also present during the first 2 days of the fermentation. Results showed that the heterofermentative LAB were primarily Leuconostoc species, thus it presents a viable method to achieve long term preservation of this root. PMID:25777679

  7. Long-term effect on some chemical parameter and microbial diversity in a conifer forest soil

    Iglesias, T.; Iglesias, M.; Francisco-Álvarez, R.; Ramírez, M.; Fernández-Bermejo, M. C.

    2009-04-01

    Soil microbiota are one of the soil components most affected by wildfires. The data from the present study were obtained from a conifer forest soil at Sierra de Gredos (Ávila, central Spain) twenty years after fire of low-to-moderate intensity. A set of soil characteristics indicated the extent to which the spontaneous recovery of the soil is produced as a result of vegetation regrowth. Ten months after fire a strong increase in soil pH, organic C and N, and exchangeable Ca and K, with respect the control soil. Eighteen years after this fire it was observed a decrease of soil organic C and N, whereas other variables such as pH, exchangeable Ca and K were slightly increased with respect to control soil. Is summe a change in soil microbiota was observed due to wildfire, with a decrease in fungi and bacteria population, Also some changes in microbial community was detected, Key words: Forest Fire, soil microbiology, chemical soil properties

  8. Climate change modifies the diversity, structure and size of N2O-producing microbial communities in montane grassland soil

    Chen, Zhe; Lu, Haiyan; Wang, Changhui; Gschwendtner, Silvia; Schloter, Michael; Butterbach-Bahl, Klaus; Dannenmann, Michael

    2015-04-01

    It is well known that soils are important sources of nitrous oxide (N2O) with microbial nitrification and denitrification being key regulators of N2Oproduction and consumption. Climate change could modify these soil processes thereby affecting net exchange of soil N2O with the atmosphere. In this study, we examined the effects of simulated climatic change (warming, reduced summer precipitation and reduced winter snow cover) on in situ N2O fluxes and associated nitrifying and denitrifying microbial community size, composition and diversity in montane grassland soils. Climate change was simulated by translocation of 200 mini-lysimeters down an elevational gradient with a control transfer within the high altitude site from the pre-alpine grassland Terrestrial Environmental Observatory (TERENO). Our results showed that simulated climate change promoted N2O fluxes in winter time due to the intensified frost and/or the thawing events favored by reduced snow cover but reduced N2O fluxes in dry summer period due to low soil WFPS (water filled pore space). Warming and lower precipitation increased the size of the nitrifying community but decreased the size of the denitrifying community. Denitrifying community composition, rather than nitrifying community composition, showed significant shifts in response to climatic changes, and soil moisture, temperature and soil ammonium concentrations were the most important factors influencing denitrifying community composition. Field N2O fluxes showed a strong positive correlation with the abundance of nitrite reductase genes (nirK+nirS) minus N2O reductase gene (nosZ). Furthermore, under climate change but not at recent climatic conditions, N2O fluxes were correlated with the abundance of ammonia oxidizing bacteria (AOB). Overall, our results illustrate that AOB and denitrifying communities of pre-alpine grassland soils can be quickly altered in a changing climate and that these changes have season-specific impacts on N2O fluxes.

  9. A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

    Lisle, John T.

    2011-01-01

    Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

  10. Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India.

    Rao, Subramanya; Chan, Yuki; Bugler-Lacap, Donnabella C; Bhatnagar, Ashish; Bhatnagar, Monica; Pointing, Stephen B

    2016-03-01

    A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca(2+) and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system. PMID:26843695

  11. Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence.

    Liu, Jinbo; Kong, Weidong; Zhang, Guoshuai; Khan, Ajmal; Guo, Guangxia; Zhu, Chunmao; Wei, Xiaojie; Kang, Shichang; Morgan-Kiss, Rachael M

    2016-10-01

    Global warming has resulted in substantial glacier retreats in high-elevation areas, exposing deglaciated soils to harsh environmental conditions. Autotrophic microbes are pioneering colonizers in the deglaciated soils and provide nutrients to the extreme ecosystem devoid of vegetation. However, autotrophic communities remain less studied in deglaciated soils. We explored the diversity and succession of the cbbL gene encoding the large subunit of form I RubisCO, a key CO2-fixing enzyme, using molecular methods in deglaciated soils along a 10-year deglaciation chronosequence on the Tibetan Plateau. Our results demonstrated that the abundance of all types of form I cbbL (IA/B, IC and ID) rapidly increased in young soils (0-2.5 years old) and kept stable in old soils. Soil total organic carbon (TOC) and total nitrogen (TN) gradually increased along the chronosequence and both demonstrated positive correlations with the abundance of bacteria and autotrophs, indicating that soil TOC and TN originated from autotrophs. Form IA/B autotrophs, affiliated with cyanobacteria, exhibited a substantially higher abundance than IC and ID. Cyanobacterial diversity and evenness increased in young soils (<6 years old) and then remained stable. Our findings suggest that cyabobacteria play an important role in accumulating TOC and TN in the deglaciated soils. PMID:27465079

  12. Gut microbial diversity studies on Ethiopian Blackhead Ogaden sheep with particular emphasis on rumen methanogenic archaea and total bacteria

    Ethiopia, which was designed to determine the rumen microbial composition of black head Ogaden sheep in comparison with highland sheep. The areas experience shorter rainy seasons (October/November and March/April) and the prolonged dry season. During the rainy season animals have access to fresh grass and water but during the dry periods animals hardly get grass pasture as the severe weather dries out the grass and what remains in the grazing field is a highly fibrous and lignified material. During the dry periods animals are usually compelled to survive on the scarcely available thorny trees and shrubs among which Acacias and Cactus are the most prominent. A total of 44 rumen fluid samples were collected both in dry and rainy seasons and kept at -80 deg C until processed and finally DNA was extracted. Also rumen samples were collected from five highland sheep (from sheep of the institute) for comparison. The randomly selected four samples (two collected in dry season, one collected in rainy season and one highland sheep samples) were tested with real time PCR against total bacteria, protozoa, anaerobic fungi, F. succinogenes, R. flavefaciens and methanogens. The study indicated that the population of methanogenes of black head Ogaden sheep showed that 12.6 to 23.58 fold lower and also R. flavifaciens 6.4 to 10.12 fold lower than highland sheep. The population of rumen microbes of Black head Ogaden sheep samples collected during rainy season were generally much lower than highland sheep (61.3 to 95.8% less), while anaerobi fungi of Blackhead Ogaden sheep samples collected during dry season was exceptionally 117 to 311 % higher than highland sheep. Generally this study indicated that Blackhead Ogaden sheep has low rumen microbial population including methanogens

  13. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates.

