WorldWideScience

Sample records for bacterial community diversity

  1. Bacterial Community Diversity Harboured by Interacting Species.

    Directory of Open Access Journals (Sweden)

    Mikaël Bili

    Full Text Available All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing. Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

  2. Bacterial community diversity in municipal waste landfill sites.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Tang, Wei; Lei, Yu

    2015-09-01

    Little is known about the bacterial diversity of landfills and how environmental factors impact the diversity. In this study, PCR-based 454 pyrosequencing was used to investigate the bacterial communities of ten landfill leachate samples from five landfill sites in China. A total of 137 K useable sequences from the V3-V6 regions of the 16S rRNA gene were retrieved from 205 K reads. These sequences revealed the presence of a large number of operational taxonomic units (OTUs) in the landfills (709-1599 OTUs per sample). The most predominant bacterial representatives in the landfills investigated, regardless of geographic area, included Gammaproteobacteria, Firmicutes, and Bacteroidetes. The phyla Fusobacteria and Tenericutes were also found for the first time to be predominant in the landfills. The phylum Fusobacteria predominated (51.5 and 48.8%) in two semi-arid landfills, and the phylum Tenericutes dominated (30.6%) at one humid, subtropical landfill. Further, a large number of Pseudomonas was detected in most samples, comprising the dominant group and accounting for 40.9 to 92.4% of the total abundance. Principal component analysis (PCA) and cluster analysis based on OTU abundance showed that the abundant taxa separated the bacterial community. Canonical correlation analysis (CCA) suggested that precipitation and landfilling age significantly impact on the bacterial community structure. The bacterial community function (e.g., cellulolytic bacteria, sulfate-reducing bacteria (SRB), sulfate-oxidizing bacteria, and xenobiotic organic compound (XOC)-degrading bacteria) was also diverse, but the pattern is unclear.

  3. Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

    Directory of Open Access Journals (Sweden)

    Raymon S Shange

    Full Text Available Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of

  4. Analysis of intestinal bacterial community diversity of adult Dastarcus helophoroides.

    Science.gov (United States)

    Zhang, Z Q; He, C; Li, M L

    2014-01-01

    Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culture-dependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial primers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Enterococcaceae), Bacillus (Bacillales: Bacillaceae), Cellvibrio (Pseudomonadales: Pseudomonadaceae), Caulobacter (Caulobacterales: Caulobacteraceae), and uncultured bacteria, whereas those isolated by the culture-dependent technique belonged to Staphylococcus (Bacillales: Staphylococcaceae), Pectobacterium Enterobacteriales: Enterobacteriaceae), and Enterobacter (Enterobacteriales: Enterobacteriaceae). These intestinal bacteria represented the groups Lactobacillales (Enterococcus), Pseudomonadales (Cellvibrio), Caulobacterales (Caulobacter), Bacilli (Bacillus and Staphylococcus), and Gammaproteobacteria (Pectobacterium and Enterobacter). Our results demonstrated that PCR-DGGE analysis and the culture-dependent technique were useful in determining the intestinal bacteria of D. helophoroides and the two methods should be integrated to characterize the microbial community and diversity. PMID:25373236

  5. Diversity surveys of soil bacterial community by cultivation-based methods and molecular fingerprinting techniques

    Institute of Scientific and Technical Information of China (English)

    LUO Hai-feng; QI Hong-yan; ZHANG Hong-xun

    2004-01-01

    By combining the cultivation methods with molecular fingerprinting techniques, the diversity surveys of soil bacterial community in 13 areas of China were carried out. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis(DGGE) by the extraction and purification of the total soil DNA, and amplification of bacterial 16S rDNA fragments by polymerase chain reaction ( PCR). The Shannon-Wiener indices of diversity (H), richness (S)and evenness( EH ) were employed to estimate the diversity of soil bacterial community. The results showed that there was an obvious diversification existed in soil from the different areas. However, the genetic diversity estimated by PCR-DGGE can provide more comprehensive information on bacterial community than the cultivation-based methods. Therefore, it is suggested to combine the traditional methods with genetic fingerprinting techniques to survey and estimate soil bacterial diversity.

  6. Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

    OpenAIRE

    Blasiak, Leah C.; Schmidt, Alex W.; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Wendy L Applequist; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P.; Schmidt, Thomas M; Hill, Russell T.

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communitie...

  7. Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas

    Science.gov (United States)

    Vences, Miguel; Lyra, Mariana L.; Kueneman, Jordan G.; Bletz, Molly C.; Archer, Holly M.; Canitz, Julia; Handreck, Svenja; Randrianiaina, Roger-Daniel; Struck, Ulrich; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; McKenzie, Valerie J.; Tebbe, Christoph C.; Haddad, Célio F. B.; Glos, Julian

    2016-04-01

    Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.

  8. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

    Science.gov (United States)

    Zha, Yinghua; Berga, Mercè; Comte, Jérôme; Langenheder, Silke

    2016-01-01

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted. PMID:27182596

  9. Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms

    NARCIS (Netherlands)

    Evans, FF; Rosado, AS; Sebastian, GV; Casella, R; Machado, PLOA; Holmstrom, C; Kjelleberg, S; van Elsas, JD; Seldin, L

    2004-01-01

    The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial popula

  10. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Science.gov (United States)

    Blasiak, Leah C; Schmidt, Alex W; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P; Schmidt, Thomas M; Hill, Russell T

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  11. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Science.gov (United States)

    Blasiak, Leah C; Schmidt, Alex W; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P; Schmidt, Thomas M; Hill, Russell T

    2014-01-01

    Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas. PMID:24465484

  12. Bacterial communities in Malagasy soils with differing levels of disturbance affecting botanical diversity.

    Directory of Open Access Journals (Sweden)

    Leah C Blasiak

    Full Text Available Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.

  13. Shifts in diversity and function of lake bacterial communities upon glacier retreat.

    Science.gov (United States)

    Peter, Hannes; Sommaruga, Ruben

    2016-07-01

    Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear. PMID:26771929

  14. Bacterial community structure and diversity in a black soil as affected by long-term fertilization

    Institute of Scientific and Technical Information of China (English)

    WEI Dan; YANG Qian; ZHANG Jun-Zheng; WANG Shuang; CHEN Xue-Li; ZHANG Xi-Lin; LI Wei-Qun

    2008-01-01

    Black soil (Mollisol) is one of the main soil types in northeastern China.Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) methods were used to examine the influence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province.Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments.The metabolic ability of the bacterial community in the manure treatment was similar to the control.DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not influenced by fertilization.However,chemical fertilizer increased the diversity of soil bacterial community.Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure.Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them.The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

  15. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    OpenAIRE

    Seung Hak Yang; Joung Soo Lim; Modabber Ahmed Khan; Bong Soo Kim; Dong Yoon Choi; Eun Young Lee; Hee Kwon Ahn

    2015-01-01

    The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gen...

  16. Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

    OpenAIRE

    Guo, Yan; Zhang, Jinliang; Yan, Yongfeng; Wu, Jian; Zhu, Nengwu; Deng, Changyan

    2015-01-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive ...

  17. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-01-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. PMID:27650273

  18. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  19. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-21

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  20. Genetic diversity of bacterial communities and gene transfer agents in northern South China Sea.

    Directory of Open Access Journals (Sweden)

    Fu-Lin Sun

    Full Text Available Pyrosequencing of the 16S ribosomal RNA gene (rDNA amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA major capsid gene (g5 was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS, temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments.

  1. Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand

    NARCIS (Netherlands)

    Hamdan, L.J.; Gillevet, P.M.; Pohlman, J.W.; Sikaroodi, M.; Greinart, J.; Coffin, R.B.

    2011-01-01

    Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and

  2. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  3. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    International Nuclear Information System (INIS)

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure (α-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  4. Petroleum-influenced beach sediments of the campeche bank, Mexico: Diversity and bacterial community structure assessment

    Energy Technology Data Exchange (ETDEWEB)

    Rosano-Hernandez, M. C.; Ramirez-Saad, H.; Fernandez-Linares, L.; Xoconostle, B.

    2009-07-01

    In Mexican, either spilled or seeped out petroleum impacts nearly 300 km of the beach between Dos Bocas (Tabasco State) to Champoton town (Campeche State), where between 9 to exceptionally 9 to exceptionally 300 tonnes of oil as tar balls have been measured. This study was focused to explore, for the first time, the bacterial diversity and community structure ({alpha}-diversity)- in a kilometric scale on petroleum influenced sediments of 100 km of sandy beach. (Author)

  5. Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity

    Institute of Scientific and Technical Information of China (English)

    HE Dan; REN Lijuan; WU Qinglong

    2012-01-01

    Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species.However,the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood.We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes:Vallisneria natans and Hydrilla verticillata in Taihu Lake,Jiangsu,China,using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes.The results show that:(1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria,and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria,including Burkholderiales,was the most abundant bacterial group on both plants.Cyanobacteria and Gammaproteobacteria were the second largest groups on V.natans and H.verticillata,respectively.Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations.Both ANOSIM of the T-RFLPdata and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants.Therefore,the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific,which may aid in understanding the ecological functions of submerged macrophytes in general.

  6. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  7. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  8. Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland.

    Science.gov (United States)

    Ganzert, Lars; Bajerski, Felizitas; Wagner, Dirk

    2014-08-01

    Greenland is one of the regions of interest with respect to climate change and global warming in the Northern Hemisphere. Little is known about the structure and diversity of the terrestrial bacterial communities in ice-free areas in northern Greenland. These soils are generally poorly developed and usually carbon- and nitrogen-limited. Our goal was to provide the first insights into the soil bacterial communities from five different sites in Northeast Greenland using culture-independent and culture-dependent methods. The comparison of environmental and biological data showed that the soil bacterial communities are diverse and significantly pH-dependent. The most frequently detected OTUs belonged to the phyla Acidobacteria, Bacteroidetes and (Alpha-, Beta-, Delta-) Proteobacteria. Low pH together with higher nitrogen and carbon concentrations seemed to support the occurrence of (Alpha-, Beta-, Delta-) Proteobacteria (at the expense of Acidobacteria), whereas Bacteroidetes were predominant at higher values of soil pH. Our study indicates that pH is the main factor for shaping bacterial community, but carbon and nitrogen concentrations as well may become important, especially for selecting oligotrophic microorganisms.

  9. Vertical Distribution of Bacterial Community Diversity and Water Quality during the Reservoir Thermal Stratification

    Directory of Open Access Journals (Sweden)

    Hai-Han Zhang

    2015-06-01

    Full Text Available Reservoir thermal stratification drives the water temperature and dissolved oxygen gradient, however, the characteristic of vertical water microbial community during thermal stratification is so far poorly understood. In this work, water bacterial community diversity was determined using the Illumina Miseq sequencing technique. The results showed that epilimnion, metalimnion and hypolimnion were formed steadily in the JINPEN drinking water reservoir. Water temperature decreased steadily from the surface (23.11 °C to the bottom (9.17 °C. Total nitrogen ranged from 1.07 to 2.06 mg/L and nitrate nitrogen ranged from 0.8 to 1.84 mg/L. The dissolved oxygen concentration decreased sharply below 50 m, and reached zero at 65 m. The Miseq sequencing revealed a total of 4127 operational taxonomic units (OTUs with 97% similarity, which were affiliated with 15 phyla including Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Caldiserica, Chlamydiae, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The highest Shannon diversity was 4.41 in 45 m, and the highest Chao 1 diversity was 506 in 5 m. Rhodobacter dominated in 55 m (23.24% and 65 m (12.58%. Prosthecobacter dominated from 0.5 to 50 m. The heat map profile and redundancy analysis (RDA indicated significant difference in vertical water bacterial community composition in the reservoir. Meanwhile, water quality properties including dissolved oxygen, conductivity, nitrate nitrogen and total nitrogen have a dramatic influence on vertical distribution of bacterial communities.

  10. Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.

    Science.gov (United States)

    Meier, Christoph; Wehrli, Bernhard; van der Meer, Jan Roelof

    2008-08-01

    Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to

  11. Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer.

    Science.gov (United States)

    Rizoulis, Athanasios; Elliott, David R; Rolfe, Stephen A; Thornton, Steven F; Banwart, Steven A; Pickup, Roger W; Scholes, Julie D

    2013-07-01

    Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.

  12. Bacterial community diversity and variation in spray water sources and the tomato fruit surface

    Directory of Open Access Journals (Sweden)

    Ottesen Andrea R

    2011-04-01

    Full Text Available Abstract Background Tomato (Solanum lycopersicum consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. Results The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. Conclusions Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an

  13. Two decades of warming increases diversity of a potentially lignolytic bacterial community

    OpenAIRE

    Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen M

    2015-01-01

    As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soi...

  14. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area

    Science.gov (United States)

    Wang, Neng Fei; Zhang, Tao; Yang, Xiao; Wang, Shuang; Yu, Yong; Dong, Long Long; Guo, Yu Dong; Ma, Yong Xing; Zang, Jia Ye

    2016-01-01

    This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments.

  15. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.

    Science.gov (United States)

    Wang, Jichen; Xue, Chao; Song, Yang; Wang, Lei; Huang, Qiwei; Shen, Qirong

    2016-01-01

    Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen-fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha

  16. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.

    Science.gov (United States)

    Wang, Jichen; Xue, Chao; Song, Yang; Wang, Lei; Huang, Qiwei; Shen, Qirong

    2016-01-01

    Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic-inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen-fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha

  17. Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity

    Science.gov (United States)

    Wang, Jichen; Xue, Chao; Song, Yang; Wang, Lei; Huang, Qiwei; Shen, Qirong

    2016-01-01

    Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of

  18. Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions.

    Science.gov (United States)

    Pérez, María Laura; Collavino, Mónica Mariana; Sansberro, Pedro Alfonso; Mroginski, Luis Amado; Galdeano, Ernestina

    2016-04-01

    The composition and diversity of the endophytic community associated with yerba mate (Ilex paraguariensis) was investigated using culture-depending methods. Fungi were identified based on their micromorphological characteristics and internal transcribed spacer rDNA sequence analysis; for bacteria 16S rDNA sequence analysis was used. Fungal and bacterial diversity did not show significant differences between organ age. The highest fungal diversity was registered during fall season and the lowest in winter. Bacterial diversity was higher in stems and increased from summer to winter, in contrast with leaves, which decreased. The most frequently isolated fungus was Fusarium, followed by Colletotrichum; they were both present in all the sampling seasons and organ types assayed. Actinobacteria represented 57.5 % of all bacterial isolates. The most dominant bacterial taxa were Curtobacterium and Microbacterium. Other bacteria frequently found were Methylobacterium, Sphingomonas, Herbiconiux and Bacillus. Nitrogen fixation and phosphate solubilization activity, ACC deaminase production and antagonism against plant fungal pathogens were assayed in endophytic bacterial strains. In the case of fungi, strains of Trichoderma, Penicillium and Aspergillus were assayed for antagonism against pathogenic Fusarium sp. All microbial isolates assayed showed at least one growth promoting activity. Strains of Bacillus, Pantoea, Curtobacterium, Methylobacterium, Brevundimonas and Paenibacillus had at least two growth-promoting activities, and Bacillus, Paenibacillus and the three endophytic fungi showed high antagonistic activity against Fusarium sp. In this work we have made a wide study of the culturable endophytic community within yerba mate plants and found that several microbial isolates could be considered as potential inoculants useful for improving yerba mate production. PMID:26925623

  19. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area.

    Science.gov (United States)

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area. PMID:26902649

  20. Relationships between host phylogeny, host type and bacterial community diversity in cold-water coral reef sponges.

    Directory of Open Access Journals (Sweden)

    Sandra Schöttner

    Full Text Available Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level, as well as sponge type (high versus low microbial abundance, and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA showed that as many as 345 (79% of the 437 different bacterial operational taxonomic units (OTUs detected in the dataset were shared between sponges and sediments, while only 70 (16% appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation, sponge family (52% or sponge type (30%, whereas mesoscale geographic distances and water depth showed comparatively small effects (<5% each. In addition, a highly significant, positive relationship between bacterial community dissimilarity and sponge phylogenetic distance was observed within the ancient family of the Geodiidae. Overall, the high diversity of sponges in cold-water coral reefs, combined with the observed sponge-related variation in bacterial community structure, support the idea that sponges represent heterogeneous, yet structured microbial habitats that contribute significantly to enhancing bacterial diversity in deep-sea ecosystems.

  1. Physicochemical control of bacterial and protist community composition and diversity in Antarctic sea ice.

    Science.gov (United States)

    Torstensson, Anders; Dinasquet, Julie; Chierici, Melissa; Fransson, Agneta; Riemann, Lasse; Wulff, Angela

    2015-10-01

    Due to climate change, sea ice experiences changes in terms of extent and physical properties. In order to understand how sea ice microbial communities are affected by changes in physicochemical properties of the ice, we used 454-sequencing of 16S and 18S rRNA genes to examine environmental control of microbial diversity and composition in Antarctic sea ice. We observed a high diversity and richness of bacteria, which were strongly negatively correlated with temperature and positively with brine salinity. We suggest that bacterial diversity in sea ice is mainly controlled by physicochemical properties of the ice, such as temperature and salinity, and that sea ice bacterial communities are sensitive to seasonal and environmental changes. For the first time in Antarctic interior sea ice, we observed a strong eukaryotic dominance of the dinoflagellate phylotype SL163A10, comprising 63% of the total sequences. This phylotype is known to be kleptoplastic and could be a significant primary producer in sea ice. We conclude that mixotrophic flagellates may play a greater role in the sea ice microbial ecosystem than previously believed, and not only during the polar night but also during summer when potential food sources are abundant.

  2. Phylogenetic diversity of dominant bacterial communities during bioremediation of crude oil-polluted soil

    Directory of Open Access Journals (Sweden)

    Eugene Thomas Cloete

    2011-08-01

    Full Text Available Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities respectively. Bacterial dynamics in crude oil-polluted soil microcosms undergoing bioremediation were investigated over a 42-day period. Four out of the five microcosms containing 4kg of pristine soil each were contaminated with 4% Arabian light crude oil. Three microcosms were amended with either 25g of NPK fertilizer, calcium ammonium nitrate or poultry droppings respectively while the fourth designated oil-contaminated control was unamended. The fifth microcosm had only pristine soil and was set up to ascertain indigenous bacterial community structure pre-contamination. Biostimulated soils were periodically tilled and watered. Hydrocarbon degradation was measured throughout the experimental period by gas chromatography. Gas chromatographic tracing of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second (day 14 till the sixth (day 42 week after contamination whereas no significant reduction in hydrocarbon peaks was seen in the oil contaminated control soil throughout the 6-week experimental period. Molecular fingerprints of bacterial communities involved in aerobic biodegradation of crude oil hydrocarbons in biostimulated soils and controls were generated with DGGE using PCR-amplification of 16S rRNA gene obtained from extracted total soil community DNA. DGGE fingerprints demonstrated that NPK, calcium ammonium nitrate and poultry droppings selected different bacterial populations during the active phase of oil

  3. [Effects of nitrogen and water addition on soil bacterial diversity and community structure in temperate grasslands in northern China].

    Science.gov (United States)

    Yang, Shan; Li, Xiao-bing; Wang, Ru-zhen; Cai, Jiang-ping; Xu, Zhu-wen; Zhang, Yu-ge; Li, Hui; Jiang, Yong

    2015-03-01

    In this study, we measured the responses of soil bacterial diversity and community structure to nitrogen (N) and water addition in the typical temperate grassland in northern China. Results showed that N addition significantly reduced microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) under regular precipitation treatment. Similar declined trends of MBC and MBN caused by N addition were also found under increased precipitation condition. Nevertheless, water addition alleviated the inhibition by N addition. N addition exerted no significant effects. on bacterial α-diversity indices, including richness, Shannon diversity and evenness index under regular precipitation condition. Precipitation increment tended to increase bacterial α-diversity, and the diversity indices of each N gradient under regular precipitation were much lower than that of the corresponding N addition rate under increased precipitation. Correlation analysis showed that soil moisture, nitrate (NO3(-)-N) and ammonium (NH4+-N) were significantly negatively correlated with bacterial evenness index, and MBC and MBN had a significant positive correlation with bacterial richness and evenness. Non-metric multidimensional scaling (NMDS) ordination illustrated that the bacterial communities were significantly separated by N addition rates, under both water ambient and water addition treatments. Redundancy analysis (RDA) revealed that soil MBC, MBN, pH and NH4+-N were the key environmental factors for shaping bacterial communities.

  4. Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity▿ †

    OpenAIRE

    Zul, Delita; Denzel, Sabine; Kotz, Andrea; Overmann, Jörg

    2007-01-01

    Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic finge...

  5. Assessment of changes in community level physiological profile and molecular diversity of bacterial communities in different stages of jute retting.

    Science.gov (United States)

    Das, Biswapriya; Chakrabarti, Kalyan; Ghosh, Sagarmoy; Chakraborty, Ashis; Saha, Manabendra Nath

    2013-12-01

    Retting of jute is essentially microbiological and biochemical in nature. Community Level Physiological Profiles (CLPP) as well as genomic diversity of bacterial communities were assessed in water samples collected during pre-retting, after 1st and 2nd charges of retting. The water samples were collected from two widely cultivated jute growing locations, Sonatikari (22 degrees 41'27"N; 88 degrees 35'44"E) and Baduria (22 degrees 44'24"N; 88 degrees 47'24"E), West Bengal, India. The CLPP, expressed as net area under substrate utilization curve, was studied by carbon source utilization patterns in BIOLOG Ecoplates. Molecular diversity was studied by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) of total DNA from water samples. Both between locations and stages of retting, substrate utilizations pattern were carbohydrates > carboxylic acids > polymers > amino acids > amines/amides > phenolic compounds. Differential substrate utilization pattern as well as variation in banding pattern in DGGE profiles was observed between the two locations and at different stages of retting. The variations in CLPP in different stages of retting were due to the change in bacterial communities. PMID:24506039

  6. Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China

    Institute of Scientific and Technical Information of China (English)

    WANG Liping; ZHENG Binghui; LEI Kun

    2015-01-01

    In order to understand the diversity and distribution of the bacterial community in the coastal sediment of the Bohai Bay, China, high-throughput barcoded pyrosequencing of the 16S rRNA gene was used. Metagenomic DNA was extracted from the sediment samples, and was sequenced using a 454 GS FLX Titanium system. At 97%similarity, the sequences were assigned to 22 884 operational taxonomic units (OTUs) which belonged to 41 phyla, 84 classes, 268 genera and 789 species. At the different taxonomic levels, both the dominants and their distribution varied significantly among the six coastal sediments. Proteobacteria was the first dominant phylum across all the six coastal sediments, representing 57.52%, 60.66%, 45.10%, 60.92%, 56.63% and 56.59%, respectively. Bacteroidetes was the second dominant phylum at Stas S1, S2 and S4, while Chloroflexi was the second dominant phylum at Stas S3, S5 and S6. At class level,γ-Proteobacteria was the first dominant class at Stas S1, S2, S4 and S6, whileδ-Proteobacteria became the first dominant class at Stas S3 and S5. In addition, a large proportion of unclassified representatives have distributed at the different taxonomic levels. Canonical correspondence analysis (CCA) results indicated that the sediment texture, water depth (D), dissolved oxygen (DO), total nitrogen (TN) and nine EPA priority control polycyclic aromatic hydrocarbons (PAHs) including naphthalene, acenaphthylene, acenaphthene, fluorine, phenanthrene, fluoranthene, pyrene, benzo[a]anthracene and indeno[1,2,3-cd]pyrene were the important factors in regulating the bacterial community composition. Those results are very important to further understand the roles of bacterial community in the coastal biogeochemical cycles.

  7. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities

    OpenAIRE

    Yinghua Zha; Mercè Berga; Jérôme Comte; Silke Langenheder

    2016-01-01

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional ...

  8. Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition

    OpenAIRE

    Chairmandurai Aravindraja; Dharmaprakash Viszwapriya; Shunmugiah Karutha Pandian

    2013-01-01

    BACKGROUND: Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. METHODS AND PRINCIPAL FINDINGS: In the present st...

  9. 454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils.

    Science.gov (United States)

    Makonde, Huxley M; Mwirichia, Romano; Osiemo, Zipporah; Boga, Hamadi I; Klenk, Hans-Peter

    2015-01-01

    Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites' gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40-58 %), Spirochaetes (10-70 %), Firmicutes (17-27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28-45 %), Actinobacteria (20-40 %) and Proteobacteria (18-24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to

  10. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... analysed by Shannon-Weaver indices, functional diversity was found to increase almost immediately after mercury addition and to remain at a level higher than the control soil for the rest of the experiment. The fraction of culturable heterotrophic bacteria increased from 1% to 10% of the total bacterial...

  11. Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest.

    Directory of Open Access Journals (Sweden)

    Zhenping Yang

    Full Text Available As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping

  12. Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest.

    Science.gov (United States)

    Yang, Zhenping; Yang, Wenping; Li, Shengcai; Hao, Jiaomin; Su, Zhifeng; Sun, Min; Gao, Zhiqiang; Zhang, Chunlai

    2016-01-01

    As the major crops in north China, spring crops are usually planted from April through May every spring and harvested in fall. Wheat is also a very common crop traditionally planted in fall or spring and harvested in summer year by year. This continuous cropping system exhibited the disadvantages of reducing the fertility of soil through decreasing microbial diversity. Thus, management of microbial diversity in the rhizosphere plays a vital role in sustainable crop production. In this study, ten common spring crops in north China were chosen sole-cropped and four were chosen intercropped with peanut in wheat fields after harvest. Denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of one 16S rDNA fragment were used to analyze the bacterial diversity and species identification. DGGE profiles showed the bacterial community diversity in rhizosphere soil samples varied among various crops under different cropping systems, more diverse under intercropping system than under sole-cropping. Some intercropping-specific bands in DGGE profiles suggested that several bacterial species were stimulated by intercropping systems specifically. Furthermore, the identification of these dominant and functional bacteria by DNA sequencing indicated that intercropping systems are more beneficial to improve soil fertility. Compared to intercropping systems, we also observed changes in microbial community of rhizosphere soil under sole-crops. The rhizosphere bacterial community structure in spring crops showed a strong crop species-specific pattern. More importantly, Empedobacter brevis, a typical plant pathogen, was only found in the carrot rhizosphere, suggesting carrot should be sown prudently. In conclusion, our study demonstrated that crop species and cropping systems had significant effects on bacterial community diversity in the rhizosphere soils. We strongly suggest sorghum, glutinous millet and buckwheat could be taken into account as intercropping crops with peanut

  13. Early Changes in Soil Metabolic Diversity and Bacterial Community Structure in Sugarcane under Two Harvest Management Systems

    Directory of Open Access Journals (Sweden)

    Lucas Carvalho Basilio Azevedo

    2015-06-01

    Full Text Available Preharvest burning is widely used in Brazil for sugarcane cropping. However, due to environmental restrictions, harvest without burning is becoming the predominant option. Consequently, changes in the microbial community are expected from crop residue accumulation on the soil surface, as well as alterations in soil metabolic diversity as of the first harvest. Because biological properties respond quickly and can be used to monitor environmental changes, we evaluated soil metabolic diversity and bacterial community structure after the first harvest under sugarcane management without burning compared to management with preharvest burning. Soil samples were collected under three sugarcane varieties (SP813250, SP801842 and RB72454 and two harvest management systems (without and with preharvest burning. Microbial biomass C (MBC, carbon (C substrate utilization profiles, bacterial community structure (based on profiles of 16S rRNA gene amplicons, and soil chemical properties were determined. MBC was not different among the treatments. C-substrate utilization and metabolic diversity were lower in soil without burning, except for the evenness index of C-substrate utilization. Soil samples under the variety SP801842 showed the greatest changes in substrate utilization and metabolic diversity, but showed no differences in bacterial community structure, regardless of the harvest management system. In conclusion, combined analysis of soil chemical and microbiological data can detect early changes in microbial metabolic capacity and diversity, with lower values in management without burning. However, after the first harvest, there were no changes in the soil bacterial community structure detected by PCR-DGGE under the sugarcane variety SP801842. Therefore, the metabolic profile is a more sensitive indicator of early changes in the soil microbial community caused by the harvest management system.

  14. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    Science.gov (United States)

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  15. Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

    Institute of Scientific and Technical Information of China (English)

    GAO Zheng; WANG Xin; Angelos K. HANNIDES; Francis J. SANSONE; WANG Guangyi

    2011-01-01

    Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry.Although biogeochemical redox stratification has been well documented in marine sediments,its impact on microbial communities remains largely unknown.In this study,we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm.A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm.They were members of nine phyla and three candidate divisions,including Proteobacteria (Alpha-,Beta-,Gamma-,Delta-,and Epsilonproteobacteria),Actinobacteria,Acidobacteria,Bacteroidetes,Chloroflexi,Cyanobacteria,Firmicutes,Verrucomicrobia,Spirochaetes,and the candidate divisions WS3,SO31 and AO19.The vast majority of these phylotypes are related to clone sequences from other marine sediments,but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments.Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences.Results from the 16S rRNA,gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments,with the highest diversity found in the anoxic layer (15-25 mm) and the least diversity in the suboxic layer (3-5 mm).Analysis of the nosZ,and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers,with their highest diversity being in the anoxic and oxic sediment layers,respectively.These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.

  16. Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

    Science.gov (United States)

    Gao, Zheng; Wang, Xin; Hannides, Angelos K.; Sansone, Francis J.; Wang, Guangyi

    2011-11-01

    Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry. Although biogeochemical redox stratification has been well documented in marine sediments, its impact on microbial communities remains largely unknown. In this study, we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm. A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm. They were members of nine phyla and three candidate divisions, including Proteobacteria ( Alpha-, Beta-, Gamma-, Delta-, and Epsilonproteobacteria), Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Verrucomicrobia, Spirochaetes, and the candidate divisions WS3, SO31 and AO19. The vast majority of these phylotypes are related to clone sequences from other marine sediments, but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments. Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences. Results from the 16S rRNA, gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments, with the highest diversity found in the anoxic layer (15-25 mm) and the least diversity in the suboxic layer (3-5 mm). Analysis of the nosZ, and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers, with their highest diversity being in the anoxic and oxic sediment layers, respectively. These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.

  17. Diversity and succession of bacterial communities in the uterine fluid of postpartum metritic, endometritic and healthy dairy cows.

    Directory of Open Access Journals (Sweden)

    Thiago M A Santos

    Full Text Available The diversity of the uterine bacterial composition in dairy cows is still poorly understood, although the emerging picture has shown to be increasingly complex. Understanding the complexity and ecology of microorganisms in the uterus of postpartum dairy cows is critical for developing strategies to block their action in reproductive disorders, such as metritis/endometritis. Here, we used PCR-Denaturing Gradient Gel Electrophoresis (DGGE and DNA pyrosequencing to provide a comprehensive description of the uterine bacterial diversity and compare its succession in healthy, metritic and endometritic Holstein dairy cows at three intervals following calving. Samples were collected from 16 dairy cows housed in a dairy farm located in upstate New York. PCR-DGGE revealed a complex profile with extensive differences in the community structure. With few exceptions, clustering analysis grouped samples from cows presenting the same health status. Analysis of >65,000 high-quality 16S rRNA gene sequences showed that the uterine bacterial consortia, regardless of the health status, is mainly composed of members of the phyla Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Tenericutes. In addition to these co-dominant phyla, sequences from Spirochaetes, Synergistetes, and Actinobacteria appear less frequently. It is possible that some sequences detected in the uterine fluid resulted from the presence of fecal or vaginal contaminants. Overall, the bacterial core community was different in uterine fluid of healthy cows, when compared to cows suffering from postpartum diseases, and the phylogenetic diversity in all the combined samples changed gradually over time. Particularly at the 34-36 days postpartum (DPP, the core community seemed to be specific for each health status. Our finding reveals that the uterine microbiota in dairy cows varies according with health status and DPP. Also, it adds further support to the hypothesis that there is uterine

  18. Changes in the potential functional diversity of the bacterial community in biofilters

    Energy Technology Data Exchange (ETDEWEB)

    Grove, J.A.; Anderson, W.A.; Moo-Young, M. [Waterloo Univ., ON (Canada). Dept. of Chemical Engineering

    2007-12-15

    The bacterial community structure in a biofilter treating ethanol was investigated using community level physiological profiling. Laboratory scale biofilters of two sizes (5 or 11.5 cm internal diameter with 30 or 67 cm packed height, respectively) were packed with compost and a humidified airstream loaded with ethanol passed through them. Good removal efficiencies (82-100%) and elimination capacities (49-205 g ethanol m{sup -3} h{sup -1}) were observed in all units. Compost packing media samples were extracted and the community level physiological profiles assayed using Biolog Ecoplates. The community structure was found to be similar over a range of a few centimetres. No differences were observed between sample sizes of 0.5-1 and 6 g, and therefore, the smaller sample size (typical of that used in previous studies) is appropriate for use in the future. Two studies of parallel systems showed that the community structure diverged during the acclimation period (10 days) in one pair, but in another pair, no divergence was observed and a similar shift in community profile was observed in both units between 25 and 40 days of operation. Community level physiological profiling with Biolog Ecoplates is a useful method for detecting differences between and changes within the bacterial communities in biofilters. (orig.)

  19. Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China.

    Science.gov (United States)

    Zhang, Bingchang; Kong, Weidong; Wu, Nan; Zhang, Yuanming

    2016-06-01

    Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as

  20. Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B [ORNL; Schadt, Christopher Warren [ORNL; Palumbo, Anthony Vito [ORNL; Ansley, R J [Texas A& M University; Boutton, Thomas W [Texas A& M University

    2010-01-01

    In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

  1. Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations

    DEFF Research Database (Denmark)

    Lipthay, Julia R. de; Johnsen, Kaare; Albrechtsen, H.-J.;

    2004-01-01

    contaminants. We examined the effect of in situ exposure to realistic low concentrations of herbicides on the microbial diversity and community structure of sub-surface sediments from a shallow aquifer near Vejen (Denmark). Three different community analyses were performed: colony morphology typing, sole......-surface aquifers to realistic low concentrations of herbicides may alter the overall structure of a natural bacterial community, although significant effects on the genetic diversity and carbon substrate usage cannot be detected. The observed impact was probably due to indirect effects. In future investigations......An increasing number of herbicides are found in our groundwater environments. This underlines the need for examining the effects of herbicide exposure on the indigenous groundwater microbial communities, as microbial degradation is the major process responsible for the complete removal of most...

  2. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

    Energy Technology Data Exchange (ETDEWEB)

    Hodkinson, Brendan P [ORNL; Gottel, Neil R [ORNL; Schadt, Christopher Warren [ORNL; Lutzoni, Francois [Duke University

    2011-01-01

    Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.

  3. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

    Directory of Open Access Journals (Sweden)

    Mu Peng

    2015-09-01

    Full Text Available Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  4. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

    Science.gov (United States)

    Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

    2015-09-24

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  5. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

    Science.gov (United States)

    Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

    2015-10-01

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future. PMID:26404329

  6. Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

    Science.gov (United States)

    Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

    2016-02-01

    Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences. PMID:26370112

  7. Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

    Science.gov (United States)

    Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

    2016-02-01

    Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

  8. Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments

    Directory of Open Access Journals (Sweden)

    Ramona Marasco

    2013-01-01

    Full Text Available Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches. According to 16S rRNA gene PCR-DGGE, the structure of endosphere and rhizosphere bacterial communities was highly diverse (P=0.03 and was associated with a cultivar/latitudinal/climatic effect. Despite being diverse, the bacterial communities associated with Egyptian grapevines shared a higher similarity with the Tunisian grapevines than those cultivated in North Italy. A similar distribution, according to the cultivar/latitude/aridity gradients, was observed for the cultivable bacteria. Many isolates (23% presented in vitro multiple stress resistance capabilities and PGP activities, the most frequent being auxin synthesis (82%, insoluble phosphate solubilisation (61%, and ammonia production (70%. The comparable numbers and types of potential PGP traits among the three different environmental settings indicate a strong functional homeostasis of beneficial bacteria associated with grape root.

  9. Discovery of Rickettsia species in Dermacentor niveus Neumann ticks by investigating the diversity of bacterial communities.

