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Microbial Community Structure (microbial + community_structure)
Selected AbstractsMicrobial community structure of ethanol type fermentation in bio-hydrogen productionENVIRONMENTAL MICROBIOLOGY, Issue 5 2007Nanqi Ren Summary Three continuous stirred-tank reactors (CSTRs) were used for H2 production from molasses wastewater at influent pH of 6.0,6.5 (reactor A), 5.5,6.0 (reactor B), or 4.0,4.5 (reactor C). After operation for 28 days, the microbial community formed ethanol type (C), propionate type (A) and ethanol-butyrate-mixed type (B) fermentation. The H2 production rate was the highest for ethanol type fermentation, 0.40 l (g VSS),1 day,1 or 0.45 l H2 (g COD removed),1. Microbial community dynamics and diversity were analysed using double-gradient denaturing gradient gel electrophoresis (DG-DGGE). Denaturing gradient gel electrophoresis profiles indicated that the community structures changed quickly in the first 14 days. Phylogenetic analysis indicated that the dominant bacterial groups were low G+C Gram-positive bacteria, Bacteroides, ,-Proteobacteria and Actinobacteria; ,-Proteobacteria, ,-Proteobacteria, ,-Proteobacteria and Spirochaetes were also presented as minor groups in the three reactors. H2 -producing bacteria were affiliated with Ethanoligenens, Acetanaerobacterium, Clostridium, Megasphaera, Citrobacter and Bacteroides. An ethanol-based H2 -producing bacterium, Ethanoligenens harbinense CGMCC1152, was isolated from reactor C and visualized using fluorescence in situ hybridization (FISH) to be 19% of the eubacteria in reactor C. In addition, isoenzyme activity staining for alcohol dehydrogenase (ADH) supported that the majority of ethanol-producing bacteria were affiliated with Ethanoligenens in the microbial community. [source] Anaerobic redox cycling of iron by freshwater sediment microorganismsENVIRONMENTAL MICROBIOLOGY, Issue 1 2006Karrie A. Weber Summary The potential for microbially mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. Most probable number enumerations revealed the presence of significant populations of Fe(III)-reducing (approximately 108 cells ml,1) and Fe(II)-oxidizing, nitrate-reducing organisms (approximately 105 cells ml,1) in the freshwater sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (approximately 1 mM) medium with a small quantity (1% v/v) of wetland sediment, and resulted in the transient accumulation of NO2, and production of a mixture of gaseous end-products (N2O and N2) and NH4+. Fe(III) oxide (high surface area goethite) reduction took place after NO3, was depleted and continued until all the acetate was utilized. Addition of NO3, after Fe(III) reduction ceased resulted in the immediate oxidation of Fe(II) coupled to reduction of NO3, to NH4+. No significant NO2, accumulation was observed during nitrate-dependent Fe(II) oxidation. No Fe(II) oxidation occurred in pasteurized controls. Microbial community structure in the enrichment was monitored by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified 16S rDNA and reverse transcription polymerase chain reaction-amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different time points during the experiment. Strong similarities in dominant members of the microbial community were observed in the Fe(III) reduction and nitrate-dependent Fe(II) oxidation phases of the experiment, specifically the common presence of organisms closely related (, 95% sequence similarity) to the genera Geobacter and Dechloromonas. These results indicate that the wetland sediments contained organisms such as Geobacter sp. which are capable of both dissimilatory Fe(III) reduction and oxidation of Fe(II) with reduction of NO3, to NH4+. Our findings suggest that microbially catalysed nitrate-dependent Fe(II) oxidation has the potential to contribute to a dynamic anaerobic Fe redox cycle in freshwater sediments. [source] Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengersBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2010Prathap Parameswaran Abstract We compared the microbial community structures that developed in the biofilm anode of two microbial electrolysis cells fed with ethanol, a fermentable substrate,one where methanogenesis was allowed and another in which it was completely inhibited with 2-bromoethane sulfonate. We observed a three-way syntrophy among ethanol fermenters, acetate-oxidizing anode-respiring bacteria (ARB), and a H2 scavenger. When methanogenesis was allowed, H2 -oxidizing methanogens were the H2 scavengers, but when methanogenesis was inhibited, homo-acetogens became a channel for electron flow from H2 to current through acetate. We established the presence of homo-acetogens by two independent molecular techniques: 16S rRNA gene based pyrosequencing and a clone library from a highly conserved region in the functional gene encoding formyltetrahydrofolate synthetase in homo-acetogens. Both methods documented the presence of the homo-acetogenic genus, Acetobacterium, only with methanogenic inhibition. Pyrosequencing also showed a predominance of ethanol-fermenting bacteria, primarily represented by the genus Pelobacter. The next most abundant group was a diverse community of ARB, and they were followed by H2 -scavenging syntrophic partners that were either H2 -oxidizing methanogens or homo-acetogens when methanogenesis was suppressed. Thus, the community structure in the biofilm anode and suspension reflected the electron-flow distribution and H2 -scavenging mechanism. Biotechnol. Bioeng. 