    Sonnenburg, Erica D; Sonnenburg, Justin L

    2014-11-01

    The gut microbiota of a healthy person may not be equivalent to a healthy microbiota. It is possible that the Western microbiota is actually dysbiotic and predisposes individuals to a variety of diseases. The asymmetric plasticity between the relatively stable human genome and the more malleable gut microbiome suggests that incompatibilities between the two could rapidly arise. The Western lifestyle, which includes a diet low in microbiota-accessible carbohydrates (MACs), has selected for a microbiota with altered membership and functionality compared to those of groups living traditional lifestyles. Interactions between resident microbes and host leading to immune dysregulation may explain several diseases that share inflammation as a common basis. The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. Studies focused on modern and traditional societies, combined with animal models, are needed to characterize the connection between diet, microbiota composition, and function. Differentiating between an optimal microbiota, one that increases disease risk, and one that is causative or potentiates disease will be required to further understand both the etiology and possible treatments for health problems related to microbiota dysbiosis. PMID:25156449

  14. The gut as reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant.

    Lisbeth E de Vries

    Full Text Available The microbiota in the human gastrointestinal tract (GIT is highly exposed to antibiotics, and may be an important reservoir of resistant strains and transferable resistance genes. Maternal GIT strains can be transmitted to the offspring, and resistances could be acquired from birth. This is a case study using a metagenomic approach to determine the diversity of microorganisms conferring tetracycline resistance (Tc(r in the guts of a healthy mother-infant pair one month after childbirth, and to investigate the potential for horizontal transfer and maternal transmission of Tc(r genes. Fecal fosmid libraries were functionally screened for Tc(r, and further PCR-screened for specific Tc(r genes. Tc(r fosmid inserts were sequenced at both ends to establish bacterial diversity. Mother and infant libraries contained Tc(r, although encoded by different genes and organisms. Tc(r organisms in the mother consisted mainly of Firmicutes and Bacteroidetes, and the main gene detected was tet(O, although tet(W and tet(X were also found. Identical Tc(r gene sequences were present in different bacterial families and even phyla, which may indicate horizontal transfer within the maternal GIT. In the infant library, Tc(r was present exclusively in streptococci carrying tet(M, tet(L and erm(T within a novel composite transposon, Tn6079. This transposon belongs to a family of broad host range conjugative elements, implying a potential for the joint spread of tetracycline and erythromycin resistance within the infant's gut. In addition, although not found in the infant metagenomic library, tet(O and tet(W could be detected in the uncloned DNA purified from the infant fecal sample. This is the first study to reveal the diversity of Tc(r bacteria in the human gut, to detect a likely transmission of antibiotic resistance from mother to infant GITs and to indicate the possible occurrence of gene transfers among distantly related bacteria coinhabiting the GIT of the same

  15. Comparative microbial diversity and redox environments of black shale and stromatolite facies in the Mesoproterozoic Xiamaling Formation

    Luo, Genming; Hallmann, Christian; Xie, Shucheng; Ruan, Xiaoyan; Summons, Roger E.

    2015-02-01

    The composition of microbial communities and their relationship to ocean redox structure in the Precambrian are topics of continuing interest in geobiology. Our knowledge of organismic diversity and environmental conditions during this time are mostly based on fragmentary paleontological and geochemical records and might be skewed accordingly. In North China the Xiamaling Formation (∼1.37 Ga) is characterized by black shales of relatively low thermal maturity (Tmax is ∼445 °C) and has been identified as a potential petroleum source rock. To date, however, the biological sources of the organic matter and the environmental conditions prevalent during the deposition of these sediments remain unclear. In this study we analyzed the hydrocarbon biomarker compositions of the Xiamaling Formation shales and a superjacent stromatolitic carbonate in order to shed light on the microbial diversity in the sedimentary environments they represent. The hydrocarbons extracted from both sediments are dominated by low-molecular-weight n-alkanes with a maximum at C15-18, suggesting that bacteria and/or algae were primary biotic precursors. Our inability to detect steranes in bitumen I, and only traces of rearranged steranes in bitumen II of black shales, indicates that modern eukaryotic algae were either ecologically insignificant or not preserved due to a taphonomic bias. The high relative concentration of hopanes and diahopanes ranging from C27 to C35, as well as monomethylalkanes, suggests that cyanobacteria may have been the dominant primary producers and could have contributed to the biologically available nitrogen pool through N2-fixation. This observation is supported by the low nitrogen isotopic composition of the kerogens. Even though all facies zones appear to have been anoxic but not sulfidic on the basis of biomarker ratios and trace metals, subtle but distinct molecular differences are observed between the stromatolite and the black shales, which can be attributed to

  16. Community Structure and Function of High-temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

    William P. Inskeep

    2013-06-01

    Full Text Available Six phototrophic microbial mat communities from different geothermal springs (YNP were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average~ 53 Mbp/site were subjected to multiple taxonomic, phylogenetic and functional analyses. All methods, including G+C content distribution, MEGAN analyses and oligonucleotide frequency-based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7 and Fischerella-like populations at White Creek (WC_6. Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp. were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae, and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria population from Bath Lake Vista Annex (BLVA_20. Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes; however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional

  17. Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity.

    Frederiek-Maarten Kerckhof

    Full Text Available The use of mixed microbial communities (microbiomes for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA. Microbiomes were selected based upon relevance towards applications: (1 a methanotrophic co-culture (MOB, with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2 an oxygen limited autotrophic nitrification/denitrification (OLAND biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3 fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB and anaerobic AOB (AnAOB, anammox in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO and DMSO plus trehalose and tryptic soy broth (DMSO+TT] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.