    Science.gov (United States)

    Zhuang, Lu; Wang, Cheng-Yan; Tong, Yi-Gang; Tang, Fang; Yang, Hong; Liu, Wei; Cao, Wu-Chun

    2014-09-01

    Ticks (Dermacentor niveus Neumann) were collected from Tacheng, Xinjiang Uygur Autonomous Region, and their bacterial diversity was investigated using the 16S RNA gene library method from one pooled sample. A total of 452 clones was successfully sequenced and assigned to 4 phyla. The dominant phylum was the Proteobacteria, accounting for 62.8% of all the clones of the 16S rRNA gene at the confidence level 80%. The other sequences were assigned to the phyla Bacteroidetes, Firmicutes, Actinobacteria and accounted for 13.5%, 12.4%, and 11.3%, respectively. These results provide an insight into the bacterial diversity associated with D. niveus ticks in the natural environment of Tacheng. They indicate the occurrence of Rickettsia raoultii and Rickettsia slovaca in D. niveus ticks in this area, and as a consequence, cases of TIBOLA/DEBONEL may occur (tick-borne lymphadenopathy/Dermacentor-borne necrosis erythema and lymphadenopathy).

  10. Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia.

    Science.gov (United States)

    Krave, Agna S; Lin, Bin; Braster, Martin; Laverman, Anniet M; van Straalen, Nico M; Röling, Wilfred F M; van Verseveld, Henk W

    2002-06-01

    In Java, Indonesia, many nutrient-poor soils are intensively reforested with Pinus merkusii (pine). Information on nutrient cycles and microorganisms involved in these cycles will benefit the management of these important forests. Here, seasonal effects on the stratification of bacterial community structure in the soil profile of a tropical pine forest are described, and differences in bacterial communities are related to chemical and physical soil parameters. Culture-independent community profiles of litter, fragmented litter and mineral soil layers were made by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA-specific polymerase chain reaction (PCR) fragments. The community profiles of the different soil layers clustered separately, correlating with significant differences in organic matter content between the three layers. The bacterial communities appeared to be stable during the wet season of 1998. The drought in 1997, caused by the El Niño climatic effect, did not influence the bacterial communities in fragmentation and mineral soil, although moisture content and other soil parameters were markedly lower than in the wet season. However, communities in litter were influenced by drought. In the litter layer, the moisture content was significantly lower than in the fragmentation and mineral layers during the dry season. A clone library was made from a litter sample taken during the wet season. Partial sequencing of 74 clones and linking the DGGE banding positions of these clones to bands in the DGGE profile of the sample from which the clone library was derived showed considerable bacterial diversity. Alpha-proteobacteria (40.5% of the clones, of which 57% belonged to the Rhizobium-Agrobacterium group) and high-G+C content, Gram-positive bacteria (36.5%) dominated the clone library. PMID:12071981

  11. Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica as revealed by 454 pyrosequencing

    Directory of Open Access Journals (Sweden)

    Neng Fei eWang

    2015-10-01

    Full Text Available This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil in the Fildes Region (King George Island, Antarctica using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01, phosphate phosphorus (p < 0.01, organic carbon (p < 0.05, and organic nitrogen (p < 0.05 were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.

  12. Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Felix, Alvina Clara; Sanabani, Sabri Saeed

    2016-02-01

    Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients. PMID:26805866

  13. Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2016-01-01

    Full Text Available Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB, bank machine keyboard buttons (BMKB, restroom surfaces, and the employee biometric time clock system (EBTCS, in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients.

  14. Genetic diversity of bacterial communities of serpentine soil and of rhizosphere of the nickel-hyperaccumulator plant Alyssum bertolonii.

    Science.gov (United States)

    Mengoni, A; Grassi, E; Barzanti, R; Biondi, E G; Gonnelli, C; Kim, C K; Bazzicalupo, M

    2004-08-01

    Serpentine soils are characterized by high levels of heavy metals (Ni, Co, Cr), and low levels of important plant nutrients (P, Ca, N). Because of these inhospitable edaphic conditions, serpentine soils are typically home to a very specialized flora including endemic species as the nickel hyperaccumulator Alyssum bertolonii. Although much is known about the serpentine flora, few researches have investigated the bacterial communities of serpentine areas. In the present study bacterial communities were sampled at various distances from A. bertolonii roots in three different serpentine areas and their genetic diversity was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The obtained results indicated the occurrence of a high genetic diversity and heterogeneity of the bacterial communities present in the different serpentine areas. Moreover, TRFs (terminal restriction fragments) common to all the investigated A. bertolonii rhizosphere samples were found. A new cloning strategy was applied to 27 TRFs that were sequenced and taxonomically interpreted as mainly belonging to Gram-positive and alpha-Proteobacteria representatives. In particular, cloned TRFs which discriminated between rhizosphere and soil samples were mainly interpreted as belonging to Proteobacteria representatives. PMID:15546041

  15. [Effects of long-term fertilization on bacterial and archaeal diversity and community structure within subtropical red paddy soils].

    Science.gov (United States)

    Yuan, Hong-zhao; Wu, Hao; Ge, Ti-da; Li, Ke-lin; Wu, Jin-shui; Wang, Jiu-rong

    2015-06-01

    Paddy soils not only function as an important sink for "missing carbon" but also play an important role in the production of greenhouse gases such as N2O and CH4. Dynamic changes in greenhouse gases in the atmosphere are closely related to microbially mediated carbon and nitrogen transformation processes occurring in soil. Using soil samples collected from a long-term fertilization experimental site in Taojiang County, subtropical China (established in 1986), we determined the effects of long-term (>25 years) non-fertilization (CK), chemical fertilization (NPK), and NPK combined with rice straw residues (NPKS) on soil bacterial and archaeal community structures. The 16S rRNA genotypes from the three differently treated soils were divided into 9 bacterial phylotypes, mainly including Proteobacteria, Acidobacteria, Chloroflexi, and archaea of Crenarchaeota and Euryarchaeota. The relative abundance of Proteobacteria, Acidobacteria and Crenarchaeota increased in the soils under NPK and NPKS treatments, with the increase being greater in the latter treatment. LUBSHUFF statistical analyses also demonstrated that there was significant difference among the microbial community compositions in CK-, NPK- and NPKS-treated soils. The abundance of bacterial and archaeal 16S rRNA genes ranged from 0.58 x 10(10) to 1.06 x 10(10) copies · g(-1) dry soil and from 1.16 x 10(6) to 1.72 x 10(6) copies · g(-1) dry soil, respectively. Application of fertilizers increased the bacterial and archaeal abundance and diversity in the treated soils, with NPKS > NPK. Long-term chemical and organic applications significantly affected the abundance, diversity and composition of bacterial and archaeal communities in paddy ecosystems. PMID:26572036

  16. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Chairmandurai Aravindraja

    Full Text Available BACKGROUND: Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. METHODS AND PRINCIPAL FINDINGS: In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62-71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. CONCLUSION: This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater and the host associated

  17. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

    Science.gov (United States)

    Siles, José A; Margesin, Rosa

    2016-07-01

    Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site. PMID:26961712

  18. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.

    Science.gov (United States)

    Aslam, Zubair; Yasir, Muhammad; Yoon, Hwan Sik; Jeon, Che Ok; Chung, Young Ryun

    2013-12-01

    Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culture-dependent method during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89-97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera. PMID:24385351

  19. H2S gas biological removal efficiency and bacterial community diversity in biofilter treating wastewater odor.

    Science.gov (United States)

    Omri, Ilhem; Bouallagui, Hassib; Aouidi, Fathia; Godon, Jean-Jacques; Hamdi, Moktar

    2011-11-01

    The objective of this study was to assess the feasibility of using a biofilter system to treat hydrogen sulfide (H2S) contaminated air and to characterize its microbial community. The biofilter system was packed with peat. During the experimental work, the peat was divided in three layers (down, middle, and up). Satisfactory removal efficiencies of H2S were proved and reached 99% for the majority of the run time at an empty bed retention time (EBRT) of 60 s. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to uncover the changes in the microbial community between the different layers. Analysis of SSCP profiles demonstrated significant differences in community structure from a layer to another with a strong decrease in species diversity towards the up layer. It was found that the used support was suitable for microorganism growth, and may have a potential application in H2S biofiltration system. PMID:21945209

  20. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

    Directory of Open Access Journals (Sweden)

    Koen Illeghems

    Full Text Available This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni. Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

  1. Presence of a loner strain maintains cooperation and diversity in well-mixed bacterial communities.

    Science.gov (United States)

    Inglis, R F; Biernaskie, J M; Gardner, A; Kümmerli, R

    2016-01-13

    Cooperation and diversity abound in nature despite cooperators risking exploitation from defectors and superior competitors displacing weaker ones. Understanding the persistence of cooperation and diversity is therefore a major problem for evolutionary ecology, especially in the context of well-mixed populations, where the potential for exploitation and displacement is greatest. Here, we demonstrate that a 'loner effect', described by economic game theorists, can maintain cooperation and diversity in real-world biological settings. We use mathematical models of public-good-producing bacteria to show that the presence of a loner strain, which produces an independent but relatively inefficient good, can lead to rock-paper-scissor dynamics, whereby cooperators outcompete loners, defectors outcompete cooperators and loners outcompete defectors. These model predictions are supported by our observations of evolutionary dynamics in well-mixed experimental communities of the bacterium Pseudomonas aeruginosa. We find that the coexistence of cooperators and defectors that produce and exploit, respectively, the iron-scavenging siderophore pyoverdine, is stabilized by the presence of loners with an independent iron-uptake mechanism. Our results establish the loner effect as a simple and general driver of cooperation and diversity in environments that would otherwise favour defection and the erosion of diversity.

  2. Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke.

    Science.gov (United States)

    Yang, Hui; Hu, Jinxiang; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0-20 cm soil layer vertically and 0-30 cm horizontally from the plant centre. Root concentrations of K(+), Na(+), Mg(2+) and particularly Ca(2+) were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0-5 cm and 5-10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities. PMID:26852800

  3. Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert.

    Science.gov (United States)

    Piubeli, Francine; de Lourdes Moreno, María; Kishi, Luciano Takeshi; Henrique-Silva, Flavio; García, María Teresa; Mellado, Encarnación

    2015-12-01

    The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations . PMID:26543264

  4. Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea.

    Science.gov (United States)

    Haldar, Shyamalina; Choudhury, Susanta Roy; Sengupta, Sanghamitra

    2011-06-01

    Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system. PMID:21380504

  5. Diversity of the bacterial community in Myanmar traditional salted fish yegyo ngapi.

    Science.gov (United States)

    Kobayashi, Takeshi; Taguchi, Chihiro; Kida, Kakeru; Matsuda, Hiroko; Terahara, Takeshi; Imada, Chiaki; Moe, Nant Kay Thwe; Thwe, Su Myo

    2016-10-01

    The distribution and characterization of bacteria including lactic acid bacteria (LAB) in the traditional and popular salted fish yegyo ngapi in Myanmar were studied to clarify the contribution of these bacteria to the curing and ripening of this product. Samples of yegyo ngapi purchased from a market in Yangon were used. Most of the isolates obtained using de Man, Rogosa and Sharpe medium containing 10 % NaCl were identified as coccoid LAB on the basis of their basic phenotypic characteristics. From the results of 16S rRNA gene sequencing and PCR-restriction fragment length polymorphism analysis of this gene, most of the isolates were identified as the halophilic LAB Tetragenococcus muriaticus. Analyses of the 16S rRNA gene based on the clone library using DNA extracted from salted fish products were also performed. The results of these molecular-analysis-based techniques showed that spore-forming and non-spore-forming anaerobic bacteria including the genera Clostridium and Halanaerobium in addition to T. muriaticus were also frequently found in bacterial communities. These findings suggest that the anaerobic condition during curing and ripening resulted in bacterial communities composed of strictly anaerobic bacteria and halophilic LAB, and that these bacteria might also contribute to the manufacturing processes of this product. In addition, DNA sequences similar to that of Clostridium botulinum were found in the clone library analysis. Therefore, despite no reports of botulism poisoning from the region where the samples were taken, closer surveillance should be carried out from the viewpoint of food safety. PMID:27565776

  6. Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash.

    Science.gov (United States)

    Joa, Jae Ho; Weon, Hang Yeon; Hyun, Hae Nam; Jeun, Young Chull; Koh, Sang Wook

    2014-12-01

    This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687-7,330 and 1,790-3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (pfertilization management, soil pH changes and characteristics of volcanic ash. PMID:25467117

  7. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    Science.gov (United States)

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  8. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem

    Directory of Open Access Journals (Sweden)

    Eric Robert Johnston

    2016-04-01

    Full Text Available How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 grams are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth by sequencing, and the recovery of twenty-seven high-quality, almost complete (>80% completeness population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity. Collectively

  9. Truffle brules have an impact on the diversity of soil bacterial communities.

    Directory of Open Access Journals (Sweden)

    Antonietta Mello

    Full Text Available BACKGROUND: The development of Tuber melanosporum mycorrhizal symbiosis is associated with the production of an area devoid of vegetation (commonly referred to by the French word 'brûlé' around the symbiotic plants and where the fruiting bodies of T. melanosporum are usually collected. The extent of the ecological impact of such an area is still being discovered. While the relationship between T. melanosporum and the other fungi present in the brûlé has been assessed, no data are available on the relationship between this fungus and the bacteria inhabiting the brûlé. METHODOLOGY/PRINCIPAL FINDINGS: We used DGGE and DNA microarrays of 16S rRNA gene fragments to compare the bacterial and archaeal communities inside and outside of truffle brûlés. Soil samples were collected in 2008 from four productive T. melanosporum/Quercus pubescens truffle-grounds located in Cahors, France, showing characteristic truffle brûlé. All the samples were analyzed by DGGE and one truffle-ground was analyzed also using phylogenetic microarrays. DGGE profiles showed differences in the bacterial community composition, and the microarrays revealed a few differences in relative richness between the brûlé interior and exterior zones, as well as differences in the relative abundance of several taxa. CONCLUSIONS/SIGNIFICANCE: The different signal intensities we have measured for members of bacteria and archaea inside versus outside the brûlé are the first demonstration, to our knowledge, that not only fungal communities, but also other microorganisms are affected by T. melanosporum. Firmicutes (e.g., Bacillus, several genera of Actinobacteria, and a few Cyanobacteria had greater representation inside the brûlé compared with outside, whereas Pseudomonas and several genera within the class Flavobacteriaceae had higher relative abundances outside the brûlé. The findings from this study may contribute to future searches for microbial bio-indicators of brûlés.

  10. Effects of rodent community diversity and composition on prevalence of an endemic bacterial pathogen - Bartonella

    Science.gov (United States)

    Bai, Y.; Kosoy, M.Y.; Calisher, C.H.; Cully, J.F.; Collinge, S.K.

    2009-01-01

    By studying Bartonella prevalence in rodent communities from 23 geographic sites in the western United States and one site in northern Mexico, the present study focused on the effects of rodent community diversity (measured by richness and Shannon index) and composition on prevalence of Bartonella infections. The analysis showed negative correlations of Bartonella prevalence with rodent richness and Shannon index. Further, Bartonella prevalence varied among rodent genera/species. Three models were applied to explain the observations. (1) Within-species/genus transmission: Bartonella strains usually are host-specific and adding non-host species would decrease Bartonella prevalence in its principal host through reduction of host contact (encounter reduction); (2) Frequency-dependence: Adding hosts would decrease the proportion of all infected individuals in the community, resulting in a reduction in the number of contacts between susceptible and infected individuals that usually leads to transmission (transmission reduction); and (3) Dominant species effect: Dominant species, if not susceptible to Bartonellae, can constrain the abundance of susceptible hosts (susceptible host regulation). These mechanisms work in concert; and the level of Bartonella prevalence is an outcome of regulation of all of these mechanisms on the entire system.

  11. Survival of bacterial indicators and the functional diversity of native microbial communities in the Floridan aquifer system, south Florida

    Science.gov (United States)

    Lisle, John T.

    2014-01-01

    model than when exposed to groundwater from the APPZ (range: 0.540–0.684 h-1). The inactivation rates for the first phase of the models for P. aeruginosa were not significantly different between the UFA (range: 0.144–0.770 h-1) and APPZ (range: 0.159–0.772 h-1) aquifer zones. The inactivation rates for the second phase of the model for this P. aeruginosa were also similar between UFA (range: 0.003–0.008 h-1) and APPZ (0.004–0.005 h-1) zones, although significantly slower than the model’s first phase rates for this bacterial species. Geochemical data were used to determine which dissimilatory biogeochemical reactions were most likely to occur under the native conditions in the UFA and APPZ zones using thermodynamics principles to calculate free energy yields and other cell-related energetics data. The biogeochemical processes of acetotrophic and hydrogenotrophic sulfate reduction, methanogenesis and anaerobic oxidation of methane dominated in all six groundwater sites. A high throughput DNA microarray sequencing technology was used to characterize the diversity in the native aquifer bacterial communities (bacteria and archaea) and assign putative physiological capabilities to the members of those communities. The bacterial communities in both zones of the aquifer were shown to possess the capabilities for primary and secondary fermentation, acetogenesis, methanogenesis, anaerobic methane oxidation, syntrophy with methanogens, ammonification, and sulfate reduction. The data from this study provide the first determination of bacterial indicator survival during exposure to native geochemical conditions of the Floridan aquifer in south Florida. Additionally, the energetics and functional bacterial diversity characterizations are the first descriptions of native bacterial communities in this region of the Floridan aquifer and reveal how these communities persist under such extreme conditions. Collectively, these types of data can be used to develop and refine

  12. The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

    OpenAIRE

    LaPara, Timothy M.; Hope Wilkinson, Katheryn; Strait, Jacqueline M.; Hozalski, Raymond M.; Sadowksy, Michael J.; Hamilton, Matthew J

    2015-01-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in t...

  13. Semiconductor Sequencing Reveals the Diversity of Bacterial Communities in an Amazon Reservoir Considered as a Methane Source

    Science.gov (United States)

    Graças, D. A.; Ramos, R. T.; Sá, P. G.; Baraúna, R. A.; Schneider, M. C.; Silva, A.

    2013-05-01

    oxygen production is considerable in this layer. The oxygen produced by Cyanobacteria coupled to atmospheric oxygen provides the ideal environment for the methanotrophic bacteria oxidize methane. Indeed, methanotrophic bacteria represented approximately 10% in the upper layers. Another bacterial phylum well represented in the upper layers was Bacteroidetes, which accounted for about 3% in the layers of 0-30m. Rarefaction analyses, using a cutoff of 3%, tell us the existence of 3212, 6657, 10171, 4209, 10533, 74, 24345 and 64683 OTUs for the layers of 0, 10, 20, 30, 40, 50, 60 and 70 meters, respectively. Bacterial diversity seems to increase with depth, probably due to the large amount of organic matter deposited in the pellet. The 50 meter depth layer showed the lowest diversity due to low quality sequencing of this barcode, which hampered the analysis. The abundance of methanotrophic bacteria shows that the microbial profile of the reservoir is able to consume much of the methane produced by methanogenic archaea in the sediment and that there is a huge diversity whose function is still unknown. The use of semiconductor sequencing proved to be a robust tool to analysis of the microbial community, as an alternative to pyrosequencing.

  14. Characterization of Bacterial Community Structure and Diversity in Rhizosphere Soils of Three Plants in Rapidly Changing Salt Marshes Using 16S rDNA

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The structure and diversity of the bacterial communities in rhizosphere soils of native Phragmites australis and Scirpus mariqueter and alien Spartina alterniflora in the Yangtze River Estuary were investigated by constructing 16S ribosomal DNA (rDNA) clone libraries. The bacterial diversity was quantified by placing the clones into operational taxonomic unit (OTU) groups at the level of sequence similarity of > 97%. Phylogenetic analysis of the resulting 398 clone sequences indicated a high diversity of bacteria in the rhizosphere soils of these plants. The members of Alphaproteobacteria,Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria of the phylum Proteobacteria were the most abundant in rhizobacteria. Chao 1 nonparametric diversity estimator coupled with the reciprocal of Simpson's index (1/D) was applied to sequence data obtained from each library to evaluate total sequence diversity and quantitatively compare the level of dominance. The results showed that Phragmites, Scirpus, and Spartina rhizosphere soils contained 200, 668, and 382 OTUs, respectively. The bacterial communities in the Spartina and Phragmites rhizosphere soils displayed species dominance revealed by 1/D, whereas the bacterial community in Scirpus rhizosphere soil had uniform distributions of species abundance. Overall, analysis of 16S rDNA clone libraries from the rhizosphere soils indicates that the changes in bacterial composition may occur concomitantly with the shift of species composition in plant communities.

  15. Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing

    Directory of Open Access Journals (Sweden)

    Cuicui Xiao

    2016-07-01

    Full Text Available Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700 clustered into 10,365 operational taxonomic units (OTUs; 97% identity, representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. Smooth rarefaction curves were suggestive of plaque microbial diversity. α diversity analysis showed that healthy plaque microbial diversity exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups and that group members were relatively constant, only showing differences in abundance. Analysis of composition differences identified 10 health-related and 21 caries-related genera. Key genera (27 that potentially contributed to plaque microbiota distributions between groups were identified. Finally, co-occurrence network analysis and function prediction were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed.

  16. Selenium hyperaccumulators harbor a diverse endophytic bacterial community characterized by high selenium resistance and plant growth promoting properties

    Directory of Open Access Journals (Sweden)

    Martina eSura - de Jong

    2015-03-01

    Full Text Available Selenium (Se-rich plants may be used to provide dietary Se to humans and livestock, and also to clean up Se-polluted soils or waters. This study focused on endophytic bacteria of plants that hyperaccumulate selenium (Se to 0.5-1% of dry weight. Terminal restriction fragment length polymorphism (T-RFLP analysis was used to compare the diversity of endophytic bacteria of hyperaccumulators Stanleya pinnata (Brassicaceae and Astragalus bisulcatus (Fabaceae with those from related non-accumulators Physaria bellii (Brassicaceae and Medicago sativa (Fabaceae collected on the same, seleniferous site. Hyperaccumulators and non-accumulators showed equal T-RF diversity. Parsimony analysis showed that T-RFs from individuals of the same species were more similar to each other than to those from other species, regardless of plant Se content or spatial proximity. Cultivable endophytes from hyperaccumulators S. pinnata and A. bisulcatus were further identified and characterized. The 66 bacterial morphotypes were shown by MS MALDI-TOF Biotyper analysis and 16S rRNA gene sequencing to include strains of Bacillus, Pseudomonas, Pantoea, Staphylococcus, Paenibacillus, Advenella, Arthrobacter and Variovorax. Most isolates were highly resistant to selenate and selenite (up to 200 mM and all could reduce selenite to red elemental Se, reduce nitrite and produce siderophores. Seven isolates were selected for plant inoculation and found to have plant growth promoting properties, both in pure culture and when co-cultivated with crop species Brassica juncea (Brassicaceae or M. sativa. There were no effects on plant Se accumulation. We conclude that Se hyperaccumulators harbor an endophytic bacterial community in their natural seleniferous habitat that is equally diverse to that of comparable non-accumulators. The hyperaccumulator endophytes are characterized by high Se resistance, capacity to produce elemental Se and plant growth promoting properties.

  17. Diversity and antibacterial activity of the bacterial communities associated with two Mediterranean sea pens, Pennatula phosphorea and Pteroeides spinosum (Anthozoa: Octocorallia).

    Science.gov (United States)

    Porporato, E M D; Lo Giudice, A; Michaud, L; De Domenico, E; Spanò, N

    2013-10-01

    A description of the bacterial communities associated with the Mediterranean pennatulids (sea pens) Pennatula phosphorea and Pteroeides spinosum from the Straits of Messina (Italy) is reported. The automated ribosomal intergenic spacer analysis showed a marked difference between coral (tissues and mucus) and non-coral (underlying sediment and surrounding water) habitats. The diversity of the coral-associated communities was more deeply analysed by sequencing the 16S rRNA genes of bacterial clones. P. phosphorea and P. spinosum harbour distinct bacterial communities, indicating the occurrence of species-specific coral-associated bacteria. In addition, only few phylotypes were shared between mucus and tissues of the same pennatulid species, suggesting that there might be a sort of microhabitat partitioning between the associated microbial communities. The predominance of Alphaproteobacteria was observed for the communities associated with both tissues and mucus of P. phosphorea (84 and 58.2 % of total sequences, respectively). Conversely, the bacterial community in the mucus layer of P. spinosum was dominated by Alphaproteobacteria (74.2 %) as opposed to the tissue library that was dominated by the Gammaproteobacteria and Mollicutes (40.6 and 35.4 %, respectively). The antibacterial activity of 78 bacterial isolates against indicator organisms was assayed. Active isolates (15.4 %), which predominantly affiliated to Vibrio spp., were mainly obtained from coral mucus. Results from the present study enlarge our knowledge on the composition and antibacterial activity of coral-associated bacterial communities. PMID:23817604

  18. Characterizing the structural diversity of a bacterial community associated with filter materials in recirculating aquaculture systems of Scortum barcoo.

    Science.gov (United States)

    Zhu, Peng; Ye, Yangfang; Pei, Fangfang; Lu, Kaihong

    2012-03-01

    The bacterial community structure associated with filter materials in the recirculating aquaculture system of Scortum barcoo was investigated using the 16S rRNA gene clone library method. Preliminary results showed that the clone library constructed from the initial operation condition was characterized by 31 taxa of bacteria belonging to eight phyla including Proteobacteria, Acidobacteria, Firmicutes, Fusobacteria, Sphingobacteria, Bacteroidetes, Verrucomicrobiae, and Actinobacteria. There were 14 taxa of bacteria belonging to four phyla including Proteobacteria, Acidobacteria, Planctomycetacia, and Nitrospirae from the stable operation condition where the water quality was well maintained. Nitrospirae was only found under the stable operation condition in this study. Our results further indicated that Nitrospira was dominated by members of the Nitrospira sp. lineages, with a minor fraction related to Nitrospira moscoviensis and an unknown Nitrospira cluster. These great differences of both diversity and composition between two operation conditions suggested that the composition of the microbial community varied with the degree of water quality in the recirculating aquaculture system of S. barcoo. PMID:22339297

  19. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

    DEFF Research Database (Denmark)

    Klümper, Uli; Riber, Leise; Dechesne, Arnaud;

    2014-01-01

    Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer...... bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids....

  20. Diversity of Ixodes ricinus tick-associated bacterial communities from different forests

    NARCIS (Netherlands)

    Overbeek, van L.S.; Gassner, F.; Lombaers-van der Plas, C.H.; Kastelein, P.; Nunes da Rocha, U.; Takken, W.

    2008-01-01

    Nymphal Ixodes ricinus ticks (n=180) were collected from three different areas in the Netherlands to investigate the effect of forest composition on tick-associated microbial communities. Sampled habitats differed in thickness of leaf litter and humus layers and vegetation associations and were loca

  1. Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices.

    Science.gov (United States)

    Battini, Fabio; Cristani, Caterina; Giovannetti, Manuela; Agnolucci, Monica

    2016-02-01

    Arbuscular Mycorrhizal Fungi (AMF) live in symbiosis with most crop plants and represent essential elements of soil fertility and plant nutrition and productivity, facilitating soil mineral nutrient uptake and protecting plants from biotic and abiotic stresses. These beneficial services may be mediated by the dense and active spore-associated bacterial communities, which sustain diverse functions, such as the promotion of mycorrhizal activity, biological control of soilborne diseases, nitrogen fixation, and the supply of nutrients and growth factors. In this work, we utilised culture-dependent methods to isolate and functionally characterize the microbiota strictly associated to Rhizophagus intraradices spores, and molecularly identified the strains with best potential plant growth promoting (PGP) activities by 16S rDNA sequence analysis. We isolated in pure culture 374 bacterial strains belonging to different functional groups-actinobacteria, spore-forming, chitinolytic and N2-fixing bacteria-and screened 122 strains for their potential PGP activities. The most common PGP trait was represented by P solubilization from phytate (69.7%), followed by siderophore production (65.6%), mineral P solubilization (49.2%) and IAA production (42.6%). About 76% of actinobacteria and 65% of chitinolytic bacteria displayed multiple PGP activities. Nineteen strains with best potential PGP activities, assigned to Sinorhizobium meliloti, Streptomyces spp., Arthrobacter phenanthrenivorans, Nocardiodes albus, Bacillus sp. pumilus group, Fictibacillus barbaricus and Lysinibacillus fusiformis, showed the ability to produce IAA and siderophores and to solubilize P from mineral phosphate and phytate, representing suitable candidates as biocontrol agents, biofertilisers and bioenhancers, in the perspective of targeted management of beneficial symbionts and their associated bacteria in sustainable food production systems. PMID:26805620

  2. Microbial communities in the saturated groundwater environment II: Diversity of bacterial communities in a Pleistocene sand aquifer and their in vitro activities.

    Science.gov (United States)

    Kölbel-Boelke, J; Anders, E M; Nehrkorn, A

    1988-07-01

    Bacterial cell numbers obtained from 103 water and sediment samples from a Pleistocene sandy aquifer in the Lower Rhine region (Bocholt, FRG) were determinated on P-agar and by direct count. Below 5 m under the surface, colony-forming unit (cfu) numbers in water samples were less than 100/ml, and in many cases less than 50/ml. In sediment samples, they were 10- to 100-fold higher (10(2)-10(4) cfu/g dry wt), but changing markedly between different depths. Direct cell counts yielded numbers two to three orders of magnitude higher.About 2,700 strains of bacteria from 60 samples were isolated randomly and characterized by morphological and physiological properties. Of all the isolates, 71.6% were gram-negative, and 52.2% were gram-negative straight rods. Water communities, with one exception, had low proportions of gram-positive bacteria (<11%), whereas in all but one of the sediment communities percentages of gram-positive isolates were three- to sevenfold higher (35-43%). Water and sediment communities, as well as communities from different sampling sites and communities from different depths of the same sampling site, differed in their qualitative and quantitative morphotype composition and physiological capabilities.The in vitro activities of strains within a single community were quite different, indicating that each community is composed of many diverse bacteria, several having extremely different capabilities. Thus, each community has its own specific activity pattern. Gram-positive bacteria showed on an average lower total activities than did gram-negative bacteria. Grampositive bacteria as well as gram-negative bacteria from sediment had higher values of in vitro activities than the corresponding groups isolated from water. Many water and sediment bacteria preferred the same substrates which were utilized at high rates. However, there were differences in the degradation of the various other substrates present, and each community showed preferences for

  3. Bacterial diversity exploration in hydrocarbon polluted soil: metabolic potential and degrader community evolution revealed by isotope labeling

    International Nuclear Information System (INIS)

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous compounds produced by incomplete combustion of organic matter. They are a source of environmental pollution, especially associated to oil product exploitation, and represent a threat for living organisms including human beings because of their toxicity. Many bacteria capable of degrading PAHs have been isolated and studied. However, since less than 5% of soil bacteria can be cultivated in the laboratory, bacterial species able to degrade PAHs in situ have been poorly studied. The first goal of this study was to identify bacteria that degrade PAHs in soil using culture-independent molecular methods. To this end, a strategy known a stable isotope probing has been implemented based on the use of phenanthrene, a three rings PAH, in which the natural isotope of carbon was replaced by 13C. This molecule has been introduced as a tracer in microcosms containing soil from a constructed wetlands collecting contaminated water from highway runoff. Bacteria having incorporated the 13C were then identified by 16S rRNA gene sequence analysis after PCR amplification from labeled genomic DNA extracted from soil. The results show that so far little studied Betaproteobacteria, belonging to the genera Acidovorax, Rhodoferax, Hydrogenophaga and Thiobacillus, as well as Rhodocyclaceae, were the key players in phenanthrene degradation. Predominance of Betaproteobacteries was established thanks to quantitative PCR measurements. A dynamic analysis of bacterial diversity also showed that the community structure of degraders depended on phenanthrene bioavailability. In addition, the phylogenetic diversity of ring-hydroxylating di-oxygenases, enzymes involved in the first step of PAH degradation, has been explored. We detected new sequences, mostly related to di-oxygenases from Sphingomonadales and Burkholderiales. For the first time, we were able to associate a catalytic activity for oxidation of PAHs to partial gene sequences amplified

  4. Diversity in soil bacterial communities structure in four high-altitude vineyards cultivated using different soil management techniques

    Science.gov (United States)

    Opsi, Francesca; Landa, Blanca; Zecca, Odoardo; Biddoccu, Marcella; Barmaz, Andrea; Cavallo, Eugenio

    2014-05-01

    Some of the major wine producing countries are located in the Mediterranean regions, where viticulture represents one of the most widespread cultivations with economic and social importance. The area devoted to vineyards can also expand to mountain and steep slope zones, often characterized by small-scale high quality wine production, where viticulture contributes to the sustainable development from the ecological and environmental point of view. Farming practices adopted in sloping vineyards have the purpose to improve the soil physicochemical but also biological properties to avoid the degradation of the soil characteristics and resulting problems such as soil erosion and organic matter losses. A preliminary study was conducted during 2013 in four commercial vineyards located in Aosta Valley (north-western Italy), within a small area located in the adjacent municipalities of Chambave and Saint-Denis in order to minimize soil variability. Two sites have been identified on the lower (about 600 m asl) and higher (about 750 m asl) zone of the slope, each of which consist of two vineyards managed since at least ten years with different soil management techniques: grass cover and chemical weed control. The four experimental soils had a sandy loam texture with abundant skeleton, and were characterized by a slightly alkaline reaction. The organic matter content was greater in the lower zone (2.4%) than in the upper (1.5%), without specific differences between treatments. The low values of the C:N ratio reported (on average 6.2) reveal the increased organic matter mineralization; furthermore the CEC values were rather low, typical of loose soils. Soil microbiota are critical for the maintenance of soil health and quality, playing an important role in agricultural soil ecosystems. A 16S rDNA pyrosequencing approach was used for investigating differences, abundance and diversity in bacterial community structure of the four studied vineyards. Data from pyrosequencing

  5. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

    OpenAIRE

    Mu Peng; Xiaoxue Zi; Qiuyu Wang

    2015-01-01

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacte...

  6. The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms.

    Science.gov (United States)

    LaPara, Timothy M; Hope Wilkinson, Katheryn; Strait, Jacqueline M; Hozalski, Raymond M; Sadowksy, Michael J; Hamilton, Matthew J

    2015-10-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

  7. Abundance and diversity of sedimentary bacterial communities in a coastal productive setting in the Western Irish Sea

    Science.gov (United States)

    O'Reilly, S. S.; Pentlavalli, P.; Flanagan, P. V.; Allen, C. C. R.; Monteys, X.; Szpak, M. T.; Murphy, B. T.; Jordan, S. F.; Kelleher, B. P.

    2016-02-01

    The bacterial community composition and biomass abundance from a depositional mud belt in the western Irish Sea and regional sands were investigated by phospholipid ester-linked fatty acid profiling, denaturing gradient gel electrophoresis and barcoded pyrosequencing of 16S rRNA genes. The study area varied by water depth (12-111 m), organic carbon content (0.09-1.57% TOC), grain size, hydrographic regime (well-mixed vs. stratified), and water column phytodetrital input (represented by algal polyunsaturated PLFA). The relative abundance of bacterial-derived PLFA (sum of methyl-branched, cyclopropyl and odd-carbon number PLFA) was positively correlated with fine-grained sediment, and was highest in the depositional mud belt. A strong association between bacterial biomass and eukaryote primary production was suggested based on observed positive correlations with total nitrogen and algal polyunsaturated fatty acids. In addition, 16S rRNA genes affiliated to the classes Clostridia and Flavobacteria represented a major proportion of total 16S rRNA gene sequences. This suggests that benthic bacterial communities are also important degraders of phytodetrital organic matter and closely coupled to water column productivity in the western Irish Sea.

  8. Intra- and Interspecific Comparisons of Bacterial Diversity and Community Structure Support Coevolution of Gut Microbiota and Termite Host†

    Science.gov (United States)

    Hongoh, Yuichi; Deevong, Pinsurang; Inoue, Tetsushi; Moriya, Shigeharu; Trakulnaleamsai, Savitr; Ohkuma, Moriya; Vongkaluang, Charunee; Noparatnaraporn, Napavarn; Kudo, Toshiaki

    2005-01-01

    We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic “termite clusters” comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites. PMID:16269686

  9. Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host.

    Science.gov (United States)

    Hongoh, Yuichi; Deevong, Pinsurang; Inoue, Tetsushi; Moriya, Shigeharu; Trakulnaleamsai, Savitr; Ohkuma, Moriya; Vongkaluang, Charunee; Noparatnaraporn, Napavarn; Kudo, Toshiaki

    2005-11-01

    We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic "termite clusters" comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.

  10. Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus.

    Directory of Open Access Journals (Sweden)

    Imen Louati

    Full Text Available The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing and Microcystis (colonial and non-N2 fixing that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere.

  11. Diversity, Dynamics and Activity of Bacterial Communities during Production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis

    OpenAIRE

    Randazzo, C.L.; Torriani, S.; Akkermans, A.D.L.; Vos, de, R.; Vaughan, E E

    2002-01-01

    The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene...