2010;105: 69,78. © 2009 Wiley Periodicals, Inc. [source] Effect of environmental variables on eukaryotic microbial community structure of land-fast Arctic sea iceENVIRONMENTAL MICROBIOLOGY, Issue 3 2010Brian Eddie Summary Sea ice microbial community structure affects carbon and nutrient cycling in polar seas, but its susceptibility to changing environmental conditions is not well understood. We studied the eukaryotic microbial community in sea ice cores recovered near Point Barrow, AK in May 2006 by documenting the composition of the community in relation to vertical depth within the cores, as well as light availability (mainly as variable snow cover) and nutrient concentrations. We applied a combination of epifluorescence microscopy, denaturing gradient gel electrophoresis and clone libraries of a section of the 18S rRNA gene in order to compare the community structure of the major eukaryotic microbial phylotypes in the ice. We find that the community composition of the sea ice is more affected by the depth horizon in the ice than by light availability, although there are significant differences in the abundance of some groups between light regimes. Epifluorescence microscopy shows a shift from predominantly heterotrophic life styles in the upper ice to autotrophy prevailing in the bottom ice. This is supported by the statistical analysis of the similarity between the samples based on the denaturing gradient gel electrophoresis banding patterns, which shows a clear difference between upper and lower ice sections with respect to phylotypes and their proportional abundance. Clone libraries constructed using diatom-specific primers confirm the high diversity of diatoms in the sea ice, and support the microscopic counts. Evidence of protistan grazing upon diatoms was also found in lower sections of the core, with implications for carbon and nutrient recycling in the ice. [source] The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cyclingENVIRONMENTAL MICROBIOLOGY, Issue 11 2008Diana R. Nemergut Summary Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0,5 cm) samples from five control and five long-term N-amended plots established and maintained at the Niwot Ridge Long-term Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N-amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N-amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G-lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function. [source] Disturbance and recovery of microbial community structure and function following Hurricane FrancesENVIRONMENTAL MICROBIOLOGY, Issue 3 2007Anthony C. Yannarell Summary Disturbance and recovery influence microbial community structure and ecosystem functions in most natural environments. This study from a hypersaline Bahamian lagoon details the response of a benthic cyanobacterial mat to disturbance by Hurricane Frances, a category-4 storm. Clone libraries of cyanobacterial small subunit r-RNA genes and nitrogenase genes revealed significant shifts in cyanobacterial and diazotroph community composition following the hurricane. Post-hurricane clone libraries were dominated by sequences that had been rare in pre-hurricane communities. In spite of this dominance shift, re-colonizing mat communities performed nitrogen fixation and photosynthesis at rates within the normal range of variation measured in the mat at similar salinities. There was a tendency for nitrogen fixation rates from mats re-colonizing sites with hurricane-related sand deposition to be higher than those from mats re-colonizing sites without significant sand deposition. This suggests that the altered communities responded to a carbon : nitrogen imbalance that was particularly pronounced in areas subjected to disturbance by sand burial. The post-hurricane dominance of organisms that had been previously rare suggests that pre-hurricane diversity and functional redundancy contributed to the rapid recovery of ecosystem function in the post-disturbance environment. [source] Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary systemENVIRONMENTAL MICROBIOLOGY, Issue 9 2005Anne E. Bernhard Summary Ammonia-oxidizing bacteria (AOB) play an important role in nitrogen cycling in estuaries, but little is known about AOB diversity, distribution and activity in relation to the chemical and physical changes encountered in estuary systems. Although estuarine salinity gradients are well recognized to influence microbial community structure, few studies have examined the influence of varying salinity on the diversity and stability of AOB populations. To investigate these relationships, we collected sediment samples from low-, mid- and high-salinity sites in Plum Island Sound estuary, MA, during spring and late summer over 3 years. Ammonia-oxidizing bacteria distribution and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) analysis of the ammonia monooxygenase (amoA) gene, and fragments were identified by screening amoA clone libraries constructed from each site. Most striking was the stability and low diversity of the AOB community at the high-salinity site, showing little variability over 3 years. Ammonia-oxidizing bacteria at the high-salinity site were not closely related to any cultured AOB, but were most similar to Nitrosospira spp. Ammonia-oxidizing bacteria at the mid- and low-salinity sites were distributed among Nitrosospira- like sequences and sequences related to Nitrosomonas ureae/oligotropha and Nitrosomonas sp. Nm143. Our study suggests that salinity is a strong environmental control on AOB diversity and distribution in this estuary. [source] Nitrogenase gene diversity and microbial community structure: a cross-system comparisonENVIRONMENTAL MICROBIOLOGY, Issue 7 2003Jonathan P. Zehr Summary 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. [source] Distribution of microbial biomass and phospholipid fatty acids in Podzol profiles under coniferous forestEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2000H. Fritze Summary Microbial-derived phospholipid fatty acids (PLFAs) can be used to characterize the microbial communities in soil without the need to isolate individual fungi and bacteria. They have been used to assess microbial communities of humus layers under coniferous forest, but nothing is known of their distribution in the deeper soil. To investigate the vertical distribution we sampled nine Podzol profiles on a 100-m-long transect in a coniferous forest and analysed for their microbial biomass and