  18. Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica.

    de la Torre, José R; Goebel, Brett M; Friedmann, E Imre; Pace, Norman R

    2003-07-01

    In the McMurdo Dry Valleys of Antarctica, microorganisms colonize the pore spaces of exposed rocks and are thereby protected from the desiccating environmental conditions on the surface. These cryptoendolithic communities have received attention in microscopy and culture-based studies but have not been examined by molecular approaches. We surveyed the microbial biodiversity of selected cryptoendolithic communities by analyzing clone libraries of rRNA genes amplified from environmental DNA. Over 1,100 individual clones from two types of cryptoendolithic communities, cyanobacterium dominated and lichen dominated, were analyzed. Clones fell into 51 relatedness groups (phylotypes) with > or =98% rRNA sequence identity (46 bacterial and 5 eucaryal). No representatives of Archaea were detected. No phylotypes were shared between the two classes of endolithic communities studied. Clone libraries based on both types of communities were dominated by a relatively small number of phylotypes that, because of their relative abundance, presumably represent the main primary producers in these communities. In the lichen-dominated community, three rRNA sequences, from a fungus, a green alga, and a chloroplast, of the types known to be associated with lichens, accounted for over 70% of the clones. This high abundance confirms the dominance of lichens in this community. In contrast, analysis of the supposedly cyanobacterium-dominated community indicated, in addition to cyanobacteria, at least two unsuspected organisms that, because of their abundance, may play important roles in the community. These included a member of the alpha subdivision of the Proteobacteria that potentially is capable of aerobic anoxygenic photosynthesis and a distant relative of Deinococcus that defines, along with other Deinococcus-related sequences from Antarctica, a new clade within the Thermus-Deinococcus bacterial phylogenetic division. PMID:12839754

  19. Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking.

    Gayle C McGhee

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPRs comprise a family of short DNA repeat sequences that are separated by non repetitive spacer sequences and, in combination with a suite of Cas proteins, are thought to function as an adaptive immune system against invading DNA. The number of CRISPR arrays in a bacterial chromosome is variable, and the content of each array can differ in both repeat number and in the presence or absence of specific spacers. We utilized a comparative sequence analysis of CRISPR arrays of the plant pathogen Erwinia amylovora to uncover previously unknown genetic diversity in this species. A total of 85 E. amylovora strains varying in geographic isolation (North America, Europe, New Zealand, and the Middle East, host range, plasmid content, and streptomycin sensitivity/resistance were evaluated for CRISPR array number and spacer variability. From these strains, 588 unique spacers were identified in the three CRISPR arrays present in E. amylovora, and these arrays could be categorized into 20, 17, and 2 patterns types, respectively. Analysis of the relatedness of spacer content differentiated most apple and pear strains isolated in the eastern U.S. from western U.S. strains. In addition, we identified North American strains that shared CRISPR genotypes with strains isolated on other continents. E. amylovora strains from Rubus and Indian hawthorn contained mostly unique spacers compared to apple and pear strains, while strains from loquat shared 79% of spacers with apple and pear strains. Approximately 23% of the spacers matched known sequences, with 16% targeting plasmids and 5% targeting bacteriophage. The plasmid pEU30, isolated in E. amylovora strains from the western U.S., was targeted by 55 spacers. Lastly, we used spacer patterns and content to determine that streptomycin-resistant strains of E. amylovora from Michigan were low in diversity and matched corresponding streptomycin-sensitive strains

  20. Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking.

    McGhee, Gayle C; Sundin, George W

    2012-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) comprise a family of short DNA repeat sequences that are separated by non repetitive spacer sequences and, in combination with a suite of Cas proteins, are thought to function as an adaptive immune system against invading DNA. The number of CRISPR arrays in a bacterial chromosome is variable, and the content of each array can differ in both repeat number and in the presence or absence of specific spacers. We utilized a comparative sequence analysis of CRISPR arrays of the plant pathogen Erwinia amylovora to uncover previously unknown genetic diversity in this species. A total of 85 E. amylovora strains varying in geographic isolation (North America, Europe, New Zealand, and the Middle East), host range, plasmid content, and streptomycin sensitivity/resistance were evaluated for CRISPR array number and spacer variability. From these strains, 588 unique spacers were identified in the three CRISPR arrays present in E. amylovora, and these arrays could be categorized into 20, 17, and 2 patterns types, respectively. Analysis of the relatedness of spacer content differentiated most apple and pear strains isolated in the eastern U.S. from western U.S. strains. In addition, we identified North American strains that shared CRISPR genotypes with strains isolated on other continents. E. amylovora strains from Rubus and Indian hawthorn contained mostly unique spacers compared to apple and pear strains, while strains from loquat shared 79% of spacers with apple and pear strains. Approximately 23% of the spacers matched known sequences, with 16% targeting plasmids and 5% targeting bacteriophage. The plasmid pEU30, isolated in E. amylovora strains from the western U.S., was targeted by 55 spacers. Lastly, we used spacer patterns and content to determine that streptomycin-resistant strains of E. amylovora from Michigan were low in diversity and matched corresponding streptomycin-sensitive strains from the

  1. Microbial diversity in Paris polyphylla var. yunnanensis rhizomes of varying ages.

    Yang, Y; Yang, S C; Zhao, J; Udikeri, S; Liu, T

    2015-01-01

    Endophyte microorganisms live inside plants without causing them any apparent damage. Recently, endophytic microorganisms have attracted attention because they can produce bioactive compounds of biotechnological interest. The endophytic microorganisms in Paris polyphylla var. yunnanensis (Liliaceae) - a species used since antiquity in traditional Chinese medicine - are under scrutiny because they may be responsible for producing the bioactive metabolites associated with the plant. The levels of bioactive metabolites in the rhizomes of P. polyphylla increase with rhizome age. To elucidate the roles played by endophytes in the accumulation of bioactive metabolites, we investigated the community structure and diversity of the endophytic microorganisms in P. polyphylla rhizomes of different ages (4, 6, and 8 years) using 16S rRNA and internal transcribed spacer (ITS) sequence analysis. 16S rDNA amplicon pyrosequencing revealed that the number of operational taxonomic units was lower in the 8-year-old samples than in the other samples. A total of 28 phyla were observed in the P. polyphylla samples and the predominant bacteria were of the Cyanobacteria and Proteobacteria phyla. Moreover, the percentage of Cyanobacteria increased with rhizome age. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes; some classes were more prevalent in the 8-year-old rhizomes than in younger rhizomes, indicating the importance in secondary metabolism in older rhizomes. Our study showed that endophyte microorganism diversity and prevalence depend on P. polyphylla rhizome age. There was also an indication that some endophyte microorganisms contribute to the higher saponin content in older P. polyphylla specimens. PMID:26782406

  2. Risk management tools and the case study Brassica napus: evaluating possible effects of genetically modified plants on soil microbial diversity.