  12. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

    Science.gov (United States)

    Stanish, Lee F; Hull, Natalie M; Robertson, Charles E; Harris, J Kirk; Stevens, Mark J; Spear, John R; Pace, Norman R

    2016-01-01

    The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

  13. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

    Directory of Open Access Journals (Sweden)

    Lee F Stanish

    Full Text Available The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria, MLE1-12 (phylum Cyanobacteria, Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

  14. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA

    Science.gov (United States)

    Stanish, Lee F.; Hull, Natalie M.; Robertson, Charles E.; Harris, J. Kirk; Stevens, Mark J.; Spear, John R.; Pace, Norman R.

    2016-01-01

    The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

  15. Application of targeted metagenomics to explore abundance and diversity of CO₂-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea.

    Science.gov (United States)

    Yousuf, Basit; Keshri, Jitendra; Mishra, Avinash; Jha, Bhavanath

    2012-09-10

    Sequestration of CO(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO(2). Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real-time PCR (qRT PCR), was 9.38 ± 0.75 × 10(7) and 5.43 ± 0.79 × 10(8) (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO(2)-fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management. PMID:22766402

  16. Composition and diversity analysis of the gut bacterial community of the Oriental armyworm, Mythimna separata, determined by culture-independent and culture-dependent techniques.

    Science.gov (United States)

    He, Cai; Nan, Xiaoning; Zhang, Zhengqing; Li, Menglou

    2013-01-01

    The intestinal bacteria community structure and diversity of the Oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), was studied by analysis of a 16S rDNA clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. The 16S rDNA clone library revealed a bacterial community diversity comprising Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes and Proteobacteria, among which Escherichia coli (Migula) (Enterobacteriales: Enterobacteriaceae) was the dominant bacteria. The intestinal bacteria isolated by PCR-denaturing gradient gel electrophoresis were classified to Firmicutes, Proteobacteria, and Gracilicutes, and E. coli was again the dominant bacteria. The culture-dependent technique showed that the intestinal bacteria belonged to Firmicutes and Actinobacteria, and Staphylococcus was the dominant bacteria. The intestinal bacteria of M. separata were widely distributed among the groups Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes, Proteobacteria, and Gracilicutes. 16S rDNA clone library, denaturing gradient gel electrophoresis, and culture-dependent techniques should be integrated to obtain precise results in terms of the microbial community and its diversity. PMID:24773514

  17. Distribution and diversity of carbon monoxide-oxidizing bacteria and bulk bacterial communities across a succession gradient on a Hawaiian volcanic deposit.

    Science.gov (United States)

    Weber, C F; King, G M

    2010-07-01

    Relatively little is known about the distribution and diversity of CO-oxidizing bacteria during succession on volcanic deposits even though they are among the primary colonists. We surveyed CO-oxidizing communities across a vegetation gradient on a 1959 cinder deposit using coxL (large subunit gene of carbon monoxide dehydrogenase) sequences. Sequences most closely related to a coxL sequence from Ktedonobacter racemifer, dominated unvegetated cinders, while Proteobacteria-like sequences dominated vegetated sites. The number of coxL operational taxonomic units (OTUs) increased threefold with increased vegetation, and correlated most strongly with the increased beta-Proteobacteria richness (r = 0.987). These compositional shifts were also reflected in overall bacterial community compositions as determined by 16S rRNA gene analysis. Notably, coxL OTU:16S rRNA OTU ratios increased with increased vegetation, indicating that CO oxidizers became a larger fraction of total bacterial richness during succession. Results from most probable number estimates and maximum potential CO uptake activity assays indicate that increased richness is paralleled by increased CO oxidizer abundance, which likely results from increased vegetation and organic carbon content. Collectively, results suggest that in contrast to patterns observed for plant succession, a versatile bacterial functional group that is important during early colonization and succession can remain important in later stages of succession, irrespective of dramatic environmental changes.

  18. Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing.

    Science.gov (United States)

    Hong, Youwei; Liao, Dan; Hu, Anyi; Wang, Han; Chen, Jinsheng; Khan, Sardar; Su, Jianqiang; Li, Hu

    2015-10-01

    Root-associated microbial communities are very important for biogeochemical cycles in wetland ecosystems and help to elaborate the mechanisms of plant invasions. In the estuary of Jiulong River (China), Spartina alterniflora has widely invaded Kandelia obovata-dominated habitats, offering an opportunity to study the influence of root-associated bacteria. The community structures of endophytic and rhizosphere bacteria associated with selected plant species were investigated using the barcoded Illumina paired-end sequencing technique. The diversity indices of bacteria associated with the roots of S. alterniflora were higher than those of the transition stands and K. obovata monoculture. Using principal coordinate analysis with UniFrac metrics, the comparison of β-diversity showed that all samples could be significantly clustered into 3 major groups, according to the bacteria communities of origin. Four phyla, namely Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, were enriched in the rhizoplane of both salt marsh plants, while they shared higher abundances of Cyanobacteria and Proteobacteria among endophytic bacteria. Members of the phyla Spirochaetes and Chloroflexi were found among the endophytic bacteria of S. alterniflora and K. obovata, respectively. One of the interesting findings was that endophytes were more sensitive in response to plant invasion than were rhizosphere bacteria. With linear discriminate analysis, we found some predominant rhizoplane and endophytic bacteria, including Methylococcales, Pseudoalteromonadacea, Clostridium, Vibrio, and Desulfovibrio, which have the potential to affect the carbon, nitrogen, and sulfur cycles. Thus, the results provide clues to the isolation of functional bacteria and the effects of root-associated microbial groups on S. alterniflora invasions. PMID:26223001

  19. Bacterial Communities: Interactions to Scale

    Science.gov (United States)

    Stubbendieck, Reed M.; Vargas-Bautista, Carol; Straight, Paul D.

    2016-01-01

    In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities. PMID:27551280

  20. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  1. Bacterial Diversity in Rhizospheres of Nontransgenic and Transgenic Corn

    OpenAIRE

    Fang, Min; Kremer, Robert J.; Motavalli, Peter P.; Davis, Georgia

    2005-01-01

    Bacterial diversity in transgenic and nontransgenic corn rhizospheres was determined. In greenhouse and field studies, metabolic profiling and molecular analysis of 16S rRNAs differentiated bacterial communities among soil textures but not between corn varieties. We conclude that bacteria in corn rhizospheres are affected more by soil texture than by cultivation of transgenic varieties.

  2. Bacterial Community Profiling of H2/CO2 or Formate-Utilizing Acetogens Enriched from Diverse Ecosystems

    Science.gov (United States)

    Han, R.; Zhang, L.; Fu, B.; Liu, H.

    2014-12-01

    Synthetic gases are usually generated from either cellulosic agricultural waste combustion or industrial release and could be subsequently transformed into acetate, ethanol, and/or butyrate by homoacetogenic bacteria, which commonly possess reductive acetyl-CoA synthesis pathway. Homoacetogen-based syngas fermentation technology provides an alternative solution to link greenhouse gas emission control and cellulosic solid waste treatment with biofuels production. The objective of our current project is to hunt for homoacetogens with capabilities of highly efficiently converting syngases to chemical solvents. In this study, we evaluated homoacetogens population dynamics during enrichments and pinpointed dominant homoacetogens representing diverse ecosystems enriched by different substrates. We enriched homoacetogens from four different samples including waste activate sludge, freshwater sediment, anaerobic methanogenic sludge, and cow manure using H2/CO2 (4:1) or formate as substrate for homoacetogen enrichment. Along with the formyltetrahydrofolate synthetase (FTHFS) gene (fhs gene)-specific real time qPCR assay and Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis, 16S rRNA based 454 high-throughput pyrosequencing was applied to reveal the population dynamic and community structure during enrichment from different origins. Enrichment of homoacetogenic populations coincided with accumulations of short chain fatty acids such as acetate and butyrate. 454 high-throughput pyrosequencing revealed Firmicutes and Spirochaetes populations became dominant while the overall microbial diversity decreased after enrichment. The most abundant sequences among the four origins belonged to the following phyla: Firmicutes, Spirochaetes, Proteobacteria, and Bacteroidetes, accounting for 62.1%-99.1% of the total reads. The major putative homoacetogenic species enriched on H2/CO2 or formate belonged to Clostridium spp., Acetobacterium spp., Acetoanaerobium spp

  3. Drivers of bacterial beta diversity in two temperate forests

    NARCIS (Netherlands)

    Wang, Xugao; Li, Hui; Bezemer, T.Martijn; Hao, Zhanqing

    2016-01-01

    Although the consequences of changes in microbial diversity have received increasing attention, our understanding of processes that drive spatial variation in microbial diversity remains limited. In this study, we sampled bacterial communities in early and late successional temperate forests in Nort

  4. Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance.

    Directory of Open Access Journals (Sweden)

    Wen Xie

    Full Text Available BACKGROUND: Bemisia tabaci (Gennadius is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. METHODOLOGY AND PRINCIPAL FINDINGS: Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45% unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10-5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. CONCLUSIONS: This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the

  5. Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD: Pitfalls and Improved Methodology to Enhance Diversity Recovery

    Directory of Open Access Journals (Sweden)

    Anna V. Piterina

    2010-03-01

    Full Text Available Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD, was performed using a number of extraction and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference to PCR and qPCR amplification was observed due to chelation, nuclease activity and the presence of thermolabile components derived from the ATAD sludge. Addition of selected adjuvant restored the ability to amplify community DNA, derived from the thermophilic sludge, via a number of primer sets of ecological importance and various DNA polymerases. Resolution of community profiles by molecular techniques was also influenced by the ATAD sludge extraction procedure as demonstrated by PCR-DGGE profiling and comparison of taxonomic affiliations of the most predominant members within 16S rRNA gene libraries constructed from ATAD DNA extracted by different methods. Several modifications have been shown to be necessary to optimize the molecular analysis of the ATAD thermal niche which may have general applicability to diversity recovery from similar environments.

  6. Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods.

    Science.gov (United States)

    Tajeddin, E; Sherafat, S J; Majidi, M R S; Alebouyeh, M; Alizadeh, A H M; Zali, M R

    2016-08-01

    Bacterial infection is considered a predisposing factor for disorders of the biliary tract. This study aimed to determine the diversity of bacterial communities in bile samples and their involvement in the occurrence of biliary tract diseases. A total of 102 bile samples were collected during endoscopic retrograde cholangiopancreatography (ERCP). Characterization of bacteria was done using culture and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods. Antimicrobial susceptibility of the isolates was determined based on the Clinical and Laboratory Standards Institute (CLSI) guidelines and identity of the nucleotide sequences of differentiated bands from the DGGE gels was determined based on GenBank data. In total, 41.2 % (42/102) of the patients showed bacterial infection in their bile samples. This infection was detected in 21 % (4/19), 45.4 % (5/11), 53.5 % (15/28), and 54.5 % (24/44) of patients with common bile duct stone, microlithiasis, malignancy, and gallbladder stone, respectively. Escherichia coli showed a significant association with gallstones. Polymicrobial infection was detected in 48 % of the patients. While results of the culture method established coexistence of biofilm-forming bacteria (Pseudomonas aeruginosa, E. coli, Klebsiella pneumoniae, Enterococcus spp., and Acinetobacter spp.) in different combinations, the presence of Capnocytophaga spp., Lactococcus spp., Bacillus spp., Staphylococcus haemolyticus, Enterobacter or Citrobacter spp., Morganella spp., Salmonella spp., and Helicobacter pylori was also characterized in these samples by the PCR-DGGE method. Multidrug resistance phenotypes (87.5 %) and resistance to third- and fourth-generation cephalosporins and quinolones were common in these strains, which could evolve through their selection by bile components. Ability for biofilm formation seems to be a need for polymicrobial infection in this organ. PMID:27193890

  7. Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community

    NARCIS (Netherlands)

    Duarte, G.F.; Rosado, A.S.; Keijzer-Wolters, A.C.; Elsas, van J.D.

    1998-01-01

    A method for the indirect (cell extraction followed by nucleic acid extraction) isolation of bacterial ribosomal RNA (rRNA) and genomic DNA from soil was developed. The protocol allowed for the rapid parallel extraction of genomic DNA as well as small and large ribosomal subunit RNA from four soils

  8. Spatial structuring of bacterial communities within individual Ginkgo biloba trees.

    Science.gov (United States)

    Leff, Jonathan W; Del Tredici, Peter; Friedman, William E; Fierer, Noah

    2015-07-01

    Plant-associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch and trunk samples and used high-throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harbouring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples' proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts.

  9. Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas).

    Science.gov (United States)

    Wichels, Antje; Würtz, Sven; Döpke, Hilke; Schütt, Christian; Gerdts, Gunnar

    2006-04-01

    The aim of this study was to investigate the diversity and variability of bacterial communities associated with the marine sponge Halichondria panicea with respect to tissue compartmentalization as well as seasonal and small-scale geographic variation. Diversity of microorganisms in sponges was investigated recently, but work on the variability and succession of associated bacterial communities is rare. Despite some information on Pacific and Mediterranean sponges, it is still uncertain whether bacteria and sponges are specifically associated. In this study, H. panicea specimens were sampled throughout the year at different stations around the island of Helgoland (North Sea) and investigated using molecular tools. The bacterial community associated with H. panicea was diverse, consisting of one denaturing gradient gel electrophoresis (DGGE) band occurring in most 'tissue' samples and additional variable bands. Variability was observed between different sponge fractions (i.e. the aquiferous system and the 'tissue'), sampling locations, and sampling dates. A PCR-DGGE specific for the Roseobacter group of marine Alphaproteobacteria displayed low diversity and a marked similarity between all samples. Phylogenetic analysis also pointed to specific Alphaproteobacteria of the Roseobacter group, which was predominant in most sponge 'tissue' samples. We conclude that H. panicea harbour a specific Roseobacter population with varying bacterial co-populations occurring seasonally or on a small-scale geographically, sometimes even dominating the bacterial community.

  10. Low Pore Connectivity Increases Bacterial Diversity in Soil▿

    OpenAIRE

    Carson, Jennifer K.; Gonzalez-Quiñones, Vanesa; Murphy, Daniel V.; Hinz, Christoph; Shaw, Jeremy A.; Gleeson, Deirdre B.

    2010-01-01

    One of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water ...

  11. Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity.

    Science.gov (United States)

    Junker, Robert R; Keller, Alexander

    2015-09-01

    Eukaryote-associated microbiomes interact with their hosts in multiple manners, thereby affecting the hosts' phenotype, physical condition and behaviour. In plants, bacteria have numerous functions, with variable net effects, both in natural and agricultural systems. However, information about the composition and diversity of the bacterial communities associated with different aboveground plant organs, particularly flowers, is lacking. In addition, the relative effects of microhabitat and environmental conditions on community establishment require further attention. Here, using culture-independent methods, we determine that leaves and three floral microhabitats (nectar, stamina and styles) of Metrosideros polymorpha (Myrtaceae), a tree endemic to Hawai'i, host unique indicator communities composed of relatively abundant bacterial taxa. These indicator communities are accompanied by a large number of ubiquitous or rare bacteria with lower abundances. In our study system, the strong effect of microhabitat filtering on plant-associated community composition and bacterial richness and diversity strongly exceeds the influence of environmental effects such as precipitation, altitude, substrate age and geographic distance. Thus, the bacterial richness of aboveground plant organs is strongly underestimated when only one microhabitat, e.g. leaves, is considered. Our study represents a first step towards a comprehensive characterization of the distribution, composition and underlying factors, of plant bacterial communities, with implications for future basic and applied research on plant health, pollination and reproduction. PMID:26253507

  12. Bacterial diversity associated with freshwater zooplankton

    DEFF Research Database (Denmark)

    Grossart, Hans-Peter; Dziallas, Claudia; Tang, Kam W.

    2009-01-01

    Bacterial community compositions (BCC) associated with the cladoceran Bosmina coregoni and the cyclopoid copepod Thermocyclops oithonoides in oligotrophic Lake Stechlin versus eutrophic Lake Dagow (northeastern Germany) were compared using molecular techniques. We also transplanted the zooplankton...

  13. Bacterial diversity in soils around a lead and zinc mine

    Institute of Scientific and Technical Information of China (English)

    HU Qing; QI Hong-yan; ZENG Jing-hai; ZHANG Hong-xun

    2007-01-01

    Five samples of soil collected from a lead and zinc mine were used to assess the effect of combined contamination of heavy metals on soil bacterial communities using a polyphasic approach including characterization of isolates by culture method, community level catabolic profiling in BIOLOG GN microplates, and genetic community fingerprinting by denaturing gradient gel electrophoresis of 16S rDNA fragments amplified by PCR from community DNA (PCR-DGGE). The structure of the bacterial community was affected to a certain extent by heavy metals. The PCR-DGGE analysis of 16S rRNA genes showed that there were significant differences in the structure of the microbial community among the soil samples, which were related to the contamination levels. The number of bacteria and the number of denaturing gradient gel electrophoresis (DGGE) bands in the soils increased with increasing distance from the lead and zinc mine tailing, whereas the concentration of lead (Pb) and cadmium (Cd) was decreased. Heavily polluted soils could be characterized by a community that differs from those of lightly polluted soils in richness and structure of dominating bacterial populations. The clustering analysis of the DGGE profiles showed that the bacteria in all the five samples of soil belonged to three clusters. The data from the BIOLOG analysis also showed the same result. This study showed that heavy metal contamination decreased both the biomass and diversity of the bacterial community in soil.

  14. Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere.

    Directory of Open Access Journals (Sweden)

    Blaz Stres

    Full Text Available BACKGROUND: The Himalaya with its altitude and geographical position forms a barrier to atmospheric transport, which produces much aqueous-particle monsoon precipitation and makes it the largest continuous ice-covered area outside polar regions. There is a paucity of data on high-altitude microbial communities, their native environments and responses to environmental-spatial variables relative to seasonal and deglaciation events. METHODOLOGY/PRINCIPAL FINDINGS: Soils were sampled along altitude transects from 5000 m to 6000 m to determine environmental, spatial and seasonal factors structuring bacterial communities characterized by 16 S rRNA gene deep sequencing. Dust traps and fresh-snow samples were used to assess dust abundance and viability, community structure and abundance of dust associated microbial communities. Significantly different habitats among the altitude-transect samples corresponded to both phylogenetically distant and closely-related communities at distances as short as 50 m showing high community spatial divergence. High within-group variability that was related to an order of magnitude higher dust deposition obscured seasonal and temporal rearrangements in microbial communities. Although dust particle and associated cell deposition rates were highly correlated, seasonal dust communities of bacteria were distinct and differed significantly from recipient soil communities. Analysis of closest relatives to dust OTUs, HYSPLIT back-calculation of airmass trajectories and small dust particle size (4-12 µm suggested that the deposited dust and microbes came from distant continental, lacustrine and marine sources, e.g. Sahara, India, Caspian Sea and Tibetan plateau. Cyanobacteria represented less than 0.5% of microbial communities suggesting that the microbial communities benefitted from (codeposited carbon which was reflected in the psychrotolerant nature of dust-particle associated bacteria. CONCLUSIONS/SIGNIFICANCE: The spatial

  15. Dynamics of seawater bacterial communities in a shellfish hatchery.

    Science.gov (United States)

    Powell, S M; Chapman, C C; Bermudes, M; Tamplin, M L

    2013-08-01

    Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.

  16. Office space bacterial abundance and diversity in three metropolitan areas.

    Directory of Open Access Journals (Sweden)

    Krissi M Hewitt

    Full Text Available People in developed countries spend approximately 90% of their lives indoors, yet we know little about the source and diversity of microbes in built environments. In this study, we combined culture-based cell counting and multiplexed pyrosequencing of environmental ribosomal RNA (rRNA gene sequences to investigate office space bacterial diversity in three metropolitan areas. Five surfaces common to all offices were sampled using sterile double-tipped swabs, one tip for culturing and one for DNA extraction, in 30 different offices per city (90 offices, 450 total samples. 16S rRNA gene sequences were PCR amplified using bar-coded "universal" bacterial primers from 54 of the surfaces (18 per city and pooled for pyrosequencing. A three-factorial Analysis of Variance (ANOVA found significant differences in viable bacterial abundance between offices inhabited by men or women, among the various surface types, and among cities. Multiplex pyrosequencing identified more than 500 bacterial genera from 20 different bacterial divisions. The most abundant of these genera tended to be common inhabitants of human skin, nasal, oral or intestinal cavities. Other commonly occurring genera appeared to have environmental origins (e.g., soils. There were no significant differences in the bacterial diversity between offices inhabited by men or women or among surfaces, but the bacterial community diversity of the Tucson samples was clearly distinguishable from that of New York and San Francisco, which were indistinguishable. Overall, our comprehensive molecular analysis of office building microbial diversity shows the potential of these methods for studying patterns and origins of indoor bacterial contamination. "[H]umans move through a sea of microbial life that is seldom perceived except in the context of potential disease and decay." - Feazel et al. (2009.

  17. 饵料对蚯蚓粪细菌群落结构多样性的影响%Characterization of Bacterial Community Diversity in Various Vermicomposts Produced from Feedstocks

    Institute of Scientific and Technical Information of China (English)

    陈浩; 赵海涛; 姚振飞; 孙红军; 胡健

    2012-01-01

    以牛粪、猪粪和污泥等有机废弃物作为蚯蚓饵料,利用细菌16S rDNA V3区特异扩增及变性梯度凝胶电泳(PCR-DGGE)技术,比较了不同饵料及饵料改变对蚯蚓粪细菌群落结构多样性的影响.结果表明:(1)与所取食的饵料相比,蚯蚓粪细菌群落结构多样性均有不同程度的下降,蚯蚓粪与对应饵料之间细菌群落结构相似性范围为15.3%~37.7%;(2)来自不同饵料的蚯蚓粪细菌群落结构相似性范围为17.2%~39.1%,其中以牛粪和猪粪为饵料时,蚯蚓粪细菌群落结构相似性最高,与对应的饵料细菌群落结构相似性相比,提高了近1倍;(3)当饵料由猪粪改为牛粪后,随着时间延长,蚯蚓粪细菌群落结构多样性逐渐下降并趋于稳定,并且蚯蚓粪与饵料牛粪的细菌群落结构相似性由0d的33.2%逐渐下降到21d的14.8%并趋于稳定.由此可知,饵料的种类及转换可以影响蚯蚓粪细菌群落结构多样性.%The earthworms were fed with different feedstocks, such as cattle manure, pig manure and sludge. Then the bacterial community diversity between feedstock and vermicompost were determined by DGGE analysis of PCR-amplified bacterial 16S rDNA V3 region. The results showed that: (1 )The diversities of bacterial community in various vermicomposts were all decreased as compared with different feedstocks. The similarity coefficients of the bacterial community between vermicompost and feedstock were different among all the tested samples, which were from 15.3% to 37.7%;(2)Feeding with different kind of feedstocks resulted in the different similarity coefficient of bacteria] community among all the types of vermicomposts, but some vermicompost samples showed similar bacterial community diversity. The highest similarity value was found between two vermicomposts derived from cattle manure and pig manure, respectively, both of which were about one fold higher than their corresponding feedstocks;( 3 )The

  18. Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery

    OpenAIRE

    Anna V. Piterina; John Bartlett; Tony Pembroke, J.

    2010-01-01

    Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD), was performed using a number of extraction and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference to PCR and qPCR amplification was observed due to chelation, nuclease activity and the presence of thermolabile components derived from the ATAD sl...

  19. Diversity, Dynamics and Activity of Bacterial Communities during Production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis

    NARCIS (Netherlands)

    Randazzo, C.L.; Torriani, S.; Akkermans, A.D.L.; Vos, de W.M.; Vaughan, E.E.

    2002-01-01

    The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and de

  20. Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.

    Science.gov (United States)

    Handl, Stefanie; Dowd, Scot E; Garcia-Mazcorro, Jose F; Steiner, Jörg M; Suchodolski, Jan S

    2011-05-01

    This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces.

  1. 细菌性阴道病患者阴道茵群特征的非培养分析%Diversity of Human Vaginal Bacterial Communities in Healthy Women and Bacterial Vaginosis

    Institute of Scientific and Technical Information of China (English)

    王克迪; 吕治; 苏建荣

    2011-01-01

    Bacterial vaginosis ( BV) is a polymicrobial infestation of the human vagina, thus an accurate understanding of the composition and ecology of the ecosystem is essential for understanding the aetiology of BV. Traditional cultivation technologies are limitative for most of the microbial species that reside in the vagina, while the method of construction 16S rRNA library is credible for illuminate the diversity of human vaginal bacterial communities. Broad-range polymerase-chain-reaction ( PCR) amplification of 16S rRNA and construction of 16S rRNA library were used to analyze the vaginal flora diversity of 30 healthy women and 30 BV positive ones, and 8 species were detected with idiographic primers, in order to know the positive rates. The results showed that diversity and kinds of organisms that comprise the vaginal microbial community varied among women. As detected by broad-range PCR of 16SrRNA, lactobacillus was the predominant species in healthy women, especially L. Crispatus. BV positive ones had greater bacterial diversity, arranged from 6 to 15 species in each sample, where Gardnerella vagmalis(23.0% ) , Prevotella species( 18. 57% ) , Megasphaera species( 14. 3% ) , Lep-totrichia species{ 10. 57% ) , Atopobium vaginae(6.4% ) were strongly associated with BV. 8 species can be detected ; however, the positive rates differ from each other. Vaginal flora predominant with Lactobacillus crispatus is a normal status, while BV positive ones have a predominant species of Gardnerella vaginalis, Prevotella, Megasphaera species, Leptotrichia species and Atopobium vaginae, et al.%细菌性阴道病( bacterial vaginosis,BV)是一种阴道菌群失调所致的常见病,许多阴道菌群为厌氧菌,培养条件要求苛刻,很难纯培养和分离鉴定.本研究旨在通过非培养方法,明确BV患者阴道菌群特征.根据Amsel标准和Nugent评分筛选BV患者和健康育龄期妇女各30例,提取细菌基因组DNA,构建细菌16SrRNA基因文库.同时,应用

  2. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

    Directory of Open Access Journals (Sweden)

    Lidianne L. Rocha

    2016-01-01

    Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

  3. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

    Science.gov (United States)

    Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

    2016-01-01

    We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

  4. Diversity rankings among bacterial lineages in soil.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2009-03-01

    We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed. PMID:18987677

  5. Bacterial Diversity in Çamalti Saltern, Turkey.

    Science.gov (United States)

    Mutlu, Mehmet Burçin; Güven, Kiymet

    2015-01-01

    A combination of culture-dependent and culture-independent approaches was employed to identify the bacterial diversity of Çamalti solar saltern in Turkey. The bacterial communities of Çamalti Saltern were analyzed by molecular techniques that included denaturing gradient gel electrophoresis of 16S rRNA gene fragments PCR amplified from DNA extracted from the water samples of the saltern and 16S rRNA gene library analysis. A total of 42 isolates were identified at the genus/species level and 17 of them were found to belong to the Bacteria domain. All bacterial isolates were phylogenetically related to Halobacillus, Virgibacillus and Halomonas genus. A total of 50 clones from 16S rRNA gene library were analyzed by ARDRA. 16S rRNA sequence analysisof these clones revealed that most (85%) of the bacterial clones were related to Salinibacter genus members of the Bacteroidetes. The sequences of DGGE bands were related to the uncultured Salinibacter, uncultured halophilic bacterium and Halomonas sp. This work highlights the halophilic bacterial diversity of Çamalti marine solar saltern. PMID:26094314

  6. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  7. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments.

    Science.gov (United States)

    Barbato, Marta; Mapelli, Francesca; Magagnini, Mirko; Chouaia, Bessem; Armeni, Monica; Marasco, Ramona; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

    2016-03-15

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments. PMID:26849913

  8. Soil bacterial community responses to global changes

    DEFF Research Database (Denmark)

    Bergmark, Lasse

    the bacterial soil population. The thesis addresses the effects of different global change manipulations on the soil microbial community composition (climate change in Manuscript 1-4 and unconventional urban fertilizers in Manuscript 5-6). A special emphasis was put on combining molecular techniques like 454......’ of climate change manipulations on soil microorganisms and nutrient availability in a Danish heathland, where the samples were taken shortly after a prolonged pre-summer drought. The major findings in the study are that warming increased measures of fungi and bacteria and drought might shift/change...... overall importance for ecosystem function in soil is poorly understood. Global change factors may affect the diversity and functioning of soil prokaryotes and thereby ecosystem functioning. To gain a better understanding of the effects of global changes it is of fundamental importance to classify...

  9. Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology

    Science.gov (United States)

    2016-01-01

    The modern age of metagenomics has delivered unprecedented volumes of data describing the genetic and metabolic diversity of bacterial communities, but it has failed to provide information about coincident cellular morphologies. Much like metabolic and biosynthetic capabilities, morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain. In this essay, we discuss the diversity of bacterial morphology and its implications for understanding both the mechanistic and the adaptive basis of morphogenesis. We consider how best to leverage genomic data and recent experimental developments in order to advance our understanding of bacterial shape and its functional importance. PMID:27695035

  10. Impact of disinfection on drinking water biofilm bacterial community.

    Science.gov (United States)

    Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-11-01

    Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination.

  11. pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

    DEFF Research Database (Denmark)

    El Azhari, Najoi

    2007-01-01

    cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to Pca......H sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices....

  12. Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands.

    Science.gov (United States)

    Jones, Ryan T; Bressan, Alberto; Greenwell, April M; Fierer, Noah

    2011-12-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants. PMID:21965398

  13. Bacterial community development in experimental gingivitis.

    Science.gov (United States)

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  14. Bacterial community development in experimental gingivitis.

    Science.gov (United States)

    Kistler, James O; Booth, Veronica; Bradshaw, David J; Wade, William G

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches

  15. Bacterial community development in experimental gingivitis.

    Directory of Open Access Journals (Sweden)

    James O Kistler

    Full Text Available Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp, and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs per sample. Principal coordinates analysis (PCoA plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new

  16. Bacterial diversity at different stages of the composting process

    Directory of Open Access Journals (Sweden)

    Paulin Lars

    2010-03-01

    Full Text Available Abstract Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.

  17. Metamorphosis of a butterfly-associated bacterial community.

    Directory of Open Access Journals (Sweden)

    Tobin J Hammer

    Full Text Available Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

  18. Changes in soil bacterial community structure with increasing disturbance frequency.

    Science.gov (United States)

    Kim, Mincheol; Heo, Eunjung; Kang, Hojeong; Adams, Jonathan

    2013-07-01

    Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

  19. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  20. Assessing the diversity of bacterial communities associated with plants Avaliação da diversidade de comunidades bacterianas associadas às plantas

    Directory of Open Access Journals (Sweden)

    Fernando Dini Andreote

    2009-09-01

    Full Text Available Plant-bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR, Denaturing Gradient Gel Electrophoresis (DGGE, clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants.As interações planta-bactéria resultam de um reconhecimento recíproco de ambas espécies. Estas interações são responsáveis por processos biológicos essenciais para o desenvolvimento e a proteção das plantas. Este trabalho revisa as metodologias aplicadas na investigação de alterações nas comunidades bacterianas associadas às plantas. Uma descrição das técnicas é feita, desde o isolamento até a aplicação de técnicas independentes de cultivo, destacando as técnicas de qPCR, Gel de Eletroforese em Gradiente Desnaturante (DGGE, construção e análise de bibliotecas de clones, a aplicação de análise multivariada em dados de ecologia microbiana, e as novas metodologias de alto processamento de amostras como microarranjos e pirosequenciamento. Em resumo, esta revisão fornece informações sobre o desenvolvimento das técnicas tradicionais e uma visão geral sobre as novas tendências dos estudos de comunidades bacterianas associadas às plantas.

  1. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.

    Science.gov (United States)

    Kembel, Steven W; O'Connor, Timothy K; Arnold, Holly K; Hubbell, Stephen P; Wright, S Joseph; Green, Jessica L

    2014-09-23

    The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

  2. Age-Related Shifts in Bacterial Diversity in a Reef Coral.

    Science.gov (United States)

    Williams, Alex D; Brown, Barbara E; Putchim, Lalita; Sweet, Michael J

    2015-01-01

    This study investigated the relationship between microbial communities in differently sized colonies of the massive coral Coelastrea aspera at Phuket, Thailand where colony size could be used as a proxy for age. Results indicated significant differences between the bacterial diversity (ANOSIM, R = 0.76, p = 0.001) of differently sized colonies from the same intertidal reef habitat. Juvenile and small colonies ( 28 cm mean diam). Bacterial diversity increased in a step-wise pattern from juveniles endolithic algal band of the coral skeleton; a result providing some support for the hypothesis that the endolithic algae of corals may directly influence the bacterial community present in coral tissues. PMID:26700869

  3. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome.

    Science.gov (United States)

    de Souza, Rafael Soares Correa; Okura, Vagner Katsumi; Armanhi, Jaderson Silveira Leite; Jorrín, Beatriz; Lozano, Núria; da Silva, Márcio José; González-Guerrero, Manuel; de Araújo, Laura Migliorini; Verza, Natália Cristina; Bagheri, Homayoun Chaichian; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes. PMID:27358031

  4. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome

    Science.gov (United States)

    de Souza, Rafael Soares Correa; Okura, Vagner Katsumi; Armanhi, Jaderson Silveira Leite; Jorrín, Beatriz; Lozano, Núria; da Silva, Márcio José; González-Guerrero, Manuel; de Araújo, Laura Migliorini; Verza, Natália Cristina; Bagheri, Homayoun Chaichian; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes. PMID:27358031

  5. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves

    Directory of Open Access Journals (Sweden)

    Xuejian eYu

    2015-08-01

    Full Text Available The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were found to be the dominant phyla despite the growth stages and fulvic acid application. Stevia growth stages strongly regulated composition of endophytic community. The genera Agrobacterium (12.3 % and Erwinia (7.2 % dominated in seedling stage were apparently declined in the vegetable and initial flowering stages, while Sphingomonas and Methylobacterium increased in mature leaves at harvest time, which showed that the mature leaves of Stevia preferred to accumulate some certain endophytic bacteria. Sphingomonas and Methylobacterium constituted an important part of the core endophytic community and were positively correlated with the stevioside content and UGT74G1 gene expression, respectively; while Erwinia, Agrobacterium and Bacillus were negatively correlated with the stevioside accumulation. Fulvic acid treatment accelerated the variation of endophytes along the growth stages.

  6. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves.

    Science.gov (United States)

    Yu, Xuejian; Yang, Jinshui; Wang, Entao; Li, Baozhen; Yuan, Hongli

    2015-01-01

    The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were found to be the dominant phyla despite the growth stages and fulvic acid application. Stevia growth stages strongly regulated composition of endophytic community. The genera Agrobacterium (12.3%) and Erwinia (7.2%) dominated in seedling stage were apparently declined in the vegetable and initial flowering stages, while Sphingomonas and Methylobacterium increased in mature leaves at harvest time, which showed that the mature leaves of Stevia preferred to accumulate some certain endophytic bacteria. Sphingomonas and Methylobacterium constituted an important part of the core endophytic community and were positively correlated with the stevioside content and UGT74G1 gene expression, respectively; while Erwinia, Agrobacterium, and Bacillus were negatively correlated with the stevioside accumulation. Fulvic acid treatment accelerated the variation of endophytes along the growth stages and increased the steviol glycosides content. This is the first study to reveal the community composition of endophytic bacteria in the Stevia leaves, to evidence the strong effects of growth stage and fulvic acid application on the endophytes of Stevia, and to demonstrate the correlation between the endophytic bacteria and the steviol glycosides accumulation.

  7. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves.

