Home About us Contact
|
Home About us Contact | ||
|
|
||
Bacterial Community Structure (bacterial + community_structure)
Selected AbstractsBacterial community structure and function in a metal-working fluidENVIRONMENTAL MICROBIOLOGY, Issue 6 2003Christopher J. Van Der Gast Summary The diversity of bacterial populations colonizing spatially and temporally separated samples of the same metal-working fluid (MWF) formulation was investigated. Analyses were performed with a view to improve strategies for bioaugmentation of waste MWF in bioreactor systems and prevention of in-use MWF biodeterioration in engineering workshops. Significantly, complementary phenotypic, genotypic and in situ methods revealed that the bacterial communities in operationally exhausted MWFs had low diversity and were similar in species composition from different locations and uses. Of the 179 bacterial isolates studied, only 11 genera and 15 species were identified using fatty acid methyl ester (FAME) analysis, with culture independent analyses by 16S rDNA denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization being congruent with these FAME data. In order to gain some insight into functional role of detected populations, we correlated the MWF chemical composition and potential pollution load with bacterial abundance and community composition detected within samples. [source] Bacterial community structure of glacier forefields on siliceous and calcareous bedrockEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2009A. Lazzaro Summary Forefields of retreating glaciers represent unique opportunities to investigate the initial phases of soil formation and microbial interactions with mineral surfaces. An open question concerns the physical and chemical driving-factors affecting the establishment of microbial communities in these young ecosystems. In this study we compared the bacterial community structure of six glacier forefield soils belonging to two contrasting bedrock categories (calcareous and siliceous) through T-RFLP profiling of the 16S rRNA gene. The community profiles were correlated with an array of physical (soil texture, water holding capacity, hours of sunshine, temperature, rainfall and exposure) and chemical (TC, TN, DOC, extractable nutrients and pH) factors using canonical correspondence analysis (CCA). A first comparison of the T-RFLP profiles suggested that the degree of operational taxonomic unit (OTU) diversity of these soils was similar, and that community structure was dominated by ubiquitous taxa. CCA showed that both physical (e.g. hours of sunshine or rainfall) and chemical factors (e.g. SO2,4 or PO3,4) played an equal role in shaping the soil bacterial communities. OTUs unique to specific sites appeared to be strongly influenced by the climatic regime and by texture. Overall, the community structure of the six glacial forefields showed no clear dependence on the bedrock categories. [source] Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewaterFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Changsoo Lee Abstract Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas -like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts. [source] Microbial community dynamics in nutrient-pulsed chemostatsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2006Militza Carrero-Colón Abstract In nature, microbes are subject to nutrient fluxes. As the periodicity of nutrient flux lengthens, different physiological traits may be selected. The competitive exclusion principle stipulates that one organism will dominate these systems; however, interspecies interactions may produce a dynamic microbial community. These issues were investigated in chemostats pulsed with gelatin. Chemostats were run over 30 days with substrate addition continuously or at intervals of 0.5, 1 or 3 days. Growth rates were similar between pulse intervals. Ectoaminopeptidase activity levels remained relatively constant within a pulse interval. Bacterial community structure was monitored using denaturing gradient gel electrophoresis of PCR products of the 16S rRNA gene. There were dynamic changes at all periodicities; however, the pace of these changes decreased over time. Final communities were not identical between different treatments. The structure of persistent vs. active microbial populations was compared by denaturing gradient gel electrophoresis of the PCR and reverse transcriptase-PCR amplicons of 16S rDNA and rRNA templates, respectively. For all the chemostats, the rRNA profiles were not identical to the rDNA profiles for a sample. These experiments demonstrate that complex community dynamics can occur under environmental heterogeneities that are modest relative to those found in natural aquatic habitats. Furthermore, the physiological functionality of these dynamic communities was stable. [source] Bacterial community structure, compartmentalization