    Canfora, Loredana; Sbrana, Cristiana; Avio, Luciano; Felici, Barbara; Scatà, Maria Carmela; Neri, Ulderico; Benedetti, Anna

    2014-09-15

    The cultivation of GMPs in Europe raises many questions about the environmental risks, in particular about their ecological impact on non-target organisms and on soil properties. The aim of a multidisciplinary group engaged in a LIFE+project (MAN-GMP-ITA) was to validate and improve an existing environmental risk assessment (ERA) methodology on GMPs within the European legislative framework on GMOs. Given the impossibility of evaluating GMO impact directly, as GMPs are banned in Italy, GMPs have not been used at any stage of the project. The project thus specifically focused on the conditions for the implementation of ERA in different areas of Italy, with an emphasis on some sensitive and protected areas located in the North, Centre, and South of the country, in order to lay the necessary baseline for evaluating the possible effects of a GMP on soil communities. Our sub-group carried out soil analyses in order to obtain soil health and fertility indicators to be used as baselines in the ERA model. Using various methods of chemical, biochemical, functional and genetic analysis, our study assessed the changes in diversity and functionality of bacterial populations, and arbuscular mycorrhizal fungi. The results show that plant identity and growth, soil characteristics, and field site climatic parameters are key factors in contributing to variation in microbial community structure and diversity, thus validating our methodological approach. Our project has come to the conclusion that the uneven composition and biological-agronomical quality of soils need to be taken into consideration in a risk analysis within the framework of ERA for the release of genetically modified plants. PMID:25014185

  3. Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility

    Nieto Pamela A

    2008-11-01

    Full Text Available Abstract Background Iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. Information on iron management mechanisms is available for organisms living at circumneutral pH. However, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 1018 times the concentration found in pH neutral environments. This study was motivated by the need to fill this lacuna in knowledge. An understanding of how microorganisms thrive in acidic ecosystems with high iron loads requires a comprehensive investigation of the strategies to acquire iron and to coordinate this acquisition with utilization, storage and oxidation of iron through metal responsive regulation. In silico prediction of iron management genes and Fur regulation was carried out for three Acidithiobacilli: Acidithiobacillus ferrooxidans (iron and sulfur oxidizer A. thiooxidans and A. caldus (sulfur oxidizers that can live between pH 1 and pH 5 and for three strict iron oxidizers of the Leptospirillum genus that live at pH 1 or below. Results Acidithiobacilli have predicted FeoB-like Fe(II and Nramp-like Fe(II-Mn(II transporters. They also have 14 different TonB dependent ferri-siderophore transporters of diverse siderophore affinity, although they do not produce classical siderophores. Instead they have predicted novel mechanisms for dicitrate synthesis and possibly also for phosphate-chelation mediated iron uptake. It is hypothesized that the unexpectedly large number and diversity of Fe(III-uptake systems confers versatility to this group of acidophiles, especially in higher pH environments (pH 4–5 where soluble iron may not be abundant. In contrast, Leptospirilla have only a FtrI-Fet3P-like permease and three TonB dependent ferri-dicitrate siderophore systems. This paucity of iron

  4. Stability Properties of Network Diversity Multiple Access with Multiple-Antenna Reception and Imperfect Collision Multiplicity Estimation

    Ramiro Samano-Robles

    2013-01-01

    Full Text Available In NDMA (network diversity multiple access, protocol-controlled retransmissions are used to create a virtual MIMO (multiple-input multiple-output system, where collisions can be resolved via source separation. By using this retransmission diversity approach for collision resolution, NDMA is the family of random access protocols with the highest potential throughput. However, several issues remain open today in the modeling and design of this type of protocol, particularly in terms of dynamic stable performance and backlog delay. This paper attempts to partially fill this gap by proposing a Markov model for the study of the dynamic-stable performance of a symmetrical and non-blind NDMA protocol assisted by a multiple-antenna receiver. The model is useful in the study of stability aspects in terms of the backlog-user distribution and average backlog delay. It also allows for the investigation of the different states of the system and the transition probabilities between them. Unlike previous works, the proposed approach considers the imperfect estimation of the collision multiplicity, which is a crucial process to the performance of NDMA. The results suggest that NDMA improves not only the throughput performance over previous solutions, but also the average number of backlogged users, the average backlog delay and, in general, the stability of random access protocols. It is also shown that when multiuser detection conditions degrade, ALOHA-type backlog retransmission becomes relevant to the stable operation of NDMA.

  5. Microbial diversity in a bagasse-based compost prepared for the production of Agaricus brasiliensis

    Silva, Cristina Ferreira; Azevedo, Raquel Santos; Braga, Claudia; da Silva, Romildo; Dias, Eustáquio Souza; Schwan, Rosane Freitas

    2009-01-01

    Edible mushrooms are renowned for their nutritional and medicinal properties and are thus of considerable commercial importance. Mushroom production depends on the chemical composition of the basic substrates and additional supplements employed in the compost as well as on the method of composting. In order to minimise the cost of mushroom production, considerable interest has been shown in the use of agro-industrial residues in the preparation of alternative compost mixtures. However, the interaction of the natural microbiota present in agricultural residues during the composting process greatly influences the subsequent colonisation by the mushroom. The aim of the present study was to isolate and identify the microbiota present in a sugar cane bagasse and coast-cross straw compost prepared for the production of Agaricus brasilienses. Composting lasted for 14 days, during which time the substrates and additives were mixed every 2 days, and this was followed by a two-step steam pasteurisation (55 - 65°C; 15 h each step). Bacteria, (mainly Bacillus and Paenibacillus spp. and members of the Enterobacteriaceae) were the predominant micro-organisms present throughout the composting process with an average population density of 3 x 108 CFU/g. Actinomycetes, and especially members of the genus Streptomyces, were well represented with a population density of 2 - 3 x 108 CFU/g. The filamentous fungi, however, exhibited much lower population densities and were less diverse than the other micro-organisms, although Aspergillus fumigatus was present during the whole composting process and after pasteurisation. PMID:24031404