    Science.gov (United States)

    Yu, Xuejian; Yang, Jinshui; Wang, Entao; Li, Baozhen; Yuan, Hongli

    2015-01-01

    The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were found to be the dominant phyla despite the growth stages and fulvic acid application. Stevia growth stages strongly regulated composition of endophytic community. The genera Agrobacterium (12.3%) and Erwinia (7.2%) dominated in seedling stage were apparently declined in the vegetable and initial flowering stages, while Sphingomonas and Methylobacterium increased in mature leaves at harvest time, which showed that the mature leaves of Stevia preferred to accumulate some certain endophytic bacteria. Sphingomonas and Methylobacterium constituted an important part of the core endophytic community and were positively correlated with the stevioside content and UGT74G1 gene expression, respectively; while Erwinia, Agrobacterium, and Bacillus were negatively correlated with the stevioside accumulation. Fulvic acid treatment accelerated the variation of endophytes along the growth stages and increased the steviol glycosides content. This is the first study to reveal the community composition of endophytic bacteria in the Stevia leaves, to evidence the strong effects of growth stage and fulvic acid application on the endophytes of Stevia, and to demonstrate the correlation between the endophytic bacteria and the steviol glycosides accumulation. PMID:26379644

  8. Targeted bacterial immunity buffers phage diversity.

    Science.gov (United States)

    Haerter, Jan O; Trusina, Ala; Sneppen, Kim

    2011-10-01

    Bacteria have evolved diverse defense mechanisms that allow them to fight viral attacks. One such mechanism, the clustered, regularly interspaced, short palindromic repeat (CRISPR) system, is an adaptive immune system consisting of genetic loci that can take up genetic material from invasive elements (viruses and plasmids) and later use them to reject the returning invaders. It remains an open question how, despite the ongoing evolution of attack and defense mechanisms, bacteria and viral phages manage to coexist. Using a simple mathematical model and a two-dimensional numerical simulation, we found that CRISPR adaptive immunity allows for robust phage-bacterium coexistence even when the number of virus species far exceeds the capacity of CRISPR-encoded genetic memory. Coexistence is predicted to be a consequence of the presence of many interdependent species that stress but do not overrun the bacterial defense system. PMID:21813617

  9. Local-global overlap in diversity informs mechanisms of bacterial biogeography.

    Science.gov (United States)

    Livermore, Joshua A; Jones, Stuart E

    2015-11-01

    Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local-global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among 'patches', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.

  10. Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities.

    Science.gov (United States)

    Yuan, Xia; Knelman, Joseph E; Gasarch, Eve; Wang, Deli; Nemergut, Diana R; Seastedt, Timothy R

    2016-06-01

    Bacterial community composition and diversity was studied in alpine tundra soils across a plant species and moisture gradient in 20 y-old experimental plots with four nutrient addition regimes (control, nitrogen (N), phosphorus (P) or both nutrients). Different bacterial communities inhabited different alpine meadows, reflecting differences in moisture, nutrients and plant species. Bacterial community alpha-diversity metrics were strongly correlated with plant richness and the production of forbs. After meadow type, N addition proved the strongest determinant of bacterial community structure. Structural Equation Modeling demonstrated that tundra bacterial community responses to N addition occur via changes in plant community composition and soil pH resulting from N inputs, thus disentangling the influence of direct (resource availability) vs. indirect (changes in plant community structure and soil pH) N effects that have remained unexplored in past work examining bacterial responses to long-term N inputs in these vulnerable environments. Across meadow types, the relative influence of these indirect N effects on bacterial community structure varied. In explicitly evaluating the relative importance of direct and indirect effects of long-term N addition on bacterial communities, this study provides new mechanistic understandings of the interaction between plant and microbial community responses to N inputs amidst environmental change.

  11. Diversity and Community Can Coexist.

    Science.gov (United States)

    Stivala, Alex; Robins, Garry; Kashima, Yoshihisa; Kirley, Michael

    2016-03-01

    We examine the (in)compatibility of diversity and sense of community by means of agent-based models based on the well-known Schelling model of residential segregation and Axelrod model of cultural dissemination. We find that diversity and highly clustered social networks, on the assumptions of social tie formation based on spatial proximity and homophily, are incompatible when agent features are immutable, and this holds even for multiple independent features. We include both mutable and immutable features into a model that integrates Schelling and Axelrod models, and we find that even for multiple independent features, diversity and highly clustered social networks can be incompatible on the assumptions of social tie formation based on spatial proximity and homophily. However, this incompatibility breaks down when cultural diversity can be sufficiently large, at which point diversity and clustering need not be negatively correlated. This implies that segregation based on immutable characteristics such as race can possibly be overcome by sufficient similarity on mutable characteristics based on culture, which are subject to a process of social influence, provided a sufficiently large "scope of cultural possibilities" exists. PMID:27217326

  12. The diversity of coral associated bacteria and the environmental factors affect their community variation.

    Science.gov (United States)

    Zhang, Yan-Ying; Ling, Juan; Yang, Qing-Song; Wang, You-Shao; Sun, Cui-Ci; Sun, Hong-Yan; Feng, Jing-Bin; Jiang, Yu-Feng; Zhang, Yuan-Zhou; Wu, Mei-Lin; Dong, Jun-De

    2015-10-01

    Coral associated bacterial community potentially has functions relating to coral health, nutrition and disease. Culture-free, 16S rRNA based techniques were used to compare the bacterial community of coral tissue, mucus and seawater around coral, and to investigate the relationship between the coral-associated bacterial communities and environmental variables. The diversity of coral associated bacterial communities was very high, and their composition different from seawater. Coral tissue and mucus had a coral associated bacterial community with higher abundances of Gammaproteobacteria. However, bacterial community in seawater had a higher abundance of Cyanobacteria. Different populations were also found in mucus and tissue from the same coral fragment, and the abundant bacterial species associated with coral tissue was very different from those found in coral mucus. The microbial diversity and OTUs of coral tissue were much higher than those of coral mucus. Bacterial communities of corals from more human activities site have higher diversity and evenness; and the structure of bacterial communities were significantly different from the corals collected from other sites. The composition of bacterial communities associated with same coral species varied with season's changes, geographic differences, and coastal pollution. Unique bacterial groups found in the coral samples from more human activities location were significant positively correlated to chemical oxygen demand. These coral specific bacteria lead to coral disease or adjust to form new function structure for the adaption of different surrounding needs further research. PMID:25833806

  13. Environmental and anthropogenic controls over bacterial communities in wetland soils

    OpenAIRE

    Hartman, Wyatt H.; Curtis J Richardson; Vilgalys, Rytas; Bruland, Gregory L.

    2008-01-01

    Soil bacteria regulate wetland biogeochemical processes, yet little is known about controls over their distribution and abundance. Bacteria in North Carolina swamps and bogs differ greatly from Florida Everglades fens, where communities studied were unexpectedly similar along a nutrient enrichment gradient. Bacterial composition and diversity corresponded strongly with soil pH, land use, and restoration status, but less to nutrient concentrations, and not with wetland type or soil carbon. Sur...

  14. Bacterial community survey of sediments at Naracoorte Caves, Australia

    OpenAIRE

    Ball Andrew S.; Kirby Greg; Bourne Steven; Cao Xiangsheng; Mazaheri Nezhad Fard Ramin; Adetutu Eric M.; Shahsavari Esamaeil; Thorpe Krystal

    2012-01-01

    Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey ...

  15. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water.

    Science.gov (United States)

    Long, Yan; Yi, Hao; Chen, Sili; Zhang, Zhengke; Cui, Kai; Bing, Yongxin; Zhuo, Qiongfang; Li, Bingxin; Xie, Shuguang; Guo, Qingwei

    2016-10-01

    Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system. PMID:27392623

  16. Mechanisms Controlling the Plant Diversity Effect on Soil Microbial Community Composition and Soil Microbial Diversity

    Science.gov (United States)

    Mellado Vázquez, P. G.; Lange, M.; Griffiths, R.; Malik, A.; Ravenek, J.; Strecker, T.; Eisenhauer, N.; Gleixner, G.

    2015-12-01

    Soil microorganisms are the main drivers of soil organic matter cycling. Organic matter input by living plants is the major energy and matter source for soil microorganisms, higher organic matter inputs are found in highly diverse plant communities. It is therefore relevant to understand how plant diversity alters the soil microbial community and soil organic matter. In a general sense, microbial biomass and microbial diversity increase with increasing plant diversity, however the mechanisms driving these interactions are not fully explored. Working with soils from a long-term biodiversity experiment (The Jena Experiment), we investigated how changes in the soil microbial dynamics related to plant diversity were explained by biotic and abiotic factors. Microbial biomass quantification and differentiation of bacterial and fungal groups was done by phospholipid fatty acid (PLFA) analysis; terminal-restriction fragment length polymorphism was used to determine the bacterial diversity. Gram negative (G-) bacteria predominated in high plant diversity; Gram positive (G+) bacteria were more abundant in low plant diversity and saprotrophic fungi were independent from plant diversity. The separation between G- and G+ bacteria in relation to plant diversity was governed by a difference in carbon-input related factors (e.g. root biomass and soil moisture) between plant diversity levels. Moreover, the bacterial diversity increased with plant diversity and the evenness of the PLFA markers decreased. Our results showed that higher plant diversity favors carbon-input related factors and this in turn favors the development of microbial communities specialized in utilizing new carbon inputs (i.e. G- bacteria), which are contributing to the export of new C from plants to soils.

  17. Molecular analysis of the bacterial diversity in uranium mill tailings

    International Nuclear Information System (INIS)

    A culture-independent molecular approach has been applied to investigate the bacterial diversity in three uranium contaminated sites. The three analysed soil samples have been collected from the uranium waste pile Haberland near Johanngeorgenstadt (Germany), from the uranium mill tailings in Gunnison, Colorado (USA) and from the uranium mill tailings in Shiprock, New Mexico (USA). The 16S rDNA fragments which has been isolated through direct lysis of the whole-DNA were amplified by the use of the universal primers 16S43f and 16S1404r and cloned. With restriction fragment length polymorphismus (RFLP) were the clones screened and one representative of all RFLP types that occurred more than once in the clone library was sequenced and analysed. In spite of the contamination a considerable diversity and significant differences in the composition of the natural bacterial communities in these three sites have been found. In the sample collected from the waste pile Haberland near Johanngeorgenstadt α-Proteobacteria and representatives of the Holophaga/Acidobacterium were numerically predominant. The distribution of bacteria in the sample collected from uranium mill tailings Gunnison was very similar to those found in the Haberland waste pile, but there were found besides α-Proteobacteria and representatives of Holophaga/Acidobacterium a lot of γ-Proteobacteria. The structure of the bacterial community in the sample collected from the uranium mill tailings Shiprock was significantly different. Only some representatives of the Holophaga/Acidobacterium and α-Proteobacteria were represented. Large populations of Bacilli, γ-Proteobacteria and green non sulfur bacteria were dominant in this sample. (orig.)

  18. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  19. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  20. Bacterial diversity and biogeography in deep-sea sediments of the South Atlantic Ocean

    DEFF Research Database (Denmark)

    Schauer, Regina; Bienhold, Christina; Ramette, Alban;

    2010-01-01

    communities in three basins of the eastern South Atlantic Ocean to determine diversity and biogeography of bacterial communities in deep-sea surface sediments. The analysis of 16S ribosomal RNA (rRNA) gene clone libraries in each basin revealed a high diversity, representing 521 phylotypes with 98% identity......Microbial biogeographic patterns in the deep sea depend on the ability of microorganisms to disperse. One possible limitation to microbial dispersal may be the Walvis Ridge that separates the Antarctic Lower Circumpolar Deep Water from the North Atlantic Deep Water. We examined bacterial...

  1. Molecular survey of bacterial communities associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers.

    Science.gov (United States)

    Jiang, Tieshan; Mandal, Rabindra K; Wideman, Robert F; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

    2015-01-01

    Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in

  2. Molecular survey of bacterial communities associated with bacterial chondronecrosis with osteomyelitis (BCO in broilers.

    Directory of Open Access Journals (Sweden)

    Tieshan Jiang

    Full Text Available Bacterial chondronecrosis with osteomyelitis (BCO is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens. Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9% comprised the most common phylum, followed by Firmicutes (6.1% and Actinobacteria (2.6%, accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia, lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions, and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of

  3. Determination Of Uncultured Endo phytic Bacterial Community From Rice Root

    International Nuclear Information System (INIS)

    Culture-independent approaches were developed for rapid analysis of microbial community diversity in various environments. Direct analysis based on 16S rDNA as the phylogenetic markers is the most ordinary, conventional and suitable methods for bacterial diversity analysis. The objective of this study is to investigate the microbial diversity from the rice root tissues using culture-independent approach by 16S rDNA library construction. The 16S rDNAs were directly extracted from a total genomic DNA by polymerase chain reaction (PCR) amplification using with the bacteria-specific primer set. The 16S rDNAs were subsequently analysed by cloning and restriction digestion. The amplified ribosomal DNA restriction analysis (ARDRA) clustered the 16S rDNAs into eight majority patterns. These predominant patterns were analysed by DNA sequencing. A better understanding at microbial diversity level is critical to potentiate the endophyte as plant growth promoters. (author)

  4. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans. PMID:26626941

  5. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.

  6. Patterns of bacterial diversity across a range of Antarctic terrestrial habitats.

    Science.gov (United States)

    Yergeau, Etienne; Newsham, Kevin K; Pearce, David A; Kowalchuk, George A

    2007-11-01

    Although soil-borne bacteria represent the world's greatest source of biological diversity, it is not well understood whether extreme environmental conditions, such as those found in Antarctic habitats, result in reduced soil-borne microbial diversity. To address this issue, patterns of bacterial diversity were studied in soils sampled along a > 3200 km southern polar transect spanning a gradient of increased climate severity over 27 degrees of latitude. Vegetated and fell-field plots were sampled at the Falkland (51 degrees S), South Georgia (54 degrees S), Signy (60 degrees S) and Anchorage Islands (67 degrees S), while bare frost-sorted soil polygons were examined at Fossil Bluff (71 degrees S), Mars Oasis (72 degrees S), Coal Nunatak (72 degrees S) and the Ellsworth Mountains (78 degrees S). Bacterial 16S rRNA gene sequences were recovered subsequent to direct DNA extraction from soil, polymerase chain reaction amplification and cloning. Although bacterial diversity was observed to decline with increased latitude, habitat-specific patterns appeared to also be important. Namely, a negative relationship was found between bacterial diversity and latitude for fell-field soils, but no such pattern was observed for vegetated sites. The Mars Oasis site, previously identified as a biodiversity hotspot within this region, proved exceptional within the study transect, with unusually high bacterial diversity. In independent analyses, geographical distance and vegetation cover were found to significantly influence bacterial community composition. These results provide insight into the factors shaping the composition of bacterial communities in Antarctic terrestrial habitats and support the notion that bacterial diversity declines with increased climatic severity.

  7. Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.

    Science.gov (United States)

    Takeuchi, Yayoi; Chaffron, Samuel; Salcher, Michaela M; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K

    2015-07-01

    Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria. PMID:26138047

  8. Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations.

    Directory of Open Access Journals (Sweden)

    Elizabeth Halliday

    Full Text Available Recreational water quality, as measured by culturable fecal indicator bacteria (FIB, may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.

  9. The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows

    OpenAIRE

    Mao Shengyong; Zhang Ruiyang; Wang Dongsheng; Zhu Weiyun

    2012-01-01

    Abstract Background Sub-acute ruminal acidosis (SARA) is a well-recognized digestive disorder found in particular in well-managed dairy herds. SARA can result in increased flow of fermentable substrates to the hindgut, which can increase the production of volatile fatty acids, alter the structure of the microbial community, and have a negative effect on animal health and productivity. However, little is known about changes in the structure of the microbial community and its relationship with ...

  10. Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Sebastian Germerodt

    2016-06-01

    Full Text Available Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability, we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.

  11. Diverse Perspectives on Inclusive School Communities

    Science.gov (United States)

    Tsokova, Diana; Tarr, Jane

    2012-01-01

    What is an inclusive school community? How do stakeholders perceive their roles and responsibilities towards inclusive school communities? How can school communities become more inclusive through engagement with individual perspectives? "Diverse Perspectives on Inclusive School Communities" captures and presents the voices of a wide range of…

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  14. Spatial scales of bacterial diversity in cold-water coral reef ecosystems.

    Directory of Open Access Journals (Sweden)

    Sandra Schöttner

    Full Text Available BACKGROUND: Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning. METHODOLOGY/PRINCIPAL FINDINGS: Bacterial community structure, as determined by Automated Ribosomal Intergenic Spacer Analysis (ARISA, was investigated with respect to (i microbial habitat type and (ii coral species and color, as well as the three spatial components (iii geomorphologic reef zoning, (iv reef boundary, and (v reef location. Communities revealed fundamental differences between coral-generated (branch surface, mucus and ambient microbial habitats (seawater, sediments. This habitat specificity appeared pivotal for determining bacterial community shifts over all other study levels investigated. Coral-derived surfaces showed species-specific patterns, differing significantly between Lophelia pertusa and Madrepora oculata, but not between L. pertusa color types. Within the reef center, no community distinction corresponded to geomorphologic reef zoning for both coral-generated and ambient microbial habitats. Beyond the reef center, however, bacterial communities varied considerably from local to regional scales, with marked shifts toward the reef periphery as well as between different in- and offshore reef sites, suggesting significant biogeographic imprinting but weak microbe-host specificity. CONCLUSIONS/SIGNIFICANCE: This study presents the first multi-scale survey of bacterial diversity in cold-water coral reefs, spanning a total of five observational levels including three spatial scales. It demonstrates that bacterial communities in cold-water coral reefs are structured by multiple factors acting at different spatial scales, which has

  15. Bacterial Community Development in Experimental Gingivitis

    OpenAIRE

    Kistler, James O; Veronica Booth; Bradshaw, David J.; Wade, William G.

    2013-01-01

    Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygi...

  16. Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

    Science.gov (United States)

    Rosselli, Riccardo; Romoli, Ottavia; Vitulo, Nicola; Vezzi, Alessandro; Campanaro, Stefano; de Pascale, Fabio; Schiavon, Riccardo; Tiarca, Maurizio; Poletto, Fabio; Concheri, Giuseppe; Valle, Giorgio; Squartini, Andrea

    2016-01-01

    The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies. PMID:27577787

  17. Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon.

    Science.gov (United States)

    Rosselli, Riccardo; Romoli, Ottavia; Vitulo, Nicola; Vezzi, Alessandro; Campanaro, Stefano; de Pascale, Fabio; Schiavon, Riccardo; Tiarca, Maurizio; Poletto, Fabio; Concheri, Giuseppe; Valle, Giorgio; Squartini, Andrea

    2016-01-01

    The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies. PMID:27577787

  18. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves

    OpenAIRE

    Yu, Xuejian; Yang, Jinshui; Wang, Entao; Li, Baozhen; Yuan, Hongli

    2015-01-01

    The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroi...

  19. Bacterial diversity, composition and temporal-spatial variation in the sediment of Jiaozhou Bay, China

    Institute of Scientific and Technical Information of China (English)

    LIU Xin; XIAO Tian; LUAN Qingshan; ZHANG Wenyan; WANG Mengqiang; YUE Haidong

    2011-01-01

    Studies on the diversity and distribution of bacterial populations will improve the overall understanding of the global patterns of marine bacteria and help to comprehend local biochemical processes and environments. We evaluated the composition and the dynamics of bacterial communities in the sediment of Jiaozhou Bay (China) using PCR-denaturing gradient gel electrophoresis (DGGE). Sediment samples were collected from 10 different sites in May, August, and November 2008 and in February 2009.There was significant temporal variation in bacterial community composition at all sites. However, the spatial variation was very small. The DGGE analyses of bacterial communities were used to divide the 10 stations into three types. Canonical correspondence analysis (CCA) revealed that the changes in bacterial communities were driven by sediment properties. Sequence analysis of DGGE band-derived 16S rRNA gene fragments revealed that the dominant bacterial groups in the sediment were of the classes γ-proteobacteria and δ-proteobacteria and phyla Bacteroidetes and Nitrospirae. Our results provide considerable insight into the bacterial community structure in Jiaozhou Bay, China.

  20. A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

    Science.gov (United States)

    Shang, Shuanghua; Yi, Yanli

    2015-12-01

    The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

  1. Analysis of the rhizosphere bacterial community and function diversity in cherry orchard of Dalian region%大连地区樱桃园根际土壤细菌群落功能多样性分析

    Institute of Scientific and Technical Information of China (English)

    吕德国; 侯爽; 秦嗣军; 刘灵芝; 马怀宇; 刘国成

    2011-01-01

    The microbial metabolic activity and functional diversities of sweet cherry orchards with clay soil,Sandy loam,Coarse soil in Dalian region were analyzed under Biolog Ecoplate method.The results showed that the amounts of soil microbe,microbial metabolic activity,Substrate richness(S),Shannon's diversity index(H)and Evenness index(J)were clay soil〉Sandy loam〉Coarse soil,and the carbon sources with highest utilization efficiency by soil microbes was carbohydrate in three soil texture.Microbes in the clay soil utilized phenolic compounds with higher efficiency and microbes in sandy loam and coarse soil utilized amines with higher efficiency.The results indicate that soil texture influences soil microbial functional diversity in cherry orchard,and the highest in clay soil,followed by in sandy loam and in coarse soil.But no significant difference was found in microbial metabolic activity,bacterial efficiency of carbon sources,bacterial variety of metabolic activity of three kinds ofsoil texture.Thus,the major factor responsible for bacterial community function diversity in cherry orchards is soil texture.%利用Biolog生态微平板法,分析了大连地区黏土、沙壤土、粗骨土3种不同质地土壤樱桃园微生物代谢活性及其功能多样性。结果表明,土壤微生物的数量、群落代谢活性、底物碳源利用数(S)、多样性指数(H)及均匀度指数(J)均为黏土〉沙壤土〉粗骨土,3种质地的土壤细菌碳源均以利用碳水化合物为主,而对芳香化合物和胺类化合物的利用喜好不同,其中黏土对芳香化合物的利用率相对较高,沙壤土和粗骨土对胺类化合物的利用率相对较高。说明,土壤质地可影响樱桃园的土壤微生物功能多样性,其中以黏土最丰富,沙壤土次之,粗骨土最差。3种土壤质地樱桃园的表土与根际土之间的土壤微生物群落代谢活性、土壤细菌碳源利用情况以及土壤细菌代谢功

  2. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    Science.gov (United States)

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-03-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.

  3. Bacterial community mapping of the mouse gastrointestinal tract.

    Directory of Open Access Journals (Sweden)

    Shenghua Gu

    Full Text Available Keeping mammalian gastrointestinal (GI tract communities in balance is crucial for host health maintenance. However, our understanding of microbial communities in the GI tract is still very limited. In this study, samples taken from the GI tracts of C57BL/6 mice were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities along the mouse GI tract, including those present in the stomach, duodenum, jejunum, ileum, cecum, colon and feces. Further analyses of the 283,234 valid sequences obtained from pyrosequencing revealed that the gastric, duodenal, large intestinal and fecal samples had higher phylogenetic diversity than the jejunum and ileum samples did. The microbial communities found in the small intestine and stomach were different from those seen in the large intestine and fecal samples. A greater proportion of Lactobacillaceae were found in the stomach and small intestine, while a larger proportion of anaerobes such as Bacteroidaceae, Prevotellaceae, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae were found in the large intestine and feces. In addition, inter-mouse variations of microbiota were observed between the large intestinal and fecal samples, which were much smaller than those between the gastric and small intestinal samples. As far as we can ascertain, ours is the first study to systematically characterize bacterial communities from the GI tracts of C57BL/6 mice.

  4. Horizontal gene transfer and bacterial diversity

    Indian Academy of Sciences (India)

    Chitra Dutta; Archana Pan

    2002-02-01

    Bacterial genomes are extremely dynamic and mosaic in nature. A substantial amount of genetic information is inserted into or deleted from such genomes through the process of horizontal transfer. Through the introduction of novel physiological traits from distantly related organisms, horizontal gene transfer often causes drastic changes in the ecological and pathogenic character of bacterial species and thereby promotes microbial diversification and speciation. This review discusses how the recent influx of complete chromosomal sequences of various microorganisms has allowed for a quantitative assessment of the scope, rate and impact of horizontally transmitted information on microbial evolution.

  5. Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow.

    Science.gov (United States)

    Li, Yaoming; Lin, Qiaoyan; Wang, Shiping; Li, Xiangzhen; Liu, Wentso; Luo, Caiyun; Zhang, Zhenhua; Zhu, Xiaoxue; Jiang, Lili; Li, Xine

    2016-01-01

    Warming and grazing significantly affect the structure and function of an alpine meadow ecosystem. Yet, the responses of soil microbes to these disturbances are not well understood. Controlled asymmetrical warming (+1.2/1.7°C during daytime/nighttime) with grazing experiments were conducted to study microbial response to warming, grazing and their interactions. Significant interactive effects of warming and grazing were observed on soil bacterial α-diversity and composition. Warming only caused significant increase in bacterial α-diversity under no-grazing conditions. Grazing induced no substantial differences in bacterial α-diversity and composition irrespective of warming. Warming, regardless of grazing, caused a significant increase in soil bacterial community similarity across space, but grazing only induced significant increases under no-warming conditions. The positive effects of warming on bacterial α-diversity and grazing on community similarity were weakened by grazing and warming, respectively. Soil and plant variables explained well the variations in microbial communities, indicating that changes in soil and plant properties may primarily regulate soil microbial responses to warming in this alpine meadow. The results suggest that bacterial communities may become more similar across space in a future, warmed climate and moderate grazing may potentially offset, at least partially, the effects of global warming on the soil microbial diversity. PMID:26635411

  6. 非抗虫转基因棉花对土壤细菌群落多样性的影响%Effects of Insect Non-resistant Transgenic Cottons on Bacterial Community Diversity in Soil

    Institute of Scientific and Technical Information of China (English)

    赵云丽; 李刚; 修伟明; 多立安; 曹璇; 雒珺瑜; 崔金杰; 杨殿林; 赵建宁

    2015-01-01

    There are increasing public concerns over the ecological risks of transgenic plants. Under field conditions, the diversity and com-position of bacterial community in soils grown with three insect non-resistant transgenic cottons(high-yield transgenic cotton expressing the RNA recognition motif 2 gene, disease-resistant transgenic cotton expressing the gastrodia antifungal protein and high-quality transgenic cotton expressing the [1-aminocyclopropane-1-carboxylate(ACC)oxidase])and one conventional cotton CCRI 12(as control)were evalu-ated at the boll-opening stage by denaturing gradient gel electrophoresis(DGGE). The results showed that planting three transgenic cottons did not show significant effects on Shannon-wiener index(H), evenness(EH)and richness(S)of soil bacteria. High degree of similarity in community structure was observed between transgenic and conventional cottons, indicating no influence of transgenic cottons on bacterial community diversity in the short term. High-yield RRM2 transgenic cotton, disease-resistant GAFP transgenic cotton, high-quality ACO2 transgenic cotton and conventional cotton had 67%similarity in community levels and were thus regarded as one group. According to the se-quence analysis of DGGE dominant bands, microorganisms which presented the highest homology belonged to families of Flavobacteria, Bacteriovorax, Segetibacter, alpha proteobacterium, Geobacte, Paenisporosarcina, and Acidobacterium, respectively, and all of them were not cultivatable.%田间试验条件下,为了探究非抗虫转基因棉花对土壤细菌群落多样性的影响,应用PCR-DGGE技术对转RRM2基因高产棉、转GAFP基因抗病棉、转ACO2基因优质棉及非转基因常规棉(中棉所12)种植后在吐絮期的土壤细菌群落多样性进行分析。结果表明,与常规棉相比,3种转基因棉的种植均未对土壤细菌香农-威纳指数(H)、均匀度(EH)和丰富度(S)造成显著影

  7. Patterning bacterial communities on epithelial cells.

    Directory of Open Access Journals (Sweden)

    Mohammed Dwidar

    Full Text Available Micropatterning of bacteria using aqueous two phase system (ATPS enables the localized culture and formation of physically separated bacterial communities on human epithelial cell sheets. This method was used to compare the effects of Escherichia coli strain MG1655 and an isogenic invasive counterpart that expresses the invasin (inv gene from Yersinia pseudotuberculosis on the underlying epithelial cell layer. Large portions of the cell layer beneath the invasive strain were killed or detached while the non-invasive E. coli had no apparent effect on the epithelial cell layer over a 24 h observation period. In addition, simultaneous testing of the localized effects of three different bacterial species; E. coli MG1655, Shigella boydii KACC 10792 and Pseudomonas sp DSM 50906 on an epithelial cell layer is also demonstrated. The paper further shows the ability to use a bacterial predator, Bdellovibriobacteriovorus HD 100, to selectively remove the E. coli, S. boydii and P. sp communities from this bacteria-patterned epithelial cell layer. Importantly, predation and removal of the P. Sp was critical for maintaining viability of the underlying epithelial cells. Although this paper focuses on a few specific cell types, the technique should be broadly applicable to understand a variety of bacteria-epithelial cell interactions.

  8. Bacterial community reconstruction using compressed sensing.

    Science.gov (United States)

    Amir, Amnon; Zuk, Or

    2011-11-01

    Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. Our method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of all known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a simple and efficient way for identifying bacterial species compositions in biological samples. All supplementary data and the MATLAB code are available at www.broadinstitute.org/?orzuk/publications/BCS/.

  9. Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra

    Directory of Open Access Journals (Sweden)

    Congcong eShen

    2015-06-01

    Full Text Available The elevational diversity pattern for microorganisms has received great attention recently but is still understudied, and phylogenetic relatedness is rarely studied for microbial elevational distributions. Using a bar-coded pyrosequencing technique, we examined the biodiversity patterns for soil bacterial communities of tundra ecosystem along 2000–2500 m elevations on Changbai Mountain in China. Bacterial taxonomic richness displayed a linear decreasing trend with increasing elevation. Phylogenetic diversity and mean nearest taxon distance (MNTD exhibited a unimodal pattern with elevation. Bacterial communities were more phylogenetically clustered than expected by chance at all elevations based on the standardized effect size of MNTD metric. The bacterial communities differed dramatically among elevations, and the community composition was significantly correlated with soil total carbon, total nitrogen, C:N ratio, and dissolved organic carbon. Multiple ordinary least squares regression analysis showed that the observed biodiversity patterns strongly correlated with soil total carbon and C:N ratio. Taken together, this is the first time that a significant bacterial diversity pattern has been observed across a small-scale elevational gradient. Our results indicated that soil carbon and nitrogen contents were the critical environmental factors affecting bacterial elevational distribution in Changbai Mountain tundra. This suggested that ecological niche-based environmental filtering processes related to soil carbon and nitrogen contents could play a dominant role in structuring bacterial communities along the elevational gradient.

  10. Biogeographic Congruency among Bacterial Communities from Terrestrial Sulfidic Springs

    Directory of Open Access Journals (Sweden)

    Brendan eHeadd

    2014-09-01

    Full Text Available Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria, up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria, but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or

  11. Effect of Metal-Rich Sewage Sludge Application on the Bacterial Communities of Grasslands

    OpenAIRE

    Barkay, Tamar; Tripp, Susan C.; Betty H. Olson

    1985-01-01

    The effect of long-term application of heavy metal-laden sewage sludge on the total heterotrophic aerobic and the cadmium-resistant soil bacterial communities was studied. Gram-positive bacteria were completely absent from resistant communities. These findings suggest that this group is highly susceptible to Cd. Shannon's diversity indices estimated for total communities did not reveal negative effects on the communities that developed in the presence of sludge. However, Cd-resistant communit...

  12. Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa.

    Science.gov (United States)

    Moroenyane, I; Chimphango, S B M; Wang, J; Kim, H-K; Adams, Jonathan Miles

    2016-08-01

    The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major

  13. Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa.

    Science.gov (United States)

    Moroenyane, I; Chimphango, S B M; Wang, J; Kim, H-K; Adams, Jonathan Miles

    2016-08-01

    The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major

  14. Deodorants and antiperspirants affect the axillary bacterial community.

    Science.gov (United States)

    Callewaert, Chris; Hutapea, Prawira; Van de Wiele, Tom; Boon, Nico

    2014-10-01

    The use of underarm cosmetics is common practice in the Western society to obtain better body odor and/or to prevent excessive sweating. A survey indicated that 95 % of the young adult Belgians generally use an underarm deodorant or antiperspirant. The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics. The microbial profiles were unique for every person. A stable bacterial community was seen when underarm cosmetics were applied on a daily basis and when no underarm cosmetics were applied. A distinct community difference was seen when the habits were changed from daily use to no use of deodorant/antiperspirant and vice versa. The richness was higher when deodorants and antiperspirants were applied. Especially when antiperspirants were applied, the microbiome showed an increase in diversity. Antiperspirant usage led toward an increase of Actinobacteria, which is an unfavorable situation with respect to body odor development. These initial results show that axillary cosmetics modify the microbial community and can stimulate odor-producing bacteria. PMID:25077920

  15. Nitrogen deposition alters soil chemical properties and bacterial communities in the Inner Mongolia grassland

    Institute of Scientific and Technical Information of China (English)

    Ximei Zhang; Xingguo Han

    2012-01-01

    Nitrogen deposition has dramatically altered biodiversity and ecosystem functioning on the earth; however,its effects on soil bacterial community and the underlying mechanisms of these effects have not been thoroughly examined.Changes in ecosystems caused by nitrogen deposition have traditionally been attributed to increased nitrogen content.In fact,nitrogen deposition not only leads to increased soil total N content,but also changes in the NH4+-N content,NO3--N content and pH,as well as changes in the heterogeneity of the four indexes.The soil indexes for these four factors,their heterogeneity and even the plant community might be routes through which nitrogen deposition alters the bacterial community.Here,we describe a 6-year nitrogen addition experiment conducted in a typical steppe ecosystem to investigate the ecological mechanism by which nitrogen deposition alters bacterial abundance,diversity and composition.We found that various characteristics of the bacterial community were explained by different environmental factors.Nitrogen deposition decreased bacterial abundance that is positively related to soil pH value.In addition,nitrogen addition decreased bacterial diversity,which is negatively related to soil total N content and positively related to soil NO3--N heterogeneity.Finally,nitrogen.addition altered bacterial composition that is significantly related to soil NH4+-N content.Although nitrogen deposition significantly altered plant biomass,diversity and composition,these characteristics of plant community did not have a significant impact on processes of nitrogen deposition that led to alterations in bacterial abundance,diversity and composition.Therefore,more sensitive molecular technologies should be adopted to detect the subtle shifts of microbial community structure induced by the changes of plant community upon nitrogen deposition.

  16. Bacterial diversity indicates dietary overlap among bats of different feeding habits.

    Science.gov (United States)

    Banskar, Sunil; Mourya, Devendra T; Shouche, Yogesh S

    2016-01-01

    Bats are among the most conspicuous mammals with extraordinary adaptations. They play a key role in the ecosystem. Frugivorous bats are important seed dispersing agents that help in maintaining forest tree diversity, while insectivorous bats are natural insect pest control agents. Several previous reports suggest that bats are reservoir of viruses; nonetheless their bacterial counterparts are relatively less explored. The present study describes the microbial diversity associated with the intestine of bats from different regions of India. Our observations stipulate that there is substantial sharing of bacterial communities between the insectivorous and frugivorous bats, which signifies fairly large dietary overlap. We also observed the presence of higher abundance of Mycoplasma in Cynopterus species of bats, indicating possible Mycoplasma infection. Considering the scarcity of literature related to microbial communities of bat intestinal tract, this study can direct future microbial diversity studies in bats with reference to their dietary habits, host-bacteria interaction and zoonosis.

  17. Pyrodiversity begets plant-pollinator community diversity.

    Science.gov (United States)

    Ponisio, Lauren C; Wilkin, Kate; M'Gonigle, Leithen K; Kulhanek, Kelly; Cook, Lindsay; Thorp, Robbin; Griswold, Terry; Kremen, Claire

    2016-05-01

    Fire has a major impact on the structure and function of many ecosystems globally. Pyrodiversity, the diversity of fires within a region (where diversity is based on fire characteristics such as extent, severity, and frequency), has been hypothesized to promote biodiversity, but changing climate and land management practices have eroded pyrodiversity. To assess whether changes in pyrodiversity will have impacts on ecological communities, we must first understand the mechanisms that might enable pyrodiversity to sustain biodiversity, and how such changes might interact with other disturbances such as drought. Focusing on plant-pollinator communities in mixed-conifer forest with frequent fire in Yosemite National Park, California, we examine how pyrodiversity, combined with drought intensity, influences those communities. We find that pyrodiversity is positively related to the richness of the pollinators, flowering plants, and plant-pollinator interactions. On average, a 5% increase in pyrodiversity led to the gain of approximately one pollinator and one flowering plant species and nearly two interactions. We also find that a diversity of fire characteristics contributes to the spatial heterogeneity (β-diversity) of plant and pollinator communities. Lastly, we find evidence that fire diversity buffers pollinator communities against the effects of drought-induced floral resource scarcity. Fire diversity is thus important for the maintenance of flowering plant and pollinator diversity and predicted shifts in fire regimes to include less pyrodiversity compounded with increasing drought occurrence will negatively influence the richness of these communities in this and other forested ecosystems. In addition, lower heterogeneity of fire severity may act to reduce spatial turnover of plant-pollinator communities. The heterogeneity of community composition is a primary determinant of the total species diversity present in a landscape, and thus, lower pyrodiversity may

  18. Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.

