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PubMed2005

Methane fluxes in permafrost habitats of the Lena Delta: effects of microbial community structure and organic matter quality.

For the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH(4) production and oxidation, the community structure and the quality of dissolved organic matter (DOM) were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for ester-linked phospholipid fatty acids (PLFAs) and differences in the fraction of unsaponifiable PLFAs and phospholipid ether lipids. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso- and anteiso-branched fatty acids related to the amount of straight-chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings first that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems, and second that these microorganisms are well adapted to the extreme temperature gradient of their environment.

Archaea↗

PubMed2005

Redox fluctuation structures microbial communities in a wet tropical soil.

Frequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated tropical soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated by Actinobacteria (especially Micrococcus and Streptomycetes), "Bacilli," "Clostridia," and Burkholderia and lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods.

Aerobiosis↗

PubMed2006

Development of microbial community structure and actvity in a high-rate anaerobic bioreactor at 18 degrees C.

Anaerobic digestion in the psychrophilic (< 20 degrees C) or sub-mesophilic temperature range has recently been proven as an effective treatment option for the mineralization of a wide variety of problematic wastewaters. In this study, an expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactor was seeded with a full-scale, mesophilic sludge and employed to evaluate the long-term operational potential, and underlying microbial ecology, of this approach for the treatment of a medium-strength (5 g chemical oxygen demand [COD] l(-1)), synthetic, volatile fatty acid-based wastewater. Throughout the trial period of 625 days, extended intervals of consistently stable and efficient wastewater treatment were sustained. These results were highlighted by a short start-up period (21 d), low hydraulic retention times (4.88h), high organic (up to 24.64kg CODm(-3)d(-1)), and volumetric loading rates (up to 4.92 m3 m(-3) d(-1)). A stable, well-settling granular sludge bed was maintained in the bioreactor for the majority of the trial; however, reduced treatment efficiency and biomass washout were observed at an imposed OLR of 36.96 kg COD m(-3) d(-1). The microbial biomass in the bioreactor was investigated using maximum specific methanogenic activity assays and polymerase chain reaction-denaturing gradient gel electrophoresis. A temporal succession of both the bacterial and archaeal populations was noted during the trial, compared to the seed sludge, in response to bioreactor operation at lower temperatures, loading rate increases and to VFA accumulation in the bioreactor. During the trial, an increased contribution of hydrogenotrophic methanogenesis as a pathway of methane production was observed, along with the overall emergence of a highly active psychrotolerent-though still mesophilic biomass.

Anaerobiosis↗

PubMed2006

[Enhanced ammonia removal and microbial community structure analysis using bacterial quinone profile in ITFB].

Water quality during the start-up period was changed in order to enhance the later nitrifying ability of the internal-circulation three-phase bio-fluidized bed (ITFB). The experimental results showed that high N/C ratio and low feeding concentration of COD were two key conditions for enhancing the ammonia removal. After the enhanced start-up, an efficient removal efficiency of both COD and ammonia was achieved with HRT 2h when treating sanitary wastewater, the average ammonia removal rate was 74% , the ammonia concentration in effluent was lower than 10 mg/L. Bacterial quinone profile of the system was also analyzed. The results showed that after the enhanced start-up, the number of nitrifying bacteria, such as Nitrosomonas europaea, in the biofilm in ITFB was increased, and the number of gamma-Proteobacteria, such as Acinetobacter sp. and Pseudomonas sp., was decreased. the equitability of the quinones (EQ) fluctuated around 0.5 showed that the distribution of the microbial community in the biofilm changed little. UQ/MK ratio of all the samples was greater than 1 indicated that Gram-negative bacteria was the dominant bacteria in the system.

Ammonia↗

PubMed2006

Microbial community structure and dynamics in the largest natural French lake (Lake Bourget).

We investigated the dynamics and diversity of heterotrophic bacteria, autotrophic and heterotrophic flagellates, and ciliates from March to July 2002 in the surface waters (0-50 m) of Lake Bourget. The heterotrophic bacteria consisted mainly of "small" cocci, but filaments (>2 microm), commonly considered to be grazing-resistant forms under increased nanoflagellate grazing, were also detected. These elongated cells mainly belonged to the Cytophaga-Flavobacterium (CF) cluster, and were most abundant during spring and early summer, when mixotrophic or heterotrophic flagellates were the main bacterial predators. The CF group strongly dominated fluorescent in situ hybridization-detected cells from March to June, whereas clear changes were observed in early summer when Beta-proteobacteria and Alpha-proteobacteria increased concomitantly with maximal protist grazing pressures. The analysis of protist community structure revealed that the flagellates consisted mainly of cryptomonad forms. The dynamics of Cryptomonas sp. and Dinobryon sp. suggested the potential importance of mixotrophs as consumers of bacteria. This point was verified by an experimental approach based on fluorescent microbeads to assess the potential grazing impact of all protist taxa in the epilimnion. From the results, three distinct periods in the functioning of the epilimnetic microbial loop were identified. In early spring, mixotrophic and heterotrophic flagellates constituted the main bacterivores, and were regulated by the availability of their resources mainly during April (phase 1). Once the "clear water phase" was established, the predation pressure of metazooplankton represented a strong top-down force on all microbial compartments. During this period only mixotrophic flagellates occasionally exerted a significant bacterivory pressure (phase 2). Finally, the early summer was characterized by the highest protozoan grazing impact and by a rapid shift in the carbon pathway transfer, with a fast change-over of the main predators contribution, i.e., mixotrophic, heterotrophic flagellates and ciliates in bacterial mortality. The high abundance of ciliates during this period was consistent with the high densities of resources (heterotrophic nanoflagellates, algae, bacteria) in deep layers containing the most chlorophyll. Bacteria, as ciliates, responded clearly to increasing phytoplankton abundance, and although bacterial grazing impact could vary largely, bacterial abundance seemed to be primarily bottom-up regulated (phase 3).

Animals↗

PubMed2004

Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE.

In order to study the effect of different chloroethenes (electron acceptors) on the bacterial composition of dechlorinating communities, two reductive dechlorinating enrichment cultures were developed that were able to reduce trichloroethene (TCE) and cis-1,2-dichloroethene (cis-DCE) to ethene using hydrogen as electron donor, respectively. The inoculum for the cultures was material from a methanogenic fluidized bed reactor (FBR), which was originally seeded with digester sludge and showed a stable capacity for tetrachloroethene (PCE) reduction to ethene for over six years. Molecular methods were used to determine and compare the microbial communities of these two enrichment cultures. A clone library of bacterial 16S rRNA genes was generated for each enrichment. The clones were screened into different groups by restriction fragment length polymorphism (RFLP) analysis using two different four base pair recognition restriction enzymes. A total of 12 sequence types were identified by phylogenetic analysis of nearly complete 16S rDNA sequences ( approximately 1450 bp). The sequences were affiliated with six recognized phyla of the domain Bacteria: Firmicutes (low G+C Gram-positives), Chloroflexi (green non-sulphur bacteria), Actinobacteria (high G+C Gram-positives), Bacteroidetes (Cytophaga-Flexibacter-Bacteroides), Nitrospira and Spirochaetes. The results led to the identification of an organism closely related to Dehalococcoides ethenogenes to be the presumptive dechlorinator in both enrichments. Different electron acceptors affected the bacterial diversity and the community profiles of the two enrichments. Most of the sequences identified in our dechlorinating enrichments shared high similarities with sequences previously obtained from other enriched dechlorinating cultures and chlorinated-compound-contaminated sediments or aquifers, suggesting these bacteria may have direct or indirect roles in reductive dechlorination.

Anaerobiosis↗

PubMed2006

Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison.

Structural shifts associated with functional dynamics in a bacterial community may provide clues for identifying the most valuable members in an ecosystem. A laboratory-scale denitrifying reactor was adapted from use of non-efficient seeding sludge and was utilized to degrade quinoline and remove the chemical oxygen demand. Stable removal efficiencies were achieved after an adaptation period of six weeks. Both denaturing gradient gel electrophoresis profiling of the 16S rRNA gene V3 region and comparison of the 16S rRNA gene sequence clone libraries (LIBSHUFF analysis) demonstrated that microbial communities in the denitrifying reactor and seeding sludge were significantly distinct. The percentage of the clones affiliated with the genera Thauera and Azoarcus was 74% in the denitrifying reactor and 4% in the seeding sludge. Real-time quantitative PCR also indicated that species of the genera Thauera and Azoarcus increased in abundance by about one order of magnitude during the period of adaptation. The greater abundance of Thauera and Azoarcus in association with higher efficiency after adaptation suggested that these phylotypes might play an important role for quinoline and chemical oxygen demand removal under denitrifying conditions.

Azoarcus↗

PubMed1999

Quinone profiles in lake sediments: Implications for microbial diversity and community structures.

Microbial quinone compositions of sediment mud samples from five different lakes in Japan were studied by spectrochromatography and mass spectrometry. The total quinone content of these samples ranged from 1.97 to 18.0 nmol/g dry weight of sediment, of which a combined fraction of ubiquinones and menaquinones accounted for 42 to 74%. The remaining fraction (26 to 58%) consisted of the photosynthetic quinones, plastoquinones and phylloquinone. The sediment samples produced PQ-9 or Q-8 as the most abundant quinone type regardless of their geographic locations and depths. These results indicate that oxygenic phototrophic microorganisms and Q-8-containing proteobacteria constituted major parts of microbial populations in the lake sediment. In the surface water of the same sampling sites, plastoquinones and phylloquinone occurred in much higher proportions. These findings suggested that the high abundance of oxygenic phototrophs in the sediment muds resulted from their constant movement or sedimentation from the surface water. Numerical analyses of the quinone profiles showed that the microbial communities of the sediment were diverse and different in different lakes but similar to each other in the diversity of bioenergetic modes. Three physiological groups of microbes showing ubiquinone-mediated aerobic respiration, oxygenic photosynthesis, and menaquinone-associated respiration were suggested to inhabit the lake sediments in balance.

Journal Article↗

PubMed2006

The effect of sample size in studies of soil microbial community structure.

Replicate soil samples of 0.01, 0.1, 0.25, 1.0 and 10.0 g were taken from a single, large, homogenized sample from a field maintained as continuous meadow. The samples were processed for direct enumeration of bacterial cells and community structure assays by DGGE analysis of PCR-amplified 16S-rDNA fragments from whole community extracts. The goal was to determine the sample size or size range that produced the most consistent results (i.e., mean values) and the lowest variance. Enumeration data were analyzed by ANOVA, and the community composition fingerprints were analyzed by discriminant analysis (DA). Acceptable results were obtained for sample sizes from 0.1 to 1.0 g for both enumeration and community fingerprinting, but the size that yielded the best results for both measures was 0.25 g. The results suggest that for well homogenized silt loam soils with moderate organic matter concentrations, this sample size should produce high quality consistent results. For soils that differ in organic concentrations or clay content, a reconnaissance survey similar to the present examination is recommended.

Bacteria↗

PubMed2004

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Acrolein↗

PubMed2006

The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities.

As researchers attempt to study quorum sensing in relevant clinical or environmental settings, it is apparent that many factors have the potential to affect signaling. These factors span a range of physical, chemical, and biological variables that can impact signal production, stability and distribution. Optimizing experimental systems to natural or clinical environments may be crucial for defining when and where quorum sensing occurs. These points are illustrated in our case study of S. aureus signaling in biofilms, where signal stability may be affected by the host environment. The basic signaling schemes have been worked out at the molecular level for a few of the major quorum-sensing systems. As these studies continue to refine our understanding of these mechanisms, an emerging challenge is to identify if and when the local environment can affect signaling.

4-Butyrolactone↗

PubMed2002

Microenvironments and microbial community structure in sediments.

The aim of this study was to explore the potential of a combined chemical and microbiological approach as part of a study of organic carbon oxidation processes in sediments. An assessment of microbiological diversity using molecular techniques was carried out in combination with high resolution chemical measurements at the sediment-water interface of a coastal lagoon affected by eutrophication in autumn 2000. There was a 0.2 mm overlap between the O2 and H2S profiles. pH showed a maximum just above the sediment-water interface coinciding with an oxygen maximum, suggesting photosynthetic activity, and a minimum coinciding with the O2-H2S interface. The redox potential was high in bottom water and surface sediment, reflecting the presence of oxygen and oxides, and reached low values after a step-wise decrease at -18 mm. Reduction of Fe occurred within the biofilm at the O2-H2S interface and was mostly due to reduction by H2S. The elevated concentrations of dissolved Mn in the oxic water may have been caused either by in situ production within organic aggregates or lateral water flow from sites nearby at which Mn2+ diffuses out of the sediment. Sequences related to sulphur chemolitotrophs were retrieved from the biofilm samples, which is consistent with the small overlap between O2 and H2S observed in this biofilm. Although the resolution of techniques used was different, sequencing results were consistent with chemical data in delineating the same horizons according to redox, pH or ecological properties.

Bacteria↗

PubMed2002

Analysis of the microbial community structure and function of a laboratory scale enhanced biological phosphorus removal reactor.

A laboratory scale sequencing batch reactor (SBR) operating for enhanced biological phosphorus removal (EBPR) and fed with a mixture of volatile fatty acids (VFAs) showed stable and efficient EBPR capacity over a four-year-period. Phosphorus (P), poly-beta-hydroxyalkanoate (PHA) and glycogen cycling consistent with classical anaerobic/aerobic EBPR were demonstrated with the order of anaerobic VFA uptake being propionate, acetate then butyrate. The SBR was operated without pH control and 63.67 +/- 13.86 mg P l-1 was released anaerobically. The P% of the sludge fluctuated between 6% and 10% over the operating period (average of 8.04 +/- 1.31%). Four main morphological types of floc-forming bacteria were observed in the sludge during one year of in-tensive microscopic observation. Two of them were mainly responsible for anaerobic/aerobic P and PHA transformations. Fluorescence in situ hybridization (FISH) and post-FISH chemical staining for intracellular polyphosphate and PHA were used to determine that 'Candidatus Accumulibacter phosphatis' was the most abundant polyphosphate accumulating organism (PAO), forming large clusters of coccobacilli (1.0-1.5 micro m) and comprising 53% of the sludge bacteria. Also by these methods, large coccobacillus-shaped gammaproteobacteria (2.5-3.5 micro m) from a recently described novel cluster were glycogen-accumulating organisms (GAOs) comprising 13% of the bacteria. Tetrad-forming organisms (TFOs) consistent with the 'G bacterium' morphotype were alphaproteobacteria, but not Amaricoccus spp., and comprised 25% of all bacteria. According to chemical staining, TFOs were occasionally able to store PHA anaerobically and utilize it aerobically.

Bacteria, Anaerobic↗

PubMed2003

Nitrogenase gene diversity and microbial community structure: a cross-system comparison.

Biological nitrogen fixation is an important source of fixed nitrogen for the biosphere. Microorganisms catalyse biological nitrogen fixation with the enzyme nitrogenase, which has been highly conserved through evolution. Cloning and sequencing of one of the nitrogenase structural genes, nifH, has provided a large, rapidly expanding database of sequences from diverse terrestrial and aquatic environments. Comparison of nifH phylogenies to ribosomal RNA phylogenies from cultivated microorganisms shows little conclusive evidence of lateral gene transfer. Sequence diversity far outstrips representation by cultivated representatives. The phylogeny of nitrogenase includes branches that represent phylotypic groupings based on ribosomal RNA phylogeny, but also includes paralogous clades including the alternative, non-molybdenum, non-vanadium containing nitrogenases. Only a few alternative or archaeal nitrogenase sequences have as yet been obtained from the environment. Extensive analysis of the distribution of nifH phylotypes among habitats indicates that there are characteristic patterns of nitrogen fixing microorganisms in termite guts, sediment and soil environments, estuaries and salt marshes, and oligotrophic oceans. The distribution of nitrogen-fixing microorganisms, although not entirely dictated by the nitrogen availability in the environment, is non-random and can be predicted on the basis of habitat characteristics. The ability to assay for gene expression and investigate genome arrangements provides the promise of new tools for interrogating natural populations of diazotrophs. The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment.

Archaea↗

PubMed2002

Persistence and functional impact of a microbial inoculant on native microbial community structure, nutrient digestion and fermentation characteristics in a rumen model.

Small sub-unit (SSU) rRNA-targeted oligonucleotide probes were used to monitor the persistence of a genetically engineered bacterium inoculated in model rumens. Eight dual flow continuous culture fermenters were operated with either standard artificial saliva buffer or buffer with chondroitin sulfate (0.5 g/l) added. After 168 h of operation, fermenters were inoculated with Bacteroides thetaiotaomicron BTX (BTX), at approximately 1% of total bacteria. B. thetaiotaomicron was quantified using a species-specific probe and shown to persist in fermenters 144 h after inoculation (relative abundance 0.48% and 1.42% of total SSU rRNA with standard and chondroitin sulfate buffers, respectively). No B. thetaiotaomicron SSU rRNA was detected in fermenter samples prior to inoculation with strain BTX. Relative abundances of Bacteria, Eucarya and Archaea were not affected by either inoculation or buffer type. Fiber digestion, in particular the hemicellulose fraction, increased after strain BTX addition. Chondroitin sulfate addition to the buffer increased bacterial nitrogen flow in fermenters, but did not alter fiber digestion. Neither inoculum nor buffer type altered total short chain fatty acid (VFA) concentrations but proportions of individual VFA differed. In model rumens, B. thetaiotaomicron BTX increased fiber digestion when added to mixed ruminal microbes, independent of chondroitin sulfate addition; but further study is needed to determine effects on other fiber-digesting bacteria.

Animals↗

PubMed2006

Microbial community structure in moraine lakes and glacial meltwaters, Mount Everest.

The bacterial diversity and abundance in two moraine lakes and two glacial meltwaters (5140, 5152, 5800 and 6350 m above sea level, respectively) in the remote Mount Everest region were examined through 16S rRNA gene clone library and flow cytometry approaches. In total, 247 clones were screened by RFLP and 60 16S rRNA gene sequences were obtained, belonging to the following groups: Proteobacteria (8% alpha subdivision, 21% beta subdivision, and 1% gamma subdivision), Cytophaga-Flavobacteria-Bacteroides (CFB) (54%), Actinobacteria (4%), Planctomycetes (2%), Verrucomicrobia (2%), Fibrobacteres (1%) and Eukaryotic chroloplast (3%), respectively. The high dominance of CFB distinguished the Mount Everest waters from other mountain lakes. The highest bacterial abundance and diversity occurred in the open moraine lake at 5152 m, and the lowest in the glacial meltwater at 6350 m. Low temperature at high altitude is considered to be critical for component dominancy. At the same altitude, nutrient availability plays a role in regulating population structure. Our results also show that the bacteria in Mount Everest may be derived from different sources.

Betaproteobacteria↗

PubMed1993

Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure.

Bacterial community structures in activated sludge samples from aeration tanks of a two-stage system with a high-load first stage and a low-load second stage were analyzed with oligonucleotide probes. The probes were complementary to conserved regions of the rRNA of the alpha, beta, and gamma subclasses of proteobacteria and of all bacteria. Group-specific cell counts were determined by in situ hybridization with fluorescent probe derivatives. Contributions of the proteobacterial subclasses to total bacterial rRNA were quantified by dot blot hybridization with digoxigenin-labeled oligonucleotides. The activated sludge samples were dominated by proteobacteria from the alpha, beta, or gamma subclass. These proteobacteria account for about 80% of all active bacteria found in the activated sludge. For both samples the community structures determined with molecular techniques were compared with the composition of the heterotrophic saprophyte flora isolated on nutrient-rich medium. Probes were used to rapidly classify the isolates and to directly monitor population shifts in nutrient-amended, activated sludge samples. The rich medium favored growth of gamma-subclass proteobacteria (e.g., enterobacteria) and selected against beta-subclass proteobacteria. The culture-dependent community structure analysis of activated sludge produced partial and heavily biased results. A more realistic view will be obtained by using in situ techniques.

Bacteria↗

PubMed2006

Microbial community structure of activated sludge during aerobic granulation in an annular gap bioreactor.

A novel annular gap reactor was designed to create a controlled shear environment in which aerobic granular sludge could be developed. The bacterial and eukaryal community structures during two aerobic granular sludge experiments were tracked using denaturing gradient gel electrophoresis (DGGE). The first granule cultivation experiment, using an organic loading rate of 1.6 kg/m3d COD, resulted in biomass that was dominated by filamentous bacteria and Zoogloea ramigera colonies. A second experiment with a higher organic loading rate of 6 kg/m3d COD developed a granule-like morphology but was ultimately dominated by filamentous fungi. Species identification via DGGE band purification and DNA sequencing closely matched the observed sludge morphology and behavior.

Aerobiosis↗