  6. Investigation of the microbial diversity of an extremely acidic, metal-rich water body (Lake Robule, Bor, Serbia

    Stanković Srđan

    2014-01-01

    Full Text Available An investigation of the microbial diversity of the extremely acidic, metal-rich Lake Robule was carried out using culture-dependant and culture-independent (T-RFLP methods, and the ability of indigenous bacteria from the lake water to leach copper from a mineral concentrate was tested. T-RFLP analysis revealed that the dominant bacteria in lake water samples were the obligate heterotroph Acidiphilium cryptum (~50% of total bacteria and the iron-oxidizing autotroph Leptospirillum ferrooxidans (~40% The iron/sulfur-oxidizing autotroph Acidithiobacillus ferrooxidans had been reported to be the most abundant bacteria in the lake in an earlier study by other authors, but it was not detected in the present study using T-RFLP. Although it was isolated on solid media and detected in enrichment (bioleaching cultures. The presence of the two bacterial species detected by T-RFLP (L. ferrooxidans and A. cryptum was also confirmed by cultivation on solid media. The presence and relative abundance of bacteria inhabiting Lake Robule was explained by the physiological characteristics of the bacteria and the physico-chemical characteristics of the lake water. [Projekat Ministarstva nauke Republike Srbije, br. 176016 i br.173048

  7. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  8. Fatty acids as a tool to understand microbial diversity and their role in food webs of Mediterranean temporary ponds.

    de Carvalho, Carla C C R; Caramujo, Maria-José

    2014-01-01

    Temporary Mediterranean ponds are complex ecosystems which support a high diversity of organisms that include heterotrophic microorganisms, algae, crustaceans, amphibians and higher plants, and have the potential to supply food and a resting place to migratory birds. The role of heterotrophs at the base of the food web in providing energy to the higher trophic levels was studied in temporary ponds in Central and Southern Portugal. The relative quantification of the hetero and autotrophic biomass at the base of the food web in each pond was derived from the polar fatty acid (PLFA) composition of seston through the application of the matrix factorization program CHEMTAX that used specific PLFA and their relative proportion as markers for e.g., classes of bacteria, algae and fungi. The species composition of the culturable microbial communities was identified through their fatty acid profiles. The biomass in the lower trophic level of some ponds presented an even proportion of auto to heterotrophic organisms whilst either bacteria or algae dominated in others. In a selected subset of ponds, the incorporation of bacterial fatty acids was observed to occur in potentially herbivorous zooplankton crustacean. Zooplankton consumed and incorporated bacterial fatty acids into their body tissues, including into their phospholipids, which indicates that energy of heterotrophic origin contributes to the aquatic food webs of temporary ponds. PMID:24786844

  9. Fatty Acids as a Tool to Understand Microbial Diversity and Their Role in Food Webs of Mediterranean Temporary Ponds

    Carla C. C. R. de Carvalho

    2014-04-01

    Full Text Available Temporary Mediterranean ponds are complex ecosystems which support a high diversity of organisms that include heterotrophic microorganisms, algae, crustaceans, amphibians and higher plants, and have the potential to supply food and a resting place to migratory birds. The role of heterotrophs at the base of the food web in providing energy to the higher trophic levels was studied in temporary ponds in Central and Southern Portugal. The relative quantification of the hetero and autotrophic biomass at the base of the food web in each pond was derived from the polar fatty acid (PLFA composition of seston through the application of the matrix factorization program CHEMTAX that used specific PLFA and their relative proportion as markers for e.g., classes of bacteria, algae and fungi. The species composition of the culturable microbial communities was identified through their fatty acid profiles. The biomass in the lower trophic level of some ponds presented an even proportion of auto to heterotrophic organisms whilst either bacteria or algae dominated in others. In a selected subset of ponds, the incorporation of bacterial fatty acids was observed to occur in potentially herbivorous zooplankton crustacean. Zooplankton consumed and incorporated bacterial fatty acids into their body tissues, including into their phospholipids, which indicates that energy of heterotrophic origin contributes to the aquatic food webs of temporary ponds.

  10. POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

    Cannon, Ethalinda K. S.; Birkett, Scott M.; Braun, Bremen L.; Kodavali, Sateesh; Jennewein, Douglas M.; Yilmaz, Alper; Antonescu, Valentin; Antonescu, Corina; Harper, Lisa C.; Gardiner, Jack M.; Schaeffer, Mary L.; Campbell, Darwin A.; Andorf, Carson M.; Andorf, Destri; Lisch, Damon

    2011-01-01

    The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics pro...

  11. Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel

    Qin, Huibin; Sun, Qinghui; Pan, Xuewei; Qiao, Zhijun; Yang, Hongjiang

    2016-01-01

    Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely.

  12. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. PMID

  13. Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel.

    Qin, Huibin; Sun, Qinghui; Pan, Xuewei; Qiao, Zhijun; Yang, Hongjiang

    2016-01-01

    Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely. PMID:27610102

  14. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    Thompson, Luke R

    2013-05-11

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. 2013 The

  15. Study of the Microbial Diversity of a Newly Discovered East Antarctic Freshwater Lake, L27C, and of a Perennially Ice-Covered Lake Untersee

    Huang, Jonathan P.; Hoover, Richard B.; Andersen, Dale; Bej, Asim K.