    Science.gov (United States)

    Cleary, D F R; Polónia, A R M; Sousa, A I; Lillebø, A I; Queiroga, H; Gomes, N C M

    2016-09-01

    In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation. PMID:27061465

  19. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

    Science.gov (United States)

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven, Luc; Navarro-Noya, Yendi E.

    2016-01-01

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health. PMID:27524305

  20. Comparative assessment of bacterial diversity associated with co-occurring eukaryotic hosts of Palk Bay origin.

    Science.gov (United States)

    Viszwapriya, Dharmaprakash; Aravindraja, Chairmandurai; Pandian, Shunmugiah Karutha

    2015-06-01

    Epibacterial communities of co-occurring eukaryotic hosts of Palk Bay origin (five seaweed species (Gracilaria sp, Padina sp, Enteromorpha sp, Sargassum sp, and Turbinaria sp) and one seagrass [Cymodaceae sp]) were analyzed for diversity and compared using 16S rRNA based Denaturant Gradient Gel Electrophoresis analysis. Diversity index revealed that Turbinaria sp hosts highest bacterial diversity while it was least in Gracilaria sp. The DGGE band profile showed that the epibacterial community differed considerably among the studied species. Statistical assessment using cluster analysis and Non-metric multidimensional scale analysis also authenticated the observed variability. Despite huge overlap, the composition of bacterial community structure differed significantly among the three closely related species namely Sargassum, Turbinaria and Padina. In addition, Enteromorpha and Sargassum, one being chlorophyta and the other phaeophyta showed about 80% similarity in bacterial composition. This differs from the general notion that epibacterial community composition will vary widely depending on the host phyla. The results extended the phenomenon of host specific epibacterial community irrespective of phylogeny and similarity in geographical location. PMID:26155683

  1. Bacterial Diversity and Composition in Oylat Cave (Turkey) with Combined Sanger/Pyrosequencing Approach.

    Science.gov (United States)

    Gulecal-Pektas, Yasemin

    2016-01-01

    The microbiology of caves is an important topic for better understanding subsurface biosphere diversity. The diversity and taxonomic composition of bacterial communities associated with cave walls of the Oylat Cave was studied first time by molecular cloning based on Sanger/pyrosequencing approach. Results showed an average of 1,822 operational taxonomic units per sample. Clones analyzed from Oylat Cave were found to belong to 10 common phyla within the domain Bacteria. Proteobacteria dominated the phyla, followed by Actinobacteria, Acidobacteria and Nitrospirae. Shannon diversity index was between to 3.76 and 5.35. The robust analysis conducted for this study demonstrated high bacterial diversity on cave rock wall surfaces. PMID:27281996

  2. Bacterial Diversity of Gut Content in Sea Cucumber (Apostichopus japonicus) and Its Habitat Surface Sediment

    Institute of Scientific and Technical Information of China (English)

    GAO Fei; TAN Jie; SUN Huiling; YAN Jingping

    2014-01-01

    This study investigated the bacterial diversity of gut content of sea cucumber (Apostichopus japonicus) and its habitat surface sediment in a bottom enhancement area using PCR-based denaturing gradient gel electrophoresis (DGGE) technique. Bacte-rial diversity evaluation showed that the value of the Shannon-Wiener index of gut content in different intestinal segments of A. ja-ponicus varied between 2.88 and 3.00, lower than that of the surrounding sediment (3.23). Phylogenetic analysis showed that bacte-rial phylotypes in gut content and the surrounding sediment of A. japonicus were closely related to Proteobacteria includingγ-,α-,δ-andε-proteobacteria, Bacteroidetes, Firmicute, and Actinobacteria, of whichγ-proteobacteria were predominant. These results sug-gested that the sea cucumber A. japonicus was capable of feeding selectively, and PCR-DGGE was applicable for characterizing the bacterial community composition in gut content and the surrounding sediment of sea cucumber. Further investigation targeting longer 16S rDNA gene fragments and/or functional genes was recommended for obtaining more information of the diversity and function of bacterial community in the gut content of sea cucumber.

  3. Bacterial Communities in Rhizosphere of Maize Studied by T-RFLP

    Directory of Open Access Journals (Sweden)

    Ondreičková Katarína

    2014-12-01

    Full Text Available The terminal restriction fragment length polymorphism munities from different collecting places was evaluated was used to determine the bacterial diversity in rhizo- by principal component analysis. Results showed that sphere of maize (Zea mays L. collected from four sites the most different bacterial community originated from of experimental field plot in two dates of the vegetation marginal part of the experimental field plot collected in season (July and September. The 16S rRNA gene was September was caused probably by combination of the amplified from metagenomic DNA using universal eubac- marginal effect and drought before sampling date in Sep- terial primers and PCR products were digested separately tember. Other rhizosphere samples showed from moderate with three restriction enzymes. Significant differences in to small differences in the structure of the bacterial com- the number of terminal restriction fragments among rhi- munity. Nevertheless, significant differences among all zosphere samples and between sampling dates were not collected bacterial communities were not observed. detected (P < 0.05. Variation within the bacterial communities from different collecting places was evaluated by principal component analysis. Results showed that the most different bacterial community originated from marginal part of the experimental field plot collected in September was caused probably by combination of the marginal effect and drought before sampling date in September. Other rhizosphere samples showed from moderate to small differences in the structure of the bacterial community. Nevertheless, significant differences among all collected bacterial communities were not observed.

  4. Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels.

    Science.gov (United States)

    Stothart, Mason R; Bobbie, Colleen B; Schulte-Hostedde, Albrecht I; Boonstra, Rudy; Palme, Rupert; Mykytczuk, Nadia C S; Newman, Amy E M

    2016-01-01

    Bacterial diversity within animals is emerging as an essential component of health, but it is unknown how stress may influence the microbiome. We quantify a proximate link between the oral microbiome and hypothalamic-pituitary-adrenal (HPA) axis activity using faecal glucocorticoid metabolites (FGM) in wild red squirrels (Tamiasciurus hudsonicus). Not only was bacterial diversity lower at higher levels of FGM, but also between capture periods a change in bacterial relative abundance was related to an increase in FGM. These linkages between the HPA axis and microbiome communities represent a powerful capacity for stress to have multi-dimensional effects on health. PMID:26740566

  5. Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

    Science.gov (United States)

    Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

    2015-11-01

    The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.

  6. SPECIES DIVERSITY AND STABILITY OF BIRD COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Matsyura M.V.

    2011-12-01

    Full Text Available When comparing the suggested stability indicators, we obtained statistically significant correlations for indicators of annual stability of species and total number and standard deviation of the logarithm of the number. Annual Stability Index can be applied with a high degree of reliability as a characteristic of the averaged structure of the community and its pyramid of abundances. The results of correlation analysis confirm our assumptions about the correlation between stability over the years and indices of species diversity and relative uniformity.The final task of the study was to create a mathematical model of stability, where the independent variables are the indices of species diversity. The calculation of these indices allows forecasting birds’ community stability. According to the result of multiple regression for the indicators of diversity and stability of the breeding birds’ community highest correlation coefficients were obtained fro Shannon index and Simpson's dominance Index.Community stability could be determined by its overall species diversity. When considering the stability of community its diversity should be considered as a combination of uniformity of their total number and number of species. The most suitable predictors for the community stability were the nonparametric index of dominance and information-statistical indices, since they considered simultaneously evenness and richness. The community stability is subject of the complexity of its internal communications pattern.

  7. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Institute of Scientific and Technical Information of China (English)

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

  8. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.

    Directory of Open Access Journals (Sweden)

    Nima Kianoush

    Full Text Available Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3-V4 region to compare microbial communities in layers ranging in pH from 4.5-7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼ 60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

  9. Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site▿ †

    OpenAIRE

    Mendez, Monica O.; Neilson, Julia W; Maier, Raina M.

    2008-01-01

    Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites. This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a v...

  10. Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest.

    Science.gov (United States)

    Shen, Ju-pei; Chen, C R; Lewis, Tom

    2016-01-20

    Effects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0-10 cm) was significantly higher in the B2 treatment compared with the B0 and B4 treatments. Non-metric multidimensional analysis (NMDS) of bacterial community showed clear separation of the soil bacterial community structure among different fire frequency regimes and between the depths. Different frequency fire did not have a substantial effect on bacterial composition at phylum level or bacterial 16S rRNA gene abundance. Soil pH and C:N ratio were the major drivers for bacterial community structure in the most frequent fire treatment (B2), while other factors (EC, DOC, DON, MBC, NH4(+), TC and TN) were significant in the less frequent burning and no burning treatments (B4 and B0). This study suggested that burning had a dramatic impact on bacterial diversity but not abundance with more frequent fire.

  11. Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest

    Science.gov (United States)

    Shen, Ju-Pei; Chen, C. R.; Lewis, Tom

    2016-01-01

    Effects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0–10 cm) was significantly higher in the B2 treatment compared with the B0 and B4 treatments. Non-metric multidimensional analysis (NMDS) of bacterial community showed clear separation of the soil bacterial community structure among different fire frequency regimes and between the depths. Different frequency fire did not have a substantial effect on bacterial composition at phylum level or bacterial 16S rRNA gene abundance. Soil pH and C:N ratio were the major drivers for bacterial community structure in the most frequent fire treatment (B2), while other factors (EC, DOC, DON, MBC, NH4+, TC and TN) were significant in the less frequent burning and no burning treatments (B4 and B0). This study suggested that burning had a dramatic impact on bacterial diversity but not abundance with more frequent fire.

  12. Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest.

    Science.gov (United States)

    Shen, Ju-pei; Chen, C R; Lewis, Tom

    2016-01-01

    Effects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0-10 cm) was significantly higher in the B2 treatment compared with the B0 and B4 treatments. Non-metric multidimensional analysis (NMDS) of bacterial community showed clear separation of the soil bacterial community structure among different fire frequency regimes and between the depths. Different frequency fire did not have a substantial effect on bacterial composition at phylum level or bacterial 16S rRNA gene abundance. Soil pH and C:N ratio were the major drivers for bacterial community structure in the most frequent fire treatment (B2), while other factors (EC, DOC, DON, MBC, NH4(+), TC and TN) were significant in the less frequent burning and no burning treatments (B4 and B0). This study suggested that burning had a dramatic impact on bacterial diversity but not abundance with more frequent fire. PMID:26787458

  13. Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations.

    Science.gov (United States)

    Ma, Jincai; Ibekwe, A Mark; Yang, Ching-Hong; Crowley, David E

    2016-09-01

    Microbial diversity of agricultural soils has been well documented, but information on leafy green producing soils is limited. In this study, we investigated microbial diversity and community structures in 32 (16 organic, 16 conventionally managed soils) from California (CA) and Arizona (AZ) using pyrosequencing, and identified factors affecting bacterial composition. Results of detrended correspondence analysis (DCA) and dissimilarity analysis showed that bacterial community structures of conventionally managed soils were similar to that of organically managed soils; while the bacterial community structures in soils from Salinas, California were different (Psoils from Yuma, Arizona and Imperial Valley, California. Canonical correspondence analysis (CCA) and artificial neural network (ANN) analysis of bacterial community structures and soil variables showed that electrical conductivity (EC), clay content, water-holding capacity (WHC), pH, total nitrogen (TN), and organic carbon (OC) significantly (Psoil physical properties (clay, EC, and WHC), soil chemical variables (pH, TN, and OC) and sampling location explained 16.3%, 12.5%, and 50.9%, respectively, of total variations in bacterial community structure, leaving 13% of the total variation unexplained. Our current study showed that bacterial community composition and diversity in major fresh produce growing soils from California and Arizona is a function of soil physiochemical characteristics and geographic distances of sampling sites. PMID:27135583

  14. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species. PMID:21108068

  15. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.

  16. Diversity of Streptococcus mutans strains in bacterial interspecies interactions

    NARCIS (Netherlands)

    X. Li; M.A. Hoogenkamp; J. Ling; W. Crielaard; D.M. Deng

    2014-01-01

    Biofilms are matrix-enclosed microbial population adhere to each other and to surfaces. Compared to planktonic bacterial cells, biofilm cells show much higher levels of antimicrobial resistance. We aimed to investigate Streptococcus mutans strain diversity in biofilm formation and chlorhexidine (CHX

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  19. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition

    DEFF Research Database (Denmark)

    Severin, Ina; Östman, Örjan; Lindström, Eva S.

    2013-01-01

    ) a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B) a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i......Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate - functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment...... in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1) changes in taxonomic diversity, 2) changes in phylogenetic diversity or 3) changes in the composition of functional traits. The experiment was conducted in two phases; (A...

  20. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments.

    Directory of Open Access Journals (Sweden)

    Xuexia Jiang

    Full Text Available Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB. In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III. Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating

  1. Exploring the diversity of protein modifications: special bacterial phosphorylation systems

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Grangeasse, Christophe; Turgay, Kürşad

    2016-01-01

    that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial...... phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial...... physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein...

  2. Bacterial community structure and function shift across a northern boreal forest fire chronosequence

    Science.gov (United States)

    Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O.; Heinonsalo, Jussi

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  3. Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific "warm pool"

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific "warm pool" (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments.Five bacterial 16S rDNA clone libraries were constructed, and t33 clones with different restriction fragment length polymorphism(RFLP) patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample.The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria (SRB) were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.

  4. Bacterial community structure and function shift across a northern boreal forest fire chronosequence.

    Science.gov (United States)

    Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O; Heinonsalo, Jussi

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs cycling pathways were present in all sites showing high redundancy in the gene profiles. However, hierarchical cluster analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  5. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Natacha Bodenhausen

    Full Text Available Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root and habitat (epiphytes vs endophytes structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024, while the reverse is true for the leaves (P = 0.032. Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001. The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

  6. Bacterial community in sclerotia of Cenococcum species and soil in sub-alpine forest, central Japan

    Science.gov (United States)

    Nonoyama, Y.; Narisawa, K.; Ohta, H.; Watanabe, M.

    2009-04-01

    Species of Cenococcum, ectomycorrhizal fungi, may be particularly abundant in cold- or nutrient-stressed habitats. The fungus is easily recognized by its jet-black hyphae, and distinct compact masses of fungal mycelium called sclerotia. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and can provide sufficient inoculums for several years. The purpose of this study is to investigate bacterial community inside sclerotia, with an interest on contribution of sclerotia to microbial diversity in rhizosphere. To investigate bacterial community inside of the fungal sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from sub-alpine forest soil in central Japan. Furthermore, three sclerotium grains were applied to investigate internal bacteria community by culture method. The isolated bacterial strains were then proceeded to determine their 16S rDNA partial sequences. The predominant group determined by clone library analysis of 16S ribosomal RNA genes with DNA from the sclerotia was Acidobacteria in both sclerotia and soil. Bacterial community of sclerotia showed higher diversity compared to soil. On the contrary, bacterial flora isolated from single sclerotium differed each other. Additionally, the bacterial community was composed by limited species of related genus.

  7. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

  8. Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities.

    Science.gov (United States)

    Xiao, Meng; Sun, Shan-Shan; Zhang, Zhong-Zhi; Wang, Jun-Ming; Qiu, Long-Wei; Sun, Hua-Yang; Song, Zhao-Zheng; Zhang, Bei-Yu; Gao, De-Li; Zhang, Guang-Qing; Wu, Wei-Min

    2016-01-01

    The community diversities of two oil reservoirs with low permeability of 1.81 × 10(-3) and 2.29 × 10(-3) μm(2) in Changqing, China, were investigated using a high throughput sequencing technique to analyze the influence of biostimulation with a nutrient activator on the bacterial communities. These two blocks differed significantly in salinity (average 17,500 vs 40,900 mg/L). A core simulation test was used to evaluate the effectiveness of indigenous microbial-enhanced oil recovery (MEOR). The results indicated that in the two high salinity oil reservoirs, one reservoir having relatively lower salinity level and a narrow salinity range had higher bacterial and phylogenetic diversity. The addition of the nutrient activator increased the diversity of the bacterial community structure and the diversity differences between the two blocks. The results of the core simulation test showed that the bacterial community in the reservoir with a salinity level of 17,500 mg/L did not show significant higher MEOR efficiency compared with the reservoir with 40,900 mg/L i.e. MEOR efficiency of 8.12% vs 6.56% (test p = 0.291 > 0.05). Therefore, salinity levels affected the bacterial diversities in the two low permeability oil blocks remarkably. But the influence of salinity for the MEOR recovery was slightly. PMID:26786765

  9. Comparison of Diversities and Compositions of Bacterial Populations Inhabiting Natural Forest Soils

    OpenAIRE

    Hackl, Evelyn; Zechmeister-Boltenstern, Sophie; Bodrossy, Levente; Sessitsch, Angela

    2004-01-01

    The diversity and composition of soil bacterial communities were compared among six Austrian natural forests, including oak-hornbeam, spruce-fir-beech, and Austrian pine forests, using terminal restriction fragment length polymorphism (T-RFLP, or TRF) analysis and sequence analysis of 16S rRNA genes. The forests studied differ greatly in soil chemical characteristics, microbial biomass, and nutrient turnover rates. The aim of this study was to relate these differences to the composition of th...

  10. Bacterial Communities in Rhizosphere of Maize Studied by T-RFLP

    OpenAIRE

    Ondreičková Katarína; Ficek Andrej; Mihálik Daniel; Gubišová Marcela; Hudcovicová Martina; Drahovská Hana; Kraic Ján

    2014-01-01

    The terminal restriction fragment length polymorphism munities from different collecting places was evaluated was used to determine the bacterial diversity in rhizo- by principal component analysis. Results showed that sphere of maize (Zea mays L.) collected from four sites the most different bacterial community originated from of experimental field plot in two dates of the vegetation marginal part of the experimental field plot collected in season (July and September). The 16S rRNA gene was ...

  11. Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia.

    Science.gov (United States)

    He, Jizheng; Xu, Zhihong; Hughes, Jane

    2006-01-01

    A major operational change in exotic pine plantations of subtropical Australia has been the decision to retain postharvest residues on site. A long-term field experiment was established in February 1996 to examine the impacts of residue management regimes [i.e. the postharvest residues removed (G0R), natural amount of residues retained (G1R) and residue quantity doubled and retained (G2R)] on tree growth (F1 hybrid pine) and sustainable soil management. Twelve soil samples, which included the above three residue regimes with four replicates, were collected at plantation age 6.4 years. A 16S rRNA gene clone library was established following soil community DNA extraction, polymerase chain reaction amplification and cloning. A total of 324 clones, including 27 from each sample, were randomly selected and sequenced to represent the bacterial composition and diversity of the clone library and thus the soil bacterial community under the residue management regimes. Phylogenetic analyses indicated that Acidobacteria (37.6%) and Proteobacteria (35.6%) were the dominant components of the soil bacterial community, followed by Actinobacteria (14.7%), Chlamydiae/Verrucomicrobia (7.3%), Unclassified Bacteria (3.8%) and Gemmatimonadetes (1.0%). Analysis of molecular variance revealed that there was no significant difference in bacterial composition and diversity among the residue management regimes or their replicated samples. PMID:16420613

  12. Associations between bacterial communities of house dust and infant gut

    Energy Technology Data Exchange (ETDEWEB)

    Konya, T.; Koster, B. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Maughan, H. [Department of Cell and Systems Biology, University of Toronto (Canada); Escobar, M. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Azad, M.B. [Department of Pediatrics, University of Alberta (Canada); Guttman, D.S. [Department of Cell and Systems Biology, University of Toronto (Canada); Sears, M.R. [Department of Medicine, McMaster University (Canada); Becker, A.B. [University of Manitoba (Canada); Brook, J.R. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Environment Canada (Canada); Takaro, T.K. [Faculty of Health Science, Simon Fraser University (Canada); Kozyrskyj, A.L. [Department of Pediatrics, University of Alberta (Canada); Scott, J.A., E-mail: james.scott@utoronto.ca [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada)

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  13. Associations between bacterial communities of house dust and infant gut

    International Nuclear Information System (INIS)

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership

  14. Associations between bacterial communities of house dust and infant gut.

    Science.gov (United States)

    Konya, T; Koster, B; Maughan, H; Escobar, M; Azad, M B; Guttman, D S; Sears, M R; Becker, A B; Brook, J R; Takaro, T K; Kozyrskyj, A L; Scott, J A

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust-stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  15. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    Full Text Available BACKGROUND: Bacterial vaginosis (BV is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. METHODOLOGY/PRINCIPAL FINDINGS: Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel's clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs significantly associated with each of the four Amsel's criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. CONCLUSIONS/SIGNIFICANCE: The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased

  16. Age, sun and substrate: triggers of bacterial communities in lichens.

    Science.gov (United States)

    Cardinale, Massimiliano; Steinová, Jana; Rabensteiner, Johannes; Berg, Gabriele; Grube, Martin

    2012-02-01

    Bacterial communities colonize the surfaces of lichens in a biofilm-like manner. The overall structure of the bacterial communities harboured by the lichens shows similarities, in particular the dominance of not yet cultured Alphaproteobacteria. Parameters causing variation in abundance, composition and spatial organization of the lichen-associated bacterial communities are so far poorly understood. As a first step, we used a microscopic approach to test the significance of both lichen-intrinsic and extrinsic environmental factors on the bacterial communities associated with 11 lichen samples, belonging to six species. Some of these species have thalli with a distinct age gradient. A statistically significant effect can be attributed to the age of the thallus parts, which is an intrinsic factor: growing parts of the lichens host bacterial communities that significantly differ from those of the ageing portions of the thalli. The substrate type (rock, tree, understory) and (at a lower extent) the exposition to the sun also affected the bacterial communities. Interestingly, the abundance of bacterial cells in the lichens was also influenced by the same structure-triggering factors. No effect on the composition with main bacterial groups was attributed to different lichen species, differentiated thallus parts or thallus growth type. Our results are important for the experimental designs in lichen-bacterial ecology. PMID:23757225

  17. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment. PMID:24600849

  18. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Science.gov (United States)

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment.

  19. Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

    Science.gov (United States)

    Gruninger, Robert J.; McAllister, Tim A.; Forster, Robert J.

    2016-01-01

    The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver. PMID:27227334

  20. Bacterial diversity in Greenlandic soils as affected by potato cropping and inorganic versus organic fertilization

    DEFF Research Database (Denmark)

    Michelsen, Charlotte Frydenlund; Pedas, Pai Rosager; Glaring, Mikkel Andreas;

    2014-01-01

    Arctic and Subarctic ecosystems will in the near future be exposed to severe environmental stresses due to global warming. For example, the microbial community structure and function may change as a result of increased temperatures. In Greenland, agriculture is carried out in the Subarctic regions...... with only limited pest management, despite the presence of plant pathogenic fungi. The microbial community composition in agricultural soils, which plays an important role for soil and plant health and for crop yield, may be affected by the use of different fertilizer treatments. Currently, only limited...... on bacterial diversity, nutrient composition and crop yield in two Greenlandic agricultural soils. An effect of fertilizer was found on soil and plant nutrient levels and on crop yields. Pyrosequencing of 16S rRNA gene sequences did not reveal any major changes in the overall bacterial community composition...

  1. Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia.

    Science.gov (United States)

    Khoo, Jing-Jing; Chen, Fezshin; Kho, Kai Ling; Ahmad Shanizza, Azzy Iyzati; Lim, Fang-Shiang; Tan, Kim-Kee; Chang, Li-Yen; AbuBakar, Sazaly

    2016-07-01

    Ticks are vectors in the transmission of many important infectious diseases in human and animals. Ticks can be readily found in the semi-forested areas such as the settlements of the indigenous people in Malaysia, the Orang Asli. There is still minimal information available on the bacterial agents associated with ticks found in Malaysia. We performed a survey of the bacterial communities associated with ticks collected from domestic animals found in two Orang Asli villages in Malaysia. We collected 62 ticks, microscopically and molecularly identified as related to Haemaphysalis wellingtoni, Haemaphysalis hystricis and Haemaphysalis bispinosa. Bacterial 16s rRNA hypervariable region (V6) amplicon libraries prepared from the tick samples were sequenced on the Ion Torrent PGM platform. We detected a total of 392 possible bacterial genera after pooling and sequencing 20 samples, indicating a diverse bacterial community profile. Dominant taxa include the potential tick endosymbiont, Coxiella. Other dominant taxa include the tick-associated pathogen, Rickettsia, and environmental bacteria such as Bacillus, Mycobacterium, Sphingomonas and Pseudomonas. Other known tick-associated bacteria were also detected, including Anaplasma, Ehrlichia, Rickettsiella and Wolbachia, albeit at very low abundance. Specific PCR was performed on selected samples to identify Rickettsia and Coxiella. Sequence of Rickettsia felis, which causes spotted fever in human and cats, was identified in one sample. Coxiella endosymbionts were detected in three samples. This study provides the baseline knowledge of the microbiome of ticks in Malaysia, focusing on tick-associated bacteria affecting the Orang Asli communities. The role of the herein found Coxiella and Rickettsia in tick physiology or disease transmission merits further investigation. PMID:27132518

  2. Phyllopshere Bacterial Community Structure of Spinach (Spinacia oleracea as Affected by Cultivar and Environmental Conditions at Time of Harvest

    Directory of Open Access Journals (Sweden)

    Joseph O. Falkinham III

    2011-12-01

    Full Text Available Modern molecular ecology techniques were used to demonstrate the effects of plant genotype and environmental conditions prior to harvest on the spinach epiphytic bacterial community. Three cultivars of spinach with different leaf topographies were collected at three different periods during the fall growing season. Leaf surface topography had an effect on diversity and number of culturable bacteria on the phylloepiphtyic community of spinach. Savoy cultivars, which had larger surface area and more stomata and glandular trichomes, where bacterial aggregates were observed, featured more diverse communities with increased richness and larger bacterial populations compared to flat-leaved cultivars. Bacterial community richness was compared using denaturant gradient gel electrophoresis (DGGE, while abundance was quantified using 16s rRNA primers for major phyla. The most diverse communities, both in richness and abundance, were observed during the first sampling period, immediately following a period of rapid spinach growth. Exposure to lower air and soil temperatures and decreased precipitation resulted in significantly reduced bacterial population size and bacterial community richness in November and December. This study describes the effect of the plant characteristics and environmental conditions that affect spinach microbiota population size and diversity, which might have implications in the survival of food and plant bacterial pathogens.

  3. Diversity of Online Community Activities

    CERN Document Server

    Hogg, Tad

    2008-01-01

    Web sites where users create and rate content as well as form networks with other users display long-tailed distributions in many aspects of behavior. Using behavior on one such community site, Essembly, we propose and evaluate plausible mechanisms to explain these behaviors. Unlike purely descriptive models, these mechanisms rely on user behaviors based on information available locally to each user. For Essembly, we find the long-tails arise from large differences among user activity rates and qualities of the rated content, as well as the extensive variability in the time users devote to the site. We show that the models not only explain overall behavior but also allow estimating the quality of content from their early behaviors.

  4. Response of bacterial communities to environmental changes in a mesoscale subtropical watershed, Southeast China.

    Science.gov (United States)

    Hu, Anyi; Yang, Xiaoyong; Chen, Nengwang; Hou, Liyuan; Ma, Ying; Yu, Chang-Ping

    2014-02-15

    This study used 16S rRNA gene-based pyrosequencing (16S-pyrotag) to investigate both planktonic and benthic bacterial communities in two main tributaries (North River and West River) of the Jiulong River Watershed (JRW), a mesoscale subtropical watershed that has experienced intensive human perturbation in recent decades. The results of 16S-pyrotag showed that benthic bacterial communities were clearly more diverse and uniform than surface bacterioplankton communities. The results of taxonomic assignments indicated that Betaproteobacteria, Actinobacteria and Firmicutes were significantly more abundant in planktonic than in benthic communities, whereas the relative abundances of Acidobacteria, Delta-, Gammaproteobacteria, Chloroflexi and Nitrospira were higher in sediment than in water samples. In particular, several sewer- and fecal-pollution bacterial indicators were observed in water samples, implying that the water bodies of the JRW were contaminated by fecal pollution. Using the typical freshwater bacteria (TFB) taxonomic framework, 57.6 ± 10%, 27.6 ± 10.9% and 10.4 ± 6.9% of sequences recovered from planktonic communities could be assigned to lineages, clades and tribes of TFB, respectively. The relatively lower abundance of TFB implied that some unknown or unique autochthonous bacterioplankton populations occurred in the JRW. The principal coordinate analysis (PCoA) and one way analysis of similarity (ANOSIM) analysis demonstrated that planktonic bacterial community structures were significantly different between North River and West River, whereas benthic communities from these two tributaries were grouped together. Multivariate statistical analysis revealed that nutrient concentrations and stoichiometry were the key drivers of both α- and β-diversity patterns of bacterioplankton communities. Overall, our results indicate that the diversity, composition and structure of planktonic bacterial communities are sensitive to water chemistry (e.g., nutrient

  5. Bacterial community structure of a full-scale biofilter treating pig house exhaust air

    DEFF Research Database (Denmark)

    Kristiansen, Anja; Pedersen, Kristina Hadulla; Nielsen, Per Halkjær;

    2011-01-01

    Biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. Quantitative fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter...

  6. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

    Science.gov (United States)

    de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

    2016-01-01

    The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem-also called "microbiome"-is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  7. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters

    2016-03-01

    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

  8. Altamira cave Paleolithic paintings harbor partly unknown bacterial communities.

    Science.gov (United States)

    Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

    2002-05-21

    Since it has been reported that microorganisms can affect painting pigments, Paleolithic painting microbiology deserves attention. The present study is the first report on the bacterial colonization of the valuable Paleolithic paintings in the famous Altamira cave (Spain). One sample taken from a painting area in the Polychromes Hall was analyzed culture-independently. This was the first time microbiologists were allowed to take sample material directly from Altamira paintings. Identification methods included PCR amplification of 16S rRNA genes (16S rDNA) and community fingerprinting by denaturing gradient gel electrophoresis (DGGE). The applied approach gave insight into a great bacterial taxonomic diversity, and allowed the detection of unexpected and unknown bacteria with potential effects on the conservation of the painting. Regarding the number of 29 visible DGGE bands in the community fingerprint, the numbers of analyzed clones described about 72% of the phylogenetic diversity present in the sample. Thirty-eight percent of the sequences analyzed were phylogenetically most closely related to cultivated bacteria, while the majority (62%) were most closely related to environmental 16S rDNA clones. Bacteria identified in Altamira were related with sequence similarities between 84.8 and 99.4% to members of the cosmopolitan Proteobacteria (52.3%), to members of the Acidobacterium division (23.8%), Cytophaga/Flexibacter/Bacteroides phylum (9.5%), green non-sulfur bacteria (4.8%), Planctomycetales (4.8%) and Actinobacteria (4.8%). The high number of clones most closely related to environmental 16S rDNA clones showed the broad spectrum of unknown and yet to be cultivated bacteria in Altamira cave. PMID:12052543

  9. Bacterial community composition of a wastewater treatment system reliant on N{sub 2} fixation

    Energy Technology Data Exchange (ETDEWEB)

    Reid, N.M.; Bowers, T.H.; Lloyd-Jones, G. [Scion, Rotorua (New Zealand)

    2008-05-15

    The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N{sub 2} fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by {alpha}-Proteobacteria and {beta}-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system. (orig.)

  10. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition.

    Directory of Open Access Journals (Sweden)

    Ina Severin

    Full Text Available Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate-functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1 changes in taxonomic diversity, 2 changes in phylogenetic diversity or 3 changes in the composition of functional traits. The experiment was conducted in two phases; (A a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i.e. their functional traits. From experiment (B we could thus estimate changes in functional traits in communities in experiment (A. Bacterial production was affected by dispersal, but not consistently among lakes. Neither change in taxonomic or phylogenetic diversity with dispersal could explain the observed dispersal-productivity relationships. Instead, changes in trait composition with dispersal, especially the communities' ability to use p-coumaric acid, an aromatic compound, could explain the observed dispersal-productivity relationships. Changes in this trait caused by dispersal seemed especially important for bacterial productivity in waters with a high aromaticity of the organic matter pool. We conclude that the effect of dispersal on bacterial communities can affect ecosystem functioning in different ways, through changes in functional key-traits which are important for the local environment.

  11. Stability of multispecies bacterial communities: signaling networks may stabilize microbiomes.

    Directory of Open Access Journals (Sweden)

    Ádám Kerényi

    Full Text Available Multispecies bacterial communities can be remarkably stable and resilient even though they consist of cells and species that compete for environmental resources. In silico models suggest that common signals released into the environment may help selected bacterial species cluster at common locations and that sharing of public goods (i.e. molecules produced and released for mutual benefit can stabilize this coexistence. In contrast, unilateral eavesdropping on signals produced by a potentially invading species may protect a community by keeping invaders away from limited resources. Shared bacterial signals, such as those found in quorum sensing systems, may thus play a key role in fine tuning competition and cooperation within multi-bacterial communities. We suggest that in addition to metabolic complementarity, signaling dynamics may be important in further understanding complex bacterial communities such as the human, animal as well as plant microbiomes.

  12. Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau.

    Science.gov (United States)

    Aguilar, Pablo; Acosta, Eduardo; Dorador, Cristina; Sommaruga, Ruben

    2016-01-01

    The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.

  13. Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

    Science.gov (United States)

    Song, Liyan; Li, Lei

    2016-08-01

    Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a

  14. Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils

    Directory of Open Access Journals (Sweden)

    Jing eLi

    2015-02-01

    Full Text Available Copper contamination on China’s arable land could pose severe economic, ecological and healthy consequences in the coming decades. As the drivers in maintaining ecosystem functioning, the responses of soil microorganisms to long-term copper contamination in different soil ecosystems are still debated. This study investigated the impacts of copper gradients on soil bacterial communities in two agricultural fields with contrasting soil properties. Our results revealed consistent reduction in soil microbial biomass carbon (SMBC with increasing copper levels in both soils, coupled by significant declines in bacterial abundance in most cases. Despite of contrasting bacterial community structures between the two soils, the bacterial diversity in the copper-contaminated soils showed considerably decreasing patterns when copper levels elevated. High-throughput sequencing revealed copper selection for major bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Chloroflexi were highly sensitive to copper. The thresholds that bacterial communities changed sharply were 800 and 200 added copper mg kg-1 in the fluvo-aquic soil and red soil, respectively, which were similar to the toxicity thresholds (EC50 values characterized by SMBC. Structural equation model (SEM analysis ascertained that the shifts of bacterial community composition and diversity were closely related with the changes of SMBC in both soils. Our results provide field-based evidence that copper contamination exhibits consistently negative impacts on soil bacterial communities, and the shifts of bacterial communities could have largely determined the variations of the microbial biomass.

  15. Bacterial Diversity of Young Seafloor Basalts: A Potential Role for Microorganisms in Ocean Crust Weathering

    Science.gov (United States)

    Santelli, C. M.; Edgcomb, V.; Bach, W.; Edwards, K.

    2005-12-01

    A growing number of studies indicate that microbial communities exist within the oceanic crust on mid-ocean ridge flanks. Young ocean crust that is exposed at the seafloor or in the shallow subseafloor interacts directly with low-temperature, oxygenated fluids and undergoes alteration. The free energy associated with oxidation of reduced species in the basalt could potentially be used by microbial communities for growth. Basaltic rock habitats at and below the seafloor, however, remain poorly studied with respect to the physiological and phylogenetic diversity of microbial communities that may be supported by oxidative weathering reactions. In this study, we have investigated the diversity of microorganisms living on or within basaltic crust at the seafloor, and the changes in these microbial communities with increasing oxidative rock alteration. Seafloor lavas representing various flow morphologies, alteration states, and ages (up to 20 kyrs) were collected from the East Pacific Rise between 9°28'N and 9°50'N. Total community DNA was extracted and bacterial 16S rRNA was amplified by PCR. Clone libraries were constructed and sequenced for phylogenetic analyses. To assess the overall extent of basalt alteration and quantify cell abundance in relation to surfacial weathering products, a combination of confocal laser scanning microscopy and scanning electron microscopy was used on natural, unprocessed samples. Phylogenetic and microscopic analyses indicate that diverse, yet distinct populations of bacteria inhabit different lavas, and these microbial communities shift with changes in basalt alteration state. A general trend from metal and sulfur-oxidizing autotrophic communities towards metal- and sulfur-reducing populations correlates with apparent increasing accumulation of weathering products (oxides, clays, etc.). These results provide insight into phylogenetic population trends among bacterial communities harbored in basalt during ocean crust weathering.

