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Sample records for active bacterial communities

  1. The active bacterial community in a pristine confined aquifer

    NASA Astrophysics Data System (ADS)

    Flynn, Theodore M.; Sanford, Robert A.; Santo Domingo, Jorge W.; Ashbolt, Nicholas J.; Levine, Audrey D.; Bethke, Craig M.

    2012-09-01

    This study of the active bacteria residing in a pristine confined aquifer provides unexpected insights into the ecology of iron-reducing and sulfate-reducing bacteria in the subsurface. At 18 wells, we trapped the microbes that attached to aquifer sediment and used molecular techniques to examine the bacterial populations. We used multivariate statistics to compare the composition of bacterial communities among the wells with respect to the chemistry of the groundwater. We found groundwater at each well was considerably richer in ferrous iron than sulfide, indicating iron-reducing bacteria should, by established criteria, dominate the sulfate reducers. Our results show, however, that areas where groundwater contains more than a negligible amount of sulfate (>0.03 mM), populations related to sulfate reducers of the generaDesulfobacter and Desulfobulbus were of nearly equal abundance with putative iron reducers related to Geobacter, Geothrix, and Desulfuromonas. Whereas sulfate is a key discriminant of bacterial community structure, we observed no statistical relationship between the distribution of bacterial populations in this aquifer and the concentration of either ferrous iron or dissolved sulfide. These results call into question the validity of using the relative concentration of these two ions to predict the nature of bacterial activity in an aquifer. Sulfate reducers and iron reducers do not appear to be segregated into discrete zones in the aquifer, as would be predicted by the theory of competitive exclusion. Instead, we find the two groups coexist in the subsurface in what we suggest is a mutualistic relationship.

  2. Bacterial communities and enzyme activities of PAHs polluted soils.

    PubMed

    Andreoni, V; Cavalca, L; Rao, M A; Nocerino, G; Bernasconi, S; Dell'Amico, E; Colombo, M; Gianfreda, L

    2004-11-01

    Three soils (i.e. a Belgian soil, B-BT, a German soil, G, and an Italian agricultural soil, I-BT) with different properties and hydrocarbon-pollution history with regard to their potential to degrade phenanthrene were investigated. A chemical and microbiological evaluation of soils was done using measurements of routine chemical properties, bacterial counts and several enzyme activities. The three soils showed different levels of polycyclic aromatic hydrocarbons (PAHs), being their contamination strictly associated to their pollution history. High values of enzyme activities and culturable heterotrophic bacteria were detected in the soil with no or negligible presence of organic pollutants. Genetic diversity of soil samples and enrichment cultures was measured as bands on denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA sequences from the soil and enrichment community DNAs. When analysed by Shannon index (H'), the highest genetic biodiversity (H'=2.87) was found in the Belgian soil B-BT with a medium-term exposition to PAHs and the poorest biodiversity (H'=0.85) in the German soil with a long-term exposition to alkanes and PAHs and where absence, or lower levels of enzyme activities were measured. For the Italian agricultural soil I-BT, containing negligible amounts of organic pollutants but the highest Cu content, a Shannon index=2.13 was found. The enrichment of four mixed cultures capable of degrading solid phenanthrene in batch liquid systems was also studied. Phenanthrene degradation rates in batch systems were culture-dependent, and simple (one-slope) and complex (two-slope) kinetic behaviours were observed. The presence of common bands of microbial species in the cultures and in the native soil DNA indicated that those strains could be potential in situ phenanthrene degraders. Consistent with this assumption are the decrease of PAH and phenanthrene contents of Belgian soil B-BT and the isolation of phenanthrene-degrading bacteria. From

  3. Comparison of bacterial communities of conventional and A-stage activated sludge systems

    PubMed Central

    Gonzalez-Martinez, Alejandro; Rodriguez-Sanchez, Alejandro; Lotti, Tommaso; Garcia-Ruiz, Maria-Jesus; Osorio, Francisco; Gonzalez-Lopez, Jesus; van Loosdrecht, Mark C. M.

    2016-01-01

    The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly loaded A-stage systems. A-stage processes are proposed as the first step in an energy producing municipal wastewater treatment process. Pyrosequencing analysis indicated that bacterial community structure of all influents was similar. Also the bacterial community of all CAS bioreactors was similar. Bacterial community structure of A-stage bioreactors showed a more case-specific pattern. A core of genera was consistently found for all influents, all CAS bioreactors and all A-stage bioreactors, respectively, showing that different geographical locations in The Netherlands and Spain did not affect the functional bacterial communities in these technologies. The ecological roles of these bacteria were discussed. Influents and A-stage bioreactors shared several core genera, while none of these were shared with CAS bioreactors communities. This difference is thought to reside in the different operational conditions of the two technologies. This study shows that bacterial community structure of CAS and A-stage bioreactors are mostly driven by solids retention time (SRT) and hydraulic retention time (HRT), as suggested by multivariate redundancy analysis. PMID:26728449

  4. Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

    PubMed Central

    Lupatini, Manoeli; Suleiman, Afnan Khalil Ahmad; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Kuramae, Eiko Eurya; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Würdig

    2013-01-01

    The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated. PMID:24146873

  5. Regulation of bacterial communities through antimicrobial activity by the coral holobiont.

    PubMed

    Kvennefors, E Charlotte E; Sampayo, Eugenia; Kerr, Caroline; Vieira, Genyess; Roff, George; Barnes, Andrew C

    2012-04-01

    Interactions between corals and associated bacteria and amongst these bacterial groups are likely to play a key role in coral health. However, the complexity of these interactions is poorly understood. We investigated the functional role of specific coral-associated bacteria in maintaining microbial communities on the coral Acropora millepora (Ehrenberg 1834) and the ability of coral mucus to support or inhibit bacterial growth. Culture-independent techniques were used to assess bacterial community structures whilst bacterial culture was employed to assess intra- and inter-specific antimicrobial activities of bacteria. Members of Pseudoalteromonas and ribotypes closely related to Vibrio coralliilyticus displayed potent antimicrobial activity against a range of other cultured isolates and grew readily on detached coral mucus. Although such bacterial ribotypes would be expected to have a competitive advantage, they were rare or absent on intact and healthy coral colonies growing in situ (analysed using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing). The most abundant bacterial ribotypes found on healthy corals were Gammaproteobacteria, previously defined as type A coral associates. Our results indicate that this group of bacteria and specific members of the Alphaproteobacteria described here as 'type B associates' may be important functional groups for coral health. We suggest that bacterial communities on coral are kept in check by a combination of host-derived and microbial interactions and that the type A associates in particular may play a key role in maintaining stability of microbial communities on healthy coral colonies. PMID:21984347

  6. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

    SciTech Connect

    Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K.; Sjoling, Sara

    2008-05-15

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  7. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

    PubMed Central

    Zhang, Yao; Zhao, Zihao; Dai, Minhan; Jiao, Nianzhi; Herndl, Gerhard J

    2014-01-01

    To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and 16S rRNA gene (V1-3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S rRNA vs. rDNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance-decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay. PMID:24684298

  8. Bacterial Community Composition and Extracellular Enzyme Activity in Temperate Streambed Sediment during Drying and Rewetting

    PubMed Central

    Pohlon, Elisabeth; Ochoa Fandino, Adriana; Marxsen, Jürgen

    2013-01-01

    Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany). Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow) for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes, especially after

  9. Bacterial Community Dynamics in Full-Scale Activated Sludge Bioreactors: Operational and Ecological Factors Driving Community Assembly and Performance

    PubMed Central

    Valentín-Vargas, Alexis; Toro-Labrador, Gladys; Massol-Deyá, Arturo A.

    2012-01-01

    The assembling of bacterial communities in conventional activated sludge (CAS) bioreactors was thought, until recently, to be chaotic and mostly unpredictable. Studies done over the last decade have shown that specific, and often, predictable random and non-random factors could be responsible for that process. These studies have also motivated a “structure–function” paradigm that is yet to be resolved. Thus, elucidating the factors that affect community assembly in the bioreactors is necessary for predicting fluctuations in community structure and function. For this study activated sludge samples were collected during a one-year period from two geographically distant CAS bioreactors of different size. Combining community fingerprinting analysis and operational parameters data with a robust statistical analysis, we aimed to identify relevant links between system performance and bacterial community diversity and dynamics. In addition to revealing a significant β-diversity between the bioreactors’ communities, results showed that the largest bioreactor had a less dynamic but more efficient and diverse bacterial community throughout the study. The statistical analysis also suggests that deterministic factors, as opposed to stochastic factors, may have a bigger impact on the community structure in the largest bioreactor. Furthermore, the community seems to rely mainly on mechanisms of resistance and functional redundancy to maintain functional stability. We suggest that the ecological theories behind the Island Biogeography model and the species-area relationship were appropriate to predict the assembly of bacterial communities in these CAS bioreactors. These results are of great importance for engineers and ecologists as they reveal critical aspects of CAS systems that could be applied towards improving bioreactor design and operation. PMID:22880016

  10. A Coexisting Fungal-Bacterial Community Stabilizes Soil Decomposition Activity in a Microcosm Experiment

    PubMed Central

    Ushio, Masayuki; Miki, Takeshi; Balser, Teri C.

    2013-01-01

    How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities. PMID:24260368

  11. Activity and stability of a complex bacterial soil community under simulated Martian conditions

    NASA Astrophysics Data System (ADS)

    Hansen, Aviaja Anna; Merrison, Jonathan; Nørnberg, Per; Aagaard Lomstein, Bente; Finster, Kai

    2005-04-01

    A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.

  12. The Active Bacterial Community in a Pristine Confined Aquifer

    EPA Science Inventory

    This study of the active bacteria residing in a pristine confined aquifer provides unexpected insights into the ecology of iron-reducing and sulfate-reducing bacteria in the subsurface. At 18 wells in east-central Illinois, we trapped the microbes that attached to aquifer sedimen...

  13. Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils

    PubMed Central

    Herzog, Sarah; Wemheuer, Franziska; Wemheuer, Bernd; Daniel, Rolf

    2015-01-01

    Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application. PMID:26694644

  14. Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils.

    PubMed

    Herzog, Sarah; Wemheuer, Franziska; Wemheuer, Bernd; Daniel, Rolf

    2015-01-01

    Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application. PMID:26694644

  15. Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

    PubMed Central

    Verastegui, Y.; Cheng, J.; Engel, K.; Kolczynski, D.; Mortimer, S.; Lavigne, J.; Montalibet, J.; Romantsov, T.; Hall, M.; McConkey, B. J.; Rose, D. R.; Tomashek, J. J.; Scott, B. R.

    2014-01-01

    ABSTRACT Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the 13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. PMID:25028422

  16. Particle-associated extracellular enzyme activity and bacterial community composition across the Canadian Arctic Ocean.

    PubMed

    Kellogg, Colleen T E; Deming, Jody W

    2014-08-01

    Microbial enzymatic hydrolysis of marine-derived particulate organic carbon (POC) can be a dominant mechanism for attenuating carbon flux in cold Arctic waters during spring and summer. Whether this mechanism depends on composition of associated microbial communities and extends into other seasons is not known. Bacterial community composition (BCC) and extracellular enzyme activity (EEA, for leucine aminopeptidases, glucosidases and chitobiases) were measured on small suspended particles and potentially sinking aggregates collected during fall from waters of the biologically productive North Water and river-impacted Beaufort Sea. Although other environmental variables appeared influential, both BCC and EEA varied along a marine productivity gradient in the two regions. Aggregates harbored the most distinctive bacterial communities, with a small number of taxa driving differences between particle-size classes (1.0-60 and > 60 μm) and free-living bacteria (0.2-1.0 μm). Significant relationships between patterns in particle-associated BCC and EEA suggest strong links between these two variables. Calculations indicated that up to 80% of POC in the euphotic zone of the North Water, and 20% in the Beaufort Sea, may be hydrolyzed enzymatically, underscoring the importance of this mechanism in attenuating carbon fluxes in Arctic waters even as winter approaches. PMID:24666253

  17. Diversity, antimicrobial and antioxidant activities of culturable bacterial endophyte communities in Aloe vera.

    PubMed

    Akinsanya, Mushafau Adewale; Goh, Joo Kheng; Lim, Siew Ping; Ting, Adeline Su Yien

    2015-12-01

    Twenty-nine culturable bacterial endophytes were isolated from surface-sterilized tissues (root, stem and leaf) of Aloe vera and molecularly characterized to 13 genera: Pseudomonas, Bacillus, Enterobacter, Pantoea, Chryseobacterium, Sphingobacterium, Aeromonas, Providencia, Cedecea, Klebsiella, Cronobacter, Macrococcus and Shigella. The dominant genera include Bacillus (20.7%), Pseudomonas (20.7%) and Enterobacter (13.8%). The crude and ethyl acetate fractions of the metabolites of six isolates, species of Pseudomonas, Bacillus, Chryseobacterium and Shigella, have broad spectral antimicrobial activities against pathogenic Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus cereus, Salmonella Typhimurium, Proteus vulgaris, Klebsiella pneumoniae, Escherichia coli, Streptococcus pyogenes and Candida albicans, with inhibition zones ranging from 6.0 ± 0.57 to 16.6 ± 0.57 mm. In addition, 80% of the bacterial endophytes produced 1,1-diphenyl-2-picrylhydrazyl (DPPH) with scavenging properties of over 75% when their crude metabolites were compared with ascorbic acid (92%). In conclusion, this study revealed for the first time the endophytic bacteria communities from A. vera (Pseudomonas hibiscicola, Macrococcus caseolyticus, Enterobacter ludwigii, Bacillus anthracis) that produce bioactive compounds with high DPPH scavenging properties (75-88%) and (Bacillus tequilensis, Pseudomonas entomophila, Chryseobacterium indologenes, Bacillus aerophilus) that produce bioactive compounds with antimicrobial activities against bacterial pathogens. Hence, we suggest further investigation and characterization of their bioactive compounds. PMID:26454221

  18. [Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

    PubMed

    Li, Min; Wu, Feng-zhi

    2014-12-01

    Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance. PMID:25876408

  19. Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments.

    PubMed

    Besaury, Ludovic; Ghiglione, Jean-François; Quillet, Laurent

    2014-04-01

    We analyzed the impact of copper mine tailing discharges on benthic Archaea and Bacteria around the city of Chanaral in northern Chile. Quantitative PCR (Q-PCR) showed that the bacteria dominated the prokaryotic community at both sites, but only the bacteria showed a decrease in abundance in the copper-contaminated site. Q-PCR on reverse transcripts indicated a higher activity of both bacterial and archaeal communities in the contaminated site, suggesting an adaptation of the two communities to copper. This hypothesis was reinforced by the concomitant augmentation of the copper-resistant copA gene coding for a P-type ATP-ase pump in the contaminated site. The metabolically active bacterial community of the contaminated site was dominated by Gammaproteobacteria related to Ectothiorhodospiraceae and Chromatiaceae and by Alphaproteobacteria phylum related to Rhodobacteraceae. The metabolically active archaeal community was dominated by one lineage belonging to unclassified Euryarchaeota and to methanogenic Archaea. PMID:24072336

  20. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Zhao, Z.; Dai, M.; Jiao, N.

    2013-12-01

    Very few studies have been devoted to understanding microbial biogeography from the viewpoint of active versus total bacterial communities. Here, we examined the bacterial community along two transects, one from the inner Pearl River estuary to the open water of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and rDNA. Bacterial community composition was strongly correlated with environmental factors and weakly correlated with geographical distance between sites, although the diversity and biogeographic patterns differed substantially between the total and active communities. Compared to the total community, the active heterotrophic bacterial community displayed higher environmental sensitivity and a greater distance effect that was in fact mainly contributed by the active assemblage from deep waters. Taken together, the 16S rRNA versus rDNA relationships and community network models implied that the active heterotrophic bacteria, in high competition with each other, have high growth rates and high loss rates from predation, and hence are less-abundant in the SCS. Thereinto, most of the taxa act as specialists in the ecosystem and the others as generalists, which could cause some dispersal limitations such that some species could not become successfully established in the new location as they were moved through drift and, therefore, the active bacterial community could be determined to have a distinct distance-decay relationship. Altogether, our results supported the proposal that the current distributions of bacteria in the SCS were actually the result of both contemporary selection and historical drift processes.

  1. Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms.

    PubMed

    Sun, Fu-Lin; Fan, Lei-Lei; Xie, Guang-Jian

    2016-08-01

    The anaerobic-anoxic-aerobic (A2O) process is a highly efficient sewage treatment method, which uses complex bacterial communities. However, the effect of copper on this process and the bacterial communities involved remains unknown. In this study, a systematic investigation of the effect of persistent exposure of copper in the A2O wastewater treatment system was performed. An A2O device was designed to examine the effect of copper on the removal efficiency and microbial community compositions of activated sludge that was continuously treated with 10, 20, and 40 mg L(-1) copper, respectively. Surprisingly, a decrease in chemical oxygen demand (COD) and ammonia nitrogen (NH4N) removal efficiency was observed, and the toxicity of high copper concentration was significantly greater at 7d than at 1d. Proteobacteria, Bacteroidetes, Acidobacteria, Chlorobi, and Nitrospirae were the dominant bacterial taxa in the A2O system, and significant changes in microbial community were observed during the exposure period. Most of the dominant bacterial groups were easily susceptible to copper toxicity and diversely changed at different copper concentrations. However, not all the bacterial taxa were inhibited by copper treatment. At high copper concentration, many bacterial species were stimulated and their abundance increased. Cluster analysis and principal coordinate analysis (PCoA) based on operational taxonomic units (OTUs) revealed clear differences in the bacterial communities among the samples. These findings indicated that copper severely affected the performance and key microbial populations in the A2O system as well as disturbed the stability of the bacterial communities in the system, thus decreasing the removal efficiency. PMID:27179238

  2. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    SciTech Connect

    Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

    2011-05-01

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  3. Molecular characterization of total and metabolically active bacterial communities of "white colonizations" in the Altamira Cave, Spain.

    PubMed

    Portillo, M Carmen; Saiz-Jimenez, Cesareo; Gonzalez, Juan M

    2009-01-01

    Caves with paleolithic paintings are influenced by bacterial development. Altamira Cave (Spain) contains some of the most famous paintings from the Paleolithic era. An assessment of the composition of bacterial communities that have colonized this cave represents a first step in understanding and potentially controlling their proliferation. In this study, areas showing colonization with uncolored microorganisms, referred to as "white colonizations", were analyzed. Microorganisms present in these colonizations were studied using DNA analysis, and those showing significant metabolic activity were detected in RNA-based RNA analysis. Bacterial community fingerprints were obtained both from DNA and RNA analyses, indicating differences between the microorganisms present and metabolically active in these white colonizations. Metabolically active microorganisms represented only a fraction of the total bacterial community present in the colonizations. 16S rRNA gene libraries were used to identify the major representative members of the studied communities. Proteobacteria constituted the most frequently found division both among metabolically active microorganisms (from RNA-based analysis) and those present in the community (from DNA analysis). Results suggest the existence of a huge variety of taxa in white colonizations of the Altamira Cave which represent a potential risk for the conservation of the cave and its paintings. PMID:18984039

  4. Correlation analysis of enzyme activities and deconstruction of ammonia-pretreated switchgrass by bacterial-fungal communities.

    PubMed

    Jain, Abhiney; Bediako, Sandra H; Henson, J Michael

    2016-10-01

    The mixed microbial communities that occur naturally on lignocellulosic feedstocks can provide feedstock-specific enzyme mixtures to saccharify lignocelluloses. Bacterial-fungal communities were enriched from switchgrass bales to deconstruct ammonia-pretreated switchgrass (DSG). Correlation analysis was carried out to elucidate the relationship between microbial decomposition of DSG by these communities, enzymatic activities produced and enzymatic saccharification of DSG using these enzyme mixtures. Results of the analysis showed that β-glucosidase and xylosidase activities limited the extent of microbial deconstruction and enzymatic saccharification of DSG. The results also underlined the importance of ligninase activity for the enzymatic saccharification of pretreated lignocellulosic feedstock. The bacterial-fungal communities developed in this research can be used to produce enzyme mixtures to deconstruct DSG, and the results from the correlation analysis can be used to optimize these enzyme mixtures for efficient saccharification of DSG to produce second-generation biofuels. PMID:27469088

  5. Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition.

    PubMed

    Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; Zhang, Li-Mei

    2016-02-01

    Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils. PMID:26803661

  6. Seasonal Transition of Active Bacterial and Archaeal Communities in Relation to Water Management in Paddy Soils

    PubMed Central

    Itoh, Hideomi; Ishii, Satoshi; Shiratori, Yutaka; Oshima, Kenshiro; Otsuka, Shigeto; Hattori, Masahira; Senoo, Keishi

    2013-01-01

    Paddy soils have an environment in which waterlogging and drainage occur during the rice growing season. Fingerprinting analysis based on soil RNA indicated that active microbial populations changed in response to water management conditions, although the fundamental microbial community was stable as assessed by DNA-based fingerprinting analysis. Comparative clone library analysis based on bacterial and archaeal 16S rRNAs (5,277 and 5,436 clones, respectively) revealed stable and variable members under waterlogged or drained conditions. Clones related to the class Deltaproteobacteria and phylum Euryarchaeota were most frequently obtained from the samples collected under both waterlogged and drained conditions. Clones related to syntrophic hydrogen-producing bacteria, hydrogenotrophic methanogenic archaea, rice cluster III, V, and IV, and uncultured crenarchaeotal group 1.2 appeared in greater proportion in the samples collected under waterlogged conditions than in those collected under drained conditions, while clones belonging to rice cluster VI related to ammonia-oxidizing archaea (AOA) appeared at higher frequency in the samples collected under drained conditions than in those collected under waterlogged conditions. These results suggested that hydrogenotrophic methanogenesis may become active under waterlogged conditions, whereas ammonia oxidation may progress by rice cluster VI becoming active under drained conditions in the paddy field. PMID:24005888

  7. Antimicrobial Activity of Heterotrophic Bacterial Communities from the Marine Sponge Erylus discophorus (Astrophorida, Geodiidae)

    PubMed Central

    Graça, Ana Patrícia; Bondoso, Joana; Gaspar, Helena; Xavier, Joana R.; Monteiro, Maria Cândida; de la Cruz, Mercedes; Oves-Costales, Daniel; Vicente, Francisca; Lage, Olga Maria

    2013-01-01

    Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds. PMID:24236081

  8. Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae).

    PubMed

    Graça, Ana Patrícia; Bondoso, Joana; Gaspar, Helena; Xavier, Joana R; Monteiro, Maria Cândida; de la Cruz, Mercedes; Oves-Costales, Daniel; Vicente, Francisca; Lage, Olga Maria

    2013-01-01

    Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds. PMID:24236081

  9. Bacterial Communities: Interactions to Scale.

    PubMed

    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

  10. Bacterial Communities: Interactions to Scale

    PubMed Central

    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

  11. Layered Structure of Bacterial and Archaeal Communities and Their In Situ Activities in Anaerobic Granules▿ †

    PubMed Central

    Satoh, Hisashi; Miura, Yuki; Tsushima, Ikuo; Okabe, Satoshi

    2007-01-01

    The microbial community structure and spatial distribution of microorganisms and their in situ activities in anaerobic granules were investigated by 16S rRNA gene-based molecular techniques and microsensors for CH4, H2, pH, and the oxidation-reduction potential (ORP). The 16S rRNA gene-cloning analysis revealed that the clones related to the phyla Alphaproteobacteria (detection frequency, 51%), Firmicutes (20%), Chloroflexi (9%), and Betaproteobacteria (8%) dominated the bacterial clone library, and the predominant clones in the archaeal clone library were affiliated with Methanosaeta (73%). In situ hybridization with oligonucleotide probes at the phylum level revealed that these microorganisms were numerically abundant in the granule. A layered structure of microorganisms was found in the granule, where Chloroflexi and Betaproteobacteria were present in the outer shell of the granule, Firmicutes were found in the middle layer, and aceticlastic Archaea were restricted to the inner layer. Microsensor measurements for CH4, H2, pH, and ORP revealed that acid and H2 production occurred in the upper part of the granule, below which H2 consumption and CH4 production were detected. Direct comparison of the in situ activity distribution with the spatial distribution of the microorganisms implied that Chloroflexi contributed to the degradation of complex organic compounds in the outermost layer, H2 was produced mainly by Firmicutes in the middle layer, and Methanosaeta produced CH4 in the inner layer. We determined the effective diffusion coefficient for H2 in the anaerobic granules to be 2.66 × 10−5 cm2 s−1, which was 57% in water. PMID:17905889

  12. Impact of titanium dioxide nanoparticles on the bacterial communities of biological activated carbon filter intended for drinking water treatment.

    PubMed

    Zhiyuan, Liu; Shuili, Yu; Heedeung, Park; Qingbin, Yuan; Guicai, Liu; Qi, Li

    2016-08-01

    Titanium dioxide nanoparticles (TiO2 NPs) are inevitably present in the aquatic environment owing to their increasing production and use. However, knowledge of the potential effects of TiO2 NPs on the treatment of drinking water is scarce. Herein, the effects of two types of anatase TiO2 NPs (TP1, 25 nm; TP2, 100 nm) on the bacterial community in a biological activated carbon (BAC) filter were investigated via quantitative polymerase chain reaction (Q-PCR) analysis, ATP quantification, and 454 pyrosequencing analysis. Both TP1 and TP2 significantly inhibited the bacterial ATP level (p < 0.01) and induced a decrease in the abundance of bacterial 16S rDNA gene copies at doses of 0.1 and 100 mg L(-1). Simultaneously, the diversity and evenness of the bacterial communities were considerably reduced. The relative abundances of bacteria annotated to OTUs from Nitrospira class and Betaproteobacteria class decreased upon TiO2 NP treatment, whereas those of Bacilli class and Gammaproteobacteria class increased. TiO2 NP size showed a greater effect on the bacterial composition than did the dose based on Bray-Curtis distances. These findings identified negative effects of TiO2 NPs on the bacterial community in the BAC filter. Given the fact that BAC filters are used widely in drinking water treatment plants, these results suggested a potential threat by TiO2 NP to drinking water treatment system. PMID:27126871

  13. Impacts of Multiwalled Carbon Nanotubes on Nutrient Removal from Wastewater and Bacterial Community Structure in Activated Sludge

    PubMed Central

    Hai, Reti; Wang, Yulin; Wang, Xiaohui; Du, Zhize; Li, Yuan

    2014-01-01

    Background The increasing use of multiwalled carbon nanotubes (MWCNTs) will inevitably lead to the exposure of wastewater treatment facilities. However, knowledge of the impacts of MWCNTs on wastewater nutrient removal and bacterial community structure in the activated sludge process is sparse. Aims To investigate the effects of MWCNTs on wastewater nutrient removal, and bacterial community structure in activated sludge. Methods Three triplicate sequencing batch reactors (SBR) were exposed to wastewater which contained 0, 1, and 20 mg/L MWCNTs. MiSeq sequencing was used to investigate the bacterial community structures in activated sludge samples which were exposed to different concentrations of MWCNTs. Results Exposure to 1 and 20 mg/L MWCNTs had no acute (1 day) impact on nutrient removal from wastewater. After long-term (180 days) exposure to 1 mg/L MWCNTs, the average total nitrogen (TN) removal efficiency was not significantly affected. TN removal efficiency decreased from 84.0% to 71.9% after long-term effects of 20 mg/L MWCNTs. After long-term exposure to 1 and 20 mg/L MWCNTs, the total phosphorus removal efficiencies decreased from 96.8% to 52.3% and from 98.2% to 34.0% respectively. Further study revealed that long-term exposure to 20 mg/L MWCNTs inhibited activities of ammonia monooxygenase and nitrite oxidoreductase. Long-term exposure to 1 and 20 mg/L MWCNTs both inhibited activities of exopolyphosphatase and polyphosphate kinase. MiSeq sequencing data indicated that 20 mg/L MWCNTs significantly decreased the diversity of bacterial community in activated sludge. Long-term exposure to 1 and 20 mg/L MWCNTs differentially decreased the abundance of nitrifying bacteria, especially ammonia-oxidizing bacteria. The abundance of PAOs was decreased after long-term exposure to 20 mg/L MWCNTs. The abundance of glycogen accumulating organisms (GAOs) was increased after long-term exposure to 1 mg/L MWCNTs. Conclusion MWCNTs have adverse effects on biological

  14. Measuring bacterial activity and community composition at high hydrostatic pressure using a novel experimental approach: a pilot study.

    PubMed

    Wannicke, Nicola; Frindte, Katharina; Gust, Giselher; Liskow, Iris; Wacker, Alexander; Meyer, Andreas; Grossart, Hans-Peter

    2015-05-01

    In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 ± 1.4 and 3.9 ± 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 ± 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 ± 1.5 and 2.9 ± 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump. PMID:25873457

  15. Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment.

    PubMed

    Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N

    2014-02-01

    The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0-6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α- and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. PMID:24443388

  16. Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment

    PubMed Central

    Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N

    2014-01-01

    The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0–6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α-and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. PMID:24443388

  17. Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet.

    PubMed

    Stibal, Marek; Schostag, Morten; Cameron, Karen A; Hansen, Lars H; Chandler, David M; Wadham, Jemma L; Jacobsen, Carsten S

    2015-04-01

    Biological processes in the supraglacial ecosystem, including cryoconite, contribute to nutrient cycling within the cryosphere and may affect surface melting, yet little is known of the diversity of the active microbes in these environments. We examined the bacterial abundance and community composition of cryoconite over a melt season at two contrasting sites at the margin and in the interior of the Greenland ice sheet, using sequence analysis and quantitative polymerase chain reaction of coextracted 16S rDNA and rRNA. Significant differences were found between bulk (rDNA) and potentially active (rRNA) communities, and between communities sampled from the two sites. Higher concentrations of rRNA than rDNA were detected at the interior site, whereas at the margin several orders of magnitude less rRNA was found compared with rDNA, which may be explained by a lower proportion of active bacteria at the margin site. The rRNA communities at both sites were dominated by a few taxa of Cyanobacteria and Alpha- and/or Betaproteobacteria. The bulk alpha diversity was higher in the margin site community, suggesting that local sources may be contributing towards the gene pool in addition to long distance transport. PMID:25405749

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

    PubMed

    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

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

    PubMed Central

    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 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; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of 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

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

    PubMed

    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; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of 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

  1. Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing.

    PubMed

    Kelly, L C; Colin, Y; Turpault, M-P; Uroz, S

    2016-08-01

    Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site. PMID:27138048

  2. The Impact of Injections of Different Nutrients on the Bacterial Community and Its Dechlorination Activity in Chloroethene-Contaminated Groundwater

    PubMed Central

    Miura, Takamasa; Yamazoe, Atsushi; Ito, Masako; Ohji, Shoko; Hosoyama, Akira; Takahata, Yoh; Fujita, Nobuyuki

    2015-01-01

    Dehalococcoides spp. are currently the only organisms known to completely reduce cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC) to non-toxic ethene. However, the activation of fermenting bacteria that generate acetate, hydrogen, and CO2 is considered necessary to enhance the dechlorination activity of Dehalococcoides and enable the complete dechlorination of chloroethenes. In the present study, we stimulated chloroethene-contaminated groundwater by injecting different nutrients prepared from yeast extract or polylactate ester using a semicontinuous culture system. We then evaluated changes in the bacterial community structure and their relationship with dechlorination activity during the biostimulation. The populations of Dehalococcoides and the phyla Bacteroidetes, Firmicutes, and Spirochaetes increased in the yeast extract-amended cultures and chloroethenes were completely dechlorinated. However, the phylum Proteobacteria was dominant in polylactate ester-amended cultures, in which almost no cis-DCE and VC were dechlorinated. These results provide fundamental information regarding possible interactions among bacterial community members involved in the dechlorination process and support the design of successful biostimulation strategies. PMID:25877696

  3. Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.

    PubMed

    Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

    2013-07-01

    The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes. PMID:23397107

  4. Effect of transportation on fecal bacterial communities and fermentative activities in horses: impact of Saccharomyces cerevisiae CNCM I-1077 supplementation.

    PubMed

    Faubladier, C; Chaucheyras-Durand, F; da Veiga, L; Julliand, V

    2013-04-01

    This study evaluated the effect of transportation on fecal bacterial communities and activities in horses with or without supplementation of live yeast and attempted to link those effects with changes in blood stress markers. Four mature horses were assigned to a crossover design and fed a basal diet (60:40 forage to concentrate; 1.45% BW on a DM basis), with or without supplementation, of 2 × 10(10) cfu/d of Saccharomyces cerevisiae CNCM I-1077. After a 14-d adaptation to dietary treatments, the 5-d experiment started 1 d before transportation (d -1). At d 0, horses were simultaneously transported in a truck for 2 h. Feces were sampled 4 h after the morning meal of concentrate at d -1, 0 (immediately after transportation), and 3 for enumeration of the main functional bacterial groups and determination of fermentative variables. Within each dietary treatment, feces were pooled before DNA extraction and molecular analysis of the bacterial communities, using temporal temperature gradient electrophoreses (TTGE). Blood samples were collected at the same time for determination of white blood cells (WBC) counts and glucose and total protein concentrations. Regardless of dietary treatment, the neutrophil to lymphocyte ratio increased during transportation (P < 0.01), indicating that horses were stressed. In both treatments, TTGE profiles were clearly different before and 3 d after transportation, and the percentage of similarity between profiles at d -1 and 3 was greater in supplemented horses compared with the controls. From d 0 to 3, the molar percentage of propionate increased and total concentration of VFA and the acetate + butyrate to propionate ratio decreased, regardless of dietary treatment (P < 0.01, P = 0.02, and P < 0.01, respectively), whereas pH decreased only in control horses (P = 0.03). Regardless of day of sampling, fecal concentrations of lactate-utilizing bacteria and cellulolytic bacteria were greater in supplemented horses than in control horses (P

  5. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    PubMed Central

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-01-01

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

  6. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    SciTech Connect

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  7. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    DOE PAGESBeta

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

  8. Biodegradation of Triton X-100 and its primary metabolites by a bacterial community isolated from activated sludge.

    PubMed

    Wyrwas, Bogdan; Dymaczewski, Zbysław; Zgoła-Grześkowiak, Agnieszka; Szymański, Andrzej; Frańska, Magdalena; Kruszelnicka, Izabela; Ginter-Kramarczyk, Dobrochna; Cyplik, Paweł; Ławniczak, Łukasz; Chrzanowski, Łukasz

    2013-10-15

    A set of studies was carried using a continuous flow biodegradation unit in order to isolate a microbial community capable of efficient and complete utilization of octylphenol ethoxylates from activated sludge. Increasing concentrations of Triton X-100 (in the range of 1-1000 mg/l) were applied over a time period of 35 days in order to select microorganisms, which exhibit high tolerance towards this surfactant. The fate of the surfactant and its primary degradation products was assessed by HPLC/MS. It was observed that even small doses of the surfactant contributed to the disruption of the activated sludge, due to adsorption of primary Triton X-100 metabolites (octylphenol and short-chained ethoxylates) on the cells, although the long-chain octylphenol ethoxylates were efficiently degraded during the isolation process. The toxicity assessment of octylphenol as well as octylphenol di- and monoethoxylates towards activated sludge allowed for determination of EC50 values (8 and 55 mg/l, respectively). The identification of the residual microorganisms revealed the presence of Acinetobacter junii, Acinetobacter calcoaceticus, Aeromonas hydrophilia, Alcaligenes spp., Pseudomonas fluorescens and Sphingomonas capsulata. The isolated community exhibited a high resistance towards Triton X-100 and was capable of growth even at 10,000 mg/l, with the highest specific growth rate (0.47 h(-1)) observed at 4000 mg/l. Under aerobic conditions both octylphenol and the short-chained ethoxylates were completely degraded while no toxic effect towards the isolated bacterial community was observed. PMID:23770380

  9. Phylogenetic organization of bacterial activity.

    PubMed

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-09-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  10. Phylogenetic organization of bacterial activity

    PubMed Central

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-01-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with 13C and 18O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  11. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches.

    PubMed

    Wemheuer, Bernd; Güllert, Simon; Billerbeck, Sara; Giebel, Helge-Ansgar; Voget, Sonja; Simon, Meinhard; Daniel, Rolf

    2014-02-01

    Despite their importance for ecosystem functioning, little is known about the composition of active marine bacterioplankton communities. Hence, this study was focused on assessing the diversity of these communities in the southern North Sea and examining the impact of a phytoplankton spring bloom on the ambient bacterioplankton community. Community composition in and outside the bloom was assessed in 14 samples by pyrosequencing-based analysis of 16S rRNA gene amplicons generated from environmental RNA. The data set comprised of 211 769 16S rRNA gene sequences. Proteobacteria were the predominant phylogenetic group with Alphaproteobacteria and Gammaproteobacteria as the most abundant classes. Actinobacteria and Bacteroidetes were identified in minor abundances. Active bacterial communities were dominated by few lineages such as the Roseobacter RCA cluster and the SAR92 clade. Community structures of three selected samples were also assessed by direct sequencing of cDNA generated from rRNA-depleted environmental RNA. Generated data sets comprised of 988 202 sequences. Taxonomic assignment of the reads confirmed the predominance of Proteobacteria. The examined phytoplankton spring bloom affected the bacterioplankton community structures significantly. Bacterial richness was reduced in the bloom area, and the abundance of certain bacterial groups was affected by bloom presence. The SAR92 clade and the Roseobacter RCA cluster were significantly more abundant and active in the bloom. Functions affected by the bloom include photosynthesis, protein metabolism, and DNA metabolism. PMID:24111503

  12. Effects of PAH biodegradation in the presence of non-ionic surfactants on a bacterial community and its exoenzymatic activity.

    PubMed

    Chang, Yi-Tang; Thirumavalavan, Munusamy; Lee, Jiunn-Fwu

    2010-01-01

    The influence of two non-ionic surfactants (TX-100 and Brij 35) on a bacterial community and its exoenzymatic activity during polycyclic aromatic hydrocarbon (naphthalene, phenanthrene and pyrene) biodegradation was evaluated in this study. The result indicated the addition of the non-ionic surfactants altered the profiles of the microbial populations and produced exoenzymes. Fluorescence in situ hybridization found that, as PAH biodegradation progressed in the presence of non-ionic surfactant, the proportion of Bacteria presents increased significantly from the range 54.79%-57.00% to 64.17%-73.4% and there was parallel decrease in Archaea. The trends in five phyla/subclass of Bacteria, namely alpha -, beta -, or gamma -Proteobacteria, HGC bacteria and LGC bacteria, were influenced significantly by the addition of Brij 35 as either monomers or micelles. A change was ascribed to different cohesive energy density (CED) value between the PAH and surfactant. The percentage of genera Pseudomonas 4.76%-12.67%, which included two signals, namely most true Pseudomonas spp. and Pseudomonas aeruginosa, were dominant during biodegradation. For exoenzymaztic activities, trends were identified by principle component analysis of the API ZYM enzymatic activity dataset. The additions of non-ionic surfactant were identified strong activities of three esterase (esterase, esterase lipase and lipase), alpha -glucosidase, beta -glucosidase, leucine arylamidase and acid phosphatase during PAH biodegradation. These enzymes are selected as possible organic pollutant indicators when the in situ bioremediation was monitored in the presence of non-ionic surfactant additives. PMID:20390887

  13. [Carbon/nitrogen Removal and Bacterial Community Structure Change in an A/O Activated Sludge System Under Different Dissolved Oxygen Conditions].

    PubMed

    Chen, Yan; Liu, Guo-hua; Fan, Qiang; Wang, Jun-yan; Qi, Lu; Wang, Hong-chen

    2015-07-01

    Carbon and nitrogen removal performance and microbial community structure under different dissolved oxygen (DO) conditions (3, 2, 1 and 0. 5 mg . L -1) in an anoxic/oxic (A/O) system were investigated. The results showed that the A/O activated sludge system still had an excellent performance in removing carbon and nutrient under low DO condition (0. 5 mg . L-1). The removal rates of chemical oxygen demand (COD), ammonia (NH4+ -N) and total nitrogen (TN) were 89. 7%, 98. 3% and 88. 0% respectively. The PCR-DGGE analysis showed that the bacterial community structure changed greatly under different DO conditions. However, there was still a high bacterial diversity even at low DO level, which ensured the functional stability of the A/O system. On the basis of the results of the phylogenetic tree, bacterial communities were observed to be very abundant, and Proteobacteria was identified as the dominant bacteria. PMID:26489332

  14. A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge.

    PubMed

    Meyer, Julie L; Jaekel, Ulrike; Tully, Benjamin J; Glazer, Brian T; Wheat, C Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P; Hulme, Samuel M; Girguis, Peter R; Huber, Julie A

    2016-01-01

    The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere. PMID:26935537

  15. A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

    PubMed Central

    Meyer, Julie L.; Jaekel, Ulrike; Tully, Benjamin J.; Glazer, Brian T.; Wheat, C. Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P.; Hulme, Samuel M.; Girguis, Peter R.; Huber, Julie A.

    2016-01-01

    The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere. PMID:26935537

  16. A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

    NASA Astrophysics Data System (ADS)

    Meyer, Julie L.; Jaekel, Ulrike; Tully, Benjamin J.; Glazer, Brian T.; Wheat, C. Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P.; Hulme, Samuel M.; Girguis, Peter R.; Huber, Julie A.

    2016-03-01

    The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.

  17. Effects of temperature and fertilization on total vs. active bacterial communities exposed to crude and diesel oil pollution in NW Mediterranean Sea.

    PubMed

    Rodríguez-Blanco, Arturo; Antoine, Virginie; Pelletier, Emilien; Delille, Daniel; Ghiglione, Jean-François

    2010-03-01

    The dynamics of total and active microbial communities were studied in seawater microcosms amended with crude or diesel oil at different temperatures (25, 10 and 4 degrees C) in the presence/absence of organic fertilization (Inipol EAP 22). Total and hydrocarbon-degrading microbes were enumerated by fluorescence microscopy and Most Probable Number (MPN) method, respectively. Total (16S rDNA-based) vs. active (16S rRNA) bacterial community structure was monitored by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting. Hydrocarbons were analyzed after 12 weeks of incubation by gas chromatography-mass spectrometry. Total and hydrocarbon-degrading microbial counts were highly influenced by fertilization while no important differences were observed between temperatures. Higher biodegradation levels were observed in fertilized microcosms. Temperature and fertilization induced changes in structure of total bacterial communities. However, fertilization showed a more important effect on active bacterial structure. The calculation of Simpson's diversity index showed similar trends among temperatures whereas fertilization reduced diversity index of both total and active bacterial communities. PMID:19906475

  18. Shifts in Bacterial Communities of Eggshells and Antimicrobial Activities in Eggs during Incubation in a Ground-Nesting Passerine

    PubMed Central

    Grizard, Stéphanie; Versteegh, Maaike A.; Ndithia, Henry K.; Salles, Joana F.; Tieleman, B. Irene

    2015-01-01

    Microbial invasion of egg contents is a cause of embryonic death. To counter infection risks, the embryo is protected physically by the eggshell and chemically by antimicrobial proteins. If microbial pressure drives embryo mortality, then females may have evolved, through natural selection, to adapt their immune investment into eggs. Although frequently hypothesized, this match between immune allocation and microorganisms has not been explored yet. To examine if correlations between microbes on eggs and immunity in eggs exist, we collected eggs from red-capped larks (Calandrella cinerea) and simultaneously examined their bacterial communities and antimicrobial components—pH, lysozyme and ovotransferrin—during natural incubation. Using molecular techniques, we find that bacterial communities are highly dynamic: bacterial abundance increases from the onset to late incubation, Shannon’s α-diversity index increases during early incubation stages, and β-diversity analysis shows that communities from 1 day-old clutches are phylogenetically more similar to each other than the older ones. Regarding the antimicrobials, we notice a decrease of pH and lysozyme concentration, while ovotransferrin concentration increases during incubation. Interestingly, we show that two eggs of the same clutch share equivalent immune protection, independent of clutch age. Lastly, our results provide limited evidence of significant correlation between antimicrobial compounds and bacterial communities. Our study examined simultaneously, for the first time in a wild bird, the dynamics of bacterial communities present on eggshells and of albumen-associated antimicrobial components during incubation and investigated their relationship. However, the link between microorganisms and immunity of eggs remains to be elucidated further. Identifying invading microbes and their roles in embryo mortality, as well as understanding the role of the eggshell microbiome, might be key to better understand

  19. Contamination of Soil by Copper Affects the Dynamics, Diversity, and Activity of Soil Bacterial Communities Involved in Wheat Decomposition and Carbon Storage▿ †

    PubMed Central

    Bernard, L.; Maron, P. A.; Mougel, C.; Nowak, V.; Lévêque, J.; Marol, C.; Balesdent, J.; Gibiat, F.; Ranjard, L.

    2009-01-01

    A soil microcosm experiment was conducted to evaluate the influence of copper contamination on the dynamics and diversity of bacterial communities actively involved in wheat residue decomposition. In the presence of copper, a higher level of CO2 release was observed, which did not arise from greater wheat decomposition but from a higher level of stimulation of soil organic matter mineralization (known as the priming effect). Such functional modifications may be related to significant modifications in the diversity of active bacterial populations characterized using the DNA stable-isotope probing approach. PMID:19801474

  20. Atmospheric cloud water contains a diverse bacterial community

    SciTech Connect

    Kourtev, P. S.; Hill, Kimberly A.; Shepson, Paul B.; Konopka, Allan

    2011-06-15

    Atmospheric cloud water contains an active microbial community which can impact climate, human health and ecosystem processes in terrestrial and aquatic systems. Most studies on the composition of microbial communities in clouds have been performed with orographic clouds that are typically in direct contact with the ground. We collected water samples from cumulus clouds above the upper U.S. Midwest. The cloud water was analyzed for the diversity of bacterial phylotypes by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene amplicons. DGGE analyses of bacterial communities detected 17e21 bands per sample. Sequencing confirmed the presence of a diverse bacterial community; sequences from seven bacterial phyla were retrieved. Cloud water bacterial communities appeared to be dominated by members of the cyanobacteria, proteobacteria, actinobacteria and firmicutes.

  1. Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil.

    PubMed

    Meynet, Paola; Hale, Sarah E; Davenport, Russell J; Cornelissen, Gerard; Breedveld, Gijs D; Werner, David

    2012-05-01

    We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. PMID:22455603

  2. Effect of Activated Carbon Amendment on Bacterial Community Structure and Functions in a PAH Impacted Urban Soil

    PubMed Central

    2012-01-01

    We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. PMID:22455603

  3. Bacterial community in the biofilm of granular activated carbon (GAC) PreBiofilter in bench-scale pilot plants for surface water pretreatment.

    PubMed

    Wu, Tiehang; Fu, George Yuzhu; Sabula, Michael; Brown, Tommy

    2014-12-01

    Biofilters of granular activated carbon (GAC) are responsible for the removal of organic matters in drinking water treatments. PreBiofilters, which operate as the first unit in a surface water treatment train, are a cost-effective pretreatment for conventional surface water treatment and provide more consistent downstream water quality. This study investigated bacterial communities from the samples of raw surface water, biofilm on the PreBiofilter, and filtrates for surface water pretreatment. A bench-scale pilot plant of PreBiofilter was constructed to pretreat surface water from the Canoochee River, GA, USA. PreBiofilter exhibited a significant reduction of total organic carbon and dissolved organic carbon. The evenness and Shannon diversity of bacterial operational taxonomic units (OTUs) were significantly higher on the biofilm of PreBiofilter than in raw water and filtrates. Similar bacteria communities were observed in the raw water and filtrates using relative abundance of bacterial OTUs. However, the bacterial communities in the filtrates became relatively similar to those in the biofilm using presence/absence of bacterial OTUs. GAC biofilm or raw water and filtrates greatly contributed to the abundance of bacteria; whereas, bacteria sheared from colonized biofilm and entered filtrates. Evenly distributed, diverse and unique bacteria in the biofilm played an important role to remove organic matters from surface water for conventional surface water pretreatment. PMID:25267475

  4. Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

    NASA Astrophysics Data System (ADS)

    Wilton, E.; Flanagan, L. B.

    2014-12-01

    Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

  5. Chemoautotrophic Carbon Fixation Rates and Active Bacterial Communities in Intertidal Marine Sediments

    PubMed Central

    Boschker, Henricus T. S.; Vasquez-Cardenas, Diana; Bolhuis, Henk; Moerdijk-Poortvliet, Tanja W. C.; Moodley, Leon

    2014-01-01

    Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m−2 d−1. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)−1, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on

  6. Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments.

    PubMed

    Boschker, Henricus T S; Vasquez-Cardenas, Diana; Bolhuis, Henk; Moerdijk-Poortvliet, Tanja W C; Moodley, Leon

    2014-01-01

    Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, The Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m(-2) d(-1). Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)(-1), which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on

  7. Characterization of Fe(II) oxidizing bacterial activities and communities at two acidic Appalachian coalmine drainage-impacted sites

    SciTech Connect

    Senko, John M.; Wanjugi, Pauline; Lucas, Melanie; Bruns, Mary Ann; Burgos, William D.

    2008-06-12

    We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalminederived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O2. Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenic spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.

  8. Identification of Active Bacterial Communities in Drinking Water Using 16S rRNA-Based Sequence Analyses

    EPA Science Inventory

    DNA-based methods have considerably increased our understanding of the bacterial diversity of water distribution systems (WDS). However, as DNA may persist after cell death, the use of DNA-based methods cannot be used to describe metabolically-active microbes. In contrast, intra...

  9. Crude Oil Treatment Leads to Shift of Bacterial Communities in Soils from the Deep Active Layer and Upper Permafrost along the China-Russia Crude Oil Pipeline Route

    PubMed Central

    Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun

    2014-01-01

    The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils. PMID:24794099

  10. Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route.

    PubMed

    Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun

    2014-01-01

    The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils. PMID:24794099

  11. 2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil.

    PubMed

    Gonod, Laure Vieublé; Martin-Laurent, Fabrice; Chenu, Claire

    2006-12-01

    The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D. PMID:17117994

  12. Sulfide-oxidizing activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system.

    PubMed

    Cytryn, Eddie; Minz, Dror; Gelfand, Ilya; Neori, Amir; Gieseke, Armin; De Beer, Dirk; Van Rijn, Jaap

    2005-03-15

    In the present work we describe a comprehensive analysis of sulfide oxidation in a fluidized bed reactor (FBR) from an environmentally sustainable, zero-discharge mariculture system. The FBR received oxygen-depleted effluent from a digestion basin (DB) that is responsible for gasification of organic matter and nitrogen. The FBR is a crucial component in this recirculating system because it safeguards the fish from the toxic sulfide produced in the DB. Microscale sulfide oxidation potential and bacterial community composition within FBR biofilms were correlated to biofilter performance by integrating bulk chemical, microsensor (O2, pH, and H2S), and molecular microbial community analyses. The FBR consistently oxidized sulfide during two years of continuous operation, with an estimated average sulfide removal rate of 1.3 g of sulfide-S L(FBR)(-1) d(-1). Maximum sulfide oxidation rates within the FBR biofilms were 0.36 and 0.21 mg of sulfide-S cm(-3) h(-1) in the oxic and anoxic layers, respectively, indicating that both oxygen and nitrate serve as electron acceptors for sulfide oxidation. The estimated anoxic sulfide removal rate, as extrapolated from bench scale, autotrophic, nitrate-amended experiments, was 0.7 g of sulfide-S L(FBR)(-1) d(-1), which is approximately 50% of the total estimated sulfide removal in the FBR. Community composition analyses using denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments from FBR samples taken at six-month intervals revealed several sequences that were closely affiliated with sulfide-oxidizing bacteria. These included the denitrifying, sulfide-oxidizing bacteria Thiomicrospira denitrificans, members of the filamentous Thiothrix genus, and sulfide-oxidizing symbionts from the Gammaproteobacteria. In addition, marine Alphaproteobacteria and Bacteroidetes species were present in all of the DGGE profiles examined. DGGE analyses showed significant shifts in the bacterial community composition between

  13. Spatial distribution of marine airborne bacterial communities.

    PubMed

    Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

    2015-06-01

    The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters - temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances. PMID:25800495

  14. Spatial distribution of marine airborne bacterial communities

    PubMed Central

    Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

    2015-01-01

    The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters – temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances. PMID:25800495

  15. Antibiotics promote aggregation within aquatic bacterial communities

    PubMed Central

    Corno, Gianluca; Coci, Manuela; Giardina, Marco; Plechuk, Sonia; Campanile, Floriana; Stefani, Stefania

    2014-01-01

    The release of antibiotics (AB) into the environment poses several threats for human health due to potential development of AB-resistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance) in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5–6 fold. These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of the effects of

  16. Antibiotics promote aggregation within aquatic bacterial communities.

    PubMed

    Corno, Gianluca; Coci, Manuela; Giardina, Marco; Plechuk, Sonia; Campanile, Floriana; Stefani, Stefania

    2014-01-01

    The release of antibiotics (AB) into the environment poses several threats for human health due to potential development of AB-resistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance) in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold. These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of the effects of AB

  17. Bacterial communities associated with the lichen symbiosis.

    PubMed

    Bates, Scott T; Cropsey, Garrett W G; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2011-02-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N(2) fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N(2) fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses. PMID:21169444

  18. Ozonation effects for excess sludge reduction on bacterial communities composition in a full-scale activated sludge plant for domestic wastewater treatment.

    PubMed

    Chiellini, C; Gori, R; Tiezzi, A; Brusetti, L; Pucciarelli, S; D'Amato, E; Chiavola, A; Sirini, P; Lubello, C; Petroni, G

    2014-01-01

    Activated sludge process is the most widely diffused system to treat wastewater to control the discharge of pollutants into the environment. Microorganisms are responsible for the removal of organic matter, nitrogen, phosphorous and other emerging contaminants. The environmental conditions of biological reactors significantly affects the ecology of the microbial community and, therefore, the performance of the treatment process. In the last years, ozone has been used to reduce excess sludge production by wastewater treatment plants (WWTPs), whose disposal represents one of the most relevant operational costs. The ozonation process has demonstrated to be a viable method to allow a consistent reduction in excess sludge. This study was carried out in a full-scale plant treating municipal wastewater in two parallel lines, one ozonated in the digestion tank and another used as a control. Bacterial communities of samples collected from both lines of digestion thanks were then compared to assess differences related to the ozonation treatment. Data were then analysed with terminal restriction fragment length polymorphism (T-RFLP) analysis on 16S rRNA gene. Differences between bacterial communities of both treated and untreated line appeared 2 weeks after the beginning of the treatment. Results demonstrated that ozonation treatment significantly affected the activated sludge in WWTP. PMID:24701944

  19. Effect of increased load of high-strength food wastewater in thermophilic and mesophilic anaerobic co-digestion of waste activated sludge on bacterial community structure.

    PubMed

    Jang, Hyun Min; Ha, Jeong Hyub; Kim, Mi-Sun; Kim, Jong-Oh; Kim, Young Mo; Park, Jong Moon

    2016-08-01

    In recent years, anaerobic co-digestion (AcoD) has been widely used to improve reactor performance, especially methane production. In this study, we applied two different operating temperatures (thermophilic and mesophilic) and gradually increased the load of food wastewater (FWW) to investigate the bacterial communities during the AcoD of waste activated sludge (WAS) and FWW. As the load of FWW was increased, methane production rate (MPR; L CH4/L d) and methane content (%) in both Thermophilic AcoD (TAcoD) and Mesophilic AcoD (MAcoD) increased significantly; the highest MPR and methane content in TAcoD (1.423 L CH4/L d and 68.24%) and MAcoD (1.233 L CH4/L d and 65.21%) were observed when the FWW mixing ratio was 75%. However, MPR and methane yield in both reactors decreased markedly and methane production in TAcoD ceased completely when only FWW was fed into the reactor, resulting from acidification of the reactor caused by accumulation of organic acids. Pyrosequencing analysis revealed a decrease in bacterial diversity in TAcoD and a markedly different composition of bacterial communities between TAcoD and MAcoD with an increase in FWW load. For example, Bacterial members belonging to two genera Petrotoga (assigned to phylum Thermotogae) and Petrimonas (assigned to phylum Bacteroidetes) became dominant in TAcoD and MAcoD with an increase in FWW load, respectively. In addition, quantitative real-time PCR (qPCR) results showed higher bacterial and archaeal populations (expressed as 16S rRNA gene concentration) in TAcoD than MAcoD with an increase in FWW load and showed maximum population when the FWW mixing ratio was 75% in both reactors. Collectively, this study demonstrated the dynamics of key bacterial communities in TAcoD and MAcoD, which were highly affected by the load of FWW. PMID:27155112

  20. Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil†

    PubMed Central

    Murase, Jun; Noll, Matthias; Frenzel, Peter

    2006-01-01

    Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a γ-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G+C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH4+ was lower and the level of extractable SO42− was higher without protists, indicating that nitrogen mineralization and SO42− reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O2 was a major

  1. Jellyfish modulate bacterial dynamic and community structure.

    PubMed

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    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 possible changes in

  2. Jellyfish Modulate Bacterial Dynamic and Community Structure

    PubMed Central

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    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

  3. Bacterial Biofilms as Complex Communities

    NASA Astrophysics Data System (ADS)

    Vlamakis, Hera

    2010-03-01

    Many microbial populations form surface-associated multicellular communities known as biofilms. These multicellular communities are encased in a self-produced extracellular matrix composed of polysaccharides and proteins. Division of labor is a key feature of these communities and different cells serve distinct functions. We have found that in biofilms of the bacterium Bacillus subtilis, different cell types including matrix-producing and sporulating cells coexist and localize to distinct regions within the structured community. We were interested in understanding how these different cell types arise. Using fluorescence reporters under the control of promoters that are specific for distinct cell types we were able to follow the dynamics of differentiation throughout biofilm development. We found that a series of extracellular signals leads to differentiation of distinct cell types during biofilm formation. In addition, we found that extracellular matrix functions as a differentiation signal for timely sporulation within a biofilm and mutants unable to produce matrix were delayed in sporulation. Our results indicate that within a biofilm, cell-cell signaling is directional in that one cell type produces a signal that is sensed by another distinct cell type. Furthermore, once differentiated, cells become resistant to the action of other signaling molecules making it possible to maintain distinct cell populations over prolonged periods.

  4. Supraglacial bacterial community structures vary across the Greenland ice sheet.

    PubMed

    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. PMID:26691594

  5. Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China.

    PubMed

    Niu, Lihua; Li, Yi; Wang, Peifang; Zhang, Wenlong; Wang, Chao; Wang, Qing

    2015-10-01

    To understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla. Betaproteobacteria, Bacteroidetes, and Firmicutes displayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations. PMID:26162883

  6. Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China

    PubMed Central

    Niu, Lihua; Wang, Peifang; Wang, Chao; Wang, Qing

    2015-01-01

    To understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla. Betaproteobacteria, Bacteroidetes, and Firmicutes displayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations. PMID:26162883

  7. A comparison of the benthic bacterial communities within and surrounding Dreissena clusters in lakes.

    PubMed

    Lohner, Rachel N; Sigler, Von; Mayer, Christine M; Balogh, Csilla

    2007-10-01

    The impact of Dreissena (Dreissena polymorpha and D. bugensis) on the benthic bacterial community in lakes is largely unknown. Therefore, we quantified differences in the structure and activity of bacterial communities living in sediments (1) associated with Dreissena clusters, and (2) unassociated with established clusters (lake bottom sediments). Dreissena clusters and sediments were collected from locations in Lake Erie, Lake Ontario, and several inland lakes. Denaturing gradient gel electrophoresis (DGGE) analysis of the benthic bacterial community showed that the bacterial populations selected for by Dreissena represent a subset of the bottom communities and are geographically distinct. Community-level physiological profiling (CLPP) showed that overall bacterial activity and metabolic diversity were enhanced by the presence of clusters in all samples, with the exception of those harvested from the two Lake Erie sites. Therefore, Dreissena appears to affect both structure and metabolic function of the benthic bacterial community and may have yet unexplored ecosystem and food web consequences. PMID:17308984

  8. Bacterial community analysis of Indonesian hot springs.

    PubMed

    Baker, G C; Gaffar, S; Cowan, D A; Suharto, A R

    2001-06-12

    We report the first attempts to describe thermophilic bacterial communities in Indonesia's thermal springs using molecular phylogenetic analyses. 16S rRNA genes from laboratory cultures and DNA directly amplified from three hot springs in West Java were sequenced. The 22 sequences obtained were assignable to the taxa Proteobacteria, Bacillus and Flavobacterium, including a number of clades not normally associated with thermophily. PMID:11410357

  9. Ion channels enable electrical communication within bacterial communities

    PubMed Central

    Prindle, Arthur; Liu, Jintao; Asally, Munehiro; Ly, San; Garcia-Ojalvo, Jordi; Süel, Gürol M.

    2016-01-01

    The study of bacterial ion channels has provided fundamental insights into the structural basis of neuronal signaling. However, the native role of ion channels in bacteria has remained elusive. Here we show that ion channels conduct long-range electrical signals within bacterial biofilm communities through spatially propagating waves of potassium. These waves result from a positive feedback loop, in which a metabolic trigger induces release of intracellular potassium, which in turn depolarizes neighboring cells. Propagating through the biofilm, this wave of depolarization coordinates metabolic states among cells in the interior and periphery of the biofilm. Deletion of the potassium channel abolishes this response. As predicted by a mathematical model, we further show that spatial propagation can be hindered by specific genetic perturbations to potassium channel gating. Together, these results demonstrate a function for ion channels in bacterial biofilms, and provide a prokaryotic paradigm for active, long-range electrical signaling in cellular communities. PMID:26503040

  10. Activity of JNJ-Q2, a new fluoroquinolone, tested against contemporary pathogens isolated from patients with community-acquired bacterial pneumonia.

    PubMed

    Biedenbach, Douglas J; Farrell, David J; Flamm, Robert K; Liverman, Lisa C; McIntyre, Gail; Jones, Ronald N

    2012-04-01

    JNJ-Q2 is a broad-spectrum fluoroquinolone with bactericidal activity against Gram-positive and Gram-negative pathogens and is currently in clinical development for the treatment of community-acquired bacterial pneumonia (CABP) and acute bacterial skin and skin-structure infections. This study determined the activity of JNJ-Q2 against a worldwide year 2010 collection (89 centres in 27 countries) of three common respiratory pathogens (3757 isolates) from patients with CABP. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis were tested by the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method, and susceptibility rates for comparators were assessed using CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoint criteria. JNJ-Q2 had activity against all three species, with 96.9% of strains inhibited at ≤0.015 mg/L. JNJ-Q2 [minimum inhibitory concentration for 50% and 90% of the organisms, respectively (MIC(50/90))=0.008/0.015 mg/L] demonstrated a 16-fold greater potency compared with moxifloxacin (MIC(50/90)=0.12/0.25 mg/L) and at least 128-fold greater activity compared with levofloxacin (MIC(50/90)=1/ 1 mg/L) and ciprofloxacin (MIC(50/90)=1/2 mg/L) against S. pneumoniae. Haemophilus influenzae isolates were 21.9-23.3% resistant to ampicillin, but JNJ-Q2 (MIC(50/90)≤0.004/0.015 mg/L) was at least two-fold more active than moxifloxacin (MIC(50/90)=0.015/0.03 mg/L) as well as being potent against M. catarrhalis (MIC(90)=0.015/0.015 mg/L). In conclusion, JNJ-Q2 demonstrated increased potency compared with other marketed fluoroquinolones that have been used to treat CABP pathogens, thus favouring further clinical development. PMID:22306239

  11. Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem.

    PubMed

    Das, Suvendu; Chou, Mon-Lin; Jean, Jiin-Shuh; Liu, Chia-Chuan; Yang, Huai-Jen

    2016-01-15

    Although rice cultivated under water-saturated conditions as opposed to submerged conditions has received considerable attention with regard to reducing As levels in rice grain, the rhizosphere microbiome potentially influencing As-biotransformation and bioavailability in a rice ecosystem has rarely been studied. In this study, the impacts of flooded, non-flooded and alternate wetting and drying (AWD) practices on rhizosphere bacterial composition and activities that could potentially impact As speciation and accumulation in rhizosphere soil and pore water, As fractions in rhizosphere soil and As speciation and distribution in plant parts were assessed. The results revealed that in addition to pore water As concentration, non-specifically sorbed As fraction, specifically sorbed As fraction and amorphous iron oxide bound As fraction in soil were bio-available to rice plants. In the flooded treatment, As(III) in the pore water was the predominant As species, accounting for 87.3-93.6% of the total As, whereas in the non-flooded and AWD treatments, As(V) was the dominant As species, accounting for 89.6-96.2% and 73.0-83.0%, respectively. The genera Ohtaekwangia, Geobacter, Anaeromyxobacter, Desulfuromonas, Desulfocapsa, Desulfobulbus, and Lacibacter were found in relatively high abundance in the flooded soil, whereas the genera Acinetobacter, Ignavibacterium, Thiobacillus, and Lysobacter were detected in relatively high abundance in the non-flooded soil. Admittedly, the decrease in As level in rice cultivated under the non-flooded and AWD conditions was mostly linked to a relatively high soil redox potential, low As(III) concentration in the soil pore water, a decrease in the relative abundance of As-, Fe- and sulfur-reducing bacteria and an increase in the relative abundance of As-, Fe- and sulfur-oxidizing bacteria in the rhizosphere soil of the rice. This study demonstrated that with substantial reduction in grain As levels and higher water productivity, AWD

  12. Bacterial Community Diversity Harboured by Interacting Species.

    PubMed

    Bili, Mikaël; Cortesero, Anne Marie; Mougel, Christophe; Gauthier, Jean Pierre; Ermel, Gwennola; Simon, Jean Christophe; Outreman, Yannick; Terrat, Sébastien; Mahéo, Frédérique; Poinsot, Denis

    2016-01-01

    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. PMID:27258532

  13. Bacterial Community Diversity Harboured by Interacting Species

    PubMed Central

    Bili, Mikaël; Cortesero, Anne Marie; Mougel, Christophe; Gauthier, Jean Pierre; Ermel, Gwennola; Simon, Jean Christophe; Outreman, Yannick; Terrat, Sébastien; Mahéo, Frédérique; Poinsot, Denis

    2016-01-01

    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. PMID:27258532

  14. Experimental warming effects on the bacterial community structure and diversity

    NASA Astrophysics Data System (ADS)

    Kim, W.; Han, S.; Adams, J.; Son, Y.

    2014-12-01

    The objective of this study is to investigate the responses of soil bacterial community to future temperature increase by conducting open-field warming experiment. We conducted an open-field experimental warming system using infra-red heater in 2011 and regulated the temperature of warmed plots by 3oC higher than that of control plots constantly. The seeds of Pinus densiflora, Abies holophylla, Abies koreana, Betula costata, Quercus variabilis, Fraxinus rhynchophylla, and Zelkova serrata were planted in each 1 m × 1 m plot (n=3) in April, 2012. We collected soil samples from the rhizosphere of 7 tree species. DNA was extracted and PCR-amplified for the bacterial 16S gene targeting V1-V3 region. The paired-end sequencing was performed at Beijing Genome Institute (BGI, Hong Kong, China) using 2× 100 bp Hiseq2000 (Illumina). This study aimed to answer the following prediction/hypothesis: 1) Experimental warming will change the structure of soil bacterial community, 2) There will be distinct 'indicator group' which response to warming treatment relatively more sensitive than other groups. 3) Warming treatment will enhance the microbial activity in terms of soil respiration. 4) The rhizoplane bacterial communities for each of 7 tree species will show different response pattern to warming treatment. Since the sequence data does not arrive before the submission deadline, therefore, we would like to present the results and discussions on December 2014, AGU Fall Meeting.

  15. Bacterial communities in petroleum oil in stockpiles.

    PubMed

    Yoshida, Nobuyuki; Yagi, Kazuhiro; Sato, Daisuke; Watanabe, Noriko; Kuroishi, Takeshi; Nishimoto, Kana; Yanagida, Akira; Katsuragi, Tohoru; Kanagawa, Takahiro; Kurane, Ryuichiro; Tani, Yoshiki

    2005-02-01

    Bacterial communities in crude-oil samples from Japanese oil stockpiles were investigated by 16S rRNA gene cloning, followed by denaturing gradient gel electrophoresis (DGGE) analysis. 16S rRNA genes were successfully amplified by PCR after isooctane treatment from three kinds of crude-oil sample collected at four oil stockpiles in Japan. DGGE profiles showed that bacteria related to Ochrobactrum anthropi, Burkholderia cepacia, Stenotrophomonas maltophilia, Propionibacterium acnes, and Brevundimonas diminuta were frequently detected in most crude-oil samples. The bacterial communities differed in the sampling time and layer. Among the predominant bacteria detected in the crude oil, only three species were found for bacteria isolated on agar plates and were related to Burkholderia, Stenotrophomonas, and Propionibacterium, while Ochrobactrum sp. could not be isolated although this species seemed to be the most abundant bacterium in crude oil from the DGGE profiles. Using an archaea-specific primer set, methanogens were found in crude-oil sludge but not in crude-oil samples, indicating that methanogens might be involved in sludge formation in oil stockpiles. PMID:16233771

  16. The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments

    PubMed Central

    Bienhold, Christina; Boetius, Antje; Ramette, Alban

    2012-01-01

    The availability of nutrients and energy is a main driver of biodiversity for plant and animal communities in terrestrial and marine ecosystems, but we are only beginning to understand whether and how energy–diversity relationships may be extended to complex natural bacterial communities. Here, we analyzed the link between phytodetritus input, diversity and activity of bacterial communities of the Siberian continental margin (37–3427 m water depth). Community structure and functions, such as enzymatic activity, oxygen consumption and carbon remineralization rates, were highly related to each other, and with energy availability. Bacterial richness substantially increased with increasing sediment pigment content, suggesting a positive energy–diversity relationship in oligotrophic regions. Richness leveled off, forming a plateau, when mesotrophic sites were included, suggesting that bacterial communities and other benthic fauna may be structured by similar mechanisms. Dominant bacterial taxa showed strong positive or negative relationships with phytodetritus input and allowed us to identify candidate bioindicator taxa. Contrasting responses of individual taxa to changes in phytodetritus input also suggest varying ecological strategies among bacterial groups along the energy gradient. Our results imply that environmental changes affecting primary productivity and particle export from the surface ocean will not only affect bacterial community structure but also bacterial functions in Arctic deep-sea sediment, and that sediment bacterial communities can record shifts in the whole ocean ecosystem functioning. PMID:22071347

  17. Bacterial community development in experimental gingivitis.

    PubMed

    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

  18. Bacterial Communities in Acidic and Circumneutral Streams †

    PubMed Central

    Palumbo, Anthony V.; Bogle, Mary Anna; Turner, Ralph R.; Elwood, Jerry W.; Mulholland, Patrick J.

    1987-01-01

    The relationship between pH and the abundance and activity of bacteria in streams was examined as part of a study of the effect of acidification on stream communities. Of the bacterial communities examined, the epilithic community appeared to be the most significantly affected by acidification. Microbial biomass, as quantified by measuring the ATP level, on rock surfaces was significantly correlated with pH. Also, bacterial production by the epilithic bacteria, indicated by incorporation of tritiated thymidine into DNA, was always higher at high-pH sites than at low-pH sites of the same stream order and elevation. Bacterioplankton concentrations varied between 0.53 × 105 and 9.42 × 105 cells · ml−1 in the first- to fourth-order streams examined. The bacterioplankton concentration in one sample from a spring was 0.17 × 105 cells · ml−1. Bacterioplankton concentrations were not correlated with pH but were significantly correlated with seston concentrations. The correlation with seston is a result of increases in particle-associated bacteria at high seston concentrations. The proportion of bacterioplankton attached to particles varied from 0 to 70%. Bacterial numbers and production in the sediments were significantly correlated with the organic content of the sediment rather than with the pH of the overlying water. Thus, reduced abundance and activity of bacteria as a result of acidification could be detected only for the relatively active community on rock surfaces; this community was exposed to the low pH because of the unbuffered nature of its environment. PMID:16347283

  19. The impact of titanium dioxide nanoparticles on biological nitrogen removal from wastewater and bacterial community shifts in activated sludge.

    PubMed

    Li, Dapeng; Cui, Fuyi; Zhao, Zhiwei; Liu, Dongmei; Xu, Yongpeng; Li, Huiting; Yang, Xiaonan

    2014-04-01

    The potential impact of titanium dioxide nanoparticles (TiO2 NPs) on nitrogen removal from wastewater in activated sludge was investigated using a sequencing batch reactor. The addition of 2-50 mg L(-1) of TiO2 NPs did not adversely affect nitrogen removal. However, when the activated sludge was exposed to 100-200 mg L(-1) of TiO2 NPs, the effluent total nitrogen removal efficiencies were 36.5 % and 20.3 %, respectively, which are markedly lower than the values observed in the control test (80 %). Further studies showed that the decrease in biological nitrogen removal induced by higher concentrations of TiO2 NPs was due to an inhibitory effect on the de-nitrification process. Denaturing gradient gel electrophoresis profiles showed that 200 mg L(-1) of TiO2 NPs significantly reduced microbial diversity in the activated sludge. The effect of light on the antibacterial activity of TiO2 NPs was also investigated, and the results showed that the levels of TiO2-dependent inhibition of biological nitrogen removal were similar under both dark and light conditions. Additional studies revealed that different TiO2 concentrations had a significant effect on dehydrogenase activity, and this effect was most likely the result of decreased microbial activity. PMID:23660752

  20. Differences in Bacterial Community Structure in Two Color Morphs of the Hawaiian Reef Coral Montipora capitata.

    PubMed

    Shore-Maggio, Amanda; Runyon, Christina M; Ushijima, Blake; Aeby, Greta S; Callahan, Sean M

    2015-10-01

    Corals harbor diverse bacterial associations that contribute to the health of the host. Using 16S rRNA pyrosequencing, we compared the bacterial communities of red and orange morphs of the Hawaiian coral Montipora capitata. Although both color morphs shared dominant bacterial genera, weighted and unweighted UniFrac analyses showed distinct bacterial communities. A single operational taxonomic unit (OTU), classified as Vibrio, represented the largest driver of differences between the color morphs. This OTU comprised 35.4% (±5.5%) of the orange morph bacterial community yet comprised 1.1% (±0.6%) of the red morph bacterial community. Cultivable bacteria from the two color morphs were also compared and tested for antibacterial activity. Cultured isolates represented 14 genera (7% of the total genera identified from sequencing data), and all but two cultured isolates had a matching OTU from the sequencing data. Half of the isolates tested (8 out of 16) displayed antibacterial activity against other cultured isolates but not against two known bacterial pathogens of M. capitata. The results from this study demonstrate that the specificity of coral-bacterial associations extends beyond the level of coral species. In addition, culture-dependent methods captured bacterial diversity that was representative of both rare and abundant members of the associated bacterial community, as characterized by culture-independent methods. PMID:26253663

  1. Differences in Bacterial Community Structure in Two Color Morphs of the Hawaiian Reef Coral Montipora capitata

    PubMed Central

    Shore-Maggio, Amanda; Runyon, Christina M.; Ushijima, Blake; Aeby, Greta S.

    2015-01-01

    Corals harbor diverse bacterial associations that contribute to the health of the host. Using 16S rRNA pyrosequencing, we compared the bacterial communities of red and orange morphs of the Hawaiian coral Montipora capitata. Although both color morphs shared dominant bacterial genera, weighted and unweighted UniFrac analyses showed distinct bacterial communities. A single operational taxonomic unit (OTU), classified as Vibrio, represented the largest driver of differences between the color morphs. This OTU comprised 35.4% (±5.5%) of the orange morph bacterial community yet comprised 1.1% (±0.6%) of the red morph bacterial community. Cultivable bacteria from the two color morphs were also compared and tested for antibacterial activity. Cultured isolates represented 14 genera (7% of the total genera identified from sequencing data), and all but two cultured isolates had a matching OTU from the sequencing data. Half of the isolates tested (8 out of 16) displayed antibacterial activity against other cultured isolates but not against two known bacterial pathogens of M. capitata. The results from this study demonstrate that the specificity of coral-bacterial associations extends beyond the level of coral species. In addition, culture-dependent methods captured bacterial diversity that was representative of both rare and abundant members of the associated bacterial community, as characterized by culture-independent methods. PMID:26253663

  2. Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis.

    PubMed

    Randazzo, Cinzia L; Torriani, Sandra; Akkermans, Antoon D L; de Vos, Willem M; Vaughan, Elaine E

    2002-04-01

    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, respectively. DGGE profiles from samples taken during cheese production indicated dramatic shifts in the microbial community structure. Cloning and sequencing of rDNA amplicons revealed that mesophilic lactic acid bacteria (LAB), including species of Leuconostoc, Lactococcus lactis, and Macrococcus caseolyticus were dominant in the raw milk, while Streptococcus thermophilus prevailed during lactic fermentation. Other thermophilic LAB, especially Lactobacillus delbrueckii and Lactobacillus fermentum, also flourished during ripening. Comparison of the rRNA-derived patterns obtained by RT-PCR to the rDNA DGGE patterns indicated a substantially different degree of metabolic activity for the microbial groups detected. Identification of cultivated LAB isolates by phenotypic characterization and 16S rDNA analysis indicated a variety of species, reflecting to a large extent the results obtained from the 16S rDNA clone libraries, with the significant exception of the Lactobacillus delbrueckii species, which dominated in the ripening cheese but was not detected by cultivation. The present molecular approaches combined with culture can effectively describe the complex ecosystem of natural fermented dairy products, giving useful information for starter culture design and preservation of artisanal fermented food technology. PMID:11916708

  3. IDENTIFICATION OF ACTIVE BACTERIAL COMMUNITIES IN A MODEL DRINKING WATER BIOFILM SYSTEM USING 16S RRNA-BASED CLONE LIBRARIES

    EPA Science Inventory

    Recent phylogenetic studies have used DNA as the target molecule for the development of environmental 16S rDNA clone libraries. As DNA may persist in the environment, DNA-based libraries cannot be used to identify metabolically active bacteria in water systems. In this study, a...

  4. Analysis of Diversity and Activity of Sulfate-Reducing Bacterial Communities in Sulfidogenic Bioreactors Using 16S rRNA and dsrB Genes as Molecular Markers▿

    PubMed Central

    Dar, Shabir A.; Yao, Li; van Dongen, Udo; Kuenen, J. Gijs; Muyzer, Gerard

    2007-01-01

    Here we describe the diversity and activity of sulfate-reducing bacteria (SRB) in sulfidogenic bioreactors by using the simultaneous analysis of PCR products obtained from DNA and RNA of the 16S rRNA and dissimilatory sulfite reductase (dsrAB) genes. We subsequently analyzed the amplified gene fragments by using denaturing gradient gel electrophoresis (DGGE). We observed fewer bands in the RNA-based DGGE profiles than in the DNA-based profiles, indicating marked differences in the populations present and in those that were metabolically active at the time of sampling. Comparative sequence analyses of the bands obtained from rRNA and dsrB DGGE profiles were congruent, revealing the same SRB populations. Bioreactors that received either ethanol or isopropanol as an energy source showed the presence of SRB affiliated with Desulfobulbus rhabdoformis and/or Desulfovibrio sulfodismutans, as well as SRB related to the acetate-oxidizing Desulfobacca acetoxidans. The reactor that received wastewater containing a diverse mixture of organic compounds showed the presence of nutritionally versatile SRB affiliated with Desulfosarcina variabilis and another acetate-oxidizing SRB, affiliated with Desulfoarculus baarsii. In addition to DGGE analysis, we performed whole-cell hybridization with fluorescently labeled oligonucleotide probes to estimate the relative abundances of the dominant sulfate-reducing bacterial populations. Desulfobacca acetoxidans-like populations were most dominant (50 to 60%) relative to the total SRB communities, followed by Desulfovibrio-like populations (30 to 40%), and Desulfobulbus-like populations (15 to 20%). This study is the first to identify metabolically active SRB in sulfidogenic bioreactors by using the functional gene dsrAB as a molecular marker. The same approach can also be used to infer the ecological role of coexisting SRB in other habitats. PMID:17098925

  5. Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum.

    PubMed

    Uroz, S; Courty, P E; Pierrat, J C; Peter, M; Buée, M; Turpault, M P; Garbaye, J; Frey-Klett, P

    2013-08-01

    An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil. PMID:23455431

  6. Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain).

    PubMed

    Portillo, Maria C; Gonzalez, Juan M

    2011-01-01

    The influence of bacterial communities on the formation of carbonate deposits such as moonmilk was investigated in Altamira Cave (Spain). The study focuses on the relationship between the bacterial communities at moonmilk deposits and those forming white colonizations, which develop sporadically throughout the cave. Using molecular fingerprinting of the metabolically active bacterial communities detected through RNA analyses, the development of white colonizations and moonmilk deposits showed similar bacterial profiles. White colonizations were able to raise the pH as a result of their metabolism (reaching in situ pH values above 8.5), which was proportional to the nutrient supply. Bacterial activity was analyzed by nanorespirometry showing higher metabolic activity from bacterial colonizations than uncolonized areas. Once carbonate deposits were formed, bacterial activity decreased drastically (down to 5.7% of the white colonization activity). This study reports on a specific type of bacterial community leading to moonmilk deposit formation in a cave environment as a result of bacterial metabolism. The consequence of this process is a macroscopic phenomenon of visible carbonate depositions and accumulation in cave environments. PMID:20717660

  7. 3D printing of microscopic bacterial communities

    PubMed Central

    Connell, Jodi L.; Ritschdorff, Eric T.; Whiteley, Marvin; Shear, Jason B.

    2013-01-01

    Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell–cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa. PMID:24101503

  8. Short scale variations in nutrients, ectoenzymatic activities and bottom-up effects on bacterial production and community structure during late summer-autumn transition in the open NW Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    van Wambeke, F.; Ghiglione, J.-F.; Nedoma, J.; Mével, G.; Raimbault, P.

    2009-01-01

    We examined the vertical and temporal dynamics of nutrients, ectoenzymatic activities under late summer-fall transition period (September-October 2004) in NW Mediterranean Sea in relation to temporal change in factors limiting bacterial production. The depth of the mixed layer (12.8±5.3 m) was extremely stable until the onset of the destratification period after 11 October, creating a zone where diffusion of nutrient from the much deeper phosphacline (69±12 m) and nitracline (50±8 m) was probably strongly limited. However during the second half of the cruise, a shallowing of nutriclines occured, particularly marked for nitracline. Hence, the nitrate to phosphate ratio within the mixed layer, although submitted to a high short term variability, shifted the last week of the cruise from 1.1±1.2 to 4.6±3.8, and nitrate increased by a factor 2 (0.092±0.049 μM). A corresponding switch from more than one limitation (PN) to P-only limitation of bacterial production was observed during the month as detected by enrichment bioassays. Differences in the identity of the limiting nutrient in surface (5 m: N and P at the beginning, strictly P at the end of the study) versus 80 m (labile carbon) influence greatly bacterial community structure shift between these two layers. The two communities (5 and 80 m) reacted rapidly (24 h) to changes in nutrient concentrations by drastic modification of total and active population assemblages resulting in changes in activity. For bacterial production values less than 10 ng C l-1h-1 (associated to deeper layers), aminopeptidase and lipase exhibited higher activity relative to production whereas phosphatase varied in the same proportions than BP on the range of activities tested. Our results illustrate the effect of bottom-up control on bacterial community structure and activities in the epipelagic NW Mediterranean Sea.

  9. Moderately thermophilic, hydrocarbonoclastic bacterial communities in Kuwaiti desert soil: enhanced activity via Ca(2+) and dipicolinic acid amendment.

    PubMed

    Al-Mailem, D M; Kansour, M K; Radwan, S S

    2015-05-01

    Pristine and oil-contaminated desert soil samples from Kuwait harbored between 10 and 100 cells g(-1) of hydrocarbonoclastic bacteria capable of growth at 50 °C. Enrichment by incubation of moistened soils for 6 months at 50 °C raised those numbers to the magnitude of 10(3) cells g(-1). Most of these organisms were moderately thermophilic and belonged to the genus Bacillus; they grew at 40-50 °C better than at 30 °C. Species belonging to the genera Amycolatopsis, Chelativorans, Isoptericola, Nocardia, Aeribacillus, Aneurinibacillus, Brevibacillus, Geobacillus, Kocuria, Marinobacter and Paenibacillus were also found. This microbial diversity indicates a good potential for hydrocarbon removal in soil at high temperature. Analysis of the same desert soil samples by a culture-independent method (combined, DGGE and 16S rDNA sequencing) revealed dramatically different lists of microorganisms, many of which had been recorded as hydrocarbonoclastic. Many species were more frequent in the oil contaminated than in the pristine soil samples, which may reflect their hydrocarbonoclastic activity in situ. The growth and hydrocarbon consumption potential of all tested isolates were dramatically enhanced by amendment of the cultures with Ca(2+) (up to 2.5 M CaSO4). This enhanced effect was even amplified when in addition 8 % w/v dipicolinic acid was amended. These novel findings are useful in suggesting biotechnologies for waste hydrocarbon remediation at moderately high temperature. PMID:25716145

  10. Community level physiological profiles of bacterial communities inhabiting uranium mining impacted sites.

    PubMed

    Kenarova, Anelia; Radeva, Galina; Traykov, Ivan; Boteva, Silvena

    2014-02-01

    Bacterial activity and physiological diversity were characterized in mining and milling impacted soils collected from three abandoned uranium mine sites, Senokos, Buhovo and Sliven, using bacterial dehydrogenase activity and Biolog (EcoPlate) tests. The elemental composition of soils revealed high levels of uranium and heavy metals (sum of technogenic coefficients of contamination; TCC(sum) pollution as follows: Sliven (uranium - 374 mg/kg; TCC(sum) - 23.40) >Buhovo (uranium - 139.20mg/kg; TCC(sum) - 3.93) >Senokos (uranium - 23.01 mg/kg; TCC(sum) - 0.86). The physiological profiles of the bacterial community level were site specific, and indicated intensive utilization of polyols, carbohydrates and carboxylic acids in low and medium polluted environments, and i-erithrytol and 2-hydroxy-benzoic acid in the highly polluted environment of Sliven waste pile. Enzymes which take part in the biodegradation of recalcitrant substances were more resistant to pollution than these from the pathways of the easily degradable carbon sources. The Shannon index indicated that the physiological diversity of bacteria was site specific but not in line with the levels of pollution. A general tendency of increasing the importance of the number of utilizable substrates to bacterial physiological diversity was observed at less polluted sites, whereas in highly polluted sites the evenness of substrate utilization rate was more significant. Dehydrogenase activity was highest in Senokos upper soil layer and positively correlated (p<0.01) with the soil organic matter content. The bacterial activity (EcoPlate) and physiological diversity (Shannon index) correlated significantly and negatively with As, Cu, Zn, Pb and U, and Co, Cr, Ni and Mn, respectively. We concluded that the observed site specific shifts in bacterial communities were complex due to both the environmental peculiarities and the bacterial tolerance to the relevant level of pollution, rather than a strong indication of uranium

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

    PubMed

    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

  12. The green alga Dicytosphaeria ocellata and its organic extracts alter natural bacterial biofilm communities.

    PubMed

    Sneed, Jennifer M; Pohnert, Georg

    2011-04-01

    Surfaces immersed in the marine environment are under intense fouling pressure by a number of invertebrates and algae. The regulation of this fouling can often be attributed to the bacterial biofilm that quickly develops on the surface of any available substratum in the ocean. The bacterial community composition on the surface of the green alga Dictyosphaeria ocellata was investigated and compared to those found on two other green algae, Batophora oerstedii and Cladophoropsis macromeres, and on a reference surface from three sites along the Florida Keys. Although the bacterial community composition of D. ocellata was not consistent across the sites, it was significantly different from the other algae and the reference surface at two of the three sites tested. Methanol extracts of D. ocellata significantly affected the abundance of bacteria and composition of the bacterial community on Phytagel™ plates when compared to solvent controls, suggesting that the alga regulates the bacterial community by producing active metabolites. PMID:21512919

  13. Enhanced bacterial decomposition with increasing addition of autochthonous to allochthonous carbon without any effect on bacterial community composition

    NASA Astrophysics Data System (ADS)

    Attermeyer, K.; Hornick, T.; Kayler, Z. E.; Bahr, A.; Zwirnmann, E.; Grossart, H.-P.; Premke, K.

    2014-03-01

    Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (13C-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (phytoplankton lysate). We then determined bacterial C consumption, activities, and community composition together with the C flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and low- and high-molecular-weight substance fractions (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. Both DOC sources (allochthonous and autochthonous DOC) were metabolized at a high bacterial growth efficiency (BGE) around 50%. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption of up to 68% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substance (HS) fraction and an increase in bacterial biomass. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover.

  14. Bacterial Community Succession in Pine-Wood Decomposition

    PubMed Central

    Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-01-01

    Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

  15. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

    PubMed Central

    McKenzie, Valerie J; Bowers, Robert M; Fierer, Noah; Knight, Rob; Lauber, Christian L

    2012-01-01

    Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens. PMID:21955991

  16. Stability and change in estuarine biofilm bacterial community diversity.

    PubMed

    Moss, Joseph A; Nocker, Andreas; Lepo, Joe E; Snyder, Richard A

    2006-09-01

    Biofouling communities contribute significantly to aquatic ecosystem productivity and biogeochemical cycling. Our knowledge of the distribution, composition, and activities of these microbially dominated communities is limited compared to other components of estuarine ecosystems. This study investigated the temporal stability and change of the dominant phylogenetic groups of the domain Bacteria in estuarine biofilm communities. Glass slides were deployed monthly over 1 year for 7-day incubations during peak tidal periods in East Sabine Bay, Fla. Community profiling was achieved by using 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes in combination with ribotyping, cloning, and sequencing to evaluate diversity and to identify dominant microorganisms. Bacterial community profiles from biofilms grown near the benthos showed distinct periods of constancy within winter and summer sampling periods. Similar periods of stability were also seen in T-RFLP patterns from floating biofilms. Alternating dominance of phylogenetic groups between seasons appeared to be associated with seasonal changes in temperature, nutrient availability, and light. The community structure appeared to be stable during these periods despite changes in salinity and in dissolved oxygen. PMID:16957182

  17. Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms.

    PubMed

    Hunting, Ellard R; Vijver, Martina G; van der Geest, Harm G; Mulder, Christian; Kraak, Michiel H S; Breure, Anton M; Admiraal, Wim

    2015-01-01

    Decomposition of organic matter is an important ecosystem process governed in part by bacteria. The process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. However, the relative importance of resource niche breadth (metabolic diversity) and resource niche overlap (functional redundancy) on decomposition and the temporal stability of ecosystem processes received little scientific attention. Therefore, this study aims to evaluate the effect of an increase in bacterial community resemblance on both decomposition and the stability of bacterial metabolism in aquatic sediments. To this end, we performed laboratory microcosm experiments in which we examined the influence of bacterial consortia differing in number and composition of species on bacterial activity (Electron Transport System Activity, ETSA), dissolved organic carbon production and wavelet transformed measurements of redox potential (Eh). Single substrate affinities of the individual bacterial species were determined in order to calculate the metabolic diversity of the microbial community. Results presented here indicate that bacterial activity and organic matter decomposition increase with widening of the resource niche breadth, and that metabolic stability increases with increasing overlap in bacterial resource niches, hinting that resource niche overlap can promote the stability of bacterial community metabolism. PMID:25759686

  18. Dynamics of Bacterial Community Composition in the Malaria Mosquito's Epithelia

    PubMed Central

    Tchioffo, Majoline T.; Boissière, Anne; Abate, Luc; Nsango, Sandrine E.; Bayibéki, Albert N.; Awono-Ambéné, Parfait H.; Christen, Richard; Gimonneau, Geoffrey; Morlais, Isabelle

    2016-01-01

    The Anopheles midgut hosts diverse bacterial communities and represents a complex ecosystem. Several evidences indicate that mosquito midgut microbiota interferes with malaria parasite transmission. However, the bacterial composition of salivary glands and ovaries, two other biologically important tissues, has not been described so far. In this study, we investigated the dynamics of the bacterial communities in the mosquito tissues from emerging mosquitoes until 8 days after a blood meal containing Plasmodium falciparum gametocytes and described the temporal colonization of the mosquito epithelia. Bacterial communities were identified in the midgut, ovaries, and salivary glands of individual mosquitoes using pyrosequencing of the 16S rRNA gene. We found that the mosquito epithelia share a core microbiota, but some bacteria taxa were more associated with one or another tissue at a particular time point. The bacterial composition in the tissues of emerging mosquitoes varied according to the breeding site, indicating that some bacteria are acquired from the environment. Our results revealed temporal variations in the bacterial community structure, possibly as a result of the mosquito physiological changes. The abundance of Serratia significantly correlated with P. falciparum infection both in the midgut and salivary glands of malaria challenged mosquitoes, which suggests that interactions occur between microbes and parasites. These bacteria may represent promising targets for vector control strategies. Overall, this study points out the importance of characterizing bacterial communities in malaria mosquito vectors. PMID:26779155

  19. Determinants of bacterial communities in Canadian agroforestry systems.

    PubMed

    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. PMID:26184386

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

    PubMed Central

    Hartman, Wyatt H.; Richardson, Curtis J.; 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. Surprisingly, wetland restoration decreased bacterial diversity, a response opposite to that in terrestrial ecosystems. Community level patterns were underlain by responses of a few taxa, especially the Acidobacteria and Proteobacteria, suggesting promise for bacterial indicators of restoration and trophic status. PMID:19004771

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

    PubMed

    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

  2. Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

    PubMed Central

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

    2013-01-01

    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. PMID:23844027

  3. Metamorphosis of a Butterfly-Associated Bacterial Community

    PubMed Central

    Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah

    2014-01-01

    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. PMID:24466308

  4. Bacterial Community Affects Toxin Production by Gymnodinium catenatum

    PubMed Central

    Albinsson, Maria E.; Negri, Andrew P.; Blackburn, Susan I.; Bolch, Christopher J. S.

    2014-01-01

    The paralytic shellfish toxin (PST)-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01) and grown with: 1) complex bacterial communities derived from each of the two parent cultures; 2) simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3) a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell) of clonal offspring (134–197 fmol STX cell−1) was similar to the parent cultures (169–206 fmol STX cell−1), however cultures grown with single bacterial types contained less toxin (134–146 fmol STX cell−1) than offspring or parent cultures grown with more complex mixed bacterial communities (152–176 fmol STX cell−1). Specific toxin production rate (fmol STX day−1) was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell−1 day−1) did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter

  5. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting.

    PubMed

    Barnard, Romain L; Osborne, Catherine A; Firestone, Mary K

    2013-11-01

    The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities. PMID:23823489

  6. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

    PubMed Central

    Barnard, Romain L; Osborne, Catherine A; Firestone, Mary K

    2013-01-01

    The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities. PMID:23823489

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

    PubMed

    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. PMID:26574105

  8. Bacterial Networks in Cells and Communities.

    PubMed

    Sourjik, Victor; Vorholt, Julia A

    2015-11-20

    Research on the bacterial regulatory networks is currently experiencing a true revival, driven by advances in methodology and by emergence of novel concepts. The biannual conference Bacterial Networks (BacNet15) held in May 2015, in Sant Feliu de Guíxols, Spain, covered progress in the studies of regulatory networks that control bacterial physiology, cell biology, stress responses, metabolism, collective behavior and evolution. It demonstrated how interdisciplinary approaches that combine molecular biology and biochemistry with the latest microscopy developments, whole cell (-omics) approaches and mathematical modeling can help understand design principles relevant in microbiology. It further showed how current biotechnology and medical microbiology could profit from our knowledge of and ability to engineer regulatory networks of bacteria. PMID:26506266

  9. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica)

    PubMed Central

    Garcias-Bonet, Neus; Arrieta, Jesus M.; de Santana, Charles N.; Duarte, Carlos M.; Marbà, Núria

    2012-01-01

    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 Denaturing Gradient Gel Electrophoresis (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. PMID:23049528

  10. Opposing phylogenetic diversity gradients of plant and soil bacterial communities.

    PubMed

    Goberna, Marta; Navarro-Cano, Jose A; Verdú, Miguel

    2016-02-24

    Plants and soil microbes show parallel patterns of species-level diversity. Diverse plant communities release a wider range of organics that are consumed by more microbial species. We speculated, however, that diversity metrics accounting for the evolutionary distance across community members would reveal opposing patterns between plant and soil bacterial phylogenetic diversity. Plant phylogenetic diversity enhances plant productivity and thus expectedly soil fertility. This, in turn, might reduce bacterial phylogenetic diversity by favouring one (or a few) competitive bacterial clade. We collected topsoils in 15 semi-arid plant patches and adjacent low-cover areas configuring a plant phylodiversity gradient, pyrosequenced the 16S rRNA gene to identify bacterial taxa and analysed soil fertility parameters. Structural equation modelling showed positive effects of both plant richness and phylogenetic diversity on soil fertility. Fertility increased bacterial richness but reduced bacterial phylogenetic diversity. This might be attributed to the competitive dominance of a lineage based on its high relative fitness. This suggests biotic interactions as determinants of the soil bacterial community assembly, while emphasizing the need to use phylogeny-informed metrics to tease apart the processes underlying the patterns of diversity. PMID:26888037

  11. Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

    PubMed Central

    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

  12. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

    PubMed Central

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; Zhou, Jizhong

    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 patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. PMID:26242625

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

    PubMed Central

    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

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

    PubMed

    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

  15. Evidence for successional development in Antarctic hypolithic bacterial communities

    PubMed Central

    Makhalanyane, Thulani P; Valverde, Angel; Birkeland, Nils-Kåre; Cary, Stephen C; Marla Tuffin, I; Cowan, Don A

    2013-01-01

    Hypoliths (cryptic microbial assemblages that develop on the undersides of translucent rocks) are significant contributors to regional C and N budgets in both hot and cold deserts. Previous studies in the Dry Valleys of Eastern Antarctica have reported three morphologically distinct hypolithic community types: cyanobacteria dominated (type I), fungus dominated (type II) and moss dominated (type III). Here we present terminal-restriction fragment length polymorphism analyses to elucidate the bacterial community structure in hypolithons and the surrounding soils. We show clear and robust distinction in bacterial composition between bulk surface soils and hypolithons. Moreover, the bacterial assemblages were similar in types II and III hypolithons and clearly distinct from those found in type I. Through 16S rRNA gene 454 pyrosequencing, we show that Proteobacteria dominated all three types of hypolithic communities. As expected, Cyanobacteria were more abundant in type I hypolithons, whereas Actinobacteria were relatively more abundant in types II and III hypolithons, and were the dominant group in soils. Using a probabilistic dissimilarity metric and random sampling, we demonstrate that deterministic processes are more important in shaping the structure of the bacterial community found in types II and III hypolithons. Most notably, the data presented in this study suggest that hypolithic bacterial communities establish via a successional model, with the type I hypolithons acting as the basal development state. PMID:23765099

  16. Evidence for successional development in Antarctic hypolithic bacterial communities.

    PubMed

    Makhalanyane, Thulani P; Valverde, Angel; Birkeland, Nils-Kåre; Cary, Stephen C; Tuffin, I Marla; Cowan, Don A

    2013-11-01

    Hypoliths (cryptic microbial assemblages that develop on the undersides of translucent rocks) are significant contributors to regional C and N budgets in both hot and cold deserts. Previous studies in the Dry Valleys of Eastern Antarctica have reported three morphologically distinct hypolithic community types: cyanobacteria dominated (type I), fungus dominated (type II) and moss dominated (type III). Here we present terminal-restriction fragment length polymorphism analyses to elucidate the bacterial community structure in hypolithons and the surrounding soils. We show clear and robust distinction in bacterial composition between bulk surface soils and hypolithons. Moreover, the bacterial assemblages were similar in types II and III hypolithons and clearly distinct from those found in type I. Through 16S rRNA gene 454 pyrosequencing, we show that Proteobacteria dominated all three types of hypolithic communities. As expected, Cyanobacteria were more abundant in type I hypolithons, whereas Actinobacteria were relatively more abundant in types II and III hypolithons, and were the dominant group in soils. Using a probabilistic dissimilarity metric and random sampling, we demonstrate that deterministic processes are more important in shaping the structure of the bacterial community found in types II and III hypolithons. Most notably, the data presented in this study suggest that hypolithic bacterial communities establish via a successional model, with the type I hypolithons acting as the basal development state. PMID:23765099

  17. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant.

    PubMed

    Flowers, Jason J; Cadkin, Tracey A; McMahon, Katherine D

    2013-12-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = -0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. PMID:24200007

  18. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant

    PubMed Central

    Flowers, Jason J.; Cadkin, Tracey A.; McMahon, Katherine D.

    2014-01-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = –0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. PMID:24200007

  19. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    SciTech Connect

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; Zhou, Jizhong; Firestone, Mary

    2015-08-04

    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 patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal

  20. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    DOE PAGESBeta

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; et al

    2015-08-04

    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 patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

  1. Experimental sulfate amendment alters peatland bacterial community structure.

    PubMed

    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

  2. Topographic diversity of fungal and bacterial communities in human skin.

    PubMed

    Findley, Keisha; Oh, Julia; Yang, Joy; Conlan, Sean; Deming, Clayton; Meyer, Jennifer A; Schoenfeld, Deborah; Nomicos, Effie; Park, Morgan; Kong, Heidi H; Segre, Julia A

    2013-06-20

    Traditional culture-based methods have incompletely defined the microbial landscape of common recalcitrant human fungal skin diseases, including athlete's foot and toenail infections. Skin protects humans from invasion by pathogenic microorganisms and provides a home for diverse commensal microbiota. Bacterial genomic sequence data have generated novel hypotheses about species and community structures underlying human disorders. However, microbial diversity is not limited to bacteria; microorganisms such as fungi also have major roles in microbial community stability, human health and disease. Genomic methodologies to identify fungal species and communities have been limited compared with those that are available for bacteria. Fungal evolution can be reconstructed with phylogenetic markers, including ribosomal RNA gene regions and other highly conserved genes. Here we sequenced and analysed fungal communities of 14 skin sites in 10 healthy adults. Eleven core-body and arm sites were dominated by fungi of the genus Malassezia, with only species-level classifications revealing fungal-community composition differences between sites. By contrast, three foot sites--plantar heel, toenail and toe web--showed high fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that physiologic attributes and topography of skin differentially shape these two microbial communities. These results provide a framework for future investigation of the contribution of interactions between pathogenic and commensal fungal and bacterial communities to the maintainenace of human health and to disease pathogenesis. PMID:23698366

  3. Soil Bacterial Community Structure Responses to Precipitation Reduction and Forest Management in Forest Ecosystems across Germany

    PubMed Central

    Felsmann, Katja; Baudis, Mathias; Gimbel, Katharina; Kayler, Zachary E.; Ellerbrock, Ruth; Bruehlheide, Helge; Bruckhoff, Johannes; Welk, Erik; Puhlmann, Heike; Weiler, Markus; Gessler, Arthur; Ulrich, Andreas

    2015-01-01

    Soil microbial communities play an important role in forest ecosystem functioning, but how climate change will affect the community composition and consequently bacterial functions is poorly understood. We assessed the effects of reduced precipitation with the aim of simulating realistic future drought conditions for one growing season on the bacterial community and its relation to soil properties and forest management. We manipulated precipitation in beech and conifer forest plots managed at different levels of intensity in three different regions across Germany. The precipitation reduction decreased soil water content across the growing season by between 2 to 8% depending on plot and region. T-RFLP analysis and pyrosequencing of the 16S rRNA gene were used to study the total soil bacterial community and its active members after six months of precipitation reduction. The effect of reduced precipitation on the total bacterial community structure was negligible while significant effects could be observed for the active bacteria. However, the effect was secondary to the stronger influence of specific soil characteristics across the three regions and management selection of overstorey tree species and their respective understorey vegetation. The impact of reduced precipitation differed between the studied plots; however, we could not determine the particular parameters being able to modify the response of the active bacterial community among plots. We conclude that the moderate drought induced by the precipitation manipulation treatment started to affect the active but not the total bacterial community, which points to an adequate resistance of the soil microbial system over one growing season. PMID:25875835

  4. Architectural Design Drives the Biogeography of Indoor Bacterial Communities

    PubMed Central

    O’Connor, Timothy K.; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G. Z.; Bohannan, Brendan J. M.; Green, Jessica L.

    2014-01-01

    Background Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Results Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Conclusions Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our

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

    PubMed

    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

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

    PubMed Central

    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

  7. Comparison of rhizosphere bacterial communities in Arabidopsis thaliana mutants for systemic acquired resistance.

    PubMed

    Hein, John W; Wolfe, Gordon V; Blee, Kristopher A

    2008-02-01

    Systemic acquired resistance (SAR) is an inducible systemic plant defense against a broad spectrum of plant pathogens, with the potential to secrete antimicrobial compounds into the soil. However, its impact on rhizosphere bacteria is not known. In this study, we examined fingerprints of bacterial communities in the rhizosphere of the model plant Arabidopsis thaliana to determine the effect of SAR on bacterial community structure and diversity. We compared Arabidopsis mutants that are constitutive and non-inducible for SAR and verified SAR activation by measuring pathogenesis-related protein activity via a beta-glucoronidase (GUS) reporter construct driven by the beta-1-3 glucanase promoter. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of MspI- and HaeIII-digested 16S rDNA to estimate bacterial rhizosphere community diversity, with Lactobacillus sp. added as internal controls. T-RFLP analysis showed a clear rhizosphere effect on community structure, and diversity analysis of both rhizosphere and bulk soil operational taxonomic units (as defined by terminal restriction fragments) using richness, Shannon-Weiner, and Simpson's diversity indices and evenness confirmed that the presence of Arabidopsis roots significantly altered bacterial communities. This effect of altered soil microbial community structure by plants was also seen upon multivariate cluster analysis of the terminal restriction fragments. We also found visible differences in the rhizosphere community fingerprints of different Arabidopsis SAR mutants; however, there was no clear decrease of rhizosphere diversity because of constitutive SAR expression. Our study suggests that SAR can alter rhizosphere bacterial communities, opening the door to further understanding and application of inducible plant defense as a driving force in structuring soil bacterial assemblages. PMID:17619212

  8. The bacterial community of entomophilic nematodes and host beetles.

    PubMed

    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

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

    PubMed

    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

  10. The dual oxidase gene BdDuox regulates the intestinal bacterial community homeostasis of Bactrocera dorsalis.

    PubMed

    Yao, Zhichao; Wang, Ailin; Li, Yushan; Cai, Zhaohui; Lemaitre, Bruno; Zhang, Hongyu

    2016-05-01

    The guts of metazoans are in permanent contact with the microbial realm that includes beneficial symbionts, nonsymbionts, food-borne microbes and life-threatening pathogens. However, little is known concerning how host immunity affects gut bacterial community. Here, we analyze the role of a dual oxidase gene (BdDuox) in regulating the intestinal bacterial community homeostasis of the oriental fruit fly Bactrocera dorsalis. The results showed that knockdown of BdDuox led to an increased bacterial load, and to a decrease in the relative abundance of Enterobacteriaceae and Leuconostocaceae bacterial symbionts in the gut. The resulting dysbiosis, in turn, stimulates an immune response by activating BdDuox and promoting reactive oxygen species (ROS) production that regulates the composition and structure of the gut bacterial community to normal status by repressing the overgrowth of minor pathobionts. Our results suggest that BdDuox plays a pivotal role in regulating the homeostasis of the gut bacterial community in B. dorsalis. PMID:26565723

  11. Dynamics of size-fractionated bacterial communities during the coastal dispersal of treated municipal effluents.

    PubMed

    Liu, SiGuang; Luo, YuanRong; Huang, LingFeng

    2016-07-01

    Everyday huge amount of treated municipal wastewater is discharged into the coastal seawater. However, microbial biomarkers for the municipal effluent instead of the fecal species from raw sewage have not been proposed. Meanwhile, bacterial taxa for degrading large amounts of input organics have not been fully understood. In this study, raw effluent and serial water samples were collected from the coastal dispersal of two sewage treatment plants in Xiamen, China. Free-living (FL) and particle-associated (PA) bacterial communities were analyzed via high-throughput sequencing of 16S rRNA gene and quantitative PCR to measure bacterial abundance. The PA bacterial communities in our samples exhibited higher cell abundance, alpha diversity, and population dynamics than the FL bacterial communities, which supports greater environmental significance of the PA bacterial communities. Two non-fecal but typical genera in activated sludge, Zoogloea and Dechloromonas, exhibited decreased but readily detectable abundance along the effluent dispersal distance. Furthermore, the dominating microbial species near the outfalls were related to well-known marine indigenous taxa, such as SAR11 clade, OM60 clade, low-GC Actinobacteria, and unclassified Flavobacteriales, as well as the less understood taxa like Pseudohongiella and Microbacteriaceae. It is interesting that these taxa exhibited two types of correlation patterns with COD concentration. Our study suggested Zoogloea as a potential indicator of municipal effluents and also proposed potential utilizers of residual effluent COD in marine environments. PMID:26944731

  12. Soil bacterial communities associated with natural and commercial Cyclopia spp.

    PubMed

    Postma, Anneke; Slabbert, Etienne; Postma, Ferdinand; Jacobs, Karin

    2016-03-01

    The commercially important plants in the genus Cyclopia spp. are indigenous to the Cape Floristic Region of South Africa and are used to manufacture an herbal tea known as honeybush tea. Growing in the low nutrient fynbos soils, these plants are highly dependent on symbiotic interactions with soil microorganisms for nutrient acquisition. The aim of this study was to investigate the soil bacterial communities associated with two commercially important Cyclopia species, namely C. subternata and C. longifolia. Specific interest was the differences between rhizosphere and bulk soil collected from natural sites and commercially grown plants. Samples were collected on two occasions to include a dry summer and wet winter season. Results showed that the dominant bacterial taxa associated with these plants included Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria. Commercial and natural as well as rhizosphere and bulk soil samples were highly similar in bacterial diversity and species richness. Significant differences were detected in bacterial community structures and co-occurrence patterns between the wet and dry seasons. The results of this study improved our knowledge on what effect commercial Cyclopia plantations and seasonal changes can have on soil bacterial communities within the endemic fynbos biome. PMID:26850159

  13. Panamanian frog species host unique skin bacterial communities

    PubMed Central

    Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N.

    2015-01-01

    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 these skin symbiont

  14. Panamanian frog species host unique skin bacterial communities.

    PubMed

    Belden, Lisa K; Hughey, Myra C; Rebollar, Eria A; Umile, Thomas P; Loftus, Stephen C; Burzynski, Elizabeth A; Minbiole, Kevin P C; House, Leanna L; Jensen, Roderick V; Becker, Matthew H; Walke, Jenifer B; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N

    2015-01-01

    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 these skin symbiont

  15. Sediment Bacterial Communities Reflect the History of a Sea Basin

    PubMed Central

    Lyra, Christina; Sinkko, Hanna; Rantanen, Matias; Paulin, Lars; Kotilainen, Aarno

    2013-01-01

    How entire microbial communities are structured across stratified sediments from the historical standpoint is unknown. The Baltic Sea is an ideal research object for historical reconstruction, since it has experienced many fresh- and brackish water periods and is depleted of dissolved oxygen, which increases the sediment's preservation potential. We investigated the bacterial communities, chemical elements (e.g. Cr, Pb Na, P, Sr and U) and sediment composition in a stratified sediment core dated by radiocarbon and spanning 8000 years of Baltic Sea history, using up-to-date multivariate statistics. The communities were analysed by 16S rRNA gene terminal restriction fragment length polymorphism. The communities of the deep Early Litorina and surface Late Litorina Sea laminae were separated from the communities of the middle Litorina Sea laminae, which were associated with elevated concentrations of U and Sr trace elements, palaeo-oxygen and palaeosalinity proxies. Thus, the Litorina Sea laminae were characterized by past oxygen deficiency and salinity increase. The communities of the laminae, bioturbated and homogeneous sediments were differentiated, based on the same historical sea phases, with correct classifications of 90%. Palaeosalinity was one of the major parameters that separated the bacterial communities of the stratified sediments. A discontinuous spatial structure with a surprising increase in community heterogeneity was detected in Litorina Sea sediments from 388 to 422 cm deep, which suggests that a salinity maximum occurred in the central Gulf of Finland app. 6200–6600 years ago. The community heterogeneity decreased from the surface down to 306 cm, which reflected downcore mineralization. The plateau of the decrease was in the app. 2000-year-old sediment layers. Bacterial community data may be used as an additional tool in ocean-drilling projects, in which it is important to detect mineralization plateaus both to determine historically comparable

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

    PubMed

    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

  17. Different bacterial communities in ectomycorrhizae and surrounding soil

    PubMed Central

    Vik, Unni; Logares, Ramiro; Blaalid, Rakel; Halvorsen, Rune; Carlsen, Tor; Bakke, Ingrid; Kolstø, Anne-Brit; Økstad, Ole Andreas; Kauserud, Håvard

    2013-01-01

    Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis. PMID:24326907

  18. Marine bacterial communities are resistant to elevated carbon dioxide levels.

    PubMed

    Oliver, Anna E; Newbold, Lindsay K; Whiteley, Andrew S; van der Gast, Christopher J

    2014-12-01

    It is well established that the release of anthropogenic-derived CO2 into the atmosphere will be mainly absorbed by the oceans, with a concomitant drop in pH, a process termed ocean acidification. As such, there is considerable interest in how changes in increased CO2 and lower pH will affect marine biota, such as bacteria, which play central roles in oceanic biogeochemical processes. Set within an ecological framework, we investigated the direct effects of elevated CO2, contrasted with ambient conditions on the resistance and resilience of marine bacterial communities in a replicated temporal seawater mesocosm experiment. The results of the study strongly indicate that marine bacterial communities are highly resistant to the elevated CO2 and lower pH conditions imposed, as demonstrated from measures of turnover using taxa–time relationships and distance–decay relationships. In addition, no significant differences in community abundance, structure or composition were observed. Our results suggest that there are no direct effects on marine bacterial communities and that the bacterial fraction of microbial plankton holds enough flexibility and evolutionary capacity to withstand predicted future changes from elevated CO2 and subsequent ocean acidification. PMID:25756110

  19. Fungal and bacterial community structure downwind of a cattle feedyard

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soils provide a complex microhabitat for harboring a diverse group of microorganisms. The interaction of soil type, crop type, agroecosystem, and land management practices may all influence agricultural bacterial communities. In a previous study, we documented the long-term environmental impacts of ...

  20. Bacterial community diversity in municipal waste landfill sites.

    PubMed

    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. PMID:25981996

  1. Bacterial Communities of Two Ubiquitous Great Barrier Reef Corals Reveals Both Site- and Species-Specificity of Common Bacterial Associates

    PubMed Central

    Kvennefors, E. Charlotte E.; Sampayo, Eugenia; Ridgway, Tyrone; Barnes, Andrew C.; Hoegh-Guldberg, Ove

    2010-01-01

    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 invertebrate associates

  2. Distinct bacterial communities dominate tropical and temperate zone leaf litter.

    PubMed

    Kim, Mincheol; Kim, Woo-Sung; Tripathi, Binu M; Adams, Jonathan

    2014-05-01

    Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial

  3. Natural bacterial communities serve as quantitative geochemical biosensors

    DOE PAGESBeta

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; et al

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination,more » even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.« less

  4. Diversity of Bacterial Communities in Container Habitats of Mosquitoes

    PubMed Central

    Ponnusamy, Loganathan; Xu, Ning; Stav, Gil; Wesson, Dawn M.; Schal, Coby

    2010-01-01

    We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n=12), cemetery urns (n=23), and miscellaneous containers that included two tree holes (n=19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species. PMID:18373113

  5. Natural bacterial communities serve as quantitative geochemical biosensors

    SciTech Connect

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; Earles, Jennifer E.; Phillips, Jana; Techtmann, Steve M.; Joyner, Dominique C.; Elias, Dwayne A.; Bailey, Kathryn L.; Hurt, Richard A.; Preheim, Sarah P.; Sanders, Matthew C.; Yang, Joy; Mueller, Marcella A.; Brooks, Scott; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, Eric A.; Adams, Paul D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, Eric J.; Hazen, Terry C.

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.

  6. Suppression of Bacterial Blight by a Bacterial Community Isolated from the Guttation Fluids of Anthuriums†

    PubMed Central

    Fukui, R.; Fukui, H.; Alvarez, A. M.

    1999-01-01

    Growth and survival of Xanthomonas campestris pv. dieffenbachiae in guttation fluids (xylem sap exuded from leaf margins) of anthuriums were suppressed by several bacterial strains indigenous to leaves of various anthurium cultivars. Inhibition of growth was not observed in filter-sterilized guttation fluids and was restored to original levels only by reintroducing specific mixtures of bacteria into filter-sterilized guttation fluids. The inhibitory effect was related to the species in the bacterial community rather than to the total numbers of bacteria in the guttation fluids. One very effective bacterial community consisted of five species isolated from inhibitory guttation fluids of two susceptible anthurium cultivars. The individual strains in this community had no effect on the pathogen, but the mixture was inhibitory to X. campestris pv. dieffenbachiae in guttation fluids. The populations of the individual strains remained near the initial inoculum levels for at least 14 days. The effect of the five inhibitory strains on reducing disease in susceptible anthurium plants was tested by using a bioluminescent strain of X. campestris pv. dieffenbachiae to monitor the progression of disease in leaves nondestructively. Invasion of the pathogen through hydathodes at leaf margins was reduced by applying the strain mixture to the leaves. When the strain mixture was applied directly to wounds created on the leaf margins, the pathogen failed to invade through the wounds. This bacterial community has potential for biological control of anthurium blight. PMID:10049858

  7. Response of soil bacterial and fungal communities to summer drought and subsequent rainfall

    NASA Astrophysics Data System (ADS)

    Barnard, R. L.; Osborne, C.; Firestone, M. K.

    2011-12-01

    Rewetting of dry Mediterranean grasslands triggers a flush of carbon substrates, fueling a large soil CO2 pulse, which constitutes an important component of the annual carbon cycle in these ecosystems. However, little is known about the dynamics of activity and resource allocation of the soil microbial community over the dry summer period, which likely sets the stage for the rapid response upon rewetting. In three California grasslands, soil prokaryotic and fungal communities were assessed (by DNA- and RNA-based sequencing) several times over a summer to track changes in the soil microbial community characteristics. In a companion greenhouse-based study, soil from a California grassland was subjected to three different Spring-summer dry-down treatments over four months: weekly water inputs, weekly water inputs for two months followed by drought, and no water input. In both experiments, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were assessed over time by sequencing, and the abundance of selected genes determined by qPCR analysis. At the end of summer, soil CO2 efflux rates were determined during a controlled wet-up and the soil microbial community was also analyzed post-wet-up. In soil samples from the field, we found an overall increase in bacterial 16S DNA and fungal 28S DNA gene copies (but not of rRNA) over the summer. At each site, the composition of the RNA-based bacterial community changed significantly as summer drought progressed, then returned to pre-drought composition within several hours of rewetting. Upon rewetting, bacterial mRNA transcript copies significantly increased at all sites, reflecting rapid resumption of activity. In the Spring dry-down experiment, we found significantly more bacterial 16S DNA and fungal 28S DNA gene copies in the dry treatment than in the weekly-watered soil treatment. Upon rewetting, bacterial mRNA transcript copies increased dramatically in both treatments that

  8. Comparison of Bacterial Communities in Sands and Water at Beaches with Bacterial Water Quality Violations

    PubMed Central

    Halliday, Elizabeth; McLellan, Sandra L.; Amaral-Zettler, Linda A.; Sogin, Mitchell L.; Gast, Rebecca J.

    2014-01-01

    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. PMID:24599478

  9. Bacterial community composition in low-flowing river water with different sources of pollutants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pollution of water resources is a major risk to human health and water quality throughout the world. The purpose of this study was to determine the influence of pollutant sources from agricultural activities, urban runoffs, and runoffs from wastewater treatment plants (WWTPs) on bacterial communitie...

  10. Bacterial communities in the fruit bodies of ground basidiomycetes

    NASA Astrophysics Data System (ADS)

    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.

  11. Distinct Phyllosphere Bacterial Communities on Arabidopsis Wax Mutant Leaves

    PubMed Central

    Reisberg, Eva E.; Hildebrandt, Ulrich; Riederer, Markus; Hentschel, Ute

    2013-01-01

    The phyllosphere of plants is inhabited by diverse microorganisms, however, the factors shaping their community composition are not fully elucidated. The plant cuticle represents the initial contact surface between microorganisms and the plant. We thus aimed to investigate whether mutations in the cuticular wax biosynthesis would affect the diversity of the phyllosphere microbiota. A set of four Arabidopsis thaliana eceriferum mutants (cer1, cer6, cer9, cer16) and their respective wild type (Landsberg erecta) were subjected to an outdoor growth period and analysed towards this purpose. The chemical distinctness of the mutant wax phenotypes was confirmed by gas chromatographic measurements. Next generation amplicon pyrosequencing of the bacterial communities showed distinct community patterns. This observation was supported by denaturing gradient gel electrophoresis experiments. Microbial community analyses revealed bacterial phylotypes that were ubiquitously present on all plant lines (termed “core” community) while others were positively or negatively affected by the wax mutant phenotype (termed “plant line-specific“ community). We conclude from this study that plant cuticular wax composition can affect the community composition of phyllosphere bacteria. PMID:24223831

  12. Bacterial Community Analysis of Drinking Water Biofilms in Southern Sweden

    PubMed Central

    Lührig, Katharina; Canbäck, Björn; Paul, Catherine J.; Johansson, Tomas; Persson, Kenneth M.; Rådström, Peter

    2015-01-01

    Next-generation sequencing of the V1–V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82–87%), with 22–40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities. PMID:25739379

  13. The bacterial communities of Drosophila suzukii collected from undamaged cherries

    PubMed Central

    James, Pamela M.; Jospin, Guillaume; Lang, Jenna M.

    2014-01-01

    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. PMID:25101226

  14. Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate.

    PubMed

    Vila-Costa, Maria; Rinta-Kanto, Johanna M; Sun, Shulei; Sharma, Shalabh; Poretsky, Rachel; Moran, Mary Ann

    2010-11-01

    Dimethylsulfoniopropionate (DMSP) is an important source of reduced sulfur and carbon for marine microbial communities, as well as the precursor of the climate-active gas dimethylsulfide (DMS). In this study, we used metatranscriptomic sequencing to analyze gene expression profiles of a bacterial assemblage from surface waters at the Bermuda Atlantic Time-series Study (BATS) station with and without a short-term enrichment of DMSP (25 nM for 30 min). An average of 303 143 reads were obtained per treatment using 454 pyrosequencing technology, of which 51% were potential protein-encoding sequences. Transcripts from Gammaproteobacteria and Bacteroidetes increased in relative abundance on DMSP addition, yet there was little change in the contribution of two bacterioplankton groups whose cultured members harbor known DMSP degradation genes, Roseobacter and SAR11. The DMSP addition led to an enrichment of transcripts supporting heterotrophic activity, and a depletion of those encoding light-related energy generation. Genes for the degradation of C3 compounds were significantly overrepresented after DMSP addition, likely reflecting the metabolism of the C3 component of DMSP. Mapping these transcripts to known biochemical pathways indicated that both acetyl-CoA and succinyl-CoA may be common entry points of this moiety into the tricarboxylic acid cycle. In a short time frame (30 min) in the extremely oligotrophic Sargasso Sea, different gene expression patterns suggest the use of DMSP by a diversity of marine bacterioplankton as both carbon and sulfur sources. PMID:20463763

  15. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    PubMed Central

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-01-01

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact. PMID:25954263

  16. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    SciTech Connect

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

  17. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    DOE PAGESBeta

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes)more » in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.« less

  18. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests.

    PubMed

    Hesse, Cedar N; Mueller, Rebecca C; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D; Zak, Donald R; Kuske, Cheryl R

    2015-01-01

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact. PMID:25954263

  19. [Analysis of the bacterial community developing in the course of Sphagnum moss decomposition].

    PubMed

    Kulichevskaia, I S; Belova, S E; Kevbrin, V V; Dedysh, S N; Zavarzin, G A

    2007-01-01

    Slow degradation of organic matter in acidic Sphagnum peat bogs suggests a limited activity of organotrophic microorganisms. Monitoring of the Sphagnum debris decomposition in a laboratory simulation experiment showed that this process was accompanied by a shift in the water color to brownish due to accumulation of humic substances and by the development of a specific bacterial community with a density of 2.4 x 10(7) cells ml(-1). About half of these organisms are metabolically active and detectable with rRNA-specific oligonucleotide probes. Molecular identification of the components of this microbial community showed the numerical dominance of bacteria affiliated with the phyla Alphaproteobacteria, Actinobacteria, and Phanctomycetes. The population sizes of Firmicutes and Bacteroidetes, which are believed to be the main agents of bacterially-mediated decomposition in eutrophic wetlands, were low. The numbers of planctomycetes increased at the final stage of Sphagnum decomposition. The representative isolates of Alphaproteobacteria were able to utilize galacturonic acid, the only low-molecular-weight organic compound detected in the water samples; the representatives of Planctomycetes were able to decompose some heteropolysaccharides, which points to the possible functional role of these groups of microorganisms in the community under study. Thus, the composition of the bacterial community responsible for Sphagnum decomposition in acidic and low-mineral oligotrophic conditions seems to be fundamentally different from that of the bacterial community which decomposes plant debris in eutrophic ecosystems at neutral pH. PMID:18069332

  20. Bacterial communities involved in soil formation and plant establishment triggered by pyrite bioweathering on arctic moraines.

    PubMed

    Mapelli, Francesca; Marasco, Ramona; Rizzi, Agostino; Baldi, Franco; Ventura, Stefano; Daffonchio, Daniele; Borin, Sara

    2011-02-01

    In arctic glacier moraines, bioweathering primed by microbial iron oxidizers creates fertility gradients that accelerate soil development and plant establishment. With the aim of investigating the change of bacterial diversity in a pyrite-weathered gradient, we analyzed the composition of the bacterial communities involved in the process by sequencing 16S rRNA gene libraries from different biological soil crusts (BSC). Bacterial communities in three BSC of different morphology, located within 1 m distance downstream a pyritic conglomerate rock, were significantly diverse. The glacier moraine surrounding the weathered site showed wide phylogenetic diversity and high evenness with 15 represented bacterial classes, dominated by Alphaproteobacteria and pioneer Cyanobacteria colonizers. The bioweathered area showed the lowest diversity indexes and only nine bacterial families, largely dominated by Acidobacteriaceae and Acetobacteraceae typical of acidic environments, in accordance with the low pH of the BSC. In the weathered BSC, iron-oxidizing bacteria were cultivated, with counts decreasing along with the increase of distance from the rock, and nutrient release from the rock was revealed by environmental scanning electron microscopy-energy dispersive X-ray analyses. The vegetated area showed the presence of Actinomycetales, Verrucomicrobiales, Gemmatimonadales, Burkholderiales, and Rhizobiales, denoting a bacterial community typical of developed soils and indicating that the lithoid substrate of the bare moraine was here subjected to an accelerated colonization, driven by iron-oxidizing activity. PMID:20953598

  1. The effect of long-term nitrate treatment on SRB activity, corrosion rate and bacterial community composition in offshore water injection systems.

    PubMed

    Bødtker, Gunhild; Thorstenson, Tore; Lillebø, Bente-Lise P; Thorbjørnsen, Bente E; Ulvøen, Rikke Helen; Sunde, Egil; Torsvik, Terje

    2008-12-01

    Biogenic production of hydrogen sulphide (H(2)S) is a problem for the oil industry as it leads to corrosion and reservoir souring. Continuous injection of a low nitrate concentration (0.25-0.33 mM) replaced glutaraldehyde as corrosion and souring control at the Veslefrikk and Gullfaks oil field (North Sea) in 1999. The response to nitrate treatment was a rapid reduction in number and activity of sulphate-reducing bacteria (SRB) in the water injection system biofilm at both fields. The present long-term study shows that SRB activity has remained low at < or =0.3 and < or =0.9 microg H(2)S/cm(2)/day at Veslefrikk and Gullfaks respectively, during the 7-8 years with continuous nitrate injection. At Veslefrikk, 16S rRNA gene based community analysis by PCR-DGGE showed that bacteria affiliated to nitrate-reducing sulphide-oxidizing Sulfurimonas (NR-SOB) formed major populations at the injection well head throughout the treatment period. Downstream of deaerator the presence of Sulfurimonas like bacteria was less pronounced, and were no longer observed 40 months into the treatment period. The biofilm community during nitrate treatment was highly diverse and relative stable for long periods of time. At the Gullfaks field, a reduction in corrosion of up to 40% was observed after switch to nitrate treatment. The present study show that nitrate injection may provide a stable long-term inhibition of SRB in sea water injection systems, and that corrosion may be significantly reduced when compared to traditional biocide treatment. PMID:18752014

  2. Sulfate reducing bacterial community and in situ activity in mature fine tailings analyzed by real time qPCR and microsensor.

    PubMed

    Liu, Hong; Tan, Shuying; Yu, Tong; Liu, Yang

    2016-06-01

    Sulfate reducing bacteria (SRB) play significant roles in anaerobic environments in oil sands mature fine tailings (MFTs). Hydrogen sulfide (H2S) is produced during the biological sulfate reduction process. The production of toxic H2S is one of the concerns because it may hinder the landscape remediation efficiency of oil sands tailing ponds. In present study, the in situ activity and the community structure of SRB in MFT and gypsum amended MFT in two settling columns were investigated. Combined techniques of H2S microsensor and dissimilatory sulfite reductase β-subunit (dsrB) genes-based real time quantitative polymerase chain reaction (qPCR) were applied to detect the in situ H2S and the abundance of SRB. A higher diversity of SRB and more H2S were observed in gypsum amended MFT than that in MFT, indicating a higher sulfate reduction activity in gypsum amended MFT; in addition, the activity of SRB varied as depth in both MFT and gypsum amended MFT: the deeper the more H2S produced. Long-term plans for tailings management can be assessed more wisely with the information provided in this study. PMID:27266310

  3. Defined spatial structure stabilizes a synthetic multispecies bacterial community

    PubMed Central

    Kim, Hyun Jung; Boedicker, James Q.; Choi, Jang Wook; Ismagilov, Rustem F.

    2008-01-01

    This paper shows that for microbial communities, “fences make good neighbors.” Communities of soil microorganisms perform critical functions: controlling climate, enhancing crop production, and remediation of environmental contamination. Microbial communities in the oral cavity and the gut are of high biomedical interest. Understanding and harnessing the function of these communities is difficult: artificial microbial communities in the laboratory become unstable because of “winner-takes-all” competition among species. We constructed a community of three different species of wild-type soil bacteria with syntrophic interactions using a microfluidic device to control spatial structure and chemical communication. We found that defined microscale spatial structure is both necessary and sufficient for the stable coexistence of interacting bacterial species in the synthetic community. A mathematical model describes how spatial structure can balance the competition and positive interactions within the community, even when the rates of production and consumption of nutrients by species are mismatched, by exploiting nonlinearities of these processes. These findings provide experimental and modeling evidence for a class of communities that require microscale spatial structure for stability, and these results predict that controlling spatial structure may enable harnessing the function of natural and synthetic multispecies communities in the laboratory. PMID:19011107

  4. Bacterial RNAs activate innate immunity in Arabidopsis.

    PubMed

    Lee, Boyoung; Park, Yong-Soon; Lee, Soohyun; Song, Geun Cheol; Ryu, Choong-Min

    2016-01-01

    The common molecular patterns of microbes play a critical role in the regulation of plant innate immunity. However, little is known about the role of nucleic acids in this process in plants. We pre-infiltrated Arabidopsis leaves with total RNAs from Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) and subsequently inoculated these plants with the same bacterial cells. Total Pto DC3000 RNAs pre-infiltrated into Arabidopsis leaves elicited plant immune responses against Pto DC3000. However, sheared RNAs and RNase A application failed to induce immunity, suggesting that intact bacterial RNAs function in plant innate immunity. This notion was supported by the positive regulation of superoxide anion levels, callose deposition, two mitogen-activated protein kinases and defense-related genes observed in bacterial RNA-pre-treated leaves. Intriguingly, the Pto DC3000 population was not compromised in known pattern recognition receptor mutants for chitin, flagellin and elongation factor-Tu (EF-Tu). Plant defense-related mutant analyses further revealed that bacterial RNA-elicited innate immunity was normally required for salicylic and jasmonic acid signaling. Notably, among total RNAs, the abundant bacterial RNA species 16S and 23S ribosomal RNAs were the major determinants of this response. Our findings provide evidence that bacterial RNA serves as a microbe-associated molecular pattern in plants. PMID:26499893

  5. Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System.

    PubMed

    Jin, Di; Zhao, Shengguo; Wang, Pengpeng; Zheng, Nan; Bu, Dengpan; Beckers, Yves; Wang, Jiaqi

    2016-01-01

    Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants. PMID:27446045

  6. Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System

    PubMed Central

    Jin, Di; Zhao, Shengguo; Wang, Pengpeng; Zheng, Nan; Bu, Dengpan; Beckers, Yves; Wang, Jiaqi

    2016-01-01

    Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants. PMID:27446045

  7. Effects of benthic macrofauna bioturbation on the bacterial community composition in lake sediments.

    PubMed

    Zeng, Jin; Zhao, Da-Yong; Liu, Peng; Yu, Zhong-Bo; Huang, Rui; Wu, Qinglong L

    2014-08-01

    Benthic macrofauna are considered to be an important part of the lacustrine ecosystem, and bioturbation may greatly affect the biogeochemical processes and microbial activities in sediments. In the present study, the bacterial community composition in sediments inhabited by 3 different types of benthic macrofauna (Corbicula fluminea, Chironomidae larvae, and tubificid worms) in the shallow and eutrophic Lake Taihu was studied to investigate the different effects of bioturbation on the composition of these communities. Microcosms were constructed, and culture-independent methods, including terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis, were performed to evaluate the bacterial communities. Analysis of similarities (ANOSIM) and multidimensional scaling (MDS) analysis of T-RFLP patterns demonstrated that differences in the bacterial community composition between the control and the macrofauna-inhabited sediments were not as great as expected, although the chemical properties of the sediments changed remarkably. Nevertheless, the dominant bacterial group in each type of macrofauna-inhabited sediment was different. Acidobacteria, Betaproteobacteria, and Deltaproteobacteria were the dominant bacterial groups in sediments inhabited by C. fluminea, tubificid worms, and Chironomidae larvae, respectively. The data obtained in this study are helpful for understanding the effects of bioturbation in a shallow, eutrophic lake. PMID:25070418

  8. Algal exudates and stream organic matter influence the structure and function of denitrifying bacterial communities.

    PubMed

    Kalscheur, Kathryn N; Rojas, Miguel; Peterson, Christopher G; Kelly, John J; Gray, Kimberly A

    2012-11-01

    Within aquatic ecosystems, periphytic biofilms can be hot spots of denitrification, and previous work has suggested that algal taxa within periphyton can influence the species composition and activity of resident denitrifying bacteria. This study tested the hypothesis that algal species composition within biofilms influences the structure and function of associated denitrifying bacterial communities through the composition of organic exudates. A mixed population of bacteria was incubated with organic carbon isolated from one of seven algal species or from one of two streams that differed in anthropogenic inputs. Pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) revealed differences in the organic composition of algal exudates and stream waters, which, in turn, selected for distinct bacterial communities. Organic carbon source had a significant effect on potential denitrification rates (DNP) of the communities, with organics isolated from a stream with high anthropogenic inputs resulting in a bacterial community with the highest DNP. There was no correlation between DNP and numbers of denitrifiers (based on nirS copy numbers), but there was a strong relationship between the species composition of denitrifier communities (as indicated by tag pyrosequencing of nosZ genes) and DNP. Specifically, the relative abundance of Pseudomonas stutzeri-like nosZ sequences across treatments correlated significantly with DNP, and bacterial communities incubated with organic carbon from the stream with high anthropogenic inputs had the highest relative abundance of P. stutzeri-like nosZ sequences. These results demonstrate a significant relationship between bacterial community composition and function and provide evidence of the potential impacts of anthropogenic inputs on the structure and function of stream microbial communities. PMID:22828897

  9. Foliar bacterial communities of trembling aspen in a common garden.

    PubMed

    Mason, Charles J; Pfammatter, Jesse A; Holeski, Liza M; Raffa, Kenneth F

    2015-02-01

    Microbial associations with plants are widely distributed and are structured by a number of biotic and physical factors. Among biotic factors, the host plant genotype may be integral to these plant-microbe interactions. Trees in the genus Populus have become models for studies in scaling effects of host plant genetics and in plant-microbe interactions. Using 454 pyrosequencing of the 16S rRNA gene, we assessed the foliar bacterial community of 7 genotypes of mature trembling aspen trees (Populus tremuloides Michx.) grown in a common garden. Trees were selected based on prior analyses showing clonal variation in their concentration of chemicals conferring resistance against insect herbivores. At broad taxonomic designations, the bacterial community of trembling aspen was similar across all plant genotypes. At a finer taxonomic scale, the foliage of these trees varied in their community composition, but there was no distinct pattern to colonization or abundance related to plant genotype. The most abundant operational taxonomic units (OTUs) were classified as Ralstonia, Bradyrhizobium, Pseudomonas, and Brucella. These OTUs varied across the common garden, but there was no significant effect of host plant genotype or spatial position on the abundance of these members. Our results suggest that aspen genotype is less important in the structuring of its foliar bacterial communities than are other, poorly understood processes. PMID:25602743

  10. Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

    PubMed Central

    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

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

    PubMed

    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

  12. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  13. Metatranscriptomics reveals overall active bacterial composition in caries lesions

    PubMed Central

    Simón-Soro, Aurea; Guillen-Navarro, Miriam; Mira, Alex

    2014-01-01

    Background Identifying the microbial species in caries lesions is instrumental to determine the etiology of dental caries. However, a significant proportion of bacteria in carious lesions have not been cultured, and the use of molecular methods has been limited to DNA-based approaches, which detect both active and inactive or dead microorganisms. Objective To identify the RNA-based, metabolically active bacterial composition of caries lesions at different stages of disease progression in order to provide a list of potential etiological agents of tooth decay. Design Non-cavitated enamel caries lesions (n=15) and dentin caries lesions samples (n=12) were collected from 13 individuals. RNA was extracted and cDNA was constructed, which was used to amplify the 16S rRNA gene. The resulting 780 bp polymerase chain reaction products were pyrosequenced using Titanium-plus chemistry, and the sequences obtained were used to determine the bacterial composition. Results A mean of 4,900 sequences of the 16S rRNA gene with an average read length of 661 bp was obtained per sample, giving a comprehensive view of the active bacterial communities in caries lesions. Estimates of bacterial diversity indicate that the microbiota of cavities is highly complex, each sample containing between 70 and 400 metabolically active species. The composition of these bacterial consortia varied among individuals and between caries lesions of the same individuals. In addition, enamel and dentin lesions had a different bacterial makeup. Lactobacilli were found almost exclusively in dentin cavities. Streptococci accounted for 40% of the total active community in enamel caries, and 20% in dentin caries. However, Streptococcus mutans represented only 0.02–0.73% of the total bacterial community. Conclusions The data indicate that the etiology of dental caries is tissue dependent and that the disease has a clear polymicrobial origin. The low proportion of mutans streptococci detected confirms that they

  14. Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms

    PubMed Central

    Lalonde, Isabelle

    2015-01-01

    Surveys of the coxL gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of coxL sequences encompassing the atypical genotype coxL type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available coxL reference genome sequences, this unusual genotype was assigned to an unknown member of the Deltaproteobacteria, with the coxL sequence from Haliangium ochraceum being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the coxL group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of Deltaproteobacteria was too small to account for the abundance of the coxL group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of coxL genotypes and CO uptake activity in soil. We found that most of the coxL genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to Actinobacteria and Alphaproteobacteria. Our analysis did not provide any evidence that coxL group x genotypes belonged to Deltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical coxL group x genotype are mixotrophic K-strategists. PMID:26682854

  15. Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms.

    PubMed

    Lalonde, Isabelle; Constant, Philippe

    2016-02-01

    Surveys of the coxL gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of coxL sequences encompassing the atypical genotype coxL type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available coxL reference genome sequences, this unusual genotype was assigned to an unknown member of the Deltaproteobacteria, with the coxL sequence from Haliangium ochraceum being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the coxL group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of Deltaproteobacteria was too small to account for the abundance of the coxL group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of coxL genotypes and CO uptake activity in soil. We found that most of the coxL genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to Actinobacteria and Alphaproteobacteria. Our analysis did not provide any evidence that coxL group x genotypes belonged to Deltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical coxL group x genotype are mixotrophic K-strategists. PMID:26682854

  16. Process-driven bacterial community dynamics are key to cured meat colour formation by coagulase-negative staphylococci via nitrate reductase or nitric oxide synthase activities.

    PubMed

    Sánchez Mainar, María; Leroy, Frédéric

    2015-11-01

    The cured colour of European raw fermented meats is usually achieved by nitrate-into-nitrite reduction by coagulase-negative staphylococci (CNS), subsequently generating nitric oxide to form the relatively stable nitrosomyoglobin pigment. The present study aimed at comparing this classical curing procedure, based on nitrate reductase activity, with a potential alternative colour formation mechanism, based on nitric oxide synthase (NOS) activity, under different acidification profiles. To this end, meat models with and without added nitrate were fermented with cultures of an acidifying strain (Lactobacillus sakei CTC 494) and either a nitrate-reducing Staphylococcus carnosus strain or a rare NOS-positive CNS strain (Staphylococcus haemolyticus G110), or by relying on the background microbiota. Satisfactory colour was obtained in the models prepared with added nitrate and S. carnosus. In the presence of nitrate but absence of added CNS, however, cured colour was only obtained when L. sakei CTC 494 was also omitted. This was ascribed to the pH dependency of the emerging CNS background microbiota, selecting for nitrate-reducing Staphylococcus equorum strains at mild acidification conditions but for Staphylococcus saprophyticus strains with poor colour formation capability when the pH decrease was more rapid. This reliance of colour formation on the composition of the background microbiota was further explored by a side experiment, demonstrating the heterogeneity in nitrate reduction of a set of 88 CNS strains from different species. Finally, in all batches prepared with S. haemolyticus G110, colour generation failed as the strain was systematically outcompeted by the background microbiota, even when imposing milder acidification profiles. Thus, when aiming at colour formation through CNS metabolism, technological processing can severely interfere with the composition and functionality of the meat-associated CNS communities, for both nitrate reductase and NOS activities

  17. Bacterial diversity and community composition from seasurface to subseafloor

    PubMed Central

    Walsh, Emily A; Kirkpatrick, John B; Rutherford, Scott D; Smith, David C; Sogin, Mitchell; D'Hondt, Steven

    2016-01-01

    We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment. PMID:26430855

  18. Bacterial diversity and community composition from seasurface to subseafloor.

    PubMed

    Walsh, Emily A; Kirkpatrick, John B; Rutherford, Scott D; Smith, David C; Sogin, Mitchell; D'Hondt, Steven

    2016-04-01

    We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450,104 pyrotags representing 29,814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment. PMID:26430855

  19. Influence of influent wastewater communities on temporal variation of activated sludge communities.

    PubMed

    Lee, Sang-Hoon; Kang, Hyun-Jin; Park, Hee-Deung

    2015-04-15

    Continuously feeding influent wastewater containing diverse bacterial species to a wastewater treatment activated sludge bioreactor may influence the activated sludge bacterial community temporal dynamics. To explore this possibility, this study tracked influent wastewater and activated sludge bacterial communities by pyrosequencing 16S rRNA genes from four full-scale wastewater treatment plants over a 9-month period. The activated sludge communities showed significantly higher richness and evenness than the influent wastewater communities. Furthermore, the two communities were different in composition and temporal dynamics. These results demonstrate that the impact of the influent wastewater communities on the activated sludge communities was weak. Nevertheless, 4.3-9.3% of the operational taxonomic units (OTUs) detected in the activated sludge were shared with the influent wastewater, implying contribution from influent wastewater communities to some extent. However, the relative OTU abundance of the influent wastewater was not maintained in the activated sludge communities (i.e., weak neutral assembly). In addition, the variability of the communities of the shared OTUs was moderately correlated with abiotic factors imposed to the bioreactors. Taken together, temporal dynamics of activated sludge communities appear to be predominantly explained by species sorting processes in response to influent wastewater communities. PMID:25655320

  20. Assessing the diversity of bacterial communities associated with plants

    PubMed Central

    Andreote, Fernando Dini; Azevedo, João Lúcio; Araújo, Welington Luiz

    2009-01-01

    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. PMID:24031382

  1. Response of soil bacterial community to metal nanoparticles in biosolids.

    PubMed

    Shah, Vishal; Jones, Jamilee; Dickman, Jenifer; Greenman, Steven

    2014-06-15

    The increasing use of engineered nanoparticles (NPs) in industrial and household applications will very likely lead to the increased release of such materials into the public sewer systems. During the wastewater treatment process, some fraction of NPs would always be concentrated in the biosolids. When biosolids is applied on the agricultural land, NPs are introduced into the soil matrix. In the current study we investigate the influence of five different metal nanoparticles present in biosolids on soil microbial community as a function of time. Results indicate that ZnO and Zero Valent Cu NPs were not toxic to soil bacterial community. Biosolids mixed with Ag NPs and TiO2 (both anatase and rutile phase) in contrast changed the bacterial richness and composition in wavering pattern as a function of time. Based on the observations made in the study, we suggest caution when interpreting the toxicity of NPs based on single time point study. PMID:24801897

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

    PubMed Central

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

    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 phylogenetic analysis, the cloned sequences were placed into several major lineages of the Bacteria domain: the Flexibacter/Cytophaga/Bacteroides phylum and the α, β, and γ subdivisions of the phylum Proteobacteria. Analysis at the subphylum level revealed that the majority of our sequences were not closely affiliated with those of known, cultured taxa, although the estimated evolutionary distances between our sequences and their nearest neighbors were always less than 0.1 (i.e., greater than 90% similar). This result suggests that the majority of sequences obtained in this study represent as yet phenotypically undescribed bacterial species and that the range of bacterial-algal interactions that occur in nature has not yet been fully described. PMID:9797295

  3. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    SciTech Connect

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  4. Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators

    PubMed Central

    Wu, Cindy H.; Sercu, Bram; Van De Werfhorst, Laurie C.; Wong, Jakk; DeSantis, Todd Z.; Brodie, Eoin L.; Hazen, Terry C.; Holden, Patricia A.; Andersen, Gary L.

    2010-01-01

    Background Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Methodology/Principal Findings Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and α-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC∶A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. Conclusions/Significance This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health. PMID:20585654

  5. Changes in bacterial community structure in a full-scale membrane bioreactor for municipal wastewater treatment.

    PubMed

    Hashimoto, Kurumi; Tsutsui, Hirofumi; Takada, Kazuki; Hamada, Hiroshi; Sakai, Kousuke; Inoue, Daisuke; Sei, Kazunari; Soda, Satoshi; Yamashita, Kyoko; Tsuji, Koji; Hashimoto, Toshikazu; Ike, Michihiko

    2016-07-01

    This study investigated changes in the structure and metabolic capabilities of the bacterial community in a full-scale membrane bioreactor (MBR) treating municipal wastewater. Microbial monitoring was also conducted for a parallel-running conventional activated sludge (CAS) process treating the same influent. The mixed-liquor suspended solid concentration in the MBR reached a steady-state on day 73 after the start-up. Then the MBR maintained higher rates of removal of organic compounds and nitrogen than the CAS process did. Terminal restriction fragment length polymorphism analysis revealed that the bacterial community structure in the MBR was similar to that in the CAS process at the start-up, but it became very different from that in the CAS process in the steady state. The bacterial community structure of the MBR continued to change dynamically even after 20 months of the steady-state operation, while that of the CAS process was maintained in a stable condition. By contrast, Biolog assay revealed that the carbon source utilization potential of the MBR resembled that of the CAS process as a whole, although it declined transiently. Overall, the results indicate that the bacterial community of the MBR has flexibility in terms of its phylogenetic structure and metabolic activity to maintain the high wastewater treatment capability. PMID:26811223

  6. Bacterial Heat Shock Protein Activity

    PubMed Central

    Maleki, Farajollah; Khosravi, Afra; Nasser, Ahmad; Taghinejad, Hamid

    2016-01-01

    Bacteria are exposed to different types of stress in their growth conditions. They have developed appropriate responses, modulated by the re-modeling of protein complexes and by phosphorylation dependent signal transduction systems, to adapt and to survive in a variety range of nature. Proteins are essential components for biologic activity in the eukaryotic and prokaryotic cell. Heat Shock Proteins (HSP) have been identified from various organisms and have critical role in cell hemostasis. Chaperone can sense environment and have different potential role in the organism evolution. PMID:27134861

  7. Propachlor degradation by a soil bacterial community.

    PubMed Central

    Villarreal, D T; Turco, R F; Konopka, A

    1991-01-01

    Soil from a pesticide disposal site was used to enrich for microorganisms that degraded the acylanilide herbicide propachlor (2-chloro-N-isopropylacetanilide). After seven transfers of the enrichment, the culture contained about six strains. The highest yield of microbial biomass occurred if just two of these isolates, strains DAK3 and MAB2, were inoculated into a mineral salts medium containing propachlor. When only strain DAK3 was grown on propachlor, a metabolite (2-chloro-N-isopropylacetamide) was released into the medium. Strain MAB2 could grow on this metabolite. The results of morphological and physiological tests suggest that strains DAK3 and MAB2 most closely resemble species belonging to the genera Moraxella and Xanthobacter, respectively. Strain DAK3 can respire and grow on N-substituted acylanilides containing methyl, ethyl, or isopropyl substitutions, but is incapable of respiration or growth on acetanilide, aniline, or the acylanilide herbicides alachlor and metolachlor. Strain DAK3 appears to use the aromatic C atoms of propachlor for growth, as suggested by the growth yield on propachlor and the induction of catechol 2,3-oxygenase activity in acylanilide-grown cells. PMID:1768085

  8. Propachlor degradation by a soil bacterial community.

    PubMed

    Villarreal, D T; Turco, R F; Konopka, A

    1991-08-01

    Soil from a pesticide disposal site was used to enrich for microorganisms that degraded the acylanilide herbicide propachlor (2-chloro-N-isopropylacetanilide). After seven transfers of the enrichment, the culture contained about six strains. The highest yield of microbial biomass occurred if just two of these isolates, strains DAK3 and MAB2, were inoculated into a mineral salts medium containing propachlor. When only strain DAK3 was grown on propachlor, a metabolite (2-chloro-N-isopropylacetamide) was released into the medium. Strain MAB2 could grow on this metabolite. The results of morphological and physiological tests suggest that strains DAK3 and MAB2 most closely resemble species belonging to the genera Moraxella and Xanthobacter, respectively. Strain DAK3 can respire and grow on N-substituted acylanilides containing methyl, ethyl, or isopropyl substitutions, but is incapable of respiration or growth on acetanilide, aniline, or the acylanilide herbicides alachlor and metolachlor. Strain DAK3 appears to use the aromatic C atoms of propachlor for growth, as suggested by the growth yield on propachlor and the induction of catechol 2,3-oxygenase activity in acylanilide-grown cells. PMID:1768085

  9. Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

    PubMed Central

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; Earles, Jennifer E.; Phillips, Jana; Techtmann, Steve M.; Joyner, Dominique C.; Elias, Dwayne A.; Bailey, Kathryn L.; Hurt, Richard A.; Preheim, Sarah P.; Sanders, Matthew C.; Yang, Joy; Mueller, Marcella A.; Brooks, Scott; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, Eric A.; Adams, Paul D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, Eric J.

    2015-01-01

    ABSTRACT Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. PMID:25968645

  10. Changes in the bacterial community structure in stored wormbed leachate.

    PubMed

    Romero-Tepal, Elda M; Contreras-Blancas, Eduardo; Navarro-Noya, Yendi E; Ruíz-Valdiviezo, Víctor M; Luna-Guido, Marco; Gutiérrez-Miceli, Federico A; Dendooven, Luc

    2014-01-01

    Organic wastes, such as cow manure, are often composted with earthworms (vermicomposting) while excess water is drained and collected. This wormbed leachate is nutrient-rich and it has been extensively used to fertilize plants. However, it is derived partially from a not yet finished compost process and could exhibit phytotoxicity or contain potentially hazardous microorganisms. The bacterial community in wormbed leachate derived from vermicomposting of cow manure was studied by pyrosequencing the 16S rRNA gene. The fresh wormbed leachate was rich in Mollicutes, particularly the genus Acholeplasma which contain phytopathogen species. The abundance of the Mollicutes decreased when the leachate was stored, while that of the Rhizobiales and the genus Pseudomonas increased. The bacterial communities changed rapidly in the leachate during storage. The changes in ammonium, nitrate and inorganic carbon content of the wormbed leachate when stored were correlated to changes in the bacterial community structure. It was found that storage of the wormbed leachate might be required before it can be applied to crops as large proportions of potentially plant pathogens were found in the fresh leachate. PMID:24577291

  11. Dynamics and functions of bacterial communities in bark, charcoal and sand filters treating greywater.

    PubMed

    Dalahmeh, Sahar S; Jönsson, Håkan; Hylander, Lars D; Hui, Nan; Yu, Dan; Pell, Mikael

    2014-05-01

    This study explored the effects of greywater application on the dynamics and functions of biofilms developed in bark, activated charcoal and sand filters used for removal of organic matter and nitrogen. Duplicate columns (20 cm diameter, 60 cm deep) were packed with bark, charcoal or sand with effective size 1.4 mm and uniformity coefficient 2.2, and dosed with 32 L m(-2) day(-1) of an artificial greywater (14 g BOD5 m(-2) day(-1)) for 116 days. Potential respiration rate (PRR), determined in filter samples after addition of excess glucose, and bacterial diversity and composition, analysed by 454-pyrosequencing of bacterial 16S ribosomal DNA, were measured at different times and depths in the filters. The bark and charcoal filters were more efficient in removing BOD5 than the sand (98, 97% and 75%, respectively). The highest PRR in the 0-2 cm layer of the columns on day 84 was found in the bark filters, followed by the charcoal and sand filters (632 ± 66, 222 ± 34 and 56 ± 2 mg O2 L(-1), respectively; n = 2). Bacterial community in the bark filters showed the highest richness. The charcoal and sand filters both developed more diverse and dynamic (changing over time and depth) bacterial communities than the bark. In addition to the greywater, the lignocelluosic composition of the bark and its lower pH probably selected for the bacterial community structure and the organic content provided additional substrate, as shown by its higher PRR and its different nitrifying bacterial genera. In the oligotrophic charcoal and sand, the composition of the greywater itself defined the bacterial community. Thus, the initially low bacterial biomass in the latter filters was enriched over time, allowing a diversified bacterial community to develop. The top layers of the bark and charcoal filters displayed a high dominance of Rhizobium, Pseudomonas and Acinetobacter, which were less evident in the 60 cm layer, whereas in the sand filters these genera were

  12. Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis▿ †

    PubMed Central

    Oakley, Brian B.; Fiedler, Tina L.; Marrazzo, Jeanne M.; Fredricks, David N.

    2008-01-01

    Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 ± 0.7 versus 5.2 ± 0.75 (mean ± standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities. PMID:18487399

  13. Environmental Factors Shape Sediment Anammox Bacterial Communities in Hypernutrified Jiaozhou Bay, China▿ †

    PubMed Central

    Dang, Hongyue; Chen, Ruipeng; Wang, Lin; Guo, Lizhong; Chen, Pingping; Tang, Zuwang; Tian, Fang; Li, Shaozheng; Klotz, Martin G.

    2010-01-01

    Bacterial anaerobic ammonium oxidation (anammox) is an important process in the marine nitrogen cycle. Because ongoing eutrophication of coastal bays contributes significantly to the formation of low-oxygen zones, monitoring of the anammox bacterial community offers a unique opportunity for assessment of anthropogenic perturbations in these environments. The current study used targeting of 16S rRNA and hzo genes to characterize the composition and structure of the anammox bacterial community in the sediments of the eutrophic Jiaozhou Bay, thereby unraveling their diversity, abundance, and distribution. Abundance and distribution of hzo genes revealed a greater taxonomic diversity in Jiaozhou Bay, including several novel clades of anammox bacteria. In contrast, the targeting of 16S rRNA genes verified the presence of only “Candidatus Scalindua,” albeit with a high microdiversity. The genus “Ca. Scalindua” comprised the apparent majority of active sediment anammox bacteria. Multivariate statistical analyses indicated a heterogeneous distribution of the anammox bacterial assemblages in Jiaozhou Bay. Of all environmental parameters investigated, sediment organic C/organic N (OrgC/OrgN), nitrite concentration, and sediment median grain size were found to impact the composition, structure, and distribution of the sediment anammox bacterial community. Analysis of Pearson correlations between environmental factors and abundance of 16S rRNA and hzo genes as determined by fluorescent real-time PCR suggests that the local nitrite concentration is the key regulator of the abundance of anammox bacteria in Jiaozhou Bay sediments. PMID:20833786

  14. Endosymbiont Dominated Bacterial Communities in a Dwarf Spider

    PubMed Central

    Vanthournout, Bram; Hendrickx, Frederik

    2015-01-01

    The microbial community of spiders is little known, with previous studies focussing primarily on the medical importance of spiders as vectors of pathogenic bacteria and on the screening of known cytoplasmic endosymbiont bacteria. These screening studies have been performed by means of specific primers that only amplify a selective set of endosymbionts, hampering the detection of unreported species in spiders. In order to have a more complete overview of the bacterial species that can be present in spiders, we applied a combination of a cloning assay, DGGE profiling and high-throughput sequencing on multiple individuals of the dwarf spider Oedothorax gibbosus. This revealed a co-infection of at least three known (Wolbachia, Rickettsia and Cardinium) and the detection of a previously unreported endosymbiont bacterium (Rhabdochlamydia) in spiders. 16S rRNA gene sequences of Rhabdochlamydia matched closely with those of Candidatus R. porcellionis, which is currently only reported as a pathogen from a woodlouse and with Candidatus R. crassificans reported from a cockroach. Remarkably, this bacterium appears to present in very high proportions in one of the two populations only, with all investigated females being infected. We also recovered Acinetobacter in high abundance in one individual. In total, more than 99% of approximately 4.5M high-throughput sequencing reads were restricted to these five bacterial species. In contrast to previously reported screening studies of terrestrial arthropods, our results suggest that the bacterial communities in this spider species are dominated by, or even restricted to endosymbiont bacteria. Given the high prevalence of endosymbiont species in spiders, this bacterial community pattern could be widespread in the Araneae order. PMID:25706947

  15. Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions.

    PubMed

    Hiller, Kenly A; Foreman, Kenneth H; Weisman, David; Bowen, Jennifer L

    2015-10-01

    Permeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole. PMID:26231655

  16. Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions

    PubMed Central

    Hiller, Kenly A.; Foreman, Kenneth H.; Weisman, David

    2015-01-01

    Permeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole. PMID:26231655

  17. Bacterial Endophytic Communities in the Grapevine Depend on Pest Management

    PubMed Central

    Campisano, Andrea; Antonielli, Livio; Pancher, Michael; Yousaf, Sohail; Pindo, Massimo; Pertot, Ilaria

    2014-01-01

    Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars. PMID:25387008

  18. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    PubMed

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community. PMID:26580738

  19. Bacterial endophytic communities in the grapevine depend on pest management.

    PubMed

    Campisano, Andrea; Antonielli, Livio; Pancher, Michael; Yousaf, Sohail; Pindo, Massimo; Pertot, Ilaria

    2014-01-01

    Microbial plant endophytes are receiving ever-increasing attention as a result of compelling evidence regarding functional interaction with the host plant. Microbial communities in plants were recently reported to be influenced by numerous environmental and anthropogenic factors, including soil and pest management. In this study we used automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and pyrosequencing of 16S rDNA to assess the effect of organic production and integrated pest management (IPM) on bacterial endophytic communities in two widespread grapevines cultivars (Merlot and Chardonnay). High levels of the dominant Ralstonia, Burkholderia and Pseudomonas genera were detected in all the samples We found differences in the composition of endophytic communities in grapevines cultivated using organic production and IPM. Operational taxonomic units (OTUs) assigned to the Mesorhizobium, Caulobacter and Staphylococcus genera were relatively more abundant in plants from organic vineyards, while Ralstonia, Burkholderia and Stenotrophomonas were more abundant in grapevines from IPM vineyards. Minor differences in bacterial endophytic communities were also found in the grapevines of the two cultivars. PMID:25387008

  20. Deodorants and antiperspirants affect the axillary bacterial community.

    PubMed

    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

  1. Composition and Metabolic Activities of the Bacterial Community in Shrimp Sauce at the Flavor-Forming Stage of Fermentation As Revealed by Metatranscriptome and 16S rRNA Gene Sequencings.

    PubMed

    Duan, Shan; Hu, Xiaoxi; Li, Mengru; Miao, Jianyin; Du, Jinghe; Wu, Rongli

    2016-03-30

    The bacterial community and the metabolic activities involved at the flavor-forming stage during the fermentation of shrimp sauce were investigated using metatranscriptome and 16S rRNA gene sequencings. Results showed that the abundance of Tetragenococcus was 95.1%. Tetragenococcus halophilus was identified in 520 of 588 transcripts annotated in the Nr database. Activation of the citrate cycle and oxidative phosphorylation, along with the absence of lactate dehydrogenase gene expression, in T. halophilus suggests that T. halophilus probably underwent aerobic metabolism during shrimp sauce fermentation. The metabolism of amino acids, production of peptidase, and degradation of limonene and pinene were very active in T. halophilus. Carnobacterium, Pseudomonas, Escherichia, Staphylococcus, Bacillus, and Clostridium were also metabolically active, although present in very small populations. Enterococcus, Abiotrophia, Streptococcus, and Lactobacillus were detected in metatranscriptome sequencing, but not in 16S rRNA gene sequencing. Many minor taxa showed no gene expression, suggesting that they were in dormant status. PMID:26978261

  2. Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage

    PubMed Central

    Breidenbach, Björn; Conrad, Ralf

    2015-01-01

    We studied the resident (16S rDNA) and the active (16S rRNA) members of soil archaeal and bacterial communities during rice plant development by sampling three growth stages (vegetative, reproductive and maturity) under field conditions. Additionally, the microbial community was investigated in two non-flooded fields (unplanted, cultivated with upland maize) in order to monitor the reaction of the microbial communities to non-flooded, dry conditions. The abundance of Bacteria and Archaea was monitored by quantitative PCR showing an increase in 16S rDNA during reproductive stage and stable 16S rRNA copies throughout the growth season. Community profiling by T-RFLP indicated a relatively stable composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the two non-flooded fields with flooded rice fields showed that the community composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded vs. flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes) was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management. PMID:25620960

  3. Hg bioavailability and impact on bacterial communities in a long-term polluted soil.

    PubMed

    Ruggiero, P; Terzano, R; Spagnuolo, M; Cavalca, L; Colombo, M; Andreoni, V; Rao, M A; Perucci, P; Monaci, E

    2011-01-01

    Different soil samples characterised by a long-term Hg-pollution were studied for Hg total content, fractionation, phytotoxicity and influence on the bacterial community. Hg pollution ranged from 1 to 50 mg kg(-1) and most of it was speciated in scarcely soluble forms. In agreement with this, the biochemical quality indexes were investigated (biomass, enzyme activities) and the bacterial community (viable heterotrophic (VH) bacteria, functional diversity) apparently was not influenced by the degree of Hg pollution. In particular, the investigated soils exhibited a low percentage of Hg-resistant (Hg(R)) bacteria ranging from less than 0.001% to 0.25% of the VH and the addition of available Hg in the form of HgCl(2) induced an enrichment of resistant Hg(R) populations. The general biodiversity of the bacterial community was evaluated by denaturing gradient gel electrophoresis of DNA of Hg spiked soil microcosms and of control soils. Hg(R) bacteria capable to grow in a minimal medium containing HgCl(2) were also isolated and identified. MerA and merB gene PCR fragments were obtained from different Hg(R) strains and the range of similarities at the DNA level and at the deduced amino acid level showed that they carried mercuric reductase and lyase. Differently from bacteria, some influence of soil Hg content on seeds' germination and root elongation was observed for Lepidium sativum L. and Solanum lycopersicum L. In conclusion, most of the Hg in these long-term polluted soils was scarcely mobile and available and did not significantly influence the soil bacterial community. The risk of potential Hg remobilization over time, that could be naturally favoured by the activity of plant roots or other inorganic processes occurring in soil, can be extenuated since bacterial community was resistant and resilient to subsequent Hg stress. PMID:21060931

  4. High Concentrations of Methyl Fluoride Affect the Bacterial Community in a Thermophilic Methanogenic Sludge

    PubMed Central

    Hao, Liping; Lü, Fan; Wu, Qing; Shao, Liming; He, Pinjing

    2014-01-01

    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. PMID:24658656

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

    PubMed Central

    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

  6. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

    PubMed

    Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G; Tang, Sen-Lin

    2016-01-01

    Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches. PMID:26934492

  7. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia

    PubMed Central

    Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G.; Tang, Sen-Lin

    2016-01-01

    Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches. PMID:26934492

  8. Effect of copper tolerant Elsholtzia splendens on bacterial community associated with Commelina communis on a copper mine spoil.

    PubMed

    Yang, Ruyi; Guo, Fuyu; Li, Jing; Su, Nannan; Shao, Zongyuan; Zan, Shuting

    2016-08-01

    Facilitation, or positive plant-plant interaction, has received increasing concern from ecologists over the last two decades. Facilitation may occur through direct mitigation of severe environments or indirect mediation by a third participant from the same or different trophic levels. The copper (Cu) tolerant species Elsholtzia splendens facilitates the establishment and growth of co-occurring Commelina communis through indirect enrichment of microbial activity. However, whether and how E. splendens impacts the microbial community that is associated with C. communis is less known. We characterized the soil bacterial community in the rhizosphere of C. communis in the absence and presence of E. splendens using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and sequencing. The result showed that the richness of the bacterial community increased, but diversity and evenness remained similar, in the presence of E. splendens. Chloroflexi, Acidobacteria and Proteobacteria were the most dominant bacteria. The relative abundance of dominant and minor bacterial groups showed distinctly different responses to E. splendens. Principal component analysis and redundancy analysis indicated that variation of the bacterial community was determined by multiple factors and might be driven by the tested soil parameters collectively, or alternatively changed through plant root exudates or other microorganisms. Our results enhance the understanding of how the bacterial community associated with a beneficiary plant responds to a benefactor plant and suggests that the changes of bacterial community composition may have far-reaching influence on plant-soil feedback and the aboveground plant community in the long run. PMID:27521948

  9. Bacterial community structure in aquifers corresponds to stratigraphy

    NASA Astrophysics Data System (ADS)

    Beyer, Andrea; Möller, Silke; Neumann, Stefan; Burow, Katja; Gutmann, Falko; Lindner, Julia; Müsse, Steffen; Kothe, Erika; Büchel, Georg

    2014-05-01

    So far, groundwater microbiology with respect to different host rocks has not been well described in the literature. However, factors influencing the communities would be of interest to provide a tool for mapping groundwater paths. The Thuringian Basin (Germany) studied here, contains formations of the Permian (Zechstein) and also Triassic period of Buntsandstein, Muschelkalk and Keuper, all of which can be found to crop out at the surface in different regions. We analyzed the bacterial community of nine natural springs and sixteen groundwater wells of the respective rock formations as well as core material from the Zechstein salts. For that we sampled in a mine 3 differnet salt rock samples (carnallitite, halite and sylvinitite). To validate the different approaches, similar rock formations were compared and a consistent microbial community for Buntsandstein could be verified. Similary, for Zechstein, the presence of halophiles was seen with cultivation, isolation directly from the rock material and also in groundwater with DNA-dependent approaches. A higher overlap between sandstone- and limestone-derived communities was visible as if compared to the salt formations. Principal component analysis confirmed formation specific patterns for Muschelkalk, Buntsandstein and Zechstein for the bacterial taxa present, with some overlaps. Bacilli and Gammaproteobacteria were the major groups, with the genera Pseudomonas, Marinomonas, Bacillus, Marinobacter and Pseudoalteromonas representing the communities. The bacteria are well adapted to their respective environment with survival strategies including a wide range of salinity which makes them suitable as tracers for fluid movement below the ground. The results indicate the usefulness and robustness of the approach taken here to investigate aquifer community structures in dependence of the stratigraphy of the groundwater reservoir.

  10. Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil*

    PubMed Central

    Zhang, Shu-ying; Wang, Qing-feng; Wan, Rui; Xie, Shu-guang

    2011-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role. PMID:21887852

  11. Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil.

    PubMed

    Zhang, Shu-ying; Wang, Qing-feng; Wan, Rui; Xie, Shu-guang

    2011-09-01

    Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role. PMID:21887852

  12. Twenty Years of Active Bacterial Core Surveillance

    PubMed Central

    Schaffner, William; Farley, Monica M.; Lynfield, Ruth; Bennett, Nancy M.; Reingold, Arthur; Thomas, Ann; Harrison, Lee H.; Nichols, Megin; Petit, Susan; Miller, Lisa; Moore, Matthew R.; Schrag, Stephanie J.; Lessa, Fernanda C.; Skoff, Tami H.; MacNeil, Jessica R.; Briere, Elizabeth C.; Weston, Emily J.; Van Beneden, Chris

    2015-01-01

    Active Bacterial Core surveillance (ABCs) was established in 1995 as part of the Centers for Disease Control and Prevention Emerging Infections Program (EIP) network to assess the extent of invasive bacterial infections of public health importance. ABCs is distinctive among surveillance systems because of its large, population-based, geographically diverse catchment area; active laboratory-based identification of cases to ensure complete case capture; detailed collection of epidemiologic information paired with laboratory isolates; infrastructure that allows for more in-depth investigations; and sustained commitment of public health, academic, and clinical partners to maintain the system. ABCs has directly affected public health policies and practices through the development and evaluation of vaccines and other prevention strategies, the monitoring of antimicrobial drug resistance, and the response to public health emergencies and other emerging infections. PMID:26292067

  13. Community dynamics of cellulose-adapted thermophilic bacterial consortia.

    PubMed

    Eichorst, Stephanie A; Varanasi, Patanjali; Stavila, Vatalie; Zemla, Marcin; Auer, Manfred; Singh, Seema; Simmons, Blake A; Singer, Steven W

    2013-09-01

    Enzymatic hydrolysis of cellulose is a key process in the global carbon cycle and the industrial conversion of biomass to biofuels. In natural environments, cellulose hydrolysis is predominately performed by microbial communities. However, detailed understanding of bacterial cellulose hydrolysis is primarily confined to a few model isolates. Developing models for cellulose hydrolysis by mixed microbial consortia will complement these isolate studies and may reveal new mechanisms for cellulose deconstruction. Microbial communities were adapted to microcrystalline cellulose under aerobic, thermophilic conditions using green waste compost as the inoculum to study cellulose hydrolysis in a microbial consortium. This adaptation selected for three dominant taxa--the Firmicutes, Bacteroidetes and Thermus. A high-resolution profile of community development during the enrichment demonstrated a community transition from Firmicutes to a novel Bacteroidetes population that clusters in the Chitinophagaceae family. A representative strain of this population, strain NYFB, was successfully isolated, and sequencing of a nearly full-length 16S rRNA gene demonstrated that it was only 86% identical compared with other validated strains in the phylum Bacteroidetes. Strain NYFB grew well on soluble polysaccharide substrates, but grew poorly on insoluble polysaccharide substrates. Similar communities were observed in companion thermophilic enrichments on insoluble wheat arabinoxylan, a hemicellulosic substrate, suggesting a common model for deconstruction of plant polysaccharides. Combining observations of community dynamics and the physiology of strain NYFB, a cooperative successional model for polysaccharide hydrolysis by the Firmicutes and Bacteroidetes in the thermophilic cellulolytic consortia is proposed. PMID:23763762

  14. Bacterial Community Structure Response to Petroleum Concentration in Groundwater

    NASA Astrophysics Data System (ADS)

    Kitts, C. L.; Wrighton, K. C.; Phillips, W. A.; Cano, R. J.; Lundegard, P. D.

    2004-12-01

    This study characterized the bacterial community present in groundwater samples from the Guadalupe Dunes Restoration Project on the central California coast. The purpose of the study was to determine the changes in bacterial community structure and function in response to variations in the concentration of dissolved phase total petroleum hydrocarbons (TPH) in groundwater plumes at the site. For the purpose of this study groundwater samples were collected at varying distance from TPH source zones in 10 different plumes. All samples were analyzed for ammonia, phosphate, TPH, methane, oxygen, carbon dioxide, nitrate, sulfate, and dissolved iron levels. Chemical analysis revealed that the groundwater chemistry varied between plumes and on a well-to-well basis within a plume. Principle component analyses (PCA) demonstrated that TPH degradation related parameters explained 28% of the variation in the groundwater chemistry. In addition to the physical and chemical analyses, four liters of each groundwater sample were filtered and bacterial DNA was isolated to determine the relationship between groundwater chemistry and bacterial community structure and function. Specific Polymerase Chain Reaction (PCR) primers were used to characterize populations of Eubacteria, and Archaea, as well as function genes for sulfate reducing, methanotrophic, and methanogenic bacteria. Terminal Restriction Fragment (TRF) Length Polymorphisms (or T-RFLP) were used to analyze community structure. Eubacterial and Archaeal groundwater communities were separated into distinct clusters which did not clearly reflect changes in groundwater chemical parameters unless individual plumes were analyzed separately. However, specific Eubacterial and Archaeal TRF peaks did correspond to known petroleum degrading organisms and methanogenic bacteria, respectively. Only one sample produced a positive result for the sulfite reductase gene (dsrAB), indicating that sulfate reduction may not be a dominant process at

  15. Sediment bacterial communities associated with anaerobic biodegradation of bisphenol A.

    PubMed

    Yang, Yuyin; Wang, Zhao; He, Tao; Dai, Yu; Xie, Shuguang

    2015-07-01

    Bisphenol A (BPA) is one of the endocrine-disrupting chemicals that are ubiquitous in aquatic environments. Biodegradation is a major way to clean up the BPA pollution in sediments. However, information on the effective BPA biodegradation in anaerobic sediments is still lacking. The present study investigated the biodegradation potential of BPA in river sediment under nitrate- or sulfate-reducing conditions. After 120-day incubation, a high removal of BPA (93 or 89%) was found in sediment microcosms (amended with 50 mg kg(-1) BPA) under these two anaerobic conditions. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Actinobacteria were the major bacterial groups in BPA-degrading sediments. The shift in bacterial community structure could occur with BPA biodegradation. PMID:25501890

  16. Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile.

    PubMed

    Zhu, Renbin; Shi, Yu; Ma, Dawei; Wang, Can; Xu, Hua; Chu, Haiyan

    2015-01-01

    Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800-2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400-1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today. PMID:26601753

  17. Characterization of Halophilic Bacterial Communities in Turda Salt Mine (Romania)

    NASA Astrophysics Data System (ADS)

    Carpa, Rahela; Keul, Anca; Muntean, Vasile; Dobrotă, Cristina

    2014-09-01

    Halophilic organisms are having adaptations to extreme salinity, the majority of them being Archaean, which have the ability to grow at extremely high salt concentrations, (from 3 % to 35 %). Level of salinity causes natural fluctuations in the halophilic populations that inhabit this particular habitat, raising problems in maintaining homeostasis of the osmotic pressure. Samples such as salt and water taken from Turda Salt Mine were analyzed in order to identify the eco-physiological bacterial groups. Considering the number of bacteria of each eco-physiological group, the bacterial indicators of salt quality (BISQ) were calculated and studied for each sample. The phosphatase, catalase and dehydrogenases enzymatic activities were quantitatively determined and the enzymatic indicators of salt quality (EISQ) were calculated. Bacterial isolates were analyzed using 16S rRNA gene sequence analysis. Universal bacterial primers, targeting the consensus region of the bacterial 16S rRNA gene were used. Analysis of a large fragment, of 1499 bp was performed to improve discrimination at the species level.

  18. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

    PubMed Central

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-01-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents. PMID:27169490

  19. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

    NASA Astrophysics Data System (ADS)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-05-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  20. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    PubMed

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-01-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents. PMID:27169490

  1. Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients

    PubMed Central

    Joss, Tom V.; Burke, Catherine M.; Hudson, Bernard J.; Darling, Aaron E.; Forer, Martin; Alber, Dagmar G.; Charles, Ian G.; Stow, Nicholas W.

    2016-01-01

    Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus. PMID:26834708

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

    PubMed

    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

  3. Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

    PubMed

    Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

    2014-04-01

    With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore. PMID:24214680

  4. Secondary bacterial symbiont community in aphids responds to plant diversity.

    PubMed

    Zytynska, Sharon E; Meyer, Sebastian T; Sturm, Sarah; Ullmann, Wiebke; Mehrparvar, Mohsen; Weisser, Wolfgang W

    2016-03-01

    Biodiversity is important for ecosystem functioning and biotic interactions. In experimental grasslands, increasing plant species richness is known to increase the diversity of associated herbivores and their predators. If these interactions can also involve endosymbionts that reside within a plant or animal host is currently unknown. In plant-feeding aphids, secondary bacterial symbionts can have strong fitness effects on the host, e.g. resistance to natural enemies or fungal pathogens. We examined the secondary symbiont community in three species of aphid, each feeding on a unique host plant across experimental plots that varied in plant species richness. Aphids were collected in May and June, and the symbiont community identified using species-specific PCR assays. Aphis fabae aphids were found to host six different symbiont species with individual aphids co-hosting up to four symbionts. Uroleucon jaceae and Macrosiphum rosae hosted two and three symbiont species, respectively. We found that, at the aphid population level, increasing plant species richness increased the diversity of the aphid symbiont community, whereas at the individual aphid level, the opposite was found. These effects are potentially driven by varying selective pressures across different plant communities of varying diversities, mediated by defensive protection responses and a changing cost-benefit trade-off to the aphid for hosting multiple secondary symbionts. Our work extends documented effects of plant diversity beyond visible biotic interactions to changes in endosymbiont communities, with potentially far-reaching consequences to related ecosystem processes. PMID:26603858

  5. Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river.

    PubMed

    Wang, Yongming; Liu, Lemian; Chen, Huihuang; Yang, Jun

    2015-11-01

    The spatiotemporal distribution of microbial diversity, community composition, and their major drivers are fundamental issues in microbial ecology. In this study, the planktonic bacterial and microeukaryotic communities of the Jiulong River were investigated across both wet and dry seasons by using denaturing gradient gel electrophoresis (DGGE). We found evidence of temporal change between wet and dry seasons and distinct spatial patterns of bacterial and microeukaryotic communities. Both bacterial and microeukaryotic communities were strongly correlated with temperature, NH4-N, PO4-P, and chlorophyll a, and these environmental factors were significant but incomplete predictors of microbial community composition. Local environmental factors combined with spatial and temporal factors strongly controlled both bacterial and microeukaryotic communities in complex ways, whereas the direct influence of spatial and temporal factors appeared to be relatively small. Path analysis revealed that the microeukaryotic community played key roles in shaping bacterial community composition, perhaps through grazing effects and multiple interactions. Both Betaproteobacteria and Actinobacteria were the most dominant and diverse taxa in bacterial communities, while the microeukaryotic communities were dominated by Ciliophora (zooplankton) and Chlorophyta (phytoplankton). Our results demonstrated that both bacterial and microeukaryotic communities along the Jiulong River displayed a distinct spatiotemporal pattern; however, microeukaryotic communities exhibited a stronger distance-decay relationship than bacterial communities and their spatial patterns were mostly driven by local environmental variables rather than season or spatial processes of the river. Therefore, we have provided baseline data to support further research on river microbial food webs and integrating different microbial groups into river models. PMID:26156239

  6. Gamma-irradiated bacterial preparation having anti-tumor activity

    SciTech Connect

    Vass, A.A.; Tyndall, R.L.; Terzaghi-Howe, P.

    1999-11-16

    This application describes a bacterial preparation from Pseudomonas species isolated {number{underscore}sign}15 ATCC 55638 that has been exposed to gamma radiation exhibits cytotoxicity that is specific for neoplastic carcinoma cells. A method for obtaining a bacterial preparation having antitumor activity consists of suspending a bacterial isolate in media and exposing the suspension to gamma radiation. A bacterial preparation of an aged culture of an amoeba-associated bacteria exhibits anti-reverse transcriptase activity. A method for obtaining a bacterial preparation having anti-reverse transcriptase activity from an amoeba-associated bacterial isolate grown to stationary phase is disclosed.

  7. Gamma-irradiated bacterial preparation having anti-tumor activity

    DOEpatents

    Vass, Arpad A.; Tyndall, Richard L.; Terzaghi-Howe, Peggy

    1999-01-01

    A bacterial preparation from Pseudomonas species isolated #15 ATCC 55638 that has been exposed to gamma radiation exhibits cytotoxicity that is specific for neoplastic carcinoma cells. A method for obtaining a bacterial preparation having antitumor activity consists of suspending a bacterial isolate in media and exposing the suspension to gamma radiation. A bacterial preparation of an aged culture of an amoeba-associated bacteria exhibits anti-reverse transcriptase activity. A method for obtaining a bacterial preparation having anti-reverse transcriptase activity from an amoeba-associated bacterial isolate grown to stationary phase is disclosed.

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

    PubMed

    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. PMID:27459784

  9. Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans.

    PubMed

    Wietz, Matthias; Wemheuer, Bernd; Simon, Heike; Giebel, Helge-Ansgar; Seibt, Maren A; Daniel, Rolf; Brinkhoff, Thorsten; Simon, Meinhard

    2015-10-01

    The bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm experiments at four contrasting locations in the Southern and Atlantic Oceans. At the Southern polar front, chitin-supplemented microcosms were characterized by higher fractions of actively growing cells and a community shift from Alphaproteobacteria to Gammaproteobacteria and Bacteroidetes. At the Antarctic ice shelf, chitin degradation was associated with growth of Bacteroidetes, with 24% higher cell numbers compared with the control. At the Patagonian continental shelf, alginate and agarose degradation covaried with growth of different Alteromonadaceae populations, each with specific temporal growth patterns. At the Mauritanian upwelling, only the alginate hydrolysis product guluronate was consumed, coincident with increasing abundances of Alteromonadaceae and possibly cross-feeding SAR11. 16S rRNA gene amplicon libraries indicated that growth of the Bacteroidetes-affiliated genus Reichenbachiella was stimulated by chitin at all cold and temperate water stations, suggesting comparable ecological roles over wide geographical scales. Overall, the predominance of location-specific patterns showed that bacterial communities from contrasting oceanic biomes have members with different potentials to hydrolyse polysaccharides. PMID:25753990

  10. Seasonal Variations and Resilience of Bacterial Communities in a Sewage Polluted Urban River

    PubMed Central

    Ouattara, Nouho Koffi; Anzil, Adriana; Verbanck, Michel A.; Brion, Natacha; Servais, Pierre

    2014-01-01

    The Zenne River in Brussels (Belgium) and effluents of the two wastewater treatment plants (WWTPs) of Brussels were chosen to assess the impact of disturbance on bacterial community composition (BCC) of an urban river. Organic matters, nutrients load and oxygen concentration fluctuated highly along the river and over time because of WWTPs discharge. Tag pyrosequencing of bacterial 16S rRNA genes revealed the significant effect of seasonality on the richness, the bacterial diversity (Shannon index) and BCC. The major grouping: -winter/fall samples versus spring/summer samples- could be associated with fluctuations of in situ bacterial activities (dissolved and particulate organic carbon biodegradation associated with oxygen consumption and N transformation). BCC of the samples collected upstream from the WWTPs discharge were significantly different from BCC of downstream samples and WWTPs effluents, while no significant difference was found between BCC of WWTPs effluents and the downstream samples as revealed by ANOSIM. Analysis per season showed that allochthonous bacteria brought by WWTPs effluents triggered the changes in community composition, eventually followed by rapid post-disturbance return to the original composition as observed in April (resilience), whereas community composition remained altered after the perturbation by WWTPs effluents in the other seasons. PMID:24667680

  11. Distribution of bacterial communities across plateau freshwater lake and upslope soils.

    PubMed

    Chen, Yihui; Dai, Yu; Wang, Yilin; Wu, Zhen; Xie, Shuguang; Liu, Yong

    2016-05-01

    Microorganisms are involved in a variety of biogeochemical processes in natural environments. The differences between bacterial communities in freshwaters and upslope soils remain unclear. The present study investigated the bacterial distribution in a plateau freshwater lake, Erhai Lake (southwestern China), and its upslope soils. Illumina MiSeq sequencing illustrated high bacterial diversity in lake sediments and soils. Sediment and soil bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Planctomycetes. However, a distinctive difference in bacterial community structure was found between soil and sediment ecosystems. Water content, nitrogen and pH affected the distribution of the bacterial community across Erhai Lake and its upslope soils. Moreover, the soil bacterial community might also be shaped by plant types. This work could provide some new insights into plateau aquatic and terrestrial microbial ecology. PMID:27155410

  12. Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa)

    PubMed Central

    Tiodjio, Rosine E.; Sakatoku, Akihiro; Nakamura, Akihiro; Tanaka, Daisuke; Fantong, Wilson Y.; Tchakam, Kamtchueng B.; Tanyileke, Gregory; Ohba, Takeshi; Hell, Victor J.; Kusakabe, Minoru; Nakamura, Shogo; Ueda, Akira

    2014-01-01

    The aim of this study was to assess the microbial diversity associated with Lake Nyos, a lake with an unusual chemistry in Cameroon. Water samples were collected during the dry season on March 2013. Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. The results indicate a stratification of both communities along the water column. Altogether, the physico-chemical data and microbial sequences suggest a close correspondence of the potential microbial functions to the physico-chemical pattern of the lake. We also obtained evidence of a rich microbial diversity likely to include several novel microorganisms of environmental importance in the large unexplored microbial reservoir of Lake Nyos. PMID:25141868

  13. Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils.

    PubMed

    Oline, David K

    2006-11-01

    I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale ( approximately 100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography. PMID:16950906

  14. Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils▿

    PubMed Central

    Oline, David K.

    2006-01-01

    I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography. PMID:16950906

  15. Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil.

    PubMed

    Leewis, Mary-Cathrine; Uhlik, Ondrej; Fraraccio, Serena; McFarlin, Kelly; Kottara, Anastasia; Glover, Catherine; Macek, Tomas; Leigh, Mary Beth

    2016-01-01

    Despite decades of research there is limited understanding of how vegetation impacts the ability of microbial communities to process organic contaminants in soil. Using a combination of traditional and molecular assays, we examined how phytoremediation with willow and/or fertilization affected the microbial community present and active in the transformation of diesel contaminants. In a pot study, willow had a significant role in structuring the total bacterial community and resulted in significant decreases in diesel range organics (DRO). However, stable isotope probing (SIP) indicated that fertilizer drove the differences seen in community structure and function. Finally, analysis of the total variance in both pot and SIP experiments indicated an interactive effect between willow and fertilizer on the bacterial communities. This study clearly demonstrates that a willow native to Alaska accelerates DRO degradation, and together with fertilizer, increases aromatic degradation by shifting microbial community structure and the identity of active naphthalene degraders. PMID:27313574

  16. Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil

    PubMed Central

    Leewis, Mary-Cathrine; Uhlik, Ondrej; Fraraccio, Serena; McFarlin, Kelly; Kottara, Anastasia; Glover, Catherine; Macek, Tomas; Leigh, Mary Beth

    2016-01-01

    Despite decades of research there is limited understanding of how vegetation impacts the ability of microbial communities to process organic contaminants in soil. Using a combination of traditional and molecular assays, we examined how phytoremediation with willow and/or fertilization affected the microbial community present and active in the transformation of diesel contaminants. In a pot study, willow had a significant role in structuring the total bacterial community and resulted in significant decreases in diesel range organics (DRO). However, stable isotope probing (SIP) indicated that fertilizer drove the differences seen in community structure and function. Finally, analysis of the total variance in both pot and SIP experiments indicated an interactive effect between willow and fertilizer on the bacterial communities. This study clearly demonstrates that a willow native to Alaska accelerates DRO degradation, and together with fertilizer, increases aromatic degradation by shifting microbial community structure and the identity of active naphthalene degraders. PMID:27313574

  17. The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing.

    PubMed

    Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

    2015-01-01

    In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

  18. The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

    PubMed Central

    Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

    2015-01-01

    In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

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

    PubMed

    Germerodt, Sebastian; Bohl, Katrin; Lück, Anja; Pande, Samay; Schröter, Anja; Kaleta, Christoph; Schuster, Stefan; Kost, Christian

    2016-06-01

    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. PMID:27314840

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

    PubMed Central

    Germerodt, Sebastian; Bohl, Katrin; Pande, Samay; Schröter, Anja; Kaleta, Christoph; Kost, Christian

    2016-01-01

    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. PMID:27314840

  1. The structure and functions of bacterial communities in an agrocenosis

    NASA Astrophysics Data System (ADS)

    Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

    2016-01-01

    The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

  2. Understanding the bacterial communities of hard cheese with blowing defect.

    PubMed

    Bassi, Daniela; Puglisi, Edoardo; Cocconcelli, Pier Sandro

    2015-12-01

    The environment of hard cheese encourages bacterial synergies and competitions along the ripening process, which might lead in defects such as clostridial blowing. In this study, Denaturing Gradient Gel Electrophoresis (DGGE), a quantitative Clostridium tyrobutyricum PCR and next-generation Illumina-based sequencing of 16S rRNA gene were applied to study 83 Grana Padano spoiled samples. The aim was to investigate the community of clostridia involved in spoilage, the ecological relationships with the other members of the cheese microbiota, and the effect of lysozyme. Three main genera were dominant in the analysed cheeses, Lactobacillus, Streptococcus and Clostridium, and the assignment at the species level was of 94.3% of 4,477,326 high quality sequences. C. tyrobutyricum and C. butyricum were the most prevalent clostridia. Hierarchical clustering based on the abundance of bacterial genera, revealed three main clusters: one characterized by the highest proportion of Clostridium, a second where Lactobacillus was predominant and the last, dominated by Streptococcus thermophilus. Ecological relationships among species were found: cheeses characterized by an high abundance of S. thermophilus and L. rhamnosus were spoiled by C. tyrobutyricum while, when L. delbrueckii was the most abundant Lactobacillus, C. butyricum was the dominant spoiling species. Lysozyme also shaped the bacterial community, reducing C. tyrobutyricum in favour of C. butyricum. Moreover, this preservative increased the proportion of L. delbrueckii and obligate heterofermentative lactobacilli and lowered L. helveticus and non-starter species, such as L. rhamnosus and L. casei. PMID:26338123

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

    PubMed

    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

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

    PubMed Central

    de Steenhuijsen Piters, Wouter A. A.

    2016-01-01

    ABSTRACT 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

  5. Phylogenetically and Spatially Close Marine Sponges Harbour Divergent Bacterial Communities

    PubMed Central

    Hardoim, Cristiane C. P.; Esteves, Ana I. S.; Pires, Francisco R.; Gonçalves, Jorge M. S.; Cox, Cymon J.; Xavier, Joana R.; Costa, Rodrigo

    2012-01-01

    Recent studies have unravelled the diversity of sponge-associated bacteria that may play essential roles in sponge health and metabolism. Nevertheless, our understanding of this microbiota remains limited to a few host species found in restricted geographical localities, and the extent to which the sponge host determines the composition of its own microbiome remains a matter of debate. We address bacterial abundance and diversity of two temperate marine sponges belonging to the Irciniidae family - Sarcotragus spinosulus and Ircinia variabilis – in the Northeast Atlantic. Epifluorescence microscopy revealed that S. spinosulus hosted significantly more prokaryotic cells than I. variabilis and that prokaryotic abundance in both species was about 4 orders of magnitude higher than in seawater. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of S. spinosulus and I. variabilis differed markedly from each other – with higher number of ribotypes observed in S. spinosulus – and from those of seawater. Four PCR-DGGE bands, two specific to S. spinosulus, one specific to I. variabilis, and one present in both sponge species, affiliated with an uncultured sponge-specific phylogenetic cluster in the order Acidimicrobiales (Actinobacteria). Two PCR-DGGE bands present exclusively in S. spinosulus fingerprints affiliated with one sponge-specific phylogenetic cluster in the phylum Chloroflexi and with sponge-derived sequences in the order Chromatiales (Gammaproteobacteria), respectively. One Alphaproteobacteria band specific to S. spinosulus was placed in an uncultured sponge-specific phylogenetic cluster with a close relationship to the genus Rhodovulum. Our results confirm the hypothesized host-specific composition of bacterial communities between phylogenetically and spatially close sponge species in the Irciniidae family, with S. spinosulus displaying higher bacterial community diversity and distinctiveness than I. variabilis. These

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

    SciTech Connect

    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.

  7. Temporal variability in detritus resource maintains diversity of bacterial communities

    NASA Astrophysics Data System (ADS)

    Hiltunen, Teppo; Laakso, Jouni; Kaitala, Veijo; Suomalainen, Lotta-Riina; Pekkonen, Minna

    2008-05-01

    Competition theory generally predicts that diversity is maintained by temporal environmental fluctuations. One of the many suggested mechanisms for maintaining diversity in fluctuating environments is the gleaner-opportunist trade-off, whereby gleaner species have low threshold resource levels and low maximum growth rates in high resource concentration while opportunist species show opposite characteristics. We measured the growth rates of eight heterotrophic aquatic bacteria under different concentrations of chemically complex plant detritus resource. The growth rates revealed gleaner-opportunist trade-offs. The role of environmental variability in maintaining diversity was tested in a 28-day experiment with three different resource fluctuation regimes imposed on two four-species bacterial communities in microcosms. We recorded population densities with serial dilution plating and total biomass as turbidity. Changes in resource availability were measured from filter-sterilised medium by re-introducing the consumer species and recording short-term growth rates. The type of environmental variation had no effect on resource availability, which declined slowly during the experiment and differed in level between the communities. However, the slowly fluctuating environment had the highest Shannon diversity index, biomass, and coefficient of variation of biomass in both communities. We did not find a clear link between the gleaner-opportunist trade-off and diversity in fluctuating environments. Nevertheless, our results do not exclude this explanation and support the general view that temporal environmental variation maintains species diversity also in communities feeding chemically complex resource.

  8. Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.

    PubMed

    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

  9. The dynamic bacterial communities of a melting High Arctic glacier snowpack.

    PubMed

    Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

    2013-09-01

    Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation. PMID:23552623

  10. The dynamic bacterial communities of a melting High Arctic glacier snowpack

    PubMed Central

    Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

    2013-01-01

    Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation. PMID:23552623

  11. Bacterial communities in the initial stage of marine biofilm formation on artificial surfaces.

    PubMed

    Lee, Jin-Woo; Nam, Ji-Hyun; Kim, Yang-Hoon; Lee, Kyu-Ho; Lee, Dong-Hun

    2008-04-01

    Succession of bacterial communities during the first 36 h of biofilm formation in coastal water was investigated at 3 approximately 15 h intervals. Three kinds of surfaces (i.e., acryl, glass, and steel substratum) were submerged in situ at Sacheon harbor, Korea. Biofilms were harvested by scraping the surfaces, and the compositions of bacterial communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of 16S rRNA genes. While community structure based on T-RFLP analysis showed slight differences by substratum, dramatic changes were commonly observed for all substrata between 9 and 24 h. Identification of major populations by 16S rRNA gene sequences indicated that gamma-Proteobacteria (Pseudomonas, Acinetobacter, Alteromonas, and uncultured gamma-Proteobacteria) were predominant in the community during 0 approximately 9 h, while the ratio of alpha-Proteobacteria (Loktanella, Methylobacterium, Pelagibacter, and uncultured alpha-Proteobacteria) increased 2.6 approximately 4.8 folds during 24 approximately 36 h of the biofilm formation, emerging as the most predominant group. Previously, alpha-Proteobacteria were recognized as the pioneering organisms in marine biofilm formation. However, results of this study, which revealed the bacterial succession with finer temporal resolution, indicated some species of gamma-Proteobacteria were more important as the pioneering population. Measures to control pioneering activities of these species can be useful in prevention of marine biofilm formation. PMID:18545967

  12. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

    PubMed Central

    Aylward, Frank O; Burnum, Kristin E; Scott, Jarrod J; Suen, Garret; Tringe, Susannah G; Adams, Sandra M; Barry, Kerrie W; Nicora, Carrie D; Piehowski, Paul D; Purvine, Samuel O; Starrett, Gabriel J; Goodwin, Lynne A; Smith, Richard D; Lipton, Mary S; Currie, Cameron R

    2012-01-01

    Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus–bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans. PMID:22378535

  13. Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity.

    PubMed

    Badin, Anne-Laure; Mustafa, Tarfa; Bertrand, Cédric; Monier, Armelle; Delolme, Cécile; Geremia, Roberto A; Bedell, Jean-Philippe

    2012-08-01

    This study focuses on the distribution of bacterial and fungal communities within the microstructure of a multi-contaminated sedimentary layer resulting from urban stormwater infiltration. Fractionation was performed on the basis of differential porosity and aggregate grain size, resulting in five fractions: leachable fitting macroporosity, < 10, 10-160, 160-1000 μm fitting aggregates, > 1000 μm. Amounts of both bacterial and fungal biomasses are greater in the < 10 μm and leachable fractions. The aggregates contain numerous bacteria but very low amounts of fungal biomass. Single-strand conformational polymorphism molecular profiles highlighted the differences between bacterial and fungal communities of the leachable fraction and those of the aggregates. Random Sanger sequencing of ssu clones revealed that these differences were mainly because of the presence of Epsilonproteobacteria and Firmicutes in the leachable fractions, while the aggregates contained more Cyanobacteria. The Cyanobacteria phylotypes in the aggregates were dominated by the sequences related to Microcoleus vaginatus while the leachable fractions presented the sequences of chloroplastic origin. Therefore, more than 50% of the phylotypes observed were related to Proteobacteria while 40% were related to Cyanobacteria and Bacteroidetes. Preferential distribution of clades in almost all the phyla or classes detected was observed. This study provides insight into the identities of dominant members of the bacterial communities of urban sediments. Microcoleus vaginatus appeared to predominate in pioneer soils. PMID:22404135

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

    PubMed

    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

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

    PubMed Central

    Peter, Hannes; Sommaruga, Ruben

    2016-01-01

    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

  16. Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

    PubMed Central

    Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

    2015-01-01

    Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

  17. [Characterization of the Gut Bacterial Community of the Japanese Sea Cucumber Apostichopus japonicus].

    PubMed

    Bogatyrenko, E A; Buzoleva, L S

    2016-01-01

    Comparative analysis of the composition and abundance of the gut bacterial community of the Japanese sea cucumber (trepang) Apostichopus japonicus and the soil from its habitat was carried out. In spite of the presence of strictly aerobic bacteria in the soil, gut microflora of this holothurian was shown to be formed by facultative anaerobes from the environment. Irrespective of the geographical location of the habitat, the sea cucmber gut community had a constant composition considered its normal microflora. Capacity of bactreia isolated from the Japanese sea cucumber for decomposition of starch, sodium alginate, chitin, chondroitin sulfate, Tweens, olive oil, casein, and gelatin was studied. Various degrees of enzymatic activity were shown for 33% of the studied bacterial strains, which indicates a considerable role of the trepang gut microflora in processing and assimilation of organic matter arriving with food. PMID:27301133

  18. Biogeographic congruency among bacterial communities from terrestrial sulfidic springs

    PubMed Central

    Headd, Brendan; Engel, Annette S.

    2014-01-01

    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 climate change. PMID

  19. The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

    PubMed

    Ibarbalz, Federico M; Pérez, María Victoria; Figuerola, Eva L M; Erijman, Leonardo

    2014-01-01

    The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

  20. Shifts in Fungal and Bacterial Community Structure During Tallgrass Prairie Restoration

    NASA Astrophysics Data System (ADS)

    Shutthanandan, J.; Bailey, V. L.; Bolton, H.; Brockman, F. J.

    2002-12-01

    The cycling of carbon through the microbial community of soils results in both the storage of freshly added carbon in the soil and the release of greenhouse gases such as carbon dioxide to the atmosphere. It is hypothesized that fungi and bacteria cycle carbon differently, and result in different proportions of carbon stored and evolved. The intensive management of a soil will affect these proportions and thus, may also affect the terrestrial carbon cycle. The soil microbial community was monitored in four soils that form a tallgrass prairie restoration chronosequence. The chronosequence was composed of: 1) native tallgrass prairie, 2) farmland restored to tallgrass prairie in 1979, 3) farmland restored to prairie in 1993, and 4) farmland still in production with row crops. The structure of the microbial community was determined by terminal restriction fragment length analysis (T-RFLP) and we focus here on comparing bacterial and fungal domains from agriculture to native conditions. Shifts in the fungal and bacterial communities were detected that indicate that the bacteria recovered faster from changing the land use from farmland back to prairie, while the fungi are more sensitive to the perturbations of invasive agriculture and appear to be taking longer to revert to their original prairie composition. However, it must also be considered that assays of the activities of these two communities indicate that as the restoration progresses, the fungi dominate the degradation of freshly added carbon (the ratio of fungal-to-bacterial activity was 13.5:1 in the 1979 restoration, but only 0.85:1 in the farmland). Identification of this shift in community structure offers insights into monitoring ecosystem restoration and may also suggest opportunities for enhancing carbon storage by allowing marginal lands to revert to a natural condition.

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

    PubMed

    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

  2. Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

    PubMed Central

    Brannen-Donnelly, Kathleen; Engel, Annette S.

    2015-01-01

    Unchanging physicochemical conditions and nutrient sources over long periods of time in cave and karst subsurface habitats, particularly aquifers, can support stable ecosystems, termed autochthonous microbial endokarst communities (AMEC). AMEC existence is unknown for other karst settings, such as epigenic cave streams. Conceptually, AMEC should not form in streams due to faster turnover rates and seasonal disturbances that have the capacity to transport large quantities of water and sediment and to change allochthonous nutrient and organic matter sources. Our goal was to investigate whether AMEC could form and persist in hydrologically active, epigenic cave streams. We analyzed bacterial diversity from cave water, sediments, and artificial substrates (Bio-Traps®) placed in the cave at upstream and downstream locations. Distinct communities existed for the water, sediments, and Bio-Trap® samplers. Throughout the study period, a subset of community members persisted in the water, regardless of hydrological disturbances. Stable habitat conditions based on flow regimes resulted in more than one contemporaneous, stable community throughout the epigenic cave stream. However, evidence for AMEC was insufficient for the cave water or sediments. Community succession, specifically as predictable exogenous heterotrophic microbial community succession, was evident from decreases in community richness from the Bio-Traps®, a peak in Bio-Trap® community biomass, and from changes in the composition of Bio-Trap® communities. The planktonic community was compositionally similar to Bio-Trap® initial colonizers, but the downstream Bio-Trap® community became more similar to the sediment community at the same location. These results can help in understanding the diversity of planktonic and attached microbial communities from karst, as well as microbial community dynamics, stability, and succession during disturbance or contamination responses over time. PMID:26257715

  3. Tagging frogs with passive integrated transponders causes disruption of the cutaneous bacterial community and proliferation of opportunistic fungi.

    PubMed

    Antwis, Rachael E; Garcia, Gerardo; Fidgett, Andrea L; Preziosi, Richard F

    2014-08-01

    Symbiotic bacterial communities play a key role in protecting amphibians from infectious diseases including chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis. Events that lead to the disruption of the bacterial community may have implications for the susceptibility of amphibians to such diseases. Amphibians are often marked both in the wild and in captivity for a variety of reasons, and although existing literature indicates that marking techniques have few negative effects, the response of cutaneous microbial communities has not yet been investigated. Here we determine the effects of passive integrated transponder (PIT) tagging on culturable cutaneous microbial communities of captive Morelet's tree frogs (Agalychnis moreletii) and assess the isolated bacterial strains for anti-B. dendrobatidis activity in vitro. We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase). Handling also caused a disruption the bacterial community, although to a lesser extent than PIT tagging. However, the effects of both tagging and handling were temporary, and after 2 weeks, the bacterial communities were similar to their original compositions. We also identify two bacterial strains that inhibit B. dendrobatidis, one of which increased in abundance on PIT-tagged frogs at 1 day postmarking, while the other was unaffected. These results show that PIT tagging has previously unobserved consequences for cutaneous microbial communities of frogs and may be particularly relevant for studies that intend to use PIT tagging to identify individuals involved in trials to develop probiotic treatments. PMID:24878599

  4. Tagging Frogs with Passive Integrated Transponders Causes Disruption of the Cutaneous Bacterial Community and Proliferation of Opportunistic Fungi

    PubMed Central

    Garcia, Gerardo; Fidgett, Andrea L.; Preziosi, Richard F.

    2014-01-01

    Symbiotic bacterial communities play a key role in protecting amphibians from infectious diseases including chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis. Events that lead to the disruption of the bacterial community may have implications for the susceptibility of amphibians to such diseases. Amphibians are often marked both in the wild and in captivity for a variety of reasons, and although existing literature indicates that marking techniques have few negative effects, the response of cutaneous microbial communities has not yet been investigated. Here we determine the effects of passive integrated transponder (PIT) tagging on culturable cutaneous microbial communities of captive Morelet's tree frogs (Agalychnis moreletii) and assess the isolated bacterial strains for anti-B. dendrobatidis activity in vitro. We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase). Handling also caused a disruption the bacterial community, although to a lesser extent than PIT tagging. However, the effects of both tagging and handling were temporary, and after 2 weeks, the bacterial communities were similar to their original compositions. We also identify two bacterial strains that inhibit B. dendrobatidis, one of which increased in abundance on PIT-tagged frogs at 1 day postmarking, while the other was unaffected. These results show that PIT tagging has previously unobserved consequences for cutaneous microbial communities of frogs and may be particularly relevant for studies that intend to use PIT tagging to identify individuals involved in trials to develop probiotic treatments. PMID:24878599

  5. A bacterial community analysis using reverse transcription (RT) PCR which detects the bacteria with high activity in a wastewater treatment reactor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This research used reverse transcription polymerase chain reaction (RT-PCR) method to help detect active bacteria in a single-tank deammonification reactor combining partial nitritation and anammox. The single-tank aerobic deammonification reactor effectively removed the ammonia in anaerobically di...

  6. Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA).

    PubMed

    Sadet-Bourgeteau, S; Philippeau, C; Dequiedt, S; Julliand, V

    2014-12-01

    The horse's hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp(®) DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples. PMID:25075719

  7. Activity and bacterial diversity of snow around Russian Antarctic stations.

    PubMed

    Lopatina, Anna; Krylenkov, Vjacheslav; Severinov, Konstantin

    2013-11-01

    The diversity and temporal dynamics of bacterial communities in pristine snow around two Russian Antarctic stations was investigated. Taxonomic analysis of rDNA libraries revealed that snow communities were dominated by bacteria from a small number of operational taxonomic units (OTUs) that underwent dramatic swings in abundance between the 54th (2008-2009) and 55th (2009-2010) Russian Antarctic expeditions. Moreover, analysis of the 55th expedition samples indicated that there was very little, if any, correspondence in abundance of clones belonging to the same OTU present in rDNA and rRNA libraries. The latter result suggests that most rDNA clones originate from bacteria that are not alive and/or active and may have been deposited on the snow surface from the atmosphere. In contrast, clones most abundant in rRNA libraries (mostly belonging to Variovorax, Janthinobacterium, Pseudomonas, and Sphingomonas genera) may be considered as endogenous Antarctic snow inhabitants. PMID:24012540

  8. Changes in bacterial and archaeal communities in anaerobic digesters treating different organic wastes.

    PubMed

    Kim, Young Mo; Jang, Hyun Min; Lee, Kwanyong; Chantrasakdakul, Phrompol; Kim, Daegi; Park, Ki Young

    2015-12-01

    The goal of this study was to characterize microbial communities in anaerobic batch digesters treating different representative organic sources (sewage sludge, food waste, septage). Among the digesters, the anaerobic digester of food waste had the highest methanogen density, producing a peak value methane yield of 813.2mLCH4/gVS. In all the digesters, acetoclastic Methanosarcinales and hydrogenotrophic Methanomicrobiales were the most dominant methanogen groups, but their proportion among the methanogens varied depending on the organic sources. The bacteria community in the anaerobic digestion (AD) of food waste and septage was distinctly different from that found in the AD of sewage sludge (primary sludge and waste activated sludge). Shifts in both bacterial and archaeal community structures could be related to differences in chemical properties, production, and accumulation of intermediates digested from organic wastes having different characteristics. These findings could prove useful in optimizing the microbial community to enhance AD process treating organic wastes. PMID:26184789

  9. Resonant activation: a strategy against bacterial persistence

    NASA Astrophysics Data System (ADS)

    Fu, Yan; Zhu, Meng; Xing, Jianhua

    2010-03-01

    A bacterial colony may develop a small number of cells genetically identical to, but phenotypically different from, other normally growing bacteria. These so-called persister cells keep themselves in a dormant state and thus are insensitive to antibiotic treatment, resulting in serious problems of drug resistance. In this paper, we proposed a novel strategy to 'kill' persister cells by triggering them to switch, in a fast and synchronized way, into normally growing cells that are susceptible to antibiotics. The strategy is based on resonant activation (RA), a well-studied phenomenon in physics where the internal noise of a system can constructively facilitate fast and synchronized barrier crossings. Through stochastic Gilliespie simulation with a generic toggle switch model, we demonstrated that RA exists in the phenotypic switching of a single bacterium. Further, by coupling single cell level and population level simulations, we showed that with RA, one can greatly reduce the time and total amount of antibiotics needed to sterilize a bacterial population. We suggest that resonant activation is a general phenomenon in phenotypic transition, and can find other applications such as cancer therapy.

  10. Antifungal activity of plant and bacterial ureases.

    PubMed

    Becker-Ritt, A B; Martinelli, A H S; Mitidieri, S; Feder, V; Wassermann, G E; Santi, L; Vainstein, M H; Oliveira, J T A; Fiuza, L M; Pasquali, G; Carlini, C R

    2007-12-01

    Ureases (EC 3.5.1.5) are nickel-dependent metalloenzymes that catalyze the hydrolysis of urea to ammonia and carbon dioxide. Produced by plants, fungi and bacteria, but not by animals, ureases share significant homology and similar mechanisms of catalysis, although differing in quaternary structures. While fungal and plant ureases are homo-oligomeric proteins of 90 kDa subunits, bacterial ureases are multimers of two (e.g. Helicobacter pylori) or three subunit complexes. It has been proposed that in plants these enzymes are involved in nitrogen bioavailability and in protection against pathogens. Previous studies by our group have shown that plant ureases, but not a bacterial (Bacillus pasteurii) urease, display insecticidal activity. Herein we demonstrate that (Glycine max) embryo-specific soybean urease, jackbean (Canavalia ensiformis) major urease and a recombinant H. pylori urease impair growth of selected phytopathogenic fungi at sub-micromolar concentrations. This antifungal property of ureases is not affected by treatment of the proteins with an irreversible inhibitor of the ureolytic activity. Scanning electron microscopy of urease-treated fungi suggests plasmolysis and cell wall injuries. Altogether, our data indicate that ureases probably contribute to the plant arsenal of defense compounds against predators and phytopathogens and that the urease defense mechanism is independent of ammonia release from urea. PMID:17825863

  11. Impact of oil on bacterial community structure in bioturbated sediments.

    PubMed

    Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

    2013-01-01

    Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria

  12. Influence of PAHs among other coastal environmental variables on total and PAH-degrading bacterial communities.

    PubMed

    Sauret, Caroline; Tedetti, Marc; Guigue, Catherine; Dumas, Chloé; Lami, Raphaël; Pujo-Pay, Mireille; Conan, Pascal; Goutx, Madeleine; Ghiglione, Jean-François

    2016-03-01

    We evaluated the relative impact of anthropogenic polycyclic aromatic hydrocarbons (PAHs) among biogeochemical variables on total, metabolically active, and PAH bacterial communities in summer and winter in surface microlayer (SML) and subsurface seawaters (SSW) across short transects along the NW Mediterranean coast from three harbors, one wastewater effluent, and one nearshore observatory reference site. At both seasons, significant correlations were found between dissolved total PAH concentrations and PAH-degrading bacteria that formed a gradient from the shore to nearshore waters. Accumulation of PAH degraders was particularly high in the SML, where PAHs accumulated. Harbors and wastewater outfalls influenced drastically and in a different way the total and active bacterial community structure, but they only impacted the communities from the nearshore zone (<2 km from the shore). By using direct multivariate statistical analysis, we confirmed the significant effect of PAH concentrations on the spatial and temporal dynamic of total and active communities in this area, but this effect was putted in perspective by the importance of other biogeochemical variables. PMID:26122564

  13. Assessing the Unseen Bacterial Diversity in Microbial Communities

    PubMed Central

    Caro-Quintero, Alejandro; Ochman, Howard

    2015-01-01

    For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs—that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations. PMID:26615218

  14. Assessing the Unseen Bacterial Diversity in Microbial Communities.

    PubMed

    Caro-Quintero, Alejandro; Ochman, Howard

    2015-12-01

    For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria--individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach--termed phyloTAGs--that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations. PMID:26615218

  15. Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor.

    PubMed

    Pischedda, Laura; Militon, Cécile; Gilbert, Franck; Cuny, Philippe

    2011-12-01

    Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system. PMID:21946148

  16. Mining bacterial genomes for novel arylesterase activity

    PubMed Central

    Wang, Lijun; Mavisakalyan, Valentina; Tillier, Elisabeth R. M.; Clark, Greg W.; Savchenko, Alexei V.; Yakunin, Alexander F.; Master, Emma R.

    2010-01-01

    Summary One hundred and seventy‐one genes encoding potential esterases from 11 bacterial genomes were cloned and overexpressed in Escherichia coli; 74 of the clones produced soluble proteins. All 74 soluble proteins were purified and screened for esterase activity; 36 proteins showed carboxyl esterase activity on short‐chain esters, 17 demonstrated arylesterase activity, while 38 proteins did not exhibit any activity towards the test substrates. Esterases from Rhodopseudomonas palustris (RpEST‐1, RpEST‐2 and RpEST‐3), Pseudomonas putida (PpEST‐1, PpEST‐2 and PpEST‐3), Pseudomonas aeruginosa (PaEST‐1) and Streptomyces avermitilis (SavEST‐1) were selected for detailed biochemical characterization. All of the enzymes showed optimal activity at neutral or alkaline pH, and the half‐life of each enzyme at 50°C ranged from < 5 min to over 5 h. PpEST‐3, RpEST‐1 and RpEST‐2 demonstrated the highest specific activity with pNP‐esters; these enzymes were also among the most stable at 50°C and in the presence of detergents, polar and non‐polar organic solvents, and imidazolium ionic liquids. Accordingly, these enzymes are particularly interesting targets for subsequent application trials. Finally, biochemical and bioinformatic analyses were compared to reveal sequence features that could be correlated to enzymes with arylesterase activity, facilitating subsequent searches for new esterases in microbial genome sequences. PMID:21255363

  17. Initial community and environment determine the response of bacterial communities to dispersant and oil contamination.

    PubMed

    Ortmann, Alice C; Lu, YueHan

    2015-01-15

    Bioremediation of seawater by natural bacterial communities is one potential response to coastal oil spills, but the success of the approach may vary, depending on geographical location, oil composition and the timing of spill. The short term response of coastal bacteria to dispersant, oil and dispersed oil was characterized using 16S rRNA gene tags in two mesocosm experiments conducted two months apart. Despite differences in the amount of oil-derived alkanes across the treatments and experiments, increases in the contributions of hydrocarbon degrading taxa and decreases in common estuarine bacteria were observed in response to dispersant and/or oil. Between the two experiments, the direction and rates of changes in particulate alkane concentrations differed, as did the magnitude of the bacterial response to oil and/or dispersant. Together, our data underscore large variability in bacterial responses to hydrocarbon pollutants, implying that bioremediation success varies with starting biological and environmental conditions. PMID:25487088

  18. Composition and Seasonal Variation of Rhipicephalus turanicus and Rhipicephalus sanguineus Bacterial Communities

    PubMed Central

    Lalzar, Itai; Harrus, Shimon; Mumcuoglu, Kosta Y.

    2012-01-01

    A 16S rRNA gene approach, including 454 pyrosequencing and quantitative PCR (qPCR), was used to describe the bacterial community in Rhipicephalus turanicus and to evaluate the dynamics of key bacterial tenants of adult ticks during the active questing season. The bacterial community structure of Rh. turanicus was characterized by high dominance of Coxiella and Rickettsia and extremely low taxonomic diversity. Parallel diagnostic PCR further revealed a novel Coxiella species which was present and numerically dominant in all individual ticks tested (n = 187). Coxiella sp. densities were significantly higher in female versus male ticks and were overall stable throughout the questing season. In addition, we revealed the presence of the novel Coxiella sp. in Rh. sanguineus adult ticks, eggs, and hatched larvae, indicating its vertical transmission. The presence of both spotted fever group Rickettsia spp. (SFGR) and non-SFGR was verified in the various individual ticks. The prevalence and density of Rickettsia spp. were very low compared to those of Coxiella sp. Furthermore, Rickettsia sp. densities were similar in males and females and significantly declined toward the end of the questing season. No correlation was found between Coxiella sp. and Rickettsia sp. densities. These results suggest different control mechanisms in the tick over its different bacterial populations and point to an obligatory and facultative association between the two tick species and Coxiella sp. and Rickettsia spp., respectively. PMID:22467507

  19. Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

    EPA Science Inventory

    Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by py...

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

    PubMed

    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

  1. Impacts of Grazing Intensity and Plant Community Composition on Soil Bacterial Community Diversity in a Steppe Grassland.

    PubMed

    Qu, Tong-Bao; Du, Wei-Chao; Yuan, Xia; Yang, Zhi-Ming; Liu, Dong-Bo; Wang, De-Li; Yu, Li-Jun

    2016-01-01

    Soil bacteria play a key role in the ecological and evolutionary responses of agricultural ecosystems. Domestic herbivore grazing is known to influence soil bacterial community. However, the effects of grazing and its major driving factors on soil bacterial community remain unknown for different plant community compositions under increasing grazing intensity. Thus, to investigate soil bacterial community diversity under five plant community compositions (Grass; Leymus chinensis; Forb; L. chinensis & Forb; and Legume), we performed a four-year field experiment with different grazing intensity treatments (no grazing; light grazing, 4 sheep·ha-1; and heavy grazing, 6 sheep·ha-1) in a grassland in China. Total DNA was obtained from soil samples collected from the plots in August, and polymerase chain reaction (PCR) analysis and denaturing gradient gel electrophoresis (DGGE) fingerprinting were used to investigate soil bacterial community. The results showed that light grazing significantly increased indices of soil bacterial community diversity for the Forb and Legume groups but not the Grass and L. chinensis groups. Heavy grazing significantly reduced these soil bacterial diversity indices, except for the Pielou evenness index in the Legume group. Further analyses revealed that the soil N/P ratio, electrical conductivity (EC), total nitrogen (TN) and pH were the major environmental factors affecting the soil bacterial community. Our study suggests that the soil bacterial community diversity was influenced by grazing intensity and plant community composition in a meadow steppe. The present study provides a baseline assessment of the soil bacterial community diversity in a temperate meadow steppe. PMID:27467221

  2. Impacts of Grazing Intensity and Plant Community Composition on Soil Bacterial Community Diversity in a Steppe Grassland

    PubMed Central

    Qu, Tong-bao; Du, Wei-chao; Yuan, Xia; Yang, Zhi-ming; Liu, Dong-bo; Wang, De-li; Yu, Li-jun

    2016-01-01

    Soil bacteria play a key role in the ecological and evolutionary responses of agricultural ecosystems. Domestic herbivore grazing is known to influence soil bacterial community. However, the effects of grazing and its major driving factors on soil bacterial community remain unknown for different plant community compositions under increasing grazing intensity. Thus, to investigate soil bacterial community diversity under five plant community compositions (Grass; Leymus chinensis; Forb; L. chinensis & Forb; and Legume), we performed a four-year field experiment with different grazing intensity treatments (no grazing; light grazing, 4 sheep·ha−1; and heavy grazing, 6 sheep·ha−1) in a grassland in China. Total DNA was obtained from soil samples collected from the plots in August, and polymerase chain reaction (PCR) analysis and denaturing gradient gel electrophoresis (DGGE) fingerprinting were used to investigate soil bacterial community. The results showed that light grazing significantly increased indices of soil bacterial community diversity for the Forb and Legume groups but not the Grass and L. chinensis groups. Heavy grazing significantly reduced these soil bacterial diversity indices, except for the Pielou evenness index in the Legume group. Further analyses revealed that the soil N/P ratio, electrical conductivity (EC), total nitrogen (TN) and pH were the major environmental factors affecting the soil bacterial community. Our study suggests that the soil bacterial community diversity was influenced by grazing intensity and plant community composition in a meadow steppe. The present study provides a baseline assessment of the soil bacterial community diversity in a temperate meadow steppe. PMID:27467221

  3. Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members

    PubMed Central

    Willsey, Graham G.; Wargo, Matthew J.

    2015-01-01

    Bacteria secrete enzymes into the extracellular space to hydrolyze macromolecules into constituents that can be imported for microbial nutrition. In bacterial communities, these enzymes and their resultant products can be modeled as community property. Our goal was to investigate the impact of individual community member absence on the resulting community production of exoenzymes (extracellular enzymes) involved in lipid and protein hydrolysis. Our model community contained nine bacteria isolated from the potable water system of the International Space Station. Bacteria were grown in static conditions individually, all together, or in all combinations of eight species and exoproduct production was measured by colorimetric or fluorometric reagents to assess short chain and long chain lipases, choline-specific phospholipases C, and proteases. The exoenzyme production of each species grown alone varied widely, however, the enzyme activity levels of the mixed communities were functionally robust to absence of any single species, with the exception of phospholipase C production in one community. For phospholipase C, absence of Chryseobacterium gleum led to increased choline-specific phospholipase C production, correlated with increased growth of Burkholderia cepacia and Sphingomonas sanguinis. Because each individual species produced different enzyme activity levels in isolation, we calculated an expected activity value for each bacterial mixture using input levels or known final composition. This analysis suggested that robustness of each exoenzyme activity is not solely mediated by community composition, but possibly influenced by bacterial communication, which is known to regulate such pathways in many bacteria. We conclude that in this simplified model of a drinking water bacterial community, community structure imposes constraints on production and/or secretion of exoenzymes to generate a level appropriate to exploit a given nutrient environment. PMID:26599415

  4. Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members.

    PubMed

    Willsey, Graham G; Wargo, Matthew J

    2015-01-01

    Bacteria secrete enzymes into the extracellular space to hydrolyze macromolecules into constituents that can be imported for microbial nutrition. In bacterial communities, these enzymes and their resultant products can be modeled as community property. Our goal was to investigate the impact of individual community member absence on the resulting community production of exoenzymes (extracellular enzymes) involved in lipid and protein hydrolysis. Our model community contained nine bacteria isolated from the potable water system of the International Space Station. Bacteria were grown in static conditions individually, all together, or in all combinations of eight species and exoproduct production was measured by colorimetric or fluorometric reagents to assess short chain and long chain lipases, choline-specific phospholipases C, and proteases. The exoenzyme production of each species grown alone varied widely, however, the enzyme activity levels of the mixed communities were functionally robust to absence of any single species, with the exception of phospholipase C production in one community. For phospholipase C, absence of Chryseobacterium gleum led to increased choline-specific phospholipase C production, correlated with increased growth of Burkholderia cepacia and Sphingomonas sanguinis. Because each individual species produced different enzyme activity levels in isolation, we calculated an expected activity value for each bacterial mixture using input levels or known final composition. This analysis suggested that robustness of each exoenzyme activity is not solely mediated by community composition, but possibly influenced by bacterial communication, which is known to regulate such pathways in many bacteria. We conclude that in this simplified model of a drinking water bacterial community, community structure imposes constraints on production and/or secretion of exoenzymes to generate a level appropriate to exploit a given nutrient environment. PMID:26599415

  5. Molecular analysis of bacterial communities from a Canadian high Arctic polythermal glacier

    NASA Astrophysics Data System (ADS)

    Bhatia, M.; Sharp, M.; Foght, J.

    2003-04-01

    The goal of this study is to characterize the bacterial communities beneath, on, and adjacent to a high Arctic polythermal glacier, with a view to understanding the origins of the subglacial microbial population. The study site is John Evans Glacier (JEG), Ellesmere Island, Canada. JEG is a polythermal glacier consisting of a core of ice at the pressure melting point, surrounded by an outer layer of cold ice. Basal melting and seasonal inputs of meltwater from the glacier surface provide liquid water for subglacial microbial life. Samples were collected from the subglacial, supraglacial, and proglacial environments at JEG. Subglacial samples included basal ice and water that had been stored beneath the glacier. Dry snow, wet snow, and water from supraglacial streams were collected as representatives of the supraglacial environment, which changes in character through the melt season. Sediments and algal mats were collected from an area directly in front of the glacier terminus and along a transect adjacent to the glacier to reflect the developing proglacial environment. Hydrochemical analyses were conducted to assess the role of microbial activity in biogeochemical processes. To compare the bacterial communities, molecular techniques were applied to total community DNA that was released from the samples by a physical cell disruption technique. The polymerase chain reaction (PCR) was used with bacterial-specific primers, one of which was fluorescently labeled, to amplify community 16S rDNA genes. Single digestions with the restriction enzymes HaeIII and HhaI were performed to conduct inter- and intra-community comparisons of the terminal restriction fragment length polymorphisms (tRFLPs) of the fluorescently tagged amplified 16S rDNA genes. Preliminary results indicate that although some species are present throughout the different environments, several species are unique to each particular habitat. Further study of replicate tRFLP data and statistical analyses will

  6. Subalpine conifers in different geographical locations host highly similar foliar bacterial endophyte communities.

    PubMed

    Carrell, Alyssa A; Carper, Dana L; Frank, A Carolin

    2016-08-01

    Pines in the subalpine environment at Niwot Ridge, CO, have been found to host communities of acetic acid bacteria (AAB) within their needles. The significance and ubiquity of this pattern is not known, but recent evidence of nitrogen (N)-fixing activity in Pinus flexilis (limber pine) foliage calls for a better understanding of the processes that regulate endophytic communities in forest tree canopies. Here, to test if AAB dominate the foliar bacterial microbiota in other subalpine locations, we compared the 16S rRNA community in needles from P. flexilis and P. contorta (lodgepole pine) growing in the Eastern Sierra Nevada, CA, and Niwot Ridge, CO. AAB made up the majority of the bacterial community in both species at both sites. Multiple distinct AAB taxa, resolved at the single nucleotide level, were shared across host species and sites, with dominant OTUs identical or highly similar to database sequences from cold environments, including high altitude air sampled in Colorado, and the endosphere of Arctic plants. Our results suggest strong selection for community composition, potentially amplified by the long lifespan of individual Pinus needles, along with low dispersal constraints on canopy bacteria. PMID:27267931

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

    PubMed

    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

  8. Imaging the Population Dynamics of Bacterial Communities in the Zebrafish Gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Zac Stephens, W.; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

    2013-03-01

    The vertebrate gut is home to a diverse microbial ecosystem whose composition has a strong influence on the development and health of the host organism. While researchers are increasingly able to identify the constituent members of the microbiome, very little is known about the spatial and temporal dynamics of commensal microbial communities, including the mechanisms by which communities nucleate, grow, and interact. We address these issues using a model organism: the larval zebrafish (Danio rerio) prepared microbe-free and inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging with light sheet fluorescence microscopy enables visualization of individual bacterial cells as well as growing colonies over the entire volume of the gut over periods up to 24 hours. We analyze the structure and dynamics of imaged bacterial communities, uncovering correlations between population size, growth rates, and the timing of inoculations that suggest the existence of active changes in the host environment induced by early bacterial exposure. Our data provide the first visualizations of gut microbiota development over an extended period of time in a vertebrate.

  9. Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima

    PubMed Central

    Zhang, Fan; Vicente, Jan; Hill, Russell T.

    2014-01-01

    Sponges that harbor microalgal or, cyanobacterial symbionts may benefit from photosynthetically derived carbohydrates, which are rich in carbon but devoid of nitrogen, and may therefore encounter nitrogen limitation. Diazotrophic communities associated with two Caribbean sponges, Ircinia strobilina and Mycale laxissima were studied in a time series during which three individuals of each sponge were collected in four time points (5:00 AM, 12:00 noon, 5:00 PM, 10:00 PM). nifH genes were successfully amplified from the corresponding gDNA and cDNA pools and sequenced by high throughput 454 amplicon sequencing. In both sponges, over half the nifH transcripts were classified as from cyanobacteria and the remainder from heterotrophic bacteria. We found various groups of bacteria actively expressing the nifH gene during the entire day-night cycle, an indication that the nitrogen fixation potential was fully exploited by different nitrogen fixing bacteria groups associated with their hosts. This study showed for the first time the dynamic changes in the activity of the diazotrophic bacterial communities in marine sponges. Our study expands understanding of the diazotrophic groups that contribute to the fixed nitrogen pool in the benthic community. Sponge bacterial community-associated diazotrophy may have an important impact on the nitrogen biogeochemical cycle in the coral reef ecosystem. PMID:25389420

  10. Species Composition of Bacterial Communities Influences Attraction of Mosquitoes to Experimental Plant Infusions

    PubMed Central

    Ponnusamy, Loganathan; Wesson, Dawn M.; Arellano, Consuelo; Schal, Coby

    2013-01-01

    In the container habitats of immature mosquitoes, catabolism of plant matter and other organic detritus by microbial organisms produces metabolites that mediate the oviposition behavior of Aedes aegypti and Aedes albopictus. Public health agencies commonly use oviposition traps containing plant infusions for monitoring populations of these mosquito species, which are global vectors of dengue viruses. In laboratory experiments, gravid females exhibited significantly diminished responses to experimental infusions made with sterilized white oak leaves, showing that attractive odorants were produced through microbial metabolic activity. We evaluated effects of infusion concentration and fermentation time on attraction of gravid females to infusions made from senescent bamboo or white oak leaves. We used plate counts of heterotrophic bacteria, total counts of 4′,6-diamidino-2-phenylindole-stained bacterial cells, and 16S ribosomal DNA (rDNA) polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) to show that changes in the relative abundance of bacteria and the species composition of bacterial communities influenced attraction of gravid A. aegypti and A. albopictus mosquitoes to infusions. DGGE profiles showed that bacterial species composition in infusions changed over time. Principal components analysis indicated that oviposition responses to plant infusions were in general most affected by bacterial diversity and abundance. Analysis of bacterial 16S rDNA sequences derived from DGGE bands revealed that Proteo-bacteria (Alpha-, Beta-, Delta-, and Gamma-) were the predominant bacteria detected in both types of plant infusions. Gravid A. aegypti were significantly attracted to a mix of 14 bacterial species cultured from bamboo leaf infusion. The oviposition response of gravid mosquitoes to plant infusions is strongly influenced by abundance and diversity of bacterial species, which in turn is affected by plant species, leaf biomass, and fermentation

  11. Salinity and Bacterial Diversity: To What Extent Does the Concentration of Salt Affect the Bacterial Community in a Saline Soil?

    PubMed Central

    Canfora, Loredana; Bacci, Giovanni; Pinzari, Flavia; Lo Papa, Giuseppe; Dazzi, Carmelo; Benedetti, Anna

    2014-01-01

    In this study, the evaluation of soil characteristics was coupled with a pyrosequencing analysis of the V2-V3 16S rRNA gene region in order to investigate the bacterial community structure and diversity in the A horizon of a natural saline soil located in Sicily (Italy). The main aim of the research was to assess the organisation and diversity of microbial taxa using a spatial scale that revealed physical and chemical heterogeneity of the habitat under investigation. The results provided information on the type of distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH. The analysis of bacterial 16S rRNA showed differences in bacterial composition and diversity due to a variable salt concentration in the soil. The bacterial community showed a statistically significant spatial variability. Some bacterial phyla appeared spread in the whole area, whatever the salinity gradient. It emerged therefore that a patchy saline soil can not contain just a single microbial community selected to withstand extreme osmotic phenomena, but many communities that can be variously correlated to one or more environmental parameters. Sequences have been deposited to the SRA database and can be accessed on ID Project PRJNA241061. PMID:25188357

  12. Functional diversity and dynamics of bacterial communities in a membrane bioreactor for the treatment of metal-working fluid wastewater.

    PubMed

    Grijalbo, Lucía; Garbisu, Carlos; Martín, Iker; Etxebarria, Javier; Gutierrez-Mañero, F Javier; Lucas Garcia, Jose Antonio

    2015-12-01

    An extensive microbiological study has been carried out in a membrane bioreactor fed with activated sludge and metal-working fluids. Functional diversity and dynamics of bacterial communities were studied with different approaches. Functional diversity of culturable bacterial communities was studied with different Biolog™ plates. Structure and dynamics of bacterial communities were studied in culturable and in non-culturable fractions using a 16S rRNA analysis. Among the culturable bacteria, Alphaproteobacteria and Gammaproteobacteria were the predominant classes. However, changes in microbial community structure were detected over time. Culture-independent analysis showed that Betaproteobacteria was the most frequently detected class in the membrane bioreactor (MBR) community with Zoogloea and Acidovorax as dominant genera. Also, among non-culturable bacteria, a process of succession was observed. Longitudinal structural shifts observed were more marked for non-culturable than for culturable bacteria, pointing towards an important role in the MBR performance. Microbial community metabolic abilities assessed with Biolog™ Gram negative, Gram positive and anaerobic plates also showed differences over time for Shannon's diversity index, kinetics of average well colour development, and the intensely used substrates by bacterial community in each plate. PMID:26608762

  13. Characteristics of extracellular polymeric substances and bacterial communities in an anaerobic membrane bioreactor coupled with online ultrasound equipment.

    PubMed

    Yu, Zhiyong; Wen, Xianghua; Xu, Meilan; Huang, Xia

    2012-08-01

    Two parallel anaerobic membrane bioreactors (MBRs), integrated with or without ultrasound equipment for online membrane fouling control (US-AnMBR, or AnMBR) were established to digest waste activated sludge (WAS). The characteristics of bound extracellular polymeric substances (EPS) and bacterial communities in the systems were investigated for further understanding of the membrane fouling mechanisms. Ultrasound was an effective method for reducing cake layer resistance. A relatively high amount of bound EPS were found in the cake layer, especially for the US-AnMBR, by responding to the external forces (i.e. cross flow and ultrasound). High-throughput pyrosequencing and denaturing gradient gel electrophoresis (DGGE) were applied to analyze the bacterial diversity. Some bacterial populations contributing to membrane fouling were identified to accumulate in the cake layer, such as Peptococcaceae, Bacteroides and Syntrophobacterales. Since the ultrasounded retentate was recirculated back to the reactor, the bacterial community in the digested sludge was affected. PMID:22621809

  14. Bacterial communities in Arctic first-year drift ice during the winter/spring transition.

    PubMed

    Eronen-Rasimus, Eeva; Piiparinen, Jonna; Karkman, Antti; Lyra, Christina; Gerland, Sebastian; Kaartokallio, Hermanni

    2016-08-01

    Horizontal and vertical variability of first-year drift-ice bacterial communities was investigated along a North-South transect in the Fram Strait during the winter/spring transition. Two different developmental stages were captured along the transect based on the prevailing environmental conditions and the differences in bacterial community composition. The differences in the bacterial communities were likely driven by the changes in sea-ice algal biomass (2.6-5.6 fold differences in chl-a concentrations). Copiotrophic genera common in late spring/summer sea ice, such as Polaribacter, Octadecabacter and Glaciecola, dominated the bacterial communities, supporting the conclusion that the increase in the sea-ice algal biomass was possibly reflected in the sea-ice bacterial communities. Of the dominating bacterial genera, Polaribacter seemed to benefit the most from the increase in algal biomass, since they covered approximately 39% of the total community at the southernmost stations with higher (>6 μg l(-1) ) chl-a concentrations and only 9% at the northernmost station with lower chl-a concentrations (<6 μg l(-1) ). The sea-ice bacterial communities also varied between the ice horizons at all three stations and thus we recommend that for future studies multiple ice horizons be sampled to cover the variability in sea-ice bacterial communities in spring. PMID:27264318

  15. Restructuring of endophytic bacterial communities in grapevine yellows-diseased and recovered Vitis vinifera L. plants.

    PubMed

    Bulgari, Daniela; Casati, Paola; Crepaldi, Paola; Daffonchio, Daniele; Quaglino, Fabio; Brusetti, Lorenzo; Bianco, Piero Attilio

    2011-07-01

    Length heterogeneity-PCR assays, combined with statistical analyses, highlighted that the endophytic bacterial community associated with healthy grapevines was characterized by a greater diversity than that present in diseased and recovered plants. The findings suggest that phytoplasmas can restructure the bacterial community by selecting endophytic strains that could elicit a plant defense response. PMID:21622794

  16. Indoor Heating Drives Water Bacterial Growth and Community Metabolic Profile Changes in Building Tap Pipes during the Winter Season

    PubMed Central

    Zhang, Hai-Han; Chen, Sheng-Nan; Huang, Ting-Lin; Shang, Pan-Lu; Yang, Xiao; Ma, Wei-Xing

    2015-01-01

    The growth of the bacterial community harbored in indoor drinking water taps is regulated by external environmental factors, such as indoor temperature. However, the effect of indoor heating on bacterial regrowth associated with indoor drinking water taps is poorly understood. In the present work, flow cytometry and community-level sole-carbon-source utilization techniques were combined to explore the effects of indoor heating on water bacterial cell concentrations and community carbon metabolic profiles in building tap pipes during the winter season. The results showed that the temperature of water stagnated overnight (“before”) in the indoor water pipes was 15–17 °C, and the water temperature decreased to 4–6 °C after flushing for 10 min (“flushed”). The highest bacterial cell number was observed in water stagnated overnight, and was 5–11 times higher than that of flushed water. Meanwhile, a significantly higher bacterial community metabolic activity (AWCD590nm) was also found in overnight stagnation water samples. The significant “flushed” and “taps” values indicated that the AWCD590nm, and bacterial cell number varied among the taps within the flushed group (p < 0.01). Heatmap fingerprints and principle component analyses (PCA) revealed a significant discrimination bacterial community functional metabolic profiles in the water stagnated overnight and flushed water. Serine, threonine, glucose-phosphate, ketobutyric acid, phenylethylamine, glycerol, putrescine were significantly used by “before” water samples. The results suggested that water stagnated at higher temperature should be treated before drinking because of bacterial regrowth. The data from this work provides useful information on reasonable utilization of drinking water after stagnation in indoor pipes during indoor heating periods. PMID:26516885

  17. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health

    PubMed Central

    Wei, Zhong; Yang, Tianjie; Friman, Ville-Petri; Xu, Yangchun; Shen, Qirong; Jousset, Alexandre

    2015-01-01

    Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity–invasion resistance relationships in bacterial rhizosphere communities. PMID:26400552

  18. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health.

    PubMed

    Wei, Zhong; Yang, Tianjie; Friman, Ville-Petri; Xu, Yangchun; Shen, Qirong; Jousset, Alexandre

    2015-01-01

    Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity-invasion resistance relationships in bacterial rhizosphere communities. PMID:26400552

  19. Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity

    PubMed Central

    Adams, Heather E.; Crump, Byron C.; Kling, George W.

    2015-01-01

    Storm events can pulse nutrients and carbon from soils and provide an important subsidy to food webs in oligotrophic streams and lakes. Bacterial nutrient limitation and the potential response of stream aquatic bacteria to storm events was investigated in arctic tundra environments by manipulating both water temperature and inorganic nutrient concentrations in short (up to 4 days) and long duration (up to 2 weeks) laboratory mesocosm experiments. Inorganic N and P additions increased bacterial production (14C-labeled leucine uptake) up to seven times over controls, and warmer incubation temperatures increased the speed of this response to added nutrients. Bacterial cell numbers also increased in response to temperature and nutrient additions with cell-specific carbon uptake initially increasing and then declining after 2 days. Bacterial community composition (BCC; determined by means of 16S denaturing gradient gel electrophoresis fingerprinting) shifted rapidly in response to changes in incubation temperature and the addition of nutrients, within 2 days in some cases. While the bacteria in these habitats responded to nutrient additions with rapid changes in productivity and community composition, water temperature controlled the speed of the metabolic response and affected the resultant change in bacterial community structure, constraining the potential responses to pulsed nutrient subsidies associated with storm events. In all cases, at higher nutrient levels and temperatures the effect of initial BCC on bacterial activity was muted, suggesting a consistent, robust interaction of temperature, and nutrients controlling activity in these aquatic systems. PMID:25873916

  20. The Matrix Reloaded: How Sensing the Extracellular Matrix Synchronizes Bacterial Communities

    PubMed Central

    Steinberg, Nitai

    2015-01-01

    In response to chemical communication, bacterial cells often organize themselves into complex multicellular communities that carry out specialized tasks. These communities are frequently referred to as biofilms, which involve the collective behavior of different cell types. Like cells of multicellular eukaryotes, the biofilm cells are surrounded by self-produced polymers that constitute the extracellular matrix (ECM), which binds them to each other and to the surface. In multicellular eukaryotes, it has been evident for decades that cell-ECM interactions control multiple cellular processes during development. While cells both in biofilms and in multicellular eukaryotes are surrounded by ECM and activate various genetic programs, until recently it has been unclear whether cell-ECM interactions are recruited in bacterial communicative behaviors. In this review, we describe the examples reported thus far for ECM involvement in control of cell behavior throughout the different stages of biofilm formation. The studies presented in this review have provided a newly emerging perspective of the bacterial ECM as an active player in regulation of biofilm development. PMID:25825428

  1. Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments.

    PubMed

    Laverock, Bonnie; Smith, Cindy J; Tait, Karen; Osborn, A Mark; Widdicombe, Steve; Gilbert, Jack A

    2010-12-01

    Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing

  2. Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

    PubMed

    Shi, Yu; Xiang, Xingjia; Shen, Congcong; Chu, Haiyan; Neufeld, Josh D; Walker, Virginia K; Grogan, Paul

    2015-01-01

    The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H') were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064

  3. Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

    PubMed Central

    Shi, Yu; Xiang, Xingjia; Shen, Congcong; Neufeld, Josh D.; Walker, Virginia K.

    2014-01-01

    The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064

  4. Bacterial diversity and active biomass in full-scale granular activated carbon filters operated at low water temperatures.

    PubMed

    Kaarela, Outi E; Härkki, Heli A; Palmroth, Marja R T; Tuhkanen, Tuula A

    2015-01-01

    Granular activated carbon (GAC) filtration enhances the removal of natural organic matter and micropollutants in drinking water treatment. Microbial communities in GAC filters contribute to the removal of the biodegradable part of organic matter, and thus help to control microbial regrowth in the distribution system. Our objectives were to investigate bacterial community dynamics, identify the major bacterial groups, and determine the concentration of active bacterial biomass in full-scale GAC filters treating cold (3.7-9.5°C), physicochemically pretreated, and ozonated lake water. Three sampling rounds were conducted to study six GAC filters of different operation times and flow modes in winter, spring, and summer. Total organic carbon results indicated that both the first-step and second-step filters contributed to the removal of organic matter. Length heterogeneity analysis of amplified 16S rRNA genes illustrated that bacterial communities were diverse and considerably stable over time. α-Proteobacteria, β-Proteobacteria, and Nitrospira dominated in all of the GAC filters, although the relative proportion of dominant phylogenetic groups in individual filters differed. The active bacterial biomass accumulation, measured as adenosine triphosphate, was limited due to low temperature, low flux of nutrients, and frequent backwashing. The concentration of active bacterial biomass was not affected by the moderate seasonal temperature variation. In summary, the results provided an insight into the biological component of GAC filtration in cold water temperatures and the operational parameters affecting it. PMID:25242545

  5. Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions

    PubMed Central

    Langenheder, Silke; Lindström, Eva S.; Tranvik, Lars J.

    2006-01-01

    The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration. PMID:16391045

  6. Changes in intestinal bacterial communities are closely associated with shrimp disease severity.

    PubMed

    Xiong, Jinbo; Wang, Kai; Wu, Jinfeng; Qiuqian, Linglin; Yang, Kunjie; Qian, Yunxia; Zhang, Demin

    2015-08-01

    Increasing evidence has revealed a close association between intestinal bacterial communities and human health. However, given that host phylogeny shapes the composition of intestinal microbiota, it is unclear whether changes in intestinal microbiota structure in relation to shrimp health status. In this study, we collected shrimp and seawater samples from ponds with healthy and diseased shrimps to understand variations in bacterial communities among habitats (water and intestine) and/or health status. The bacterial communities were clustered according to the original habitat and health status. Habitat and health status constrained 14.6 and 7.7 % of the variation in bacterial communities, respectively. Changes in shrimp intestinal bacterial communities occurred in parallel with changes in disease severity, reflecting the transition from a healthy to a diseased state. This pattern was further evidenced by 38 bacterial families that were significantly different in abundance between healthy and diseased shrimps; moderate changes were observed in shrimps with sub-optimal health. In addition, within a given bacterial family, the patterns of enrichment or decrease were consistent with the known functions of those bacteria. Furthermore, the identified 119 indicator taxa exhibited a discriminative pattern similar to the variation in the community as a whole. Overall, this study suggests that changes in intestinal bacterial communities are closely associated with the severity of shrimp disease and that indicator taxa can be used to evaluate shrimp health status. PMID:25947250

  7. Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.

    PubMed

    Barbosa Lima, Amanda; Cannavan, Fabiana Souza; Navarrete, Acacio Aparecido; Teixeira, Wenceslau Geraldes; Kuramae, Eiko Eurya; Tsai, Siu Mui

    2015-05-01

    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes. PMID:25103911

  8. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

    SciTech Connect

    Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.; Suen, Garret; Tringe, Susannah G.; Adams, Sandra M.; Barry, Kerrie W.; Nicora, Carrie D.; Piehowski, Paul D.; Purvine, Samuel O.; Starrett, Gabriel J.; Goodwin, Lynne A.; Smith, Richard D.; Lipton, Mary S.; Currie, Cameron R.

    2012-09-01

    Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant Neotropical herbivores cultivate symbiotic fungus gardens on massive quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers in mature Atta colonies. Here we use metagenomic, and metaproteomic techniques to characterize the bacterial diversity and overall physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that, in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter, and Escherichia. We show that these bacterial communities possess genes commonly associated with lignocellulose degradation, and likely participate in the processing of plant biomass. Additionally, we demonstrate that bacteria in these environments encode a diverse suite of biosynthetic pathways, and that they may enrich the nitrogen-poor forage of the ants with B-vitamins, amino acids, and proteins. These results are consistent with the hypothesis that fungus gardens are highly-specialized fungus-bacteria communities that efficiently convert plant material into usable energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities to the ecology and evolution of herbivorous metazoans.

  9. Metagenomic analysis of bacterial communities on Dokdo Island.

    PubMed

    Kim, Ye-Eun; Yoon, Hyeokjun; Kim, Miae; Nam, Yoon-Jong; Kim, Hyun; Seo, Yeonggyo; Lee, Gyeong-Min; Ja Kim, Young; Kong, Won-Sik; Kim, Jong-Guk; Seu, Young-Bae

    2014-01-01

    Dokdo, located east of the mainland of South Korea, is a volcanic island designated as a natural monument of South Korea due to its ecological value. Dokdo is divided into Dongdo and Seodo, islands with geological differences. The soil bacterial communities on Dokdo (Dongdo and Seodo) were analyzed using the pyrosequencing method. There were 1,693 and 1,408 operational taxonomic units (OTU) from Dongdo and Seodo, respectively. The statistical analyses (rarefaction curves as well as Chao1, Shannon, and Simpson indices) showed that bacterial diversity was slightly higher in Dongdo than Seodo. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. From the phylum level down to the species level, the number of classified reads considerably decreased due to the absence of information concerning unculturable or unidentified bacteria to date. Among the 36 phyla identified, three phyla (Proteobacteria, Actinobacteria and Acidobacteria) accounted for around 74.64%. The taxonomic composition was similar at the higher ranks (family and above) between Dongdo and Seodo, but a little different at the genus level. There were also various differences in the relative abundance of taxonomic ranks between Dongdo and Seodo. In particular, the proportion of the genus Acidobacterium (of the phylum Acidobacteria) was about six times higher in Seodo than Dongdo. In addition, the percentage of the genus Mycobacterium (of the phylum Actinobacteria) was nearly three times higher in Seodo than Dongdo, and the proportion of the genus Gaiella was about 3.7 times higher in Dongdo than Seodo. Overall, through the metagenomic analysis, the number of species identified in Dongdo and Seodo was 1,239 and 1,055, respectively. This information on the numerous culturable and unculturable bacteria is expected to help in the screening of new species in Dokdo. PMID:24859864

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

    PubMed

    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. PMID:26924012

  11. Spatial and temporal variability of bacterial communities within a combined sewer system.

    PubMed

    Jensen, Henriette Stokbro; Sekar, Raju; Shepherd, Will J; Osborn, Andrew M; Tait, Simon; Biggs, Catherine A

    2016-08-01

    This study describes the temporal and spatial variability of bacterial communities within a combined sewer system in England. Sampling was conducted over 9 months in a sewer system with intensive monitoring of hydraulic conditions. The bacterial communities were characterized by 16S rRNA gene-targeted terminal restriction fragment length polymorphism analysis. These data were related to the hydraulic data as well as the sample type, location, and time. Temporal and spatial variation was observed between and within wastewater communities and biofilm communities. The bacterial communities in biofilm were distinctly different from the communities in wastewater and exhibited greater spatial variation, while the wastewater communities exhibited variability between different months of sampling. This study highlights the variation of bacterial communities between biofilm and wastewater, and has shown both spatial and temporal variations in bacterial communities in combined sewers. The temporal variation is of interest for in-sewer processes, for example, sewer odor generation, as field measurements for these processes are often carried out over short durations and may therefore not capture the influence of this temporal variation of the bacterial communities. PMID:27063341

  12. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice.

    PubMed

    Howe, Adina; Ringus, Daina L; Williams, Ryan J; Choo, Zi-Ning; Greenwald, Stephanie M; Owens, Sarah M; Coleman, Maureen L; Meyer, Folker; Chang, Eugene B

    2016-05-01

    To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health. PMID:26473721

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Biodegradation of Leonardite by an alkali-producing bacterial community and characterization of the degraded products.

    PubMed

    Gao, Tong-Guo; Jiang, Feng; Yang, Jin-Shui; Li, Bao-Zhen; Yuan, Hong-Li

    2012-03-01

    In this study, three bacterial communities were obtained from 12 Leonardite samples with the aim of identifying a clean, effective, and economic technique for the dissolution of Leonardite, a type of low-grade coal, in the production of humic acid (HA). The biodegradation ability and characteristics of the degraded products of the most effective bacterial community (MCSL-2), which degraded 50% of the Leonardite within 21 days, were further investigated. Analyses of elemental composition, (13)C NMR, and Fourier transform infrared revealed that the contents of C, O, and aliphatic carbon were similar in biodegraded humic acid (bHA) and chemically (alkali) extracted humic acid (cHA). However, the N and carboxyl carbon contents of bHA was higher than that of cHA. Furthermore, a positive correlation was identified between the degradation efficiency and the increasing pH of the culture medium, while increases of manganese peroxidase and esterase activities were also observed. These data demonstrated that both alkali production and enzyme reactions were involved in Leonardite solubilization by MCSL-2, although the former mechanism predominated. No fungus was observed by microscopy. Only four bacterial phylotypes were recognized, and Bacillus licheniformis-related bacteria were identified as the main group in MCSL-2 by analysis of amplified 16S rRNA genes, thus demonstrating that Leonardite degradation ability has a limited distribution in bacteria. Hormone-like bioactivities of bHA were also detected. In this study, a bacterial community capable of Leonardite degradation was identified and the products characterized. These data implicate the use of such bacteria for the exploitation of Leonardite as a biofertilizer. PMID:22075634

  15. Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry

    PubMed Central

    Kumari, Priyanka; Choi, Hong L.; Sudiarto, Sartika I. A.

    2015-01-01

    The bacterial community assembly patterns and processes are poorly understood in pig manure slurry. We collected pig manure slurry samples during the winter and summer seasons from eight commercial pig farms in South Korea. The V3 region of 16S rRNA genes was PCR amplified and sequenced using paired-end Illumina technology for in-depth characterization of bacterial community. Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Tenericutes were the predominant bacterial phyla present in slurry samples. Bacterial taxonomic community composition was not influenced by the season; however, phylogenetic community composition was affected by seasonal variations. The community composition and diversity patterns were strongly influenced by pH. The bacterial diversity indices showed a unimodal relationship with pH. Phylogenetic signals were detected over only short phylogenetic distances, revealing that closely related bacterial operational taxonomic units (OTUs) tend to co-occur in the same environment; hence, they are ecologically similar. Across all samples, a niche-based process, through strong environmental filtering imposed by pH, primarily governed bacterial community assembly; however, in samples close to the neutral pH range, the role of environmental filtering was decreased due to neutral community assembly. In summary, pH emerged as the major physico-chemical variable in pig manure slurry that regulates the relative importance of niche-based and neutral processes in shaping the community assembly of bacteria. PMID:26422375

  16. Pyrosequencing Reveals a Core Community of Anodic Bacterial Biofilms in Bioelectrochemical Systems from China

    PubMed Central

    Xiao, Yong; Zheng, Yue; Wu, Song; Zhang, En-Hua; Chen, Zheng; Liang, Peng; Huang, Xia; Yang, Zhao-Hui; Ng, I-Son; Chen, Bor-Yann; Zhao, Feng

    2015-01-01

    Bioelectrochemical systems (BESs) are promising technologies for energy and product recovery coupled with wastewater treatment, and the core microbial community in electrochemically active biofilm in BESs remains controversy. In the present study, 7 anodic communities from 6 bioelectrochemical systems in 4 labs in southeast, north and south-central of China are explored by 454 pyrosequencing. A total of 251,225 effective sequences are obtained for 7 electrochemically active biofilm samples at 3% cutoff level. While Alpha-, Beta-, and Gamma-proteobacteria are the most abundant classes (averaging 16.0–17.7%), Bacteroidia and Clostridia are the two sub-dominant and commonly shared classes. Six commonly shared genera i.e., Azospira, Azospirillum, Acinetobacter, Bacteroides, Geobacter, Pseudomonas, and Rhodopseudomonas dominate the electrochemically active communities and are defined as core genera. A total of 25 OTUs with average relative abundance >0.5% were selected and designated as core OTUs, and some species relating to these OTUs have been reported electrochemically active. Furthermore, cyclic voltammetry and chronoamperometry tests show that two strains from Acinetobacter guillouiae and Stappia indica, bacteria relate to two core OTUs, are electrochemically active. Using randomly selected bioelectrochemical systems, the study has presented extremely diverse bacterial communities in anodic biofilms, though, we still can suggest some potentially microbes for investigating the electrochemical mechanisms in bioelectrochemical systems. PMID:26733958

  17. Pyrosequencing Reveals a Core Community of Anodic Bacterial Biofilms in Bioelectrochemical Systems from China.

    PubMed

    Xiao, Yong; Zheng, Yue; Wu, Song; Zhang, En-Hua; Chen, Zheng; Liang, Peng; Huang, Xia; Yang, Zhao-Hui; Ng, I-Son; Chen, Bor-Yann; Zhao, Feng

    2015-01-01

    Bioelectrochemical systems (BESs) are promising technologies for energy and product recovery coupled with wastewater treatment, and the core microbial community in electrochemically active biofilm in BESs remains controversy. In the present study, 7 anodic communities from 6 bioelectrochemical systems in 4 labs in southeast, north and south-central of China are explored by 454 pyrosequencing. A total of 251,225 effective sequences are obtained for 7 electrochemically active biofilm samples at 3% cutoff level. While Alpha-, Beta-, and Gamma-proteobacteria are the most abundant classes (averaging 16.0-17.7%), Bacteroidia and Clostridia are the two sub-dominant and commonly shared classes. Six commonly shared genera i.e., Azospira, Azospirillum, Acinetobacter, Bacteroides, Geobacter, Pseudomonas, and Rhodopseudomonas dominate the electrochemically active communities and are defined as core genera. A total of 25 OTUs with average relative abundance >0.5% were selected and designated as core OTUs, and some species relating to these OTUs have been reported electrochemically active. Furthermore, cyclic voltammetry and chronoamperometry tests show that two strains from Acinetobacter guillouiae and Stappia indica, bacteria relate to two core OTUs, are electrochemically active. Using randomly selected bioelectrochemical systems, the study has presented extremely diverse bacterial communities in anodic biofilms, though, we still can suggest some potentially microbes for investigating the electrochemical mechanisms in bioelectrochemical systems. PMID:26733958

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

    PubMed

    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

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

    PubMed Central

    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. Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities.

    PubMed

    Ceja-Navarro, Javier A; Rivera-Orduña, Flor N; Patiño-Zúñiga, Leonardo; Vila-Sanjurjo, Antón; Crossa, José; Govaerts, Bram; Dendooven, Luc

    2010-06-01

    Bacterial communities are important not only in the cycling of organic compounds but also in maintaining ecosystems. Specific bacterial groups can be affected as a result of changes in environmental conditions caused by human activities, such as agricultural practices. The aim of this study was to analyze the effects of different forms of tillage and residue management on soil bacterial communities by using phylogenetic and multivariate analyses. Treatments involving zero tillage (ZT) and conventional tillage (CT) with their respective combinations of residue management, i.e., removed residue (-R) and kept residue (+R), and maize/wheat rotation, were selected from a long-term field trial started in 1991. Analysis of bacterial diversity showed that soils under zero tillage and crop residue retention (ZT/+R) had the highest levels of diversity and richness. Multivariate analysis showed that beneficial bacterial groups such as fluorescent Pseudomonas spp. and Burkholderiales were favored by residue retention (ZT/+R and CT/+R) and negatively affected by residue removal (ZT/-R). Zero-tillage treatments (ZT/+R and ZT/-R) had a positive effect on the Rhizobiales group, with its main representatives related to Methylosinus spp. known as methane-oxidizing bacteria. It can be concluded that practices that include reduced tillage and crop residue retention can be adopted as safer agricultural practices to preserve and improve the diversity of soil bacterial communities. PMID:20382808

  1. Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces

    PubMed Central

    Frias-Lopez, Jorge; Zerkle, Aubrey L.; Bonheyo, George T.; Fouke, Bruce W.

    2002-01-01

    Distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (BBD) on the southern Caribbean island of Curaçao, Netherlands Antilles. PCR amplification and sequencing of bacterial 16S rRNA genes (rDNA) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. The molecular sequences exhibited less than 5% similarity in bacterial community composition between seawater and the healthy, black band diseased, and dead coral surfaces. The BBD bacterial mat rapidly migrates across and kills the coral tissue. Clone libraries constructed from the BBD mat were comprised of eight bacterial divisions and 13% unknowns. Several sequences representing bacteria previously found in other marine and terrestrial organisms (including humans) were isolated from the infected coral surfaces, including Clostridium spp., Arcobacter spp., Campylobacter spp., Cytophaga fermentans, Cytophaga columnaris, and Trichodesmium tenue. PMID:11976091

  2. Critical appraisal of ceftaroline in the management of community-acquired bacterial pneumonia and skin infections

    PubMed Central

    Goodman, Julian J; Martin, Stanley I

    2012-01-01

    Ceftaroline is a novel broad-spectrum cephalosporin β-lactam antibiotic with activity against methicillin-resistant Staphylococcus aureus (MRSA) as well as multidrug-resistant Streptococcus pneumoniae among other routine Gram positive and Gram negative organisms. It has been approved by the US Food and Drug Administration for treatment of community-acquired bacterial pneumonia and acute bacterial skin and skin structure infections (ABSSSIs). Ceftaroline is approved for treatment of ABSSSI due to MRSA, however currently there are no data for pneumonia due to MRSA in humans. Herein we review the major clinical trials as well as ceftaroline microbiology, pharmacokinetics, and safety, followed by a look at further directions for investigation of this new agent. PMID:22547933

  3. Impacts of dimethyl phthalate on the bacterial community and functions in black soils

    PubMed Central

    Wang, Zhi-Gang; Hu, Yun-Long; Xu, Wei-Hui; Liu, Shuai; Hu, Ying; Zhang, Ying

    2015-01-01

    Dimethyl phthalate (DMP), a known endocrine disruptor and one of the phthalate esters (PAEs), is a ubiquitous pollutant. Its impacts on living organisms have aroused great concern. In this study, the impacts of DMP contamination on bacterial communities and functions were tested by using microcosm model in black soils. The results showed that the operational taxonomic unit (OTUs) richness and bacterial diversity were reduced by DMP contamination. The relative percentages of some genera associated with nitrogen metabolism were increased by DMP contamination, while the relative percentages of some other genera that were extremely beneficial to soil health were decreased by DMP contamination. Further, the relative percentages of some genera that possessed the capability to degrade DMP were increased by the DMP treatment at low concentrations (5, 10, and 20 mg/kg), but were decreased by the high concentration DMP treatment (40 mg/kg). Clearly, DMP contamination changed the bacterial community structure and disturbed the metabolic activity and functional diversity of the microbes in black soils. Our results suggest that DMP pollution can alter the metabolism and biodiversity of black soil microorganisms, thereby directly impact fertility and ecosystem functions. PMID:25999932

  4. Effect of organic carbon and metal accumulation on the bacterial communities in sulphidogenic sediments.

    PubMed

    Bueche, Matthieu; Junier, Pilar

    2016-06-01

    A unique geochemical setting in Lake Cadagno, Switzerland, has led to the accumulation of insoluble metal sulphides in the sedimentary record as the result of past airborne pollution. This offers an exceptional opportunity to study the effect of these metals on the bacterial communities in sediments, and in particular to investigate further the link between metal contamination and an increase in the populations of endospore-forming bacteria observed previously in other metal-contaminated sediments. A decrease in organic carbon and total bacterial counts was correlated with an increase in the numbers of endospores in the oldest sediment samples, showing the first environmental evidence of a decrease in nutrient availability as a trigger of sporulation. Proteobacteria and Firmicutes were the two dominant bacterial phyla throughout the sediment, the former in an area with high sulphidogenic activity, and the latter in the oldest samples. Even though the dominant Firmicutes taxa were stable along the sediment core and did not vary with changes in metal contamination, the prevalence of some molecular species like Clostridium sp. was positively correlated with metal sulphide concentration. However, this cannot be generalized to all endospore-forming species. Overall, the community composition supports the hypothesis of sporulation as the main mechanism explaining the dominance of endospore formers in the deepest part of the sediment core, while metal contamination in the form of insoluble metal sulphide deposits appears not to be linked with sporulation as a mechanism of metal tolerance in this sulphidogenic ecosystem. PMID:26780045

  5. Bacterial community migration in the ripening of doenjang, a traditional Korean fermented soybean food.

    PubMed

    Jeong, Do-Won; Kim, Hye-Rim; Jung, Gwangsick; Han, Seulhwa; Kim, Cheong-Tae; Lee, Jong-Hoon

    2014-05-01

    Doenjang, a traditional Korean fermented soybean paste, is made by mixing and ripening meju with high salt brine (approximately 18%). Meju is a naturally fermented soybean block prepared by soaking, steaming, and molding soybean. To understand living bacterial community migration and the roles of bacteria in the manufacturing process of doenjang, the diversity of culturable bacteria in meju and doenjang was examined using media supplemented with NaCl, and some physiological activities of predominant isolates were determined. Bacilli were the major bacteria involved throughout the entire manufacturing process from meju to doenjang; some of these bacteria might be present as spores during the doenjang ripening process. Bacillus siamensis was the most populous species of the genus, and Bacillus licheniformis exhibited sufficient salt tolerance to maintain its growth during doenjang ripening. Enterococcus faecalis and Enterococcus faecium, the major lactic acid bacteria (LAB) identified in this study, did not continue to grow under high NaCl conditions in doenjang. Enterococci and certain species of coagulase-negative staphylococci (CNS) were the predominant acid-producing bacteria in meju fermentation, whereas Tetragenococcus halophilus and CNS were the major acid-producing bacteria in doenjang fermentation. We conclude that bacilli, LAB, and CNS may be the major bacterial groups involved in meju fermentation and that these bacterial communities undergo a shift toward salt-tolerant bacilli, CNS, and T. halophilus during the doenjang fermentation process. PMID:24548930

  6. Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

    PubMed Central

    Verni, Franco; Petroni, Giulio

    2013-01-01

    Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution. PMID:24227997

  7. Pyrosequencing-based analysis of the bacterial community in Korean traditional seafood, ojingeo jeotgal.

    PubMed

    Jung, Jaejoon; Choi, Sungjong; Jeon, Che Ok; Park, Woojun

    2013-10-28

    Jeotgal fermentation is dependent upon a diverse microbial community, although a detailed understanding of its microbial composition is limited to a relatively small number of jeotgal. Pyrosequencing-based bacterial community analysis was performed in fermented squid, ojingeo jeotgal. Leuconostoc was identified as the predominant bacterial genus, with Bacillus and Staphylococcus also accounting for a large proportion of the bacterial community. Phylogenetic analysis with 16S rRNA genes of Leuconostoc type species indicated that L. citreum- and L. holzapfelii-like strains could be the major Leuconostoc strains in jeotgal. High concentrations of NaCl were thought to be an important factor determining the makeup of the bacterial community in the fermented squid; however, a genomic survey with osmotic stress-related genes suggests the existence of more complex factors selecting the dominant bacterial species in fermented squid. PMID:23851268

  8. Pyrosequencing based profiling of the bacterial community in the Chilika Lake, the largest lagoon of India

    PubMed Central

    Pramanik, Arnab; Basak, Pijush; Banerjee, Satabdi; Sengupta, Sanghamitra; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

    2015-01-01

    Brackish water lake is the most extraordinary reservoir for bacterial community with an adaptability of tolerance to saline stress. In the present study, metagenomic approach was implemented utilising 454-pyrosequencing platform to gain deeper insights into the bacterial diversity profile of the soil sediment of Chilika Lake, Odisha, India. Metagenome contained 68,150 sequences with 31,896,430 bp and 56.79% G + C content. Metagenome sequences data are now available at NCBI under the Sequence Read Archive (SRA) database with accession no. SRX753382. Bacterial community metagenome sequences were analysed by MG-RAST server representing the presence of 16,212 species belonging to 45 different phyla. The dominating phyla were Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Bacteroidetes and Planctomycetes. The analysis of bacterial community datasets obtained from two different saline soil sediments revealed significant differences in bacterial community composition and diversity value providing better understanding of the ecosystem dynamics of Chilika Lake. PMID:26484193

  9. Diversity of bacterial community during spring phytoplankton blooms in the central Yellow Sea.

    PubMed

    Liu, Min; Dong, Yi; Zhang, Wuchang; Sun, Jun; Zhou, Feng; Ren, Jingling; Bao, Shixiang; Xiao, Tian

    2013-05-01

    Bacterial community diversity and the effects of environmental factors on bacterial community composition during 2 spring phytoplankton blooms in the central Yellow Sea were investigated by using denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analysis. The Shannon-Weaver indices (H') of bacterial diversity from samples at station B23 were higher than those at station B20. Cluster analysis based on DGGE band patterns indicated temporal variations of bacterial community at the 2 bloom stations but a vertical distribution pattern only at station B20. The predominant bacterial groups were affiliated with Alphaproteobacteria, Gammaproteobacteria, Cytophaga-Flavobacterium-Bacteroides, Deltaproteobacteria, and Actinobacteria. The effects of environmental factors on bacterial community were analyzed by canonical correspondence analysis. Bacterial community structures were significantly affected by silicate at station B20 and by Paralia sulcata and Heterocapsa spp. at station B23. From the results, phytoplankton species composition had a significant effect on bacterial community structure during phytoplankton blooms in the central Yellow Sea. PMID:23647345

  10. Characterization of bacterial communities in heavy metal contaminated soils.

    PubMed

    Roane, T M; Kellogg, S T

    1996-06-01

    Heavy metal pollution is a principle source of environmental contamination. We analyzed heavy metal impacted soil microbial communities and found that, in general, although lead adversely affected biomass, metabolic activity, and diversity, autochthonous lead- and cadmium-resistant isolates were found. In several metal-stressed soils, the microbial community consisted of two populations, either resistant or sensitive to lead. Additionally, a lead-resistant isolate was isolated from a control soil with no known previous exposure to lead, suggesting widespread lead resistance. Lead-resistant genera isolated included Pseudomonas, Bacillus, Corynebacterium, and Enterobacter species. Plasmids, ranging from 5 to 260 kb, were not detected through standard purifications from lead-resistant isolates. Positive correlations existed between antibiotic resistance and isolation habitat for lead-resistant strains, microbial metabolic activity and soil type, soluble lead concentration and microbial diversity, and arsenic concentration and total or viable cell concentrations. PMID:8801006

  11. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

    PubMed Central

    Schmitt, Susanne; Tsai, Peter; Bell, James; Fromont, Jane; Ilan, Micha; Lindquist, Niels; Perez, Thierry; Rodrigo, Allen; Schupp, Peter J; Vacelet, Jean; Webster, Nicole; Hentschel, Ute; Taylor, Michael W

    2012-01-01

    Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations. PMID:21993395

  12. Quantum dot conjugates for SEM of bacterial communities

    NASA Astrophysics Data System (ADS)

    Nadeau, Jay; Mielke, Randall; Clarke, Samuel

    2009-05-01

    Biologically compatible quantum dot (QD) nanoparticles are hybrid inorganic-organic materials with increasing popularity as fluorescent probes for studying biological specimens. QDs have several advantageous optical features compared to fluorescent dyes and they are electron-dense, allowing for correlated fluorescence and electron microscopic imaging. Despite these features, widespread use of QDs as biological probes has generally been limited by the complex chemistry required for their synthesis and the conjugation. In this work, we show that easily prepared quantum dot (QD) probes provide excellent contrast for fluorescent confocal and environmental scanning electron microscopy (ESEM) analysis of pure microbial cultures and microbial communities. Two conjugation strategies were employed in order to specifically target the QDs to bacterial cell surfaces. The first was biotinylation of the bacteria followed by labeling with commercially available QDs incorporating the high-affinity partner for biotin (QD-streptavidin). Second, we designed a novel QD probe for Gram negative bacteria: QD-polymyxin B (PMB), which binds to lipopolysaccharide (LPS) in the Gram negative cell wall. Pure cultures of Gram positive and Gram negative strains were used to illustrate that QDs impart electron density and irradiation stability to the cells, and so no other preparation apart from QD labeling is required. The techniques were then extended to a set of recently characterized microbial communities of perennial cold springs in the Canadian High Arctic, which live in close association with unusual sulfur crystals. Using correlated confocal and and ESEM, we were able to image these organisms in living samples and illustrate their relationship to the minerals.

  13. Assessment of denitrifying bacterial composition in activated sludge.

    PubMed

    Srinandan, C S; Shah, Mrinal; Patel, Bhavita; Nerurkar, Anuradha S

    2011-10-01

    The abundance and structure of denitrifying bacterial community in different activated sludge samples were assessed, where the abundance of denitrifying functional genes showed nirS in the range of 10(4)-10(5), nosZ with 10(4)-10(6) and 16S rRNA gene in the range 10(9)-10(10) copy number per ml of sludge. The culturable approach revealed Pseudomonas sp. and Alcaligenes sp. to be numerically high, whereas culture independent method showed betaproteobacteria to dominate the sludge samples. Comamonas sp. and Pseudomonas fluorescens isolates showed efficient denitrification, while Pseudomonas mendocina, Pseudomonas stutzeri and Brevundimonas diminuta accumulated nitrite during denitrification. Numerically dominant RFLP OTUs of the nosZ gene from the fertilizer factory sludge samples clustered with the known isolates of betaproteobacteria. The data also suggests the presence of different truncated denitrifiers with high numbers in sludge habitat. PMID:21868215

  14. Comparison of soil bacterial communities under diverse agricultural land management and crop production practices.

    PubMed

    Wu, Tiehang; Chellemi, Dan O; Graham, Jim H; Martin, Kendall J; Rosskopf, Erin N

    2008-02-01

    The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity

  15. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    PubMed

    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

  16. Using in situ bacterial communities to monitor contaminants in river sediments.

    PubMed

    Xie, Yuwei; Wang, Jizhong; Wu, Yaketon; Ren, Chen; Song, Chao; Yang, Jianghua; Yu, Hongxia; Giesy, John P; Zhang, Xiaowei

    2016-05-01

    Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments. PMID:26866572

  17. Denitrification in Agriculturally Impacted Streams: Seasonal Changes in Structure and Function of the Bacterial Community

    PubMed Central

    Manis, Erin; Royer, Todd V.; Johnson, Laura T.; Leff, Laura G.

    2014-01-01

    Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage), whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ) and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO3-) and that seasonal drying of stream channels has a negative impact on NO3- removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change in abundance or

  18. Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

    NASA Astrophysics Data System (ADS)

    Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

    2015-12-01

    Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of

  19. Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

    PubMed

    Adair, Karen L; Wratten, Steve; Lear, Gavin

    2013-06-01

    Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers. PMID:23754721

  20. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids.

    PubMed

    Ren, Tiantian; Glatt, Dominique Ulrike; Nguyen, Tam Nhu; Allen, Emma Kaitlynn; Early, Stephen V; Sale, Michele; Winther, Birgit; Wu, Martin

    2013-02-01

    Adenoid microbiota plays an important role in the development of various infectious and non-infectious diseases of the upper airways, such as otitis media, adenotonsillitis, rhinosinusitis and adenoid hypertrophy. Studies have suggested that adenoids could act as a potential reservoir of opportunistic pathogens. However, previous bacterial surveys of adenoids were mainly culture based and therefore might only provide an incomplete and potentially biased assessment of the microbial diversity. To develop an in-depth and comprehensive understanding of the adenoid microbial communities and test the 'pathogen reservoir hypothesis', we carried out a 16S rRNA based, culture-independent survey of bacterial communities on 67 human adenoids removed by surgery. Our survey revealed highly diverse adenoid bacterial communities distinct from those of other body habitats. Despite large interpersonal variations, adenoid microbiota shared a core set of taxa and can be classified into at least five major types based on its bacterial species composition. Our results support the 'pathogen reservoir hypothesis' as we found common pathogens of otitis media to be both prevalent and abundant. Co-occurrence analyses revealed evidence consistent with the bacterial interference theory in that multiple common pathogens showed 'non-coexistence' relationships with non-pathogenic members of the commensal microflora. PMID:23113966

  1. Light availability affects stream biofilm bacterial community composition and function, but not diversity

    PubMed Central

    Wagner, Karoline; Besemer, Katharina; Burns, Nancy R.; Battin, Tom J.

    2015-01-01

    Summary Changes in riparian vegetation or water turbidity and browning in streams alter the local light regime with potential implications for stream biofilms and ecosystem functioning. We experimented with biofilms in microcosms grown under a gradient of light intensities (range: 5–152 μmole photons s−1 m−2) and combined 454‐pyrosequencing and enzymatic activity assays to evaluate the effects of light on biofilm structure and function. We observed a shift in bacterial community composition along the light gradient, whereas there was no apparent change in alpha diversity. Multifunctionality, based on extracellular enzymes, was highest under high light conditions and decoupled from bacterial diversity. Phenol oxidase activity, involved in the degradation of polyphenolic compounds, was twice as high on average under the lowest compared with the highest light condition. This suggests a shift in reliance of microbial heterotrophs on biofilm phototroph‐derived organic matter under high light availability to more complex organic matter under low light. Furthermore, extracellular enzyme activities correlated with nutrient cycling and community respiration, supporting the link between biofilm structure–function and biogeochemical fluxes in streams. Our findings demonstrate that changes in light availability are likely to have significant impacts on biofilm structure and function, potentially affecting stream ecosystem processes. PMID:26013911

  2. Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea.

    PubMed

    De Tender, Caroline A; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Ruttink, Tom; Dawyndt, Peter

    2015-08-18

    Bacterial colonization of marine plastic litter (MPL) is known for over four decades. Still, only a few studies on the plastic colonization process and its influencing factors are reported. In this study, seafloor MPL was sampled at different locations across the Belgian part of the North Sea to study bacterial community structure using 16S metabarcoding. These marine plastic bacterial communities were compared with those of sediment and seawater, and resin pellets sampled on the beach, to investigate the origin and uniqueness of plastic bacterial communities. Plastics display great variation of bacterial community composition, while each showed significant differences from those of sediment and seawater, indicating that plastics represent a distinct environmental niche. Various environmental factors correlate with the diversity of MPL bacterial composition across plastics. In addition, intrinsic plastic-related factors such as pigment content may contribute to the differences in bacterial colonization. Furthermore, the differential abundance of known primary and secondary colonizers across the various plastics may indicate different stages of bacterial colonization, and may confound comparisons of free-floating plastics. Our studies provide insights in the factors that shape plastic bacterial colonization and shed light on the possible role of plastic as transport vehicle for bacteria through the aquatic environment. PMID:26204244

  3. Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River

    PubMed Central

    Staley, Christopher; Gould, Trevor J.; Wang, Ping; Phillips, Jane; Cotner, James B.; Sadowsky, Michael J.

    2014-01-01

    Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of 14 bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046) between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River. PMID:25339945

  4. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska

    PubMed Central

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-01-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0–10 cm to 10–20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen ( and ). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. PMID:24893754

  5. Molecular ecological analysis of planktonic bacterial communities in constructed wetlands invaded by Culex (Diptera: Culicidae) mosquitoes.

    PubMed

    Popko, David A; Han, Suk-Kyun; Lanoil, Brian; Walton, William E

    2006-11-01

    The succession of the planktonic bacterial community during the colonization by Culex (Diptera: Culicidae) mosquitoes of 0.1-ha treatment wetlands was studied using denaturing gradient gel electrophoresis (DGGE) methodology. Relationships between apparent bacterial diversity and ecological factors (water quality, total bacterial counts, and immature mosquito abundance) were determined during a 1-mo flooding period. Analysis of DGGE banding patterns indicated that days postflooding and temporal changes in water quality were the primary and secondary determinants, respectively, of diversity in bacterial communities. Lower levels of diversity were associated with later postflood stages and increases in ammoniacal nitrogen concentration and total bacterial counts. Diversity was therefore most similar for bacteria present on the same sampling date at wetland locations with similar flooding regimes and water quality, suggesting that wastewater input was the driving force shaping bacterial communities. Comparatively small changes in bacterial diversity were connected to natural processes as water flowed through the wetlands. Greater immature mosquito abundance coincided with less diverse communities composed of greater total numbers of bacteria. Five individual DGGE bands were directly associated with fluctuations in mosquito production, and an additional 16 bands were associated with hydrological aspects of the environment during the rise and fall of mosquito populations. A marked decline in mosquito numbers 21 d after inundation may have masked associations of bacterial communities and mosquito recruitment into the sparsely vegetated wetlands. DGGE was an effective tool for the characterization of bacteria in mosquito habitat in our study, and its potential application in mosquito ecology is discussed. PMID:17162947

  6. Diversity in gut bacterial community of school-age children in Asia.

    PubMed

    Nakayama, Jiro; Watanabe, Koichi; Jiang, Jiahui; Matsuda, Kazunori; Chao, Shiou-Huei; Haryono, Pri; La-Ongkham, Orawan; Sarwoko, Martinus-Agus; Sujaya, I Nengah; Zhao, Liang; Chen, Kang-Ting; Chen, Yen-Po; Chiu, Hsueh-Hui; Hidaka, Tomoko; Huang, Ning-Xin; Kiyohara, Chikako; Kurakawa, Takashi; Sakamoto, Naoshige; Sonomoto, Kenji; Tashiro, Kousuke; Tsuji, Hirokazu; Chen, Ming-Ju; Leelavatcharamas, Vichai; Liao, Chii-Cherng; Nitisinprasert, Sunee; Rahayu, Endang S; Ren, Fa-Zheng; Tsai, Ying-Chieh; Lee, Yuan-Kun

    2015-01-01

    Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. To address the diversity in their gut microbiota, we characterized the bacterial community in fecal samples obtained from 303 school-age children living in urban or rural regions in five countries spanning temperate and tropical areas of Asia. The microbiota profiled for the 303 subjects were classified into two enterotype-like clusters, each driven by Prevotella (P-type) or Bifidobacterium/Bacteroides (BB-type), respectively. Majority in China, Japan and Taiwan harbored BB-type, whereas those from Indonesia and Khon Kaen in Thailand mainly harbored P-type. The P-type microbiota was characterized by a more conserved bacterial community sharing a greater number of type-specific phylotypes. Predictive metagenomics suggests higher and lower activity of carbohydrate digestion and bile acid biosynthesis, respectively, in P-type subjects, reflecting their high intake of diets rich in resistant starch. Random-forest analysis classified their fecal species community as mirroring location of resident country, suggesting eco-geographical factors shaping gut microbiota. In particular, children living in Japan harbored a less diversified microbiota with high abundance of Bifidobacterium and less number of potentially pathogenic bacteria, which may reflect their living environment and unique diet. PMID:25703686

  7. Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

    PubMed Central

    Koyama, Akihiro; Wallenstein, Matthew D.; Simpson, Rodney T.; Moore, John C.

    2014-01-01

    The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-Proteobacteria and β-Proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming. PMID:25324836

  8. Diversity in gut bacterial community of school-age children in Asia

    PubMed Central

    Nakayama, Jiro; Watanabe, Koichi; Jiang, Jiahui; Matsuda, Kazunori; Chao, Shiou-Huei; Haryono, Pri; La-ongkham, Orawan; Sarwoko, Martinus-Agus; Sujaya, I. Nengah; Zhao, Liang; Chen, Kang-Ting; Chen, Yen-Po; Chiu, Hsueh-Hui; Hidaka, Tomoko; Huang, Ning- Xin; Kiyohara, Chikako; Kurakawa, Takashi; Sakamoto, Naoshige; Sonomoto, Kenji; Tashiro, Kousuke; Tsuji, Hirokazu; Chen, Ming-Ju; Leelavatcharamas, Vichai; Liao, Chii-Cherng; Nitisinprasert, Sunee; Rahayu, Endang S.; Ren, Fa-Zheng; Tsai, Ying-Chieh; Lee, Yuan-Kun

    2015-01-01

    Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. To address the diversity in their gut microbiota, we characterized the bacterial community in fecal samples obtained from 303 school-age children living in urban or rural regions in five countries spanning temperate and tropical areas of Asia. The microbiota profiled for the 303 subjects were classified into two enterotype-like clusters, each driven by Prevotella (P-type) or Bifidobacterium/Bacteroides (BB-type), respectively. Majority in China, Japan and Taiwan harbored BB-type, whereas those from Indonesia and Khon Kaen in Thailand mainly harbored P-type. The P-type microbiota was characterized by a more conserved bacterial community sharing a greater number of type-specific phylotypes. Predictive metagenomics suggests higher and lower activity of carbohydrate digestion and bile acid biosynthesis, respectively, in P-type subjects, reflecting their high intake of diets rich in resistant starch. Random-forest analysis classified their fecal species community as mirroring location of resident country, suggesting eco-geographical factors shaping gut microbiota. In particular, children living in Japan harbored a less diversified microbiota with high abundance of Bifidobacterium and less number of potentially pathogenic bacteria, which may reflect their living environment and unique diet. PMID:25703686

  9. Fluorescence in situ hybridization and spectral imaging of coral-associated bacterial communities.

    PubMed

    Ainsworth, T D; Fine, M; Blackall, L L; Hoegh-Guldberg, O

    2006-04-01

    Microbial communities play important roles in the functioning of coral reef communities. However, extensive autofluorescence of coral tissues and endosymbionts limits the application of standard fluorescence in situ hybridization (FISH) techniques for the identification of the coral-associated bacterial communities. This study overcomes these limitations by combining FISH and spectral imaging. PMID:16598010

  10. Manure Refinement Affects Apple Rhizosphere Bacterial Community Structure: A Study in Sandy Soil

    PubMed Central

    Zhang, Qiang; Sun, Jian; Liu, Songzhong; Wei, Qinping

    2013-01-01

    We used DNA-based pyrosequencing to characterize the bacterial community structure of the sandy soil of an apple orchard with different manure ratios. Five manure percentages (5%, 10%, 15%, 20% and 25%) were examined. More than 10,000 valid reads were obtained for each replicate. The communities were composed of five dominant groups (Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Bacteroidetes), of which Proteobacteria content gradually decreased from 41.38% to 37.29% as manure ratio increased from 0% to 25%, respectively. Redundancy analysis showed that 37 classes were highly correlated with manure ratio, 18 of which were positively correlated. Clustering revealed that the rhizosphere samples were grouped into three components: low manure (control, 5%) treatment, medium manure (10%, 15%) treatment and high manure (20%, 25%) treatment. Venn analysis of species types of these three groups revealed that the bacteria community difference was primarily reflected by quantity ratio rather than species variety. Although greater manure content led to higher soil organic matter content, the medium manure improved soil showed the highest urease activity and saccharase activity, while 5% to 20% manure ratio improvement also resulted in higher bacteria diversity than control and 25% manure ratio treatment. Our experimental results suggest that the use of a proper manure ratio results in significantly higher soil enzyme activity and different bacteria community patterns, whereas the use of excessive manure amounts has negative effect on soil quality. PMID:24155909

  11. Effect of wastewater disposal on the bacterial and archaeal community of sea sediment in an industrial area in China.

    PubMed

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Liu, Rui; Wen, Donghui

    2014-05-01

    Human activities usually leave footprints in the environment. By using 454 pyrosequencing, the impact of effluent from an industrial park on the coastal microecology in Hangzhou Bay, China, was interpreted by analysing the microbial communities of the activated sludge from three wastewater treatment plants and the sediment from the effluent receiving area. Based on richness and biodiversity, the sediments were more diversified than the activated sludge, although the seawater environment was highly contaminated. Both bacterial and archaeal communities were niche-determined. The bacterial phylum Proteobacteria dominated in all samples; and certain pollutant-resistant genera, such as Thauera and Truepera, were found in all samples. Archaeal phyla Euryarchaeota and Thaumarchaeota dominated the activated sludge and sediment samples, respectively. According to the analysis of shared operational taxonomic units (OTUs) and reads among different samples, more bacterial OTUs and reads were shared between two samples from sites with a direct effluent connection, showing a clear correlation between the wastewater treatment plants and the effluent receiving bay area. The impact of second-hand pollution can be evaluated by comparing the bacterial community in different eco-environments with a direct effluent connection, especially when pristine samples are not available. PMID:24697989

  12. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species

    PubMed Central

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Background Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. Methodology and Results To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. Conclusions The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation. PMID:27008327

  13. Bacterial communities associated with four ctenophore genera from the German Bight (North Sea).

    PubMed

    Hao, Wenjin; Gerdts, Gunnar; Peplies, Jörg; Wichels, Antje

    2015-01-01

    Intense research has been conducted on jellyfish and ctenophores in recent years. They are increasingly recognized as key elements in the marine ecosystem that serve as critical indicators and drivers of ecosystem performance and change. However, the bacterial community associated with ctenophores is still poorly investigated. Based on automated ribosomal intergenic spacer analysis (ARISA) and 16S ribosomal RNA gene amplicon pyrosequencing, we investigated bacterial communities associated with the frequently occurring ctenophore species Mnemiopsis leidyi, Beroe sp., Bolinopsis infundibulum and Pleurobrachia pileus at Helgoland Roads in the German Bight (North Sea). We observed significant differences between the associated bacterial communities of the different ctenophore species based on ARISA patterns. With respect to bacterial taxa, all ctenophore species were dominated by Proteobacteria as revealed by pyrosequencing. Mnemiopsis leidyi and P. pileus mainly harboured Gammaproteobacteria, with Marinomonas as the dominant phylotype of M. leidyi. By contrast, Pseudoalteromonas and Psychrobacter were the most abundant Gammaproteobacteria in P. pileus. Beroe sp. was mainly dominated by Alphaproteobacteria, particularly by the genus Thalassospira. For B. infundibulum, the bacterial community was composed of Alphaproteobacteria and Gammaproteobacteria in equal parts, which consisted of the genera Thalassospira and Marinomonas. In addition, the bacterial communities associated with M. leidyi display a clear variation over time that needs further investigation. Our results indicate that the bacterial communities associated with ctenophores are highly species- specific. PMID:25764531

  14. pH affects bacterial community composition in soils across the Huashan Watershed, China.

    PubMed

    Huang, Rui; Zhao, Dayong; Zeng, Jin; Shen, Feng; Cao, Xinyi; Jiang, Cuiling; Huang, Feng; Feng, Jingwei; Yu, Zhongbo; Wu, Qinglong L

    2016-09-01

    To investigate soil bacterial richness and diversity and to determine the correlations between bacterial communities and soil properties, 8 soil samples were collected from the Huashan watershed in Anhui, China. Subsequently, 454 high-throughput pyrosequencing and bioinformatics analyses were performed to examine the soil bacterial community compositions. The operational taxonomic unit richness of the bacterial community ranged from 3664 to 5899, and the diversity indices, including Chao1, Shannon-Wiener, and Faith's phylogenetic diversity ranged from 7751 to 15 204, 7.386 to 8.327, and 415.77 to 679.11, respectively. The 2 most dominant phyla in the soil samples were Actinobacteria and Proteobacteria. The richness and diversity of the bacterial community were positively correlated with soil pH. The Mantel test revealed that the soil pH was the dominant factor influencing the bacterial community. The positive modular structure of co-occurrence patterns at the genus level was discovered by network analysis. The results obtained in this study provide useful information that enhances our understanding of the effects of soil properties on the bacterial communities. PMID:27374919

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

    PubMed

    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

  16. The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

    PubMed Central

    Figuerola, Eva L. M.; Erijman, Leonardo

    2014-01-01

    The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

  17. Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth

    PubMed Central

    Singh, Mangal; Awasthi, Ashutosh; Soni, Sumit K.; Singh, Rakshapal; Verma, Rajesh K.; Kalra, Alok

    2015-01-01

    An assessment of roles of rhizospheric microbial diversity in plant growth is helpful in understanding plant-microbe interactions. Using random combinations of rhizospheric bacterial species at different richness levels, we analysed the contribution of species richness, compositions, interactions and identity on soil microbial respiration and plant biomass. We showed that bacterial inoculation in plant rhizosphere enhanced microbial respiration and plant biomass with complementary relationships among bacterial species. Plant growth was found to increase linearly with inoculation of rhizospheric bacterial communities with increasing levels of species or plant growth promoting trait diversity. However, inoculation of diverse bacterial communities having single plant growth promoting trait, i.e., nitrogen fixation could not enhance plant growth over inoculation of single bacteria. Our results indicate that bacterial diversity in rhizosphere affect ecosystem functioning through complementary relationship among plant growth promoting traits and may play significant roles in delivering microbial services to plants. PMID:26503744

  18. Identification and ecology of bacterial communities associated with necroses of three cactus species.

    PubMed

    Foster, J L; Fogleman, J C

    1993-01-01

    To compare the bacterial communities residing in necrotic tissues of columnar cacti of the Sonoran Desert, isolates from 39 organ pipe, 19 saguaro, and 16 senita cacti were obtained. The isolates were clustered into 28 conspecific groups on the basis of their fatty acid profiles. The distributions of the individual bacterial isolates varied among cactus species. Seven of the 28 species groups were unique to a particular cactus species, whereas 8 species groups were found in all three cacti. The effective number of bacterial species for each cactus species was positively correlated with both the chemical complexity and glucose concentration of the plant tissues. The effective number of bacterial species and bacterial distribution patterns were compared with those known for communities of cactophilic yeasts. The observed bacterial distribution patterns are most likely due to differences in the chemical compositions of the three cactus species. PMID:8439142

  19. Bacterial community diversity in a low-permeability oil reservoir and its potential for enhancing oil recovery.

    PubMed

    Xiao, Meng; Zhang, Zhong-Zhi; Wang, Jing-Xiu; Zhang, Guang-Qing; Luo, Yi-Jing; Song, Zhao-Zheng; Zhang, Ji-Yuan

    2013-11-01

    The diversity of indigenous bacterial community and the functional species in the water samples from three production wells of a low permeability oil reservoir was investigated by high-throughput sequencing technology. The potential of application of indigenous bacteria for enhancing oil recovery was evaluated by examination of the effect of bacterial stimulation on the formation water-oil-rock surface interactions and micromodel test. The results showed that production well 88-122 had the most diverse bacterial community and functional species. The broth of indigenous bacteria stimulated by an organic nutrient activator at aerobic condition changed the wettability of the rock surface from oil-wet to water-wet. Micromodel test results showed that flooding using stimulated indigenous bacteria following water flooding improved oil recovery by 6.9% and 7.7% in fractured and unfractured micromodels, respectively. Therefore, the zone of low permeability reservoir has a great potential for indigenous microbial enhanced oil recovery. PMID:23994957

  20. Diversity and Abundance of the Bacterial Community of the Red Macroalga Porphyra umbilicalis: Did Bacterial Farmers Produce Macroalgae?

    PubMed Central

    Miranda, Lilibeth N.; Hutchison, Keith; Grossman, Arthur R.; Brawley, Susan H.

    2013-01-01

    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 unexpected

  1. Bacterial activities driving arsenic speciation and solubility in marine sediments

    NASA Astrophysics Data System (ADS)

    Battaglia-Brunet, F.; Seby, F.; Crouzet, C.; Joulian, C.; Mamindy-Pajany, Y.; Guezennec, A. G.; Hurel, C.; Marmier, N.; Bataillard, P.

    2012-04-01

    include dissolution of FeS (which confers to the muddy sediment its deep dark color), oxidation of Fe(II) to Fe(III), oxidation of As(III) to As(V), oxidation of S(-II) to S°, S(VI) and maybe other intermediate species, adsorption of As(V) onto fresh iron oxides. Bacterial activity tests applied to the crude sediments indicated that As(III)-oxidizing and As(V)-reducing micro-organisms have the potential to be active at both sites. Detection of aoxB and arrA genes, respectively specific to As(III)-oxidation and respiratory As(V)-reduction, revealed the presence of diverse bacterial communities able to contribute to As transformation in both St-Mandrier and l'Estaque marina sediments. As(III)-oxidizing bacteria probably contribute to the biogeochemical stabilization of arsenic, wherever electron acceptors are available. Whereas reducing conditions prevail in organic carbon-rich marina sediment, bacteria able to oxidize As(III) are present and can be rapidly active as soon as electron acceptors are available. The present study showed that arsenic, which inorganic forms As(III) and As(V) are particularly toxic, is one of the most mobile pollutants in polluted marina sediments. The biogeochemical reactions governing its mobility should thus be considered in the management of sediment dredging operations. This work was performed in the framework of ASEDMAR project supported by the French National Research Agency, under reference "2008 CESA-003".

  2. Removal of methyl acrylate by ceramic-packed biotrickling filter and their response to bacterial community.

    PubMed

    Wu, Hao; Yin, Zhenhao; Quan, Yue; Fang, Yingyu; Yin, Chengri

    2016-06-01

    Methyl acrylate is a widely used raw chemical materials and it is toxic in humans. In order to treat the methyl acrylate waste gas, a 3-layer BTF packed with ceramic particles and immobilized with activated sludge was set up. The BTF exhibited excellent removal efficiency that no methyl acrylate could be detected when EBRT was larger than 266s and inlet concentration was lower than 0.19g/m(3). The 1st layer performed the best at fixed inlet concentration of 0.42g/m(3). PCR combined with DGGE was performed to detect the differences in different layers of the BTF. Phylum Proteobacteria (e.g. α-, β-, γ-, δ-) was predominantly represented in the bacterial community, followed by Actinobacteria and Firmicutes. Desulfovibrio gigas, Variovorax paradoxus, Dokdonella koreensis, Pseudoxanthomonas suwonensis, Azorhizobium caulinodans, Hyphomicrobium denitrificans, Hyphomicrobium sp. and Comamonas testosteroni formed the bacteria community to treat methyl acrylate waste gas in the BTF. PMID:26970927

  3. Large scale distribution of bacterial communities in the upper Paraná River floodplain

    PubMed Central

    Chiaramonte, Josiane Barros; Roberto, Maria do Carmo; Pagioro, Thomaz Aurélio

    2014-01-01

    A bacterial community has a central role in nutrient cycle in aquatic habitats. Therefore, it is important to analyze how this community is distributed throughout different locations. Thirty-six different sites in the upper Paraná River floodplain were surveyed to determine the influence of environmental variable in bacterial community composition. The sites are classified as rivers, channels, and floodplain lakes connected or unconnected to the main river channel. The bacterial community structure was analyzed by fluorescent in situ hybridization (FISH) technique, based on frequency of the main domains Bacteria and Archaea, and subdivisions of the phylum Proteobacteria (Alpha-proteobacteria, Beta-proteobacteria, Gamma-proteobacteria) and the Cytophaga-Flavobacterium cluster. It has been demonstrated that the bacterial community differed in density and frequency of the studied groups. And these differences responded to distinct characteristics of the three main rivers of the floodplain as well as to the classification of the environments found in this floodplain. We conclude that dissimilarities in the bacterial community structure are related to environmental heterogeneity, and the limnological variables that most predicted bacterial communities in the upper Paraná River floodplain was total and ammoniacal nitrogen, orthophosphate and chlorophyll-a. PMID:25763022

  4. Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau.

    PubMed

    Yuan, Yanli; Si, Guicai; Wang, Jian; Luo, Tianxiang; Zhang, Gengxin

    2014-01-01

    The Tibetan Plateau, 'the third pole', is a region that is very sensitive to climate change. A better understanding of response of soil microorganisms to climate warming is important to predict soil organic matter preservation in future scenario. We selected a typically altitudinal gradient (4400 m-5200 m a.s.l) along south-facing slope of Nyainqentanglha Mountains on central Tibetan Plateau. Bacterial communities were investigated using terminal restriction fragment length polymorphism analysis (T-RFLP) combined with sequencing methods. Acidobacteria and Proteobacteria were dominant bacteria in this alpine soil. Redundancy analysis revealed that soil bacterial communities were significantly different along the large altitudinal gradient, although the dominant environmental driving factors varied at different soil depth. Specifically, our results showed that precipitation and soil NH4 + were dominant environmental factors that influence bacterial communities at 0-5 cm depth along the altitudinal gradients, whereas pH was a major influential factor at 5-20 cm soil. In this semi-arid region, precipitation rather than temperature was a main driving force on soil bacterial communities as well as on plant communities. We speculate that an increase in temperature might not significantly change soil bacterial community structures along the large altitudinal gradient, whereas precipitation change would play a more important role in affecting soil bacterial communities. PMID:23991911

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

    PubMed

    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

  6. Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

    PubMed

    Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

    2016-10-01

    Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were

  7. A comparison of bacterial communities in deep terrestrial and deep sub-seafloor biospheres (Invited)

    NASA Astrophysics Data System (ADS)

    Toner, B. M.; Lesniewski, R.; Alexander, E. C.; Gralnick, J.; Orcutt, B.

    2009-12-01

    The distribution and community structure of microorganisms within the Earth’s crust are thought to be influenced - even controlled - by environmental factors. However, significant uncertainty remains in our understanding of microbial species distributions generally, and especially in the deep biosphere where 325 - 518 Pg of microbial biomass is estimated to reside globally. The potential magnitude and global significance of deep biosphere microbial communities has prompted active research focused on sub-seafloor biogeochemistry. Taxonomic analyses based on bacterial 16S rRNA gene libraries from over 200 deep terrestrial and marine microbial communities, suggests that the deep terrestrial biosphere is distinct from the deep-sea biosphere in terms of microbial community composition. Therefore, our rapidly expanding understanding of the distribution, ecology, and biogeochemical significance of microorganisms in the deep sub-seafloor may not be transferable to deep terrestrial systems representing up to 70 % of the deep subsurface biomass globally. The long-term goal of this research is an integration of local and regional microbial community and geochemistry data into a global perspective on the biogeography of deep biosphere systems.

  8. Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds.

    PubMed

    Negandhi, Karita; Laurion, Isabelle; Lovejoy, Connie

    2016-08-01

    One consequence of High Arctic permafrost thawing is the formation of small ponds, which release greenhouse gases (GHG) from stored carbon through microbial activity. Under a climate with higher summer air temperatures and longer ice-free seasons, sediments of shallow ponds are likely to become warmer, which could influence enzyme kinetics or select for less cryophilic microbes. There is little data on the direct temperature effects on GHG production and consumption or on microbial communities' composition in Arctic ponds. We investigated GHG production over 16 days at 4°C and 9°C in sediments collected from four thaw ponds. Consistent with an enzymatic response, production rates of CO2 and CH4 were significantly greater at higher temperatures, with Q10 varying from 1.2 to 2.5. The bacterial community composition from one pond was followed through the incubation by targeting the V6-V8 variable regions of the 16S rRNA gene and 16S rRNA. Several rare taxa detected from rRNA accounted for significant community compositional changes. At the higher temperature, the relative community contribution from Bacteroidetes decreased by 15% with compensating increases in Betaproteobacteria, Alphaproteobacteria, Firmicutes, Acidobacteria, Verrucomicrobia and Actinobacteria. The increase in experimental GHG production accompanied by changes in community indicates an additional factor to consider in sediment environments when evaluating future climate scenarios. PMID:27288196

  9. Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil

    PubMed Central

    Kielak, Anna M.; Cretoiu, Mariana Silvia; Semenov, Alexander V.; Sørensen, Søren J.

    2013-01-01

    Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and chiA genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of chiA gene types in soil is enormous and (i) that different chiA gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in the immediate response to the added chitin (based on 16S rRNA gene abundance and chiA gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes. PMID:23104407

  10. Bacterial chitinolytic communities respond to chitin and pH alteration in soil.

    PubMed

    Kielak, Anna M; Cretoiu, Mariana Silvia; Semenov, Alexander V; Sørensen, Søren J; van Elsas, Jan Dirk

    2013-01-01

    Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and chiA genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of chiA gene types in soil is enormous and (i) that different chiA gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in the immediate response to the added chitin (based on 16S rRNA gene abundance and chiA gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes. PMID:23104407

  11. Profiling of root canal bacterial communities associated with chronic apical periodontitis from Brazilian and Norwegian subjects.

    PubMed

    Siqueira, José F; Rôças, Isabela N; Debelian, Gilberto J; Carmo, Flávia L; Paiva, Simone S M; Alves, Flávio R F; Rosado, Alexandre S

    2008-12-01

    The aim of this study was to compare the bacterial community profiles of the root canal microbiota associated with chronic apical periodontitis from Brazilian and Norwegian patients using the denaturing gradient gel electrophoresis (DGGE) and the ribosomal intergenic spacer analysis (RISA) approaches. DNA extracted from root canal samples was subjected to polymerase chain reaction using primers appropriate for further DGGE or RISA analysis. The resulting banding patterns representative of the bacterial community structures in samples from the two locations were compared. DGGE and RISA fingerprints showed a great interindividual variability in the bacterial community profiles, irrespective of the geographic location of the patient. However, similarities among the bacterial community DGGE profiles revealed the existence of a geography-related pattern. PMID:19026873

  12. Description of Drinking Water Bacterial Communities Using 16S rRNA Gene Sequence Analyses

    EPA Science Inventory

    Descriptions of bacterial communities inhabiting water distribution systems (WDS) have mainly been accomplished using culture-based approaches. Due to the inherent selective nature of culture-based approaches, the majority of bacteria inhabiting WDS remain uncharacterized. The go...

  13. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi River water

    EPA Science Inventory

    Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is kn...

  14. Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities.

    PubMed

    Arenz, Brett E; Schlatter, Dan C; Bradeen, James M; Kinkel, Linda L

    2015-10-01

    A blocking primer set based on the technique described by Vestheim and Jarman (2008) was developed to reduce amplification of non-target plant DNA when conducting metagenomic studies on bacterial endophyte communities. Bacterial amplification efficiency was increased 300-fold compared to standard PCR in an Illumina-based study of Sorghastrum nutans leaves. PMID:26159909

  15. Comparison of soil bacterial communities under diverse agricultural land management and crop production practices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The composition and structure of bacterial communities was examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profile...

  16. [Impact of biocontrol agent Bacillus subtilis on bacterial communities in tobacco rhizospheric soil].

    PubMed

    You, Cai; Zhang, Li-Meng; Ji, Si-Gui; Gao, Jia-Ming; Zhang, Cheng-Sheng; Kong, Fan-Yu

    2014-11-01

    The impact of inoculation with the biocontrol agent Bacillus subtilis on bacterial communities and bacterial diversity in rhizospheric soil of Nicotiana tabacum was assessed by constructing a 16S rRNA gene clone library and conducting amplified ribosomal DNA restriction analysis (ARDRA). The bacterial diversity was evaluated by coverage value (C), Shannon index (H), Pielou evenness index (E) and Margalef richness index (R). Phylogenetic analysis revealed that the inoculation significantly affected the composition of bacterial communities in tobacco rhizospheric soil. A total of twelve bacterial groups including Acidobacteria, Proteobacteria (including α-, β-, δ-, γ-Proteobacteria) , Planctomycetes, Firmicutes, Nitrospirae, Gemmatimonadetes, Actinobacteria, Chloroflexi and Bacteroidetes were detected to be shared by inoculated soil and control soil. The community composition and proportions of different bacteria in the communities showed significant variations between the two samples. The dominant bacteria were Acidobacteria (27.1%) and Proteobacteria (26.5%) in control soil, while in the inoculated soil Proteobacteria (38.0%) and Acidobacteria (29.6%) were dominant. B. subtilis inoculation increased the numbers of γ-Proteobacteria and α-Proteobacteria but reduced the numbers of bacterial groups such as β-Proteobacteria, Planctomycetes, Firmicutes. Diversity analysis showed that bacterial diversity was rich for both soil samples, and soil bacterial Shannon index and Margalef richness index were promoted after inoculation. PMID:25898632

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

    PubMed

    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. Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

    PubMed Central

    Kao-Kniffin, J.; Woodcroft, B.J.; Carver, S.M.; Bockheim, J.G.; Handelsman, J.; Tyson, G.W.; Hinkel, K.M.; Mueller, C.W.

    2015-01-01

    We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures. PMID:26681584

  19. Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

    SciTech Connect

    Kao-Kniffin, J.; Woodcroft, B. J.; Carver, S. M.; Bockheim, J. G.; Handelsman, J.; Tyson, G. W.; Hinkel, K. M.; Mueller, C. W.

    2015-12-18

    We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.

  20. Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska.

    PubMed

    Kao-Kniffin, J; Woodcroft, B J; Carver, S M; Bockheim, J G; Handelsman, J; Tyson, G W; Hinkel, K M; Mueller, C W

    2015-01-01

    We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus 'Methanoflorens stordalenmirensis' were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus 'M. stordalenmirensis' across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures. PMID:26681584

  1. Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China

    PubMed Central

    Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; Stegen, James C.; An, Lizhe; Feng, Huyuan

    2015-01-01

    Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent

  2. Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China.

    PubMed

    Hu, Weigang; Zhang, Qi; Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; Stegen, James C; An, Lizhe; Feng, Huyuan

    2015-01-01

    Understanding the processes that influence the structure of biotic communities is one of the major ecological topics, and both stochastic and deterministic processes are expected to be at work simultaneously in most communities. Here, we investigated the vertical distribution patterns of bacterial communities in a 10-m-long soil core taken within permafrost of the Qinghai-Tibet Plateau. To get a better understanding of the forces that govern these patterns, we examined the diversity and structure of bacterial communities, and the change in community composition along the vertical distance (spatial turnover) from both taxonomic and phylogenetic perspectives. Measures of taxonomic and phylogenetic beta diversity revealed that bacterial community composition changed continuously along the soil core, and showed a vertical distance-decay relationship. Multiple stepwise regression analysis suggested that bacterial alpha diversity and phylogenetic structure were strongly correlated with soil conductivity and pH but weakly correlated with depth. There was evidence that deterministic and stochastic processes collectively drived bacterial vertically-structured pattern. Bacterial communities in five soil horizons (two originated from the active layer and three from permafrost) of the permafrost core were phylogenetically random, indicator of stochastic processes. However, we found a stronger effect of deterministic processes related to soil pH, conductivity, and organic carbon content that were structuring the bacterial communities. We therefore conclude that the vertical distribution of bacterial communities was governed primarily by deterministic ecological selection, although stochastic processes were also at work. Furthermore, the strong impact of environmental conditions (for example, soil physicochemical parameters and seasonal freeze-thaw cycles) on these communities underlines the sensitivity of permafrost microorganisms to climate change and potentially subsequent

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

    PubMed Central

    Shen, Congcong; Ni, Yingying; Liang, Wenju; Wang, Jianjun; Chu, Haiyan

    2015-01-01

    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 (TC), 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 TC 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. PMID:26217308

  4. Bacterial communities and their association with the bio-drying of sewage sludge.

    PubMed

    Cai, Lu; Chen, Tong-Bin; Gao, Ding; Yu, Jie

    2016-03-01

    Bio-drying is a technology that aims to remove water from a material using the microbial heat originating from organic matter degradation. However, the evolution of bacterial communities that are associated with the drying process has not been researched systematically. This study was performed to investigate the variations of bacterial communities and the relationships among bacterial communities, water evaporation, water generation, and organic matter degradation during the bio-drying of sewage sludge. High-throughput pyrosequencing was used to analyze the bacterial communities, while water evaporation and water generation were determined based on an in situ water vapor monitoring device. The values of water evaporation, water generation, and volatile solids degradation were 412.9 g kg(-1) sewage sludge bio-drying material (SSBM), 65.0 g kg(-1) SSBM, and 70.2 g kg(-1) SSBM, respectively. Rarefaction curves and diversity indices showed that bacterial diversity plummeted after the temperature of the bio-drying pile dramatically increased on d 2, which coincided with a remarkable increase of water evaporation on d 2. Bacterial diversity increased when the pile cooled. During the thermophilic phase, in which Acinetobacter and Bacillus were the dominant genera, the rates of water evaporation, water generation, and VS degradation peaked. These results implied that the elevated temperature reshaped the bacterial communities, which played a key role in water evaporation, and the high temperature also contributed to the effective elimination of pathogens. PMID:26724438

  5. Metabolic and phylogenetic profile of bacterial community in Guishan coastal water (Pearl River Estuary), South China Sea

    NASA Astrophysics Data System (ADS)

    Hu, Xiaojuan; Liu, Qing; Li, Zhuojia; He, Zhili; Gong, Yingxue; Cao, Yucheng; Yang, Yufeng

    2014-10-01

    Characteristics of a microbial community are important as they indicate the status of aquatic ecosystems. In the present study, the metabolic and phylogenetic profile of the bacterioplankton community in Guishan coastal water (Pearl River Estuary), South China Sea, at 12 sites (S1-S12) were explored by community-level physiological profiling (CLPP) with BIOLOG Eco-plate and denaturing gradient gel electrophoresis (DGGE). Our results showed that the core mariculture area (S6, S7 and S8) and the sites associating with human activity and sewage discharge (S11 and S12) had higher microbial metabolic capability and bacterial community diversity than others (S1-5, S9-10). Especially, the diversity index of S11 and S12 calculated from both CLPP and DGGE data ( H>3.2) was higher than that of others as sewage discharge may increase water nitrogen and phosphorus nutrient. The bacterial community structure of S6, S8, S11 and S12 was greatly influenced by total phosphorous, salinity and total nitrogen. Based on DGGE fingerprinting, proteobacteria, especially γ- and α-proteobacteria, were found dominant at all sites. In conclusion, the aquaculture area and wharf had high microbial metabolic capability. The structure and composition of bacterial community were closely related to the level of phosphorus, salinity and nitrogen.

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

    PubMed

    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

  7. Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea).

    PubMed

    Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje

    2015-06-01

    Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea. PMID:25500510

  8. Does the aboveground herbivore assemblage influence soil bacterial community composition and richness in subalpine grasslands?

    PubMed

    Hodel, Melanie; Schütz, Martin; Vandegehuchte, Martijn L; Frey, Beat; Albrecht, Matthias; Busse, Matt D; Risch, Anita C

    2014-10-01

    Grassland ecosystems support large communities of aboveground herbivores that are known to directly and indirectly affect belowground properties such as the microbial community composition, richness, or biomass. Even though multiple species of functionally different herbivores coexist in grassland ecosystems, most studies have only considered the impact of a single group, i.e., large ungulates (mostly domestic livestock) on microbial communities. Thus, we investigated how the exclusion of four groups of functionally different herbivores affects bacterial community composition, richness, and biomass in two vegetation types with different grazing histories. We progressively excluded large, medium, and small mammals as well as invertebrate herbivores using exclosures at 18 subalpine grassland sites (9 per vegetation type). We assessed the bacterial community composition using terminal restriction fragment length polymorphism (T-RFLP) at each site and exclosure type during three consecutive growing seasons (2009-2011) for rhizosphere and mineral soil separately. In addition, we determined microbial biomass carbon (MBC), root biomass, plant carbon:nitrogen ratio, soil temperature, and soil moisture. Even though several of these variables were affected by herbivore exclusion and vegetation type, against our expectations, bacterial community composition, richness, or MBC were not. Yet, bacterial communities strongly differed between the three growing seasons as well as to some extent between our study sites. Thus, our study indicates that the spatiotemporal variability in soil microclimate has much stronger effects on the soil bacterial communities than the grazing regime or the composition of the vegetation in this high-elevation ecosystem. PMID:24889285

  9. Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea)

    PubMed Central

    Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje

    2015-01-01

    Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea. PMID:25500510

  10. Influence of temperature and soil water content on bacterial, archaeal and denitrifying microbial communities in drained fen grassland soil microcosms.

    PubMed

    Stres, Blaz; Danevcic, Tjasa; Pal, Levin; Fuka, Mirna Mrkonjić; Resman, Lara; Leskovec, Simona; Hacin, Janez; Stopar, David; Mahne, Ivan; Mandic-Mulec, Ines

    2008-10-01

    In this study, microcosms were used to investigate the influence of temperature (4 and 28 degrees C) and water content (45% and 90% WHC) on microbial communities and activities in carbon-rich fen soil. Bacterial, archaeal and denitrifier community composition was assessed during incubation of microcosms for 12 weeks using terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA and nitrous oxide reductase (nosZ) genes. In addition, microbial and denitrifier abundance, potential denitrification activity and production of greenhouse gases were measured. No detectable changes were observed in prokaryote or denitrifier abundance. In general, cumulatively after 12 weeks more carbon was respired at the higher temperature (3.7 mg CO(2) g(-1) soil), irrespective of the water content, whereas nitrous oxide production was greater under wet conditions (98-336 microg N(2)O g(-1) soil). After an initial lag phase, methane emissions (963 microg CH(4) g(-1) soil) were observed only under warm and wet conditions. T-RFLP analyses of bacterial 16S rRNA and nosZ genes revealed small or undetectable community changes in response to temperature and water content, suggesting that bacterial and denitrifying microbial communities are stable and do not respond significantly to seasonal changes in soil conditions. In contrast, archaeal microbial community structure was more dynamic and was strongly influenced by temperature. PMID:18710395

  11. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

    PubMed Central

    Srinivasan, Sujatha; Hoffman, Noah G.; Morgan, Martin T.; Matsen, Frederick A.; Fiedler, Tina L.; Hall, Robert W.; Ross, Frederick J.; McCoy, Connor O.; Bumgarner, Roger; Marrazzo, Jeanne M.; Fredricks, David N.

    2012-01-01

    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 incidence of BV in

  12. Characterisation of the bacterial community structures in the intestine of Lampetra morii.

    PubMed

    Li, Yingying; Xie, Wenfang; Li, Qingwei

    2016-07-01

    The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response. PMID:27180095

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