    2010-01-01

    The microbial communities that reside within freshwater lakes of Schirmacher and Untersee Oases in East Antarctica must cope with extreme conditions that may include cold temperature, annual freeze-thaw cycles, exposure to UV radiation, especially during the austral summer months, low light beneath thick ice-cover, followed by seasonal darkness. The objective of this study was to assess the microbial biodiversity and distribution from samples taken from two freshwater lakes (L27C and Lake Untersee) that were collected during the Tawani 2008 International Antarctic Expedition that conducted research in this region of Antarctica. L27C is a small, previously unreported lake residing 2 km WNW of Maitri Station at Schirmacher Oasis. Biodiversity and distribution of microorganisms within the lake were studied using both culture-independent and culture-dependent methodologies based upon the analysis of eubacterial 16S rRNA gene sequences. Lake Untersee, a perennially ice-covered, ultra-oligotrophic, lake in the Otto-von-Gruber-Gebirge (Gruber Mountains) of central Dronning Maud Land was also sampled and the microbial diversity was analyzed by eubacterial 16S rRNA gene sequences derived from pure cultures. Direct culturing of water samples from each lake on separate R2A growth medium exhibited a variety of microorganisms including: Janthinobacterium, Hymenobacter, Sphingamonas, Subtercola, Deinococcus, Arthrobacter, Flavobacterium, Polaromonas, Rhodoferax and Duganella. The evaluation of samples from L27C through culture-independent methodology identified a rich microbial diversity consisting of six different phyla of bacteria. The culture-independent analysis also displayed the majority of bacteria (56%) belonged to the Class gamma-proteobacteria within the phylum Proteobacteria. Within the Class gamma-proteobacteria, Acinetobacter dominated (48%) the total microbial load. Overall, L27C exhibited 7 different phyla of bacteria and 20 different genera. Statistical analysis

  16. Microbial Diversity and Ecology in the Interfaces of the Deep-sea Anoxic Brine Pools in the Red Sea

    Hikmawan, Tyas I.

    2015-05-01

    Deep-sea anoxic brine pools are one of the most extreme ecosystems on Earth, which are characterized by drastic changes in salinity, temperature, and oxygen concentration. The interface between the brine and overlaying seawater represents a boundary of oxic-anoxic layer and a steep gradient of redox potential that would initiate favorable conditions for divergent metabolic activities, mainly methanogenesis and sulfate reduction. This study aimed to investigate the diversity of Bacteria, particularly sulfate-reducing communities, and their ecological roles in the interfaces of five geochemically distinct brine pools in the Red Sea. Performing a comprehensive study would enable us to understand the significant role of the microbial groups in local geochemical cycles. Therefore, we combined culture-dependent approach and molecular methods, such as 454 pyrosequencing of 16S rRNA gene, phylogenetic analysis of functional marker gene encoding for the alpha subunits of dissimilatory sulfite reductase (dsrA), and single-cell genomic analysis to address these issues. Community analysis based on 16S rRNA gene sequences demonstrated high bacterial diversity and domination of Bacteria over Archaea in most locations. In the hot and multilayered Atlantis II Deep, the bacterial communities were stratified and hardly overlapped. Meanwhile in the colder brine pools, sulfatereducing Deltaproteobacteria were the most prominent bacterial groups inhabiting the interfaces. Corresponding to the bacterial community profile, the analysis of dsrA gene sequences revealed collectively high diversity of sulfate-reducing communities. Desulfatiglans-like dsrA was the prevalent group and conserved across the Red Sea brine pools. In addition to the molecular studies, more than thirty bacterial strains were successfully isolated and remarkably were found to be cytotoxic against the cancer cell lines. However, none of them were sulfate reducers. Thus, a single-cell genomic analysis was used to study

  17. PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp ( Marsupenaeus japonicus)

    Liu, Huaide; Liu, Mei; Wang, Baojie; Jiang, Keyong; Jiang, Shan); Sun, Shujuan; Wang, Lei

    2010-07-01

    In this study, the intestinal microbiota of kuruma shrimp ( Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.

  18. Microbial diversity and metal pollution from a platinum mine tailings dam in the North-West Province (RSA) / by Molemi Evelyn Rauwane.

    Rauwane, Molemi Evelyn

    2008-01-01

    The aim of this study was to determine the effects of the heavy metal pollution on microbial diversity along the gradient from a platinum mine tailings dam using culture-dependent (plating methods) and molecular methods. Tailings and soil samples were collected from seven sites (6 samples per site) at increasing distances from the tailings dam. Samples were collected over a two year period and included two rainy and two dry periods. Concentrations of various heavy metals were determi...

  19. Microbial diversity and Its relationship to physicochemical characteristics of the water in two extreme acidic pit lakes from the Iberian Pyrite Belt (SW Spain)

    Santofimia, Esther; González-Toril, Elena; López-Pamo, Enrique; Gomariz, María; Amils, Ricardo; Aguilera, Ángeles

    2013-01-01

    The Iberian Pyrite Belt (IPB) hosts one of the world's largest accumulations of acidic mine wastes and pit lakes. The mineralogical and textural characteristics of the IPB ores have favored the oxidation and dissolution of metallic sulfides, mainly pyrite, and the subsequent formation of acidic mining drainages. This work reports the physical properties, hydrogeochemical characteristics, and microbial diversity of two pit lakes located in the IPB. Both pit lakes are acidic and showed high con...

  20. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

    Guo, Shaogui; Zhang, Jianguo; Sun, Honghe;

    2013-01-01

    evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and......Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an...

  1. Genetic diversity of wild sunflower (Helianthus sp. accessions with different tolerance to mid-stalk white rot

    Miladinović Dragana

    2014-01-01

    Full Text Available Random amplified polymorphic DNA (RAPD markers were used to detect polymorphism among accessions of wild sunflower species Hеlianthus maximiliani, Helianthus tuberosus, Helianthus mollis and Helianthus rigidus with different tolerance to mid-stalk white rot and selection of potential markers for different levels of tolerance to this disease. Estimates of genetic variation showed that genetic diversity was equally distributed between Helianthus species and within them. Cluster analysis corresponded to the phylogenetic relations within the genus Helianthus. The results obtained by principal coordinates analysis (PCoA, where the first two principal coordinates accounted for 83.7% of total variation, perfectly coincided with the results of cluster analysis. Contingency coefficient significance test showed that most of the used primers generated bands associated with some level of tolerance or susceptibility to mid- stalk white rot. Furthermore, contingency analysis showed that primer C12 generated bands associated with resistance (100% to mid-stalk white rot both in H. mollis and in all accessions, while primer X18 generated bands significantly associated with high tolerance (75% in H. rigidus, H. mollis as well as in all tested accessions. The C15-600 bp locus was found to be significantly associated with high tolerance (75% in all accessions, and medium tolerance (50% in H. mollis. [Projekat Ministarstva nauke Republike Srbije, br. TR 31025