PLFA pattern to a depth of 0.4 m. The transect covered a fertility gradient from Vaccinium vitis-idaea forest site type to Vaccinium myrtillus forest site type. The cores were divided into humus (O) and eluvial (E) layers and below that into 10-cm sections and designated as either illuvial (B) or parent material (C), or as a combination (BC). Two measures of microbial biomass analyses were applied: substrate-induced respiration (SIR) to determine microbial biomass C (Cmic), and the sum of the extracted microbial-derived phospholipid fatty acids (totPLFA). The soil fertility had no effect on the results. The Cmic correlated well with totPLFA (r=,0.86). The microbial biomass decreased with increasing depth. In addition the PLFA pattern changed with increased depth as assessed with principal component analysis, indicating a change in the microbial community structure. The composition of the PLFAs in the O layer differed from that in the E layer and both differed from the upper part of the B layer and from the rest of the BC layers. The deeper parts of the B layer (BC1, BC2 and BC3) were similar to one other. The O layer had more 18:2,6, a PLFA indicator of fungi, whereas the E layer contained relatively more of the PLFAs 16:1,9, 18:1,7 and cy19:0 common in gram-negative bacteria. With increased depth the relative amount of 10Me18:0, the PLFA indicator for actinomycetes, increased. We conclude that the PLFA method is a promising discriminator between the microbial community structures of the horizons in Podzols. [source] Effect of temperature change on the composition of the bacterial and archaeal community potentially involved in the turnover of acetate and propionate in methanogenic rice field soilFEMS MICROBIOLOGY ECOLOGY, Issue 2 2010Matthias Noll Abstract The microbial community structure was investigated together with the path of methane production in Italian rice field soil incubated at moderate (35 °C) and high (45 °C) temperature using terminal restriction fragment length polymorphism and stable isotope fractionation. The structure of both the archaeal and bacterial communities differed at 35 °C compared with 45 °C, and acetoclastic and hydrogenotrophic methanogenesis dominated, respectively. Changing the incubation of the 45 °C soil to different temperatures (25, 30, 35, 40, 45, 50 °C) resulted in a dynamic change of both microbial community structure and stable isotope fractionation. In all treatments, acetate first accumulated and then decreased. Propionate was also transiently produced and consumed. It is noteworthy that acetate was also consumed at thermophilic conditions, although archaeal community composition and stable isotope fractionation indicated that acetoclastic methanogenesis did not operate. Instead, acetate must have been consumed by syntrophic acetate oxidizers. The transient accumulation and subsequent consumption of acetate at thermophilic conditions was specifically paralleled by terminal restriction fragments characteristic for clostridial cluster I, whereas those of clostridial clusters I and III, Acidaminococcaceae and Heliobacteraceae, paralleled the thermophilic turnover of both acetate and propionate. [source] Microbial ecology of corals, sponges, and algae in mesophotic coral environmentsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2010Julie B. Olson Abstract Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone. [source] Soil microbial community structure in cucumber rhizosphere of different resistance cultivars to fusarium wiltFEMS MICROBIOLOGY ECOLOGY, Issue 3 2010Huaiying Yao Abstract Cucumber fusarium wilt is a common soil-borne disease. We hypothesize that there is a relationship between the severity of disease and soil microbial ecology. In this work, culturable microbial populations, lipid fatty acid and community-level physiological profiles (CLPP) from rhizosphere soils of four different cucumber cultivars were investigated. Comparatively higher actinomycetes, mycorrhizal colonization and higher ratios of bacteria to fungi were found in the two resistant cultivars compared with the two susceptible cultivars. CLPP analysis showed that catabolic diversity indices were higher in the presence of two resistant cultivars. Phospholipid fatty acid (PLFA) profiles suggested that fungal (18:2,6,9c) PLFA was enriched in the rhizosphere soils of the two susceptible cultivars, but some bacterial (16:0 and 15:0a) PLFAs were found in a lower relative abundance in these soils. The neutral lipid fatty acid 16:1,5, which is an indicator of arbuscular mycorrhizal fungi, was enriched in the rhizosphere soils of the two resistant cultivars. All the three methods suggested that plant genotype had a significant impact on the soil microbial community composition and activity, and the differences in the rhizosphere microbial community may result in the differences in the resistance to fusarium wilt. [source] Reproducibility of a microbial river water community to self-organize upon perturbation with the natural chemical enantiomers, R - and S -carvoneFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Katja Lehmann Abstract A river water microbial community was studied in response to perturbation with the monoterpene enantiomers R - and S -carvone. The microbial community structure and function was also evaluated after enantiomers exposure was switched. Microbial communities were evaluated by length heterogeneity PCR. The addition of R - and S -carvone enriched for a range of functionally different communities: enantiomer-selective, racemic and ones that contain both. After 5 days incubation, the R - and S -carvone treatments developed a range of dominant microbial communities, which were increasingly dissimilar from the ones in which no carvone degradation had taken place (R -values: R -carvone 0.743, S -carvone 0.5007). There was an increase in the evenness of the microbial community structure upon carvone depletion. After the cross-over, the rate of carvone utilization was significantly faster