  16. Spatial Distribution of Bacterial Communities Driven by Multiple Environmental Factors in a Beach Wetland of the Largest Freshwater Lake in China

    Directory of Open Access Journals (Sweden)

    Xia eDing

    2015-02-01

    Full Text Available The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction and vertical (sediment depth gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH4+ concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

  17. Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Lucas William Mendes

    2014-12-01

    Full Text Available Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%, which presented differences according to the depth, where the classes Betaproteobacteria (21% and Deltaproteobacteria (16% were abundant at 10 cm and Epsilonproteobacteria (35% was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively, Chloroflexi (2.8% and 0.75%, and Acidobacteria (2.75% and 0.57% according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth.

  18. Age-Related Shifts in Bacterial Diversity in a Reef Coral.

    Directory of Open Access Journals (Sweden)

    Alex D Williams

    Full Text Available This study investigated the relationship between microbial communities in differently sized colonies of the massive coral Coelastrea aspera at Phuket, Thailand where colony size could be used as a proxy for age. Results indicated significant differences between the bacterial diversity (ANOSIM, R = 0.76, p = 0.001 of differently sized colonies from the same intertidal reef habitat. Juvenile and small colonies ( 28 cm mean diam. Bacterial diversity increased in a step-wise pattern from juveniles < small < medium colonies, which was then followed by a slight decrease in the two largest size classes. These changes appear to resemble a successional process which occurs over time, similar to that observed in the ageing human gut. Furthermore, the dominant bacterial ribotypes present in the tissues of medium and large sized colonies of C. aspera, (such as Halomicronema, an Oscillospira and an unidentified cyanobacterium were also the dominant ribotypes found within the endolithic algal band of the coral skeleton; a result providing some support for the hypothesis that the endolithic algae of corals may directly influence the bacterial community present in coral tissues.

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

    OpenAIRE

    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...

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

    OpenAIRE

    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...

  1. Soil bacterial communities respond to mowing and nutrient addition in a steppe ecosystem.

    Science.gov (United States)

    Zhang, Ximei; Chen, Quansheng; Han, Xingguo

    2013-01-01

    In many grassland ecosystems, nitrogen (N) and phosphorus (P) are added to improve plant productivity, and the aboveground plant biomass is mowed and stored as hay for the bullamacow. Nutrient addition and mowing affect the biodiversity and ecosystem functioning, and most of the previous studies have primarily focused on their effects on macro-organisms, neglecting the responses of soil microbial communities. In this study, we examined the changes in three community attributes (abundance, richness, and composition) of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to mowing, N addition, P addition, and their combinations, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Overall, N addition had a greater effect than mowing and P addition on most of these bacterial groups, as indicated by changes in the abundance, richness and composition in response to these treatments. N addition affected these soil bacterial groups primarily through reducing soil pH and increasing available N content. Meanwhile, the 16 bacterial phyla/classes responded differentially to these experimental treatments, with Acidobacteria, Acidimicrobidae, Deltaproteobacteria, and Gammaproteobacteria being the most sensitive. The changes in the abundance, richness, and composition of various bacterial groups could imply some potential shift in their ecosystem functions. Furthermore, the important role of decreased soil pH caused by N addition in affecting soil bacterial communities suggests the importance of restoring acidified soil to maintain soil bacterial diversity. PMID:24391915

  2. Emergence of Collective Territorial Defense in Bacterial Communities: Horizontal Gene Transfer Can Stabilize Microbiomes

    OpenAIRE

    János Juhász; Attila Kertész-Farkas; Dóra Szabó; Sándor Pongor

    2014-01-01

    Multispecies bacterial communities such as the microbiota of the gastrointestinal tract can be remarkably stable and resilient even though they consist of cells and species that compete for resources and also produce a large number of antimicrobial agents. Computational modeling suggests that horizontal transfer of resistance genes may greatly contribute to the formation of stable and diverse communities capable of protecting themselves with a battery of antimicrobial agents while preserving ...

  3. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China.

    Science.gov (United States)

    Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Tang, Shu-Kun; Jiang, Hong-Chen; Zhang, Chuanlun L; Dong, Hailiang; Li, Wen-Jun

    2013-04-01

    Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.

  4. The microbiome of Folsomia candida: an assessment of bacterial diversity in a Wolbachia-containing animal.

    Science.gov (United States)

    Agamennone, Valeria; Jakupović, Dennis; Weedon, James T; Suring, Wouter J; van Straalen, Nico M; Roelofs, Dick; Röling, Wilfred F M

    2015-11-01

    The springtail Folsomia candida is an important model organism for soil ecology, ecotoxicology and ecogenomics. The decomposer activities of soil invertebrates like Folsomia depend on their relationship with microbial communities including gut symbionts. In this paper, we apply high-throughput sequencing to provide a detailed characterization of the bacterial community associated with parthenogenetic F. candida. First, we evaluated a method to suppress the amplification of DNA from the endosymbiont Wolbachia, to prevent it from interfering with the identification of less abundant operational taxonomic units (OTUs). The suppression treatment applied was effective against Wolbachia and did not interfere with the detection of the most abundant OTUs (59 OTUs, contributing over 87% of the reads). However, this method did affect the inferred community composition. Significant differences were subsequently observed in the composition of bacterial communities associated with two different strains of F. candida. A total of 832 OTUs were found, of which 45% were only present in one strain and 17% only in the other. Among the 20 most abundant OTUs, 16 were shared between strains. Denaturing gradient gel electrophoresis and clone libraries, although unable to capture the full diversity of the bacterial community, provided results that supported the NGS data. PMID:26499484

  5. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

    Directory of Open Access Journals (Sweden)

    Qi eYe

    2016-01-01

    Full Text Available Submarine groundwater (SGD is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

  6. Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata.

    Science.gov (United States)

    Daniels, Camille; Breitbart, Mya

    2012-10-01

    Residing in a phylum of their own, ctenophores are gelatinous zooplankton that drift through the ocean's water column. Although ctenophores are known to be parasitized by a variety of eukaryotes, no studies have examined their bacterial associates. This study describes the bacterial communities associated with the lobate ctenophore Mnemiopsis leidyi and its natural predator Beroe ovata in Tampa Bay, Florida, USA. Investigations using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes demonstrated that ctenophore bacterial communities were distinct from the surrounding water. In addition, each ctenophore genus contained a unique microbiota. Ctenophore samples contained fewer bacterial operational taxonomic units (OTUs) by T-RFLP and lower diversity communities by 16S rRNA gene sequencing than the water column. Both ctenophore genera contained sequences related to bacteria previously described in marine invertebrates, and sequences similar to a sea anemone pathogen were abundant in B. ovata. Temporal sampling revealed that the ctenophore-associated bacterial communities varied over time, with no single OTU detected at all time points. This is the first report of distinct and dynamic bacterial communities associated with ctenophores, suggesting that these microbial consortia may play important roles in ctenophore ecology. Future work needs to elucidate the functional roles and mode of acquisition of these bacteria. PMID:22571334

  7. Microbial communities in high altitude altiplanic wetlands in northern Chile: phylogeny, diversity and function

    OpenAIRE

    Dorador Ortiz, C.

    2007-01-01

    The phylogeny, diversity and function of microbial communities from several altiplanic wetlands was examined using an array of different but complimentary techniques. Results highlighted that microbial diversity exhibited a specific pattern in each wetland. Bacteria were dominant over Archaea in both freshwater and saline systems. Bacterial and archaeal diversity were both higher in sediment than in water samples. Lago Chungará, Laguna de Piacota and Bofedal de Parinacota are freshwater wetla...

  8. Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington

    KAUST Repository

    Lee, O. O.

    2009-04-10

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  9. Impacts of poultry house environment on poultry litter bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Michael D Dumas

    Full Text Available Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD. Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  10. Impacts of poultry house environment on poultry litter bacterial community composition.

    Science.gov (United States)

    Dumas, Michael D; Polson, Shawn W; Ritter, Don; Ravel, Jacques; Gelb, Jack; Morgan, Robin; Wommack, K Eric

    2011-01-01

    Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  11. Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms.

    Science.gov (United States)

    Landa, Marine; Blain, Stéphane; Christaki, Urania; Monchy, Sébastien; Obernosterer, Ingrid

    2016-01-01

    Marine microbes have a pivotal role in the marine biogeochemical cycle of carbon, because they regulate the turnover of dissolved organic matter (DOM), one of the largest carbon reservoirs on Earth. Microbial communities and DOM are both highly diverse components of the ocean system, yet the role of microbial diversity for carbon processing remains thus far poorly understood. We report here results from an exploration of a mosaic of phytoplankton blooms induced by large-scale natural iron fertilization in the Southern Ocean. We show that in this unique ecosystem where concentrations of DOM are lowest in the global ocean, a patchwork of blooms is associated with diverse and distinct bacterial communities. By using on-board continuous cultures, we identify preferences in the degradation of DOM of different reactivity for taxa associated with contrasting blooms. We used the spatial and temporal variability provided by this natural laboratory to demonstrate that the magnitude of bacterial production is linked to the extent of compositional changes. Our results suggest that partitioning of the DOM resource could be a mechanism that structures bacterial communities with a positive feedback on carbon cycling. Our study, focused on bacterial carbon processing, highlights the potential role of diversity as a driving force for the cycling of biogeochemical elements. PMID:26196334

  12. Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia

    Directory of Open Access Journals (Sweden)

    Dominik eSchneider

    2015-12-01

    Full Text Available Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use system comprised rubber agroforests (jungle rubber, rubber plantation and oil plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 20,494 bacterial and 1,762 archaeal Operational Taxonomic Units at species level (97% genetic identity. Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to

  13. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

    Science.gov (United States)

    Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D.; Scheu, Stefan; Daniel, Rolf

    2015-01-01

    Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio

  14. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    Science.gov (United States)

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  15. Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects.

    Science.gov (United States)

    Tobler, Dominique J; Benning, Liane G

    2011-07-01

    The microbial ecology associated with siliceous sinters was studied in five geochemically diverse Icelandic geothermal systems. Bacterial 16S rRNA clone libraries were constructed from water-saturated precipitates from each site resulting in a total of 342 bacterial clone sequences and 43 species level phylotypes. In near-neutral, saline (2.6-4.7% salinity) geothermal waters where sinter growth varied between 10 and ~300 kg year(-1) m(-2), 16S rRNA gene analyses revealed very low (no OTUs could be detected) to medium (9 OTUs) microbial activity. The most dominant phylotypes found in these waters belong to marine genera of the Proteobacteria. In contrast, in alkaline (pH = 9-10), meteoric geothermal waters with temperature = 66-96°C and geothermal waters; alkaliphilic thermophilic microbial communities with phylotypes related to heterotrophic and autotrophic microorganisms developed in alkaline high temperature waters, whereas halophilic mesophilic communities dominated coastal geothermal waters.

  16. Changes in soil bacterial communities induced by the invasive plant Pennisetum setaceum in a semiarid environment

    Science.gov (United States)

    Rodriguez-Caballero, Gema; Caravaca, Fuensanta; del Mar Alguacil, María; Fernández-López, Manuel; José Fernández-González, Antonio; García-Orenes, Fuensanta; Roldán, Antonio

    2016-04-01

    Invasive alien species are considered as a global threat being among the main causes of biodiversity loss. Plant invasions have been extensively studied from different disciplines with the purpose of identifying predictor traits of invasiveness and finding solutions. However, less is known about the implication of the rhizosphere microbiota in these processes, even when it is well known the importance of the interaction between plant rhizosphere and microbial communities. The objective of this study was to determine whether native and invasive plants support different bacterial communities in their rhizospheres and whether there are bacterial indicator species that might be contributing to the invasion process of these ecosystems. We carried out a study in five independent locations under Mediterranean semiarid conditions, where the native Hyparrhenia hirta is being displaced by Pennisetum setaceum, an aggressive invasive Poaceae and soil bacterial communities were amplified and 454-pyrosequenced. Changes in the composition and structure of the bacterial communities, owing to the invasive status of the plant, were detected when the richness and alpha-diversity estimators were calculated as well as when we analyzed the PCoA axes scores. The Indicator Species Analysis results showed a higher number of indicators for invaded communities at all studied taxonomic levels. In conclusion, the effect of the invasiveness and its interaction with the soil location has promoted shifts in the rhizosphere bacterial communities which might be facilitating the invader success in these ecosystems.

  17. Potential mechanisms and environmental controls of TiO2 nanoparticle effects on soil bacterial communities.

    Science.gov (United States)

    Ge, Yuan; Priester, John H; Van De Werfhorst, Laurie C; Schimel, Joshua P; Holden, Patricia A

    2013-12-17

    It has been reported that engineered nanoparticles (ENPs) alter soil bacterial communities, but the underlying mechanisms and environmental controls of such effects remain unknown. Besides direct toxicity, ENPs may indirectly affect soil bacteria by changing soil water availability or other properties. Alternatively, soil water or other environmental factors may mediate ENP effects on soil bacterial communities. To test, we incubated nano-TiO2-amended soils across a range of water potentials for 288 days. Following incubation, the soil water characteristics, organic matter, total carbon, total nitrogen, and respiration upon rewetting (an indicator of bioavailable organic carbon) were measured. Bacterial community shifts were characterized by terminal restriction fragment length polymorphism (T-RFLP). The endpoint soil water holding had been reported previously as not changing with this nano-TiO2 amendment; herein, we also found that some selected soil properties were unaffected by the treatments. However, we found that nano-TiO2 altered the bacterial community composition and reduced diversity. Nano-TiO2-induced community dissimilarities increased but tended to approach a plateau when soils became drier. Taken together, nano-TiO2 effects on soil bacteria appear to be a result of direct toxicity rather than indirectly through nano-TiO2 affecting soil water and organic matter pools. However, such directs effects of nano-TiO2 on soil bacterial communities are mediated by soil water. PMID:24256577

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  20. Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora.

    Directory of Open Access Journals (Sweden)

    Jie Li

    Full Text Available Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.

  1. Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island, Mexico.

    Science.gov (United States)

    Aguirre-Garrido, José Félix; Ramírez-Saad, Hugo César; Toro, Nicolás; Martínez-Abarca, Francisco

    2016-01-01

    Isabel Lake is a moderate saline soda crater lake located in Isabel Island in the eastern tropical Pacific coast of Mexico. Lake is mainly formed by rainfall and is strongly affected by evaporation and high input of nutrients derived from excretions of a large bird community inhabiting the island. So far, only the island macrobiota has been studied. The knowledge of the prokaryotic biota inhabiting the upper layers of this meromictic lake can give clues for the maintenance of this ecosystem. We assessed the diversity and composition of prokaryotic community in sediments and water of the lake by DGGE profiling, 16S rRNA gene amplicon pyrosequencing, and cultivation techniques. The bacterial community is largely dominated by halophilic and halotolerant microorganisms. Alpha diversity estimations reveal higher value in sediments than in water (P > 0.005). The lake water is dominated by γ-Proteobacteria belonging to four main families where Halomonadaceae presents the highest abundance. Aerobic, phototrophic, and halotolerant prokaryotes such as Cyanobacteria GPIIa, Halomonas, Alcanivorax, Idiomarina, and Cyclobacterium genera are commonly found. However, in sediment samples, Formosa, Muricauda, and Salegentibacter genera corresponding to Flavobacteriaceae family accounted for 15-20 % of the diversity. Heterotrophs like those involved in sulfur cycle, Desulfotignum, Desulfuromonas, Desulfofustis, and Desulfopila, appear to play an important role in sediments. Finally, a collection of aerobic halophilic bacterial isolates was created from these samples; members of the genus Halomonas were predominantly isolated from lake water. This study contributes to state the bacterial diversity present in this particular soda saline crater lake. PMID:26391805

  2. Molecular Characterization of Epiphytic Bacterial Communities on Charophycean Green Algae

    OpenAIRE

    Fisher, Madeline M.; Wilcox, Lee W.; Linda E Graham

    1998-01-01

    Epiphytic bacterial communities within the sheath material of three filamentous green algae, Desmidium grevillii, Hyalotheca dissiliens, and Spondylosium pulchrum (class Charophyceae, order Zygnematales), collected from a Sphagnum bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phyl...

  3. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    Science.gov (United States)

    Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

    2016-07-01

    Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system. PMID:27070460

  4. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    Science.gov (United States)

    Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

    2016-07-01

    Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system.

  5. Bacterial and Archaeal Diversity From the Eastern Lau Spreading Center

    Science.gov (United States)

    Reysenbach, A.; Banta, A.; Kelly, S.; Kirshstein, J.; Voytek, M.

    2005-12-01

    Due to the diversity of venting styles, geological settings and variations in fluid geochemistry, the Valu Fa Ridge and Eastern Lau Spreading Center (ELSC) provide a unique opportunity to explore the effects geological and geochemical variables on patterns of microbial phylogenetic and metabolic diversity. High temperature sulfides, diffuse flow fluids and microbial mats were collected from six active vent fields on the Valu Fa Ridge and Eastern Lau Spreading Center during the R/V Melville cruise TUIM05MV. All samples were subsampled for molecular and microbial culturing purposes. The archaeal and bacterial 16S rRNA genes were amplified by PCR from a selection of samples. Additionally, the presence of Aquificales and an unidentified lineage, the DHVE archaeal group, was explored using PCR primers specific for these groups. A selection of DNAs were also screened for functional genes that are diagnostic for certain pathways, viz, aclB (reductive TCA cycle), mcrA (methanogenesis), nirS and nirK (nitrite reduction), amoA (ammonia oxidation). Culturing of thermophiles, both acidophiles and neutrophiles, was initiated. Over 20 hydrogen oxidizing (hydrogen and oxygen) or nitrate reducing (hydrogen and nitrate) chemolithoautotrophs were isolated as colonies and grow at 70 degrees C. All are related to Persephonella hydrogenophila, with the exception of 2 cultures that perhaps represent new species of Hydrogenivirga and Aquifex. Preliminary analysis of patterns of Aquificales diversity using both culturing and molecular approaches suggest that the distributions of this group alone are very different from that observed at other hydrothermal sites such as along the East Pacific Rise or Central Indian Ridge. As yet, the most commonly isolated Aquificales, P. marina, has not been detected in enrichment cultures from ELSC, and the diversity of Aquificales-related sequences is much greater than detected from sites along the EPR. It is therefore also likely, that patterns of

  6. Functional recovery of biofilm bacterial communities after copper exposure

    Energy Technology Data Exchange (ETDEWEB)

    Boivin, Marie-Elene Y. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands) and Vrije Universiteit, Department of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands)]. E-mail: marie-elene.boivin@rivm.nl; Massieux, Boris [Netherlands Institutes of Ecology, Centre for Limnology, Rijkstraatweg 6, 3631 AC Nieuwersluis (Netherlands); Breure, Anton M. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Greve, Gerdit D. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Vrije Universiteit, Department of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands); Rutgers, Michiel [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Admiraal, Wim [University of Amsterdam, Department of Aquatic Ecology and Ecotoxicology, Kruislaan 320, 1098 SM Amsterdam (Netherlands)

    2006-03-15

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 {mu}mol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 {mu}mol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 {mu}mol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper.

  7. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems.

  8. Phylogenetic diversity of Amazonian tree communities

    OpenAIRE

    Honorio Coronado, Eurídice N.; Dexter, Kyle G.; Pennington, R. Toby; Chave, Jérôme; Lewis, Simon L.; Alexiades, Miguel N.; Alvarez, Esteban; Alves de Oliveira, Atila; Amaral, Iêda L.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard, Gerardo A.; Baraloto, Christopher; Bonal, Damien; Brienen, Roel

    2015-01-01

    Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses...

  9. Bacterial communities associated with the surfaces of fresh fruits and vegetables.

    Directory of Open Access Journals (Sweden)

    Jonathan W Leff

    Full Text Available Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically

  10. Diversity of Dominant Bacterial Taxa in Activated Sludge Promotes Functional Resistance following Toxic Shock Loading

    KAUST Repository

    Saikaly, Pascal

    2010-12-14

    Examining the relationship between biodiversity and functional stability (resistance and resilience) of activated sludge bacterial communities following disturbance is an important first step towards developing strategies for the design of robust biological wastewater treatment systems. This study investigates the relationship between functional resistance and biodiversity of dominant bacterial taxa by subjecting activated sludge samples, with different levels of biodiversity, to toxic shock loading with cupric sulfate (Cu[II]), 3,5-dichlorophenol (3,5-DCP), or 4-nitrophenol (4-NP). Respirometric batch experiments were performed to determine the functional resistance of activated sludge bacterial community to the three toxicants. Functional resistance was estimated as the 30 min IC50 or the concentration of toxicant that results in a 50% reduction in oxygen utilization rate compared to a referential state represented by a control receiving no toxicant. Biodiversity of dominant bacterial taxa was assessed using polymerase chain reaction-terminal restriction fragment length polymorphism (PCR-T-RFLP) targeting the 16S ribosomal RNA (16S rRNA) gene. Statistical analysis of 30 min IC50 values and PCR-T-RFLP data showed a significant positive correlation (P<0.05) between functional resistance and microbial diversity for each of the three toxicants tested. To our knowledge, this is the first study showing a positive correlation between biodiversity of dominant bacterial taxa in activated sludge and functional resistance. In this system, activated sludge bacterial communities with higher biodiversity are functionally more resistant to disturbance caused by toxic shock loading. © 2010 Springer Science+Business Media, LLC.

  11. Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities.

    Directory of Open Access Journals (Sweden)

    Thierry Bouvier

    Full Text Available The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.

  12. Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities.

    Science.gov (United States)

    Bouvier, Thierry; Venail, Patrick; Pommier, Thomas; Bouvier, Corinne; Barbera, Claire; Mouquet, Nicolas

    2012-01-01

    The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations. PMID:22701572

  13. Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill▿ †

    OpenAIRE

    Alonso-Gutiérrez, Jorge; Figueras, Antonio; Albaigés Riera, Joan; Jiménez, N.; Viñas, Marc; Solanas, Anna M.; Novoa, Beatriz

    2009-01-01

    The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaro...

  14. Assessment of anaerobic bacterial diversity and its effects on anaerobic system stability and the occurrence of antibiotic resistance genes.

    Science.gov (United States)

    Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2016-05-01

    This study evaluated the link between anaerobic bacterial diversity and, the biodegradation of antibiotic combinations and assessed how amending antibiotic combination and increasing concentration of antibiotics in a stepwise fashion influences the development of resistance genes in anaerobic reactors. The biodegradation, sorption and occurrence of the known antibiotic resistance genes (ARGs) of erythromycin and tetracycline were investigated using the processes of UV-HPLC and qPCR analysis respectively. Ion Torrent sequencing was used to detect microbial community changes in response to the addition of antibiotics. The overall results indicated that changes in the structure of a microbial community lead to changes in biodegradation capacity, sorption of antibiotics combinations and occurrence of ARGs. The enhanced biodegradation efficiency appeared to generate variations in the structure of the bacterial community. The results suggested that controlling the ultimate Gram-negative bacterial community, especially Acinetobacter-related populations, may promote the successful biodegradation of antibiotic combinations and reduce the occurrence of ARGs. PMID:26897411

  15. Soil microbial community diversity and driving mechanisms

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To study the structure of soil microbial communities, DNA was extracted from different environmental soil samples, and 16S rDNA clone libraries were constructed. The diversity of these 16S libraries were analyzed with restriction fragment length polymorphism based on amplification ribosomal DNA restriction analysis (RFLP-ARDRA)method. The results reveal a high diversity of the soil microbial communities, and striking differences in community structure at different depths. In the surface soil environment, there is no dominant gene pattern, but in the subsurface samples some dominant gene patterns are much more common. With the increasing depth the preference dominance becomes more significant. A spatial isolation hypothesis is proposed to explain the different community structures at different soil depths. Microcosms are set to simulate competition between populations at different degrees of spatial isolation. These studies reveal that spatial isolation caused by low moisture affects the competitive interactions of the two populations. In the two-strain microcosm there is one dominant population at high moisture, and no dominance in very dry environments

  16. Changes in assembly processes in soil bacterial communities following a wildfire disturbance.

    Science.gov (United States)

    Ferrenberg, Scott; O'Neill, Sean P; Knelman, Joseph E; Todd, Bryan; Duggan, Sam; Bradley, Daniel; Robinson, Taylor; Schmidt, Steven K; Townsend, Alan R; Williams, Mark W; Cleveland, Cory C; Melbourne, Brett A; Jiang, Lin; Nemergut, Diana R

    2013-06-01

    Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

  17. Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats

    Science.gov (United States)

    Ni, Jiajia; Yu, Yuhe; Zhang, Tanglin; Gao, Lei

    2012-09-01

    The intestinal bacteria of vertebrates form a close relationship with their host. External and internal conditions of the host, including its habitat, affect the intestinal bacterial community. Similarly, the intestinal bacterial community can, in turn, influence the host, particularly with respect to disease resistance. We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake. We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes, from which 66 different operational taxonomic units were identified. Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination, we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish, except for DF-7, and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities (Mantel one-tailed test, R=0.157, P=0.175). Cetobacterium appeared more frequently in the intestine of grass carp collected from pond. A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  18. Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats

    Institute of Scientific and Technical Information of China (English)

    NI Jiajia; YU Yuhe; ZHANG Tanglin; GAO Lei

    2012-01-01

    The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.

  19. Chronic N-amended soils exhibit an altered bacterial community structure in Harvard Forest, MA, USA.

    Science.gov (United States)

    Turlapati, Swathi A; Minocha, Rakesh; Bhiravarasa, Premsai S; Tisa, Louis S; Thomas, William K; Minocha, Subhash C

    2013-02-01

    At the Harvard Forest, Petersham, MA, the impact of 20 years of annual ammonium nitrate application to the mixed hardwood stand on soil bacterial communities was studied using 16S rRNA genes pyrosequencing. Amplification of 16S rRNA genes was done using DNA extracted from 30 soil samples (three treatments × two horizons × five subplots) collected from untreated (control), low N-amended (50 kg ha(-1) year(-1)) and high N-amended (150 kg ha(-1) year(-1)) plots. A total of 1.3 million sequences were processed using qiime. Although Acidobacteria represented the most abundant phylum based on the number of sequences, Proteobacteria were the most diverse in terms of operational taxonomic units (OTUs). UniFrac analyses revealed that the bacterial communities differed significantly among soil horizons and treatments. Microsite variability among the five subplots was also evident. Nonmetric multidimensional scaling ordination of normalized OTU data followed by permutational manova further confirmed these observations. Richness indicators and indicator species analyses revealed higher bacterial diversity associated with N amendment. Differences in bacterial diversity and community composition associated with the N treatments were also observed at lower phylogenetic levels. Only 28-35% of the 6 936 total OTUs identified were common to three treatments, while the rest were specific to one treatment or common to two. PMID:22974374

  20. Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals

    KAUST Repository

    Apprill, Amy

    2013-03-21

    Cultivation-based studies have demonstrated that yellow-band disease (YBD), a lesion-producing ailment affecting diverse species of coral, is caused by a consortium of Vibrio spp. This study takes the first cultivation-independent approach to examine the whole bacterial community associated with YBD-like lesioned corals. Two species of Fungiidae corals, Ctenactis crassa and Herpolitha limax, displaying YBD-like lesions were examined across diverse reefs throughout the Red Sea. Using a pyrosequencing approach targeting the V1-V3 regions of the SSU rRNA gene, no major differences in bacterial community composition or diversity were identified between healthy and lesioned corals of either species. Indicator species analysis did not find Vibrio significantly associated with the lesioned corals. However, operational taxonomic units belonging to the Ruegeria genus of Alphaproteobacteria and NS9 marine group of Flavobacteria were significantly associated with the lesioned corals. The most striking trend of this dataset was that reef location was found to be the most significant influence on the coral-bacterial community. It is possible that more pronounced lesion-specific bacterial signatures might have been concealed by the strong influence of environmental conditions on coral-bacteria. Overall, this study demonstrates inconsistencies between cultivation-independent and cultivation-based studies regarding the role of specific bacteria in coral diseases. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  1. Do honeybees shape the bacterial community composition in floral nectar?

    Directory of Open Access Journals (Sweden)

    Yana Aizenberg-Gershtein

    Full Text Available Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers. Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

  2. Assessment of bacterial community structure in nitrifying biofilm under inorganic carbon-sufficient and -limited conditions.

    Science.gov (United States)

    Bae, Hyokwan; Chung, Yun-Chul; Yang, Heejeong; Lee, Changsoo; Aryapratama, Rio; Yoo, Young J; Lee, Seockheon

    2015-01-01

    In this work, nitrification and changes in the composition of the total bacterial community under inorganic carbon (IC)-limited conditions, in a nitrifying moving bed biofilm reactor, was investigated. A culture-independent analysis of cloning and sequencing based on the 16S rRNA gene was applied to quantify the bacterial diversity and to determine bacterial taxonomic assignment. IC concentrations had significant effects on the stability of ammonia-oxidation as indicated by the reduction of the nitrogen conversion rate with high NH4(+)-N loadings. The predominance of Nitrosomonas europaea was maintained in spite of changes in the IC concentration. In contrast, heterotrophic bacterial species contributed to a high bacterial diversity, and to a dynamic shift in the bacterial community structure, under IC-limited conditions. In this study, individual functions of heterotrophic bacteria were estimated based on taxonomic information. Possible key roles of coexisting heterotrophic bacteria are the assimilation of organic compounds of extracellular polymeric substances produced by nitrifiers, and biofilm formation by providing a filamentous structure and aggregation properties.

  3. Changes of Bacterial Community Structure in Copper Mine Tailings After Colonization of Reed (Phragmites communis)

    Institute of Scientific and Technical Information of China (English)

    CHEN Yu-Qing; REN Guan-Ju; AN Shu-Qing; SUN Qing-Ye; LIU Chang-Hong; SHUANG Jing-Lei

    2008-01-01

    Soil samples were collected from both bare and vegetated mine tailings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed (Phragmites communis) colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic (pH = 3.78), whereas the vegetated mine tailing was near neutral (pH = 7.28). The contents of organic matter, total nitrogen, and ammonium acetate-extractable otassium in vegetated mine tailings were significantly higher than those in the bare mine tailings (P < 0.01), whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings (P < 0.01). The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.

  4. Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity.

    Science.gov (United States)

    Kanokratana, Pattanop; Mhuanthong, Wuttichai; Laothanachareon, Thanaporn; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Kruetreepradit, Trongtham; Mayes, Shawn; Champreda, Verawat

    2016-08-01

    Pitchers are specialized digestive organs of carnivorous plants which evolved for trapping prey and represent a unique environment harboring hidden diversity of unexplored microbes forming transient hydrolytic microcosms. In this study, the diversity of bacterial communities in the pitcher fluids of seven local Nepenthes found in Thailand was assessed by tagged 16S ribosomal RNA (rRNA) gene amplicon sequencing on an Ion PGM™ platform. A total of 1,101,000 filtered sequences were obtained which were taxonomically classified into 20 phyla, 48 classes, 72 orders, 153 families, and 442 genera while the remainder (1.43 %) could not be assigned to any existing taxa. Proteobacteria represented the predominant members in closed pitchers and more diversified bacterial taxa particularly Bacteriodetes and Actinobacteria, showed increasing abundance in open pitchers containing insect bodies. Principal coordinate analysis revealed that distribution of bacterial taxa was not significantly related to the Nepenthes species but strongly correlated to the pH of the pitcher fluids (pH 1.7-6.7). Acidicella was a highly dominant bacterial genus in acidic pitcher fluids while Dyella and Mycobacterium were also common genera in most pitchers. A unique microbial community structure was found in Nepenthes ampullaria which could reflect their adaptation to digest leaf litter, in addition to insect prey. The work revealed the highly unexplored nature of bacterial microcosms in Nepenthes pitcher fluids and provides insights into their community structure in this unique ecological system. PMID:27287538

  5. Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest

    OpenAIRE

    Shen, Ju-Pei; Chen, C. R.; Lewis, Tom

    2016-01-01

    Effects of fire on biogeochemical cycling in terrestrial ecosystem are widely acknowledged, while few studies have focused on the bacterial community under the disturbance of long-term frequent prescribed fire. In this study, three treatments (burning every two years (B2), burning every four years (B4) and no burning (B0)) were applied for 38 years in an Australian wet sclerophyll forest. Results showed that bacterial alpha diversity (i.e. bacterial OTU) in the top soil (0–10 cm) was signific...

  6. The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert.

    Science.gov (United States)

    Gombeer, S; Ramond, J-B; Eckardt, F D; Seely, M; Cowan, D A

    2015-09-01

    Notwithstanding, the severe environmental conditions, deserts harbour a high diversity of adapted micro-organisms. In such oligotrophic environments, soil physicochemical characteristics play an important role in shaping indigenous microbial communities. This study investigates the edaphic bacterial communities of three contrasting desert terrain types (gravel plains, sand dunes and ephemeral rivers) with different surface geologies in the Central Namib Desert. For each site, we evaluated surface soil physicochemistries and used explorative T-RFLP methodology to get an indication of bacterial community diversities. While grain size was an important parameter in separating the three terrain types physicochemically and specific surface soil types could be distinguished, the desert edaphic bacterial communities displayed a high level of local spatial heterogeneity. Ten variables contributed significantly (P Namib Desert and stress the importance of recording a wide variety of environmental descriptors to comprehensively assess the role of edaphic parameters in shaping microbial communities. PMID:25939371

  7. Cuticles of European and American lobsters harbor diverse bacterial species and differ in disease susceptibility.

    Science.gov (United States)

    Whitten, Miranda M A; Davies, Charlotte E; Kim, Anita; Tlusty, Michael; Wootton, Emma C; Chistoserdov, Andrei; Rowley, Andrew F

    2014-06-01

    Diseases of lobster shells have a significant impact on fishing industries but the risk of disease transmission between different lobster species has yet to be properly investigated. This study compared bacterial biofilm communities from American (Homarus americanus) and European lobsters (H. gammarus), to assess both healthy cuticle and diseased cuticle during lesion formation. Culture-independent molecular techniques revealed diversity in the bacterial communities of cuticle biofilms both within and between the two lobster species, and identified three bacterial genera associated with shell lesions plus two putative beneficial bacterial species (detected exclusively in healthy cuticle or healing damaged cuticle). In an experimental aquarium shared between American and European lobsters, heterospecific transmission of potentially pathogenic bacteria appeared to be very limited; however, the claws of European lobsters were more likely to develop lesions when reared in the presence of American lobsters. Aquarium biofilms were also examined but revealed no candidate pathogens for environmental transmission. Aquimarina sp. 'homaria' (a potential pathogen associated with a severe epizootic form of shell disease) was detected at a much higher prevalence among American than European lobsters, but its presence correlated more with exacerbation of existing lesions rather than with lesion initiation. PMID:24817518

  8. Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

    Science.gov (United States)

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  9. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    Science.gov (United States)

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  10. Supraglacial bacterial community structures vary across the Greenland ice sheet

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Zarsky, Jakub D.;

    2016-01-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across t...

  11. Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization

    Directory of Open Access Journals (Sweden)

    Heather eManching

    2014-08-01

    Full Text Available Plant leaves are inhabited by a diverse group of microorganisms that are important contributors to optimal growth. Biotic and abiotic effects on plant growth are usually studied in controlled settings examining response to variation in single factors and in field settings with large numbers of variables. Multi-factor experiments with combinations of stresses bridge this gap, increasing our understanding of the genotype-environment-phenotype functional map for the host plant and the affiliated epiphytic community. The maize inbred B73 was exposed to single and combination abiotic and the biotic stress treatments: low nitrogen fertilizer and high levels of infection with southern leaf blight (causal agent Cochliobolus heterostrophus. Microbial epiphyte samples were collected at the vegetative early-season phase and species composition was determined using 16S ribosomal intergenic spacer analysis. Plant traits and level of southern leaf blight disease were measured late-season. Bacterial diversity was different among stress treatment groups (P< 0.001. Lower species richness—alpha diversity--was correlated with increased severity of southern leaf blight disease when disease pressure was high. Nitrogen fertilization intensified the decline in bacterial alpha diversity. While no single bacterial ribotype was consistently associated with disease severity, small sets of ribotypes were good predictors of disease levels. Difference in leaf bacterial-epiphyte diversity early in the season were correlated with plant disease severity, supporting further tests of microbial epiphyte-disease correlations for use in predicting disease progression.

  12. Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs.

    Science.gov (United States)

    Choudhury, Md Abu; Marsh, Nicole; Banu, Shahera; Paterson, David L; Rickard, Claire M; McMillan, David J

    2016-01-01

    Skin bacteria at peripheral intravenous catheter (PIVC) insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs). Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, pskin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%), Pseudomonas spp., (10%) and Acinetobacter spp. (10%) were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.

  13. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  14. Evaluation of five antibiotics on larval gut bacterial diversity of Plutella xylostella (Lepidoptera: Plutellidae).

    Science.gov (United States)

    Lin, Xiao-Li; Kang, Zhi-Wei; Pan, Qin-Jian; Liu, Tong-Xian

    2015-10-01

    Larvae of the diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae), have rich microbial communities inhabiting the gut, and these bacteria contribute to the fitness of the pest. In this study we evaluated the effects of five antibiotics (rifampicin, ampicillin, tetracycline, streptomycin sulfate and chloramphenicol) on the gut bacterial diversity of P. xylostella larvae. We screened five different concentrations for each antibiotic in a leaf disc assay, and found that rifampicin and streptomycin sulfate at 3 mg/mL significantly reduced the diversity of the bacterial community, and some bacterial species could be rapidly eliminated. The number of gut bacteria in the rifampicin group and streptomycin sulfate group decreased more rapidly than the others. With the increase of antibiotic concentration, the removal efficiency was improved, whereas toxic effects became more apparent. All antibiotics reduced larval growth and development, and eventually caused high mortality, malformation of the prepupae, and hindered pupation and adult emergence. Among the five antibiotics, tetracycline was the most toxic and streptomycin sulfate was a relatively mild one. Some dominant bacteria were not affected by feeding antibiotics alone. Denaturing gradient gel electrophoresis graph showed that the most abundant and diverse bacteria in P. xylostella larval gut appeared in the cabbage feeding group, and diet change and antibiotics intake influenced gut flora abundance. Species diversity was significantly reduced in the artificial diet and antibiotics treatment groups. After feeding on the artificial diet with rifampicin, streptomycin sulfate and their mixture for 10 days, larval gut bacteria could not be completely removed as detected with the agarose gel electrophoresis method. PMID:25183343

  15. Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

    Science.gov (United States)

    Ellegaard, Kirsten M.; Engel, Philipp

    2016-01-01

    Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

  16. Safe-site effects on rhizosphere bacterial communities in a high-altitude alpine environment.

    Science.gov (United States)

    Ciccazzo, Sonia; Esposito, Alfonso; Rolli, Eleonora; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2014-01-01

    The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P < 0.05) on 16S rRNA gene diversity revealed significant differences (P < 0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  17. Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

    Directory of Open Access Journals (Sweden)

    Sonia Ciccazzo

    2014-01-01

    Full Text Available The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05 on 16S rRNA gene diversity revealed significant differences (P<0.05 between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

  18. Long- term manure exposure increases soil bacterial community potential for plasmid uptake

    DEFF Research Database (Denmark)

    Musovic, Sanin; Klümper, Uli; Dechesne, Arnaud;

    2014-01-01

    Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and main......Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive...... and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent...

  19. Association of host and microbial species diversity across spatial scales in desert rodent communities.

    Directory of Open Access Journals (Sweden)

    Yoni Gavish

    Full Text Available Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.

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

    Science.gov (United States)

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

    2014-07-01

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

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

    Science.gov (United States)

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

    2014-07-01

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

  2. Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines.

    Science.gov (United States)

    Huang, Qiuyuan; Jiang, Hongchen; Briggs, Brandon R; Wang, Shang; Hou, Weiguo; Li, Gaoyuan; Wu, Geng; Solis, Ramonito; Arcilla, Carlo A; Abrajano, Teofilo; Dong, Hailiang

    2013-09-01

    The microbial diversity was investigated in sediments of six acidic to circumneutral hot springs (Temperature: 60-92 °C, pH 3.72-6.58) in the Philippines using an integrated approach that included geochemistry and 16S rRNA gene pyrosequencing. Both bacterial and archaeal abundances were lower in high-temperature springs than in moderate-temperature ones. Overall, the archaeal community consisted of sequence reads that exhibited a high similarity (nucleotide identity > 92%) to phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea. The bacterial community was composed of sequence reads moderately related (nucleotide identity > 90%) to 17 phyla, with Aquificae and Firmicutes being dominant. These phylogenetic groups were correlated with environmental conditions such as temperature, dissolved sulfate and calcium concentrations in spring water, and sediment properties including total nitrogen, pyrite, and elemental sulfur. Based on the phylogenetic inference, sulfur metabolisms appear to be key physiological functions in these hot springs. Sulfobacillus (within phylum Firmicutes) along with members within Sulfolobales were abundant in two high-temperature springs (> 76 °C), and they were hypothesized to play an important role in regulating the sulfur cycling under high-temperature conditions. The results of this study improve our understanding of microbial diversity and community composition in acidic to circumneutral terrestrial hot springs and their relationships with geochemical conditions.

  3. Pesticide Side Effects in an Agricultural Soil Ecosystem as Measured by amoA Expression Quantification and Bacterial Diversity Changes.

    Directory of Open Access Journals (Sweden)

    Louise Feld

    Full Text Available Assessing the effects of pesticide hazards on microbiological processes in the soil is currently based on analyses that provide limited insight into the ongoing processes. This study proposes a more comprehensive approach. The side effects of pesticides may appear as changes in the expression of specific microbial genes or as changes in diversity. To assess the impact of pesticides on gene expression, we focused on the amoA gene, which is involved in ammonia oxidation. We prepared soil microcosms and exposed them to dazomet, mancozeb or no pesticide. We hypothesized that the amount of amoA transcript decreases upon pesticide application, and to test this hypothesis, we used reverse-transcription qPCR. We also hypothesized that bacterial diversity is affected by pesticides. This hypothesis was investigated via 454 sequencing and diversity analysis of the 16S ribosomal RNA and RNA genes, representing the active and total soil bacterial communities, respectively.Treatment with dazomet reduced both the bacterial and archaeal amoA transcript numbers by more than two log units and produced long-term effects for more than 28 days. Mancozeb also inhibited the numbers of amoA transcripts, but only transiently. The bacterial and archaeal amoA transcripts were both sensitive bioindicators of pesticide side effects. Additionally, the numbers of bacterial amoA transcripts correlated with nitrate production in N-amended microcosms. Dazomet reduced the total bacterial numbers by one log unit, but the population size was restored after twelve days. The diversity of the active soil bacteria also seemed to be re-established after twelve days. However, the total bacterial diversity as reflected in the 16S ribosomal RNA gene sequences was largely dominated by Firmicutes and Proteobacteria at day twelve, likely reflecting a halt in the growth of early opportunists and the re-establishment of a more diverse population. We observed no effects of mancozeb on diversity.

  4. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica

    Directory of Open Access Journals (Sweden)

    Neus eGarcias-Bonet

    2012-09-01

    Full Text Available Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes and leaves by DGGE. A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ and δ subclasses and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

  5. Bacterial community in sediment from the Western Pacific "Warm Pool" and its relationship to environment

    Institute of Scientific and Technical Information of China (English)

    ZENG Runying; ZHAO Jing; ZHANG Rui; LIN Nianwei

    2005-01-01

    Total DNAs were extracted from different sections of deep sea sediment core sample collected from the Western Pacific "Warm Pool". The bacterial 16S ribosomal DNA (rDNA) clone libraries were constructed and analyzed by PCR-restriction fragment length polymorphism (RFLP) and DNA sequencing. The bacterial communities in these samples and their relationship to environment were analyzed consequently. The results indicated that among eight main bacterial groups found in these sediments, members of the γ-Proteobacteria were most abundant in each section of sediment core sample and the genus Colwellia belonging to γ-Proteobacteria was dominant in this area. Members of the α-Proteobacteria were found commonly existing in these samples, while members belonging to β-Proteobacteria were seldom detected. The diversity of bacterial communities from different sections of sediment core sample was δ- and ε-Proteo- bacteria and the bacterial group including genera Cytopahga, Flexibacteria and Bacteroides (CFB group). These bacteria all were inversely proportional to the depth of sediment. Phylogenetic analysis showed that there were 18%-30% and 15%-25% of total bacterial communities related to methane and sulfur metabolism respectively in each section of core sample, implicating that the metabolism of sulfur and methane played an important role in the substance and energy cycles of the Western Pacific "Warm Pool".

  6. Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose.

    Science.gov (United States)

    Bogas, Andréa Cristina; Ferreira, Almir José; Araújo, Welington Luiz; Astolfi-Filho, Spartaco; Kitajima, Elliot Watanabe; Lacava, Paulo Teixeira; Azevedo, João Lúcio

    2015-01-01

    Endophytes colonize an ecological niche similar to that of phytopathogens, which make them candidate for disease suppression. Anthracnose is a disease caused by Colletotrichum spp., a phytopathogen that can infect guarana (Paullinia cupana), an important commercial crop in the Brazilian Amazon. We investigated the diversity of endophytic bacteria inhabiting the phyllosphere of asymptomatic and symptomatic anthracnose guarana plants. The PCR-denaturation gradient gel electrophoresis (PCR-DGGE) fingerprints revealed differences in the structure of the evaluated communities. Detailed analysis of endophytic bacteria composition using culture-dependent and 16S rRNA clone libraries revealed the presence of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria phyla. Firmicutes comprised the majority of isolates in asymptomatic plants (2.40E(-4)). However, cloning and sequencing of 16S rRNA revealed differences at the genus level for Neisseria (1.4E(-4)), Haemophilus (2.1E(-3)) and Arsenophonus (3.6E(-5)) in asymptomatic plants, Aquicella (3.5E(-3)) in symptomatic anthracnose plants, and Pseudomonas (1.1E(-3)), which was mainly identified in asymptomatic plants. In cross-comparisons of the endophytic bacterial communities as a whole, symptomatic anthracnose plants contained higher diversity, as reflected in the Shannon-Weaver and Simpson indices estimation (P < 0.05). Similarly, comparisons using LIBSHUFF and heatmap analysis for the relative abundance of operational taxonomic units (OTUs) showed differences between endophytic bacterial communities. These data are in agreement with the NMSD and ANOSIM analysis of DGGE profiles. Our results suggest that anthracnose can restructure endophytic bacterial communities by selecting certain strains in the phyllosphere of P. cupana. The understanding of these interactions is important for the development of strategies of biocontrol for Colletotrichum. PMID:26090305

  7. Bacterial Community Mapping of the Mouse Gastrointestinal Tract

    OpenAIRE

    Gu, Shenghua; Chen, Dandan; Zhang, Jin-Na; Lv, Xiaoman; WANG Kun; Duan, Li-Ping; Nie, Yong; Wu, Xiao-Lei

    2013-01-01

    Keeping mammalian gastrointestinal (GI) tract communities in balance is crucial for host health maintenance. However, our understanding of microbial communities in the GI tract is still very limited. In this study, samples taken from the GI tracts of C57BL/6 mice were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities along the mouse GI tract, including those present in the stomach, duodenum, jejunum, ileum, cecum, colon and feces. Further a...

  8. Bacterial community of biofilms developed under different water supply conditions in a distribution system.

    Science.gov (United States)

    Sun, Huifang; Shi, Baoyou; Bai, Yaohui; Wang, Dongsheng

    2014-02-15

    In order to understand the bacterial community characteristics of biofilms developed under different finished water supply histories in drinking water distribution systems (DWDS), biofilm samples on different type of iron corrosion scales in a real DWDS were collected and systematically investigated using 454 pyrosequencing of 16S rRNA gene. The richness and diversity estimators showed that biofilms formed in DWDS transporting finished groundwater (GW) had the lowest level of bacterial diversity. From phylum to genus level, the dominant bacterial groups found in the biofilms under finished surface water (SW) and GW conditions were distinct. Proteobacteria was the dominant group in all biofilm samples (in the range of 40%-97%), but was relatively higher in biofilms with GW. The relative abundance of Firmicutes in biofilms with SW (28%-35%) was significantly higher (psupply condition. Several potential opportunistic pathogens, such as Burkholderia fungorum, Mycobacterium neoaurum, Mycobacterium frederiksbergense were detected in the biofilms.

  9. Bacterial diversity associated with wild caught Anopheles mosquitoes from Dak Nong Province, Vietnam using culture and DNA fingerprint.

    Directory of Open Access Journals (Sweden)

    Chung Thuy Ngo

    Full Text Available Microbiota of Anopheles midgut can modulate vector immunity and block Plasmodium development. Investigation on the bacterial biodiversity in Anopheles, and specifically on the identification of bacteria that might be used in malaria transmission blocking approaches, has been mainly conducted on malaria vectors of Africa. Vietnam is an endemic country for both malaria and Bancroftian filariasis whose parasitic agents can be transmitted by the same Anopheles species. No information on the microbiota of Anopheles mosquitoes in Vietnam was available previous to this study.The culture dependent approach, using different mediums, and culture independent (16S rRNA PCR - TTGE method were used to investigate the bacterial biodiversity in the abdomen of 5 Anopheles species collected from Dak Nong Province, central-south Vietnam. Molecular methods, sequencing and phylogenetic analysis were used to characterize the microbiota.The microbiota in wild-caught Anopheles was diverse with the presence of 47 bacterial OTUs belonging to 30 genera, including bacterial genera impacting Plasmodium development. The bacteria were affiliated with 4 phyla, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, the latter being the dominant phylum. Four bacterial genera are newly described in Anopheles mosquitoes including Coxiella, Yersinia, Xanthomonas, and Knoellia. The bacterial diversity per specimen was low ranging from 1 to 4. The results show the importance of pairing culture and fingerprint methods to better screen the bacterial community in Anopheles mosquitoes.Sampled Anopheles species from central-south Vietnam contained a diverse bacterial microbiota that needs to be investigated further in order to develop new malaria control approaches. The combination of both culture and DNA fingerprint methods allowed a thorough and complementary screening of the bacterial community in Anopheles mosquitoes.

  10. Bacterial Diversity Associated with Wild Caught Anopheles Mosquitoes from Dak Nong Province, Vietnam Using Culture and DNA Fingerprint

    Science.gov (United States)

    Ngo, Chung Thuy; Aujoulat, Fabien; Veas, Francisco; Jumas-Bilak, Estelle; Manguin, Sylvie

    2015-01-01

    Background Microbiota of Anopheles midgut can modulate vector immunity and block Plasmodium development. Investigation on the bacterial biodiversity in Anopheles, and specifically on the identification of bacteria that might be used in malaria transmission blocking approaches, has been mainly conducted on malaria vectors of Africa. Vietnam is an endemic country for both malaria and Bancroftian filariasis whose parasitic agents can be transmitted by the same Anopheles species. No information on the microbiota of Anopheles mosquitoes in Vietnam was available previous to this study. Method The culture dependent approach, using different mediums, and culture independent (16S rRNA PCR – TTGE) method were used to investigate the bacterial biodiversity in the abdomen of 5 Anopheles species collected from Dak Nong Province, central-south Vietnam. Molecular methods, sequencing and phylogenetic analysis were used to characterize the microbiota. Results and Discussion The microbiota in wild-caught Anopheles was diverse with the presence of 47 bacterial OTUs belonging to 30 genera, including bacterial genera impacting Plasmodium development. The bacteria were affiliated with 4 phyla, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, the latter being the dominant phylum. Four bacterial genera are newly described in Anopheles mosquitoes including Coxiella, Yersinia, Xanthomonas, and Knoellia. The bacterial diversity per specimen was low ranging from 1 to 4. The results show the importance of pairing culture and fingerprint methods to better screen the bacterial community in Anopheles mosquitoes. Conclusion Sampled Anopheles species from central-south Vietnam contained a diverse bacterial microbiota that needs to be investigated further in order to develop new malaria control approaches. The combination of both culture and DNA fingerprint methods allowed a thorough and complementary screening of the bacterial community in Anopheles mosquitoes. PMID:25747513

  11. Pulmonary bacterial communities in surgically resected noncystic fibrosis bronchiectasis lungs are similar to those in cystic fibrosis.

    Science.gov (United States)

    Maughan, Heather; Cunningham, Kristopher S; Wang, Pauline W; Zhang, Yu; Cypel, Marcelo; Chaparro, Cecilia; Tullis, D Elizabeth; Waddell, Thomas K; Keshavjee, Shaf; Liu, Mingyao; Guttman, David S; Hwang, David M

    2012-01-01

    Background. Recurrent bacterial infections play a key role in the pathogenesis of bronchiectasis, but conventional microbiologic methods may fail to identify pathogens in many cases. We characterized and compared the pulmonary bacterial communities of cystic fibrosis (CF) and non-CF bronchiectasis patients using a culture-independent molecular approach. Methods. Bacterial 16S rRNA gene libraries were constructed from lung tissue of 10 non-CF bronchiectasis and 21 CF patients, followed by DNA sequencing of isolates from each library. Community characteristics were analyzed and compared between the two groups. Results. A wide range of bacterial diversity was detected in both groups, with between 1 and 21 bacterial taxa found in each patient. Pseudomonas was the most common genus in both groups, comprising 49% of sequences detected and dominating numerically in 13 patients. Although Pseudomonas appeared to be dominant more often in CF patients than in non-CF patients, analysis of entire bacterial communities did not identify significant differences between these two groups. Conclusions. Our data indicate significant diversity in the pulmonary bacterial community of both CF and non-CF bronchiectasis patients and suggest that this community is similar in surgically resected lungs of CF and non-CF bronchiectasis patients. PMID:22448327

  12. Pulmonary Bacterial Communities in Surgically Resected Noncystic Fibrosis Bronchiectasis Lungs Are Similar to Those in Cystic Fibrosis

    Directory of Open Access Journals (Sweden)

    Heather Maughan

    2012-01-01

    Full Text Available Background. Recurrent bacterial infections play a key role in the pathogenesis of bronchiectasis, but conventional microbiologic methods may fail to identify pathogens in many cases. We characterized and compared the pulmonary bacterial communities of cystic fibrosis (CF and non-CF bronchiectasis patients using a culture-independent molecular approach. Methods. Bacterial 16S rRNA gene libraries were constructed from lung tissue of 10 non-CF bronchiectasis and 21 CF patients, followed by DNA sequencing of isolates from each library. Community characteristics were analyzed and compared between the two groups. Results. A wide range of bacterial diversity was detected in both groups, with between 1 and 21 bacterial taxa found in each patient. Pseudomonas was the most common genus in both groups, comprising 49% of sequences detected and dominating numerically in 13 patients. Although Pseudomonas appeared to be dominant more often in CF patients than in non-CF patients, analysis of entire bacterial communities did not identify significant differences between these two groups. Conclusions. Our data indicate significant diversity in the pulmonary bacterial community of both CF and non-CF bronchiectasis patients and suggest that this community is similar in surgically resected lungs of CF and non-CF bronchiectasis patients.

  13. Changes in the bacterial community of soil from a neutral mine drainage channel.

    Directory of Open Access Journals (Sweden)

    Letícia Bianca Pereira

    Full Text Available Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.

  14. Experimental sulfate amendment alters peatland bacterial community structure.

    Science.gov (United States)

    Strickman, R J S; Fulthorpe, R R; Coleman Wasik, J K; Engstrom, D R; Mitchell, C P J

    2016-10-01

    As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group. PMID:27267720

  15. Biological support media influence the bacterial biofouling community in reverse osmosis water reclamation demonstration plants.

    Science.gov (United States)

    Ferrera, Isabel; Mas, Jordi; Taberna, Elisenda; Sanz, Joan; Sánchez, Olga

    2015-01-01

    The diversity of the bacterial community developed in different stages of two reverse osmosis (RO) water reclamation demonstration plants designed in a wastewater treatment plant (WWTP) in Tarragona (Spain) was characterized by applying 454-pyrosequencing of the 16S rRNA gene. The plants were fed by secondary treated effluent to a conventional pretreatment train prior to the two-pass RO system. Plants differed in the material used in the filtration process, which was sand in one demonstration plant and Scandinavian schists in the second plant. The results showed the presence of a highly diverse and complex community in the biofilms, mainly composed of members of the Betaproteobacteria and Bacteroidetes in all stages, with the presence of some typical wastewater bacteria, suggesting a feed water origin. Community similarities analyses revealed that samples clustered according to filter type, highlighting the critical influence of the biological supporting medium in biofilm community structure.

  16. A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.

    Science.gov (United States)

    Pascault, Noémie; Roux, Simon; Artigas, Joan; Pesce, Stéphane; Leloup, Julie; Tadonleke, Rémy D; Debroas, Didier; Bouchez, Agnès; Humbert, Jean-François

    2014-12-01

    The pollution of lakes and rivers by pesticides is a growing problem worldwide. However, the impacts of these substances on microbial communities are still poorly understood, partly because next-generation sequencing (NGS) has rarely been used in an ecotoxicology context to study bacterial communities despite its interest for accessing rare taxa. Microcosm experiments were carried out to evaluate the effects of tebuconazole (TBZ) on the structure and composition of bacterial communities from two types of freshwater ecosystem (lakes and rivers) with differing histories of pollutant contamination (pristine vs. previously exposed sites). Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously exposed sites than in pristine sites. Lakes and river stations shared very few OTUs, and differences at the phylum level were identified between these ecosystems (i.e. the relative importance of Actinobacteria and Gammaproteobacteria). Despite differences between these ecosystems and their contamination history, no significant effect of TBZ on bacterial community structure or composition was observed. Compared to functional parameters that displayed variable responses, we demonstrated that a combination of classical methods and NGS is necessary to investigate the ecotoxicological responses of microbial communities to pollutants.

  17. Effects of food on bacterial community composition associated with the copepod Acartia tonsa Dana

    DEFF Research Database (Denmark)

    Tang, Kam; Dziallas, Claudia; Hutalle-Schmelzer, Kristine;

    2009-01-01

    The estuarine copepod Acartia tonsa naturally carried diverse strains of bacteria on its body. The bacterial community composition (BCC) remained very conservative even when the copepod was fed different axenic algal species, indicating that the food per se did not much affect BCC associated...... composition and copepod life history therefore serve to regulate BCC associated with copepods, and spatial and temporal variations in algal species composition and copepod origin would alter bacteria-copepod interactions....

  18. The under-recognized dominance of Verrucomicrobia in soil bacterial communities

    OpenAIRE

    Bergmann, Gaddy T.; Bates, Scott T; Eilers, Kathryn G.; Lauber, Christian L; Caporaso, J. Gregory; Walters, William A.; Knight, Rob; Fierer, Noah

    2011-01-01

    Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples)....

  19. Bacterial communities and species-specific associations with the mucus of Brazilian coral species.

    Science.gov (United States)

    Carlos, Camila; Torres, Tatiana T; Ottoboni, Laura M M

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in samples of mucus, water, and sediment differed according to the composition and relative frequency of OTUs. The coral mucus community seemed to be more stable and resistant to seasonal variations, compared to the water and sediment communities. There was no influence of geographic location on the composition of the communities. The sediment community was extremely diverse and might act as a "seed bank" for the entire environment. Species-specific OTUs were found in P. caribaeorum, T. coccinea, and M. hispida. PMID:23567936

  20. Monitoring bacterial diversity of the marine sponge Ircinia strobilina upon transfer into aquaculture.

    Science.gov (United States)

    Mohamed, Naglaa M; Rao, Venkateswara; Hamann, Mark T; Kelly, Michelle; Hill, Russell T

    2008-07-01

    Marine sponges in the genus Ircinia are known to be good sources of secondary metabolites with biological activities. A major obstacle in the development of sponge-derived metabolites is the difficulty in ensuring an economic, sustainable supply of the metabolites. A promising strategy is the ex situ culture of sponges in closed or semiclosed aquaculture systems. In this study, the marine sponge Ircinia strobilina (order Dictyoceratida: family Irciniidae) was collected from the wild and maintained for a year in a recirculating aquaculture system. Microbiological and molecular community analyses were performed on freshly collected sponges and sponges maintained in aquaculture for 3 months and 9 months. Chemical analyses were performed on wild collected sponges and individuals maintained in aquaculture for 3 months and 1 year. Denaturing gradient gel electrophoresis was used to assess the complexity of and to monitor changes in the microbial communities associated with I. strobilina. Culture-based and molecular techniques showed an increase in the Bacteroidetes and Alpha- and Gammaproteobacteria components of the bacterial community in aquaculture. Populations affiliated with Beta- and Deltaproteobacteria, Clostridia, and Planctomycetes emerged in sponges maintained in aquaculture. The diversity of bacterial communities increased upon transfer into aquaculture. PMID:18469126

  1. Diversidade e potencial biotecnológico da comunidade bacteriana endofítica de sementes de soja Diversity and biotechnological potential of endophytic bacterial community of soybean seeds

    Directory of Open Access Journals (Sweden)

    Laura de Castro Assumpção

    2009-05-01

    Full Text Available O objetivo deste trabalho foi isolar, caracterizar e identificar a comunidade bacteriana endofítica de sementes de soja e avaliar o seu potencial biotecnológico. Foram utilizadas sementes de 12 cultivares de soja. Os isolados bacterianos endofíticos obtidos foram avaliados in vitro quanto ao antagonismo a fungos fitopatogênicos, síntese de ácido indolacético (AIA e solubilização de fosfato. A caracterização foi realizada com técnicas de isolamento, análise de restrição do DNA ribossomal amplificado (ARDRA e sequenciamento parcial do gene 16S rDNA. Os isolados com maior potencial biotecnológico foram inoculados em sementes de soja, para se avaliar a capacidade de promoção de crescimento de plantas. Foi possível identificar 12 ribótipos por meio da ARDRA, que foram classificados como: Acinetobacter, Bacillus, Brevibacterium, Chryseobacterium, Citrobacter, Curtobacterium, Enterobacter, Methylobacterium, Microbacterium, Micromonospora, Pantoea, Paenibacillus, Pseudomonas, Ochrobactrum, Streptomyces e Tsukamurella. Quanto ao potencial biotecnológico da comunidade, 18% dos isolados controlaram o crescimento de fungos fitopatogênicos, 100% produziram AIA, e 39% solubilizaram fosfato. O isolado 67A(57 de Enterobacter sp. aumentou significativamente a massa de matéria seca da raiz. A inoculação de isolados com elevado potencial biotecnológico em avaliações in vitro não promoveu o crescimento de plantas de soja na maioria dos casos.The objectives of this work were to isolate, characterize and identify the endophytic bacterial community of soybean seeds, and to test the biotechnological potential of this community. Seeds from 12 soybean cultivars were used. The endophytic bacterial isolates were evaluated for in vitro antagonism against phytopathogenic fungi, synthesis of indoleacetic acid (IAA, and capacity to solubilize phosphate. Isolation techniques, amplified ribosomal DNA restriction analysis (ARDRA grouping, and

  2. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata

    KAUST Repository

    Closek, Collin J.

    2014-06-20

    Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD. © 2014 International Society for Microbial Ecology. All rights reserved.

  3. Phytochemical diversity drives plant–insect community diversity

    OpenAIRE

    Richards, Lora A.; Dyer, Lee A.; Forister, Matthew L.; Smilanich, Angela M.; Dodson, Craig D.; Leonard, Michael D.; Jeffrey, Christopher S.

    2015-01-01

    Phytochemical diversity is a key component of functional diversity. Challenges in quantifying phytochemical diversity have limited our understanding of the causes and consequences of variation in phytochemical diversity across plant species and families. Here we show that phytochemical diversity across dozens of plant species predicts herbivore diversity, herbivore specialization, phototoxicity, herbivory, and attack by natural enemies. Our approach and findings provide a framework for future...

  4. Bacterial diversity in oil-polluted marine coastal sediments.

    Science.gov (United States)

    Acosta-González, Alejandro; Marqués, Silvia

    2016-04-01

    Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.

  5. Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil

    Directory of Open Access Journals (Sweden)

    Gaidi eRen

    2015-01-01

    Full Text Available Understanding the potential for PAH degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene at three dosages (5, 30, and 70 mg.kg-1. Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1 at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0% including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while 3 phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria were significantly increased; and (2 at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community

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

    OpenAIRE

    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'...

  7. Supraglacial bacterial community structures vary across the Greenland ice sheet.

    Science.gov (United States)

    Cameron, Karen A; Stibal, Marek; Zarsky, Jakub D; Gözdereliler, Erkin; Schostag, Morten; Jacobsen, Carsten S

    2016-02-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community dissimilarities (2.3% of total variability calculated). The majority of dissimilarities found between cryoconite 16S rRNA gene amplicons from DNA and RNA was calculated to be the result of changes in three taxa, Pseudanabaenaceae, Sphingobacteriaceae and WPS-2, which together contributed towards 80.8 ± 12.6% of dissimilarities between samples. Bacterial communities across the GrIS are spatially variable active communities that are likely influenced by localized biological inputs and physicochemical conditions.

  8. Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

    Directory of Open Access Journals (Sweden)

    Patrick M Erwin

    Full Text Available BACKGROUND: Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP, might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6% of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil. CONCLUSIONS/SIGNIFICANCE: The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities

  9. Methods Used to Study Bacterial Diversity in the Marine Environment around Qingdao

    Institute of Scientific and Technical Information of China (English)

    Robertson P. A. W.; MacInnes J; Sparagano O. A. E.; Purdom I.; LI Y.; YU D.H; DU Z.J.; XU H.S.; Austin B.

    2002-01-01

    Pollution has a considerable effect on biological communities, in terms of size and diversity of the populations.Yet, the precise consequences of human activity on microbial communities in the marine environment are poorly understood.Therefore, in an ongoing collaborative research programme between Heriot-Watt University and the Ocean University ofQingdao, bacteria were isolated in 1999 and 2000 from marine sediment, seawater, seaweed, fish and shellfish, taken fromlocations in Shandong Province adjacent to Qingdao. Sampling locations were comprised of industrial and aquacultural sitesand a clean, control site. In order to analyse microbial diversity, a polyphasic approach was adopted for characterisation ofthese isolates, specifically through examination of key phenotypic traits, i.e. using Biolog GN MicroPlateTM profiles, bacteri-al whole cell protein profiles and 16S and 23S rRNA gene sequences. These techniques yielded complex taxonomic data,which were subjected to statistical and cluster analyses. The application of these methods to studies of microbial communitiesis discussed.

  10. Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

    Institute of Scientific and Technical Information of China (English)

    Yue-Jian Hu; Qian Wang; Yun-Tao Jiang; Rui Ma; Wen-Wei Xia; Zi-Sheng Tang; Zheng Liu; Jing-Ping Liang; Zheng-Wei Huang

    2013-01-01

    The objective of this study was to investigate the compositional profiles and microbial shifts of oral microbiota during head-and-neck radiotherapy. Bioinformatic analysis based on 16S rRNA gene pyrosequencing was performed to assess the diversity and variation of oral microbiota of irradiated patients. Eight patients with head and neck cancers were involved in this study. For each patient, supragingival plaque samples were collected at seven time points before and during radiotherapy. A total of 147232 qualified sequences were obtained through pyrosequencing and bioinformatic analysis, representing 3460 species level operational taxonomic units (OTUs) and 140 genus level taxa. Temporal variations were observed across different time points and supported by cluster analysis based on weighted UniFrac metrics, Moreover, the low evenness of oral microbial communities in relative abundance was revealed by Lorenz curves. This study contributed to a better understanding of the detailed characterization of oral bacterial diversity of irradiated patients.

  11. Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem.

    Directory of Open Access Journals (Sweden)

    Guo-Chun Ding

    Full Text Available Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.

  12. Spatial diversity of bacterioplankton communities in surface water of northern South China Sea.

    Directory of Open Access Journals (Sweden)

    Jialin Li

    Full Text Available The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS. Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.

  13. The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin

    Science.gov (United States)

    Salgado, Vanessa R; de Queiroz, Artur TL; Sanabani, Sabri S; de Oliveira, Camila I; Carvalho, Edgar M; Costa, Jackson ML; Barral-Netto, Manoel; Barral, Aldina

    2016-01-01

    Localised cutaneous leishmaniasis (LCL) is the most common form of cutaneous leishmaniasis characterised by single or multiple painless chronic ulcers, which commonly presents with secondary bacterial infection. Previous culture-based studies have found staphylococci, streptococci, and opportunistic pathogenic bacteria in LCL lesions, but there have been no comparisons to normal skin. In addition, this approach has strong bias for determining bacterial composition. The present study tested the hypothesis that bacterial communities in LCL lesions differ from those found on healthy skin (HS). Using a high throughput amplicon sequencing approach, which allows for better populational evaluation due to greater depth coverage and the Quantitative Insights Into Microbial Ecology pipeline, we compared the microbiological signature of LCL lesions with that of contralateral HS from the same individuals.Streptococcus, Staphylococcus,Fusobacterium and other strict or facultative anaerobic bacteria composed the LCL microbiome. Aerobic and facultative anaerobic bacteria found in HS, including environmental bacteria, were significantly decreased in LCL lesions (p < 0.01). This paper presents the first comprehensive microbiome identification from LCL lesions with next generation sequence methodology and shows a marked reduction of bacterial diversity in the lesions. PMID:27074253

  14. Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production

    KAUST Repository

    Belila, A.

    2016-02-18

    Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m3/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during

  15. Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production.

    Science.gov (United States)

    Belila, A; El-Chakhtoura, J; Otaibi, N; Muyzer, G; Gonzalez-Gil, G; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

    2016-05-01

    Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m(3)/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during

  16. Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production.

    Science.gov (United States)

    Belila, A; El-Chakhtoura, J; Otaibi, N; Muyzer, G; Gonzalez-Gil, G; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

    2016-05-01

    Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m(3)/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during

  17. Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

    Science.gov (United States)

    Pajares, Silvia; Bonilla-Rosso, German; Travisano, Michael; Eguiarte, Luis E; Souza, Valeria

    2012-08-01

    Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.

  18. Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

    Science.gov (United States)

    Pajares, Silvia; Bonilla-Rosso, German; Travisano, Michael; Eguiarte, Luis E; Souza, Valeria

    2012-08-01

    Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment. PMID:22460437

  19. Comparative approach to capture bacterial diversity in coastal waters

    DEFF Research Database (Denmark)

    Na, Hyunsoo; Kim, Ok-Sun; Yoon, Suk-hwan;

    2011-01-01

    described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation...... to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions...... from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1% of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high...

  20. Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture.

    Directory of Open Access Journals (Sweden)

    Marcela S Montecchia

    Full Text Available The Southern Andean Yungas in Northwest Argentina constitute one of the main biodiversity hotspots in the world. Considerable changes in land use have taken place in this ecoregion, predominantly related to forest conversion to croplands, inducing losses in above-ground biodiversity and with potential impact on soil microbial communities. In this study, we used high-throughput pyrosequencing of the 16S ribosomal RNA gene to assess whether land-use change and time under agriculture affect the composition and diversity of soil bacterial communities. We selected two areas dedicated to sugarcane and soybean production, comprising both short- and long-term agricultural sites, and used the adjacent native forest soils as a reference. Land-use change altered the composition of bacterial communities, with differences between productive areas despite the similarities between both forests. At the phylum level, only Verrucomicrobia and Firmicutes changed in abundance after deforestation for sugarcane and soybean cropping, respectively. In cultivated soils, Verrucomicrobia decreased sharply (~80%, while Firmicutes were more abundant. Despite the fact that local diversity was increased in sugarcane systems and was not altered by soybean cropping, phylogenetic beta diversity declined along both chronosequences, evidencing a homogenization of soil bacterial communities over time. In spite of the detected alteration in composition and diversity, we found a core microbiome resistant to the disturbances caused by the conversion of forests to cultivated lands and few or none exclusive OTUs for each land-use type. The overall changes in the relative abundance of copiotrophic and oligotrophic taxa may have an impact in soil ecosystem functionality. However, communities with many taxa in common may also share many functional attributes, allowing to maintain at least some soil ecosystem services after forest conversion to croplands.

  1. Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture.

    Science.gov (United States)

    Montecchia, Marcela S; Tosi, Micaela; Soria, Marcelo A; Vogrig, Jimena A; Sydorenko, Oksana; Correa, Olga S

    2015-01-01

    The Southern Andean Yungas in Northwest Argentina constitute one of the main biodiversity hotspots in the world. Considerable changes in land use have taken place in this ecoregion, predominantly related to forest conversion to croplands, inducing losses in above-ground biodiversity and with potential impact on soil microbial communities. In this study, we used high-throughput pyrosequencing of the 16S ribosomal RNA gene to assess whether land-use change and time under agriculture affect the composition and diversity of soil bacterial communities. We selected two areas dedicated to sugarcane and soybean production, comprising both short- and long-term agricultural sites, and used the adjacent native forest soils as a reference. Land-use change altered the composition of bacterial communities, with differences between productive areas despite the similarities between both forests. At the phylum level, only Verrucomicrobia and Firmicutes changed in abundance after deforestation for sugarcane and soybean cropping, respectively. In cultivated soils, Verrucomicrobia decreased sharply (~80%), while Firmicutes were more abundant. Despite the fact that local diversity was increased in sugarcane systems and was not altered by soybean cropping, phylogenetic beta diversity declined along both chronosequences, evidencing a homogenization of soil bacterial communities over time. In spite of the detected alteration in composition and diversity, we found a core microbiome resistant to the disturbances caused by the conversion of forests to cultivated lands and few or none exclusive OTUs for each land-use type. The overall changes in the relative abundance of copiotrophic and oligotrophic taxa may have an impact in soil ecosystem functionality. However, communities with many taxa in common may also share many functional attributes, allowing to maintain at least some soil ecosystem services after forest conversion to croplands. PMID:25793893

  2. Dynamics of bacterial communities in soils of rainforest fragments under restoration processes

    Science.gov (United States)

    Vasconcellos, Rafael; Zucchi, Tiago; Taketani, Rodrigo; Andreote, Fernando; Cardoso, Elke

    2014-05-01

    The Brazilian Atlantic Forest ("Mata Atlântica") has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10% of its original area still remains. Many projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different ages of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant diversity highly influenced the bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, one with the youngest (10 years) and the other with the oldest (native) site suggests their use as bioindicators of soil quality and soil recovery of forest fragments under restoration.

  3. Functionally and phylogenetically diverse plant communities key to soil biota.

    Science.gov (United States)

    Milcu, Alexandru; Allan, Eric; Roscher, Christiane; Jenkins, Tania; Meyer, Sebastian T; Flynn, Dan; Bessler, Holger; Buscot, François; Engels, Christof; Gubsch, Marlén; König, Stephan; Lipowsky, Annett; Loranger, Jessy; Renker, Carsten; Scherber, Christoph; Schmid, Bernhard; Thébault, Elisa; Wubet, Tesfaye; Weisser, Wolfgang W; Scheu, Stefan; Eisenhauer, Nico

    2013-08-01

    Recent studies assessing the role of biological diversity for ecosystem functioning indicate that the diversity of functional traits and the evolutionary history of species in a community, not the number of taxonomic units, ultimately drives the biodiversity--ecosystem-function relationship. Here, we simultaneously assessed the importance of plant functional trait and phylogenetic diversity as predictors of major trophic groups of soil biota (abundance and diversity), six years from the onset of a grassland biodiversity experiment. Plant functional and phylogenetic diversity were generally better predictors of soil biota than the traditionally used species or functional group richness. Functional diversity was a reliable predictor for most biota, with the exception of soil microorganisms, which were better predicted by phylogenetic diversity. These results provide empirical support for the idea that the diversity of plant functional traits and the diversity of evolutionary lineages in a community are important for maintaining higher abundances and diversity of soil communities.

  4. The bacterial community of entomophilic nematodes and host beetles.

    Science.gov (United States)

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. PMID:26992100

  5. Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China.

    Science.gov (United States)

    Huang, Qiuyuan; Dong, Christina Z; Dong, Raymond M; Jiang, Hongchen; Wang, Shang; Wang, Genhou; Fang, Bin; Ding, Xiaoxue; Niu, Lu; Li, Xin; Zhang, Chuanlun; Dong, Hailiang

    2011-09-01

    The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.

  6. Distribution of Archaeal and Bacterial communities in a subtropical reservoir

    Directory of Open Access Journals (Sweden)

    Laís Américo Soares

    2015-12-01

    Full Text Available Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.

  7. Low Functional beta-Diversity Despite High Taxonomic beta-Diversity among Tropical Estuarine Fish Communities

    OpenAIRE

    Sébastien Villéger; Julia Ramos Miranda; Domingo Flores Hernandez; David Mouillot

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic a...

  8. Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices.

    Science.gov (United States)

    Dellagnezze, Bruna Martins; Vasconcellos, Suzan Pantaroto de; Melo, Itamar Soares de; Santos Neto, Eugênio Vaz Dos; Oliveira, Valéria Maia de

    2016-01-01

    Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam) as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM), Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA). Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material. PMID:27282730

  9. Bacterial communities in the gut and reproductive organs of Bactrocera minax (Diptera: Tephritidae based on 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Ailin Wang

    Full Text Available The citrus fruit fly Bactrocera minax is associated with diverse bacterial communities. We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax. Our dataset consisted of 100,749 reads with an average length of 400 bp. The saturated rarefaction curves and species richness indices indicate that the sampling was comprehensive. We found highly diverse bacterial communities, with individual sample containing approximately 361 microbial operational taxonomic units (OTUs. A total of 17 bacterial phyla were obtained from the flies. A phylogenetic analysis of 16S rDNA revealed that Proteobacteria was dominant in all samples (75%-95%. Actinobacteria and Firmicutes were also commonly found in the total clones. Klebsiella, Citrobacter, Enterobacter, and Serratia were the major genera. However, bacterial diversity (Chao1, Shannon and Simpson indices and community structure (PCA analysis varied across samples. Female ovary has the most diverse bacteria, followed by male testis, and the bacteria diversity of reproductive organs is richer than that of the gut. The observed variation can be caused by sex and tissue, possibly to meet the host's physiological demands.

  10. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

    OpenAIRE

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Eoin L. Brodie; Zhou, Jizhong; Firestone, Mary

    2015-01-01

    ABSTRACT It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional p...

  11. Spatial Scales of Bacterial Diversity in Cold-Water Coral Reef Ecosystems

    OpenAIRE

    Sandra Schöttner; Christian Wild; Friederike Hoffmann; Antje Boetius; Alban Ramette

    2012-01-01

    Background: Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning. Methodology/Principal Findings: Bacterial community structure, as determined by Automated Riboso...

  12. Seasonality in molecular and cytometric diversity of marine bacterioplankton: the reshuffling of bacterial taxa by vertical mixing

    KAUST Repository

    García, Francisca C.

    2015-07-17

    The ’cytometric diversity’ of phytoplankton communities has been studied based on single-cell properties, but the applicability of this method to characterize bacterioplankton has been unexplored. Here, we analysed seasonal changes in cytometric diversity of marine bacterioplankton along a decadal time-series at three coastal stations in the Southern Bay of Biscay. Shannon-Weaver diversity estimates and Bray-Curtis similarities obtained by cytometric and molecular (16S rRNA tag sequencing) methods were significantly correlated in samples from a 3.5-year monthly time-series. Both methods showed a consistent cyclical pattern in the diversity of surface bacterial communities with maximal values in winter. The analysis of the highly resolved flow cytometry time-series across the vertical profile showed that water column mixing was a key factor explaining the seasonal changes in bacterial composition and the winter increase in bacterial diversity in coastal surface waters. Due to its low cost and short processing time as compared to genetic methods, the cytometric diversity approach represents a useful complementary tool in the macroecology of aquatic microbes.

  13. Sea Ice Microbial Communities: Distribution, Abundance, and Diversity of Ice Bacteria in McMurdo Sound, Antarctica, in 1980

    OpenAIRE

    Sullivan, Cornelius W.; Palmisano, Anna C.

    1984-01-01

    An abundant and diverse bacterial community was found within brine channels of annual sea ice and at the ice-seawater interface in McMurdo Sound, Antarctica, in 1980. The mean bacterial standing crop was 1.4 × 1011 cells m−2 (9.8 mg of C m−2); bacterial concentrations as high as 1.02 × 1012 cells m−3 were observed in ice core melt water. Vertical profiles of ice cores 1.3 to 2.5 m long showed that 47% of the bacterial numbers and 93% of the bacterial biomass were located in the bottom 20 cm o...

  14. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events

    Science.gov (United States)

    Sison-Mangus, Marilou P.; Jiang, Sunny; Kudela, Raphael M.; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6–65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12–86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  15. Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children.

    Science.gov (United States)

    Dannemiller, K C; Gent, J F; Leaderer, B P; Peccia, J

    2016-04-01

    Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structures were non-random and demonstrated species segregation (C-score, P children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building's physical and occupant characteristics. PMID:25833176

  16. High concentrations of methyl fluoride affect the bacterial community in a thermophilic methanogenic sludge.

    Directory of Open Access Journals (Sweden)

    Liping Hao

    Full Text Available To precisely control the application of methyl fluoride (CH3F for analysis of methanogenic pathways, the influence of 0-10% CH3F on bacterial and archaeal communities in a thermophilic methanogenic sludge was investigated. The results suggested that CH3F acts specifically on acetoclastic methanogenesis. The inhibitory effect stabilized at an initial concentration of 3-5%, with around 90% of the total methanogenic activity being suppressed, and a characteristic of hydrogenotrophic pathway in isotope fractionation was demonstrated under this condition. However, extended exposure (12 days to high concentrations of CH3F (>3% altered the bacterial community structure significantly, resulting in increased diversity and decreased evenness, which can be related to acetate oxidation and CH3F degradation. Bacterial clone library analysis showed that syntrophic acetate oxidizing bacteria Thermacetogenium phaeum were highly enriched under the suppression of 10% CH3F. However, the methanogenic community did not change obviously. Thus, excessive usage of CH3F over the long term can change the composition of the bacterial community. Therefore, data from studies involving the use of CH3F as an acetoclast inhibitor should be interpreted with care. Conversely, CH3F has been suggested as a factor to stimulate the enrichment of syntrophic acetate oxidizing bacteria.

  17. Diversity of Bacterial Community on the Surface of Marine Paint in Temperate Coastal Marine Waters%两种船用防污涂层实海挂片表面细菌群落多样性分析

    Institute of Scientific and Technical Information of China (English)

    栾鑫; 段继周; 陈永伟; 池振明

    2013-01-01

    应用16S rDNA基因文库技术分析了实海全浸15 d的两种船用漆A和B表面的细菌多样性.样品A表面附着细菌的OTU数为26,分别属于变形菌门和拟杆菌门,其中y-变形菌为优势菌,占总克隆数的65.1%;样品B表面附着细菌的OTU数为27,分别属于变形菌门、拟杆菌门和浮霉菌门,其中优势菌分别为占据总克隆数38.7%的γ-变形菌和39.8%α-变形菌.B表面附着的细菌无论在种类还是数量上都多于A,这表明这种新的环境友好型防污涂料对细菌的杀伤力不如添加氧化亚铜和杀菌剂的传统船用漆.同时,在两种船用漆表面都附着了大量的解环菌属(Cycloclasticus)的细菌,这种海洋多环芳香烃(PAHs)分解菌是海水中分解萘和菲的关键菌,可以对涂层造成破坏.%The bacterial community structures on the surface of two kinds of marine paint,A and B,were immersed in seawater and investigated by 16S rDNA analysis.Phylogenetic analysis of 26 OTUs showed that the bacterial phylotypes of the A sample included two phylums of bacteria,Bacteroides and Proteobacteria,with y-Proteobacteria accounting for 65.1% of the clone number.The bacterial phylotypes of sample B included three phylums bacteria,Bacteroides,Planctomycetes and Proteobacteria,with γ-Proteobacteria and α-Proteobacteria as the dominant components,accounting for 38.7% and 39.8%,respectively.B is a tin free self-smoothening and self-polishing antifouling paint,which does not contain any harmful active agents to environment,nevertheless,its bactericidal efficiency is lower than traditional marine paint with cuprous oxide and fungicides.In addition,we found on the surface of both marine paints Cycloclasticus,a marine polycyclic aromatic hydrocarbons (PAHs) decomposing bacteria that can biodegrade naphthalene and phenanthrene and cause damage to the coating.

  18. Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China.

    Science.gov (United States)

    Ren, Chengjie; Sun, Pingsheng; Kang, Di; Zhao, Fazhu; Feng, Yongzhong; Ren, Guangxin; Han, Xinhui; Yang, Gaihe

    2016-01-01

    In the present paper, we investigated the effects of afforestation on nitrogen fractions and microbial communities. A total of 24 soil samples were collected from farmland (FL) and three afforested lands, namely Robinia pseudoacacia L (RP), Caragana korshinskii Kom (CK), and abandoned land (AL), which have been arable for the past 40 years. Quantitative PCR and Illumina sequencing of 16S rRNA genes were used to analyze soil bacterial abundance, diversity, and composition. Additionally, soil nitrogen (N) stocks and fractions were estimated. The results showed that soil N stock, N fractions, and bacterial abundance and diversity increased following afforestation. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacterial compositions. Overall, soil bacterial compositions generally changed from Actinobacteria (Acidobacteria)-dominant to Proteobacteria-dominant following afforestation. Soil N fractions, especially for dissolved organic nitrogen (DON), were significantly correlated with most bacterial groups and bacterial diversity, while potential competitive interactions between Proteobacteria (order Rhizobiales) and Cyanobacteria were suggested. In contrast, nitrate nitrogen (NO3(-)-N) influenced soil bacterial compositions less than other N fractions. Therefore, the present study demonstrated that bacterial diversity and specific species respond to farmland-to-forest conversion and hence have the potential to affect N dynamic processes in the Loess Plateau. PMID:27334692

  19. Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland.

    Science.gov (United States)

    Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

    2014-01-01

    Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities.

  20. Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland.

    Directory of Open Access Journals (Sweden)

    Markus Lange

    Full Text Available Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs. In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities.

  1. Functional recovery of biofilm bacterial communities after copper exposure.

    NARCIS (Netherlands)

    Boivin, Marie-Elène Y; Massieux, Boris; Breure, Anton M; Greve, Gerdit D; Rutgers, Michiel; Admiraal, Wim

    2006-01-01

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 micromol/l copper amended surface water and a reference and subsequently to un-amended surface wat

  2. Hydrocephalus in adults with community-acquired bacterial meningitis

    NARCIS (Netherlands)

    E. Soemirien Kasanmoentalib; M.C. Brouwer; A. van der Ende; D. van de Beek

    2010-01-01

    Objective: To evaluate the occurrence, treatment, and outcome of hydrocephalus complicating community-acquired bacterial meningitis in adults. Methods: Case series from a prospective nationwide cohort study from Dutch hospitals from 2006 to 2009. Results: Hydrocephalus was diagnosed in 26 of 577 epi

  3. Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

    Science.gov (United States)

    Neher, Deborah A.; Weicht, Thomas R.; Bates, Scott T.; Leff, Jonathan W.; Fierer, Noah

    2013-01-01

    Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed

  4. Microbial activity and bacterial community structure during degradation of microcystins

    DEFF Research Database (Denmark)

    Christoffersen, K.; Lyck, Susanne; Winding, A.

    2002-01-01

    experiment to evaluate the effects of organic lysates on bacterial proliferation in the absence of microcystin. An exponential decline of the dissolved toxins was observed in all cases with toxins present, and the degradation rates ranged between 0.5 and 1.0 d(-1). No lag phases were observed but slow...... including microcystins, and this resulted in a net accumulation of bacterial cells. The heterotrophic nanoflagellates responded quickly to the bacterial growth and probably consumed a considerable amount of the bacteria. The microbial activities returned to initial values within 5 to 6 d as the toxins....... It was hypothesised that the bacterial community from a lake with frequent occurrence of toxic cyanobacteria can degrade microcystin along with other organic compounds. The initial dissolved microcystin concentrations ranged between 10 and 136 mug 1(-1) (microcystin-LR equivalents) in the laboratory experiment, using...

  5. Bacterial community composition of sediments from artificial Lake Maslak, Istanbul, Turkey.

    Science.gov (United States)

    Balcı, Nurgul; Vardar, Nurcan; Yelboga, Emrah; Karaguler, Nevin Gul

    2012-09-01

    Small artificial lakes are ubiquitous in various natural environments. Small impoundments increase the residence time of water, thereby increasing the potential for retention of nutrients through biological and physical processes. We examined bacterial community structure of Lake Maslak, a small freshwater impoundment located in a densely populated region. The objective of our study was to investigate bacterial communities of the lake sediment which has not been determined and to elucidate the factors controlling bacterial diversity and the biogeochemical processes within the lake. For these purposes, surface water, lake bed sediments, and one core sample were collected. Microbiological characteristic of the lake bed and core sediments was determined by denaturing gradient gel electrophoresis targeting the 16S rRNA gene. Along with the microbiological studies, physicochemical (O(2), pH, temperature) and geochemical properties of the surface (NO (3) (-) , NO (2) (-) , NH (4) (+) ,PO (4) (-) ,SO (4) (2-) , K(+), Mg(2+), Ca(2+)) and pore water (K(+), Mg(2+), Ca(2+)) were determined in addition to heavy metals contents (Co Cu, Fe, Zn, Pb, Cd). Eight lake bed and one core sediments were also collected and analyzed for heavy metals and elemental compositions. Nitrate concentration in the surface water ranges from 0.27-1.8 mg/L, and ammonium (0.0-0.83 mg/L) appears to follow nitrate concentration. Sulfate concentration in the surface water (mean 60 mg/L) is greater than those measured in the pore water (mean, 37.5 mg/L). Fe, Zn, Pb, and Cd were not determined in the surface water, whereas Co was significantly higher both in the surface and pore water. Unlike Co, Pb, Zn, and Cd were not measured in the pore water. Lakebed and core sediments show significant enrichment in Pb, Zn, and Cu, indicating anthropogenic pollution. Consistent with geochemical parameters, microbiological analysis suggests a diverse bacterial community in the lake sediments and influence of

  6. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters.

    Science.gov (United States)

    Bacosa, Hernando P; Liu, Zhanfei; Erdner, Deana L

    2015-01-01

    Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters. PMID:26648916

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

    International Nuclear Information System (INIS)

    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

  8. Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China

    Science.gov (United States)

    Gao, Peike; Tian, Huimei; Wang, Yansen; Li, Yanshu; Li, Yan; Xie, Jinxia; Zeng, Bing; Zhou, Jiefang; Li, Guoqiang; Ma, Ting

    2016-02-01

    To investigate the spatial distribution of microbial communities and their drivers in petroleum reservoir environments, we performed pyrosequencing of microbial partial 16S rRNA, derived from 20 geographically separated water-flooding reservoirs, and two reservoirs that had not been flooded, in China. The results indicated that distinct underground microbial communities inhabited the different reservoirs. Compared with the bacteria, archaeal alpha-diversity was not strongly correlated with the environmental variables. The variation of the bacterial and archaeal community compositions was affected synthetically, by the mining patterns, spatial isolation, reservoir temperature, salinity and pH of the formation brine. The environmental factors explained 64.22% and 78.26% of the total variance for the bacterial and archaeal communities, respectively. Despite the diverse community compositions, shared populations (48 bacterial and 18 archaeal genera) were found and were dominant in most of the oilfields. Potential indigenous microorganisms, including Carboxydibrachium, Thermosinus, and Neptunomonas, were only detected in a reservoir that had not been flooded with water. This study indicates that: 1) the environmental variation drives distinct microbial communities in different reservoirs; 2) compared with the archaea, the bacterial communities were highly heterogeneous within and among the reservoirs; and 3) despite the community variation, some microorganisms are dominant in multiple petroleum reservoirs.

  9. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

  10. Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China.

    Directory of Open Access Journals (Sweden)

    Yaohui Bai

    Full Text Available Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake--Dianchi--was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ demonstrated that ammonia-oxidizing bacteria (AOB were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria.

  11. Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

    Science.gov (United States)

    Nacke, Heiko; Thürmer, Andrea; Wollherr, Antje; Will, Christiane; Hodac, Ladislav; Herold, Nadine; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2011-01-01

    Background Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. Methodology/Principal Findings We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. Conclusions/Significance Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland

  12. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils.

    Directory of Open Access Journals (Sweden)

    Heiko Nacke

    Full Text Available BACKGROUND: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. METHODOLOGY/PRINCIPAL FINDINGS: We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. CONCLUSIONS/SIGNIFICANCE: Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land

  13. Bacterial diversity in sediments of core MD05-2902 from the Xisha Trough, the South China Sea

    Institute of Scientific and Technical Information of China (English)

    LI Tao; WANG Peng

    2014-01-01

    A sediment core MD05-2902 was collected from the deep-sea basin of the Xisha Trough. The vertical dis-tribution and diversity of bacteria in the core was investigated through ten sub-sampling with an interval of 1 m using bacterial 16S rRNA gene as a phylogenetic bio-marker. Eighteen phylogenetic groups were identified from 16S rRNA gene clone libraries. The dominant bacterial groups were JS1, Planctomycetes and Chloroflexi, which accounted for 30.6%, 16.6%, and 15.6%of bacterial clones in the libraries, respectively. In order to reveal the relationship between biotic and abiotic data, a nonmetric multidimensional scaling analysis was performed. The result revealed that theδ15N,δ13C, total organic carbon and total organic ni-trogen possibly influenced the bacterial community structure. This study expanded our knowledge of the biogeochemical cycling in the Xisha Trough sediment.

  14. Influence of Starvation on the Structure of Gut-Associated Bacterial Communities in the Chinese White Pine Beetle (Dendroctonus armandi

    Directory of Open Access Journals (Sweden)

    Xia Hu

    2016-06-01

    Full Text Available This study investigated the influence of starvation on the structure of the gut bacterial community in the Chinese white pine beetle (Dendroctonus armandi. A total of 14 operational taxonomic units (OTUs0.03 clusters belonging to nine genera were identified. Denaturing gradient gel electrophoresis (DGGE profiles of bacterial PCR-amplified 16S rRNA gene fragments from the guts of starved male and female adults revealed that the bacterial community diversity increased after starvation. The dominant genus Citrobacter decreased significantly, whereas the genus Serratia increased in both starved female and starved male adults. The most predominant bacterial genus in D. armandi adults was Citrobacter, except for starved male adults, in which Serratia was the most abundant genus (27%. Our findings reveal that starvation affects gut bacterial dynamics in D. armandi, as has been observed in other insect species.

  15. Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

    Science.gov (United States)

    Balmonte, John Paul; Arnosti, Carol; Underwood, Sarah; McKee, Brent A.; Teske, Andreas

    2016-01-01

    Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities

  16. Community structure of actively growing bacterial populations in plant pathogen suppressive soil

    NARCIS (Netherlands)

    Hjort, K.; Lembke, A.; Speksnijder, A.G.C.L.; Smalla, K.; Jansson, J.K.

    2007-01-01

    The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations a

  17. Composition of bacterial and archaeal communities during landfill refuse decomposition processes.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Zhao, Heping; Long, David T

    2015-12-01

    Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales, and of bacteria were Proteobacteria, Firmicutes, and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus, Fibrobacter, and Eubacterium, while SMP harbored groups of Microbacterium. Both phases had Clostridium with different abundance, 4-5 folds higher in SMP.

  18. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  19. Reconcilable differences? Human diversity, cultural relativity, and sense of community.

    Science.gov (United States)

    Townley, Greg; Kloos, Bret; Green, Eric P; Franco, Margarita M

    2011-03-01

    Sense of community (SOC) is one of the most widely used and studied constructs in community psychology. As proposed by Sarason in (The Psychological sense of community: prospects for a community psychology, Jossey-Bass, San Francisco, 1974), SOC represents the strength of bonding among community members. It is a valuable component of community life, and it has been linked to positive mental health outcomes, citizen participation, and community connectedness. However, promotion of SOC can become problematic in community psychology praxis when it conflicts with other core values proposed to define the field, namely values of human diversity, cultural relativity, and heterogeneity of experience and perspective. Several commentators have noted that promotion of SOC can conflict with multicultural diversity because it tends to emphasize group member similarity and appears to be higher in homogeneous communities. In this paper, we introduce the idea of a community-diversity dialectic as part of praxis and research in community psychology. We argue that systematic consideration of cultural psychology perspectives can guide efforts to address a community-diversity dialectic and revise SOC formulations that ultimately will invigorate community research and action. We provide a working agenda for addressing this dialectic, proposing that systematic consideration of the creative tension between SOC and diversity can be beneficial to community psychology.

  20. Effects of sulfadiazine on soil bacterial communities

    DEFF Research Database (Denmark)

    Hangler, Martin

    and transport of SDZ at the interphase between dewatered SDZ-amended sewage sludge and soil. SDZ was not mineralized within sludge aggregates and travelled more than 10 mm into the surrounding soil. The strongest PICT response was observed in soils fertilized with organic fertilizers or inorganic NPK fertilizer...... to increasing SDZ-concentrations. Surprisingly, induced community tolerance was not detected either by [3H]-leucine incorporation or by quantification of two genes conferring resistance to sulfonamides. In contrast did SDZ-amendments lead to detection of PICT in soil samples from a long-term field experiment...... designed to test effects on soil quality of a range of different fertilizers in agriculture. In manuscript II extracted bacteria from soil samples representing a broad range of natural soil pH values were tested for their toxicity response to SDZ when amended at different assay pH. Toxicity clearly...

  1. Bacterial diversity and bioaugmentation in floodwater of a paddy field in the presence of the herbicide molinate

    OpenAIRE

    Barreiros, Luisa; Manaia, Célia M; Nunes, Olga C.

    2011-01-01

    This work aimed at studying variations on the diversity and composition of the bacterial community of a rice paddy field floodwater, subjected to conventional management, namely by using the herbicide molinate. The promotion of the herbicide biodegradation either by the autochthonous microbiota or by a bioaugmentation process was also assessed. This study comprehended four sampling campaigns at key dates of the farming procedures (seeding, immediately and 6 days aft...

  2. The Importance of Temperature and Nitrogen Speciation on Bacterial Diversity in Stream Sediments in the McMurdo Dry Valleys

    Science.gov (United States)

    Baeseman, J. L.; Ward, B. B.

    2006-12-01

    Once called the Valleys of the Dead, the McMurdo Dry Valleys in Antarctica have been shown to harbor life that can withstand some of the coldest, windiest, driest and extreme conditions on Earth. The Dry Valleys are often referred to as `ecosystems waiting for water' because of the rapid response of biological activity when liquid water appears. Although our understanding of life in the Valleys is progressing, there are numerous unanswered questions about how the organisms survive there. Most of the attention in this delicate ecosystem has been focused on nematodes and lake and stream algal mat communities. Microbe abundances in stream sediments not associated with mats are only an order of a magnitude lower than those found in temporal streams. Yet very little is known about the metabolic capabilities, energy demands, nutrient requirements and genomes of these organisms. In December of 2004, sediment and water quality samples were collected from 19 streams in Taylor Valley. Bacterial DNA was extracted from the sediments and 16S rRNA amplified using 8f and 926r bacterial primers. Terminal Restriction Length Polymorphism (tRFLP) analysis was used to obtain community diversity fingerprints for all stream sites. The Bonney Basin had the most diverse bacterial assemblages on the basis of such fingerprints. There was no correlation between bacterial diversity and algal mat presence or absence, indicating that bacterial diversity does not depend on mats. Statistical analysis comparing water chemistry data and diversity indicates that temperature and nitrogen speciation and concentration are important factors contributing to diversity in these oligotrophic streams. Five clone libraries were sequenced and used to determine the major bacteria present in the streams. Approximately 15% of the sequences had less than a 97% similarity to any known bacterial sequence present in GenBank, suggesting a high incidence of bacterial species unique to the Dry Valleys. This research is

  3. Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.

    Directory of Open Access Journals (Sweden)

    Robert E Tyx

    Full Text Available The bacterial communities present in smokeless tobacco (ST products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae. The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products.

  4. Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.

    Science.gov (United States)

    Tyx, Robert E; Stanfill, Stephen B; Keong, Lisa M; Rivera, Angel J; Satten, Glen A; Watson, Clifford H

    2016-01-01

    The bacterial communities present in smokeless tobacco (ST) products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae). The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products.

  5. Bacterial communities in the fruit bodies of ground basidiomycetes

    Science.gov (United States)

    Zagryadskaya, Yu. A.; Lysak, L. V.; Chernov, I. Yu.

    2015-06-01

    Fruit bodies of basidiomycetes at different stages of decomposition serve as specific habitats in forest biocenoses for bacteria and differ significantly with respect to the total bacterial population and abundance of particular bacterial genera. A significant increase in the total bacterial population estimated by the direct microscopic method with acridine orange staining and in the population of saprotrophic bacteria (inoculation of glucose peptone yeast agar) in fruit bodies of basidiomycetes Armillaria mellea and Coprinus comatus was recorded at the final stage of their decomposition in comparison with the initial stage. Gramnegative bacteria predominated in the tissues of fruit bodies at all the stages of decomposition and were represented at the final stage by the Aeromonas, Vibrio, and Pseudomonas genera (for fruit bodies of A. mellea) the Pseudomonas genus (for fruit bodies of C. comatus). The potential influence of bacterial communities in the fruit bodies of soil basidiomycetes on the formation of bacterial communities in the upper soil horizons in forest biocenoses is discussed. The loci connected with the development and decomposition of fruit bodies of basidiomycetes on the soil surface are promising for targeted search of Gram-negative bacteria, the important objects of biotechnology.

  6. The bacterial communities of Drosophila suzukii collected from undamaged cherries

    Directory of Open Access Journals (Sweden)

    James Angus Chandler

    2014-07-01

    Full Text Available Drosophila suzukii is an introduced pest insect that feeds on undamaged, attached fruit. This diet is distinct from the fallen, discomposing fruits utilized by most other species of Drosophila. Since the bacterial microbiota of Drosophila, and of many other animals, is affected by diet, we hypothesized that the bacteria associated with D. suzukii are distinct from that of other Drosophila. Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. We find that the bacterial communities associated with these samples of D. suzukii contain a high frequency of Tatumella. Gluconobacter and Acetobacter, two taxa with known associations with Drosophila, were also found, although at lower frequency than Tatumella in four of the five samples examined. Sampling D. suzukii from different locations and/or while feeding on different fruits is needed to determine the generality of the results determined by these samples. Nevertheless this is, to our knowledge, the first study characterizing the bacterial communities of this ecologically unique and economically important species of Drosophila.

  7. Autotrophic and heterotrophic bacterial diversity from Yucca Mountain

    International Nuclear Information System (INIS)

    A basic understanding of the types and functions of microbiota present within the deep subsurface of Yucca Mountain will be important in terms of modeling the long term stability of a nuclear waste repository. Microorganisms can degrade building materials used in tunnel construction such as concrete and steel. For example, high concentrations of nitrifying bacteria, may cause corrosion of concrete due to the release of nitric acid. Likewise, sulfur-oxidizing and iron-oxidizing bacteria have been implicated in microbially influenced corrosion (MIC), and may contribute to the degradation of waste packages. In addition, the metabolic activities of microbiota may alter the geochemistry of surrounding environments, which may in turn influence the permeability of subsurface strata and the fate of radioactive compounds. Microorganisms that play roles in these processes have diverse methods of obtaining the energy required for growth and metabolism and have been recovered from a wide range of environments, including the deep subsurface. The purpose of this research was to determine if these bacterial groups, important to the long-term success of a high-level nuclear waste repository, were indigenous to Yucca Mountain

  8. Depth-related distribution of bacterial community in sediments of eutrophic Guanting reservoir

    Institute of Scientific and Technical Information of China (English)

    QU; Jianhang; YUAN; Hongli; HUANG; Huaizeng; WANG; Entao

    2005-01-01

    In this study, DNAs were extracted from sediment samples at depths of 5, 35, and 69 cm from eutrophic Guanting reservoir, China. 16S rDNAs were amplified by PCR and clone libraries were constructed. The depth-related distribution of bacterial community in the sediment was characterized by using amplified 16S rDNA restriction analysis (ARDRA) and sequencing of the dominant clones. The results indicated that species diversity in the sediment of Guanting reservoir was rather high with the Shannon-Wiener index about 5.8. Bacterial richness varied in different depths: the highest in the sample of 35 cm in depth; followed by the sample of 5 cm in depth; and the lowest bacterial richness in the sample of 69 cm. Dominant species from the three samples were different although there were some common clones. PhyIogenetic analysis showed that all of the dominant clones in the three layers were uncultured bacteria and distantly related to the previously reported species in beta or gamma subclass of proteobacteria, including bacterial groups that have the ability to degrade aromatic hydrocarbons, n-all:anes, chlorinated organic compounds, or to accumulate polyphosphate, etc. Changes of deptt-related bacterial community in the Guanting reservoir sediment might reflect the pollution history and the water quality of the reservoir. In addition, the cloned sequences from the Guanting reservoir sediment were all different from the presently reported ones, indicating that there were some particular bacteria in that environment.

  9. Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

    Science.gov (United States)

    Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

    2015-08-01

    Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

  10. New Primers for Denaturing Gradient Gel Electrophoresis Analysis of Nitrate-Reducing Bacterial Community in Soil

    Institute of Scientific and Technical Information of China (English)

    R.PASTORELLI; R.PICCOLO; S.SIMONCINI; S.LANDI

    2013-01-01

    The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis.In this study,a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay.The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy.Specificity of the primers was determined by excision,amplification,and sequencing of bands resolved by DGGE.A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria.These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.

  11. Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host.

    Science.gov (United States)

    Yun, Ji-Hyun; Roh, Seong Woon; Whon, Tae Woong; Jung, Mi-Ja; Kim, Min-Soo; Park, Doo-Sang; Yoon, Changmann; Nam, Young-Do; Kim, Yun-Ji; Choi, Jung-Hye; Kim, Joon-Yong; Shin, Na-Ri; Kim, Sung-Hee; Lee, Won-Jae; Bae, Jin-Woo

    2014-09-01

    Insects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (± 97.7) OTUs per sample. The insect gut microbiota were dominated by Proteobacteria (62.1% of the total reads, including 14.1% Wolbachia sequences) and Firmicutes (20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities. PMID:24928884

  12. Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures.

    Science.gov (United States)

    Männistö, Minna K; Kurhela, Emilia; Tiirola, Marja; Häggblom, Max M

    2013-04-01

    The timing and extent of snow cover is a major controller of soil temperature and hence winter-time microbial activity and plant diversity in Arctic tundra ecosystems. To understand how snow dynamics shape the bacterial communities, we analyzed the bacterial community composition of windswept and snow-accumulating shrub-dominated tundra heaths of northern Finland using DNA- and RNA-based 16S rRNA gene community fingerprinting (terminal restriction fragment polymorphism) and clone library analysis. Members of the Acidobacteria and Proteobacteria dominated the bacterial communities of both windswept and snow-accumulating habitats with the most abundant phylotypes corresponding to subdivision (SD) 1 and 2 Acidobacteria in both the DNA- and RNA-derived community profiles. However, different phylotypes within Acidobacteria were found to dominate at different sampling dates and in the DNA- vs. RNA-based community profiles. The results suggest that different species within SD1 and SD2 Acidobacteria respond to environmental conditions differently and highlight the wide functional diversity of these organisms even within the SD level. The acidic tundra soils dominated by ericoid shrubs appear to select for diverse stress-tolerant Acidobacteria that are able to compete in the nutrient poor, phenolic-rich soils. Overall, these communities seem stable and relatively insensitive to the predicted changes in the winter-time snow cover.

  13. Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities.

    Science.gov (United States)

    Delgado-Serrano, Luisa; López, Gina; Bohorquez, Laura C; Bustos, José R; Rubiano, Carolina; Osorio-Forero, César; Junca, Howard; Baena, Sandra; Zambrano, María M

    2014-07-01

    Microbial explorations of hot springs have led to remarkable discoveries and improved our understanding of life under extreme conditions. The Andean Mountains harbor diverse habitats, including an extensive chain of geothermal heated water sources. In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. The diversity and structure of the microbial communities were assessed by pyrosequencing the V5 - V6 region of the 16S rRNA gene. The planktonic communities varied in terms of diversity indexes and were dominated by the bacterial phyla Proteobacteria, Aquificae, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, and Thermotogae, with site-specific bacterial taxa also observed in some cases. Statistical analyses showed that these microbial communities were distinct from one another and that they clustered in a manner consistent with physicochemical parameters of the environment sampled. Multivariate analysis suggested that pH and sulfate were among the main variables influencing population structure and diversity. The results show that despite their geographical proximity and some shared geochemical characteristics, there were few shared operational taxonomic units (OTUs) and that community structure was influenced mainly by environmental factors that have resulted in different microbial populations.

  14. Huanglongbing, a systemic disease, restructures the bacterial community associated with citrus roots.

    Science.gov (United States)

    Trivedi, Pankaj; Duan, Yongping; Wang, Nian

    2010-06-01

    To examine the effect of pathogens on the diversity and structure of plant-associated bacterial communities, we carried out a molecular analysis using citrus and huanglongbing as a host-disease model. 16S rRNA gene clone library analysis of citrus roots revealed shifts in microbial diversity in response to pathogen infection. The clone library of the uninfected root samples has a majority of phylotypes showing similarity to well-known plant growth-promoting bacteria, including Caulobacter, Burkholderia, Lysobacter, Pantoea, Pseudomonas, Stenotrophomonas, Bacillus, and Paenibacillus. Infection by "Candidatus Liberibacter asiaticus" restructured the native microbial community associated with citrus roots and led to the loss of detection of most phylotypes while promoting the growth of bacteria such as Methylobacterium and Sphingobacterium. In pairwise comparisons, the clone library from uninfected roots contained significantly higher 16S rRNA gene diversity, as reflected in the higher Chao 1 richness estimation (P citrus by "Ca. Liberibacter asiaticus" has a profound effect on the structure and composition of the bacterial community associated with citrus roots.

  15. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    Science.gov (United States)

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals.