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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

    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.

  11. 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

  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. 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

  14. 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...

  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. 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

  18. 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

  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. 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.

  12. 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

  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. 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....

  14. 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

  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. 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.

  1. 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.

  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 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

  18. 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.

  19. 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

  20. 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.

  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. 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...

  6. 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

  7. 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...

  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. 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.

  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. 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.

  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. 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

  7. 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.

  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. 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

  11. 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

  12. 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

  13. 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.

  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. 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...

  17. 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

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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

  4. 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'...

  5. 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...

  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. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  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. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  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. 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

  5. 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.

  6. 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

  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. 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.

  9. 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.

  10. 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%....

  11. 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

  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: 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.

  20. 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

  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. 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...

  4. 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

  5. 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...

  6. 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

  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. 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.

  11. 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

  12. 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

  13. 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.

  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. 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

  17. 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...

  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