  2. Effects of fumigants on microbial diversity and persistence of E. coli O15:H7 in contrasting soil microcosms

    Persistence of E. coli O157 in the environment is a serious public health concern. However, little is known about the persistence of this pathogen after exposure to chemical compounds like fumigants in the environment. In this study, the persistence behavior of pathogenic E. coli O157:H7 was investigated after fumigation with methyl bromide (MeBr; CH3Br) and methyl iodide (MeI, iodomethane; CH3I) in soil microcosms under laboratory conditions. Our goal was to assess changes in soil microbial community structure and persistence of E. coli O157:H7 in microcosm soils after fumigation. PCR was used to amplify 16S rRNA genes from total bacterial community composition, and the products were subjected to denaturing gradient gel electrophoresis (DGGE). Microbial diversity as determined by DGGE was significantly higher in clay soil than sandy soil. Real-time PCR and plate counts were used to quantify the survival of E. coli O157:H7 in the two soils after fumigation with MeBr and MeI. The survival of the pathogen was higher in the non fumigated controls than the fumigated treatments when determined using plate counts. These results were confirmed by real time PCR analysis targeting the stx1, stx2, and the eae genes. E. coli O157:H7 survived for about 35 days when determined using the plate count method but continued to be detected at about the detection limit of 102 by real time PCR for more than 86 days. Our results showed that there was a fast inactivation of the pathogen during the first 35 days. After this period, a small proportion of the pathogen continued to survive in the soil microcosms. Subsequent enrichment of soil samples and immunomagnetic separation revealed the continuous presence of viable cells after 86 days of incubation. The data presented contribute to a better understanding of the behavior of E. coli O157:H7 in soil, and showed the need for more investigation of the role of dormant cells in soil that may be a source for recontamination of the environment.

  3. Characterization of bacterial diversity associated with microbial mats, gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava, Salar de Atacama, Chile.

    Farías, M E; Contreras, M; Rasuk, M C; Kurth, D; Flores, M R; Poiré, D G; Novoa, F; Visscher, P T

    2014-03-01

    In this paper, we report the presence of sedimentary microbial ecosystems in wetlands of the Salar de Atacama. These laminated systems, which bind, trap and precipitate mineral include: microbial mats at Laguna Tebenquiche and Laguna La Brava, gypsum domes at Tebenquiche and carbonate microbialites at La Brava. Microbial diversity and key biogeochemical characteristics of both lakes (La Brava and Tebenquiche) and their various microbial ecosystems (non-lithifying mats, flat and domal microbialites) were determined. The composition and abundance of minerals ranged from trapped and bound halite in organic-rich non-lithifying mats to aragonite-dominated lithified flat microbialites and gypsum in lithified domal structures. Pyrosequencing of the V4 region of the 16s rDNA gene showed that Proteobacteria comprised a major phylum in all of the microbial ecosystems studied, with a marked lower abundance in the non-lithifying mats. A higher proportion of Bacteroidetes was present in Tebenquiche sediments compared to La Brava samples. The concentration of pigments, particularly that of Chlorophyll a, was higher in the Tebenquiche than in La Brava. Pigments typically associated with anoxygenic phototrophic bacteria were present in lower amounts. Organic-rich, non-lithifying microbial mats frequently formed snake-like, bulbous structures due to gas accumulation underneath the mat. We hypothesize that the lithified microbialites might have developed from these snake-like microbial mats following mineral precipitation in the surface layer, producing domes with endoevaporitic communities in Tebenquiche and carbonate platforms in La Brava. Whereas the potential role of microbes in carbonate platforms is well established, the contribution of endoevaporitic microbes to formation of gypsum domes needs further investigation. PMID:24442191

  4. Microbial Profiling Of Cyanobacteria From VIT Lake

    Swati Singh

    2015-08-01

    Full Text Available The application of molecular biological methods to study the diversity and ecology of micro-organisms in natural environments has been practice in mid-1980. The aim of our research is to access the diversity composition and functioning of complex microbial community found in VIT Lake. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA or RNA level which is useful for constructing genetically modified microbes by recombinant DNA technology for reputed use in the environment. In this research first we will isolate cyanobacteria in lab using conventional methods like broth culture and spread plate method then we will analyze their morphology using various staining methods and DNA and protein composition using electrophoresis method. The applications of community profiling approaches will advance our understanding of the functional role of microbial diversity in VIT Lake controls on microbial community composition.

  5. Language Accessibility in the Classroom: How UDL Can Promote Success for Linguistically Diverse Learners

    Rice Doran, Patricia

    2015-01-01

    This article provides an overview of the Universal Design for Learning (UDL) framework, which is based on brain-structure research and which incorporates multiple means of instruction, action and expression, and engagement. The article describes the relevance of this framework to linguistically diverse and culturally and linguistically diverse…

  6. South Africa: Distance Higher Education Policies for Access, Social Equity, Quality, and Social and Economic Responsiveness in a Context of the Diversity of Provision

    Badat, Saleem

    2005-01-01

    The principal concern of this paper is the implication of the increasing diversity of higher education provision in South Africa for equity of access and opportunity for historically disadvantaged social groups, high-quality provision, and social and economic responsiveness in distance higher education. This diversity is signalled by a variety of…

  7. Mineral, flavonoid, and fatty acid concentrations in ten diverse Lablab purpureus (L.) sweet accessions.

    Seeds of Hyacinth bean (Lablab purpureus [L.]) Sweet containing high concentrations of minerals, flavonoids and fatty acids may provide government agencies with a nutrient-dense and health-beneficial food for use in hunger stricken and nutrient deprived people. Seeds from ten hyacinth bean accession...

  8. Structural and functional diversity of microbial communities beneath the hydrothermal vent at the Iheya North field of the Mid-Okinawa Trough (IODP Expedition 331)

    Yanagawa, K.; Nunoura, T.; Kawagucci, S.; Hirai, M.; Sunamura, M.; Breuker, A.; Brandt, L.; House, C. H.; McAllister, S. M.; Moyer, C. L.; Takai, K.

    2012-12-01

    Complex and diverse microbial communities in deep-sea hydrothermal fluids are apparently different from those in ambient seawater, some of which are predicted to migrate along hydrothermal vein from "subvent biosphere". Subseafloor environment just beneath active hydrothermal vent has been expected to be one of the most conceivable habitats for metabolically active and diverse microbial community. We conducted the scientific ocean drilling (IODP Expedition 331) for the Iheya North hydrothermal field in the Mid-Okinawa Trough in Sept. 2010, and collected core samples from the subseafloor biosphere beneath the hydrothermal vent. IODP Site C0014 was located 450 m east off the main hydrothermal vent. Temperature exceeded the limit of life at the depth of approximately 40 m below the seafloor. Both microscopy and quantitative PCR analyses successfully detected microbial populations in the shallower zone above 15 mbsf. However, the cultivation attempts of (hyper-)thermophiles were unsuccessful all over the depth. Culture-independent molecular biological experiments showed that microbial community composition distinctly changed with depth, possibly because of physicochemical conditions such as methane, sulfate and temperature. Microbial activities of methanogenesis and anaerobic methane oxidation were in accordance with the geochemical profiles of methane and sulfate. These results indicated the presence of functionally active subseafloor microbial communities but those were different from expected members in subvent biosphere. Site C0017 located 1.6 km east off the hydrothermal vent is a potential seawater recharge zone of the hydrothermal system, where seawater penetrates into the oceanic crust. The lithostratigraphy consists of characteristic coarse angular pumiceous gravel, lying above and below hemipelagic mud, in which high permeability may allow entrainment of seawater. As is the case with sedimentary subsurface environments, uncultivated archaeal groups were

  9. Evaluation of microbial diversity in sulfite-added and sulfite-free wine by culture-dependent and -independent methods.

    Takahashi, Masayuki; Ohta, Tami; Masaki, Kazuo; Mizuno, Akihiro; Goto-Yamamoto, Nami

    2014-05-01

    The difference in microbiota including non-lactic acid bacteria, non-acetic acid bacteria, and wild yeast during winemaking and in the end-products between sulfite-added and sulfite-free wine, was investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and a culture-dependent method. There were differences between the microorganisms detected by PCR-DGGE and those detected by the culture-dependent method, probably because of the selectivity of culture medium and the characteristics of PCR-based method. In both the red wine and white wine, the microbial diversity of the sulfite-added wine was lower than that of the sulfite-free wine during fermentation. Tatumella terrea was detected from the fermenting must by PCR-DGGE and by the culture-dependent method, even though sulfite inhibited its growth to some extent. We confirmed that the addition of sulfite plays an important role in winemaking by inhibiting the growth of unexpected microorganisms, but on the other hand, it was revealed that some microorganisms can survive and grow in sulfite-added fermenting must. We also analyzed 15 samples of commercial wines by the PCR-DGGE method and detected various microorganisms. Among them, Sphingomonas sp., Pseudozyma sp., Ochromonas sp. and Methylophilus sp. were found for the first time in wine as far as we know. We did not identify a specific microorganism that was detected only from wines without sulfite addition. Thus, the microbiota of end-products seemed to be influenced by other factors, such as filtration before bottling, the production equipment and the storage environment. PMID:24239025

  10. Assessment of morphological attributes of date palm accessions of diverse agro-ecological origin

    Sixteen Pakistani date palm cultivars from diverse origins were characterized morphologically to assess the similarity level, the overall point of polymorphism and important agronomic traits existing in the germplasm present in Pakistan. Forty two qualitative and quantitative features were explored and subjected to multivariate analyses. The results brought out important differences in phenotypic characters in all date palm cultivars. Principal component analysis (PCA) indicated that trunk length and diameter, total number of leaves, rachis length, leaflets length and width, number of leaflets per side, number of pinnae planes, length and grouping of spines were highly divergent. Similarly cluster analyses (CA) also revealed phenotypic diversity among date palm cultivars and, some close association or heterogeneity was also observed within cultivars of the same origin. (author)

  11. Access to genetic resources in indigenous peoples and the Convention on Biological Diversity

    Diana Rocío Bernal Camargo

    2013-01-01

    After the Convention on Biological Diversity a deepening debate is taking place concerning the protection of genetic resources and traditional knowledge of indigenous peoples, which involves a discussion about the application of biotechnology and its impact on the protection of life and environment, and an analysis of the participation of these in the process of developing strategies to protect their resources and traditional knowledge, which gives rise to legal pluralism from the development...

  12. Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis

    Rajesh, M. K.; Sabana, A. A.; Rachana, K. E.; Rahman, Shafeeq; Jerard, B. A.; Karun, Anitha

    2015-01-01

    Coconut (Cocos nucifera L.) is one of the important palms grown both as a homestead and plantation crop in countries and most island territories of tropical regions. Different DNA-based marker systems have been utilized to assess the extent of genetic diversity in coconut. Advances in genomics research have resulted in the development of novel gene-targeted markers. In the present study, we have used a simple and novel marker system, start codon targeted polymorphism (SCoT), for its evaluatio...

  13. On Low-Complexity Full-diversity Detection In Multi-User MIMO Multiple-Access Channels

    Ismail, Amr

    2014-01-28

    Multiple-input multiple-output (MIMO) techniques are becoming commonplace in recent wireless communication standards. This newly introduced dimension (i.e., space) can be efficiently used to mitigate the interference in the multi-user MIMO context. In this paper, we focus on the uplink of a MIMO multiple access channel (MAC) where perfect channel state information (CSI) is only available at the destination. We provide new sufficient conditions for a wide range of space-time block codes (STBC)s to achieve full-diversity under partial interference cancellation group decoding (PICGD) with or without successive interference cancellation (SIC) for completely blind users. Interference cancellation (IC) schemes for two and three users are then provided and shown to satisfy the full-diversity criteria. Beside the complexity reduction due to the fact that PICGD enables separate decoding of distinct users without sacrificing the diversity gain, further reduction of the decoding complexity may be obtained. In fact, thanks to the structure of the proposed schemes, the real and imaginary parts of each user\\'s symbols may be decoupled without any loss of performance. Our new IC scheme is shown to outperform recently proposed two-user IC scheme especially for high spectral efficiency while requiring significantly less decoding complexity.

  14. Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

    Yongcui Deng

    Full Text Available The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance, Actinobacteria (17.3% and Bacteroidetes (11% had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%. In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales. Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta and methanotrophs (mainly Methylocystis compared with the other two wetlands. Principal coordinate analysis (PCoA indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands o