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Sample records for bacterial community composition

  1. Urban greenness influences airborne bacterial community composition.

    PubMed

    Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

    2016-11-15

    Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

  2. Composition and development of oral bacterial communities

    PubMed Central

    Palmer, Robert J.

    2012-01-01

    The oral bacterial microbiome encompasses ca. 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy has resulted in the discovery of new phylotypes and, more importantly, the speed and detail of molecular analyses are impossible to achieve through classical approaches. Community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. PMID:24320954

  3. Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

    PubMed Central

    Hosen, Jacob D.; Febria, Catherine M.; Crump, Byron C.; Palmer, Margaret A.

    2017-01-01

    Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition of headwater streams

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

    PubMed

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

    2015-01-01

    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.

  5. 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

  6. 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

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

    PubMed

    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.

  8. Interaction between resource identity and bacterial community composition regulates bacterial respiration in aquatic ecosystems.

    PubMed

    Pires, A P F; Caliman, A; Laque, T; Esteves, F A; Farjalla, V F

    2015-11-01

    Resource identity and composition structure bacterial community, which in turn determines the magnitude of bacterial processes and ecological services. However, the complex interaction between resource identity and bacterial community composition (BCC) has been poorly understood so far. Using aquatic microcosms, we tested whether and how resource identity interacts with BCC in regulating bacterial respiration and bacterial functional diversity. Different aquatic macrophyte leachates were used as different carbon resources while BCC was manipulated through successional changes of bacterial populations in batch cultures. We observed that the same BCC treatment respired differently on each carbon resource; these resources also supported different amounts of bacterial functional diversity. There was no clear linear pattern of bacterial respiration in relation to time succession of bacterial communities in all leachates, i.e. differences on bacterial respiration between different BCC were rather idiosyncratic. Resource identity regulated the magnitude of respiration of each BCC, e.g. Ultricularia foliosa leachate sustained the greatest bacterial functional diversity and lowest rates of bacterial respiration in all BCC. We conclude that both resource identity and the BCC interact affecting the pattern and the magnitude of bacterial respiration in aquatic ecosystems.

  9. Composition of epiphytic bacterial communities differs on petals and leaves.

    PubMed

    Junker, R R; Loewel, C; Gross, R; Dötterl, S; Keller, A; Blüthgen, N

    2011-11-01

    The epiphytic bacterial communities colonising roots and leaves have been described for many plant species. In contrast, microbiologists have rarely considered flowers of naturally growing plants. We identified bacteria isolated from the surface of petals and leaves of two plant species, Saponaria officinalis (Caryophyllaceae) and Lotus corniculatus (Fabaceae). The bacterial diversity was much lower on petals than on leaves of the same plants. Moreover, the bacterial communities differed strongly in composition: while Pseudomonadaceae and Microbacteriaceae were the most abundant families on leaves, Enterobacteriaceae dominated the floral communities. We hypothesise that antibacterial floral volatiles trigger the low diversity on petals, which is supported by agar diffusion assays using substances emitted by flowers and leaves of S. officinalis. These results suggest that bacteria should be included in the interpretation of floral traits, and possible effects of bacteria on pollination are proposed and discussed.

  10. 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

  11. Diversity and composition of the bacterial community in Amphioxus feces.

    PubMed

    Pan, Minming; Yuan, Dongjuan; Chen, Shangwu; Xu, Anlong

    2015-11-01

    Amphioxus is a typical filter feeder animal and is confronted with a complex bacterial community in the seawater of its habitat. It has evolved a strong innate immune system to cope with the external bacterial stimulation, however, the ecological system of the bacterial community in Amphioxus remains unknown. Through massive parallel 16S rRNA gene tag pyrosequencing, the investigation indicated that the composition of wild and lab-cultured Amphioxus fecal bacteria was complex with more than 85,000 sequence tags being assigned to 12/13 phyla. The bacterial diversity between the two fecal samples was similar according to OTU richness of V4 tag, Chao1 index, Shannon index and Rarefaction curves, however, the most prominent bacteria in wild feces were genera Pseudoalteromonas (gamma Proteobacteria) and Arcobacter (epsilon Proteobacteria); the highly abundant bacteria in lab-cultured feces were other groups, including Leisingera, Phaeobacter (alpha Proteobacteria), and Vibrio (gamma Proteobacteria). Such difference indicates the complex fecal bacteria with the potential for multi-stability. The bacteria of habitat with 28 assigned phyla had the higher bacterial diversity and species richness than both fecal bacteria. Shared bacteria between wild feces and its habitat reached to approximately 90% (153/169 genera) and 28% (153/548 genera), respectively. As speculative, the less diversity of both fecal bacteria compared to its habitat partly because Amphioxus lives buried and the feces will ultimately end up in the sediment. Therefore, our study comprehensively investigates the complex bacterial community of Amphioxus and provides evidence for understanding the relationship of this basal chordate with the environment.

  12. The Importance of Dispersal for Bacterial Community Composition and Functioning

    PubMed Central

    Lindström, Eva S.; Östman, Örjan

    2011-01-01

    We conducted a metacommunity experiment to investigate the role of dispersal for bacterial community composition (BCC) and function of freshwater bacteria. Bacteria were dispersed from a common source pool into three different lake communities in their natural lake water. The experiment was conducted in dialysis bags to enable a decoupling between a change in the local environment and dispersal. BCC was determined by terminal restriction fragment length polymorphism (tRFLP) of the 16S rRNA gene. We show that the greatest changes in BCC occurred between 10% and 43% of dispersal of standing stock per day. Functioning, measured as growth rate, was also affected by dispersal in all three communities but the qualitative pattern differed between communities, sometimes showing a hump-shaped relationship to dispersal and sometimes decreasing with increasing dispersal. In all waters, functioning was related to BCC. Our results show that dispersal does affect BCC and functioning but that high dispersal rates are needed. Further, the effect of dispersal on BCC and function seem to depend on the quality of the habitat to which bacteria disperse into. PMID:21998714

  13. Pyridine-type alkaloid composition affects bacterial community composition of floral nectar

    PubMed Central

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T.; Halpern, Malka

    2015-01-01

    Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness. PMID:26122961

  14. Camparison of benthic bacterial community composition in nine streams

    Treesearch

    Xuqing Gao; Ola A. Olapade; Laura G. Leff

    2005-01-01

    In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental conditions. Taxa examined...

  15. Comparison of benthic bacterial community composition in nine streams

    Treesearch

    Xueqing Gao; Ola A. Olapade; Laura G. Leff

    2005-01-01

    In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental...

  16. Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia

    PubMed Central

    Kegler, Hauke F.; Lukman, Muhammad; Teichberg, Mirta; Plass-Johnson, Jeremiah; Hassenrück, Christiane; Wild, Christian; Gärdes, Astrid

    2017-01-01

    Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial

  17. Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

    PubMed Central

    Lear, Gavin; Bellamy, Julia; Case, Bradley S; Lee, Jack E; Buckley, Hannah L

    2014-01-01

    The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24–38% and 17–39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17–32% and 15–20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally ‘redundant'. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water. PMID:24577354

  18. Effects of triclosan on bacterial community composition and ...

    EPA Pesticide Factsheets

    Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, Vibrio, a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm) can induce a significant Vibrio growth response (68–1,700 fold increases) in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary), Doctors Arm Canal (Big Pine Key, FL), and Clam Bank Landing (North Inlet Estuary, Georgetown, SC). Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of Vibrionaceae (17-fold), Pseudoalteromonadaceae (65-fold), Alteromonadaceae (108-fold), Colwelliaceae (430-fold), and Oceanospirillaceae (1,494-fold). While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to u

  19. Seasonal and Successional Influences on Bacterial Community Composition Exceed That of Protozoan Grazing in River Biofilms

    PubMed Central

    Jürgens, Klaus; Weitere, Markus

    2012-01-01

    The effects of protozoa (heterotrophic flagellates and ciliates) on the morphology and community composition of bacterial biofilms were tested under natural background conditions by applying size fractionation in a river bypass system. Confocal laser scanning microscopy (CLSM) was used to monitor the morphological structure of the biofilm, and fingerprinting methods (single-stranded conformation polymorphism [SSCP] and denaturing gradient gel electrophoresis [DGGE]) were utilized to assess changes in bacterial community composition. Season and internal population dynamics had a greater influence on the bacterial biofilm than the presence of protozoa. Within this general framework, bacterial area coverage and microcolony abundance were nevertheless enhanced by the presence of ciliates (but not by the presence of flagellates). We also found that the richness of bacterial operational taxonomic units was much higher in planktonic founder communities than in the ones establishing the biofilm. Within the first 2 h of colonization of an empty substrate by bacteria, the presence of flagellates additionally altered their biofilm community composition. As the biofilms matured, the number of bacterial operational taxonomic units increased when flagellates were present in high abundances. The additional presence of ciliates tended to at first reduce (days 2 to 7) and later increase (days 14 to 29) bacterial operational taxonomic unit richness. Altogether, the response of the bacterial community to protozoan grazing pressure was small compared to that reported in planktonic studies, but our findings contradict the assumption of a general grazing resistance of bacterial biofilms toward protozoa. PMID:22247162

  20. Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

    PubMed Central

    Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

    2017-01-01

    The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

  1. Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function

    PubMed Central

    Berga, Mercè; Székely, Anna J.; Langenheder, Silke

    2012-01-01

    Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, we implemented two independent short-term experiments with dialysis bags containing natural bacterial communities, which were transplanted between ambient and ‘disturbed’ incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. We followed changes in community composition by terminal restriction fragment analysis (T-RFLP) and measured various community functions (bacterial production, carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community composition and functions. In the disturbance intensity experiment, the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency experiment, effects on the different functions were more consistent and recovery was not observed. Moreover, in case of the intensity experiment, there was also a time lag in the responses of community composition and functions, with functional responses being faster than compositional ones. To summarize, our study shows that disturbance strength has the potential to change the functional performance and composition of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community composition and functioning along disturbance gradients depend on the type of function and the character of the disturbance. PMID:22606316

  2. Bacterial community structure in patagonian Andean Lakes above and below timberline: from community composition to community function.

    PubMed

    Bastidas Navarro, Marcela; Balseiro, Esteban; Modenutti, Beatriz

    2014-10-01

    Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.

  3. Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

    PubMed

    Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

    2013-07-01

    Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks.

  4. 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

  5. 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.

  6. Changes in bacterial community composition in the system of rice intensification (SRI) in Chiang Mai, Thailand.

    PubMed

    Sooksa-Nguan, Thanwalee; Gypmantasiri, Phrek; Boonkerd, Nantakorn; Thies, Janice E; Teaumroong, Neung

    2010-01-01

    The factors of alternating flooding and draining during the vegetative growth phase and applying compost to investigate changes in bacterial community composition between the system of rice intensification (SRI) and conventionally managed rice were investigated. 16S rRNA gene T-RFLP analysis showed the major changes in the bacterial communities from the beginning of cultivation to vegetative phase, at which time the groups formed remained consistent until the end of cropping season. Significant and consistent separations of microbial communities between the two systems were revealed. These results suggested that the differences in rice cultivation practice can cause the changes in microbial communities.

  7. 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.

  8. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

    PubMed Central

    Crary, Benjamin C.; Shade, Ashley; Owens, Sarah; Gilbert, Jack A.; Knight, Rob; McMahon, Katherine D.

    2017-01-01

    ABSTRACT Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “Candidatus Omnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial

  9. Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.

    PubMed

    Linz, Alexandra M; Crary, Benjamin C; Shade, Ashley; Owens, Sarah; Gilbert, Jack A; Knight, Rob; McMahon, Katherine D

    2017-01-01

    Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and "Candidatus Omnitrophica" in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community

  10. Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee.

    PubMed

    McFrederick, Quinn S; Rehan, Sandra M

    2016-05-01

    Many insects obtain gut microbes from their diet, but how a mother's foraging patterns influence the microbes found in her offspring's food remains an open question. To address this gap, we studied a bee that forages for pollen from multiple species of plants and may therefore acquire diverse bacteria from different plants. We tested the hypothesis that pollen diversity correlates with bacterial diversity by simultaneously characterizing these two communities in bee brood provisions for the first time. We used deep sequencing of the plant RBCL gene and the bacterial 16S rRNA gene to characterize pollen and bacterial diversity. We then tested for associations between pollen and bacterial species richness and community composition, as well as co-occurrence of specific bacteria and pollen types. We found that both pollen and bacterial communities were extremely diverse, indicating that mother bees visit a wide variety of flowers for pollen and nectar and subsequently bring a diversity of microbes back into their nests. Pollen and bacterial species richness and community composition, however, were not correlated. Certain pollen types significantly co-occurred with the most proportionally abundant bacteria, indicating that the plants these pollen types came from may serve as reservoirs for these bacteria. Even so, the overall diversity of these communities appears to mask these associations at a broader scale. Further study of these pollen and bacteria associations will be important for understanding the complicated relationship between bacteria and wild bees.

  11. Role of shear stress on composition, diversity and dynamics of biofilm bacterial communities.

    PubMed

    Rochex, Alice; Godon, Jean-Jacques; Bernet, Nicolas; Escudié, Renaud

    2008-12-01

    This article evaluates the effect of shear stress on the composition of biofilm bacterial communities. For the first time, a Conical Couette-Taylor Reactor (CCTR) was used to develop biofilms at varying shear stresses (from 0.055 to 0.27 Pa) and provided a useful model for studying the effect of hydrodynamics on biofilms. The composition, diversity and dynamics of biofilm bacterial communities were analysed using the PCR-SSCP fingerprint method. Results clearly demonstrate a link between shear stress and composition of the microbial communities. High shear stresses decrease biofilm diversity and the analysis of biofilm community dynamics suggests that shear stress would slow down biofilm maturation and tend to maintain a young biofilm.

  12. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    PubMed Central

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

    2014-01-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

  13. High-resolution melt analysis for rapid comparison of bacterial community compositions.

    PubMed

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Baelum, Jacob; Feld, Louise; Holben, William E; Jacobsen, Carsten Suhr

    2014-06-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.

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

    PubMed Central

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

    2016-01-01

    This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p < 0.001), water content (p < 0.01), ammonium nitrogen (NH4+-N, p < 0.01), silicate silicon (SiO42--Si, p < 0.01), nitrite nitrogen (NO2--N, p < 0.05), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the bacterial community composition. The results suggest soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments. PMID:27516761

  15. 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

  16. pH Dynamics and Bacterial Community Composition in the Rumen of Lactating Dairy Cows

    USDA-ARS?s Scientific Manuscript database

    The influence of pH dynamics on ruminal bacterial community composition was studied in 8 ruminally cannulated Holstein cows fitted with indwelling electrodes that recorded pH at 10-min intervals over a 3-d period. Cows were fed a silage-based TMR supplemented with monensin. Ruminal samples were col...

  17. pH Dynamics and Bacterial Community Composition in the Rumen of Lactating Dairy Cows

    USDA-ARS?s Scientific Manuscript database

    The effect of pH dynamics on ruminal bacterial community composition (BCC) was studied in 8 ruminally cannulated Holstein cows fitted with indwelling electrodes that recorded pH at 10-min intervals over a 2.4-d period. Cows were fed a silage-based TMR supplemented with monensin. Ruminal samples wer...

  18. Composition, Diversity, and Origin of the Bacterial Community in Grass Carp Intestine

    PubMed Central

    Wu, Shangong; Wang, Guitang; Angert, Esther R.; Wang, Weiwei; Li, Wenxiang; Zou, Hong

    2012-01-01

    Gut microbiota has become an integral component of the host, and received increasing attention. However, for many domestic animals, information on the microbiota is insufficient and more effort should be exerted to manage the gastrointestinal bacterial community. Understanding the factors that influence the composition of microbial community in the host alimentary canal is essential to manage or improve the microbial community composition. In the present study, 16S rRNA gene sequence-based comparisons of the bacterial communities in the grass carp (Ctenopharyngodon idellus) intestinal contents and fish culture-associated environments are performed. The results show that the fish intestinal microbiota harbors many cellulose-decomposing bacteria, including sequences related to Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, and Citrobacter. The most abundant bacterial operational taxonomic units (OTUs) in the grass carp intestinal content are those related to feed digestion. In addition, the potential pathogens and probiotics are important members of the intestinal microbiota. Further analyses show that grass carp intestine holds a core microbiota composed of Proteobacteria, Firmicutes, and Actinobacteria. The comparison analyses reveal that the bacterial community in the intestinal contents is most similar to those from the culture water and sediment. However, feed also plays significant influence on the composition of gut microbiota. PMID:22363439

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

    PubMed

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

    2016-01-01

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

  20. Watershed Urbanization Alters the Composition and Function of Stream Bacterial Communities

    PubMed Central

    Wang, Si-Yi; Sudduth, Elizabeth B.; Wallenstein, Matthew D.; Wright, Justin P.; Bernhardt, Emily S.

    2011-01-01

    Watershed urbanization leads to dramatic changes in draining streams, with urban streams receiving a high frequency of scouring flows, together with the nutrient, contaminant, and thermal pollution associated with urbanization. These changes are known to cause significant losses of sensitive insect and fish species from urban streams, yet little is known about how these changes affect the composition and function of stream microbial communities. Over the course of two years, we repeatedly sampled sediments from eight central North Carolina streams affected to varying degrees by watershed urbanization. For each stream and sampling date, we characterized both overall and denitrifying bacterial communities and measured denitrification potentials. Denitrification is an ecologically important process, mediated by denitrifying bacteria that use nitrate and organic carbon as substrates. Differences in overall and denitrifying bacterial community composition were strongly associated with the gradient in urbanization. Denitrification potentials, which varied widely, were not significantly associated with substrate supply. By incorporating information on the community composition of denitrifying bacteria together with substrate supply in a linear mixed-effects model, we explained 45% of the variation in denitrification potential (p-value<0.001). Our results suggest that (1) the composition of stream bacterial communities change in response to watershed urbanization and (2) such changes may have important consequences for critical ecosystem functions such as denitrification. PMID:21857975

  1. The bacterial community composition of the surface microlayer in a high mountain lake

    PubMed Central

    Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

    2010-01-01

    The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air–water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 μm) and the underlying water (ULW) (0.2–0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers. PMID:20528985

  2. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

    PubMed

    Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

    2017-08-06

    Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ((3) H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the

  3. Mineral composition and charcoal determine the bacterial community structure in artificial soils.

    PubMed

    Ding, Guo-Chun; Pronk, Geertje Johanna; Babin, Doreen; Heuer, Holger; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

    2013-10-01

    To study the influence of the clay minerals montmorillonite (M) and illite (I), the metal oxides ferrihydrite (F) and aluminum hydroxide (A), and charcoal (C) on soil bacterial communities, seven artificial soils with identical texture provided by quartz (Q) were mixed with sterilized manure as organic carbon source before adding a microbial inoculant derived from a Cambisol. Bacterial communities established in artificial soils after 90 days of incubation were compared by DGGE analysis of bacterial and taxon-specific 16S rRNA gene amplicons. The bacterial community structure of charcoal-containing soils highly differed from the other soils at all taxonomic levels studied. Effects of montmorillonite and illite were observed for Bacteria and Betaproteobacteria, but not for Actinobacteria or Alphaproteobacteria. A weak influence of metal oxides on Betaproteobacteria was found. Barcoded pyrosequencing of 16S rRNA gene amplicons done for QM, QI, QIF, and QMC revealed a high bacterial diversity in the artificial soils. The composition of the artificial soils was different from the inoculant, and the structure of the bacterial communities established in QMC soil was most different from the other soils, suggesting that charcoal provided distinct microenvironments and biogeochemical interfaces formed. Several populations with discriminative relative abundance between artificial soils were identified.

  4. Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalga Fucus vesiculosus.

    PubMed

    Stratil, Stephanie B; Neulinger, Sven C; Knecht, Henrik; Friedrichs, Anette K; Wahl, Martin

    2013-04-01

    The thallus surface of the brown macroalga Fucus vesiculosus is covered by a specific biofilm community. This biofilm supposedly plays an important role in the interaction between host and environment. So far, we know little about compositional or functional shifts of this epibiotic bacterial community under changing environmental conditions. In this study, the response of the microbiota to different temperatures with respect to cell density and community composition was analyzed by nonculture-based methods (denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene). Redundancy analysis showed that despite high variability among host individuals temperature accounted for 20% of the variation in the bacterial community composition, whereas cell density did not differ between groups. Across all samples, 4341 bacterial operational taxonomic units (OTUs) at a 97% similarity level were identified. Eight percent of OTUs were significantly correlated with low, medium, and high temperatures. Notably, the family Rhodobacteraceae increased in relative abundance from 20% to 50% with increasing temperature. OTU diversity (evenness and richness) was higher at 15 °C than at the lower and higher temperatures. Considering their known and presumed ecological functions for the host, change in the epibacterial community may entail shifts in the performance of the host alga.

  5. Effects of Functionalized and Raw Multi-Walled Carbon Nanotubes on Soil Bacterial Community Composition

    PubMed Central

    Kerfahi, Dorsaf; Tripathi, Binu M.; Singh, Dharmesh; Kim, Hyoki; Lee, Sujin; Lee, Junghoon; Adams, Jonathan M.

    2015-01-01

    Carbon nanotubes (CNTs) are widely used in industry, but their environmental impacts on soil microbial communities are poorly known. In this paper, we compare the effect of both raw and acid treated or functionalized (fCNTs) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Soil DNA was extracted at 0, 2 and 8 weeks and the V3 region of the 16S rRNA gene was PCR-amplified and sequenced using paired-end Illumina bar-coded sequencing. The results show that bacterial diversity was not affected by either type of MWCNT. However, overall soil bacterial community composition, as illustrated by NMDS, was affected only by fMWCNT at high concentrations. This effect, detectable at 2 weeks, remained equally strong by 8 weeks. In the case of fMWCNTs, overall changes in relative abundance of the dominant phyla were also found. The stronger effect of fMWCNTs could be explained by their intrinsically acidic nature, as the soil pH was lower at higher concentrations of fMWCNTs. Overall, this study suggests that fMWCNTs may at least temporarily alter microbial community composition on the timescale of at least weeks to months. It appears, by contrast, that raw MWCNTs do not affect soil microbial community composition. PMID:25825905

  6. Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalga Fucus vesiculosus

    PubMed Central

    Stratil, Stephanie B; Neulinger, Sven C; Knecht, Henrik; Friedrichs, Anette K; Wahl, Martin

    2013-01-01

    The thallus surface of the brown macroalga Fucus vesiculosus is covered by a specific biofilm community. This biofilm supposedly plays an important role in the interaction between host and environment. So far, we know little about compositional or functional shifts of this epibiotic bacterial community under changing environmental conditions. In this study, the response of the microbiota to different temperatures with respect to cell density and community composition was analyzed by nonculture-based methods (denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene). Redundancy analysis showed that despite high variability among host individuals temperature accounted for 20% of the variation in the bacterial community composition, whereas cell density did not differ between groups. Across all samples, 4341 bacterial operational taxonomic units (OTUs) at a 97% similarity level were identified. Eight percent of OTUs were significantly correlated with low, medium, and high temperatures. Notably, the family Rhodobacteraceae increased in relative abundance from 20% to 50% with increasing temperature. OTU diversity (evenness and richness) was higher at 15°C than at the lower and higher temperatures. Considering their known and presumed ecological functions for the host, change in the epibacterial community may entail shifts in the performance of the host alga. PMID:23568841

  7. Effects of functionalized and raw multi-walled carbon nanotubes on soil bacterial community composition.

    PubMed

    Kerfahi, Dorsaf; Tripathi, Binu M; Singh, Dharmesh; Kim, Hyoki; Lee, Sujin; Lee, Junghoon; Adams, Jonathan M

    2015-01-01

    Carbon nanotubes (CNTs) are widely used in industry, but their environmental impacts on soil microbial communities are poorly known. In this paper, we compare the effect of both raw and acid treated or functionalized (fCNTs) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Soil DNA was extracted at 0, 2 and 8 weeks and the V3 region of the 16S rRNA gene was PCR-amplified and sequenced using paired-end Illumina bar-coded sequencing. The results show that bacterial diversity was not affected by either type of MWCNT. However, overall soil bacterial community composition, as illustrated by NMDS, was affected only by fMWCNT at high concentrations. This effect, detectable at 2 weeks, remained equally strong by 8 weeks. In the case of fMWCNTs, overall changes in relative abundance of the dominant phyla were also found. The stronger effect of fMWCNTs could be explained by their intrinsically acidic nature, as the soil pH was lower at higher concentrations of fMWCNTs. Overall, this study suggests that fMWCNTs may at least temporarily alter microbial community composition on the timescale of at least weeks to months. It appears, by contrast, that raw MWCNTs do not affect soil microbial community composition.

  8. Epiphytic bacterial community composition on two common submerged macrophytes in brackish water and freshwater

    PubMed Central

    Hempel, Melanie; Blume, Maja; Blindow, Irmgard; Gross, Elisabeth M

    2008-01-01

    Background Plants and their heterotrophic bacterial biofilm communities possibly strongly interact, especially in aquatic systems. We aimed to ascertain whether different macrophytes or their habitats determine bacterial community composition. We compared the composition of epiphytic bacteria on two common aquatic macrophytes, the macroalga Chara aspera Willd. and the angiosperm Myriophyllum spicatum L., in two habitats, freshwater (Lake Constance) and brackish water (Schaproder Bodden), using fluorescence in situ hybridization. The bacterial community composition was analysed based on habitat, plant species, and plant part. Results The bacterial abundance was higher on plants from brackish water [5.3 × 107 cells (g dry mass)-1] than on plants from freshwater [1.3 × 107 cells (g dry mass)-1], with older shoots having a higher abundance. The organic content of freshwater plants was lower than that of brackish water plants (35 vs. 58%), and lower in C. aspera than in M. spicatum (41 vs. 52%). The content of nutrients, chlorophyll, total phenolic compounds, and anthocyanin differed in the plants and habitats. Especially the content of total phenolic compounds and anthocyanin was higher in M. spicatum, and in general higher in the freshwater than in the brackish water habitat. Members of the Cytophaga-Flavobacteria-Bacteroidetes group were abundant in all samples (5–35% of the total cell counts) and were especially dominant in M. spicatum samples. Alphaproteobacteria were the second major group (3–17% of the total cell counts). Betaproteobacteria, gammaproteobacteria, and actinomycetes were present in all samples (5 or 10% of the total cell counts). Planctomycetes were almost absent on M. spicatum in freshwater, but present on C. aspera in freshwater and on both plants in brackish water. Conclusion Bacterial biofilm communities on the surface of aquatic plants might be influenced by the host plant and environmental factors. Distinct plant species, plant part and

  9. Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters

    PubMed Central

    Roiha, Toni; Peura, Sari; Cusson, Mathieu; Rautio, Milla

    2016-01-01

    In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions. PMID:27686416

  10. Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters.

    PubMed

    Roiha, Toni; Peura, Sari; Cusson, Mathieu; Rautio, Milla

    2016-09-30

    In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions.

  11. Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters

    NASA Astrophysics Data System (ADS)

    Roiha, Toni; Peura, Sari; Cusson, Mathieu; Rautio, Milla

    2016-09-01

    In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions.

  12. Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

    PubMed

    Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

    2013-03-01

    We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics.

  13. Factors influencing the composition of bacterial communities found at abandoned copper-tailings dumps.

    PubMed

    De la Iglesia, R; Castro, D; Ginocchio, R; van der Lelie, D; González, B

    2006-03-01

    To study the effect that copper residues exert on bacterial communities and the ability of bacteria to colonize different microhabitats in abandoned tailing dumps. We used the terminal-restriction fragment length polymorphism technique, a culture-independent molecular approach based on PCR amplification of ribosomal genes, to compare the structure of the bacterial communities from samples taken at two nearby located abandoned tailing dumps found in the Mediterranean-climate area of central Chile. Our results show that elevated available copper content in tailings has a strong effect on the bacterial community composition, but that other factors like pH and organic matter content also play an important role in the structure of these communities. We also found that the number of abundant bacteria in these samples was significantly lower than in soils not exposed to metal pollution. In addition to bioavailable copper, bacterial communities found in copper-tailings dumps are also affected by several other environmental factors. This first report on environmental factors influencing microbial communities in copper-tailings dumps will help to devise appropriate restoration procedures in this type of polluted habitat.

  14. From source to filter: changes in bacterial community composition during potable water treatment.

    PubMed

    Zanacic, Enisa; McMartin, Dena W; Stavrinides, John

    2017-06-01

    Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

  15. The role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar.

    PubMed

    Samuni-Blank, Michal; Izhaki, Ido; Laviad, Sivan; Bar-Massada, Avi; Gerchman, Yoram; Halpern, Malka

    2014-01-01

    Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs.

  16. The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar

    PubMed Central

    Samuni-Blank, Michal; Izhaki, Ido; Laviad, Sivan; Bar-Massada, Avi; Gerchman, Yoram; Halpern, Malka

    2014-01-01

    Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that “everything is everywhere, but the environment selects”. Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs. PMID:24922317

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

    PubMed

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

    2011-01-01

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

  18. Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition

    PubMed Central

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

    2011-01-01

    Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly Gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens. PMID:21949751

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

    PubMed Central

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

    2016-01-01

    The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the “green” pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L-1) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L-1) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity. PMID:27446017

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

    PubMed

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

    2016-01-01

    The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the "green" pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L(-1)) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L(-1)) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.

  1. Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition.

    PubMed

    Bang-Andreasen, Toke; Nielsen, Jeppe T; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C B; Jacobsen, Carsten S

    2017-01-01

    Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha(-1). We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha(-1) to alkaline at 167 t ha(-1). Bacterial numbers significantly increased up to a wood ash dose of 22 t ha(-1) followed by significant decrease at 167 t ha(-1) wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha(-1) while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha(-1) with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha(-1) whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can

  2. Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

    PubMed Central

    Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C. B.; Jacobsen, Carsten S.

    2017-01-01

    Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha-1 to alkaline at 167 t ha-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha-1 followed by significant decrease at 167 t ha-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly

  3. Within-lake heterogeneity of environmental factors structuring bacterial community composition in Lake Dongting, China.

    PubMed

    Niu, Yuan; Yu, Hui; Jiang, Xia

    2015-11-01

    Within-lake heterogeneity of bacterial community composition (BCC) was investigated in the large and shallow regulating Lake Dongting. Samples were collected at 13 sites located in different areas of the lake. PCR-denaturing gradient gel electrophoresis (DGGE) and redundancy analysis (RDA) were used for revealing spatial distribution of BCC and the relationships between BCC and environmental variables. The DGGE banding patterns revealed a remarkable spatial heterogeneity which was closely related to their geographical positions. RDA result demonstrated that TP and TN, as well as Secchi depth, were the three most influential factors, responsible for a major part of the observed variation in BCC. Total bacterial abundances were significantly higher in Eastern Dongting due to high TP and suspended solids. In conclusion, bacterial community diversity in Lake Dongting was mainly shaped by within-lake heterogeneity of nutrient and transparency.

  4. Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce.

    PubMed

    Rastogi, Gurdeep; Sbodio, Adrian; Tech, Jan J; Suslow, Trevor V; Coaker, Gitta L; Leveau, Johan H J

    2012-10-01

    The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009-2010 crop cycle. Total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial 'core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.

  5. Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

    PubMed Central

    Rastogi, Gurdeep; Sbodio, Adrian; Tech, Jan J; Suslow, Trevor V; Coaker, Gitta L; Leveau, Johan H J

    2012-01-01

    The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009–2010 crop cycle. Total bacterial populations averaged between 105 and 106 per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial ‘core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment. PMID:22534606

  6. Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms.

    PubMed

    Lawes, Jasmin C; Neilan, Brett A; Brown, Mark V; Clark, Graeme F; Johnston, Emma L

    2016-01-01

    Biofilms are integral to many marine processes but their formation and function may be affected by anthropogenic inputs that alter environmental conditions, including fertilisers that increase nutrients. Density composition and connectivity of biofilms developed in situ (under ambient and elevated nutrients) were compared using 454-pyrosequencing of the 16S gene. Elevated nutrients shifted community composition from bacteria involved in higher processes (eg Pseudoalteromonas spp. invertebrate recruitment) towards more nutrient-tolerant bacterial species (eg Terendinibacter sp.). This may enable the persistence of biofilm communities by increasing resistance to nutrient inputs. A core biofilm microbiome was identified (predominantly Alteromonadales and Oceanospirillales) and revealed shifts in abundances of core microbes that could indicate enrichment by fertilisers. Fertiliser decreased density and connectivity within biofilms indicating that associations were disrupted perhaps via changes to energetic allocations within the core microbiome. Density composition and connectivity changes suggest nutrients can affect the stability and function of these important marine communities.

  7. Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought?

    PubMed

    Evans, Sarah E; Wallenstein, Matthew D; Burke, Ingrid C

    2014-01-01

    Both biogeographical and rainfall manipulation studies show that soil water content can be a strong driver of microbial community composition. However, we do not yet know if these patterns emerge because certain bacterial taxa are better able to survive at dry soil moisture regimes or if they are due to other drought-sensitive ecosystem properties indirectly affecting microbial community composition. In this study, we evaluated (1) whether bacterial community composition changed under an 11-year drought manipulation and (2) whether shifts under drought could be explained by variation in the moisture sensitivity of growth among bacterial taxa (moisture niche partitioning). Using 454 pyrosequencing of 16S rRNA, we observed shifts in bacterial community composition under drought, coincident with changes in other soil properties. We wet-up dry soils from drought plots to five moisture levels, and measured respiration and the composition of actively growing communities using bromodeoxyuridine (BrdU) labeling of DNA. The field drought experiment affected the composition of the active community when incubated at different moisture levels in the laboratory, as well as short-term (36-hour) respiration rates. Independent of history, bacterial communities also displayed strong niche partitioning across the wet-up moisture gradient. Although this indicates that moisture has the potential to drive bacterial community composition under long-term drought, species distributions predicted by response to moisture did not reflect the community composition of plots that were subjected to long-term drought. Bacterial community structure was likely more strongly driven by other environmental factors that changed under long-term drought, or not shaped by response to water level upon wet-up. The approach that we present here for linking niches to community composition could be adapted for other environmental variables to aid in predicting microbial species distributions and community

  8. Activation of the Jasmonic Acid Plant Defence Pathway Alters the Composition of Rhizosphere Bacterial Communities

    PubMed Central

    Carvalhais, Lilia C.; Dennis, Paul G.; Badri, Dayakar V.; Tyson, Gene W.; Vivanco, Jorge M.; Schenk, Peer M.

    2013-01-01

    Jasmonic acid (JA) signalling plays a central role in plant defences against necrotrophic pathogens and herbivorous insects, which afflict both roots and shoots. This pathway is also activated following the interaction with beneficial microbes that may lead to induced systemic resistance. Activation of the JA signalling pathway via application of methyl jasmonate (MeJA) alters the composition of carbon containing compounds released by roots, which are implicated as key determinants of rhizosphere microbial community structure. In this study, we investigated the influence of the JA defence signalling pathway activation in Arabidopsis thaliana on the structure of associated rhizosphere bacterial communities using 16S rRNA gene amplicon pyrosequencing. Application of MeJA did not directly influence bulk soil microbial communities but significant changes in rhizosphere community composition were observed upon activation of the jasmonate signalling pathway. Our results suggest that JA signalling may mediate plant-bacteria interactions in the soil upon necrotrophic pathogen and herbivorous insect attacks. PMID:23424661

  9. Antibiotic resistance, antimicrobial residues and bacterial community composition in urban wastewater.

    PubMed

    Novo, Ana; André, Sandra; Viana, Paula; Nunes, Olga C; Manaia, Célia M

    2013-04-01

    This study was based on the hypothesis that the occurrence of antimicrobial residues and antibiotic resistant bacteria in the sewage could be correlated with the structure and composition of the bacterial community and the antibiotic resistance loads of the final effluent. Raw and treated wastewater composite samples were collected from an urban treatment plant over 14 sampling dates. Samples were characterized for the i) occurrence of tetracyclines, penicillins, sulfonamides, quinolones, triclosan, arsenic, cadmium, lead, chromium and mercury; ii) antibiotic resistance percentages for tetracycline, sulfamethoxazole, ciprofloxacin and amoxicillin and iii) 16S rRNA gene-DGGE patterns. The data of corresponding samples, taking into account the hydraulic residence time, was analyzed using multivariate analysis. Variations on the bacterial community structure of the final effluent were significantly correlated with the occurrence of tetracyclines, penicillins, sulfonamides, quinolones and triclosan in the raw inflow. Members of the class Epsilonproteobacteria presented positive correlations with those antimicrobials, whereas negative correlations were observed with Beta and Gammaproteobacteria and Firmicutes. Antibiotic resistance percentages presented different trends of variation in heterotrophs/enterobacteria and in enterococci, varied over time and after wastewater treatment. Antibiotic resistance was positively correlated with the occurrence of tetracyclines residues and high temperature. A relationship between antibiotic residues, bacterial community structure and composition and antibiotic resistance is demonstrated. Further studies, involving more wastewater treatment plants may help to elucidate this complex relationship. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Aspen defense chemicals influence midgut bacterial community composition of gypsy moth.

    PubMed

    Mason, Charles J; Rubert-Nason, Kennedy F; Lindroth, Richard L; Raffa, Kenneth F

    2015-01-01

    Microbial symbionts are becoming increasingly recognized as mediators of many aspects of plant - herbivore interactions. However, the influence of plant chemical defenses on gut associates of insect herbivores is less well understood. We used gypsy moth (Lymantria dispar L.), and differing trembling aspen (Populus tremuloides Michx.) genotypes that vary in chemical defenses, to assess the influence of foliar chemistry on bacterial communities of larval midguts. We evaluated the bacterial community composition of foliage, and of midguts of larvae feeding on those leaves, using next-generation high-throughput sequencing. Plant defense chemicals did not influence the composition of foliar communities. In contrast, both phenolic glycosides and condensed tannins affected the bacterial consortia of gypsy moth midguts. The two most abundant operational taxonomic units were classified as Ralstonia and Acinetobacter. The relative abundance of Ralstonia was higher in midguts than in foliage when phenolic glycoside concentrations were low, but lower in midguts when phenolic glycosides were high. In contrast, the relative abundance of Ralstonia was lower in midguts than in foliage when condensed tannin concentrations were low, but higher in midguts when condensed tannins were high. Acinetobacter showed a different relationship with host chemistry, being relatively more abundant in midguts than with foliage when condensed tannin concentrations were low, but lower in midguts when condensed tannins were high. Acinetobacter tended to have a greater relative abundance in midguts of insects feeding on genotypes with high phenolic glycoside concentrations. These results show that plant defense chemicals influence herbivore midgut communities, which may in turn influence host utilization.

  11. Characterisation of the soil bacterial community structure and composition of natural and constructed wetlands.

    PubMed

    Ansola, Gemma; Arroyo, Paula; Sáenz de Miera, Luis E

    2014-03-01

    In the present study, the pyrosequencing of 16S ribosomal DNA was used to characterise the soil bacterial community composition of a constructed wetland receiving municipal wastewater and a nearby natural wetland. Soil samples were taken from different locations in each wetland (lagoon, zone with T. latifolia, zone with S. atrocinerea). Moreover, the water quality parameters were evaluated (pH, Tª, conductivity, dissolved oxygen, redox potential, nutrients and suspended solids), revealing that the organic matter and nutrient contents were significantly higher in the constructed wetland than in the natural one. In general, the bacterial communities of the natural wetland were more diverse than those of the constructed wetland. The major phylogenic groups of all soils included Proteobacteria, Verrucomicrobia and Chloroflexi, with Proteobacteria being the majority of the community composition. The Verrucomicrobia and Chloroflexi phyla were more abundant in the natural wetland than the constructed wetland; in contrast, the Proteobacteria phylum was more abundant in the constructed wetland than the natural wetland. Beta diversity analyses reveal that the soil bacterial communities in the natural wetland were less dissimilar to each other than to those of the constructed wetland.

  12. Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment

    PubMed Central

    Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C.

    2017-01-01

    ABSTRACT Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of Py

  13. Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment.

    PubMed

    Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C; Xu, Jianming

    2017-01-01

    Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and

  14. Impact of warming on phyto-bacterioplankton coupling and bacterial community composition in experimental mesocosms.

    PubMed

    von Scheibner, Markus; Dörge, Petra; Biermann, Antje; Sommer, Ulrich; Hoppe, Hans-Georg; Jürgens, Klaus

    2014-03-01

    Global warming is assumed to alter the trophic interactions and carbon flow patterns of aquatic food webs. The impact of temperature on phyto-bacterioplankton coupling and bacterial community composition (BCC) was the focus of the present study, in which an indoor mesocosm experiment with natural plankton communities from the western Baltic Sea was conducted. A 6 °C increase in water temperature resulted, as predicted, in tighter coupling between the diatom-dominated phytoplankton and heterotrophic bacteria, accompanied by a strong increase in carbon flow into bacterioplankton during the phytoplankton bloom phase. Suppressed bacterial development at cold in situ temperatures probably reflected lowered bacterial production and grazing by protists, as the latter were less affected by low temperatures. BCC was strongly influenced by the phytoplankton bloom stage and to a lesser extent by temperature. Under both temperature regimes, Gammaproteobacteria clearly dominated during the phytoplankton peak, with Glaciecola sp. as the single most abundant taxon. However, warming induced the appearance of additional bacterial taxa belonging to Betaproteobacteria and Bacteroidetes. Our results show that warming during an early phytoplankton bloom causes a shift towards a more heterotrophic system, with the appearance of new bacterial taxa suggesting a potential for utilization of a broader substrate spectrum. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

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

    PubMed

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

    2016-01-01

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

  16. Rhizosphere and non-rhizosphere bacterial community composition of the wild medicinal plant Rumex patientia.

    PubMed

    Qi, Xiaojuan; Wang, Ensi; Xing, Ming; Zhao, Wei; Chen, Xia

    2012-05-01

    To investigate bacterial communities between rhizosphere and non-rhizosphere soils of the wild medicinal plant Rumex patientia of Jilin, China, small subunit rRNAs (16S rDNA) from soil metagenome were amplified by polymerase chain reaction using primers specific to the domain bacteria and analysed by cloning and sequencing. The relative proportion of bacterial communities in rhizosphere soils was similar to non-rhizosphere soils in five phylogenetic groups (Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Planctomycetes). But there were differences in five other phylogenetic groups (Firmicutes, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Unclassified bacteria). Over 97.24 % of the sequenced clones were found to be unique to rhizosphere and non-rhizosphere soils, while 2.76 % were shared by both of them. Our results indicate that there are differences in the composition and proportion of bacterial communities between rhizosphere and non-rhizosphere soils. Furthermore, the unique bacterial clones between rhizosphere and non-rhizosphere soils of the wild medicinal plant R. patientia have obvious differences.

  17. Bacterial Community Composition in Oligosaline Lake Bosten: Low Overlap of Betaproteobacteria and Bacteroidetes with Freshwater Ecosystems

    PubMed Central

    Tang, Xiangming; Xie, Guijuan; Shao, Keqiang; Dai, Jiangyu; Chen, Yuangao; Xu, Qiujin; Gao, Guang

    2015-01-01

    Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication. PMID:25985930

  18. Bacterial Community Composition in Oligosaline Lake Bosten: Low Overlap of Betaproteobacteria and Bacteroidetes with Freshwater Ecosystems.

    PubMed

    Tang, Xiangming; Xie, Guijuan; Shao, Keqiang; Dai, Jiangyu; Chen, Yuangao; Xu, Qiujin; Gao, Guang

    2015-01-01

    Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication.

  19. Key role of selective viral-induced mortality in determining marine bacterial community composition.

    PubMed

    Bouvier, T; del Giorgio, P A

    2007-02-01

    Viral infection is thought to play an important role in shaping bacterial community composition and diversity in aquatic ecosystems, but the strength of this interaction and the mechanisms underlying this regulation are still not well understood. The consensus is that viruses may impact the dominant bacterial strains, but there is little information as to how viruses may affect the less abundant taxa, which often comprise the bulk of the total bacterial diversity. The potential effect of viruses on the phylogenetic composition of marine bacterioplankton was assessed by incubating marine bacteria collected along a North Pacific coastal-open ocean transect in seawater that was greatly depleted of ambient viruses. The ambient communities were dominated by typical marine groups, including alphaproteobacteria and the Bacteroidetes. Incubation of these communities in virus-depleted ambient water yielded an unexpected and dramatic increase in the relative abundance of bacterial groups that are generally undetectable in the in situ assemblages, such as betaproteobacteria and Actinobacteria. Our results suggest that host susceptibility is not necessarily only proportional to its density but to other characteristics of the host, that rare marine bacterial groups may be more susceptible to viral-induced mortality, and that these rare groups may actually be the winners of competition for resources. These observations are not inconsistent with the 'phage kills the winner' hypothesis but represent an extreme and yet undocumented case of this paradigm, where the potential winners apparently never actually develop beyond a very low abundance threshold in situ. We further suggest that this mode of regulation may influence not just the distribution of single strains but of entire phylogenetic groups.

  20. Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

    NASA Astrophysics Data System (ADS)

    Beman, J. Michael; Carolan, Molly T.

    2013-10-01

    Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans’ largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

  1. Deoxygenation alters bacterial diversity and community composition in the ocean's largest oxygen minimum zone.

    PubMed

    Beman, J Michael; Carolan, Molly T

    2013-01-01

    Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans' largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

  2. Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

    PubMed

    Kumar, Arvind; Rai, Lal Chand

    2017-07-01

    Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

  3. Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments.

    PubMed

    Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina

    2017-01-01

    Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios.

  4. Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments

    PubMed Central

    Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina

    2017-01-01

    Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios. PMID:28286496

  5. Similar bacterial community composition in acidic mining lakes with different pH and lake chemistry.

    PubMed

    Kampe, Heike; Dziallas, Claudia; Grossart, Hans-Peter; Kamjunke, Norbert

    2010-10-01

    As extreme environmental conditions strongly affect bacterial community composition (BCC), we examined whether differences in pH-even at low pH-and in iron and sulfate concentrations lead to changes in BCC of acidic mining lakes. Thereby, we tested the following hypotheses: (1) diversity of the bacterial community in acidic lakes decreases with reducing pH, (2) BCC differs between epilimnion and hypolimnion, and (3) BCC in extremely acidic environments does not vary much over time. Therefore, we investigated the BCC of three acidic lakes with different pH values (2.3, 2.7, and 3.2) by denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of DGGE bands as well as catalyzed reporter deposition-FISH (CARD-FISH). BCC did not significantly vary among the studied lakes nor differ much between water layers. In contrast, BCC significantly changed over time, which is contradictory to our hypotheses. Bacterial communities were dominated by Alpha-, Beta-, and Gammaproteobacteria, whereas Actino- and Acidobacteria rarely occurred. Cell numbers of both free and attached bacteria were positively related to DOC concentration. Overall, low pH and extreme chemical conditions of the studied lakes led to similar assemblages of bacteria with pronounced temporal differences. This notion indicates that temporal changes in environmental conditions including food web structure also affect unique communities of bacteria thriving at low pH.

  6. The Effects of Nutrient Stoichiometry on Bacterial Community Composition in Streams

    NASA Astrophysics Data System (ADS)

    Rubin, M. A.; Leff, L. G.

    2005-05-01

    Bacterial biofilm community composition in streams may be affected by the nutrient stoichiometry of the surrounding water. Specifically, varying nitrogen to phosphorus (N:P) molar ratios potentially can select for or against different taxa, such as various subclasses of Proteobacteria, and thus alter community structure. In this study, bacterial communities at three sites along the Mahoning River (Ohio) with different inorganic nutrient concentrations were compared. Bacteria in biofilms on cobbles were enumerated using fluorescent in situ hybridization (FISH) to determine the abundance of alpha-, beta-, and gamma-Proteobacteria, and the Cytophaga-Flavobacterium-cluster. Nitrate, ammonia, and soluble reactive phosphate (SRP) concentrations in the water ranged from undetectable to 0.05 g/L of SRP and 0.3 g/L of ammonia. Beta-Proteobacteria appeared to be the most affected by N:P (ranging from 11 to 150) showing a positive correlation between their abundance and the N:P ratio. The Cytophaga-Flavobacterium showed effects that were nearly opposite of the beta-Proteobacteria. These findings provide evidence that limitation by single nutrients may not be as good a predictor of bacterial community structure as the molar ratios of these nutrients. Also, the nutrient stoichiometry could have a bottom up effect on stream ecosystems because of the central role that microbes play in stream food webs.

  7. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

    PubMed Central

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  8. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

    PubMed

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

  9. 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

  10. Bacterial community composition of sediments from artificial Lake Maslak, Istanbul, Turkey.

    PubMed

    Balcı, Nurgul; Vardar, Nurcan; Yelboga, Emrah; Karaguler, Nevin Gul

    2012-09-01

    Small artificial lakes are ubiquitous in various natural environments. Small impoundments increase the residence time of water, thereby increasing the potential for retention of nutrients through biological and physical processes. We examined bacterial community structure of Lake Maslak, a small freshwater impoundment located in a densely populated region. The objective of our study was to investigate bacterial communities of the lake sediment which has not been determined and to elucidate the factors controlling bacterial diversity and the biogeochemical processes within the lake. For these purposes, surface water, lake bed sediments, and one core sample were collected. Microbiological characteristic of the lake bed and core sediments was determined by denaturing gradient gel electrophoresis targeting the 16S rRNA gene. Along with the microbiological studies, physicochemical (O(2), pH, temperature) and geochemical properties of the surface (NO (3) (-) , NO (2) (-) , NH (4) (+) ,PO (4) (-) ,SO (4) (2-) , K(+), Mg(2+), Ca(2+)) and pore water (K(+), Mg(2+), Ca(2+)) were determined in addition to heavy metals contents (Co Cu, Fe, Zn, Pb, Cd). Eight lake bed and one core sediments were also collected and analyzed for heavy metals and elemental compositions. Nitrate concentration in the surface water ranges from 0.27-1.8 mg/L, and ammonium (0.0-0.83 mg/L) appears to follow nitrate concentration. Sulfate concentration in the surface water (mean 60 mg/L) is greater than those measured in the pore water (mean, 37.5 mg/L). Fe, Zn, Pb, and Cd were not determined in the surface water, whereas Co was significantly higher both in the surface and pore water. Unlike Co, Pb, Zn, and Cd were not measured in the pore water. Lakebed and core sediments show significant enrichment in Pb, Zn, and Cu, indicating anthropogenic pollution. Consistent with geochemical parameters, microbiological analysis suggests a diverse bacterial community in the lake sediments and influence of

  11. Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils.

    PubMed

    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.

  12. Microbial response to a mesoscale iron enrichment in the NE Subarctic Pacific: Bacterial community composition

    NASA Astrophysics Data System (ADS)

    Agawin, Nona S. R.; Hale, Michelle S.; Rivkin, Richard B.; Matthews, Paul; Li, William K. W.

    2006-10-01

    Changes in microbial community composition were determined during the subarctic ecosystem response to iron enrichment study (SERIES), a mesoscale Fe enrichment conducted in a high-nutrient low-chlorophyll (HNLC) region of the Northeast Subarctic Pacific, in July 2002. Phylogenetic composition using fluorescence in situ hybridization (FISH), relative DNA content using flow cytometry (FCM), and cellular morphometrics (shape and volume) of heterotrophic bacteria were used to characterize community composition from samples collected within and below the mixed layer, inside and outside the Fe-patch. The proportion of total cells detected as members of the Cytophaga-Flavobacterium cluster increased in a log-linear manner from 16 (±1.0)% to 47 (±1.9)% in samples within the mixed layer, inside the Fe-enriched patch, while outside the patch, the proportion remained ⩽21 (±2.2)%. Temporal changes in the proportion of cells in the mixed layer with high DNA content (% HDNA) were significantly different inside and outside the Fe-enriched patch, where inside the patch % HDNA increased 2-fold after a week, reaching 93% towards the end of the observation period. Coupling in situ observations with the results of manipulation experiments allowed us to determine the relative contributions of bottom-up (nutrient limitation) and top-down (grazing) processes on heterotrophic bacterial abundance and community composition. Shifts in heterotrophic bacterial community composition inside the Fe-enriched patch were mainly controlled by top-down processes and moderately controlled by bottom-up controls (organic substrate limitation).

  13. Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu

    PubMed Central

    Li, Junfeng; Zhang, Junyi; Liu, Liyang; Fan, Yucai; Li, Lianshuo; Yang, Yunfeng; Lu, Zuhong; Zhang, Xuegong

    2015-01-01

    Bacterioplankton plays a key role in nutrient cycling and is closely related to water eutrophication and algal bloom. We used high-throughput 16S rRNA gene sequencing to profile archaeal and bacterial community compositions in the surface water of Lake Taihu. It is one of the largest lakes in China and has suffered from recurring cyanobacterial bloom. A total of 81 water samples were collected from 9 different sites in 9 different months of 2012. We found that temporal variation of the microbial community was significantly greater than spatial variation (adonis, n = 9999, P < 1e−4). The composition of bacterial community in December was similar to that in January, and so was the archaeal community, suggesting potential annual periodicity. Unsupervised K-means clustering was used to identify the synchrony of abundance variations between different taxa. We found that the cluster consisting mostly of ACK-M1, C111 (members of acIV), Pelagibacteraceae (alfV-A) and Synechococcaceae showed relatively higher abundance in autumn. On the contrary, the cluster of Comamonadaceae and Methylophilaceae (members of lineage betI and betIV) had higher abundance in spring. The co-occurrence relationships between taxa were greatly altered during the cyanobacterial bloom according to our further network module analysis. PMID:26503553

  14. Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

    PubMed

    Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

    2015-02-15

    Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics.

  15. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

    PubMed

    Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

    2009-09-01

    Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

  16. Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea

    PubMed Central

    Herlemann, Daniel P. R.; Lundin, Daniel; Andersson, Anders F.; Labrenz, Matthias; Jürgens, Klaus

    2016-01-01

    Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity. PMID:27933046

  17. Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters.

    PubMed

    Stressmann, Franziska A; Couve-Deacon, Elodie; Chainier, Delphine; Chauhan, Ashwini; Wessel, Aimee; Durand-Fontanier, Sylvaine; Escande, Marie-Christine; Kriegel, Irène; Francois, Bruno; Ploy, Marie-Cécile; Beloin, Christophe; Ghigo, Jean-Marc

    2017-01-01

    Totally implanted venous access ports (TIVAPs) are commonly used catheters for the management of acute or chronic pathologies. Although these devices improve health care, repeated use of this type of device for venous access over long periods of time is also associated with risk of colonization and infection by pathogenic bacteria, often originating from skin. However, although the skin microbiota is composed of both pathogenic and nonpathogenic bacteria, the extent and the consequences of TIVAP colonization by nonpathogenic bacteria have rarely been studied. Here, we used culture-dependent and 16S rRNA gene-based culture-independent approaches to identify differences in bacterial colonization of TIVAPs obtained from two French hospitals. To explore the relationships between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection, we analyzed the bacterial community parameters between TIVAPs suspected (symptomatic) or not (asymptomatic) of infection. Although we did not find a particular species assemblage or community marker to distinguish infection risk on an individual sample level, we identified differences in bacterial community composition, diversity, and structure between clinically symptomatic and asymptomatic TIVAPs that could be explored further. This study therefore provides a new view of bacterial communities and colonization patterns in intravascular TIVAPs and suggests that microbial ecology approaches could improve our understanding of device-associated infections and could be a prognostic tool to monitor the evolution of bacterial communities in implants and their potential susceptibility to infections. IMPORTANCE Totally implanted venous access ports (TIVAPs) are commonly used implants for the management of acute or chronic pathologies. Although their use improves the patient's health care and quality of life, they are associated with a risk of infection and subsequent clinical complications, often leading to implant removal

  18. Tempo-spatial patterns of bacterial community composition in the western North Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Kataoka, Takafumi; Hodoki, Yoshikuni; Suzuki, Koji; Saito, Hiroaki; Higashi, Seigo

    2009-04-01

    In the western North Pacific, where subarctic Oyashio waters encounter subtropical Kuroshio waters, phylotype composition of heterotrophic bacteria was estimated by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial 16S ribosomal DNA. Total bacterial abundance was also measured by flow cytometry. The study area was divided into four water masses: coastal, Oyashio, Kuroshio, and the Kuroshio-Oyashio transition. Abundances of heterotrophic bacteria in the Oyashio, Kuroshio, and Kuroshio-Oyashio transition regions ranged from 0.2 × 10 5 cells mL - 1 to 1.4 × 10 5 cells mL - 1 and were not significantly different, except in the Oyashio region during September. Bacterial compositions were distinct in each water mass. Furthermore, phylotype distributions differed between surface and subsurface waters in the Kuroshio-Oyashio transition region. Out of 61 DGGE bands obtained, 41 were successfully identified as 31 phylotypes: 22 Gammaproteobacteria, 4 Alphaproteobacteria, 2 unknown bacteria, 2 cyanobacteria, and 1 plastid. Although the Gammaproteobacteria OM60 clade was eurytopic in the study area, Psychrobacter glacincola and the uncultured Gammaproteobacteria SAR92 clade were often observed in the Oyashio region. Overall, our results indicated that Gammaproteobacteria were predominant in the bacterial community, which was influenced by the hydrographic properties of each water mass in the study area.

  19. Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia.

    PubMed

    Cleary, Daniel F R; de Voogd, Nicole J; Polónia, Ana R M; Freitas, Rossana; Gomes, Newton C M

    2015-11-01

    In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus

  20. Bacterial Community Composition in Three Freshwater Reservoirs of Different Alkalinity and Trophic Status

    PubMed Central

    Llirós, Marc; Inceoğlu, Özgül; García-Armisen, Tamara; Anzil, Adriana; Leporcq, Bruno; Pigneur, Lise-Marie; Viroux, Laurent; Darchambeau, François; Descy, Jean-Pierre; Servais, Pierre

    2014-01-01

    In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga–Flavobacteria–Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions. PMID:25541975

  1. Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status.

    PubMed

    Llirós, Marc; Inceoğlu, Özgül; García-Armisen, Tamara; Anzil, Adriana; Leporcq, Bruno; Pigneur, Lise-Marie; Viroux, Laurent; Darchambeau, François; Descy, Jean-Pierre; Servais, Pierre

    2014-01-01

    In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga-Flavobacteria-Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.

  2. The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics.

    PubMed

    Shade, Ashley; Jones, Stuart E; McMahon, Katherine D

    2008-04-01

    Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.

  3. RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

    PubMed Central

    McCarthy, Ann; Chiang, Edna; Schmidt, Marian L.; Denef, Vincent J.

    2015-01-01

    Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA samples. PMID:25798612

  4. RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition.

    PubMed

    McCarthy, Ann; Chiang, Edna; Schmidt, Marian L; Denef, Vincent J

    2015-01-01

    Bias is a pervasive problem when characterizing microbial communities. An important source is the difference in lysis efficiencies of different populations, which vary depending on the extraction protocol used. To avoid such biases impacting comparisons between gene and transcript abundances in the environment, the use of one protocol that simultaneously extracts both types of nucleic acids from microbial community samples has gained popularity. However, knowledge regarding tradeoffs to combined nucleic acid extraction protocols is limited, particularly regarding yield and biases in the observed community composition. Here, we evaluated a commercially available protocol for simultaneous extraction of DNA and RNA, which we adapted for freshwater microbial community samples that were collected on filters. DNA and RNA yields were comparable to other commonly used, but independent DNA and RNA extraction protocols. RNA protection agents benefited RNA quality, but decreased DNA yields significantly. Choice of extraction protocol influenced the perceived bacterial community composition, with strong method-dependent biases observed for specific phyla such as the Verrucomicrobia. The combined DNA/RNA extraction protocol detected significantly higher levels of Verrucomicrobia than the other protocols, and those higher numbers were confirmed by microscopic analysis. Use of RNA protection agents as well as independent sequencing runs caused a significant shift in community composition as well, albeit smaller than the shift caused by using different extraction protocols. Despite methodological biases, sample origin was the strongest determinant of community composition. However, when the abundance of specific phylogenetic groups is of interest, researchers need to be aware of the biases their methods introduce. This is particularly relevant if different methods are used for DNA and RNA extraction, in addition to using RNA protection agents only for RNA samples.

  5. Bacterial community composition in the water column of a lake formed by a former uranium open pit mine.

    PubMed

    Edberg, Frida; Andersson, Anders F; Holmström, Sara J M

    2012-11-01

    Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

  6. 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. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  7. The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem.

    PubMed

    Wymore, Adam S; Liu, Cindy M; Hungate, Bruce A; Schwartz, Egbert; Price, Lance B; Whitham, Thomas G; Marks, Jane C

    2016-05-01

    Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.

  8. Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

    NASA Astrophysics Data System (ADS)

    Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

    2013-12-01

    The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order

  9. 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

  10. Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice.

    PubMed

    Hatam, Ido; Lange, Benjamin; Beckers, Justin; Haas, Christian; Lanoil, Brian

    2016-10-01

    Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.

  11. Longitudinal Changes in the Bacterial Community Composition of the Danube River: a Whole-River Approach▿ †

    PubMed Central

    Winter, Christian; Hein, Thomas; Kavka, Gerhard; Mach, Robert L.; Farnleitner, Andreas H.

    2007-01-01

    The Danube River is the second longest river in Europe, and its bacterial community composition has never been studied before over its entire length. In this study, bacterial community composition was determined by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified portions of the bacterial 16S rRNA gene from a total of 98 stations on the Danube River (73 stations) and its major tributaries (25 stations), covering a distance of 2,581 km. Shifts in the bacterial community composition were related to changes in environmental conditions found by comparison with physicochemical parameters (e.g., temperature and concentration of nutrients) and the concentration of chlorophyll a (Chl a). In total, 43 distinct DGGE bands were detected. Sequencing of selected bands revealed that the phylotypes were associated with typical freshwater bacteria. Apparent bacterial richness in the Danube varied between 18 and 32 bands and correlated positively with the concentration of P-PO4 (r = 0.56) and negatively with Chl a (r = −0.52). An artificial neural network-based model explained 90% of the variation of apparent bacterial richness using the concentrations of N-NO2 and P-PO4 and the distance to the Black Sea as input parameters. Between the cities of Budapest and Belgrade, apparent bacterial richness was significantly lower than that of other regions of the river, and Chl a showed a pronounced peak. Generally, the bacterial community composition developed gradually; however, an abrupt and clear shift was detected in the section of the phytoplankton bloom. Large impoundments did not have a discernible effect on the bacterial community of the water column. In conclusion, the riverine bacterial community was largely influenced by intrinsic factors. PMID:17085708

  12. Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils.

    PubMed

    Li, Jing; Hu, Hang-Wei; Ma, Yi-Bing; Wang, Jun-Tao; Liu, Yu-Rong; He, Ji-Zheng

    2015-07-01

    Nickel pollution imposes deleterious effects on soil ecosystem. The responses of soil microorganisms to long-term nickel pollution under field conditions remain largely unknown. Here, we used high-throughput sequencing to elucidate the impacts of long-term nickel pollution on soil bacterial communities in two contrasting agricultural soils. Our results found that the soil microbial biomass carbon consistently decreased along the nickel gradients in both soils. Nickel pollution selectively favored or impeded the prevalence of several dominant bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Planctomycetes displayed sensitivity. Despite the apparent shifts in the bacterial community composition, no clear tendency in the bacterial diversity and abundance was identified along the nickel gradients in either soil. Collectively, we provide evidence that long-term nickel pollution shifted the soil bacterial communities, resulting in the decrease of microbial biomass although the bacterial diversity was not significantly changed.

  13. Phylogenetic analysis of bacterial community composition in sediments with organic contaminants from the Jiaojiang estuary in China.

    PubMed

    Jiang, Ran; Wang, Jian-Xin; Huang, Bei; Yu, Kai-Cheng; Zhang, Pan; Zheng, Jun-Wei; Liu, Xue-Zhu

    2016-08-15

    The aim of this study was to investigate the bacterial community composition, the concentration of organic contaminants, and their relationship in the sediments of Jiaojiang estuary. Sediments were collected from seven stations and the environmental parameters were analyzed. The results showed that the site closest to the chemical industry zone was the most polluted. Bacterial communities were determined using 16S rRNA clone libraries and phylogenetic analysis. These results revealed that there were 13 known bacterial phyla in the sediments and that Proteobacteria were the dominant group. Using these data, we assessed the correlation between bacterial communities and organic contaminants using cluster, multidimensional scaling, and redundancy analyses. These showed that there was no simple relationship between organic contaminants and bacterial community diversity in the sediments, but polycyclic aromatic hydrocarbons were more influential than the other pollutants and negatively affected Chloroflexi. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water.

    PubMed

    Tang, Junying; Bu, Yuanqing; Zhang, Xu-Xiang; Huang, Kailong; He, Xiwei; Ye, Lin; Shan, Zhengjun; Ren, Hongqiang

    2016-10-01

    The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river.

  15. Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing

    PubMed Central

    Tzanetakis, Giorgos N.; Azcarate-Peril, Andrea M.; Zachaki, Sophia; Panopoulos, Panos; Kontakiotis, Evangelos G.; Madianos, Phoebus N.; Divaris, Kimon

    2015-01-01

    Introduction Elucidating the microbial ecology of endodontic infections (EI) is a necessary step in developing effective intra-canal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population, using high throughput sequencing methods. Methods 16S amplicon pyrosequencing of 48 root canal bacterial samples was conducted and sequencing data were analyzed using an oral microbiome-specific (HOMD) and a generic (Greengenes; GG) database. Bacterial abundance and diversity were examined by EI type (primary or persistent) and statistical analysis was performed by using non-parametric and parametric tests accounting for clustered data. Results Bacteroidetes was the most abundant phylum in both infection groups. Significant, albeit weak associations of bacterial diversity were found, as measured by UniFrac distances with infection type (ANOSIM R=0.087, P=0.005) and symptoms (ANOSIM R=0.055, P=0.047). Persistent infections were significantly enriched for Proteobacteria and Tenericutes as compared to primary ones; at the genus level, significant differences were noted for 14 taxa, including increased enrichment of persistent infections for Lactobacillus, Streptococcus, and Sphingomonas. More but less-abundant phyla were identified using the GG database; among those, Cyanobacteria (0.018%) and Acidobacteria (0.007%) were significantly enriched among persistent infections. Persistent infections showed higher Phylogenetic Diversity (asymptomatic: PD=9.2, [standard error (se)=1.3]; symptomatic: PD=8.2, se=0.7) compared to primary infections (asymptomatic: PD=5.9, se=0.8; symptomatic: PD=7.4 se=1.0). Conclusions The present study revealed a high bacterial diversity of EI and suggests that persistent infections may have more diverse bacterial communities than primary infections. PMID:25906920

  16. 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

  17. ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

    PubMed

    Koslicki, David; Chatterjee, Saikat; Shahrivar, Damon; Walker, Alan W; Francis, Suzanna C; Fraser, Louise J; Vehkaperä, Mikko; Lan, Yueheng; Corander, Jukka

    2015-01-01

    Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging. There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity. An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.

  18. Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes.

    PubMed

    Muylaert, Koenraad; Van Der Gucht, Katleen; Vloemans, Nele; Meester, Luc De; Gillis, Moniek; Vyverman, Wim

    2002-10-01

    Bacterial community composition was monitored in four shallow eutrophic lakes during one year using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified prokaryotic rDNA genes. Of the four lakes investigated, two were of the clearwater type and had dense stands of submerged macrophytes while two others were of the turbid type characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had high nutrient levels (total phosphorus, >100 micro g liter(-1)) while the other lakes had relatively low nutrient levels (total phosphorus, <100 micro g liter(-1)). For each lake, seasonal changes in the bacterial community were related to bottom-up (resources) and top-down (grazers) variables by using canonical correspondence analysis (CCA). Using an artificial model dataset to which potential sources of error associated with the use of relative band intensities in DGGE analysis were added, we found that preferential amplification of certain rDNA genes over others does not obscure the relationship between bacterial community composition and explanatory variables. Besides, using this artificial dataset as well as our own data, we found a better correlation between bacterial community composition and explanatory variables by using relative band intensities compared to using presence/absence data. While bacterial community composition was related to phytoplankton biomass in the high-nutrient lakes no such relation was found in the low-nutrient lakes, where the bacterial community is probably dependent on other organic matter sources. We used variation partitioning to evaluate top-down regulation of bacterial community composition after bottom-up regulation has been accounted for. Using this approach, we found no evidence for top-down regulation of bacterial community composition in the turbid lakes, while grazing by ciliates and daphnids (Daphnia and Ceriodaphnia) was significantly related to changes in the bacterial community in the

  19. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    PubMed Central

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-01-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing. PMID:27934957

  20. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    NASA Astrophysics Data System (ADS)

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-12-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

  1. Soil bacterial community composition and diversity respond to cultivation in Karst ecosystems.

    PubMed

    Chen, Xiangbi; Su, Yirong; He, Xunyang; Wei, Yawei; Wei, Wenxue; Wu, Jinshui

    2012-01-01

    Soil microorganisms play vital roles in recovering and maintaining the health of ecosystems, particularly in fragile Karst ecosystems that are easily degraded after cultivation. We investigated the composition and diversity of soil bacterial communities, based on RFLP and 16S rDNA sequencing, in a cropland, a naturally revegetated land with former cultivation disturbance and a primeval forest in the subtropical Karst of southwest China. Our results illustrated that Proteobacteria accounted for 44.8% of the 600 tested clones, making it the most dominant phylum observed. This phylum was followed by Acidobacteria and Planctomycetes for the three Karst soils analyzed. Compared with the primeval forest soil, the proportions of Proteobacteria were decreased by 30.2 and 37.9%, while Acidobacteria increased by 93.9 and 87.9%, and the Shannon-Wiener diversity indices and the physicochemical parameters declined in the cropland and the revegetated land, respectively. Among the three soils, the proportion of dominant bacterial phyla and the diversity indices in the revegetated land were similar to the cropland, implying the bacterial community in the cropland was relatively stable, and the after-effects of cultivation were difficult to eliminate. However, similar distributions of the four Proteobacteria subphyla were observed between the revegetated land and the primeval forest soil. Furthermore, the proportion of Rhizobiales belonging to α-Proteobacteria was sharply decreased with cultivation compared to the primeval forest soil, while a small cluster of Rhizobiales recurred with vegetation recovery. These results indicated that although the subphyla of the dominant bacterial phylum had some positive responses to 20 years of vegetation recovery, it is a slow process. Our results suggest that priority should be given to conserve the primeval forest and inoculation of functional microorganisms on the basis of vegetation recovery may be more effective for the restoration of

  2. Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil.

    PubMed

    Frenk, Sammy; Dag, Arnon; Yermiyahu, Uri; Zipori, Isaac; Hadar, Yitzhak; Minz, Dror

    2015-09-01

    Several anthropogenic interventions, common in agriculture, may influence active bacterial communities in soil without affecting their total composition. Therefore, the composition of an active bacterial community in soil may reflect its relation to biogeochemical processes. This issue was addressed during two consecutive years in olive-orchard soil, irrigated with treated wastewater (TWW) in a Mediterranean climate, by following the active (rRNA) and total (rRNA gene) bacterial community in the soil. Although TWW irrigation did not affect the composition of the total soil bacterial community, it had an effect on the active fraction of the community. These results, based on 16S rRNA data, indicate that the organic matter and minerals in TWW were not directly utilized for the rapid proliferation of specific taxonomic groups. Activity levels, manifested by variance in the relative abundance of the active and total communities of selected operational taxonomic units, revealed annual and seasonal fluctuations and fluctuations dependent on the type of irrigation. The potential activity (nitrification rates) and community composition of ammonia-oxidizing bacteria were affected by TWW irrigation, and this group of bacteria was therefore further explored. It was concluded that irrigation with TWW had little effect on "who is there", i.e. which bacteria were present, but influenced "who is active", with a distinct effect on bacteria associated with the biochemical cycling of nitrogen.

  3. Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons.

    PubMed

    Laque, Thaís; Farjalla, Vinicius F; Rosado, Alexandre S; Esteves, Francisco A

    2010-05-01

    Bacterial community composition (BCC) has been extensively related to specific environmental conditions. Tropical coastal lagoons present great temporal and spatial variation in their limnological conditions, which, in turn, should influence the BCC. Here, we sought for the limnological factors that influence, in space and time, the BCC in tropical coastal lagoons (Rio de Janeiro State, Brazil). The Visgueiro lagoon was sampled monthly for 1 year and eight lagoons were sampled once for temporal and spatial analysis, respectively. BCC was evaluated by bacteria-specific PCR-DGGE methods. Great variations were observed in limnological conditions and BCC on both temporal and spatial scales. Changes in the BCC of Visgueiro lagoon throughout the year were best related to salinity and concentrations of NO (3) (-) , dissolved phosphorus and chlorophyll-a, while changes in BCC between lagoons were best related to salinity and dissolved phosphorus concentration. Salinity has a direct impact on the integrity of the bacterial cell, and it was previously observed that phosphorus is the main limiting nutrient to bacterial growth in these lagoons. Therefore, we conclude that great variations in limnological conditions of coastal lagoons throughout time and space resulted in different BCCs and salinity and nutrient concentration, particularly dissolved phosphorus, are the main limnological factors influencing BCC in these tropical coastal lagoons.

  4. Composition of activated sludge settling and planktonic bacterial communities treating industrial effluent and their correlation to settling problems.

    PubMed

    Nadarajah, Nalina; Allen, D Grant; Fulthorpe, Roberta R

    2010-11-01

    Problems with deflocculation and solids separation in biological wastewater treatment systems are linked to fluctuations in physicochemical conditions. This study examined the composition of activated sludge bacterial communities in lab-scale sequencing batch reactors treating bleached kraft mill effluent, under transient temperature conditions (30 to 45 °C) and their correlation to sludge settleability problems. The bacterial community composition of settled and planktonic biomass samples in the reactors was monitored via denaturing gradient gel electrophoresis of 16S ribosomal RNA gene fragments. Our analysis showed that settled biomass has a different community composition from the planktonic biomass (49 ± 7% difference based on Jaccard similarity coefficients; p < 0.01). During times of poor sludge compression, the settled and planktonic biomass became more similar. This observation supports the hypothesis that settling problems observed were due to deflocculation of normally settling flocs rather than the outgrowth of non-settling bacterial species.

  5. Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators.

    PubMed

    Galimanas, Vaia; Hall, Michael William; Singh, Natasha; Lynch, Michael David Joseph; Goldberg, Michael; Tenenbaum, Howard; Cvitkovitch, Dennis Gerard; Neufeld, Josh David; Senadheera, Dilani Braziunas

    2014-01-01

    Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the disease. Until now, microbial plaque obtained from the subgingival (SubG) sites has been the primary focus for bacterial community analysis using deep sequencing. In addition to the use of SubG plaque, here, we investigated whether plaque obtained from supragingival (SupG) and tongue dorsum sites can serve as alternatives for monitoring CP-associated bacterial biomarkers. Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (approximately 200 bases) of the 16S rRNA gene using Illumina sequencing. After quality filtering, approximately 4.1 million sequences were collapsed into operational taxonomic units (OTUs; sequence identity cutoff of >97%) that were classified to a total of 19 phyla spanning 114 genera. Bacterial community diversity and overall composition was not affected by health or disease, and multiresponse permutation procedure (MRPP) on Bray-Curtis distance measures only supported weakly distinct bacterial communities in SubG and tongue plaque depending on health or disease status (P < 0.05). Nonetheless, in SubG and tongue sites, the relative abundance of Firmicutes was increased significantly from health to disease and members of Synergistetes were found in higher abundance across all sites in disease. Taxa indicative of CP were identified in all three locations (for example, Treponema denticola, Porphyromonas gingivalis, Synergistes oral taxa 362 and 363). For the first time, this study demonstrates that SupG and tongue dorsum plaque can serve as alternative sources for detecting and enumerating known and novel bacterial biomarkers of CP. This finding is clinically important because, in contrast

  6. Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators

    PubMed Central

    2014-01-01

    Background Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the disease. Until now, microbial plaque obtained from the subgingival (SubG) sites has been the primary focus for bacterial community analysis using deep sequencing. In addition to the use of SubG plaque, here, we investigated whether plaque obtained from supragingival (SupG) and tongue dorsum sites can serve as alternatives for monitoring CP-associated bacterial biomarkers. Results Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (approximately 200 bases) of the 16S rRNA gene using Illumina sequencing. After quality filtering, approximately 4.1 million sequences were collapsed into operational taxonomic units (OTUs; sequence identity cutoff of >97%) that were classified to a total of 19 phyla spanning 114 genera. Bacterial community diversity and overall composition was not affected by health or disease, and multiresponse permutation procedure (MRPP) on Bray-Curtis distance measures only supported weakly distinct bacterial communities in SubG and tongue plaque depending on health or disease status (P < 0.05). Nonetheless, in SubG and tongue sites, the relative abundance of Firmicutes was increased significantly from health to disease and members of Synergistetes were found in higher abundance across all sites in disease. Taxa indicative of CP were identified in all three locations (for example, Treponema denticola, Porphyromonas gingivalis, Synergistes oral taxa 362 and 363). Conclusions For the first time, this study demonstrates that SupG and tongue dorsum plaque can serve as alternative sources for detecting and enumerating known and novel bacterial biomarkers of CP. This finding is clinically

  7. 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

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

    PubMed

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

    2015-10-01

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

  9. Bacterial and fungal community composition and functioning of two different peatlands in China

    NASA Astrophysics Data System (ADS)

    Wang, Meng; Tian, Jianqing; Bu, Zhaojun; Chen, Huai; Zhu, Qiuan; Peng, Changhui

    2017-04-01

    Peatlands are important carbon sinks which store one third of the global soil carbon ( 550 Gt) with only 3% of the land surface. The slow rate of organic matter decomposition associated with low microbial diversity and limited functioning under cold, acidic and anoxic condition is of critical importance in controlling biogeochemical cycles in northern peatlands. To evaluate the variation in microbial community composition and functionality can advance our understanding of the underlying mechanisms of the biogeochemical processes and interactions. However, there is still a lack of information for Chinese peatlands. Here, we sampled peat profiles at three different depths (10-20, 30-40 and 60-70 cm) from two typical peatlands in China: a rich fen in Qinghai-Tibet Plateau (QTP) and a poor fen in the Changbai Mountains (CBM). We investigated the bacterial (16S rRNA) and fungal (ITS2) community composition and diversity with high-throughput sequencing and predicted the metagenome functioning with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States). The results showed that Proteobacteria, Acidobacteria and Actinobacteria were the most abundant bacterial phyla in the upper peat layer (10-20 cm) for both sites, with increasing abundance of Chloroflexi and Bacteroidetes down to the saturated zone (60-70 cm in CMB; 30-40 and 60-70 cm in QTP). For fungi, Ascomycota, Ciliophora and Basidiomycota were the most abundant phyla in both sites, with decreasing Ciliophora abundance down to the saturated zone. The α-diversity of both bacterial and fungal showed a decreasing trend with depth in QTP, with the largest diversity occurring at the depth of 30-40 cm in CMB. Regardless of sampling sites, the bacterial communities at the depth of 60-70 cm were more similar than the other depths. The fungal community was clustered into two groups, corresponding to two sampling sites. The variation in fungal community with depth was larger in QTP than in

  10. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles.

    PubMed

    van Agtmaal, Maaike; van Os, Gera J; Hol, W H Gera; Hundscheid, Maria P J; Runia, Willemien T; Hordijk, Cornelis A; de Boer, Wietse

    2015-01-01

    There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the

  11. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

    PubMed Central

    van Agtmaal, Maaike; van Os, Gera J.; Hol, W.H. Gera; Hundscheid, Maria P.J.; Runia, Willemien T.; Hordijk, Cornelis A.; de Boer, Wietse

    2015-01-01

    There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the

  12. Antibiotics, Antibiotic Resistance Genes, and Bacterial Community Composition in Fresh Water Aquaculture Environment in China.

    PubMed

    Xiong, Wenguang; Sun, Yongxue; Zhang, Tong; Ding, Xueyao; Li, Yafei; Wang, Mianzhi; Zeng, Zhenling

    2015-08-01

    Environmental antibiotic resistance has drawn increasing attention due to its great threat to human health. In this study, we investigated concentrations of antibiotics (tetracyclines, sulfonamides and (fluoro)quinolones) and abundances of antibiotic resistance genes (ARGs), including tetracycline resistance genes, sulfonamide resistance genes, and plasmid-mediated quinolone resistance genes, and analyzed bacterial community composition in aquaculture environment in Guangdong, China. The concentrations of sulfametoxydiazine, sulfamethazine, sulfamethoxazole, oxytetracycline, chlorotetracycline, doxycycline, ciprofloxacin, norfloxacin, and enrofloxacin were as high as 446 μg kg(-1) and 98.6 ng L(-1) in sediment and water samples, respectively. The relative abundances (ARG copies/16S ribosomal RNA (rRNA) gene copies) of ARGs (sul1, sul2, sul3, tetM, tetO, tetW, tetS, tetQ, tetX, tetB/P, qepA, oqxA, oqxB, aac(6')-Ib, and qnrS) were as high as 2.8 × 10(-2). The dominant phyla were Proteobacteria, Bacteroidetes, and Firmicutes in sediment samples and Proteobacteria, Actinobacteria and Bacteroidetes in water samples. The genera associated with pathogens were also observed, such as Acinetobacter, Arcobacter, and Clostridium. This study comprehensively investigated antibiotics, ARGs, and bacterial community composition in aquaculture environment in China. The results indicated that fish ponds are reservoirs of ARGs and the presence of potential resistant and pathogen-associated taxonomic groups in fish ponds might imply the potential risk to human health.

  13. Changes of bacterial and fungal community compositions during vermicomposting of vegetable wastes by Eisenia foetida.

    PubMed

    Huang, Kui; Li, Fusheng; Wei, Yongfen; Chen, Xuemin; Fu, Xiaoyong

    2013-12-01

    Changes of bacterial and fungal community during vermicomposting of vegetable wastes by hatchling, juvenile and adult Eisenia foetida were investigated through analysis of the extracted bacterial 16S rDNA and fungal 18S rDNA with quantitative polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) and sequencing. After 60days of composting, significantly lower values of microbial activity and bacterial and fungal densities were revealed in the products of composting with earthworms than in the control (without earthworms). PCR-DGGE images showed vermicomposting significantly enhanced the diversities of bacterial and fungal communities. However, for their structures, sequencing results revealed that, compared to the control where the bacterial Firmicutes were predominant, in the composts with earthworms, the bacterial Bacteroidetes and Actinomycetes, and the fungal Sordariomycetes were found dominant. In addition, some beneficial species of bacteria and fungi against pathogens were also isolated from the vermicomposting products. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects.

    PubMed

    Paulino, Gustavo Vasconcelos Bastos; Broetto, Leonardo; Pylro, Victor Satler; Landell, Melissa Fontes

    2017-01-30

    Corals harbor abundant and diverse prokaryotic communities that may be strongly influenced by human activities, which in turn compromise the normal functioning of coral species and predispose them to opportunistic infections. In this study, we investigated the effect of sewage dumping on the bacterial communities associated with the soft coral Palythoa caribaeorum at two sites in the Brazilian coast. We observed a dominance of bacterial species classified as human pathogens at sites exposed to untreated sewage discharge. The microbial diversity of undisturbed sites was more homogeneous and diverse and showed greater abundance. In addition, bacterial communities differed substantially between the exposed and undisturbed areas. The microbial community associated with the samples collected from the exposed sites revealed the anthropogenic effect caused by organic matter from untreated sewage dumping, with an abundance of pathogenic bacterial species.

  15. Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons.

    PubMed

    Oliveira, Vanessa; Gomes, Newton C M; Cleary, Daniel F R; Almeida, Adelaide; Silva, Artur M S; Simões, Mário M Q; Silva, Helena; Cunha, Ângela

    2014-12-01

    In this study, two molecular techniques [denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing] were used to evaluate the composition of bacterial communities in salt marsh microhabitats [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis ssp. perennis] that have been differentially affected by oil hydrocarbon (OH) pollution. Both DGGE and pyrosequencing revealed that bacterial composition is structured by microhabitat. Rhizosphere sediment from both plant species revealed enrichment of operational taxonomic units closely related to Acidimicrobiales, Myxococcales and Sphingomonadales. The in silico metagenome analyses suggest that homologous genes related to OH degradation appeared to be more frequent in both plant rhizospheres than in bulk sediment. In summary, this study suggests that halophyte plant colonization is an important driver of hydrocarbonoclastic bacterial community composition in estuarine environments, which can be exploited for in situ phytoremediation of OH in salt marsh environments.

  16. Variations in the bacterial community compositions at different sites in the tomb of Emperor Yang of the Sui Dynasty.

    PubMed

    Huang, Zhi; Zhao, Fei; Li, Yonghui; Zhang, Jianwei; Feng, Youzhi

    2017-03-01

    To fully understand the bacterial processes in tomb environments, it is necessary to investigate the details of the bacterial communities present under such oligotrophic conditions. Here, high-throughput sequencing based on partial 16S rRNA gene sequences was used to fully evaluate the bacterial communities at different sites in the tomb of Emperor Yang of the Sui Dynasty. We also aimed to identify the soil factors that were significant related to bacterial diversity and community composition. The results showed the presence of a broad taxonomic diversity that included nine major phyla. Actinobacteria, Firmicutes and Proteobacteria dominated the bacterial profiles in all tomb soil samples. However, significant differences between deposited soils (DS) and covering soils (CSA, CSB and CSC) were revealed by chemistry-based principal component analysis (PCA), the number of OTUs, and the Chao 1 and Shannon indexes. At the family level, hierarchically clustered heatmap and LefSe analyses showed differences in the bacterial community compositions at different sampling sites. Notably, CSA contained significant populations of Nocardioidaceae, Pseudonocardiaceae and Streptomycetaceae, which are often reported to be associated with biodeterioration in cave environments. Further, the most abundant group (>10%) in all soil samples was Streptococcaceae, whose abundance decreased from 34.66% to 13.43% with increasing soil depth. The results of redundancy analysis (RDA) and the Monte Carlo permutation test indicated that soil pH and Cu and Mn levels were significantly related to the bacterial communities in this tomb. This research offers new insight into bacterial communities in cave environments and also provides important information for the protection of this historically important tomb.

  17. Seasonal dynamics of bacterial community structure and composition in cold and hot drinking water derived from surface water reservoirs.

    PubMed

    Henne, Karsten; Kahlisch, Leila; Höfle, Manfred G; Brettar, Ingrid

    2013-10-01

    In temperate regions, seasonal variability of environmental factors affects the bacterial community in source water and finished drinking water. Therefore, the bacterial core community and its seasonal variability in cold and the respective hot drinking water was investigated. The bacterial core community was studied by 16S rRNA-based SSCP fingerprint analyses and band sequencing of DNA and RNA extracts of cold and hot water (60 °C). The bacterial communities of cold and hot drinking water showed a highly different structure and phylogenetic composition both for RNA and DNA extracts. For cold drinking water substantial seasonal dynamics of the bacterial community was observed related to environmental factors such as temperature and precipitation affecting source and drinking water. Phylogenetic analyses of the cold water community indicated that the majority of phylotypes were very closely affiliated with those detected in former studies of the same drinking water supply system (DWSS) in the preceding 6 years, indicating a high stability over time. The hot water community was very stable over time and seasons and highly distinct from the cold water with respect to structure and composition. The hot water community displayed a lower diversity and its phylotypes were mostly affiliated with bacteria of high temperature habitats with high growth rates indicated by their high RNA content. The conversion of the cold to the hot water bacterial community is considered as occurring within a few hours by the following two processes, i) by decay of most of the cold water bacteria due to heating, and ii) rapid growth of the high temperature adapted bacteria present in the hot water (co-heated with the cold water in the same device) using the nutrients released from the decaying cold water bacteria. The high temperature adapted bacteria originated partially from low abundant but beforehand detected members of the cold water; additionally, the rare members ("seed bank ") of the

  18. Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp.

    PubMed

    Zhu, Jinyong; Dai, Wenfang; Qiu, Qiongfen; Dong, Chunming; Zhang, Jinjie; Xiong, Jinbo

    2016-11-01

    Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.

  19. Composition of bacterial communities associated with natural and laboratory populations of Asobara tabida infected with Wolbachia.

    PubMed

    Zouache, Karima; Voronin, Denis; Tran-Van, Van; Mavingui, Patrick

    2009-06-01

    Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.

  20. Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification.

    PubMed

    O'Neill, B; Grossman, J; Tsai, M T; Gomes, J E; Lehmann, J; Peterson, J; Neves, E; Thies, J E

    2009-07-01

    Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.

  1. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

    PubMed

    Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

    2014-01-01

    Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to

  2. Changes in ruminal bacterial community composition following feeding of alfalfa ensiled with a lactic acid bacterial inoculant.

    PubMed

    Mohammed, R; Stevenson, D M; Beauchemin, K A; Muck, R E; Weimer, P J

    2012-01-01

    Some silage inoculants help to improve silage quality and promote an increase in milk production, possibly through altering the rumen microflora. We hypothesized that rumen bacterial community composition (BCC) would be different in cows fed alfalfa ensiled with the inoculant Lactobacillus plantarum MTD/1 (LP) compared with those fed alfalfa ensiled without the inoculant (Ctrl). Eight ruminally cannulated Holstein cows were allotted to 2 diets (Ctrl or LP) in a double crossover design with four 28-d periods. Diets were formulated to contain (% dry matter basis) 28.0% neutral detergent fiber and 16.2% crude protein, and contained alfalfa silage, 50.9; corn silage, 20.6; high-moisture shelled corn, 21.4; soy hulls, 4.7; plus minerals and vitamins, 2.4. Ruminal digesta were collected just before feeding on 3 consecutive days near the end of each period, and were separated into solid and liquid phases. Microbial DNA was extracted from each phase, amplified by PCR using domain-level bacterial primers, and subjected to automated ribosomal intergenic spacer analysis. The pH was 4.56 and 4.86 and the lactate-to-acetate ratio 9.8 and 4.4, respectively, for the treated and untreated alfalfa silages. Dry matter intakes and milk production data were not influenced by diets but showed a cow effect. Total volatile fatty acids (mM) tended to be greater for LP compared with Ctrl. Individual volatile fatty acids were not influenced by diets but showed a significant cow effect. Ruminal acetate (mol/100 mol) and acetate-to-propionate ratio were lower and propionate (mol/100 mol) greater for the 2 milk fat-depressed (MFD; <3.2% fat content) cows compared with the other 6 cows. Correspondence analysis of the 265 peaks in the automated ribosomal intergenic spacer analysis profile across the 188 samples revealed that the first 2 components contributed 7.1 and 3.8% to the total variation in the profile. The ordination points representing the liquid and solid phases clustered separately

  3. Contrasting Effects of Singlet Oxygen and Hydrogen Peroxide on Bacterial Community Composition in a Humic Lake

    PubMed Central

    Glaeser, Stefanie P.; Berghoff, Bork A.; Stratmann, Verena; Grossart, Hans-Peter; Glaeser, Jens

    2014-01-01

    Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (1O2) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (14C-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased 1O2 and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized 1O2 exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to 1O2 but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to 1O2 exposure compared to free-living populations. These results imply that 1O2 acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype

  4. Bacterial community composition in rainwater associated with synoptic weather in an area downwind of the Asian continent.

    PubMed

    Hu, Wei; Murata, Kotaro; Horikawa, Yuka; Naganuma, Ayumi; Zhang, Daizhou

    2017-12-01

    Bacteria are abundant in atmospheric waters and can be disseminated by precipitation to the surface of the Earth, potentially influencing ecosystems, public health and climate. However, data on bacterial communities in rainwater, especially on the association with weather, are very limited. In this study, rainwater was collected at the coastal city Kumamoto, southwestern Japan, in 2015. The bacterial communities in fourteen samples were identified using 16S rRNA sequencing and compared according to the rain types at the synoptic scale, i.e., cyclones, Meiyu and non-Meiyu stationary fronts, and typhoons. Diverse bacterial communities were present in all four types of rainwater and were dominated by the phyla Proteobacteria (37%), Bacteroidetes (16%), Cyanobacteria (14%), Actinobacteria (9%), Acidobacteria (8%) and Firmicutes (5%). Approximately half of the phyla (16 out of 33) were common among the rain types. The operational taxonomic units (OTUs) common among the four types of rainwater represented the majority (averagely 74%) of the sequences, indicating the predominance of common bacterial OTUs regardless of rain type. On the other hand, the synoptic weather systems and the origins of air masses associated with the rain likely resulted in distinct bacterial communities. High fractions of bacterial soil indicator taxa signified the large contribution of bacteria from soils. Genera containing ice nucleation-active bacteria were identified in all samples except one typhoon rain sample. Marine bacterial taxa, e.g., Pseudoalteromonas, Synechococcus and Marinobacter, were detected in several samples, indicating the dispersal of marine bacteria via clouds and rainwater. Fecal indicator bacteria were also detected in all samples. Thus, the bacteria in the four types of rainwater were characterized by largely overlapping communities with some differences in community composition, indicating that rain is an efficient pathway for the dissemination of bacterial communities

  5. Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

    PubMed Central

    Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

    2016-01-01

    Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

  6. Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

    PubMed Central

    Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P. A.; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

    2014-01-01

    Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescomposition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to

  7. Response of bacterial community compositions to different sources of pollutants in sediments of a tributary of Taihu Lake, China.

    PubMed

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

    2016-07-01

    Sediment bacterial communities are sensitive to water conditions in river ecosystems. The objective of this study was to compare the influences of different pollution sources, including urban areas, wastewater treatment plants (WWTPs), suburban areas, and agricultural areas, on sediment bacterial communities along a typical tributary of Taihu Lake, China. The dominant composition of the sediment bacterial community was determined using a combination of terminal restriction fragment length polymorphism (T-RFLP) and a 16S rRNA clone library. The results showed that the sediment bacterial communities were distinctly affected by the four pollution sources. Alphaproteobacteria, Betaproteobacteria, and Actinobacteria (>50 % in total) were the predominant bacterial taxa across the sediment samples. Apart from those, the sediment bacterial community composition (BCC) affected by WWTP effluent was subsequently dominated by Nitrospira (12.4 %) and Bacteroidetes (11.5 %), agriculture was dominated by Firmicutes (13.2 %) and Deltaproteobacteria (7.2 %), while urban and suburban were dominated by Bacteroidetes (7.6 and 7.9 %, respectively) and Deltaproteobacteria (7.9 and 7.6 %, respectively). Cluster analysis indicated that the BCC affected by WWTP effluent was distinct from the BCC in urban, suburban, and agricultural areas. In addition, the bacterial community richness and evenness affected by WWTP effluent were much less than those by the other pollution sources. Redundancy analysis (RDA) indicated that the variation in BCC across the sediment samples was significantly associated with ammonium (17 %), organic matter (12 %), and cadmium (3 %) (p < 0.01). Overall, the results indicated that the four different pollution sources (WWTP, urban, suburban, and agriculture) have dissimilar impacts on the sediment BCC in the tributary of Taihu Lake, while WWTPs exhibited the greatest potential to lead to biotic homogenization in river sediments.

  8. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events.

    PubMed

    Sison-Mangus, Marilou P; Jiang, Sunny; Kudela, Raphael M; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  9. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events

    PubMed Central

    Sison-Mangus, Marilou P.; Jiang, Sunny; Kudela, Raphael M.; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6–65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12–86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  10. Identification of Bacterial Community Composition in Freshwater Aquaculture System Farming of Litopenaeus vannamei Reveals Distinct Temperature-Driven Patterns

    PubMed Central

    Tang, Yuyi; Tao, Peiying; Tan, Jianguo; Mu, Haizhen; Peng, Li; Yang, Dandan; Tong, Shilu; Chen, Lanming

    2014-01-01

    Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL). Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT) and at lower (WLT) temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry. PMID:25105725

  11. Identification of bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei reveals distinct temperature-driven patterns.

    PubMed

    Tang, Yuyi; Tao, Peiying; Tan, Jianguo; Mu, Haizhen; Peng, Li; Yang, Dandan; Tong, Shilu; Chen, Lanming

    2014-08-07

    Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL). Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT) and at lower (WLT) temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

  12. Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland

    NASA Astrophysics Data System (ADS)

    Wasserstrom, Haggai; Kublik, Susanne; Wasserstrom, Rachel; Schulz, Stefanie; Schloter, Michael; Steinberger, Yosef

    2017-01-01

    Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above- and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting. Our data indicates a significant influence of season and site on bacterial community structure. We showed that during the wet season soil organic matter, pH and salinity strongly influence bacterial community composition, whereas during the dry period bacterial diversity was mainly driven by the shortage of water at all sites. Consequently diversity was lowest during dry season at dunes close to the shore, whereas during the wet season the higher water content and the reduced salinity at the dunes which are more at the inland induced an increase in diversity, which illustrates the pronounced dynamics of microbial communities in soil over a season mainly at inland dunes.

  13. Diversity analysis of bacterial community compositions in sediments of urban lakes by terminal restriction fragment length polymorphism (T-RFLP).

    PubMed

    Zhao, Dayong; Huang, Rui; Zeng, Jin; Yan, Wenming; Wang, Jianqun; Ma, Ting; Wang, Meng; Wu, Qinglong L

    2012-11-01

    Bacteria are crucial components in lake sediments and play important role in various environmental processes. Urban lakes in the densely populated cities are often small, shallow, highly artificial and hypereutrophic compared to rural and natural lakes and have been overlooked for a long time. In the present study, bacterial community compositions in surface sediments of three urban lakes (Lake Mochou, Lake Qianhu and Lake Zixia) in Nanjing City, China, were investigated using the terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene and clone libraries. Remarkable differences in the T-RFLP patterns were observed in different lakes or different sampling stations of the same lake. Canonical correspondence analysis indicated that total nitrogen (TN) had significant effects on bacterial community structure in the lake sediments. Chloroflexi were the most dominant bacterial group in the clone library from Lake Mochou (21.7 % of the total clones) which was partly associated with its higher TN and organic matters concentrations. However, Bacteroidetes appeared to be dominated colonizers in the sediments of Lake Zixia (20.4 % of the total clones). Our study gives a comprehensive insight into the structure of bacterial community of urban lake sediments, indicating that the environmental factors played a key role in influencing the bacterial community composition in the freshwater ecosystems.

  14. Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland

    PubMed Central

    Wasserstrom, Haggai; Kublik, Susanne; Wasserstrom, Rachel; Schulz, Stefanie; Schloter, Michael; Steinberger, Yosef

    2017-01-01

    Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above- and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting. Our data indicates a significant influence of season and site on bacterial community structure. We showed that during the wet season soil organic matter, pH and salinity strongly influence bacterial community composition, whereas during the dry period bacterial diversity was mainly driven by the shortage of water at all sites. Consequently diversity was lowest during dry season at dunes close to the shore, whereas during the wet season the higher water content and the reduced salinity at the dunes which are more at the inland induced an increase in diversity, which illustrates the pronounced dynamics of microbial communities in soil over a season mainly at inland dunes. PMID:28074923

  15. Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing.

    PubMed

    Kurilkina, Maria I; Zakharova, Yulia R; Galachyants, Yuri P; Petrova, Darya P; Bukin, Yuri S; Domysheva, Valentina M; Blinov, Vadim V; Likhoshway, Yelena V

    2016-07-01

    The composition of bacterial communities in Lake Baikal in different hydrological periods and at different depths (down to 1515 m) has been analyzed using pyrosequencing of the 16S rRNA gene V3 variable region. Most of the resulting 34 562 reads of the Bacteria domain have clustered into 1693 operational taxonomic units (OTUs) classified with the phyla Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Acidobacteria and Cyanobacteria. It has been found that their composition at the family level and relative contributions to bacterial communities distributed over the water column vary depending on hydrological period. The number of OTUs and the parameters of taxonomic richness (ACE, Chao1 indices) and diversity (Shannon and inverse Simpson index) reach the highest values in water layers. The composition of bacterial communities in these layers remains relatively constant, whereas that in surface layers differs between hydrological seasons. The dynamics of physicochemical conditions over the water column and their relative constancy in deep layers are decisive factors in shaping the pattern of bacterial communities in Lake Baikal. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time.

    PubMed

    Noble, Peter A; Park, Hee-Deung; Olson, Betty H; Asvapathanagul, Pitiporn; Hunter, M Colby; Garrido-Baserba, Manel; Lee, Sang-Hoon; Rosso, Diego

    2016-07-01

    Aeration diffusers in wastewater treatment plants generate air bubbles that promote mixing, distribution of dissolved oxygen, and microbial processing of dissolved and suspended matter in bulk solution. Biofouling of diffusers represents a significant problem to wastewater treatment plants because biofilms decrease oxygen transfer efficiency and increase backpressure on the blower. To better understand biofouling, we conducted a pilot study to survey the bacterial community composition and function of biofilms on different diffuser substrates and compare them to those in the bulk solution. DNA was extracted from the surface of ethylene-propylene-diene monomer (EPDM), polyurethane, and silicone diffusers operated for 15 months in a municipal treatment plant and sampled at 3 and 9 months. The bacterial community composition and function of the biofilms and bulk solution were determined by amplifying the 16S rRNA genes and pyrosequencing the amplicons and raw metagenomic DNA. The ordination plots and dendrograms of the 16S rRNA and functional genes showed that while the bacterial community composition and function of the bulk solution was independent of sampling time, the composition and function of the biofilms differed by diffuser type and testing time. For the EPDM and silicone diffusers, the biofilm communities were more similar in composition to the bulk solution at 3 months than 9 months. In contrast, the bacteria on the polyurethane diffusers were more dissimilar to the bulk solution at 3 months than 9 months. Taken together, the survey showed that the community composition and function of bacterial biofilms depend on the diffuser substrate and testing time, which warrants further elucidation.

  17. Bacterial communities associated with surfaces of leafy greens: shift in composition and decrease in richness over time.

    PubMed

    Dees, Merete Wiken; Lysøe, Erik; Nordskog, Berit; Brurberg, May Bente

    2015-02-01

    The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.

  18. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils.

    PubMed

    Girvan, Martina S; Bullimore, Juliet; Pretty, Jules N; Osborn, A Mark; Ball, Andrew S

    2003-03-01

    Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

  19. Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

    PubMed Central

    Lysøe, Erik; Nordskog, Berit; Brurberg, May Bente

    2014-01-01

    The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development. PMID:25527554

  20. Bacterial community composition and chitinase gene diversity of vermicompost with antifungal activity.

    PubMed

    Yasir, Muhammad; Aslam, Zubair; Kim, Seon Won; Lee, Seon-Woo; Jeon, Che Ok; Chung, Young Ryun

    2009-10-01

    Bacterial communities and chitinase gene diversity of vermicompost (VC) were investigated to clarify the influence of earthworms on the inhibition of plant pathogenic fungi in VC. The spore germination of Fusarium moniliforme was reduced in VC aqueous extracts prepared from paper sludge and dairy sludge (fresh sludge, FS). The bacterial communities were examined by culture-dependent and -independent analyses. Unique clones selected from 16S rRNA libraries of FS and VC on the basis of restriction fragment length polymorphism (RFLP) fell into the major lineages of the domain bacteria Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria and Firmicutes. Among culture isolates, Actinobacteria dominated in VC, while almost equal numbers of Actinobacteria and Proteobacteria were present in FS. Analysis of chitinolytic isolates and chitinase gene diversity revealed that chitinolytic bacterial communities were enriched in VC. Populations of bacteria that inhibited plant fungal pathogens were higher in VC than in FS and particularly chitinolytic isolates were most active against the target fungi.

  1. Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets.

    PubMed

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-Dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.

  2. Comparative Analysis of the Composition of Intestinal Bacterial Communities in Dastarcus helophoroides Fed Different Diets

    PubMed Central

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-Dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides. PMID:25199878

  3. Bacterial ‘cosmopolitanism’ and importance of local environmental factors for community composition in remote high-altitude lakes

    PubMed Central

    SOMMARUGA, RUBEN; CASAMAYOR, EMILIO O.

    2010-01-01

    SUMMARY In October 2004, plankton samples were collected from six permanent lakes located between 4960 and 5440 m a.s.l. in the Mount Everest region (Nepal) to assess how spatial and local environmental factors affect natural bacterial community composition. Fingerprinting analysis of the bacterial 16S rRNA gene fragment was done by denaturing gradient gel electrophoresis (DGGE). The number of DGGE bands (range: 12–23) was not correlated with lake area or remoteness, but there was a strong negative correlation with the ratio of catchment to lake area (r = −0.826, P < 0.05), suggesting that hydraulic retention time affects the establishment of the bacterial community in these seepage lakes. Most dominant sequences belonged to Betaproteobacteria except in two lakes where members of Bacteroidetes made the largest relative contribution. Up to 81% of the phylotypes had high similarity (>98 to 100%) in partial 16S rRNA gene sequence to those reported from other alpine lakes and glaciers around the world, suggesting the presence of ‘cosmopolitan’ bacteria. An analysis based on dissimilarity matrices and the Mantel test revealed the existence of dissimilarities in bacterial community composition related to geographical distance over a small spatial scale (<6 km), but determined by local environmental constraints. Our results suggest that several bacterial phylotypes are ubiquitous in the freshwater aquatic realm, but taxon sorting by local environmental constraints is important. PMID:20543908

  4. Composition and extracellular enzymatic function of pelagic, particle-associated, and benthic bacterial communities in the central Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Balmonte, J. P.; Teske, A.; Arnosti, C.

    2016-02-01

    The structure and function of Arctic bacterial communities have rarely been studied in concert, but are crucial to our understanding of biogeochemical cycles. As the Arctic transitions to become seasonally-ice free, a critical priority is to elucidate the present ecological role and environmental dependence of Arctic bacterial communities. We investigated the depth and regional variations in Central Arctic bacterial community composition (BCC) and extracellular enzymatic activities (EEA)—the initial step in organic matter breakdown—to explore links between community structure and function. Samples were collected across a gradient of sea-ice cover (open ocean, first year ice, multi-year ice) from 79°N to 88°N and from surface to bottom waters ( 3.5 to 4.5 km). Pelagic BCC most strongly varies with hydrography and with particle-association, which likely selects for a specialized community of heterotrophic opportunists; benthic BCC show little regional variation. In contrast, EEA reveal significant depth and regional differences in hydrolysis rates as well as in the spectrum of substrates hydrolyzed. Particle-associated EEA reveal an equal or greater range of enzymatic capabilities than in bulk-seawater measurements, supporting previous findings that particles are hotspots of microbial heterotrophic activity. These patterns suggest a complex relationship between BCC, EEA, and the environment: while water mass characteristics consistently differentiate bacterial communities, additional local factors shape their capabilities to hydrolyze organic matter. Multivariate analyses will be used to further explore the relationships between composition and function as well as their correlations with environmental data. Our findings provide a baseline for future comparisons and initial insight into the functionality and biogeography of Arctic bacterial communities.

  5. Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages.

    PubMed

    Kong, Yunhong; Teather, Ronald; Forster, Robert

    2010-12-01

    The species composition, distribution, and biodiversity of the bacterial communities in the rumen of cows fed alfalfa or triticale were investigated using 16S rRNA gene clone library analyses. The rumen bacterial community was fractionated and analyzed as three separate fractions: populations in the planktonic, loosely attached to rumen digesta particles, and tightly attached to rumen digesta particles. Six hundred and thirteen operational taxonomic units (OTUs) belonging to 32 genera, 19 families, and nine phyla of the domain Bacteria were identified from 1014 sequenced clones. Four hundred and fifty one of the 613 OTUs were identified as new species. These bacterial sequences were distributed differently among the three fractions in the rumen digesta of cows fed alfalfa or triticale. Chao 1 estimation revealed that, in both communities, the populations tightly attached to particulates were more diverse than the planktonic and those loosely attached to particulates. S-Libshuff detected significant differences in the composition between any two fractions in the rumen of cows with the same diet and between the communities fed alfalfa and triticale diets. The species richness estimated for the communities fed alfalfa and triticale is 1027 and 662, respectively. The diversity of the rumen bacterial community examined in this study is greater than previous studies have demonstrated and the differences in the community composition between two high-fiber diets have implications for sample selection for downstream metagenomics applications. © 2010 Federation of European Microbiological Societies and Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada.

  6. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea.

    PubMed

    Singh, Sanjay Kumar; Ramaiah, Nagappa

    2011-05-01

    Denaturing gradient gel electrophoresis (DGGE) was used to elucidate spatial and temporal variations in bacterial community composition (BCC) from four locations along the central west coast of India. DNA extracts from 36 water samples collected from surface, mid-depth (-10 m) and dose to bottom (-20 m) during premonsoon, postmonsoon, monsoon were analyzed by PCRfor amplifying variable region of 16S rRNAgene and subsequently through DGGE. Prominent bands were excised, cloned and sequenced indicated the preponderance of gammaproteobacteria, bacteroidetes and cyanobacteria. Non-metric dimensional scaling of the DGGE gels indicated that the spatial variations in BCC were prominent among the sampling locations. Temporal variations in the BCC appear to be influenced by monsoonal processes. The canonical correspondence analyses suggest that the concentration of chlorophyll a and nitrate are two important environmental factors for both spatial and temporal variations in BCC. Chlorophyll a seems to be impart a top-down control of BCC while nitrate, the bottom-up control. Our results also suggest that BCC can vary over a small geographic distance in highly dynamic, seasonally predisposed tropical coastal waters.

  7. Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure.

    PubMed

    Berg, Jeanette; Brandt, Kristian K; Al-Soud, Waleed A; Holm, Peter E; Hansen, Lars H; Sørensen, Søren J; Nybroe, Ole

    2012-10-01

    Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g(-1)) stemming from industrial contamination with CuSO(4) more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [(3)H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the Proteobacteria, Bacteroidetes, Verrumicrobia, Chloroflexi, WS3, and Planctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, the Actinobacteria, showed no response and members of the Acidobacteria showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.

  8. Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure

    PubMed Central

    Berg, Jeanette; Brandt, Kristian K.; Al-Soud, Waleed A.; Holm, Peter E.; Hansen, Lars H.; Sørensen, Søren J.

    2012-01-01

    Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g−1) stemming from industrial contamination with CuSO4 more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [3H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the Proteobacteria, Bacteroidetes, Verrumicrobia, Chloroflexi, WS3, and Planctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, the Actinobacteria, showed no response and members of the Acidobacteria showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa. PMID:22904046

  9. Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

    PubMed Central

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

    2013-01-01

    Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m. PMID:24205246

  10. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    PubMed

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

    2013-01-01

    Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  11. Phylogenetic analysis of the composition of bacterial communities in human-exploited coastal environments from Mallorca Island (Spain).

    PubMed

    Aguiló-Ferretjans, M M; Bosch, R; Martín-Cardona, C; Lalucat, J; Nogales, B

    2008-08-01

    The phylogenetic analysis of bacterial communities in environments receiving anthropogenic impact could help us to understand its effects and might be useful in the development of monitoring or management strategies. A study of the composition of 16S rDNA clone libraries prepared from bacterial communities in water samples from a marina and a beach on the coast of Mallorca (W. Mediterranean) was undertaken at two time points, corresponding to periods of maximum and minimum anthropogenic use of this area for nautical and recreational activities. Libraries generated from the marina were significantly different from those from the beach and a non-impacted, bay sample. In the marina, a predominance of sequence types was observed related to bacterioplankton from nutrient-enriched environments or typically associated with phytoplankton, such as certain phylotypes of the Roseobacter clade, OM60 clade and Bacteroidetes. Similar results were found in the summer beach library but not in the winter one, in which there was an increase in the number of clones from oligotrophic groups, in agreement with lower chlorophyll content and bacterial counts. Therefore, nutrient enrichment seemed to be an important driver of the composition of bacterial communities in sites receiving direct human impact. Interesting sequence types from the Cryomorphaceae and group agg58 (Bacteroidetes) were exclusively found in beach libraries, and the reasons for this distribution deserve further study. Clones related to putative hydrocarbon-degrading bacteria of the genus Acinetobacter were observed in the marina, in agreement with a certain degree of pollution at this site. Non-marine sequences belonging to the Actinobacteria predominated over marine groups in the summer library from the marina and, therefore, unusual communities might be transiently present in this enclosed environment. Overall, the composition of the bacterial communities in these environments agreed well with the defining

  12. Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system.

    PubMed

    Douterelo, I; Sharpe, R L; Boxall, J B

    2013-02-01

    Microbial biofilms formed on the inner-pipe surfaces of drinking water distribution systems (DWDS) can alter drinking water quality, particularly if they are mechanically detached from the pipe wall to the bulk water, such as due to changes in hydraulic conditions. Results are presented here from applying 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene to investigate the influence of different hydrological regimes on bacterial community structure and to study the potential mobilisation of material from the pipe walls to the network using a full scale, temperature-controlled experimental pipeline facility accurately representative of live DWDS. Analysis of pyrosequencing and water physico-chemical data showed that habitat type (water vs. biofilm) and hydraulic conditions influenced bacterial community structure and composition in our experimental DWDS. Bacterial community composition clearly differed between biofilms and bulk water samples. Gammaproteobacteria and Betaproteobacteria were the most abundant phyla in biofilms while Alphaproteobacteria was predominant in bulk water samples. This suggests that bacteria inhabiting biofilms, predominantly species belonging to genera Pseudomonas, Zooglea and Janthinobacterium, have an enhanced ability to express extracellular polymeric substances to adhere to surfaces and to favour co-aggregation between cells than those found in the bulk water. Highest species richness and diversity were detected in 28 days old biofilms with this being accentuated at highly varied flow conditions. Flushing altered the pipe-wall bacterial community structure but did not completely remove bacteria from the pipe walls, particularly under highly varied flow conditions, suggesting that under these conditions more compact biofilms were generated. This research brings new knowledge regarding the influence of different hydraulic regimes on the composition and structure of bacterial communities within DWDS and the implication that this

  13. Phenanthrene and Pyrene Modify the Composition and Structure of the Cultivable Endophytic Bacterial Community in Ryegrass (Lolium multiflorum Lam)

    PubMed Central

    Zhu, Xuezhu; Jin, Li; Sun, Kai; Li, Shuang; Li, Xuelin; Ling, Wanting

    2016-01-01

    This study provides new insights into the dynamics of bacterial community structure during phytoremediation. The communities of cultivable autochthonous endophytic bacteria in ryegrass exposed to polycyclic aromatic hydrocarbons (PAHs) were investigated with regard to their potential to biodegrade PAHs. Bacterial counts and 16S rRNA gene sequence were used in the microbiological evaluation. A total of 33 endophytic bacterial strains were isolated from ryegrass plants, which represented 15 different genera and eight different classes, respectively. Moreover, PAH contamination modified the composition and structure of the endophytic bacterial community in the plants. Bacillus sp., Pantoea sp., Pseudomonas sp., Arthrobacter sp., Pedobacter sp. and Delftia sp. were only isolated from the seedlings exposed to PAHs. Furthermore, the dominant genera in roots shifted from Enterobacter sp. to Serratia sp., Bacillus sp., Pantoea sp., and Stenotrophomonas sp., which could highly biodegrade phenanthrene (PHE). However, the diversity of endophytic bacterial community was decreased by exposure to the mixture of PAHs, and increased by respective exposure to PHE and pyrene (PYR), while the abundance was increased by PAH exposure. The results clearly indicated that the exposure of plants to PAHs would be beneficial for improving the effectiveness of phytoremediation of PAHs. PMID:27827894

  14. Composition dynamics of epilithic intertidal bacterial communities exposed to high copper levels.

    PubMed

    De la Iglesia, Rodrigo; Valenzuela-Heredia, Daniel; Andrade, Santiago; Correa, Juan; González, Bernardo

    2012-03-01

    Copper has a dual role for organisms, both as micronutrient and toxic element. Copper mining activities have an enormous ecological impact because of the extraction process and the consequent release of copper-containing waste materials to the environment. In northern Chile, mainly in the Chañaral coastal area, this phenomenon is clearly evident. The released waste material has caused a strong modification of the area, and copper enrichment of beaches and rocky shores has provoked a decrease in the richness and diversity of many species of macroorganisms. However, the effects that copper enrichment has on microbial (e.g. bacterial epilithic) communities associated with the rocky shore environment are poorly understood. Using a culture-independent molecular approach, field sampling and laboratory microcosm experiments, we determined the effects of copper enrichment on bacterial communities inhabiting the rocky shore environment. Field samples showed a strong effect of copper on the structure of the natural bacterial epilithic communities, and microcosm experiments demonstrated rapid changes in bacterial community when copper is added, and reversibility of this effect within 48 h after copper is removed. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed

    Ganzert, Lars; Bajerski, Felizitas; Wagner, Dirk

    2014-08-01

    Greenland is one of the regions of interest with respect to climate change and global warming in the Northern Hemisphere. Little is known about the structure and diversity of the terrestrial bacterial communities in ice-free areas in northern Greenland. These soils are generally poorly developed and usually carbon- and nitrogen-limited. Our goal was to provide the first insights into the soil bacterial communities from five different sites in Northeast Greenland using culture-independent and culture-dependent methods. The comparison of environmental and biological data showed that the soil bacterial communities are diverse and significantly pH-dependent. The most frequently detected OTUs belonged to the phyla Acidobacteria, Bacteroidetes and (Alpha-, Beta-, Delta-) Proteobacteria. Low pH together with higher nitrogen and carbon concentrations seemed to support the occurrence of (Alpha-, Beta-, Delta-) Proteobacteria (at the expense of Acidobacteria), whereas Bacteroidetes were predominant at higher values of soil pH. Our study indicates that pH is the main factor for shaping bacterial community, but carbon and nitrogen concentrations as well may become important, especially for selecting oligotrophic microorganisms. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  17. Prevalence of Antibiotic Resistance Genes and Bacterial Community Composition in a River Influenced by a Wastewater Treatment Plant

    PubMed Central

    Marti, Elisabet; Jofre, Juan; Balcazar, Jose Luis

    2013-01-01

    Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs), their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP) effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, blaTEM, blaCTX-M, blaSHV, erm(B), sul(I), sul(II), tet(O) and tet(W) were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river. PMID:24205347

  18. Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

    PubMed

    Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

    2015-06-01

    The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

  19. Comparative analysis of the composition of bacterial communities from two constructed wetlands for municipal and swine wastewater treatment.

    PubMed

    Arroyo, Paula; Ansola, Gemma; Blanco, Ivan; Molleda, Patricia; de Luis Calabuig, Estanislao; Sáenz de Miera, Luis E

    2010-03-01

    This work provides information about bacterial community structure in natural wastewater treatment systems treating different types of wastewater. The diversity and composition of bacterial communities associated with the rhizosphere of Typha latifolia and Salix atrocinerea were studied and compared among two different natural wastewater treatment systems, using the direct sequencing of the 16S ribosomal RNA codifying genes. Phylogenetic affiliations of the bacteria detected allowed us to define the main groups present in these particular ecosystems. Moreover, bacterial community structure was studied through two diversity indices. Ten identified and five non-identified phyla were found in the samples; the phylum Proteobacteria was the predominant group in the four ecosystems. The results showed a bacterial community dominated by beta-proteobacteria and a lower diversity value in the swine wastewater treatment system. The municipal wastewater treatment system presented a high diverse community in both macrophytes (Typha latifolia and Salix atrocinerea), with gamma-proteobacteria and alpha-proteobacteria, respectively, as the most abundant groups.

  20. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    PubMed

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors.

  1. Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis

    PubMed Central

    Burke, Catherine; Thomas, Torsten; Lewis, Matt; Steinberg, Peter; Kjelleberg, Staffan

    2011-01-01

    Green Ulvacean marine macroalgae are distributed worldwide in coastal tidal and subtidal ecosystems. As for many living surfaces in the marine environment, little is known concerning the epiphytic bacterial biofilm communities that inhabit algal surfaces. This study reports on the largest published libraries of near full-length 16S rRNA genes from a marine algal surface (5293 sequences from six samples) allowing for an in-depth assessment of the diversity and phylogenetic profile of the bacterial community on a green Ulvacean alga. Large 16S rRNA gene libraries of surrounding seawater were also used to determine the uniqueness of this bacterial community. The surface of Ulva australis is dominated by sequences of Alphaproteobacteria and the Bacteroidetes, especially within the Rhodobacteriaceae, Sphingomonadaceae, Flavobacteriaceae and Sapropiraceae families. Seawater libraries were also dominated by Alphaproteobacteria and Bacteroidetes sequences, but were shown to be clearly distinct from U. australis libraries through the clustering of sequences into operational taxonomic units and Bray–Curtis similarity analysis. Almost no similarity was observed between these two environments at the species level, and only minor similarity was observed at levels of sequence clustering representing clades of bacteria within family and genus taxonomic groups. Variability between libraries of U. australis was relatively high, and a consistent sub-population of bacterial species was not detected. The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface. PMID:21048801

  2. 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.

  3. 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

  4. 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.

  5. Geographic and environmental sources of variation in bacterial community composition in a large-scale municipal landfill site in China.

    PubMed

    Song, Liyan; Yang, Shu; Liu, Hongjie; Xu, Jing

    2017-01-01

    Little is known regarding how bacterial communities assemble at landfill, as well as how the environment shapes the composition of bacterial community. In this study, up to 42 refuse samples from a large-scale landfill in China were physicochemically and phylogenetically investigated. 16S ribosomal RNA (rRNA) gene-based Illumina MiSeq sequencing (nine samples) revealed that representatives of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes were dominant in the refuse samples, which was similar to a previous study on landfill leachate by using 454 pyrosequencing. Although 741 operational taxonomic units (OTUs) were detected across all nine samples, 6 of these OTUs were detected in all of the data sets, suggesting difference between bacterial community structures. Geographical differences between the samples, irrespective of depths, were revealed by a principal component analysis (PCA) based on the terminal restriction fragment length polymorphism (TRFLP) profiles of 42 refuse samples. Redundancy analysis (RDA) suggested that environmental heterogeneity (pH, landfilling ages, and depths) and the abundance of bacteria (represented by 16S rRNA gene copy numbers) were the main drivers shaping the bacterial community structure.

  6. Bacterial community composition and diversity in an ancestral ant fungus symbiosis.

    PubMed

    Kellner, Katrin; Ishak, Heather D; Linksvayer, Timothy A; Mueller, Ulrich G

    2015-07-01

    Fungus-farming ants (Hymenoptera: Formicidae, Attini) exhibit some of the most complex microbial symbioses because both macroscopic partners (ants and fungus) are associated with a rich community of microorganisms. The ant and fungal microbiomes are thought to serve important beneficial nutritional and defensive roles in these symbioses. While most recent research has investigated the bacterial communities in the higher attines (e.g. the leaf-cutter ant genera Atta and Acromyrmex), which are often associated with antibiotic-producing Actinobacteria, very little is known about the microbial communities in basal lineages, labeled as 'lower attines', which retain the ancestral traits of smaller and more simple societies. In this study, we used 16S amplicon pyrosequencing to characterize bacterial communities of the lower attine ant Mycocepurus smithii among seven sampling sites in central Panama. We discovered that ant and fungus garden-associated microbiota were distinct from surrounding soil, but unlike the situation in the derived fungus-gardening ants, which show distinct ant and fungal microbiomes, microbial community structure of the ants and their fungi were similar. Another surprising finding was that the abundance of actinomycete bacteria was low and instead, these symbioses were characterized by an abundance of Lactobacillus and Pantoea bacteria. Furthermore, our data indicate that Lactobacillus strains are acquired from the environment rather than acquired vertically.

  7. Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin.

    PubMed

    Sette, Lara D; Simioni, Karen C M; Vasconcellos, Suzan P; Dussan, Lucia J; Neto, Eugênio V S; Oliveira, Valéria M

    2007-04-01

    The aim of this study was to characterize and compare the bacterial community structure of two distinct oil samples from a petroleum field in Brazil by using both molecular, based on the construction of 16S rRNA gene libraries, and cultivation methods. Statistical comparisons of libraries based on Amplified Ribosomal DNA Restriction Analysis (ARDRA) data revealed no significant differences between the communities recovered in the non-biodegraded (NBD) and highly biodegraded oils (HBD). BlastN analysis of the 16S rRNA gene sequences representative of distinct ribotypes from both oils showed the presence of nine different bacterial genera in these samples, encompassing members of the genera Arcobacter, Halanaerobium, Marinobacter, Propionibacterium, Streptomyces, Leuconostoc, Acinetobacter, Bacillus and Streptococcus. Enrichments obtained using oil as inoculum and sole carbon source yielded bacterial isolates showing high 16S rRNA gene sequence similarity with Achromobacter xylosoxidans, Bacillus subtilis, Brevibacillus sp., Dietzia sp. and Methylobacterium sp. Comparison between the data obtained using cultivation-independent and enrichment cultures suggests that different selection of community members may occur when using distinct approaches. All the organisms found, except for Leuconostoc sp. and Streptococus sp., have been previously reported in the literature as hydrocarbon degraders and/or associated to oil field environments.

  8. Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow.

    PubMed

    Thiele, Stefan; Fuchs, Bernhard M; Amann, Rudolf; Iversen, Morten H

    2015-02-01

    Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

  9. Diversification of Bacterial Community Composition along a Temperature Gradient at a Thermal Spring

    PubMed Central

    Everroad, R. Craig; Otaki, Hiroyo; Matsuura, Katsumi; Haruta, Shin

    2012-01-01

    To better understand the biogeography and relationship between temperature and community structure within microbial mats, the bacterial diversity of mats at a slightly alkaline, sulfide-containing hot spring was explored. Microbial mats that developed at temperatures between 75–52°C were collected from an area of approximately 1 m2 in Nakabusa, Nagano, Japan. Bacterial 16S rRNA genes from these samples were examined by terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis. T-RFLP profiles revealed 66 unique fragments (T-RFs). Based on total T-RFs observed in environmental profiles and clone libraries, a temperature effect on diversity was determined, with complexity in the community increasing as temperature decreased. The T-RF pattern indicated four distinct community assemblages related to temperature. Members of the Aquificales and particularly the sulfuroxidizing bacterium Sulfurihydrogenibium were present at all temperatures and were the dominant component of mats taken at 75–67°C. Sulfide oxidation, which persisted throughout the temperature gradient, was the presumed dominant pathway of primary production above 67°C. As temperature decreased, successive additions of anoxygenic and oxygenic phototrophs increased primary productivity, allowing for diversification of the community. PMID:22673306

  10. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

    PubMed

    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium.

    PubMed

    Pereira, Arthur Prudêncio de Araujo; Andrade, Pedro Avelino Maia de; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

    2017-01-01

    Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.

  12. Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium

    PubMed Central

    de Andrade, Pedro Avelino Maia; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

    2017-01-01

    Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil. PMID:28686690

  13. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    PubMed

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Phylogenetic and functional alterations in bacterial community compositions in broiler ceca as a result of mannan oligosaccharide supplementation.

    PubMed

    Corrigan, A; de Leeuw, Marcel; Penaud-Frézet, Stéphanie; Dimova, Diliana; Murphy, R A

    2015-05-15

    This study focused on identifying reproducible effects of dietary supplementation with a mannan oligosaccharide (MOS) on the broiler cecal bacterial community structure and function in a commercial production setting. Two separate trials, each with a control and a supplemented group, were carried out in the same commercial location and run concurrently. Approximately 10,000 birds from the same commercial hatchery were mirror imaged into each of four commercial broiler sheds and fed either a control or supplemented diet. Cecal contents were obtained on days 7, 21, and 35 posthatch from 12 randomly caught broilers from each group. Bacterial pyrosequencing was performed on all samples, with approximately 250,000 sequences obtained per treatment per time point. The predominant phyla identified at all three time points in both trials were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Tenericutes, representing >99% of all sequences. MOS supplementation altered the bacterial community composition from 7 days supplementation through 35 days supplementation. Bacteroidetes appeared to be replacing Firmicutes as a result of supplementation, with the most noticeable effects after 35 days. The effects of supplementation were reproducible across both trials. PICRUSt was used to identify differences between the functional potentials of the bacterial communities as a result of MOS supplementation. Using level 3 KEGG ortholog function predictions, differences between control and supplemented groups were observed, with very strong segregation noted on day 35 posthatch in both trials. This indicated that alterations of bacterial communities as a result of MOS are likely to alter the functional capability of the cecum. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. 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.

  16. Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes.

    PubMed

    Rofner, Carina; Peter, Hannes; Catalán, Núria; Drewes, Fabian; Sommaruga, Ruben; Pérez, María Teresa

    2016-11-01

    Lakes at high altitude and latitude are typically unproductive ecosystems where external factors outweigh the relative importance of in-lake processes, making them ideal sentinels of climate change. Climate change is inducing upward vegetation shifts at high altitude and latitude regions that translate into changes in the pools of soil organic matter. Upon mobilization, this allochthonous organic matter may rapidly alter the composition and function of lake bacterial communities. Here, we experimentally simulate this potential climate-change effect by exposing bacterioplankton of two lakes located above the treeline, one in the Alps and one in the subarctic region, to soil organic matter from below and above the treeline. Changes in bacterial community composition, diversity and function were followed for 72 h. In the subarctic lake, soil organic matter from below the treeline reduced bulk and taxon-specific phosphorus uptake, indicating that bacterial phosphorus limitation was alleviated compared to organic matter from above the treeline. These effects were less pronounced in the alpine lake, suggesting that soil properties (phosphorus and dissolved organic carbon availability) and water temperature further shaped the magnitude of response. The rapid bacterial succession observed in both lakes indicates that certain taxa directly benefited from soil sources. Accordingly, the substrate uptake profiles of initially rare bacteria (copiotrophs) indicated that they are one of the main actors cycling soil-derived carbon and phosphorus. Our work suggests that climate-induced changes in soil characteristics affect bacterioplankton community structure and function, and in turn, the cycling of carbon and phosphorus in high altitude and latitude aquatic ecosystems.

  17. Structure and community composition of sprout-like bacterial aggregates in a Dinaric Karst subterranean stream.

    PubMed

    Kostanjšek, Rok; Pašić, Lejla; Daims, Holger; Sket, Boris

    2013-07-01

    The Vjetrenica cave in the Dinaric Karst hosts a worldwide extraordinarily high cave biodiversity. Beside a diverse and specialized cave fauna, sprout-like formations attached to the bed of the cave stream were observed and described, but not further characterized, almost a century ago. Here we investigated these sprout-like microbial aggregates by the rRNA approach and detailed microscopy. Based on fluorescence in situ hybridization and ultrastructural analysis, the sprout-like formations are morphologically highly organized, and their core consists of a member of a novel deep-branching lineage in the bacterial phylum Nitrospirae. This organism displays an interesting cellular ultrastructure with different kinds of cytoplasmic inclusions and is embedded in a thick extracellular matrix, which contributes to the stability and shape of the aggregates. This novel bacterium has been provisionally classified as "Candidatus Troglogloea absoloni." The surface of the sprout-like aggregates is more diverse than the core. It is colonized by a bacterial biofilm consisting primarily of filamentous Betaproteobacteria, whereas other microbial populations present in the crust include members of the Bacteriodetes, Gammaproteobacteria, Actinombacteria, Alphaproteobacteria, and Planctomycetes, which are intermingled with mineral inclusions. This study represents the first thorough molecular and ultrastructural characterization of the elusive sprout-like bacterial aggregates, which are also found in other cave systems of the Dinaric Karst. The discovery of Ca. Troglogloea absoloni contributes to the known biodiversity of subterranean ecosystems and especially of macroscopic structures formed in caves by microorganisms, whose composition and ecological function often remain enigmatic.

  18. Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants.

    PubMed

    Marques, Joana M; da Silva, Thais F; Vollu, Renata E; Blank, Arie F; Ding, Guo-Chun; Seldin, Lucy; Smalla, Kornelia

    2014-05-01

    The hypothesis that sweet potato genotypes containing different starch yields in their tuberous roots can affect the bacterial communities present in the rhizosphere (soil adhering to tubers) was tested in this study. Tuberous roots of field-grown sweet potato of genotypes IPB-149 (commercial genotype), IPB-052, and IPB-137 were sampled three and six months after planting and analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analysis of 16S rRNA genes PCR-amplified from total community DNA. The statistical analysis of the DGGE fingerprints showed that both plant age and genotypes influenced the bacterial community structure in the tuber rhizosphere. Pyrosequencing analysis showed that the IPB-149 and IPB-052 (both with high starch content) displayed similar bacterial composition in the tuber rhizosphere, while IPB-137 with the lowest starch content was distinct. In comparison with bulk soil, higher 16S rRNA gene copy numbers (qPCR) and numerous genera with significantly increased abundance in the tuber rhizosphere of IPB-137 (Sphingobium, Pseudomonas, Acinetobacter, Stenotrophomonas, Chryseobacterium) indicated a stronger rhizosphere effect. The genus Bacillus was strongly enriched in the tuber rhizosphere samples of all sweet potato genotypes studied, while other genera showed a plant genotype-dependent abundance. This is the first report on the molecular identification of bacteria being associated with the tuber rhizosphere of different sweet potato genotypes.

  19. Bacterial community composition and diversity in Kalakuli, an alpine glacial-fed lake in Muztagh Ata of the westernmost Tibetan Plateau.

    PubMed

    Liu, Keshao; Liu, Yongqin; Jiao, Nianzhi; Xu, Baiqing; Gu, Zhengquan; Xing, Tingting; Xiong, Jinbo

    2017-07-01

    It is widely accepted that bacterial community composition and diversity in remote alpine lakes are structured by environmental conditions such as nutrient status and temperature. However, the mechanisms that underlie and structure bacterial community composition and diversity in alpine lakes remain unclear. We used 16S rRNA gene-based Illumina MiSeq sequencing to investigate the complex ecological interactions between bacterial communities and nutrient status in Kalakuli Lake, an alpine glacial-fed lake in Muztagh Ata of the westernmost Tibetan Plateau. Our results indicated that the bacterial community was dominated by the Actinobacteria and Proteobacteria. The results of threshold estimates showed that there were apparent shifts in dominance from the Proteobacteria to Actinobacteria groups associated with increasing carbon to nitrogen (C:N) ratio, and the change points were 6.794 and 2.448, respectively. Using multiple statistical methods, we found that the abiotic factors of dissolved organic carbon and total nitrogen had substantial impacts on bacterial diversity, while bacterial community compositions were significantly correlated with both the biotic element of bacterial abundance and the abiotic ones, temperature and pH. These findings demonstrated that the C:N ratio played a significant role in shifting dominant bacterial assemblages in the Kalakuli watershed and provided evidence of nutrients affecting bacterial community composition and diversity. We argue that this study could further shed light on how climate change-induced glacial retreat may impact bacterial communities in glacial-fed lakes under future global warming scenarios. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

    PubMed Central

    Weiland-Bräuer, Nancy; Neulinger, Sven C.; Pinnow, Nicole; Künzel, Sven; Baines, John F.

    2015-01-01

    The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. PMID:26116680

  1. Overall bacterial community composition and abundance of nitrifiers and denitrifiers in a typical macrotidal estuary.

    PubMed

    Zhu, Weijing; Wang, Cheng; Sun, Faqian; Zhao, Liancheng; Dou, Wenjie; Mao, Zhihua; Wu, Weixiang

    2017-10-01

    Coupled nitrogen cycling processes can alleviate the negative effects of eutrophication caused by excessive nitrogen load in estuarine ecosystems. The abundance and diversity of nitrifiers and denitrifiers across different environmental gradients were examined in the sediment of Hangzhou Bay. Quantitative PCR and Pearson's correlation analyses suggested that the bacterial ammonia-oxidizers (AOB) were the dominant phylotypes capable of ammonia oxidation, while the nirS-encoding denitrifiers predominated in the denitrification process. Simultaneously, nitrite and pH were found to be the two major factors influencing amoA and nir gene abundances, and the distribution of bacterial communities. Moreover, the ratio of nirS/AOB amoA gene abundance showed negative correlation with nitrite concentration. Fluorescence in situ hybridization further demonstrated that AOB and acetate-denitrifying cells were closely connected and formed obvious aggregates in the sediment. Together, all these results provided us a preliminary insight for coupled nitrification-denitrification processes in the sediment of Hangzhou Bay. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets.

    PubMed

    Li, Zhipeng; Wright, André-Denis G; Liu, Hanlu; Bao, Kun; Zhang, Tietao; Wang, Kaiying; Cui, Xuezhe; Yang, Fuhe; Zhang, Zhigang; Li, Guangyu

    2015-02-01

    Sika deer (Cervus nippon) rely on microorganisms living in the rumen to convert plant materials into chemical compounds, such as volatile fatty acids (VFAs), but how the rumen bacterial community is affected by different forages and adapt to altered diets remains poorly understood. The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design. Three sika deer were fed oak leaves (OL), corn stover (CS), or corn silage (CI), respectively. After a 7-day feeding period, when compared to the CS and CI groups, the OL group had a lower proportion of Prevotella spp. and a higher proportion of unclassified bacteria belonging to the families Succinivibrionaceae and Paraprevotellaceae (P<0.05). Meanwhile, the concentration of isobutyrate was significantly lower (P<0.05) in the OL group than in the CS and CI groups. There was no significant change of dominant bacterial genera in the OL group after 28 days of feeding. Conversely, total volatile fatty acids (TVFAs) showed an increase after 28 days of feeding, mainly due to the increasing of acetate, propionate, and valerate (P<0.05). The interplay between bacteria and metabolism in the OL group differed from that in the CS and CI groups, especially for the interaction of TVFAs and acetate/propionate. Overall, the current study suggested that Prevotella spp. played critical roles in the fermentation of feed in the rumen of sika deer. However, the differences in interplay patterns between rumen bacterial community composition and metabolic phenotypes were altered in the native and domesticated diets indicating the changed fermentation patterns in the rumen of sika deer.

  3. Degradation of chloroacetanilide herbicides and bacterial community composition in lab-scale wetlands.

    PubMed

    Elsayed, Omniea Fawzy; Maillard, Elodie; Vuilleumier, Stéphane; Millet, Maurice; Imfeld, Gwenaël

    2015-07-01

    Degradation of chloroacetanilide herbicides rac-metolachlor, acetochlor, and alachlor, as well as associated bacterial populations, were evaluated in vertical upflow wetland columns using a combination of hydrochemical and herbicide analyses, and DNA-based approaches. Mass dissipation of chloroacetanilides, continuously supplied at 1.8-1.9 μM for 112 days, mainly occurred in the rhizosphere zone under nitrate and sulphate-reducing conditions, and averaged 61±14%, 52±12% and 29±19% for acetochlor, alachlor and rac-metolachlor, respectively. Metolachlor enantiomer fractions of 0.494±0.009 in the oxic zone and 0.480±0.005 in the rhizosphere zone indicated preferential biodegradation of the S-enantiomer. Chloroacetanilide ethane sulfonic acid and oxanilic acid degradates were detected at low concentrations only (0.5 nM), suggesting extensive degradation and the operation of yet unknown pathways for chloroacetanilide degradation. Hydrochemical parameters and oxygen concentration were major drivers of bacterial composition, whereas exposure to chloroacetanilides had no detectable impact. Taken together, the results underline the importance of anaerobic degradation of chloroacetanilides in wetlands, and highlight the potential of complementary chemical and biological approaches to characterise processes involved in the environmental dissipation of chloroacetanilides.

  4. Bacterial community composition characterization of a lead-contaminated Microcoleus sp. consortium.

    PubMed

    Giloteaux, Ludovic; Solé, Antoni; Esteve, Isabel; Duran, Robert

    2011-08-01

    A Microcoleus sp. consortium, obtained from the Ebro delta microbial mat, was maintained under different conditions including uncontaminated, lead-contaminated, and acidic conditions. Terminal restriction fragment length polymorphism and 16S rRNA gene library analyses were performed in order to determine the effect of lead and culture conditions on the Microcoleus sp. consortium. The bacterial composition inside the consortium revealed low diversity and the presence of specific terminal-restriction fragments under lead conditions. 16S rRNA gene library analyses showed that members of the consortium were affiliated to the Alpha, Beta, and Gammaproteobacteria and Cyanobacteria. Sequences closely related to Achromobacter spp., Alcaligenes faecalis, and Thiobacillus species were exclusively found under lead conditions while sequences related to Geitlerinema sp., a cyanobacterium belonging to the Oscillatoriales, were not found in presence of lead. This result showed a strong lead selection of the bacterial members present in the Microcoleus sp. consortium. Several of the 16S rRNA sequences were affiliated to nitrogen-fixing microorganisms including members of the Rhizobiaceae and the Sphingomonadaceae. Additionally, confocal laser scanning microscopy and scanning and transmission electron microscopy showed that under lead-contaminated condition Microcoleus sp. cells were grouped and the number of electrodense intracytoplasmic inclusions was increased.

  5. Analysis of the bacterial community composition in acidic well water used for drinking in Guinea-Bissau, West Africa.

    PubMed

    Machado, Ana; Bordalo, Adriano A

    2014-08-01

    Potable water is a resource out of reach for millions worldwide, and the available water may be chemically and microbiologically compromised. This is particularly acute in Africa, where water-networks may be non-existent or restricted to a small fraction of the urban population, as in the case of Guinea-Bissau, West Africa. This study was carried out seasonally in Bolama (11°N), where unprotected hand-dug wells with acidic water are the sole source of water for the population. We inspected the free-living bacterial community dynamics by automated rRNA intergenic spacer analyses, quantitative polymerase chain reaction and cloning approaches. The results revealed a clear seasonal shift in bacterial assemblage composition and microbial abundance within the same sampling site. Temperature, pH and turbidity, together with the infiltration and percolation of surface water, which takes place in the wet season, seemed to be the driving factors in the shaping and selection of the bacterial community and deterioration of water quality. Analysis of 16S rDNA sequences revealed several potential pathogenic bacteria and uncultured bacteria associated with water and sediments, corroborating the importance of a culture-independent approach in drinking water monitoring. Copyright © 2014. Published by Elsevier B.V.

  6. Effects of partial mixed rations and supplement amounts on milk production and composition, ruminal fermentation, bacterial communities, and ruminal acidosis.

    PubMed

    Golder, H M; Denman, S E; McSweeney, C; Wales, W J; Auldist, M J; Wright, M M; Marett, L C; Greenwood, J S; Hannah, M C; Celi, P; Bramley, E; Lean, I J

    2014-09-01

    and quadratically increased with supplement feeding amount. The Bacteroidetes and Firmicutes were the dominant bacterial phyla identified. The Prevotellaceae, Ruminococcaceae, and Lachnospiraceae were the dominant bacterial families, regardless of feeding group, and were influenced by feeding strategy, supplement feeding amount, or both. The Veillonellaceae family decreased in relative abundance in PMR-fed cows compared with controls, and the Streptococcaeae and Lactobacillaceae families were present in only minor relative abundances, regardless of feeding group. Despite large among- and within-group variation in bacterial community composition, distinct bacterial communities occurred among feeding strategies, supplement amounts, and sample times and were associated with ruminal fermentation measures. Control cows fed 16kg of DM of total supplement per day had the most distinct ruminal bacterial community composition. Bacterial community composition was most significantly associated with supplement feeding amount and ammonia, butyrate, valerate, and propionate concentrations. Feeding supplements in a PMR reduced the incidence of ruminal acidosis and altered ruminal bacterial communities, regardless of supplement feeding amount, but did not result in increased milk measures compared with isoenergetic control diets component-fed to late-lactation cows.

  7. Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

    PubMed

    Tian, Ren-Mao; Lee, On On; Wang, Yong; Cai, Lin; Bougouffa, Salim; Chiu, Jill Man Ying; Wu, Rudolf Shiu Sun; Qian, Pei-Yuan

    2014-01-01

    Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2',4,4'-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.

  8. Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis

    PubMed Central

    Tian, Ren-Mao; Lee, On On; Wang, Yong; Cai, Lin; Bougouffa, Salim; Chiu, Jill Man Ying; Wu, Rudolf Shiu Sun; Qian, Pei-Yuan

    2014-01-01

    Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2′,4,4′-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge. PMID:25642227

  9. 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.

  10. Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale.

    PubMed

    Van Horn, David J; Van Horn, M Lee; Barrett, John E; Gooseff, Michael N; Altrichter, Adam E; Geyer, Kevin M; Zeglin, Lydia H; Takacs-Vesbach, Cristina D

    2013-01-01

    Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when

  11. Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale

    PubMed Central

    Van Horn, David J.; Van Horn, M. Lee; Barrett, John E.; Gooseff, Michael N.; Altrichter, Adam E.; Geyer, Kevin M.; Zeglin, Lydia H.; Takacs-Vesbach, Cristina D.

    2013-01-01

    Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when

  12. Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate.

    PubMed

    Yan, Lijuan; Sinkko, Hanna; Penttinen, Petri; Lindström, Kristina

    2016-01-15

    The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

    PubMed Central

    Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid

    2012-01-01

    The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity. PMID:22389373

  14. Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany.

    PubMed

    Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid; Höfle, Manfred G

    2012-05-01

    The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

  15. Monitoring nutrient impact on bacterial community composition during bioremediation of anoxic PAH-contaminated sediment.

    PubMed

    Kim, Myungsu; Bae, Seung Seob; Seol, Mijin; Lee, Jung-Hyun; Oh, Young-Sook

    2008-12-01

    Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.

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

    USGS Publications Warehouse

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

    2009-01-01

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

  17. Terrestrial runoff controls the bacterial community composition of biofilms along a water quality gradient in the Great Barrier Reef.

    PubMed

    Witt, Verena; Wild, Christian; Uthicke, Sven

    2012-11-01

    16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyll a concentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.

  18. Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes

    NASA Astrophysics Data System (ADS)

    Riemann, Lasse; Steward, Grieg F.; Fandino, Laura B.; Campbell, Lisa; Landry, Michael R.; Azam, Farooq

    1999-08-01

    Horizontal and vertical variations in bacterial community composition were examined in samples collected during two Joint Global Ocean Flux Study (JGOFS) Arabian Sea cruises in 1995. The cruises, 11 months apart, took place during two consecutive NE Monsoon periods (January and December). Bacteria were harvested by filtration from samples collected in the mixed layer, mid-water, and deep sea at stations across the study area. Total bacterial community genomic DNA was analyzed by PCR amplification of 16S rRNA gene fragments, followed by denaturing gradient gel electrophoresis (DGGE). In total, 20 DGGE bands reflecting unique or varying phylotypes were excised, cloned and sequenced. Amplicons were dominated by bacterial groups commonly found in oceanic waters (e.g., the SAR11 cluster of α-Proteobacteria and cyanobacteria), but surprisingly none of the sequenced amplicons were related to γ-Proteobacteria or to members of the Cytophaga-Flavobacter-Bacteroides phylum. Amplicons related to magnetotactic bacteria were found for the first time in pelagic oceanic waters. The DGGE banding patterns revealed a dominance of ≈15 distinguishable amplicons in all samples. In the mixed layer the bacterial community was dominated by the same ≈15 phylotypes at all stations, but unique phylotypes were found with increasing depth. Except for cyanobacteria, comparison of the bacterial community composition in surface waters from January and December 1995 showed only minor differences, despite significant differences in environmental parameters. These data suggest a horizontal homogeneity and some degree of seasonal predictability of bacterial community composition in the Arabian Sea.

  19. Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency.

    PubMed

    Jewell, Kelsea A; McCormick, Caroline A; Odt, Christine L; Weimer, Paul J; Suen, Garret

    2015-07-01

    Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.

  20. Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

    PubMed Central

    Jewell, Kelsea A.; McCormick, Caroline A.; Odt, Christine L.; Weimer, Paul J.

    2015-01-01

    Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles. PMID:25934629

  1. Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms.

    PubMed

    Buse, Helen Y; Ji, Pan; Gomez-Alvarez, Vicente; Pruden, Amy; Edwards, Marc A; Ashbolt, Nicholas J

    2017-07-01

    It is unclear how the water-based pathogen, Legionella pneumophila (Lp), and associated free-living amoeba (FLA) hosts change or are changed by the microbial composition of drinking water (DW) biofilm communities. Thus, this study characterized the bacterial community structure over a 7-month period within mature (> 600-day-old) copper DW biofilms in reactors simulating premise plumbing and assessed the impact of temperature and introduction of Lp and its FLA host, Vermamoeba vermiformis (Vv), co-cultures (LpVv). Sequence and quantitative PCR (qPCR) analyses indicated a correlation between LpVv introduction and increases in Legionella spp. levels at room temperature (RT), while at 37°C, Lp became the dominant Legionella spp. qPCR analysis suggested Vv presence may not be directly associated with Lp biofilm growth at RT and 37°C, but may contribute to or be associated with non-Lp legionellae persistence at RT. Two-way PERMANOVA and PCoA revealed that temperature was a major driver of microbiome diversity. Biofilm community composition also changed over the seven-month period and could be associated with significant shifts in dissolved oxygen, alkalinity and various metals in the influent DW. Hence, temperature, biofilm age, DW quality and transient intrusions/amplification of pathogens and FLA hosts may significantly impact biofilm microbiomes and modulate pathogen levels over extended periods. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  2. Effects of subinhibitory ciprofloxacin concentrations on the abundance of qnrS and composition of bacterial communities from water supply reservoirs.

    PubMed

    Marti, Elisabet; Huerta, Belinda; Rodríguez-Mozaz, Sara; Barceló, Damià; Balcázar, Jose Luis; Marcé, Rafael

    2016-10-01

    We used a short-term microcosm approach to investigate the influence of two different subinhibitory concentrations of ciprofloxacin (0.01 and 0.1 μg/ml) on both the abundance of a plasmid-mediated quinolone resistance determinant (qnrS) and the structure and composition of bacterial communities from impaired and pristine water supply reservoirs. The results showed that the abundance of the qnrS gene increases in water samples exposed to both subinhibitory concentrations of ciprofloxacin, especially in water samples from La Llosa del Cavall, which represents the pristine system. Subinhibitory ciprofloxacin concentrations also induced changes in bacterial community composition as indicated by the relative abundances of each operational taxonomic unit (OTU) across treatments. Therefore, our findings may be of significant importance because subinhibitory ciprofloxacin concentrations may promote antibiotic resistance and affect bacterial community composition in environmental settings. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. The effect of organic loading on bacterial community composition of membrane biofilms in a submerged polyvinyl chloride membrane bioreactor.

    PubMed

    Xia, Siqing; Li, Jixiang; He, Shuying; Xie, Kang; Wang, Xiaojia; Zhang, Yanhao; Duan, Liang; Zhang, Zhiqiang

    2010-09-01

    The effect of organic loading on bacterial community composition of membrane biofilms was investigated using a submerged polyvinyl chloride membrane bioreactor. The low and high loadings were set at 0.33 and 0.52 gCOD/(gVSSd), respectively. The results showed that membrane fouling occurred earlier and faster under the high loading conditions. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the similarity of bacterial community in the membrane biofilms between the two loadings was 0.67, higher than that in the mixed liquors (0.52-0.55), which indicated that some specific bacteria were selected preferentially on the membranes. Clone library analysis of the membrane biofilms indicated that Betaproteobacteria and Bacteroidetes under the high loading were 54.72% and 19.81%, respectively. Microarray results further confirmed that the two bacteria were the dominant microorganisms in the high loading biofilm. The severe membrane fouling may be aroused mainly by the enrichment of the two bacteria under the high loading. (c) 2010 Elsevier Ltd. All rights reserved.

  4. Analysis of bacterial community composition of a spring water from the Western Ghats, India using culture dependent and molecular approaches.

    PubMed

    Ruckmani, Arunachalam; Chakrabarti, Tapan

    2011-01-01

    Cultivation based and culture independent molecular approaches were used to characterize the composition and structure of bacterial community from a natural warm spring in the Western Ghats, a biodiversity 'hotspot'. Dilution plating was done on three types of media with varying nutrient levels. Relatively nutritionally poor medium supported growth of highest number of bacteria (4.98 × 10(3) ml(-1)) compared to nutritionally rich media. On the basis of different morphological features on the plate, 62 aerobic and heterotrophic bacterial strains were isolated and their 16S rRNA genes were sequenced and analyzed. On the basis of sequence similarity these isolates were found to be distributed in 21 different genera belonging to Proteobacteria (58%) followed by Firmicutes (26%), Actinobacteria (13%) and Bacteroidetes (3%). Amplification of 16S rRNA gene of the community DNA using eubacterial primers, followed by cloning and sequencing revealed that predominant members of the habitat belong to the phylum Cyanobacteria (60%) followed by Proteobacteria (19.5%), Bacteroidetes (6.67%), Actinobacteria (4.4%) and Firmicutes (2.2%) and small ribosomal subunit of a plastid (of Chlorophyta, 2.2%).

  5. Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method.

    PubMed

    Paz, Henry A; Anderson, Christopher L; Muller, Makala J; Kononoff, Paul J; Fernando, Samodha C

    2016-01-01

    The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling of both the liquid and solid fraction of the rumen contents. Alpha diversity metrics, Chao1 and observed OTUs estimates, displayed higher (P = 0.02) bacterial richness in Holstein compared to Jersey cows and no difference (P > 0.70) in bacterial community richness due to sampling method. The principal coordinate analysis displayed distinct clustering of bacterial communities by breed suggesting that Holstein and Jersey cows harbor different rumen bacterial communities. Family level classification of most abundant (>1%) differential OTUs displayed that OTUs from the bacterial families Lachnospiraceae and p-2534-18B5 to be predominant in Holstein cows compared to Jersey cows. Additionally, OTUs belonging to family Prevotellaceae were differentially abundant in the two breeds. Overall, the results from this study suggest that the bacterial community between Holstein and Jersey cows differ and that esophageal tubing with collection of feed particles associated with the strainer provides a representative rumen sample similar to a sample collected via the rumen cannula. Thus, in future studies esophageal tubing with addition of retained particles can be used to collect rumen samples reducing the cost of cannulation and increasing the number of animals used in microbiome investigations, thus increasing the statistical power of rumen microbial

  6. Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method

    PubMed Central

    Paz, Henry A.; Anderson, Christopher L.; Muller, Makala J.; Kononoff, Paul J.; Fernando, Samodha C.

    2016-01-01

    The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling of both the liquid and solid fraction of the rumen contents. Alpha diversity metrics, Chao1 and observed OTUs estimates, displayed higher (P = 0.02) bacterial richness in Holstein compared to Jersey cows and no difference (P > 0.70) in bacterial community richness due to sampling method. The principal coordinate analysis displayed distinct clustering of bacterial communities by breed suggesting that Holstein and Jersey cows harbor different rumen bacterial communities. Family level classification of most abundant (>1%) differential OTUs displayed that OTUs from the bacterial families Lachnospiraceae and p-2534-18B5 to be predominant in Holstein cows compared to Jersey cows. Additionally, OTUs belonging to family Prevotellaceae were differentially abundant in the two breeds. Overall, the results from this study suggest that the bacterial community between Holstein and Jersey cows differ and that esophageal tubing with collection of feed particles associated with the strainer provides a representative rumen sample similar to a sample collected via the rumen cannula. Thus, in future studies esophageal tubing with addition of retained particles can be used to collect rumen samples reducing the cost of cannulation and increasing the number of animals used in microbiome investigations, thus increasing the statistical power of rumen microbial

  7. 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.

  8. Investigation of total bacterial and ammonia-oxidizing bacterial community composition in a full-scale aerated submerged biofilm reactor for drinking water pretreatment in China.

    PubMed

    Qin, Ying-Ying; Li, Dao-Tang; Yang, Hong

    2007-03-01

    The community composition of total bacteria and ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment was characterized by analysis of 16S rRNA gene and the functional gene amoA, respectively. Sampling was performed in February and in July. 16S rRNA gene clone libraries revealed 13 bacterial divisions. At both sampling dates, the majority of clone sequences were related to the Alpha- and Betaproteobacteria. A minor proportion belonged to the following groups: Gammaproteobacteria, Deltaproteobacteria, Nitrospira, Firmicutes, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, Chloroflexi, Gemmatimonadetes and the Cytophaga-Flavobacterium-Bacteroides group. Some sequences related to bacteria owning high potential metabolic capacities were detected in both samples, such as Rhodobacter-like rRNA gene sequences. Surveys of cloned amoA genes from the two biofilm samples revealed ammonia-oxidizing bacterial sequences affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage. An unknown Nitrosomonas group of amoA gene sequences was also detected.

  9. Bacterial community composition of three candidate insect vectors of palm phytoplasma (Texas Phoenix Palm Decline and Lethal Yellowing).

    PubMed

    Powell, Christopher M; Hail, Daymon; Potocnjak, Julia; Hanson, J Delton; Halbert, Susan H; Bextine, Blake R

    2015-02-01

    Texas Phoenix Palm Decline (TPPD) and Lethal Yellowing are two phytoplasma-linked diseases in palms. The phytoplasma causing TPPD is thought to be transmitted by three putative planthopper vectors, Ormenaria rufifascia, Omolicna joi, and Haplaxius crudus. These insects have been morphologically and molecularly described, and have screened positive for Candidatus Phytoplasma palmae. Individuals from each species were subjected to 16S bacterial community sequencing using the Roche 454 platform, providing new information regarding the previously unexplored bacterial communities present in putative vectors.

  10. Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes▿ †

    PubMed Central

    Beier, Sara; Witzel, Karl-Paul; Marxsen, Jürgen

    2008-01-01

    The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions. PMID:18024682

  11. NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

    DOE PAGES

    Penton, C. Ryan; Yang, Caiyun; Wu, Liyou; ...

    2016-11-24

    Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated tomore » differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.« less

  12. NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

    SciTech Connect

    Penton, C. Ryan; Yang, Caiyun; Wu, Liyou; Wang, Qiong; Zhang, Jin; Liu, Feifei; Qin, Yujia; Deng, Ye; Hemme, Christopher L.; Zheng, Tianling; Schuur, Edward A. G.; Tiedje, James; Zhou, Jizhong

    2016-11-24

    Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

  13. NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient.

    PubMed

    Penton, C Ryan; Yang, Caiyun; Wu, Liyou; Wang, Qiong; Zhang, Jin; Liu, Feifei; Qin, Yujia; Deng, Ye; Hemme, Christopher L; Zheng, Tianling; Schuur, Edward A G; Tiedje, James; Zhou, Jizhong

    2016-01-01

    Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

  14. NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

    PubMed Central

    Penton, C. Ryan; Yang, Caiyun; Wu, Liyou; Wang, Qiong; Zhang, Jin; Liu, Feifei; Qin, Yujia; Deng, Ye; Hemme, Christopher L.; Zheng, Tianling; Schuur, Edward A. G.; Tiedje, James; Zhou, Jizhong

    2016-01-01

    Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites. PMID:27933054

  15. Rhizosphere bacterial community composition responds to arbuscular mycorrhiza, but not to reductions in microbial activity induced by foliar cutting.

    PubMed

    Vestergård, Mette; Henry, Frédéric; Rangel-Castro, Juan Ignacio; Michelsen, Anders; Prosser, James I; Christensen, Søren

    2008-04-01

    Differences in bacterial community composition (BCC) between bulk and rhizosphere soil and between rhizospheres of different plant species are assumed to be strongly governed by quantitative and qualitative rhizodeposit differences. However, data on the relationship between rhizodeposit amounts and BCC are lacking. Other soil microorganisms, e.g. arbuscular mycorrhizal fungi (AMF), may also influence BCC. We simulated foliar herbivory (cutting) to reduce belowground carbon allocation and rhizodeposition of pea plants grown either with or without AMF. This reduced soil respiration, rhizosphere microbial biomass and bacteriovorous protozoan abundance, whereas none of these were affected by AMF. After labelling plants with (13)CO(2), root and rhizosphere soil (13)C enrichment of cut plants were reduced to a higher extent (24-46%) than shoot (13)C enrichment (10-24%). AMF did not affect (13)C enrichment. Despite these clear indications of reduced rhizosphere carbon-input, denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes PCR-amplified targeting DNA and RNA from rhizosphere soil did not reveal any effects of cutting on banding patterns. In contrast, AMF induced consistent differences in both DNA- and RNA-based DGGE profiles. These results show that a reduction in rhizosphere microbial activity is not necessarily accompanied by changes in BCC, whereas AMF presence inhibits proliferation of some bacterial taxa while stimulating others.

  16. Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation

    PubMed Central

    de Camargo, André Ferreira; Goulart, Karla Cristina Stropa; Lemos, Eliana Gertrudes de Macedo

    2016-01-01

    Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management. PMID:27528875

  17. Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil.

    PubMed

    Pan, Yao; Cassman, Noriko; de Hollander, Mattias; Mendes, Lucas W; Korevaar, Hein; Geerts, Rob H E M; van Veen, Johannes A; Kuramae, Eiko E

    2014-10-01

    Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.

  18. Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows

    USDA-ARS?s Scientific Manuscript database

    The objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) prior to exchange and over time post-exchange. Three pai...

  19. Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment

    NASA Astrophysics Data System (ADS)

    Polónia, Ana Rita Moura; Cleary, Daniel Francis Richard; Freitas, Rossana; Gomes, Newton Carlos Marcial; de Voogd, Nicole Joy

    2017-01-01

    Little is known about the microbial diversity, composition and predicted functional similarities and dissimilarities between prokaryotic kingdoms and among coral reef biotopes located in close spatial proximity to one other. In this study, we compared communities of Archaea and Bacteria in two distinct biotopes, namely, the sponge Xestospongia testudinaria and sediment of the Berau reef system, Indonesia. Using a 16S rRNA gene barcoded pyrosequencing approach and a recently developed predictive metagenomic approach (PICRUSt), we tested to what extent sediment and X. testudinaria host compositionally and functionally distinct communities of Archaea and Bacteria. Although Crenarchaeota (Archaea) and Proteobacteria (Bacteria) were the dominant phyla in the microbial communities of both sediment and sponge, there were significant differences in composition between them. Biotope proved to be the main identifiable factor affecting composition. In line with the compositional differences between sediment and sponge prokaryote communities, there were also differences in predicted functions. The archaeal and bacterial communities of sediment were enriched for functions associated with the Metabolism and Environmental Information Processing categories; those of X. testudinaria were enriched for functions associated with the Genetic Information Processing category. The significant levels of concordance between archaeal and bacterial communities and the similar enrichment of these communities in the same functional categories suggests a certain degree of functional redundancy between Archaea and Bacteria in the studied biotopes, which for the sponge may result in an increased resilience to environmental perturbations.

  20. Composition and stability of bacterial communities associated with granular activated carbon and anthracite filters in a pilot scale municipal drinking water treatment facility.

    PubMed

    Shirey, T B; Thacker, R W; Olson, J B

    2012-06-01

    Granular activated carbon (GAC) is an alternative filter substrate for municipal water treatment as it provides a high surface area suitable for microbial colonization. The resulting microbial growth promotes biodegradation of organic materials and other contaminants from influent waters. Here, the community structure of the bacteria associated with three GAC and two anthracite filters was examined over 12 months to monitor changes in community composition. Nearly complete 16S rRNA genes were polymerase chain reaction amplified for terminal restriction fragment length polymorphism (T-RFLP) analyses. The identity of commonly occurring peaks was determined through the construction of five representative 16S rRNA clone libraries. Based on sequence analysis, the bacterial communities associated with both anthracite and GAC filters appear to be composed of environmentally derived bacteria, with no known human pathogens. Analysis of similarity tests revealed that significant differences in bacterial community structure occurred over time, with filter substrate playing an important role in determining community composition. GAC filters exhibited the greatest degree of bacterial community variability over the sampling period, while anthracite filters showed a lower degree of variability and less change in community composition. Thus, GAC may be a suitable biologically active filter substrate for the treatment of municipal drinking water.

  1. Minor changes in soil bacterial and fungal community composition occur in response to monsoon precipitation in a semiarid grassland.

    PubMed

    McHugh, Theresa A; Koch, George W; Schwartz, Egbert

    2014-08-01

    Arizona and New Mexico receive half of their annual precipitation during the summer monsoon season, making this large-scale rain event critical for ecosystem productivity. We used the monsoon rains to explore the responses of soil bacterial and fungal communities to natural moisture pulses in a semiarid grassland. Through 454 pyrosequencing of the 16S rRNA gene and ITS region, we phylogenetically characterized these communities at 22 time points during a summer season. Relative humidity increased before the rains arrived, creating conditions in soil that allowed for the growth of microorganisms. During the course of the study, the relative abundances of most bacterial phyla showed little variation, though some bacterial populations responded immediately to an increase in soil moisture once the monsoon rains arrived. The Firmicutes phylum experienced over a sixfold increase in relative abundance with increasing water availability. Conversely, Actinobacteria, the dominant taxa at our site, were negatively affected by the increase in water availability. No relationship was found between bacterial diversity and soil water potential. Bacterial community structure was unrelated to all environmental variables that we measured, with the exception of a significant relationship with atmospheric relative humidity. Relative abundances of fungal phyla fluctuated more throughout the season than bacterial abundances did. Variation in fungal community structure was unrelated to soil water potential and to most environmental variables. However, ordination analysis showed a distinct fungal community structure late in the season, probably due to plant senescence.

  2. Detection and Composition of Bacterial Communities in Waters using RNA-based Methods

    EPA Science Inventory

    In recent years, microbial water quality assessments have shifted from solely relying on pure culture-based methods to monitoring bacterial groups of interest using molecular assays such as PCR and qPCR. Furthermore, coupling next generation sequencing technologies with ribosomal...

  3. Detection and Composition of Bacterial Communities in Waters using RNA-based Methods

    EPA Science Inventory

    In recent years, microbial water quality assessments have shifted from solely relying on pure culture-based methods to monitoring bacterial groups of interest using molecular assays such as PCR and qPCR. Furthermore, coupling next generation sequencing technologies with ribosomal...

  4. A longitudinal assessment of changes in bacterial community composition associated with the development of periodontal disease in dogs.

    PubMed

    Wallis, Corrin; Marshall, Mark; Colyer, Alison; O'Flynn, Ciaran; Deusch, Oliver; Harris, Stephen

    2015-12-31

    Periodontal disease is the most widespread oral disease in dogs. Whilst the involvement of bacteria in the aetiology of periodontitis is well established the role of individual species and their complex interactions with the host is not well understood. The objective of this research was therefore to perform a longitudinal study in dogs to identify the changes that occur in subgingival bacterial communities during the transition from mild gingivitis to the early stages of periodontitis (<25% attachment loss). Subgingival plaque samples were collected from individual teeth of 52 miniature schnauzer dogs every six weeks for up to 60 weeks. The microbial composition of plaque samples was determined using 454-pyrosequencing of the 16S rDNA. A group of aerobic Gram negative species, including Bergeyella zoohelcum COT-186, Moraxella sp. COT-017, Pasteurellaceae sp. COT-080, and Neisseria shayeganii COT-090 decreased in proportion as teeth progressed to mild periodontitis. In contrast, there was less evidence that increases in the proportion of individual species were associated with the onset of periodontitis, although a number of species (particularly members of the Firmicutes) became more abundant as gingivitis severity increased. There were small increases in Shannon diversity, suggesting that plaque community membership remains relatively stable but that bacterial proportions change during progression into periodontitis. This is the first study to demonstrate the temporal dynamics of the canine oral microbiota; it showed that periodontitis results from a microbial succession predominantly characterised by a reduction of previously abundant, health associated taxa. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  5. The Effect of Lactobacillus isolates on growth performance, immune response, intestinal bacterial community composition of growing Rex Rabbits.

    PubMed

    Wang, C; Zhu, Y; Li, F; Huang, L

    2017-10-01

    The objective of this experiment was to investigate the effect of Lactobacillus isolates on intestinal bacterial community composition of growing Rex Rabbits. A total of 120 weaned Rex Rabbits (30 days old, 30 per group) were used for the experiment, which started after an adaptation period of 7 days. The control group was fed with basal diet only, while the treatment I, II and III groups were fed with basal diet adding antibiotics, Lactobacillus zeae (LB1) and Lactobacillus casei (L3) respectively. Growth performance, immune response and intestinal flora have been examined. The results obtained were as follows: (i) F/G of the rabbits fed with Lactobacillus isolates was significantly lower than that of the control group (p < 0.05). (ii) The concentration of ALT decreased significantly (p < 0.05) and that of IgG and IgM increased significantly (p < 0.05) after feeding rabbits with Lactobacillus isolates. (iii) Lactobacillus isolates had no influence on the number of mast cells in duodenum and jejunum, but increased the number of mast cells in caecum significantly (p < 0.05). (iv) The data from pyrosequencing-based analysis suggested that the bacterial community in the rabbit's intestinal flora can be changed by Lactobacillus isolates and antibiotics, especially for the microbial diversity and abundance in the caecum. In conclusion, the application of proper Lactobacillus isolates can improve the growth performance, enhance the immunological function and adjust the intestinal micro-ecosystem of growing Rex Rabbits. Journal of Animal Physiology and Animal Nutrition © 2017 Blackwell Verlag GmbH.

  6. Does the aboveground herbivore assemblage influence soil bacterial community composition and richness in subalpine grasslands?

    Treesearch

    Melanie Hodel; Martin Schütz; Martijn L. Vandegehuchte; Beat Frey; Matthias Albrecht; Matt D. Busse; Anita C. Risch

    2014-01-01

    Grassland ecosystems support large communities of aboveground herbivores that can alter ecosystem processes. Thus, grazing by herbivores can directly and indirectly affect belowground properties such as the microbial community structure and diversity. Even though multiple species of functionally different herbivores coexist in grassland ecosystems, most studies have...

  7. Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms

    EPA Science Inventory

    Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for select...

  8. Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

    PubMed Central

    Terrat, Sebastien; Plassart, Pierre; Bourgeois, Emilie; Ferreira, Stéphanie; Dequiedt, Samuel; Adele-Dit-De-Renseville, Nathalie; Lemanceau, Philippe; Bispo, Antonio; Chabbi, Abad; Maron, Pierre-Alain; Ranjard, Lionel

    2015-01-01

    This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard. PMID:25195809

  9. Fine-scale transition to lower bacterial diversity and altered community composition precedes shell disease in laboratory-reared juvenile American lobster.

    PubMed

    Feinman, Sarah G; Unzueta Martínez, Andrea; Bowen, Jennifer L; Tlusty, Michael F

    2017-03-30

    The American lobster Homarus americanus supports a valuable commercial fishery in the Northeastern USA and Maritime Canada; however, stocks in the southern portion of the lobster's range have shown declines, in part due to the emergence of shell disease. Epizootic shell disease is a bacterially induced cuticular erosion that renders even mildly affected lobsters unmarketable because of their appearance, and in more severe cases can cause mortality. Despite the importance of this disease, the associated bacterial communities have not yet been fully characterized. We sampled 2 yr old, laboratory-reared lobsters that displayed signs of shell disease at the site of disease as well as at 0.5, 1, and 1.5 cm away from the site of disease to determine how the bacterial community changed over this fine spatial scale. Illumina sequencing of the 16S rRNA gene revealed a distinct bacterial community at the site of disease, with significant reductions in bacterial diversity and richness compared to more distant sampling locations. The bacterial community composition 0.5 cm from the site of disease was also altered, and there was an observable decrease in bacterial diversity and richness, even though there were no signs of disease at that location. Given the distinctiveness of the bacterial community at the site of disease and 0.5 cm from the site of disease, we refer to these communities as affected and transitionary, and suggest that these bacteria, including the previously proposed causative agent, Aquimarina 'homaria', are important for the initiation and progression of this laboratory model of shell disease.

  10. Influence of seasonality, air mass origin and particulate matter chemical composition on airborne bacterial community structure in the Po Valley, Italy.

    PubMed

    Innocente, Elena; Squizzato, Stefania; Visin, Flavia; Facca, Chiara; Rampazzo, Giancarlo; Bertolini, Valentina; Gandolfi, Isabella; Franzetti, Andrea; Ambrosini, Roberto; Bestetti, Giuseppina

    2017-03-28

    The integration of chemical and biological data in aerosol studies represents a new challenge in atmospheric science. In this perspective it will be possible to gain a clearer and deeper comprehension of biogeochemical cycles in the atmosphere. In this view, this study aimed to investigate the relationships occurring between bacterial populations and PM chemical composition in one of the most polluted and urbanized areas in Europe: the Po Valley (Italy). Moreover, seasonality, long- and short-range transports were also evaluated to investigate the influence on airborne bacterial communities. PM samples were collected in two cities of the Po Valley (Milan and Venice) characterized by different meteorological conditions and atmospheric pollutant sources. Samples were analysed for water-soluble inorganic ions (WSIIs) and bacterial community structure. Chemical and biological data were jointly processed by using redundancy discriminate analysis (RDA), while the influence of atmospheric circulation was evaluated by using wind ground data and back-trajectories analysis. Results showed strong seasonal shifts of bacterial community structure in both cities, while a different behaviour was observed for air mass circulation at Milan ad Venice sites: long-range transport significantly affected bacterial populations in Milan whereas local ground wind had more influence in the Venice area. Moreover, difference in taxonomic composition can be mostly addressed to the characteristics of sampling sites. This evidence could suggest that, while PM composition is influenced by long-range transport, bacterial populations are affected, besides transport, by other factors (i.e., season and sampling site location). This perspective allow to better understand and explain airborne bacterial community behaviour.

  11. Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing

    PubMed Central

    Li, Xiaohong; Duan, Jizhou; Xiao, Hui; Li, Yongqian; Liu, Haixia; Guan, Fang; Zhai, Xiaofan

    2017-01-01

    Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student’s t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student’s t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance

  12. Experimental manipulation of sponge/bacterial symbiont community composition with antibiotics: sponge cell aggregates as a unique tool to study animal/microorganism symbiosis.

    PubMed

    Richardson, Crystal; Hill, Malcolm; Marks, Carolyn; Runyen-Janecky, Laura; Hill, April

    2012-08-01

    Marine sponges can harbor dense and diverse bacterial communities, yet we have a limited understanding of important aspects of this symbiosis. We developed an experimental methodology that permits manipulating the composition of the microbial community. Specifically, we evaluated sponge cell aggregates (SCA) from Clathria prolifera that had been treated with different classes of antibiotics to determine whether this system might offer novel experimental approaches to the study of sponge/bacterial symbioses. Microscopic analysis of the SCA demonstrated that two distinct morphological types of microbiota existed on the external surface vs. the internal regions of the SCA. Denaturing gradient gel electrophoresis and sequence analysis of 16S rRNA gene clone libraries indicated that we were unable to create entirely aposymbiotic SCA but that different classes of antibiotics produced distinctive shifts in the SCA-associated bacterial community. After exposure to antibiotics, some bacterial species were 'revealed', thus uncovering novel components of the sponge-associated community. The antibiotic treatments used here had little discernible effect on the formation of SCA or subsequent development of the adult. The experimental approach we describe offers empirical options for studying the role symbionts play in sponge growth and development and for ascertaining relationships among bacterial species in communities residing in sponges.

  13. Acute Effects of TiO2 Nanomaterials on the Viability and Taxonomic Composition of Aquatic Bacterial Communities Assessed via High-Throughput Screening and Next Generation Sequencing

    PubMed Central

    Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-François; Gray, Kimberly A.; Kelly, John J.

    2014-01-01

    The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally

  14. Acute effects of TiO2 nanomaterials on the viability and taxonomic composition of aquatic bacterial communities assessed via high-throughput screening and next generation sequencing.

    PubMed

    Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-François; Gray, Kimberly A; Kelly, John J

    2014-01-01

    The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally

  15. Forest floor bacterial community composition and catabolic profiles in relation to landscape features in Québec's southern boreal forest.

    PubMed

    Lamarche, Josyanne; Bradley, Robert L; Hooper, Elaine; Shipley, Bill; Simao Beaunoir, Anne-Marie; Beaulieu, Carole

    2007-07-01

    Bacterial communities mediate many of the processes in boreal forest floors that determine the functioning of these ecosystems, yet it remains uncertain whether the composition of these communities is distributed nonrandomly across the landscape. In a study performed in the southern boreal mixed wood forest of Québec, Canada, we tested the hypothesis that stand type (spruce/fir, aspen, paper birch), stand age (57, 78-85, and 131 years old), and geologic parent material (clay and till) were correlated with forest floor bacterial community composition. Forest floors in 54 independent forest stands were sampled to comprise a full factorial array of the three predictor variables. Bacterial community structure was examined by terminal restriction fragment (T-RF) length polymorphism analysis of genes encoding for 16S rRNA. Distance-based redundancy analysis of T-RF assemblages revealed that each predictor variable, as well as their interaction terms, had a significant effect on bacterial community composition, geologic parent material being the most discriminating factor. A survey of the 15 T-RFs with the highest percentage fit on the first two ordination axes describing the main effects indicated that each landscape feature correlated to a distinct group of bacteria. A survey of the most discriminant T-RFs describing the effect of stand type within each combination of stand age and geologic parent material indicated a strong dependency of several T-RFs on geologic parent material. Given the possible link between bacterial community composition and forest floor functioning, we also assessed the effects of the same three landscape features on community-level catabolic profiles (CLCP) of the extractable forest floor microbiota. Geologic parent material and stand type had significant effects on CLCPs. On clay plots, the effects of landscape features on T-RF patterns were highly consistent with their effects on CLCPs. In light of our results, we suggest that future research

  16. Increasing addition of autochthonous to allochthonous carbon in nutrient-rich aquatic systems stimulates carbon consumption but does not alter bacterial community composition

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    Dissolved organic carbon (DOC) concentrations - mainly of terrestrial origin - are increasing worldwide in inland waters. The biodegradability of the DOC varies depending on quantity and chemical quality. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. It is therefore crucial to understand the processes controlling the bacterial turnover of additional allochthonous and autochthonous DOC in aquatic systems. 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 (algae lysate). We then determined bacterial carbon consumption, activities, and community composition together with the carbon flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and fractions of low and high molecular weight substances (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. In parallel to these differences in chemical composition, we observed a higher availability of allochthonous C as evidenced by increased DOC consumption and bacterial growth efficiencies (BGE) when solely allochthonous C was provided. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption from 52 to 68% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substances (HS) fraction and an increase in bacterial biomass. Stable C isotope analyses of phospholipid fatty acids (PLFA) and respired dissolved inorganic carbon (DIC) supported a preferential assimilation of autochthonous C and respiration of the

  17. 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

  18. Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors.

    PubMed

    Szabó, Enikö; Liébana, Raquel; Hermansson, Malte; Modin, Oskar; Persson, Frank; Wilén, Britt-Marie

    2017-09-05

    Granulation of activated sludge is an increasingly important area within the field of wastewater treatment. Granulation is usually achieved by high hydraulic selection pressure, which results in the wash-out of slow settling particles. The effect of the harsh wash-out conditions on the granular sludge ecosystem is not yet fully understood, but different bacterial groups may be affected to varying degrees. In this study, we used high-throughput amplicon sequencing to follow the community composition in granular sludge reactors for 12 weeks, both in the granular phase and the suspended phase (effluent). The microbiome of the washed out biomass was similar but not identical to the microbiome of the granular biomass. Certain taxa (e.g. Flavobacterium spp. and Bdellovibrio spp.) had significantly (p < 0.05) higher relative abundance in the granules compared to the effluent. Fluorescence in situ hybridization images indicated that these taxa were mainly located in the interior of granules and therefore protected from erosion. Other taxa (e.g. Meganema sp. and Zooglea sp.) had significantly lower relative abundance in the granules compared to the effluent, and appeared to be mainly located on the surface of granules and therefore subject to erosion. Despite being washed out, these taxa were among the most abundant members of the granular sludge communities and were likely growing fast in the reactors. The ratio between relative abundance in the granular biomass and in the effluent did not predict temporal variation of the taxa in the reactors, but it did appear to predict the spatial location of the taxa in the granules.

  19. Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades.

    PubMed

    Chauhan, Ashvini; Pathak, Ashish; Ogram, Andrew

    2012-10-01

    Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.

  20. Plant community richness and microbial interactions structure bacterial communities in soil.

    PubMed

    Schlatter, Daniel C; Bakker, Matthew G; Bradeen, James M; Kinkel, Linda L

    2015-01-01

    Plant species, plant community diversity and microbial interactions can significantly impact soil microbial communities, yet there are few data on the interactive effects of plant species and plant community diversity on soil bacterial communities. We hypothesized that plant species and plant community diversity affect soil bacterial communities by setting the context in which bacterial interactions occur. Specifically, we examined soil bacterial community composition and diversity in relation to plant "host" species, plant community richness, bacterial antagonists, and soil edaphic characteristics. Soil bacterial communities associated with four different prairie plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, and' Lupinus perennis) grown in plant communities of increasing species richness (1, 4, 8, and 16 species) were sequenced. Additionally, soils were evaluated for populations of antagonistic bacteria and edaphic characteristics. Plant species effects on soil bacterial community composition were small and depended on plant community richness. In contrast, increasing plant community richness significantly altered soil bacterial community composition and was negatively correlated with bacterial diversity. Concentrations of soil carbon, organic matter, nitrogen, phosphorus, and potassium were similarly negatively correlated with bacterial diversity, whereas the proportion of antagonistic bacteria was positively correlated with soil bacterial diversity. Results suggest that plant species influences on soil bacterial communities depend on plant community diversity and are mediated through the effects of plant-derived resources on antagonistic soil microbes.

  1. Pyrosequencing and mid-infrared spectroscopy techniques reveal distinct aggregate stratification of soil bacterial communities and organic matter composition

    USDA-ARS?s Scientific Manuscript database

    This study integrated physical, chemical, and molecular techniques to assess relationships between soil bacterial community structures and the quantity and quality of soil organic carbon (SOC) at the soil microenvironment scale (e.g., within different aggregate size-fractions). To accomplish this g...

  2. Aggregate stratification assessment of soil bacterial communities and organic matter composition: Coupling pyrosequencing and mid-infrared spectroscopy techniques

    USDA-ARS?s Scientific Manuscript database

    This study integrated physical, chemical, and molecular techniques to assess relationships between soil bacterial communities and the quantity and quality of soil organic carbon (SOC) at the soil microenvironment scale (e.g., within different aggregate size-fractions). To accomplish this goal soil ...

  3. Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say) (Coloptera) colonizing red pine

    Treesearch

    Italo Jr. Delalibera; Archana Vasanthakumar; Benjamin J. Burwitz; Patrick D. Schloss; Kier D. Klepzig; Jo Handelsman; Kenneth F. Raffa

    2007-01-01

    The gut bacterial community of a bark beetle, the pine engraver Ips pini (Say), was characterized using culture-dependent and culture-independent methods. Bacteria from individual guts of larvae, pupae and adults were cultured and DNA was extracted from samples of pooled larval guts. Analysis of 16S rRNA gene sequences amplified directly from the gut...

  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. Start-up and bacterial community compositions of partial nitrification in moving bed biofilm reactor.

    PubMed

    Liu, Tao; Mao, Yan-Jun; Shi, Yan-Ping; Quan, Xie

    2017-03-01

    Partial nitrification (PN) has been considered as one of the promising processes for pretreatment of ammonium-rich wastewater. In this study, a kind of novel carriers with enhanced hydrophilicity and electrophilicity was implemented in a moving bed biofilm reactor (MBBR) to start up PN process. Results indicated that biofilm formation rate was higher on modified carriers. In comparison with the reactor filled with traditional carriers (start-up period of 21 days), it took only 14 days to start up PN successfully with ammonia removal efficiency and nitrite accumulation rate of 90 and 91%, respectively, in the reactor filled with modified carriers. Evident changes of spatial distributions and community structures had been detected during the start-up. Free-floating cells existed in planktonic sludge, while these microorganisms trended to form flocs in the biofilm. High-throughput pyrosequencing results indicated that Nitrosomonas was the predominant ammonia-oxidizing bacterium (AOB) in the PN system, while Comamonas might also play a vital role for nitrogen oxidation. Additionally, some other bacteria such as Ferruginibacter, Ottowia, Saprospiraceae, and Rhizobacter were selected to establish stable footholds. This study would be potentially significant for better understanding the microbial features and developing efficient strategies accordingly for MBBR-based PN operation.

  6. Effect of sulfate on the transformation of corrosion scale composition and bacterial community in cast iron water distribution pipes

    EPA Science Inventory

    The stability of iron corrosion products and the bacterial composition of biofilm in drinking water distribution systems (DWDS) could have great impact on the water safety at the consumer ends. In this work, pipe loops were setup to investigate the transformation characteristics ...

  7. Effect of sulfate on the transformation of corrosion scale composition and bacterial community in cast iron water distribution pipes

    EPA Science Inventory

    The stability of iron corrosion products and the bacterial composition of biofilm in drinking water distribution systems (DWDS) could have great impact on the water safety at the consumer ends. In this work, pipe loops were setup to investigate the transformation characteristics ...

  8. Bacterial and fungal taxon changes in soil microbial community composition induced by short-term biochar amendment in red oxidized loam soil.

    PubMed

    Hu, Liao; Cao, Lixiang; Zhang, Renduo

    2014-03-01

    To take full advantage of biochar as a soil amendment, the objective of this study was to investigate the effects of biochar addition on soil bacterial and fungal diversity and community composition. Incubation experiments with a forest soil (a red oxidized loam soil) with and without biochar amendment were conducted for 96 days. The culture-independent molecular method was utilized to analyze soil bacterial and fungal species after the incubation experiments. Results showed that bacteria and fungi responded differently to the biochar addition during the short-term soil incubation. Twenty four and 18 bacterial genara were observed in the biochar amended and unamended soils, respectively, whereas 11 and 8 fungal genera were observed in the biochar amended and unamended soils, respectively. Microbial taxa analysis indicated that the biochar amendment resulted in significant shifts in both bacterial and fungal taxa during the incubation period. The shift for bacteria occurred at the genus and phylum levels, while for fungi only at the genus level. Specific taxa, such as Actinobacteria of bacteria and Trichoderma and Paecilomyces of fungi, were enriched in the biochar amended soil. The results reveal a pronounced impact of biochar on soil microbial community composition and an enrichment of key bacterial and fungal taxa in the soil during the short time period.

  9. Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine

    PubMed Central

    Cousteix, Elodie; Xu, Yong; Munns, Krysty; Selinger, Lorna J.; Barbieri, Rutn; Alexander, Trevor; McAllister, Tim A.; Selinger, L. Brent

    2017-01-01

    Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting > 104 E. coli O157:H7 CFU g-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders. PMID:28141846

  10. Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine.

    PubMed

    Zaheer, Rahat; Dugat-Bony, Eric; Holman, Devon; Cousteix, Elodie; Xu, Yong; Munns, Krysty; Selinger, Lorna J; Barbieri, Rutn; Alexander, Trevor; McAllister, Tim A; Selinger, L Brent

    2017-01-01

    Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting > 104 E. coli O157:H7 CFU g-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders.

  11. Differential composition of bacterial communities as influenced by phenanthrene and dibenzo[a,h]anthracene in the rhizosphere of ryegrass (Lolium perenne L.).

    PubMed

    Corgié, S C; Beguiristain, T; Leyval, C

    2006-12-01

    Bioremediation technologies of Polycyclic Aromatic Hydrocarbons (PAH) are often limited by the recalcitrance to biodegradation of high molecular weight (HMW) PAH. Rhizosphere is known to increase the biodegradation of PAH but little is known about the biodegradability of these HMW compounds by rhizosphere bacteria. This study compared the effects of a 3 and a 5-ring PAH, phenanthrene (PHE) and dibenzo[a,h]anthracene (dBA) respectively, on the composition of bacterial community, the bacterial density and the biodegradation activity. Compartmentalized devices were designed to harvest three consecutive sections of the rhizosphere. Rhizosphere and non-rhizosphere compartments were filled with PHE or dBA spiked or unspiked sand and inoculated with a soil bacterial inoculum. Different bacterial communities and degradation values were found 5 weeks after spiking with PHE (41-76% biodegradation) and dBA (12-51% biodegradation). In sections closer to the root surface, bacterial populations differed as a function of the distance to roots and the PAH added, whereas in further rhizosphere sections, communities were closer to those of the non-planted treatments. Biodegradation of PHE was also a function of the distance to roots, and decreased from 76 to 42% within 9 mm from the roots. However, biodegradation of dBA was significantly higher in the middle section (3-6 mm from roots) than the others. Rhizosphere degradation of PAH varies with the nature of the PAH, and C fluxes from roots could limit the degradation of dBA.

  12. 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

  13. Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

    PubMed Central

    Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

    2006-01-01

    Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS

  14. Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting.

    PubMed

    Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G

    2006-03-01

    Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS

  15. Does urbanization shape bacterial community composition in urban park soils? A case study in 16 representative Chinese cities based on the pyrosequencing method.

    PubMed

    Xu, Hui-Juan; Li, Shun; Su, Jian-Qiang; Nie, San'an; Gibson, Valerie; Li, Hu; Zhu, Yong-Guan

    2014-01-01

    Although the geographical distribution patterns of microbes have been studied for years, few studies have focused on urban soils. Urbanization may have detrimental effects on the soil ecosystem through pollution discharge and changes in urban climate. It is unclear whether urbanization-related factors have any effect on soil bacterial communities. Therefore we investigated geographical patterns of soil microbial communities in parks in 16 representative Chinese cities. The microbial communities in these 95 soil samples were revealed by 454-pyrosequencing. There were 574,442 effective sequences among the total of 980,019 16S rRNA gene sequences generated, showing the diversity of the microbial communities. Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Chloroflexi and Bacteroidetes were found to be the six dominant phyla in all samples. Canonical correspondence analysis showed that pH, followed by annual average precipitation, annual average temperature, annual average relative humidity and city sunshine hours, Mn and Mg were the factors most highly correlated with the bacterial community variance. Urbanization did have an effect on bacterial community composition of urban park soils but it contributed less to the total variance compared with geographical locations and soil properties, which explained 6.19% and 16.78% of the variance, respectively.

  16. Laboratory silo type and inoculation effects on nutritional composition, fermentation, and bacterial and fungal communities of oat silage.

    PubMed

    Romero, J J; Zhao, Y; Balseca-Paredes, M A; Tiezzi, F; Gutierrez-Rodriguez, E; Castillo, M S

    2017-03-01

    The objectives were to evaluate (1) the use of 2 types of experimental silos (S) to characterize whole-crop oat (Avena sativa L.) silage with or without addition of an inoculant (I), and (2) the effect of inoculation on the microbial community structure of oats ensiled using only plastic bucket silos (BKT). From each of 6 sections in a field, oats were harvested, treated (INO) or not (CON) with inoculant, packed into 19-L BKT or vacuum bags (BG), and ensiled for 217 d. The inoculant added contained Lactobacillus buchneri and Pediococcus pentosaceus (4 × 10(5) and 1 × 10(5) cfu/g of fresh oats, respectively). The experimental design was a complete randomized design replicated 6 times. Treatment design was the factorial combination of 2 S × 2 I. Some differences existed between BG versus BKT at silo opening (217 d), including a decreased CP (7.73 vs. 7.04 ± 0.247% of DM) and ethanol (1.93 vs. 1.55 ± 0.155) and increased lactic acid (4.28 vs. 3.65 ± 0.241), respectively. Also, WSC and mold counts were reduced in BG versus BKT for CON (1.78 vs. 2.70 ± 0.162% of DM and 0.8 vs. 2.82 ± 0.409 log cfu/fresh g) but not for INO (∼1.53 and 1.55), respectively. Application of INO increased DM recovery (96.1 vs. 92.9 ± 0.63%), aerobic stability (565 vs. 133 ± 29.2 h), acetic acid (2.38 vs. 1.22 ± 0.116% of DM), and reduced NDF (65.0 vs. 67.0 ± 0.57), ADF (36.7 vs. 38.1 ± 0.60), ethanol (0.63 vs. 2.85 ± 0.155), and yeast counts (1.10 vs. 4.13 ± 0.484 log cfu/fresh g) in INO versus CON, respectively. At d 0, no differences were found for S and I on the nutritional composition and background microbial counts. Leuconostocaceae (82.9 ± 4.27%) and Enterobacteriaceae (15.2 ± 3.52) were the predominant bacterial families and unidentified sequences were predominant for fungi. A higher relative abundance of the Davidiellaceae fungal family (34.3 vs. 19.6 ± 4.47) was observed in INO versus CON. At opening (217 d), INO had a lower relative abundance of Leuconostocaceae

  17. Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

    USGS Publications Warehouse

    McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

    2017-01-01

    Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

  18. Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues

    PubMed Central

    Ng, Jenny C. Y.; Chan, Yuki; Tun, Hein M.; Leung, Frederick C. C.; Shin, Paul K. S.; Chiu, Jill M. Y.

    2015-01-01

    Corals are rapidly declining globally due to coral diseases. Skeletal growth anomalies (SGA) or “coral tumors” are a group of coral diseases that affect coral reefs worldwide, including Hong Kong waters in the Indo-Pacific region. To better understand how bacterial communities may vary in corals with SGA, for the first time, we examined the bacterial composition associated with the apparently healthy and the diseased tissues of SGA-affected Platgyra carnosus using 16S ribosomal rRNA gene pyrosequencing. Taxonomic analysis revealed Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria as the main phyla in both the apparently healthy and the diseased tissues. A significant difference in the bacterial community composition was observed between the two conditions at the OTU level. Diseased tissues were associated with higher abundances of Acidobacteria and Gemmatimonadetes, and a lower abundance of Spirochaetes. Several OTUs belonging to Rhodobacteraceae, Rhizobiales, Gammaproteobacteria, and Cytophaga-Flavobacterium-Bacteroidetes (CFB) were strongly associated with the diseased tissues. These groups of bacteria may contain potential pathogens involved with the development of SGA or opportunistic secondary or tertiary colonizers that proliferated upon the health-compromised coral host. We suggest that these bacterial groups to be further studied based on inoculation experiments and testing of Koch's postulates in efforts to understand the etiology and progression of SGA. PMID:26539174

  19. Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues.

    PubMed

    Ng, Jenny C Y; Chan, Yuki; Tun, Hein M; Leung, Frederick C C; Shin, Paul K S; Chiu, Jill M Y

    2015-01-01

    Corals are rapidly declining globally due to coral diseases. Skeletal growth anomalies (SGA) or "coral tumors" are a group of coral diseases that affect coral reefs worldwide, including Hong Kong waters in the Indo-Pacific region. To better understand how bacterial communities may vary in corals with SGA, for the first time, we examined the bacterial composition associated with the apparently healthy and the diseased tissues of SGA-affected Platgyra carnosus using 16S ribosomal rRNA gene pyrosequencing. Taxonomic analysis revealed Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria as the main phyla in both the apparently healthy and the diseased tissues. A significant difference in the bacterial community composition was observed between the two conditions at the OTU level. Diseased tissues were associated with higher abundances of Acidobacteria and Gemmatimonadetes, and a lower abundance of Spirochaetes. Several OTUs belonging to Rhodobacteraceae, Rhizobiales, Gammaproteobacteria, and Cytophaga-Flavobacterium-Bacteroidetes (CFB) were strongly associated with the diseased tissues. These groups of bacteria may contain potential pathogens involved with the development of SGA or opportunistic secondary or tertiary colonizers that proliferated upon the health-compromised coral host. We suggest that these bacterial groups to be further studied based on inoculation experiments and testing of Koch's postulates in efforts to understand the etiology and progression of SGA.

  20. 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

  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. Effect of host tree species on cellulase activity and bacterial community composition in the gut of larval Asian longhorned beetle.

    PubMed

    Geib, Scott M; Jimenez-Gasco, Maria Del Mar; Carlson, John E; Tien, Ming; Hoover, Kelli

    2009-06-01

    Anoplophora glabripennis, the Asian longhorned beetle, is a wood-boring insect that can develop in a wide range of healthy deciduous hosts and requires gut microbes to aid in wood degradation and digestion. Here we show that larval A. glabripennis harbor a diverse gut bacterial community, and this community can be extremely variable when reared in different host trees. A. glabripennis reared in a preferred host (Acer saccharum) had the highest gut bacterial diversity compared with larvae reared either in a secondary host (Quercus palustris), a resistant host (Pyrus calleryana), or on artificial diet. The gut microbial community of larval A. glabripennis collected from field populations on Brooklyn, NY, showed the highest degree of complexity among all samples in this study. Overall, when larvae fed on a preferred host, they harbored a broad diversity of gut bacteria spanning the alpha-, beta-, gamma-Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Cellulase activities (beta-1,4-endoglucanase, beta-1,4-exoglucanase, and beta-1,4-glucosidase) in the guts of larvae fed in a preferred host (A. saccharum) or a secondary host (Q. palustris) were significantly higher than that of artificial diet fed larvae. Larvae that fed on wood from a resistant host (P. calleryana) showed suppressed total gut cellulase activity. Results show that the host tree can impact both gut microbial community complexity and cellulase activity in A. glabripennis.

  3. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia.

    PubMed

    de Voogd, Nicole J; Cleary, Daniel F R; Polónia, Ana R M; Gomes, Newton C M

    2015-04-01

    In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.

  4. Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis.

    PubMed

    Wu, Lan; Ge, Gang; Zhu, Guofeng; Gong, Shijie; Li, Siguang; Wan, Jinbao

    2012-01-01

    Poyang Lake is the largest fresh water lake in China. In this study, the objective was to examine the diversity of bacterial community in this environment. The phylogenetic composition of bacterioplankton communities from two sites and two dates (northern and southern sub-basins in October 2006 and in May 2007, respectively) in the water column of Poyang Lake were investigated by partially sequencing cloned 16SrRNA genes. Moreover, restriction fragment length polymorphism (RFLP) was applied in the 16SrRNA gene clones. In total, four clone libraries were constructed and 347 clones were screened by RFLP, yielding 153 operational taxonomic units, which mainly belonged to the proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia and Planctomycetes. Our results showed that Beta-proteobacteria was the most significant lineage, with dominant numbers of operational taxonomic units in the northern October 2006, southern October 2006 and May 2007 libraries. The highest bacterial diversity occurred in the library from the southern sub-basin in May 2007 and the lowest in the library from the northern sub-basin in May 2007. Horizontal and temporal differences associated with the concentration of total phosphorus, water temperature and pH suggested that the trophic state and the physicochemical properties of lake play key roles in sustaining bacterial community composition structure.

  5. Composition, richness and nonrandom assembly of culturable bacterial-microfungal communities in floral nectar of Mediterranean plants.

    PubMed

    Alvarez-Pérez, Sergio; Herrera, Carlos M

    2013-03-01

    The recent upsurge of interest in the role of floral nectar as a habitat for microorganisms has led to some detailed analyses of nectarivorous yeasts. In contrast, very little is known on the occurrence and diversity of nectar-dwelling bacteria, and bacterial-fungal interactions within nectar remain unexplored. In this work, we studied both the culturable bacteria and microfungi found in the floral nectar of wild Mediterranean plants. In general, bacteria and yeasts were found coexisting in nectar more often than would be expected by chance, and such positive association persisted after accounting for phylogenetic nonindependence of the plant species surveyed. Metschnikowia species were confirmed as the main fungal components of nectar communities, and Acinetobacter was identified as the main bacterial taxa. Finally, individual Operational Taxonomic Units (OTUs) were found to co-occur less frequently than predicted by random expectations. There existed, however, some pairwise associations between OTUs that seemed to account for the general pattern of positive bacteria-yeasts coexistence. We conclude that the culturable communities of nectar microorganisms associated with wild Mediterranean plants are nonrandom assemblages of bacterial and yeast species. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  6. Structure and composition of bacterial and fungal community in soil under soybean monoculture in the Brazilian Cerrado

    PubMed Central

    Bresolin, J.D; Bustamante, M.M.C; Krüger, R.H; Silva, M.R.S.S; Perez, K.S

    2010-01-01

    Soybean is the most important oilseed cultivated in the world and Brazil is the second major producer. Expansion of soybean cultivation has direct and indirect impacts on natural habitats of high conservation value, such as the Brazilian savannas (Cerrado). In addition to deforestation, land conversion includes the use of fertilizers and pesticides and can lead to changes in the soil microbial communities. This study evaluated the soil bacterial and fungal communities and the microbial biomass C in a native Cerrado and in a similar no-tillage soybean monoculture area using PCR-DGGE and sequencing of bands. Compared to the native area, microbial biomass C was lower in the soybean area and cluster analysis indicated that the structure of soil microbial communities differed. 16S and 18S rDNA dendrograms analysis did not show differences between row and inter-row samples, but microbial biomass C values were higher in inter-rows during soybean fructification and harvest. The study pointed to different responses and alterations in bacterial and fungal communities due to soil cover changes (fallow x growth period) and crop development. These changes might be related to differences in the pattern of root exudates affecting the soil microbial community. Among the bands chosen for sequencing there was a predominance of actinobacteria, γ-proteobacteria and ascomycetous divisions. Even under no-tillage management methods, the soil microbial community was affected due to changes in the soil cover and crop development, hence warning of the impacts caused by changes in land use. PMID:24031510

  7. Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals.

    PubMed

    Szekeres, Edina; Baricz, Andreea; Chiriac, Cecilia Maria; Farkas, Anca; Opris, Ocsana; Soran, Maria-Loredana; Andrei, Adrian-Stefan; Rudi, Knut; Balcázar, Jose Luis; Dragos, Nicolae; Coman, Cristian

    2017-06-01

    Antimicrobial resistance represents a growing and significant public health threat, which requires a global response to develop effective strategies and mitigate the emergence and spread of this phenomenon in clinical and environmental settings. We investigated, therefore, the occurrence and abundance of several antibiotics and antibiotic resistance genes (ARGs), as well as bacterial community composition in wastewater effluents from different hospitals located in the Cluj County, Romania. Antibiotic concentrations ranged between 3.67 and 53.05 μg L(-1), and the most abundant antibiotic classes were β-lactams, glycopeptides, and trimethoprim. Among the ARGs detected, 14 genes confer resistance to β-lactams, aminoglycosides, chloramphenicol, macrolide-lincosamide-streptogramin B (MLSB) antibiotics, sulfonamides, and tetracyclines. Genes encoding quaternary ammonium resistance and a transposon-related element were also detected. The sulI and qacEΔ1 genes, which confer resistance to sulfonamides and quaternary ammonium, had the highest relative abundance with values ranging from 5.33 × 10(-2) to 1.94 × 10(-1) and 1.94 × 10(-2) to 4.89 × 10(-2) copies/16 rRNA gene copies, respectively. The dominant phyla detected in the hospital wastewater samples were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Among selected hospitals, one of them applied an activated sludge and chlorine disinfection process before releasing the effluent to the municipal collector. This conventional wastewater treatment showed moderate removal efficiency of the studied pollutants, with a 55-81% decrease in antibiotic concentrations, 1-3 order of magnitude lower relative abundance of ARGs, but with a slight increase of some potentially pathogenic bacteria. Given this, hospital wastewaters (raw or treated) may contribute to the spread of these emerging pollutants in the receiving environments. To the best of our knowledge, this study quantified for the first time

  8. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

    DOE PAGES

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; ...

    2014-10-07

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean ismore » the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.« less

  9. Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean

    PubMed Central

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.

    2014-01-01

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea. PMID:25289937

  10. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean.

    PubMed

    Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Gray, Michael A; Andersen, Gary L

    2014-01-01

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.

  11. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

    USGS Publications Warehouse

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.

    2014-01-01

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.

  12. The effects of antibiotic cocktails at environmentally relevant concentrations on the community composition and acetate biodegradation kinetics of bacterial biofilms.

    PubMed

    Wunder, David B; Tan, David T; LaPara, Timothy M; Hozalski, Raymond M

    2013-02-01

    Antibiotics and antibacterials are present in water bodies worldwide but little is known about their effects on the biological processes often used to treat water. In this research, the effect of antibiotics on bacterial activity and community structure was investigated by growing biofilms in the presence and absence of a mixture of three compounds (sulfamethoxazole, erythromycin, and ciprofloxacin) in a continuous-flow rotating annular bioreactor fed acetate as a carbon and energy source. Steady-state, surface area-normalized substrate utilization rates for all antibiotic treatments (all at 0.33 μg L(-1), all at 3.33 μg L(-1), and 1 at 3.33 μg L(-1) with the other 2 at 0.33 μg L(-1)) were similar to the control experiments. Higher attached biomass levels in the experiments with ciprofloxacin at 3.33 μg L(-1) resulted in lower steady-state biomass-normalized substrate utilization rates in comparison to other runs. Microbial community analyses via automated ribosomal intergenic spacer analysis revealed significant shifts in community structure for the experiments dosed with the highest concentrations of ciprofloxacin, suggesting that the antibiotic selected for more resistant bacterial strains. The results of this research also suggest that mixtures of antibiotics at the sub-μg L(-1) concentrations typically observed in surface waters are unlikely to affect biological process performance, at least in terms of the degradation of easily assimilable compounds. Conversely, changes to community structure and biofilm quantity might be expected with ciprofloxacin at μg L(-1) concentrations. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters.

    PubMed

    Borsodi, Andrea K; Szirányi, Barbara; Krett, Gergely; Márialigeti, Károly; Janurik, Endre; Pekár, Ferenc

    2016-09-01

    Geothermal waters exploited in the southeastern region of Hungary are alkali-hydrogen-carbonate type, and beside the high amount of dissolved salt, they contain a variety of aromatic, heteroaromatic, and polyaromatic hydrocarbons. The majority of these geothermal waters used for heating are directed into surface waters following a temporary storage in reservoir lakes. The aim of this study was to gain information about the temporal and spatial changes of the water quality as well as the bacterial community composition of an alkaline and saline oxbow lake operated as reservoir of used geothermal water. On the basis of the water physical and chemical measurements as well as the denaturing gradient gel electrophoresis (DGGE) patterns of the bacterial communities, temporal changes were more pronounced than spatial differences. During the storage periods, the inflow, reservoir water, and sediment samples were characterized with different bacterial community structures in both studied years. The 16S ribosomal RNA (rRNA) gene sequences of the bacterial strains and molecular clones confirmed the differences among the studied habitats. Thermophilic bacteria were most abundant in the geothermal inflow, whereas the water of the reservoir was dominated by cyanobacteria and various anoxygenic phototrophic prokaryotes. In addition, members of several facultative anaerobic denitrifying, obligate anaerobic sulfate-reducing and syntrophic bacterial species capable of decomposition of different organic compounds including phenols were revealed from the water and sediment of the reservoir. Most of these alkaliphilic and/or halophilic species may participate in the local nitrogen and sulfur cycles and contribute to the bloom of phototrophs manifesting in a characteristic pink-reddish discoloration of the water of the reservoir.

  14. Forensic identification using skin bacterial communities.

    PubMed

    Fierer, Noah; Lauber, Christian L; Zhou, Nick; McDonald, Daniel; Costello, Elizabeth K; Knight, Rob

    2010-04-06

    Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object. Here we describe a series of studies de-monstrating the validity of this approach. We show that skin-associated bacteria can be readily recovered from surfaces (including single computer keys and computer mice) and that the structure of these communities can be used to differentiate objects handled by different individuals, even if those objects have been left untouched for up to 2 weeks at room temperature. Furthermore, we demonstrate that we can use a high-throughput pyrosequencing-based ap-proach to quantitatively compare the bacterial communities on objects and skin to match the object to the individual with a high degree of certainty. Although additional work is needed to further establish the utility of this approach, this series of studies introduces a forensics approach that could eventually be used to independently evaluate results obtained using more traditional forensic practices.

  15. Planktonic bacterial community composition of an extremely shallow soda pond during a phytoplankton bloom revealed by cultivation and molecular cloning.

    PubMed

    Borsodi, Andrea K; Knáb, Mónika; Czeibert, Katalin; Márialigeti, Károly; Vörös, Lajos; Somogyi, Boglárka

    2013-07-01

    Böddi-szék is one of the shallow soda ponds located in the Kiskunság National Park, Hungary. In June 2008, immediately prior to drying out, an extensive algal bloom dominated by a green alga (Oocystis submarina Lagerheim) was observed in the extremely saline and alkaline water of the pond. The aim of the present study was to reveal the phylogenetic diversity of the bacterial communities inhabiting the water of Böddi-szék during the blooming event. Using two different selective media, altogether 110 aerobic bacterial strains were cultivated. According to the sequence analysis of the 16S rRNA gene, most of the strains belonged to alkaliphilic or alkalitolerant and moderately halophilic species of the genera Bacillus and Gracilibacillus (Firmicutes), Algoriphagus and Aquiflexum (Bacteroidetes), Alkalimonas and Halomonas (Gammaproteobacteria). Other strains were closely related to alkaliphilic and phototrophic purple non-sulfur bacteria of the genera Erythrobacter and Rhodobaca (Alphaproteobacteria). Analysis of the 16S rRNA gene-based clone library indicated that most of the total of 157 clone sequences affiliated with the anoxic phototrophic bacterial genera of Rhodobaca and Rhodobacter (Alphaproteobacteria), Ectothiorhodospira (Gammaproteobacteria) and Heliorestis (Firmicutes). Phylotypes related to the phylum Bacteroidetes formed the second most abundant group. Clones related to the mainly anaerobic and alkaliphilic bacterial genera of Anoxynatronum (Firmicutes), Spirochaeta (Spirochaetes) and Desulfonatronum (Deltaproteobacteria) were also abundant. Further clone sequences showed less than 95 % similarity values to cultivated species of the phyla Actinobacteria, Cyanobacteria, Deinococcus-Thermus, Fibrobacteres, Gemmatimonadetes and Lentisphaerae.

  16. Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River.

    PubMed

    Suriya, Jayaraman; Chandra Shekar, Mootapally; Nathani, Neelam Mustakali; Suganya, Thangaiyan; Bharathiraja, Subramanian; Krishnan, Muthukalingan

    2017-01-01

    Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. Recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the Cauvery River has significantly increased the concentration of uranium (U) and other heavy metals. To perceive the impact of uranium on bacterial diversity in Cauvery River, sediment samples collected from polluted (UP) site with 32.4 Bq/K of U concentration and control (UNP) site were scrutinized for bacterial diversity through metagenomic analysis of the V3 region of 16S rDNA by Illumina sequencing. Taxonomic assignment revealed that the unpolluted sample was dominated by Bacteroidetes (27.7 %), and Firmicutes (25.9 %), while sediment sample from the highly polluted site revealed abundance of Proteobacteria (47.5 %) followed by Bacteroidetes (22.4 %) and Firmicutes (14.6 %). Among Proteobacteria, Gammaproteobacteria was the most prevalent group followed by alpha, delta, epsilon, and beta in the uranium-polluted sample. Rare and abundant species analysis revealed that species like Idiomarina loihiensis was abundant in the pollutant sample; however, it was rare (<0.1 %) in the sample from pristine environment. Similarly, the species distribution in both the samples varied, with the bacteria potentially active in redox activity and biosorption potential dominating in the polluted sample. Outcomes of the present study demonstrated the impact of uranium and metal accumulation on the bacterial communities and further confirmed the promising candidature of specific bacterial species as bioindicators of contamination.

  17. Community-acquired bacterial meningitis.

    PubMed

    van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G; Wijdicks, Eelco

    2016-11-03

    Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma (nosocomial bacterial meningitis). Despite advances in treatment and vaccinations, community-acquired bacterial meningitis remains one of the most important infectious diseases worldwide. Streptococcus pneumoniae and Neisseria meningitidis are the most common causative bacteria and are associated with high mortality and morbidity; vaccines targeting these organisms, which have designs similar to the successful vaccine that targets Haemophilus influenzae type b meningitis, are now being used in many routine vaccination programmes. Experimental and genetic association studies have increased our knowledge about the pathogenesis of bacterial meningitis. Early antibiotic treatment improves the outcome, but the growing emergence of drug resistance as well as shifts in the distribution of serotypes and groups are fuelling further development of new vaccines and treatment strategies. Corticosteroids were found to be beneficial in high-income countries depending on the bacterial species. Further improvements in the outcome are likely to come from dampening the host inflammatory response and implementing preventive measures, especially the development of new vaccines.

  18. Effect of sulfate on the transformation of corrosion scale composition and bacterial community in cast iron water distribution pipes.

    PubMed

    Yang, Fan; Shi, Baoyou; Bai, Yaohui; Sun, Huifang; Lytle, Darren A; Wang, Dongsheng

    2014-08-01

    The chemical stability of iron corrosion scales and the microbial community of biofilm in drinking water distribution system (DWDS) can have great impact on the iron corrosion and corrosion product release, which may result in "red water" issues, particularly under the situation of source water switch. In this work, experimental pipe loops were set up to investigate the effect of sulfate on the dynamical transformation characteristics of iron corrosion products and bacterial community in old cast iron distribution pipes. All the test pipes were excavated from existing DWDS with different source water supply histories, and the test water sulfate concentration was in the range of 50-350 mg/L. Pyrosequencing of 16S rRNA was used for bacterial community analysis. The results showed that iron release increased markedly and even "red water" occurred for pipes with groundwater supply history when feed water sulfate elevated abruptly. However, the iron release of pipes with only surface water supply history changed slightly without noticeable color even the feed water sulfate increased multiply. The thick-layered corrosion scales (or densely distributed tubercles) on pipes with surface water supply history possessed much higher stability due to the larger proportion of stable constituents (mainly Fe3O4) in their top shell layer; instead, the rather thin and uniform non-layered corrosion scales on pipes with groundwater supply history contained relatively higher proportion of less stable iron oxides (e.g. β-FeOOH, FeCO3 and green rust). The less stable corrosion scales tended to be more stable with sulfate increase, which was evidenced by the gradually decreased iron release and the increased stable iron oxides. Bacterial community analysis indicated that when switching to high sulfate water, iron reducing bacteria (IRB) maintained dominant for pipes with stable corrosion scales, while significant increase of sulfur oxidizing bacteria (SOB), sulfate reducing bacteria (SRB

  19. Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.

    PubMed

    Chen, Zhaojin; Zheng, Yuan; Ding, Chuanyu; Ren, Xuemin; Yuan, Jian; Sun, Feng; Li, Yuying

    2017-11-01

    Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot(-1), respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg(-1) cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

    PubMed

    Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

    2015-03-01

    In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs.

  1. Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays

    USGS Publications Warehouse

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Zawada, David G.; Andersen, Gary L.

    2013-01-01

    Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (Orbicella annularis, formerly of the genus Montastraea [1]) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to Aurantimonas coralicida, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™ data presented here provide a broader characterization of the bacterial community changes that occur within Orbicella annularis during the shift from a healthy to diseased state.

  2. Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in Orbicella annularis Using PhyloChip™ G3 Microarrays

    PubMed Central

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Zawada, David G.; Andersen, Gary L.

    2013-01-01

    Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (Orbicella annularis, formerly of the genus Montastraea [1]) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to Aurantimonas coralicida, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™data presented here provide a broader characterization of the bacterial community changes that occur within Orbicella annularis during the shift from a healthy to diseased state. PMID:24278181

  3. Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays.

    PubMed

    Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Gray, Michael A; Zawada, David G; Andersen, Gary L

    2013-01-01

    Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes 'white plague.' PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (Orbicella annularis, formerly of the genus Montastraea[1]) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to Aurantimonas coralicida, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™data presented here provide a broader characterization of the bacterial community changes that occur within Orbicella annularis during the shift from a healthy to diseased state.

  4. The relationship between instability of H2 production and compositions of bacterial communities within a dark fermentation fluidized-bed bioreactor.

    PubMed

    Koskinen, Perttu E P; Kaksonen, Anna H; Puhakka, Jaakko A

    2007-07-01

    Microbial community composition dynamics was studied during H(2) fermentation from glucose in a fluidized-bed bioreactor (FBR) aiming at obtaining insight into the H(2) fermentation microbiology and factors resulting in the instability of biofilm processes. FBR H(2) production performance was characterised by an instable pattern of prompt onset of H(2) production followed by rapid decrease. Gradual enrichment of organisms increased the diversity of FBR attached and suspended-growth phase bacterial communities during the operation. FBR bacteria included potential H(2) producers, H(2) consumers and neither H(2) producers nor consumers, and those distantly related to any known organisms. The prompt onset of H(2) production was due to rapid growth of Clostridium butyricum (99-100%) affiliated strains after starting continuous feed. The proportion trend of C. butyricum in FBR attached and suspended-growth phase communities coincided with H(2) and butyrate production. High glucose loading rate favoured the H(2) production by Escherichia coli (100%) affiliated strain. Decrease in H(2) production, associated with a shift from acetate-butyrate to acetate-propionate production, was due to changes in FBR attached and suspended-growth phase bacterial community compositions. During the shift, organisms, including potential propionate producers, were enriched in the communities while the proportion trend of C. butyricum decreased. We suggest that the instability of H(2) fermentation in biofilm reactors is due to enrichment and efficient adhesion of H(2) consumers on the carrier and, therefore, biofilm reactors may not favour mesophilic H(2) fermentation.

  5. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    PubMed Central

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our

  6. Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.

    PubMed

    Müller, Bettina; Sun, Li; Westerholm, Maria; Schnürer, Anna

    2016-01-01

    Syntrophic acetate oxidation (SAO) is the predominant pathway for methane production in high ammonia anaerobic digestion processes. The bacteria (SAOB) occupying this niche and the metabolic pathway are poorly understood. Phylogenetic diversity and strict cultivation requirements hinder comprehensive research and discovery of novel SAOB. Most SAOB characterised to date are affiliated to the physiological group of acetogens. Formyltetrahydrofolate synthetase is a key enzyme of both acetogenic and SAO metabolism. The encoding fhs gene has therefore been identified as a suitable functional marker, using a newly designed primer pair. In this comparative study, we used a combination of terminal restriction fragment length polymorphism profiling, clone-based comparison, qPCR and Illumina amplicon sequencing to assess the bacterial community and acetogenic sub-community prevailing in high- and low-ammonia laboratory-scale digesters in order to delineate potential SAOB communities. Potential candidates identified were further tracked in a number of low-ammonia and high-ammonia laboratory-scale and large-scale digesters in order to reveal a potential function in SAO. All methodical approaches revealed significant changes in the bacterial community composition concurrently with increasing ammonia and predominance of SAO. The acetogenic community under high ammonia conditions was revealed to be generally heterogeneous, but formed distinct phylogenetic clusters. The clusters differed clearly from those found under low-ammonia conditions and represented an acetogenic assemblage unique for biogas processes and recurring in a number of high-ammonia processes, indicating potential involvement in SAO. The phylogenetic affiliation and population dynamics observed point to a key community, belonging mainly to the Clostridia class, in particular to the orders Clostridiales and Thermoanaerobacterales, which appear to specialise in SAO rather than being metabolically versatile. Overall

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

    PubMed

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

    2015-07-01

    Plant-associated microorganisms affect the health of their hosts in diverse ways, yet the distribution of these organisms within individual plants remains poorly understood. To address this knowledge gap, we assessed the spatial variability in bacterial community diversity and composition found on and in aboveground tissues of individual Ginkgo biloba trees. We sampled bacterial communities from > 100 locations per tree, including leaf, branch and trunk samples and used high-throughput sequencing of the 16S rRNA gene to determine the diversity and composition of these communities. Bacterial community structure differed strongly between bark and leaf samples, with bark samples harbouring much greater bacterial diversity and a community composition distinct from leaves. Within sample types, we observed clear spatial patterns in bacterial diversity and community composition that corresponded to the samples' proximity to the exterior of the tree. The composition of the bacterial communities found on trees is highly variable, but this variability is predictable and dependent on sampling location. Moreover, this work highlights the importance of carefully considering plant spatial structure when characterizing the microbial communities associated with plants and their impacts on plant hosts. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Changes in the Epilimnetic Bacterial Community Composition, Production, and Protist-Induced Mortality along the Longitudinal Axis of a Highly Eutrophic Reservoir.

    PubMed

    Simek, K.; Armengol, J.; Comerma, M.; Garcia, J.C.; Kojecka, P.; Nedoma, J.; Hejzlar, J.

    2001-10-01

    We studied changes in the epilimnetic bacterial community composition (BCC), bacterial biomass and production, and protistan succession and bacterivory along the longitudinal axis of the canyon-shaped, highly eutrophic Sau Reservoir (NE Spain) during two sampling campaigns, in April and July 1997. Longitudinal changes in BCC from the river inflow to the dam area of the reservoir were detected by using oligonucleotide probes targeted to the kingdom Bacteria, to the alpha, beta, and gamma subclasses (ALFA, BETA, and GAMA) of the class Proteobacteria, and to the Cytophaga/Flavobacterium (CF) cluster. In general, the inflow of the organically loaded Ter river, with highly abundant allochthonous bacterial populations, induced a clearly distinguishable longitudinal succession of the structure of the microbial food web. The most dynamic changes in microbial parameters occurred at the plunge point, the mixing area of river water and the reservoir epilimnion. Changes within members of BETA and CF were the most important in determining changes in BCC, bacterial abundance and biomass. Much less relevant changes occurred within the less abundant ALFA and GAMA bacteria. From the plunge point downstream, we described a significant shift in BCC in the form of decreased proportions of BETA and CF. This shift spatially coincided with the highest values of heterotrophic nanoflagellate bacterivory (roughly doubled the bacterial production). CF numerically dominated throughout the reservoir without any marked longitudinal changes in their mean cell volume. In contrast, very large cells affiliated to BETA clearly dominated in the allochthonous bacterial biomass brought by the river. BETA showed a marked downstream trend of decreasing mean cell volume. We conclude that the observed BCC shift and the longitudinal shift in food web structure (bacteria-heterotrophic nanoflagellates-ciliates) resulted from highly complex interactions brought about by several major factors: varying hydrology

  9. 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

  10. The contribution of species richness and composition to bacterial services.

    PubMed

    Bell, Thomas; Newman, Jonathan A; Silverman, Bernard W; Turner, Sarah L; Lilley, Andrew K

    2005-08-25

    Bacterial communities provide important services. They break down pollutants, municipal waste and ingested food, and they are the primary means by which organic matter is recycled to plants and other autotrophs. However, the processes that determine the rate at which these services are supplied are only starting to be identified. Biodiversity influences the way in which ecosystems function, but the form of the relationship between bacterial biodiversity and functioning remains poorly understood. Here we describe a manipulative experiment that measured how biodiversity affects the functioning of communities containing up to 72 bacterial species constructed from a collection of naturally occurring culturable bacteria. The experimental design allowed us to manipulate large numbers of bacterial species selected at random from those that were culturable. We demonstrate that there is a decelerating relationship between community respiration and increasing bacterial diversity. We also show that both synergistic interactions among bacterial species and the composition of the bacterial community are important in determining the level of ecosystem functioning.

  11. Bacterial community composition and physiological shifts associated with the El Niño Southern Oscillation (ENSO) in the Patos Lagoon estuary.

    PubMed

    They, Ng Haig; Ferreira, Lise Maria Holanda; Marins, Luís Fernando; Abreu, Paulo Cesar

    2015-04-01

    The Patos Lagoon estuary is a microtidal system that is strongly regulated by atmospheric forces, including remote large-scale phenomena such as the El Niño Southern Oscillation (ENSO), which affects precipitation patterns in the region. In this study, we investigated whether the bacterial community composition (BCC), community-level physiological profiles (CLPP), and a set of environmental variables were affected by the transition from a moderate El Niño to a strong La Niña event (June 2010 to May 2011). We identified two distinct periods: a period following El Niño that was characterized by low salinity and high concentrations of NO3(-) and PO4(-3) and low molecular weight (LMW) substances and a period following La Niña during which salinity, temperature, and transparency increased and the concentrations of nutrients and LMW substances decreased. The BCC and CLPP were significantly altered in response to this transition. This is the first study addressing the effect of ENSO on bacteria at the community level in an estuarine system. Our results suggest that there is a link between ENSO and bacteria, indicating the role of climate variability in bacterial activities and, hence, the cycling of organic matter by these microorganisms.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  14. Bacterial community reconstruction using compressed sensing.

    PubMed

    Amir, Amnon; Zuk, Or

    2011-11-01

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

  15. Silica fertilization and nano-MnO₂ amendment on bacterial community composition in high arsenic paddy soils.

    PubMed

    Shao, Jihai; He, Yaxian; Zhang, Huiling; Chen, Anwei; Lei, Ming; Chen, Junfeng; Peng, Liang; Gu, Ji-Dong

    2016-03-01

    Silica fertilization and nano-MnO2 amendment are reported as useful approaches in lowering the accumulation of arsenic in rice grains, but the effects of silica fertilization or nano-MnO2 amendment on microbial community in the paddy soils containing high concentration of arsenic are still unknown. In order to elucidate this question, the structures and composition of microbial community in the paddy soils, in response to silica fertilization and nano-MnO2 amendment, were investigated using pyrosequencing technique. The results indicated that Proteobacteria, Chloroflexi, and Acidobacteria were the main dominating phyla in these paddy soils. A decrease in the relative abundance of Chloroflexi and Cyanobacteria, but an increase in the relative abundance of Acidobacteria was observed after silica fertilization and nano-MnO2 amendment. The changes of Acidobacteria, Chloroflexi, and Cyanobacteria were strongly correlated with pH and the concentration of bioavailable arsenic in the paddy soils. The α-diversity of bacteria in the paddy soils increased in response to silica fertilization at low amendment level, but decreased under silica or nano-MnO2 amendment at high amendment level. Results of β-diversity analysis indicated that the microbial communities in the control treatment shared more similarity with that of those received low level of nano-MnO2 amendment, and the two silica fertilization treatments also shared more similarity with each other.

  16. Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows.

    PubMed

    Weimer, Paul J; Cox, Madison S; Vieira de Paula, Tania; Lin, Miao; Hall, Mary Beth; Suen, Garret

    2017-09-01

    The objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) before exchange and over time postexchange. Three pairs of ruminally cannulated, third-lactation cows were selected whose MPE (energy-corrected milk per unit of dry matter intake) differed over their first 2 lactations. Approximately 95% of ruminal contents were exchanged between cows within each pair. Ruminal pH and volatile fatty acid (VFA) profiles, along with BCC (characterized by sequencing of the variable 4 region of 16S rRNA genes), were assessed just before feeding on d -8, -7, -5, -4, -1, 1, 2, 3, 7, 10, 14, 21, 28, 35, 42, and 56, relative to the exchange date. High-MPE cows had higher total ruminal VFA concentrations, higher molar percentages of propionate and valerate, and lower molar percentages of acetate and butyrate than did LE cows, and re-established these differences 1 d after contents exchange. Across all LE cows, MPE increased during 7 d postexchange but declined thereafter. Two of the 3 HE cows displayed decreases in MPE following introduction of the ruminal contents from the corresponding LE cow, but MPE increased in the third HE cow, which was determined to be an outlier. For all 6 cows, both liquid- and solids-associated BCC differed between individuals within a pair before contents exchange. Upon exchange, BCC of both phases in all 3 pairs was more similar to that of the donor inoculum than to preexchange host BCC. For 5 of 6 cows, the solids-associated community returned within 10 d to more resemble the preexchange community of that host than that of the donor community. Individual variability before the exchange was greater in liquids than in solids, as was the variability in response of bacterial communities to the exchange. Individual cows varied in their response, but generally moved toward re

  17. Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil

    PubMed Central

    Al-Kindi, Sumaiya; Abed, Raeid M. M.

    2016-01-01

    Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO2 and by using gas chromatography–mass spectrometry (GC–MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2–3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO2, given the high respiration activities of the soybean meal alone. GC–MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7–1.8 fold increase in the degraded C14 to C30 alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C14 to C30 alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5–86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95–98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils. PMID:26973618

  18. Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil.

    PubMed

    Al-Kindi, Sumaiya; Abed, Raeid M M

    2016-01-01

    Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO2 and by using gas chromatography-mass spectrometry (GC-MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2-3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO2, given the high respiration activities of the soybean meal alone. GC-MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7-1.8 fold increase in the degraded C14 to C30 alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C14 to C30 alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5-86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95-98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils.

  19. Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.

    PubMed

    Cornejo-Granados, Fernanda; Lopez-Zavala, Alonso A; Gallardo-Becerra, Luigui; Mendoza-Vargas, Alfredo; Sánchez, Filiberto; Vichido, Rodrigo; Brieba, Luis G; Viana, Maria Teresa; Sotelo-Mundo, Rogerio R; Ochoa-Leyva, Adrián

    2017-09-18

    Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.

  20. The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing.

    PubMed

    Li, Jun-Gang; Wang, Chuan-Dong; Tang, Zhong-Hai; Guo, Ying-Qiu; Zheng, Tian-Cai; Li, Yue-Zhong; You, Zhang-Qiang

    2017-09-01

    Cervus albirostris (white-lipped deer) is an endemic species in China. As the name implies, C. albirostris has a characteristic pure white marking around their mouth and on the underside of the throat. The animal is a typical alpine species normally living at the height of 3500-4300 m. In this study, by pyrosequencing the 16S rRNA gene sequences, we for the first time analyzed the gut bacterial community composition in eight feces samples of wild C. albirostris. From a total of 243,634 high-quality sequences, we identified 186 genera, included in 17 prokaryotic phyla in the feces. The relative proportions of Firmicutes and Bacteroidetes were highly consistent in each individual sample. The most frequently detected genus was Ruminococcaceae UCG-005, ranging from 6.70 to 21.00%, displaying positively connections with the Rikenellaceae RC9 gut group. The bacterial communities associated with C. albirostris provide the basic knowledge for further microbiological studies and facilitates the conservation efforts of this vulnerable deer species.

  1. Bacterial community compositions of tomato (Lycopersicum esculentum Mill.) seeds and plant growth promoting activity of ACC deaminase producing Bacillus subtilis (HYT-12-1) on tomato seedlings.

    PubMed

    Xu, Mingshuang; Sheng, Jiping; Chen, Lin; Men, Yejun; Gan, Lin; Guo, Shuntang; Shen, Lin

    2014-03-01

    Study of endophytic bacteria within plant seeds is very essential and meaningful on account of their heritability and versatility. This study investigated Bacillus bacterial communities within the seeds of four commercial tomato varieties, by 16S rRNA gene PCR-RFLP (restriction fragment length polymorphism). Phylogenetic analysis of 16S rRNA gene sequences indicated that the 22 representative isolates belonged to five species of genus Bacillus and the bacterial compositions showed remarkable differences among tomato varieties. Isolates exhibited multiple plant growth promoting (PGP) traits: 37 % of indole-3-acetic acid production; 37 % of phosphate solubilization; 24 % of siderophores production; 85 % of potential nitrogen fixation and 6 % of 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Isolate HYT-12-1 was shown to have highest ACC deaminase activity (112.02 nmol α-ketobutyrate mg⁻¹ protein h⁻¹) among the five ACC deamiase producing strains. 16S rRNA gene sequencing indicated that the isolate HYT-12-1 shared the highest sequence similarity (100 %) with B. subtilis. PGP experiments under gnotobiotic and greenhouse conditions revealed the ability of strain HYT-12-1 to enhance the growth of tomato seedlings. This is the first study to describe endophytic Bacillus communities within tomato seeds, and the results suggest that B. subtilis strain HYT-12-1 would have a great potential for industrial application as biofertilizer in the future.

  2. 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.

  3. Exploration of bacterial community classes in major human habitats

    PubMed Central

    2014-01-01

    Background Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project. Results We identify distinct community group patterns in the anterior nares, four skin sites, and vagina at the genus level. We also confirm three enterotypes previously identified in stools. We identify two clusters with low silhouette values in most oral sites, in which bacterial communities are more homogeneous. Subjects sharing a community class in one habitat do not necessarily share a community class in another, except in the three vaginal sites and the symmetric habitats of the left and right retroauricular creases. Demographic factors, including gender, age, and ethnicity, significantly influence community composition in several habitats. Community classes in the vagina, retroauricular crease and stool are stable over approximately 200 days. Conclusion The community composition, association of demographic factors with community classes, and demonstration of community stability deepen our understanding of the variability and dynamics of human microbiomes. This also has significant implications for experimental designs that seek microbial correlations with clinical phenotypes. PMID:24887286

  4. Changes in dissolved organic matter composition and metabolic diversity of bacterial community during the degradation of organic matter in swine effluent.

    PubMed

    Li, Lei; Liu, Ming; Li, Yanli; Ma, Xiaoyan; Tang, Xiaoxue; Li, Zhongpei

    2016-07-01

    In this study, an incubation experiment was conducted with effluent collected from the concentrated swine-feeding operations (CSFOs) located in Yujiang County of Jiangxi Province, China. The purpose of this study was to elucidate the relationships between the composition of dissolved organic matter (DOM) and the community-level physiological profiles (CLPPs) of microorganisms in swine effluent. For all samples examined, the concentrations of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were decreased by an average of 58.2 ± 30.4 and 49.2 ± 38.7 %, whereas total dissolved phosphorus (TDP) exhibited an average final accumulation of 141.5 ± 43.0 %. In the original samples, ammonium nitrogen accounted for 88.9 ± 4.9 % of the TDN, which was reduced to a final average of 83.9 ± 9.6 %. Two protein-like (tyrosine and tryptophan) and two humic-like (fulvic acids and humic acids) components were identified using a three-dimensional excitation-emission matrix. With the increase in incubation time, the relative concentrations of two protein-like components in effluent were reduced by an average of 83.2 ± 24.7 %. BIOLOG(™) ECO plates were used to determine the metabolic fingerprint of the bacterial community, and a shift in the utilization patterns of substrates was observed over the study period. Additionally, the Shannon-Wiener index of CLPP was ultimately reduced by an average of 43.5 ± 8.5 %, corresponding to the metabolic diversity of the bacterial community. The redundancy analysis identified significant relationships between environmental parameters and the CLPP of microorganisms. To a certain degree, the DOM compositions were linked with the substrate utilization patterns of the bacterial community during the degradation of organic matter in swine effluent.

  5. 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

  6. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

    USGS Publications Warehouse

    Ward, B.B.; Eveillard, D.; Kirshtein, J.D.; Nelson, J.D.; Voytek, M.A.; Jackson, G.A.

    2007-01-01

    The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2???s largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean. ?? 2007 The Authors.

  7. Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water

    PubMed Central

    Magnabosco, Cara; Tekere, Memory; Lau, Maggie C. Y.; Linage, Borja; Kuloyo, Olukayode; Erasmus, Mariana; Cason, Errol; van Heerden, Esta; Borgonie, Gaetan; Kieft, Thomas L.; Olivier, Jana; Onstott, Tullis C.

    2014-01-01

    South Africa has numerous thermal springs that represent topographically driven meteoric water migrating along major fracture zones. The temperature (40–70°C) and pH (8–9) of the thermal springs in the Limpopo Province are very similar to those of the low salinity fracture water encountered in the South African mines at depths ranging from 1.0 to 3.1 km. The major cation and anion composition of these thermal springs are very similar to that of the deep fracture water with the exception of the dissolved inorganic carbon and dissolved O2, both of which are typically higher in the springs than in the deep fracture water. The in situ biological relatedness of such thermal springs and the subsurface fracture fluids that feed them has not previously been evaluated. In this study, we evaluated the microbial diversity of six thermal spring and six subsurface sites in South Africa using high-throughput sequencing of 16S rRNA gene hypervariable regions. Proteobacteria were identified as the dominant phylum within both subsurface and thermal spring environments, but only one genera, Rheinheimera, was identified among all samples. Using Morisita similarity indices as a metric for pairwise comparisons between sites, we found that the communities of thermal springs are highly distinct from subsurface datasets. Although the Limpopo thermal springs do not appear to provide a new window for viewing subsurface bacterial communities, we report that the taxonomic compositions of the subsurface sites studied are more similar than previous results would indicate and provide evidence that the microbial communities sampled at depth are more correlated to subsurface conditions than geographical distance. PMID:25566203

  8. Changes in bacterial community metabolism and composition during the degradation of dissolved organic matter from the jellyfish Aurelia aurita in a Mediterranean coastal lagoon.

    PubMed

    Blanchet, Marine; Pringault, Olivier; Bouvy, Marc; Catala, Philippe; Oriol, Louise; Caparros, Jocelyne; Ortega-Retuerta, Eva; Intertaglia, Laurent; West, Nyree; Agis, Martin; Got, Patrice; Joux, Fabien

    2015-09-01

    Spatial increases and temporal shifts in outbreaks of gelatinous plankton have been observed over the past several decades in many estuarine and coastal ecosystems. The effects of these blooms on marine ecosystem functioning and particularly on the dynamics of the heterotrophic bacteria are still unclear. The response of the bacterial community from a Mediterranean coastal lagoon to the addition of dissolved organic matter (DOM) from the jellyfish Aurelia aurita, corresponding to an enrichment of dissolved organic carbon (DOC) by 1.4, was assessed for 22 days in microcosms (8 l). The high bioavailability of this material led to (i) a rapid mineralization of the DOC and dissolved organic nitrogen from the jellyfish and (ii) the accumulation of high concentrations of ammonium and orthophosphate in the water column. DOM from jellyfish greatly stimulated heterotrophic prokaryotic production and respiration rates during the first 2 days; then, these activities showed a continuous decay until reaching those measured in the control microcosms (lagoon water only) at the end of the experiment. Bacterial growth efficiency remained below 20%, indicating that most of the DOM was respired and a minor part was channeled to biomass production. Changes in bacterial diversity were assessed by tag pyrosequencing of partial bacterial 16S rRNA genes, DNA fingerprints, and a cultivation approach. While bacterial diversity in control microcosms showed little changes during the experiment, the addition of DOM from the jellyfish induced a rapid growth of Pseudoalteromonas and Vibrio species that were isolated. After 9 days, the bacterial community was dominated by Bacteroidetes, which appeared more adapted to metabolize high-molecular-weight DOM. At the end of the experiment, the bacterial community shifted toward a higher proportion of Alphaproteobacteria. Resilience of the bacterial community after the addition of DOM from the jellyfish was higher for metabolic functions than diversity

  9. 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

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

    PubMed

    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.

  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. Composition and diversity of ammonia-oxidising bacterial communities in wastewater treatment reactors of different design treating identical wastewater.

    PubMed

    Rowan, Arlene K; Snape, Jason R; Fearnside, David; Barer, Michael R; Curtis, Thomas P; Head, Ian M

    2003-03-01

    Autotrophic ammonia-oxidising bacteria (AOB) are a crucial component of the microbial communities of nitrifying wastewater treatment systems. Nitrification is known to occur in reactors of different configuration, but whether AOB communities are different in reactors of different design is unknown. We compared the diversity and community structure of the betaproteobacterial AOB in two full-scale treatment reactors - a biological aerated filter (BAF) and a trickling filter - receiving the same wastewater. Polymerase chain reaction (PCR) of 16S ribosomal RNA (rRNA) gene fragments with AOB-selective primers was combined with denaturing gradient gel electrophoresis (DGGE) to allow comparative analysis of the dominant AOB populations. The phylogenetic affiliation of the dominant AOB was determined by cloning and sequencing PCR-amplified 16S rRNA gene fragments. DGGE profiles were compared using a probability-based similarity index (Raup and Crick). The use of a probability-based index of similarity allowed us to evaluate if the differences and similarities observed in AOB community structure in different samples were statistically significant or could be accounted for by chance matching of bands in DGGE profiles, which would suggest random colonisation of the reactors by different AOB. The community structure of AOB was different in different sections of each of the reactors and differences were also noted between the reactors. All AOB-like sequences identified, grouped within the genus Nitrosomonas. A greater diversity of AOB was detected in the trickling filters than in the BAF though all samples analysed appeared to be dominated by AOB most closely related to Nitrosococcus mobilis. Numerical analysis of DGGE profiles indicated that the AOB communities in depth profiles from the filter beds were selected in a non-random manner.

  13. 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

  14. Bacterial Community Development in Experimental Gingivitis

    PubMed Central

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

    2013-01-01

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

  15. Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing.

    PubMed

    Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

    2015-01-01

    This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence.

  16. Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing

    PubMed Central

    Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

    2015-01-01

    This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence. PMID:25938416

  17. Do diet and taxonomy influence insect gut bacterial communities?

    PubMed

    Colman, D R; Toolson, E C; Takacs-Vesbach, C D

    2012-10-01

    Many insects contain diverse gut microbial communities. While several studies have focused on a single or small group of species, comparative studies of phylogenetically diverse hosts can illuminate general patterns of host-microbiota associations. In this study, we tested the hypotheses that (i) host diet and (ii) host taxonomy structure intestinal bacterial community composition among insects. We used published 16S rRNA gene sequence data for 58 insect species in addition to four beetle species sampled from the Sevilleta National Wildlife Refuge to test these hypotheses. Overall, gut bacterial species richness in these insects was low. Decaying wood xylophagous insects harboured the richest bacterial gut flora (102.8 species level operational taxonomic units (OTUs)/sample ± 71.7, 11.8 ± 5.9 phylogenetic diversity (PD)/sample), while bees and wasps harboured the least rich bacterial communities (11.0 species level OTUs/sample ± 5.4, 2.6 ± 0.8 PD/sample). We found evidence to support our hypotheses that host diet and taxonomy structure insect gut bacterial communities (P < 0.001 for both). However, while host taxonomy was important in hymenopteran and termite gut community structure, diet was an important community structuring factor particularly for insect hosts that ingest lignocellulose-derived substances. Our analysis provides a baseline comparison of insect gut bacterial communities from which to test further hypotheses concerning proximate and ultimate causes of these associations.

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

    PubMed

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

    2013-07-01

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

  19. 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.

  20. Desert gerbils affect bacterial composition of soil.

    PubMed

    Kuznetsova, Tatyana A; Kam, Michael; Khokhlova, Irina S; Kostina, Natalia V; Dobrovolskaya, Tatiana G; Umarov, Marat M; Degen, A Allan; Shenbrot, Georgy I; Krasnov, Boris R

    2013-11-01

    Rodents affect soil microbial communities by burrow architecture, diet composition, and foraging behavior. We examined the effect of desert rodents on nitrogen-fixing bacteria (NFB) communities by identifying bacteria colony-forming units (CFU) and measuring nitrogen fixation rates (ARA), denitrification (DA), and CO2 emission in soil from burrows of three gerbil species differing in diets. Psammomys obesus is folivorous, Meriones crassus is omnivorous, consuming green vegetation and seeds, and Dipodillus dasyurus is predominantly granivorous. We also identified NFB in the digestive tract of each rodent species and in Atriplex halimus and Anabasis articulata, dominant plants at the study site. ARA rates of soil from burrows of the rodent species were similar, and substantially lower than control soil, but rates of DA and CO2 emission differed significantly among burrows. Highest rates of DA and CO2 emission were measured in D. dasyurus burrows and lowest in P. obesus. CFU differed among bacteria isolates, which reflected dietary selection. Strains of cellulolytic representatives of the family Myxococcaceae and the genus Cytophaga dominated burrows of P. obesus, while enteric Bacteroides dominated burrows of D. dasyurus. Burrows of M. crassus contained both cellulolytic and enteric bacteria. Using discriminant function analysis, differences were revealed among burrow soils of all rodent species and control soil, and the two axes accounted for 91 % of the variance in bacterial occurrences. Differences in digestive tract bacterial occurrences were found among these rodent species. Bacterial colonies in P. obesus and M. crassus burrows were related to bacteria of A. articulata, the main plant consumed by both species. In contrast, bacteria colonies in the burrow soil of D. dasyurus were related to bacteria in its digestive tract. We concluded that gerbils play an important role as ecosystem engineers within their burrow environment and affect the microbial complex of

  1. The steady state anaerobic digestion of Laminaria hyperborea--effect of hydraulic residence on biogas production and bacterial community composition.

    PubMed

    Hinks, Jamie; Edwards, Stephen; Sallis, Paul J; Caldwell, Gary S

    2013-09-01

    Methane production by anaerobic digestion (AD) of macroalgae (seaweed) is a promising algal bioenergy option. Work presented here is primarily based on the AD of Laminaria hyperborea using batch and continuously stirred tank reactors. Extrapolation of data from batch studies to long term continuous reactors was unreliable. A conservative organic loading rate (OLR) of 1 g L(-1) d(-1) was used due to difficulties experienced in achieving steady state performance at an OLR of 1.5 g L(-1) d(-1). Biogas composition and methane yields (60-70%) were near to values expected from terrestrial feedstocks. Biomass washout, as imposed by the dilution rate (i.e., hydraulic residence), had considerable bearing on the biogas generation profile, particularly at >3 hydraulic residences. Inhibition of methanogen growth was linked to nutrient deficiency and potentially antimicrobial compounds associated with the feedstock. Anaerobic digestion of L. hyperborea proved feasible over extended operational periods. Copyright © 2013. Published by Elsevier Ltd.

  2. Effects of glucose on microcystin-LR removal and the bacterial community composition through anoxic biodegradation in drinking water sludge.

    PubMed

    Ma, Guangxiang; Pei, Haiyan; Hu, Wenrong; Xu, Xiangchao; Ma, Chunxia; Pei, Ruoting

    2016-01-01

    To enhance the degradation efficiency of microcystin (MC) in drinking water sludge (DWS), the underlying mechanisms between organic carbon (glucose) and the biodegradation of MC-LR under anoxic conditions were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis technology. The addition of glucose reduced the rate of the MC-LR biodegradation indicating the occurrence of inhibition of degradation, and an increased inhibition was observed with increases in glucose concentration (0-10,000 mg/L). In addition, the community analysis indicated that the variety and the number of the microbes increased with the concentration of glucose amended (0 -1000 mg/L), but they decreased substantially with the addition of 10,000 mg/L of glucose. The phyla Firmicutes, Proteobacteria and Chloroflexi were found to be the dominant. Methylobacterium and Sphingomonas were MC-degrading bacteria and used glucose as a prior carbon source instead of MC, resulting in the decrease in the MC-LR biodegradation rate under anoxic conditions. Thus, reducing organic carbon could improve the anoxic biodegradation efficiency of MC in DWS.

  3. Elevation gradient of soil bacterial communities in bamboo plantations.

    PubMed

    Lin, Yu-Te; Chiu, Chih-Yu

    2016-12-01

    Elevation trends of macro organisms have long been well studied. However, whether microbes also exhibit such patterns of elevation change is unknown. Here, we investigated the changes in bamboo forest soil bacterial communities along six elevation gradients, from 600 to 1800 m a.s.l. in Mt. Da-an, a subtropical montane area in Nantou county at central Taiwan. Data from 16S rRNA gene clone libraries revealed that more than 70 % of the six communities contained Acidobacteria and Proteobacteria, although the relative abundance differed. Nonmetric multidimensional scaling analysis of the distribution of operational taxonomic units showed differences in bamboo soil bacterial communities across gradients. The bacterial communities at 1000 and 1200 m showed greater diversity than the communities at both lower (600 and 800 m) and higher (1400 and 1800 m) elevations. In contrast to the bacterial community trend, soil C and N and microbial biomass properties increased linearly with elevation. The bamboo soil bacterial community could interact with multiple factors such as soil organic matter content and temperature, for differences in composition and diversity with change in elevation.

  4. 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

  5. Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life

    PubMed Central

    Jiao, Jinzhen; Wu, Jian; Zhou, Chuanshe; Tang, Shaoxun; Wang, Min; Tan, Zhiliang

    2016-01-01

    The establishment of gut microbiota is increasingly recognized as a crucial action in neonatal development, host health and productivity. We hypothesized that the ileal microbiome shifted as goats matured, and this colonization process would be associated with host fermentation capacity. To this end, 18 Liuyang black grazing goats were randomly slaughtered at d 0, 7, 28, 42, and 70. Ileal microbiota was profiled by Miseq sequencing of 16S rRNA gene of bacteria, and fermentation capacity [volatile fatty acid, activities of amylase, carboxymethylcellulase (CMCase) and xylanase] was determined using digesta sample. Principal coordinate analysis revealed that each age group harbored its distinct bacteria. Total bacteria copy number and most alpha diversity indexes increased (P < 0.01) from d 0 to 70. At the phylum level, abundances of Cyanobacteria (P = 0.018) and TM7 (P = 0.010) increased linearly, abundances of Bacteroidetes (P = 0.075) and Fibrobacteres (P = 0.076) tended to increase linearly, whist Proteobacteria abundance tended to decline quadratically (P = 0.052) with age. At the genus level, Enterococcus (30.9%), Lactobacillus (32.8%), and Escherichia (2.0%) dominated at d 0, while Prevotella, Butyrivibrio, Ruminococcus, SMB53, and Fibrobacter surged in abundance after day 20. The highest amylase activity was observed at day 42, while xylanase activity increased quadratically (P = 0.002) from days 28 to 70. Correlation analysis indicated that abundances of Bacteroides, Clostridium, Lactobacillus, Propionibacterium, Enterococcus, and p-75-a5 positively correlated with enzyme activity. Collectively, ileal bacteria in grazing goats assemble into distinct communities throughout development, and might participate in the improvement of host fermentation capacity. PMID:27656165

  6. 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

  7. Metamorphosis of a butterfly-associated bacterial community.

    PubMed

    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.

  8. MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot.

    PubMed

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

    2016-06-01

    Caves in Mizoram, Northeast India, are potential hotspot diversity regions due to the historical significance of the formation of the Indo-Burman plateau and also because of their unexplored and unknown diversity. High-throughput paired end Illumina sequencing of the V4 region of 16S rRNA was performed to study the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (OTUs) (based on 97 % cutoff) comprising of 21 major and 21 candidate phyla with a sequencing depth of 1,140,013 were found in this study. The overall taxonomic profile obtained by the RDP classifier and Greengenes OTU database revealed high diversity within the bacterial communities. Communities were dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of Archaea were less varied and mostly comprising of Eukaryoarchea. Analysis revealed that Farpuk (CFP) cave sediment has low microbial diversity and is mainly dominated by Actinobacteria (80 % reads), whereas different bacterial communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis also revealed that a major portion of the identified OTUs was classified under rare biosphere. Importantly, all these caves recorded a high number of unclassified OTUs, which might represent new species. Further analysis with whole genome sequencing is needed to validate the unknown species as well as to determine their functional role.

  9. Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans.

    PubMed

    Teira, Eva; Hernando-Morales, Víctor; Cornejo-Castillo, Francisco M; Alonso-Sáez, Laura; Sarmento, Hugo; Valencia-Vila, Joaquín; Serrano Catalá, Teresa; Hernández-Ruiz, Marta; Varela, Marta M; Ferrera, Isabel; Gutiérrez Morán, Xosé Anxelu; Gasol, Josep M

    2015-12-01

    The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu(-1) and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean.

  10. Sample Dilution and Bacterial Community Composition Influence Empirical Leucine-to-Carbon Conversion Factors in Surface Waters of the World's Oceans

    PubMed Central

    Hernando-Morales, Víctor; Cornejo-Castillo, Francisco M.; Alonso-Sáez, Laura; Sarmento, Hugo; Valencia-Vila, Joaquín; Serrano Catalá, Teresa; Hernández-Ruiz, Marta; Varela, Marta M.; Ferrera, Isabel; Gutiérrez Morán, Xosé Anxelu; Gasol, Josep M.

    2015-01-01

    The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu−1 and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean. PMID:26407885

  11. Exploring gastric bacterial community in young pigs.

    PubMed

    Motta, Vincenzo; Trevisi, Paolo; Bertolini, Francesca; Ribani, Anisa; Schiavo, Giuseppina; Fontanesi, Luca; Bosi, Paolo

    2017-01-01

    Microbiota plays an important role in the homeostasis of the gastrointestinal tract. Understanding the variations of the commensal microbiota composition is crucial for a more efficient control of enteric infectious diseases and for the reduction of the use of antibiotics in animal production, which are the main points of interest for improved animal healthcare and welfare and for consumer health protection. Even though the intestinal microbiota has been extensively studied, little is known about the gastric microbiota. This pilot study was aimed at a descriptive analysis of the gastric microbiota in healthy pigs and at the identification of any differences among four potentially distinct microbial niches in the stomach. Gastric mucosal samples from the oxyntic area, the pylorus and the gastric groove, and a sample of gastric contents were collected from four healthy weaned pigs. Bacterial DNA was isolated and extracted from each sample and amplicons from the V6 region of the 16S rRNA gene were sequenced using Ion Torrent PGM. The data were analysed by an "unsupervised" and a "supervised" approach in the Ribosomal Database Project (RDP) pipeline. Proteobacteria was the dominant phylum in all the samples. Differences in bacterial community composition were found between mucosal and content samples (one-way ANOSIM pairwise post hoc test, p < 0.05); instead, the different mucosal regions did not show differences between them. The mucosal samples were characterised by Herbiconiux and Brevundimonas, two genera which include cellulolytic and xylanolytic strains. Nevertheless, additional larger trials are needed to support the data presented in this pilot study and to increase the knowledge regarding the resident microbiota of the stomach.

  12. Exploring gastric bacterial community in young pigs

    PubMed Central

    Motta, Vincenzo; Trevisi, Paolo; Bertolini, Francesca; Ribani, Anisa; Schiavo, Giuseppina; Fontanesi, Luca; Bosi, Paolo

    2017-01-01

    Microbiota plays an important role in the homeostasis of the gastrointestinal tract. Understanding the variations of the commensal microbiota composition is crucial for a more efficient control of enteric infectious diseases and for the reduction of the use of antibiotics in animal production, which are the main points of interest for improved animal healthcare and welfare and for consumer health protection. Even though the intestinal microbiota has been extensively studied, little is known about the gastric microbiota. This pilot study was aimed at a descriptive analysis of the gastric microbiota in healthy pigs and at the identification of any differences among four potentially distinct microbial niches in the stomach. Gastric mucosal samples from the oxyntic area, the pylorus and the gastric groove, and a sample of gastric contents were collected from four healthy weaned pigs. Bacterial DNA was isolated and extracted from each sample and amplicons from the V6 region of the 16S rRNA gene were sequenced using Ion Torrent PGM. The data were analysed by an “unsupervised” and a “supervised” approach in the Ribosomal Database Project (RDP) pipeline. Proteobacteria was the dominant phylum in all the samples. Differences in bacterial community composition were found between mucosal and content samples (one-way ANOSIM pairwise post hoc test, p < 0.05); instead, the different mucosal regions did not show differences between them. The mucosal samples were characterised by Herbiconiux and Brevundimonas, two genera which include cellulolytic and xylanolytic strains. Nevertheless, additional larger trials are needed to support the data presented in this pilot study and to increase the knowledge regarding the resident microbiota of the stomach. PMID:28249050

  13. 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.

  14. Bacterial community composition in relation to bedrock type and macrobiota in soils from the Sør Rondane Mountains, East Antarctica.

    PubMed

    Tytgat, Bjorn; Verleyen, Elie; Sweetlove, Maxime; D'hondt, Sofie; Clercx, Pia; Van Ranst, Eric; Peeters, Karolien; Roberts, Stephen; Namsaraev, Zorigto; Wilmotte, Annick; Vyverman, Wim; Willems, Anne

    2016-09-01

    Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high-altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analyzed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica), using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km(2) Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP-dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock.

  15. 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.

  16. Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques.

    PubMed

    Nunan, Naoise; Daniell, Timothy J; Singh, Brajesh K; Papert, Artemis; McNicol, James W; Prosser, James I

    2005-11-01

    Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed "bulk" rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.

  17. Changes in the bacterial community and composition of fermentation products during ensiling of wilted Italian ryegrass and wilted guinea grass silages.

    PubMed

    Li, Yanbing; Nishino, Naoki

    2013-08-01

    To gain further insights into temperate and tropical grass ensiling, fermentation products and bacterial communities were examined at both the initial and late stages of ensiling of wilted Italian ryegrass and wilted guinea grass silages. 2,3-Butanediol and ethanol fermentation were observed in wilted Italian ryegrass silage. Enterobacteria such as Rahnella sp. and Enterobacter sp. may have been involved in fermentation; however, alcohol production was intensified after the silage enterobacterial community overwhelmed the pre-ensiled enterobacterial community. Pediococcus spp. appeared in silage stored for 4 months, when a significant increase in lactic acid content was seen compared with that at 2 months. Prolonged storage enhanced acetic acid fermentation in wilted guinea grass silage. The disappearance of Enterococcus sulfureus and appearance of Lactobacillus plantarum may have been associated with the increased acetic acid content. Although many species of enterobacteria were found in common between the pre-ensiled crop and silages of Italian ryegrass and guinea grass, marked differences were seen in the type of fermentation from the initial stages. These results indicate that the bacterial community of pre-ensiled crops may be immediately replaced by one that is adapted to ensiling environments, although metabolic changes may continue over the course of ensiling.

  18. 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

  19. 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.

  20. Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae

    PubMed Central

    Robertson, Veronica; Haltli, Brad; McCauley, Erin P.; Overy, David P.; Kerr, Russell G.

    2016-01-01

    Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome. PMID:27681917

  1. Soil bacterial community shifts associated with sugarcane straw removal

    NASA Astrophysics Data System (ADS)

    Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

    2017-04-01

    In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

  2. Pyrosequencing analysis of the bacterial community in drinking water wells.

    PubMed

    Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

    2013-07-01

    Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

  3. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

    SciTech Connect

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.; Mormile, Melanie R.

    2014-10-07

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.

  4. Bacterial community composition in the rhizosphere of a transgenic, herbicide-resistant maize (Zea mays) and comparison to its non-transgenic cultivar Bosphore.

    PubMed

    Schmalenberger, Achim; Tebbe, Christoph C

    2002-04-01

    Bacterial communities in rhizospheres of transgenic maize (Zea mays, with the pat-gene conferring resistance to the herbicide glufosinate; syn. l-phosphinothricin) were compared to its isogenic, non-transgenic cultivar. Total DNA was extracted from bacterial cell consortia collected from rhizospheres of plants grown in an agricultural field. With the use of three different primer pairs binding to evolutionarily conserved regions of the bacterial 16S rRNA gene, partial sequences were amplified by polymerase chain reaction (PCR). The PCR products were subjected to single-strand conformation polymorphism (SSCP) to generate genetic profiles which corresponded to the diversity of the amplified sequences. Genetic profiles of rhizospheres consisted of 40-60 distinguishable bands depending on the chosen primer pairs, and the variability between independent replicates was very low. Neither the genetic modification nor the use of the herbicide Liberty (syn. Basta; active ingredient: glufosinate) affected the SSCP profiles as investigated with digital image analysis. In contrast, PCR-SSCP profiles of bacterial communities from rhizospheres of sugar beet, grown in the same field as a control crop, were clearly different. A less pronounced but significant difference was also observed with rhizosphere samples from fine roots of maize plants collected 35 and 70 days after sowing. Sequencing of the dominant 30 products from one typical SSCP profile generated from transgenic maize rhizospheres indicated the presence of typical soil and rhizosphere bacteria: half of the bands could be attributed to Proteobacteria, mainly of the alpha- and beta-subgroups. Other SSCP bands could be assigned to members of the following phylogenetic groups: Cytophaga-Flavobacterium-Bacteroides, Chlamydiales-Verrucomicrobium, Planctomyces, Holophaga and to Gram-positive bacteria with a high G+C DNA content.

  5. 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.

  6. Stream Hydrological Fragmentation Drives Bacterioplankton Community Composition

    PubMed Central

    Fazi, Stefano; Vázquez, Eusebi; Casamayor, Emilio O.; Amalfitano, Stefano; Butturini, Andrea

    2013-01-01

    In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow re-convergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition. PMID:23741302

  7. Stream hydrological fragmentation drives bacterioplankton community composition.

    PubMed

    Fazi, Stefano; Vázquez, Eusebi; Casamayor, Emilio O; Amalfitano, Stefano; Butturini, Andrea

    2013-01-01

    In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow re-convergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition.

  8. 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.

  9. 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

  10. Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

    PubMed Central

    Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

    2014-01-01

    Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

  11. 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

  12. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica.

    PubMed

    Kim, Mincheol; Cho, Ahnna; 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.

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

    PubMed

    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.

  14. 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

  15. Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries).

    PubMed

    Qian, Wenxi; Li, ZhiPeng; Ao, Weiping; Zhao, Guangyong; Li, Guangyu; Wu, JianPing

    2017-05-01

    The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer, and sheep and measured rumen fermentation products. Overall, 548 218 high-quality sequences were obtained and then classified into 6034 operational taxonomic units. Prevotella spp., Succiniclasticum spp., and unclassified bacteria within the families Succinivibrionaceae, Lachnospiraceae, and Veillonellaceae were the dominant bacteria in the rumen across the 3 hosts. Principal coordinate analysis identified significant differences in the bacterial communities across the 3 hosts. Pseudobutyrivibrio spp., Oscillospira spp., and Prevotella spp. were more prevalent in the rumen of the cattle, red deer, and sheep, respectively. Among the 3 hosts, the red deer rumen had the greatest amounts of acetate and butyrate and the lowest pH value. These results showed that Prevotella spp. are the dominant bacteria in the rumen of the cattle, red deer, and sheep, providing new insight into the rumen fermentation of ruminants distributed in the Tarim Basin.

  16. Bacterial community associated with Pfiesteria-like dinoflagellate cultures.

    PubMed

    Alavi, M; Miller, T; Erlandson, K; Schneider, R; Belas, R

    2001-06-01

    Dinoflagellates (Eukaryota; Alveolata; Dinophyceae) are single-cell eukaryotic microorganisms implicated in many toxic outbreaks in the marine and estuarine environment. Co-existing with dinoflagellate communities are bacterial assemblages that undergo changes in species composition, compete for nutrients and produce bioactive compounds, including toxins. As part of an investigation to understand the role of the bacteria in dinoflagellate physiology and toxigenesis, we have characterized the bacterial community associated with laboratory cultures of four 'Pfiesteria-like' dinoflagellates isolated from 1997 fish killing events in Chesapeake Bay. A polymerase chain reaction with oligonucleotide primers specific to prokaryotic 16S rDNA gene sequences was used to characterize the total bacterial population, including culturable and non-culturable species, as well as possible endosymbiotic bacteria. The results indicate a diverse group of over 30 bacteria species co-existing in the dinoflagellate cultures. The broad phylogenetic types of dinoflagellate-associated bacteria were generally similar, although not identical, to those bacterial types found in association with other harmful algal species. Dinoflagellates were made axenic, and the culturable bacteria were added back to determine the contribution of the bacteria to dinoflagellate growth. Confocal scanning laser fluorescence microscopy with 16S rDNA probes was used to demonstrate a physical association of a subset of the bacteria and the dinoflagellate cells. These data point to a key component in the bacterial community being species in the marine alpha-proteobacteria group, most closely associated with the alpha-3 or SAR83 cluster.

  17. Novel microarray design strategy to study complex bacterial communities.

    PubMed

    Huyghe, Antoine; Francois, Patrice; Charbonnier, Yvan; Tangomo-Bento, Manuela; Bonetti, Eve-Julie; Paster, Bruce J; Bolivar, Ignacio; Baratti-Mayer, Denise; Pittet, Didier; Schrenzel, Jacques

    2008-03-01

    Assessing bacterial flora composition appears to be of increasing importance to fields as diverse as physiology, development, medicine, epidemiology, the environment, and the food industry. We report here the development and validation of an original microarray strategy that allows analysis of the phylogenic composition of complex bacterial mixtures. The microarray contains approximately 9,500 feature elements targeting 16S rRNA gene-specific regions. Probe design was performed by selecting oligonucleotide sequences specific to each node of the seven levels of the bacterial phylogenetic tree (domain, phylum, class, order, family, genus, and species). This approach, based on sequence information, allows analysis of the bacterial contents of complex bacterial mixtures to detect both known and unknown microorganisms. The presence of unknown organisms can be suspected and mapped on the phylogenetic tree, indicating where to refine analysis. Initial proof-of-concept experiments were performed on oral bacterial communities. Our results show that this hierarchical approach can reveal minor changes (

  18. Terrestrial origin of bacterial communities in complex boreal freshwater networks.

    PubMed

    Ruiz-González, Clara; Niño-García, Juan Pablo; Del Giorgio, Paul A

    2015-08-25

    Bacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal aquatic network by determining the taxonomic composition of bacterial communities along the entire terrestrial/aquatic continuum, including soil and soilwaters, headwater streams, large rivers and lakes. We show that the network metacommunity has a directional spatial structure driven by a common terrestrial origin of aquatic communities, which are numerically dominated by taxa recruited from soils. Local community assembly is driven by variations along the hydrological continuum in the balance between mass effects and species sorting of terrestrial taxa, and seems further influenced by priority effects related to the spatial sequence of entry of soil bacteria into the network.

  19. The Bacterial Community of Entomophilic Nematodes and Host Beetles

    PubMed Central

    Koneru, Sneha L.; Salinas, Heilly; Flores, Gilberto E.; Hong, Ray L.

    2016-01-01

    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 geographic origin. Anaerobes Synergistaceae and sulfate-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 sulfate-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

  20. Canopy soil bacterial communities altered by severing host tree limbs

    PubMed Central

    Dangerfield, Cody R.; Nadkarni, Nalini M.

    2017-01-01

    Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities. PMID:28894646

  1. 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. © 2016 John Wiley & Sons Ltd.

  2. Comparative analysis of bacterial community composition in bulk tank raw milk by culture-dependent and culture-independent methods using the viability dye propidium monoazide.

    PubMed

    Weber, Mareike; Geißert, Janina; Kruse, Myriam; Lipski, André

    2014-11-01

    Microbial diversity of 3 raw milk samples after 72 h of storage at 4 °C in a bulk tank was analyzed by culture-dependent and -independent methods. The culture-dependent approach was based on the isolation of bacteria on complex and selective media, chemotaxonomic differentiation of isolates, and subsequent identification by 16S rRNA gene sequencing. The culture-independent approach included the treatment of raw milk with the dye propidium monoazide before direct DNA extraction by mechanic and enzymatic cell lysis approaches, and cloning and sequencing of the 16S rRNA genes. The selective detection of viable bacteria improved the comparability between bacterial compositions of raw milk based on culture-dependent and -independent methods, which was the major objective of this study. Several bacterial species of the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were detected by the culture-dependent method, whereas mainly bacteria of the phylum Proteobacteria as well as low proportions of the phyla Bacteroidetes and Actinobacteria were detected by the culture-independent method. This led to the conclusion that the phylum Firmicutes was strongly discriminated by the culture-independent approach. Generally, species richness detected by the culture-dependent method was higher than that detected by the culture-independent method for all samples. However, few taxa could be detected solely by the direct DNA-based method. In conclusion, the combination of culture-dependent and -independent methods led to the detection of the highest bacterial diversity for the raw milk samples analyzed. It was shown that DNA extraction from raw milk as the essential step in culture-independent methods causes the discrimination of taxa by incomplete cell lysis. Treatment of raw milk with the viability dye propidium monoazide was optimized for the application in raw milk without former removal of milk ingredients and proved to be a suitable tool to ensure comparability

  3. UV radiation and organic matter composition shape bacterial functional diversity in sediments

    PubMed Central

    Hunting, Ellard R.; White, Christopher M.; van Gemert, Maarten; Mes, Daan; Stam, Eva; van, Harm G.; der Geest; Kraak, Michiel H. S.; Admiraal, Wim

    2013-01-01

    UV radiation and organic matter (OM) composition are known to influence the species composition of bacterioplankton communities. Potential effects of UV radiation on bacterial communities residing in sediments remain completely unexplored to date. However, it has been demonstrated that UV radiation can reach the bottom of shallow waters and wetlands and alter the OM composition of the sediment, suggesting that UV radiation may be more important for sediment bacteria than previously anticipated. It is hypothesized here that exposure of shallow OM-containing sediments to UV radiation induces OM source-dependant shifts in the functional composition of sediment bacterial communities. This study therefore investigated the combined influence of both UV radiation and OM composition on bacterial functional diversity in laboratory sediments. Two different OM sources, labile and recalcitrant OM, were used and metabolic diversity was measured with Biolog GN. Radiation exerted strong negative effects on the metabolic diversity in the treatments containing recalcitrant OM, more than in treatments containing labile OM. The functional composition of the bacterial community also differed significantly between the treatments. Our findings demonstrate that a combined effect of UV radiation and OM composition shapes the functional composition of microbial communities developing in sediments, hinting that UV radiation may act as an important sorting mechanism for bacterial communities and driver for bacterial functioning in shallow waters and wetlands. PMID:24194736

  4. 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.

  5. 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

  6. 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.

  7. Bacterial communities in neonatal feces are similar to mothers' placentae.

    PubMed

    Dong, Xu-Dong; Li, Xiao-Ran; Luan, Jian-Jun; Liu, Xiao-Feng; Peng, Juan; Luo, Yi