than after the first carvone addition (P=0.008) as demonstrated by concomitant carvone and oxygen depletion. The main R -degrading community (450,456 bp) appeared enantioselective and largely unable to degrade S -carvone, whereas the S -carvone-degrading community (502,508 bp) appeared to have racemic catabolic capacity. In conclusion, chemical perturbations, such as enantiomers, might generate a significant shift in the river microbial ecology that can have implications for the function of a river in both a spatial and temporal context. [source] Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2004Christian Rudolph Abstract Recently, a unique microbial community, growing in a whitish, macroscopically visible strings-of-pearls-like structure was discovered in the cold, sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. The pearls interior is predominated by microcolonies of the non-methanogenic SM1 euryarchaeon; the outer part of the pearls is mainly composed of Thiothrix. To screen sulfidic ecosystems for the distribution of such unique microbial communities, comparative microbial and geochemical analyses of cold, sulfidic springs of three geographically distinct locations in Bavaria, Germany, and Dalyan, Turkey, were performed. Here, we report on the discovery and study of another type of strings-of-pearls revealing a new microbial community structure. While the SM1 euryarchaeon is again the predominant archaeal constituent, the bacterial partner is the so-called IMB1 ,-proteobacterium. Due to the predominance of the IMB1 ,-proteobacterium, the strings-of-pearls reveal a fluffy and greyish macroscopical appearance. The phylogenetic survey revealed SM1 euryarchaeal relatives, designated as SM1 group, in all sites studied, indicating a widespread distribution of these archaea in terrestrial ecosystems. [source] Field-scale 13C-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic carbon: tracing acetate assimilation and mineralization in a petroleum hydrocarbon-contaminated aquiferFEMS MICROBIOLOGY ECOLOGY, Issue 3 2002Silvina A. Pombo Abstract This study was conducted to determine the feasibility of labeling phospholipid-derived fatty acids (PLFA) of an active microbial population with a 13C-labeled organic substrate in the denitrifying zone of a petroleum hydrocarbon-contaminated aquifer during a single-well push-pull test. Anoxic test solution was prepared from 500 l of groundwater with addition of 0.5 mM Br, as a conservative tracer, 0.5 mM NO3,, and 0.25 mM [2- 13C]acetate. At 4, 23 and 46 h after injection, 1000 l of test solution/groundwater mixture were sequentially extracted. During injection and extraction phases we measured Br,, NO3, and acetate concentrations, characterized the microbial community structure by PLFA and fluorescent in situ hybridization (FISH) analyses, and determined 13C/12C ratios in dissolved inorganic carbon (DIC) and PLFA. Computed first-order rate coefficients were 0.63±0.08 day,1 for NO3, and 0.70±0.05 day,1 for acetate consumption. Significant 13C incorporation in DIC and PLFA was detected as early as 4 h after injection. At 46 h we measured ,13C values of up to 5614, in certain PLFA (especially monounsaturated fatty acids), and up to 59.8, in extracted DIC. Profiles of enriched PLFA and FISH analysis suggested the presence of active denitrifiers. Our results demonstrate the applicability of 13C labeling of PLFA and DIC in combination with FISH to link microbial structure and activities at the field scale during a push-pull test. [source] Freshwater and marine virioplankton: a brief overview of commonalities and differencesFRESHWATER BIOLOGY, Issue 6 2008STEVEN W. WILHELM Summary 1. Viruses are a pervasive component of microbial food webs in both marine and freshwater systems. The abundance of viruses in individual aquatic systems appears to be independent of salinity but related to the biomass of primary and secondary producers as well as seasonal effects. Burst size, virus production rate and the percentage of microbial cells carrying a viral burden also appear to be more closely correlated to trophic status than to salinity. 2. In marine environments, the roles of planktonic viruses as regulators of carbon and nutrient cycling as well as microbial community structure have been a focus of numerous studies, yet the roles of freshwater virioplankton remain much less studied. Nevertheless, a survey of published freshwater studies demonstrates that virioplankton recycle important quantities of growth-limiting nutrients from hosts via generation of dead particulate and dissolved organic matter during cell lysis, and suggests that both the chemical speciation and concentration of these organic compounds and nutrients may have important influences on the microbial community. 3. Parallel observations on the spatial patterns and dynamics of microbial mortality due to viruses or grazing are more advanced in freshwaters than in marine environments. However, the constraints that determine whether virus- or grazer-mediated mortality dominates are not yet understood in either environment. 4. Application of molecular approaches has facilitated the examination of the diversity and ecological dynamics of specific viral populations and entire communities. The depth of detail achieved in marine environments towards characterizing these populations and communities is just beginning to be matched in freshwater systems. The few available data suggest that viruses targeting-related hosts in freshwater and marine systems may be genetically distinct. 5. Although the role of viruses in aquatic systems is complex and remains insufficiently studied, our survey of the literature indicates that, despite some differences, many of the controls on virioplankton activity and diversity are similar in marine and freshwater environments. [source] Effects of short- and long-term water-level drawdown on the populations and activity of aerobic decomposers in a boreal peatlandGLOBAL CHANGE BIOLOGY, Issue 2 2007KRISTA JAATINEN Abstract We analysed the response of microbial communities, characterized by phospholipid fatty acids (PLFAs), to changing hydrological conditions at sites with different nutrient levels in a southern boreal peatland. Although PLFAs of Gram-negative bacteria were characteristic of the peatland complex, microbial communities differed among sites (ombrotrophic bog, oligotrophic fen, mesotrophic fen) and sampling depths (0,5, 5,10, 10,20, 20,30 cm). The microbial communities in each site changed significantly following water-level drawdown. The patterns of change varied among sites and sampling depths. The relative proportion of Gram-negative bacteria decreased in the upper 10 cm but increased in deeper layers of the fen sites. Fungi benefited from water-level drawdown in the upper 5 cm of the mesotrophic fen, but suffered in the drier surfaces of the ombrotrophic bog, especially in the 5,10 cm layer. In contrast, actinobacteria suffered from water-level drawdown in the mesotrophic fen, but benefited in the drier surfaces of the ombrotrophic bog. Basal respiration rate correlated positively with pH and fungal PLFA, and negatively with depth. We suggest that the changes in microbial community structure after persistent water-level drawdown follow not only the hydrological conditions but also the patterns of vegetation change. Our results imply that changes in structure and activity of the microbial community in response to climate change will be strongly dependent on the type of peatland. [source] Characterization of an enrichment culture debrominating tetrabromobisphenol A and optimization of its activity under anaerobic conditionsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2010L. Iasur-Kruh Abstract Aim:, To study the effects of incubation conditions on the microbial community structure and activity of a TBBPA-debrominating enrichment culture composed of bacterial and archaeal species. Methods and Results:, The effects of the methanogen inhibitor 2-bromoethanesulfonate (BES), of the antibiotic ampicillin, of substrate (tetrabromobisphenol A, TBBPA) omission and availability of different electron donors on microbial community structure and activity were examined under anaerobic conditions. Debromination of TBBPA was blocked in the presence of ampicillin, while long-term incubation with BES resulted in delayed debromination activity. The results suggest that the bacterial species responsible for the debromination of TBBPA, while archaeal species involved in electron donor metabolism. The enrichment culture lost its debromination activity after cultivation for 9 months without TBBPA, concomitantly with the disappearance of two DNA bands in a denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments corresponding to Pelobacter carbinolicus and Sphaerochaeta sp. TQ1 that were present in the original culture. When butyrate was used as an electron donor, TBBPA debromination activity was attenuated. When acetate was used as the electron donor, no debromination was observed and in addition, there was a decrease in the abundance of the mcrA gene. Conclusions:, The results indicate that to maintain a high rate of TBBPA debromination activity, it is essential to preserve the microbial community structure (bacterial and archaeal members) of this culture and supply an electron donor that produces high amounts of hydrogen when fermented. Significance and Impact of the Study:, The study provides important information for the management of cultures to be used in bioremediation of TBBPA contaminated sites. [source] Aerobic granules for low-strength wastewater treatment: formation, structure, and microbial communityJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 7 2009Shu-Guang Wang Abstract BACKGROUND: To validate the possibility of aerobic granulation at a lower organic loading rate (OLR) than 2 kg COD m,3 day,1 (GS 1) in a sequencing batch reactor (SBR), the formation, structure, and microbial community of granular sludge (GS) were investigated. RESULTS: The overall experimental process involved the following stages: acclimation, granulation, maturation, and stabilization. The optical microscopic showed the structural changes from fluffy activated sludge (AS) to GS and scanning electron microscope (SEM) examination revealed that GS 1 was irregular filamentous aggregates composed mainly of various filamentous species, while the aerobic granules cultivated at OLR 1.68,4.20 kg COD m,3 day,1 (GS 2) was mycelial pellets consisting of fungi and filamentous microorganisms. A Biolog Ecoplate analysis indicated that significant differences existed between the microbial community structure and the substrate's utilization of AS and different GS samples. CONCLUSION: GS 1 was achieved and different from GS 2 in the formation, structure, and microbial community. Aerobic granulation with low strength wastewater is of importance for the full-scale application of this technology. Copyright © 2009 Society of Chemical Industry [source] Recovery of soil microbial community structure after fire in a sagebrush-grassland ecosystemLAND DEGRADATION AND DEVELOPMENT, Issue 5 2010S. R. Dangi Abstract Recovery of the soil microbial community after fire in a sagebrush-grassland ecosystem was examined using a chronosequence of four sites ranging in time since fire from 3,39 years. The successional stage communities examined included Recent Burn (3,years since fire, ysf), Establishment (7,ysf), Expansion (21,ysf), and Mature (39,ysf). Aboveground standing plant biomass increased with time since disturbance to the Mature stage where sagebrush became dominant over herbaceous species. Phospholipid fatty acid (PLFA) analysis was used to characterize the microbial community structure. Soil microbial community productivity generally appeared to be similar to the Mature site soil (39,ysf) within 7,years of fire. Diversity of PLFAs detected in soils, at both depths, increased from a low value of 29 at the Recent site to a high of 37 at the Establishment site and then decreased again to 31 at the Mature stage site. Canonical variates analysis indicated important disparities in microbial community structure at the four sites. Greatest disparities were observed in microbial community structure between the Recent and Establishment stages but greater similarity between the Recent stage and the sagebrush dominated Mature stage. This study emphasizes both short-term and long-term changes in the belowground community and suggests that soil microbial communities are highly resilient to disturbances after prescribed fire. Copyright © 2010 John Wiley & Sons, Ltd. [source] Cultivation of low-temperature (15°C), anaerobic, wastewater treatment granulesLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2009J. O'Reilly Abstract Aims:, Anaerobic sludge granules underpin high-rate waste-to-energy bioreactors. Granulation is a microbiological phenomenon involving the self-immobilization of several trophic groups. Low-temperature anaerobic digestion of wastes is of intense interest because of the economic advantages of unheated bioenergy production technologies. However, low-temperature granulation of anaerobic sludge has not yet been demonstrated. The aims of this study were to (i) investigate the feasibility of anaerobic sludge granulation in cold (15°C) bioreactors and (ii) observe the development of methanogenic activity and microbial community structure in developing cold granules. Methods and Results:, One mesophilic (R1; 37°C) and two low-temperature (R2 and R3, 15°C) laboratory-scale, expanded granular sludge bed bioreactors were seeded with crushed (diameter <0·4 mm) granules and were fed a glucose-based wastewater for 194 days. Bioreactor performance was assessed by chemical oxygen demand removal, biogas production, granule growth and temporal methanogenic activity. Granulation was observed in R2 and R3 (up to 33% of the sludge). Elevated hydrogenotrophic methanogenesis was observed in psychrophilically cultivated biomass, but acetoclastic methanogenic activity was also retained. Denaturing gradient gel electrophoresis of archaeal 16S rRNA gene fragments indicated that a distinct community was associated with developing and mature granules in the low-temperature (LT) bioreactors. Conclusions:, Granulation was observed at 15°C in anaerobic bioreactors and was associated with H2/CO2 -mediated methanogenesis and distinct community structure development. Significance and Impact of the Study:, Granulation underpins high-rate anaerobic waste treatment bioreactors. Most LT bioreactor trials have employed mesophilic seed sludge, and granulation <20°C was not previously documented. [source] The effect of carbon source on microbial community structure and Cr(VI) reduction rateBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Athanasia G. Tekerlekopoulou Abstract In the present work, the effect of the carbon source on microbial community structure in batch cultures derived from industrial sludge and hexavalent chromium reduction was studied. Experiments in aerobic batch reactors were carried out by amending industrial sludge with two different carbon sources: sodium acetate and sucrose. In each of the experiments performed, four different initial Cr(VI) concentrations of: 6, 13, 30 and 115,mg/L were tested. The change of carbon source in the batch reactor from sodium acetate to sucrose led to a 1.3,2.1 fold increase in chromium reduction rate and to a 5- to 9.5-fold increase in biomass. Analysis of the microbial structure in the batch reactor showed that the dominant communities were bacterial species (Acinetobacter lwoffii, Defluvibacter lusatiensis, Pseudoxanthomonas japonensis, Mesorhizium chacoense, and Flavobacterium suncheonense) when sodium acetate was used as carbon source and fungal strains (Trichoderma viride and Pichia jadinii), when sodium acetate was replaced by sucrose. These results indicate that the carbon source is a key parameter for microbial dynamics and enhanced chromium reduction and should be taken into account for efficient bioreactor design. Biotechnol. Bioeng. 2010;107: 478,487. © 2010 Wiley Periodicals, Inc. [source] Perturbation-independent community development in low-temperature anaerobic biological wastewater treatment bioreactorsBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2010Pádhraig Madden Abstract The reproducibility and stability of low- temperature anaerobic wastewater treatment systems undergoing transient perturbations was investigated. Three identical anaerobic expanded granular sludge bed-based bioreactors were used to degrade a volatile fatty acid and glucose-based wastewater under sub-ambient (15°C) conditions. The effect of a variety of environmental perturbations on bioreactor performance was assessed by chemical oxygen demand removal. Temporal microbial community development was monitored by denaturation gradient gel electrophoresis (DGGE) of 16S rRNA genes extracted from sludge granules. Methanogenic activity was monitored using specific methanogenic activity assays. Bioreactor performance and microbial population dynamics were each well replicated between both experimental bioreactors and the control bioreactor prior to, and after the implementation of most of the applied perturbations. Gene fingerprinting data indicated that Methanosaeta sp. were the persistent, keystone members of the archaeal community, and likely were pivotal for the physical stability and maintenance of the granular biofilms. Cluster analyses of DGGE data suggested that temporal shifts in microbial community structure were predominantly independent of the applied perturbations. Biotechnol. Bioeng. 2010;105: 79,87. © 2009 Wiley Periodicals, Inc. [source] The utilization of glycogen accumulating organisms for mixed culture production of polyhydroxyalkanoatesBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2009*Article first published online: 15 JUN 200, Simon Bengtsson Abstract Production of polyhydroxyalkanoates (PHAs) by an open mixed culture enriched in glycogen accumulating organisms (GAOs) under alternating anaerobic,aerobic conditions with acetate as carbon source was investigated. The culture exhibited a stable enrichment performance over the 450-day operating period with regards to phenotypic behavior and microbial community structure. Candidatus Competibacter phosphatis dominated the culture at between 54% and 70% of the bacterial biomass throughout the study, as determined by fluorescence in situ hybridization. In batch experiments under anaerobic conditions, PHA containing 3-hydroxybutyrate (3HB) and 27,mol-% 3-hydroxyvalerate (3HV) was accumulated up to 49% of cell dry weight utilizing the glycogen pool stored in the SBR cycle. Under aerobic and ammonia limited conditions, PHA comprising only 3HB was accumulated to 60% of cell dry weight. Glycogen was consumed during aerobic PHA accumulation as well as under anaerobic conditions, but with different stoichiometry. Under aerobic conditions 0.31 C-mol glycogen was consumed per consumed C-mol acetate compared to 0.99 under anaerobic conditions. Both the PHA biomass content and the specific PHA production rate obtained were similar to what is typically obtained using the more commonly applied aerobic dynamic feeding strategy. Biotechnol. Bioeng. 2009; 104: 698,708 © 2009 Wiley Periodicals, Inc. [source] Effect of oxygen gradients on the activity and microbial community structure of a nitrifying, membrane-aerated biofilmBIOTECHNOLOGY & BIOENGINEERING, Issue 6 2008Leon S. Downing Abstract Shortcut nitrogen removal, that is, removal via formation and reduction of nitrite rather than nitrate, has been observed in membrane-aerated biofilms (MABs), but the extent, the controlling factors, and the kinetics of nitrite formation in MABs are poorly understood. We used a special MAB reactor to systematically study the effects of the dissolved oxygen (DO) concentration at the membrane surface, which is the biofilm base, on nitrification rates, extent of shortcut nitrification, and microbial community structure. The focus was on anoxic bulk liquids, which is typical in MAB used for total nitrogen (TN) removal, although aerobic bulk liquids were also studied. Nitrifying MABs were grown on a hollow-fiber membrane exposed to 3 mg,N/L ammonium. The MAB intra-membrane air pressure was varied to achieve different DO concentrations at the biofilm base, and the bulk liquid was anoxic or with 2 g,m,3 DO. With 2.2 and 3.5 g,m,3 DO at the biofilm base, and with an anoxic bulk-liquid, the ammonium fluxes were 0.75 and 1.0 g,N,m,2,day,1, respectively, and nitrite was the main oxidized nitrogen product. However, with membrane DO of 5.5 g,m,3, and either zero or 2 g,m,3 DO in the bulk, the ammonium flux was around 1.3 g,N,m,2,day,1, and nitrate flux increased significantly. For all experiments, the cell density of ammonium oxidizing bacteria (AOB) was relatively uniform throughout the biofilm, but the density of nitrite oxidizing bacteria (NOB) decreased with decreasing biofilm DO. Among NOB, Nitrobacter spp. were dominant in biofilm regions with 2 g,m,3 DO or greater, while Nitrospira spp. were dominant in regions with less than 2 g,m,3 DO. A biofilm model, including AOB, Nitrobacter spp., and Nitrospira spp., was developed and calibrated with the experimental results. The model predicted the greatest extent of nitrite formation (95%) and the lowest ammonium oxidation flux (0.91 g,N,m,2,day,1) when the membrane DO was 2 g,m,3 and the bulk liquid was anoxic. Conversely, the model predicted the lowest extent of nitrite formation (40%) and the highest ammonium oxidation flux (1.5 g,N,m,2,day,1) when the membrane-DO and bulk-DO were 8 g,m,3 and 2 g,m,3, respectively. The estimated kinetic parameters for Nitrospira spp., revealed a high affinity for nitrite and oxygen. This explains the dominance of Nitrospira spp. over Nitrobacter spp. in regions with low nitrite and oxygen concentrations. Our results suggest that shortcut nitrification can effectively be controlled by manipulating the DO at the membrane surface. A tradeoff is made between increased nitrite accumulation at lower DO, and higher nitrification rates at higher DO. Biotechnol. Bioeng. © 2008 Wiley Periodicals, Inc. [source] Modified implant surfaces show different biofilm compositions under in vivo conditionsCLINICAL ORAL IMPLANTS RESEARCH, Issue 8 2009Birte Größner-Schreiber Abstract Objective: Plaque accumulation on implant surfaces can result in peri-implantitis with potential implant loss. The aim of the present study was to examine the influence of zirconium nitride (ZrN) as a potential implant surface on the biofilm composition and diversity in vivo. Material and methods: ZrN- or titanium (Ti)-coated glass specimens and ZrN or roughened Ti discs were used as substrates. Pure glass and polished titanium served as controls. The specimens were mounted on removable intraoral splints in five adults. After 24 h of intraoral exposure, the biofilms were analyzed applying single-strand conformation polymorphism (SSCP analysis) of 16S rRNA genes. Sequence analysis of the dominant bands excised from the SSCP fingerprints allowed to taxonomically describe bacteria derived from biofilm samples. Results: The highest number of bands was counted on pure glass and Ti 800. ZrN-coated glass and ZrN-coated titanium discs showed the lowest values for species richness. However, no significant differences were observed regarding the diversity of the identified bacterial species among all the surfaces examined. A total of 46 different bacteria were identified. The dominant bands within the fingerprints indicated bacteria belonging to the Streptococcus group as identified by their 16S rDNA sequence. Conclusion: A coating of glass surfaces with ZrN significantly reduced the species richness in early bacterial colonization but the diversity was not significantly changed. In consideration of the results obtained by this and former studies a ZrN coating appears to rather modify the quantity of early bacterial adherence than the quality of the microbial community structure. [source] Active bacterial community structure along vertical redox gradients in Baltic Sea sedimentENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Anna Edlund Summary Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, ,64 and ,337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths. [source] Distribution of microbial biomass and phospholipid fatty acids in Podzol profiles under coniferous forestEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2000H. Fritze Summary Microbial-derived phospholipid fatty acids (PLFAs) can be used to characterize the microbial communities in soil without the need to isolate individual fungi and bacteria. They have been used to assess microbial communities of humus layers under coniferous forest, but nothing is known of their distribution in the deeper soil. To investigate the vertical distribution we sampled nine Podzol profiles on a 100-m-long transect in a coniferous forest and analysed for their microbial biomass and PLFA pattern to a depth of 0.4 m. The transect covered a fertility gradient from Vaccinium vitis-idaea forest site type to Vaccinium myrtillus forest site type. The cores were divided into humus (O) and eluvial (E) layers and below that into 10-cm sections and designated as either illuvial (B) or parent material (C), or as a combination (BC). Two measures of microbial biomass analyses were applied: substrate-induced respiration (SIR) to determine microbial biomass C (Cmic), and the sum of the extracted microbial-derived phospholipid fatty acids (totPLFA). The soil fertility had no effect on the results. The Cmic correlated well with totPLFA (r=,0.86). The microbial biomass decreased with increasing depth. In addition the PLFA pattern changed with increased depth as assessed with principal component analysis, indicating a change in the microbial community structure. The composition of the PLFAs in the O layer differed from that in the E layer and both differed from the upper part of the B layer and from the rest of the BC layers. The deeper parts of the B layer (BC1, BC2 and BC3) were similar to one other. The O layer had more 18:2,6, a PLFA indicator of fungi, whereas the E layer contained relatively more of the PLFAs 16:1,9, 18:1,7 and cy19:0 common in gram-negative bacteria. With increased depth the relative amount of 10Me18:0, the PLFA indicator for actinomycetes, increased. We conclude that the PLFA method is a promising discriminator between the microbial community structures of the horizons in Podzols. [source] Determination of microbial community structures of shrimp floc cultures by biomarkers and analysis of floc amino acid profilesAQUACULTURE RESEARCH, Issue 2 2008Zhi Yong Ju Abstract Simple, rapid and reliable methods are required to monitor the microbial community change in aquatic pond for better animal performance. Four floc (suspended organic matter) samples were collected from outdoor raceways and tanks used for culturing Pacific white shrimp Litopenaeus vannamei. Twenty-two chlorophyll (Chl) and carotenoid pigments were separated, identified and quantified using high-performance liquid chromatography,ultraviolet/Vis-mass spectrometry in the freeze-dried floc samples. Algal community composition (diatoms, chlorophytes, cyanobacteria, dinoflagellates and cryptophytes) was determined by measuring concentrations of the respective taxonomic biomarkers (carotenoid fucoxanthin, lutein, zeaxanthin, peridinin and alloxanthin) as independent variables and Chl a as the dependent variable using a multiple regression model. This analysis found that the phytoplankton community of the floc samples from two groups of shrimp tanks (32 g L,1 -salinity) were diatom-dominated (81.7% and 84.4%); and two floc samples from shrimp raceways (5 and 18 g L,1 -salinity) were chlorophyte-dominated (75.4% and 82.3%). Assessment of total algal and bacterial biomass by quantification of Chl a and muramic acid, respectively, indicated that the 18 g L,1 -salinity raceway sample was bacteria-dominated, whereas the other three floc samples were algae-dominated. Sample protein quality was evaluated by its essential amino acid (AA) score and index. Arginine and lysine were found to be the two most limiting AAs for all floc samples. [source] Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengersBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2010Prathap Parameswaran Abstract We compared the microbial community structures that developed in the biofilm anode of two microbial electrolysis cells fed with ethanol, a fermentable substrate,one where methanogenesis was allowed and another in which it was completely inhibited with 2-bromoethane sulfonate. We observed a three-way syntrophy among ethanol fermenters, acetate-oxidizing anode-respiring bacteria (ARB), and a H2 scavenger. When methanogenesis was allowed, H2 -oxidizing methanogens were the H2 scavengers, but when methanogenesis was inhibited, homo-acetogens became a channel for electron flow from H2 to current through acetate. We established the presence of homo-acetogens by two independent molecular techniques: 16S rRNA gene based pyrosequencing and a clone library from a highly conserved region in the functional gene encoding formyltetrahydrofolate synthetase in homo-acetogens. Both methods documented the presence of the homo-acetogenic genus, Acetobacterium, only with methanogenic inhibition. Pyrosequencing also showed a predominance of ethanol-fermenting bacteria, primarily represented by the genus Pelobacter. The next most abundant group was a diverse community of ARB, and they were followed by H2 -scavenging syntrophic partners that were either H2 -oxidizing methanogens or homo-acetogens when methanogenesis was suppressed. Thus, the community structure in the biofilm anode and suspension reflected the electron-flow distribution and H2 -scavenging mechanism. Biotechnol. Bioeng. 2010;105: 69,78. © 2009 Wiley Periodicals, Inc. [source] | ||||||||||||||||||||||||||||