and activity in a microbial fuel cellJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2006G.T. Kim Abstract Aims:, To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. Methods and Results:, Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. Conclusions:, Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. Significance and Impact of the Study:, This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell. [source] Field studies on the environmental fate of the Cry1Ab Bt-toxin produced by transgenic maize (MON810) and its effect on bacterial communities in the maize rhizosphereMOLECULAR ECOLOGY, Issue 8 2005SUSANNE BAUMGARTE Abstract Field studies were done to assess how much of the transgenic, insecticidal protein, Cry1Ab, encoded by a truncated cry1Ab gene from Bacillus thuringiensis (Bt), was released from Bt-maize MON810 into soil and whether bacterial communities inhabiting the rhizosphere of MON810 maize were different from those of the rhizosphere of nontransgenic maize cultivars. Bacterial community structure was investigated by SSCP (single-strand conformation polymorphism) of PCR-amplified 16S rRNA genes from community DNA. Using an improved extraction and detection protocol based on a commercially available ELISA, it was possible to detect Cry1Ab protein extracted from soils to a threshold concentration of 0.07 ng/g soil. From 100 ng of purified Cry1Ab protein added per gram of soil, only an average of 37% was extractable. At both field sites investigated, the amount of Cry1Ab protein in bulk soil of MON810 field plots was always lower than in the rhizosphere, the latter ranging from 0.1 to 10 ng/g soil. Immunoreactive Cry1Ab protein was also detected at 0.21 ng/g bulk soil 7 months after harvesting, i.e. in April of the following year. At this time, however, higher values were found in residues of leaves (21 ng/g) and of roots (183 ng/g), the latter corresponding to 12% of the Cry1Ab protein present in intact roots. A sampling 2 months later indicated further degradation of the protein. Despite the detection of Cry1Ab protein in the rhizosphere of MON810 maize, the bacterial community structure was less affected by the Cry1Ab protein than by other environmental factors, i.e. the age of the plants or field heterogeneities. The persistence of Cry1Ab protein emphasizes the importance of considering post-harvest effects on nontarget organisms. [source] The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genesENVIRONMENTAL MICROBIOLOGY, Issue 5 2010David L. Kirchman Summary Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the ,seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones. [source] Anthropogenic disturbance affects the structure of bacterial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 3 2010Duane Ager Summary Patterns of taxa abundance distributions are the result of the combined effects of historical and biological processes and as such are central to ecology. It is accepted that a taxa abundance distribution for a given community of animals or plants following a perturbation will typically change in structure from one of high evenness to increasing dominance. Subsequently, such changes in evenness have been used as indicators of biological integrity and environmental assessment. Here, using replicated experimental treehole microcosms perturbed with different concentrations of the pollutant pentachlorophenol, we investigated whether changes in bacterial community structure would reflect the effects of anthropogenic stress in a similar manner to larger organisms. Community structure was visualized using rank,abundance plots fitted with linear regression models. The slopes of the regression models were used as a descriptive statistic of changes in evenness over time. Our findings showed that bacterial community structure reflected the impact and the recovery from an anthropogenic disturbance. In addition, the intensity of impact and the rate of recovery to pre-perturbation structure were dose-dependent. These properties of bacterial community structures may potentially provide a metric for environmental assessment and regulation. [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] The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimesENVIRONMENTAL MICROBIOLOGY, Issue 6 2008Achim Schmalenberger Summary Sulfonates are a key component of the sulfur present in agricultural soils. Their mobilization as part of the soil sulfur cycle is mediated by rhizobacteria, and involves the oxidoreductase AsfA. In this study, the effect of fertilization regime on rhizosphere bacterial asfA distribution was examined at the Broadbalk long-term wheat experiment, Rothamsted, UK, which was established in 1843, and has included a sulfur-free treatment since 2001. Direct isolation of desulfonating rhizobacteria from the wheat rhizospheres led to the identification of several Variovorax and Polaromonas strains, all of which contained the asfA gene. Rhizosphere DNA was isolated from wheat rhizospheres in plots fertilized with inorganic fertilizer with and without sulfur, with farmyard manure or from unfertilized plots. Genetic profiling of 16S rRNA gene fragments [denaturing gradient gel electrophoresis (DGGE)] from the wheat rhizospheres revealed that the level of inorganic sulfate in the inorganic fertilizer was correlated with changes in the general bacterial community structure and the betaproteobacterial community structure in particular. Community analysis at the functional gene level (asfA) showed that 40% of clones in asfAB clone libraries were affiliated to the genus Variovorax. Analysis of asfAB -based terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed considerable differences between sulfate-free treatments and those where sulfate was applied. The results suggest the occurrence of desulfonating bacterial communities that are specific to the fertilization regime chosen and that arylsulfonates play an important role in rhizobacterial sulfur nutrition. [source] Detection of glycolate oxidase gene glcD diversity among cultured and environmental marine bacteriaENVIRONMENTAL MICROBIOLOGY, Issue 10 2006W. W. Y. Lau Summary Of eight laboratory cultures of marine ,- and ,- Proteobacteria tested, growth on glycolate as a sole carbon source was detected for only three species: Pseudomonas stutzeri, Oceanimonas doudoroffii and Roseobacter sp. isolate Y3F. Degenerate polymerase chain reaction (PCR) primers were designed to amplify glcD, which encodes the D-subunit of the enzyme glycolate oxidase; glcD could be amplified only from those cultures that grew on glycolate. The PCR primers were used to explore glcD diversity in four field samples collected from different ocean environments: an Atlantic Gulf Stream Ring, sampled above and below the thermocline and two Pacific coastal sites, Parks Bay and San Juan Channel, WA. Environmental glcD sequences belonged to six major bacterial phylogenetic groups, with most sequences forming novel clades with no close relatives. Different patterns of glcD diversity were observed within and between the two nutrient regimes. Comparison of glcD and 16S rDNA diversity and analyses of available bacterial genomes and a metgenomic library from the Sargasso Sea show that glycolate-utilizing potential exists in only a subset of bacteria. Glycolate is produced in marine environments mainly by phytoplankton. Examination of glcD diversity will aid in understanding the influence of phytoplankton on bacterial community structure. [source] Structural diversity of bacterial communities in a heavy metal mineralized granite outcropENVIRONMENTAL MICROBIOLOGY, Issue 3 2006Deirdre Gleeson Summary This laboratory study of a variably mineralized and hydrothermally altered granite outcrop investigated the influences of rock-surface chemistry and heavy metal content on resident bacterial populations. Results indicated that elevated heavy metal concentrations had a profound impact on bacterial community structure, with strong relationships found between certain ribotypes and particular chemical/heavy metal elements. Automated ribosomal intergenic sequence analysis (ARISA) was used to assess the nature and extent of bacterial diversity, and this was combined with chemical analysis and multivariate statistics to identify the main geochemical factors influencing bacterial community structure. A randomization test revealed significant changes in bacterial structure between samples, while canonical correspondence analysis (CCA) related each individual ARISA profile to linear combinations of the chemical variables (mineralogy, major element and heavy metal concentrations) revealing the geochemical factors that correlated with changes in the ARISA data. anova was performed to further explore interactions between individual ribotypes and chemical/heavy metal composition, and revealed that a high proportion of ribotypes correlated significantly with heavy metals. [source] Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis)ENVIRONMENTAL MICROBIOLOGY, Issue 7 2005Hong Yang Summary Differences in microenvironment and interactions of microorganisms within and across habitat boundaries should influence structure and diversity of the microbial communities within an ecosystem. We tested this hypothesis using the well characterized gut tract of the European subterranean termite Reticulitermes santonensis as a model. By cloning and sequencing analysis and molecular fingerprinting (terminal restriction fragment length polymorphism), we characterized the bacterial microbiota in the major intestinal habitats , the midgut, the wall of the hindgut paunch, the hindgut fluid and the intestinal protozoa. The bacterial community was very diverse (> 200 ribotypes) and comprised representatives of several phyla, including Firmicutes (mainly clostridia, streptococci and Mycoplasmatales -related clones), Bacteroidetes, Spirochaetes and a number of Proteobacteria, all of which were unevenly distributed among the four habitats. The largest group of clones fell into the so-called Termite group 1 (TG-1) phylum, which has no cultivated representatives. The majority of the TG-1 clones were associated with the protozoa and formed two phylogenetically distinct clusters, which consisted exclusively of clones previously retrieved from the gut of this and other Reticulitermes species. Also the other clones represented lineages of microorganisms that were exclusively recovered from the intestinal tract of termites. The termite specificity of these lineages was underscored by the finding that the closest relatives of the bacterial clones obtained from R. santonensis were usually derived also from the most closely related termites. Overall, differences in diversity between the different gut habitats and the uneven distribution of individual phylotypes support conclusively that niche heterogeneity is a strong determinant of the structure and spatial organization of the microbial community in the termite gut. [source] Adaptation to nickel spiking of bacterial communities in neocaledonian soilsENVIRONMENTAL MICROBIOLOGY, Issue 1 2003Marina Héry Summary Adaptation to nickel of bacterial communities of two extreme neocaledonian soils (an ultramafic soil and an acidic soil) was investigated by nickel spiking and compared with adaptation in a non-neocaledonian soil used as reference. Soil microcosms were amended with nickel chloride (NiCl2), and bacterial community structure was analysed with the ribosomal intergenic spacer analysis (RISA) technique. Then, bacterial populations that respond to nickel stress were identified by cloning and sequencing. In the ultramafic soil, a shift occurred on day zero on the assay profiles and consisted of the emergence of a bacterial group closely related to the Ralstonia/Oxalobacter/Burkholderia group. It is hypothesized that NiCl2 had a physico-chemical impact on soil structure. Fourteen days after nickel spiking, another shift occurred in the two soils that concerned a bacterial group belonging to the Actinomycete group. Only a few changes occurred in the bacterial community structure of the neocaledonian soils compared with those of the reference soil, which is more affected by nickel spiking. These results suggest that neocaledonian soil bacteria are particularly well adapted to nickel. [source] Bacterial community structure of glacier forefields on siliceous and calcareous bedrockEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2009A. Lazzaro Summary Forefields of retreating glaciers represent unique opportunities to investigate the initial phases of soil formation and microbial interactions with mineral surfaces. An open question concerns the physical and chemical driving-factors affecting the establishment of microbial communities in these young ecosystems. In this study we compared the bacterial community structure of six glacier forefield soils belonging to two contrasting bedrock categories (calcareous and siliceous) through T-RFLP profiling of the 16S rRNA gene. The community profiles were correlated with an array of physical (soil texture, water holding capacity, hours of sunshine, temperature, rainfall and exposure) and chemical (TC, TN, DOC, extractable nutrients and pH) factors using canonical correspondence analysis (CCA). A first comparison of the T-RFLP profiles suggested that the degree of operational taxonomic unit (OTU) diversity of these soils was similar, and that community structure was dominated by ubiquitous taxa. CCA showed that both physical (e.g. hours of sunshine or rainfall) and chemical factors (e.g. SO2,4 or PO3,4) played an equal role in shaping the soil bacterial communities. OTUs unique to specific sites appeared to be strongly influenced by the climatic regime and by texture. Overall, the community structure of the six glacial forefields showed no clear dependence on the bedrock categories. [source] Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environmentsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Rui Zhang Abstract Bacterioplankton community structures under contrasting subtropical marine environments (Hong Kong waters) were analyzed using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of predominant bands for samples collected bimonthly from 2004 to 2006 at five stations. Generally, bacterial abundance was significantly higher in the summer than in the winter. The general seasonal variations of the bacterial community structure, as indicated by cluster analysis of the DGGE pattern, were best correlated with temperature at most stations, except for the station close to a sewage discharge outfall, which was best explained by pollution-indicating parameters (e.g. biochemical oxygen demand). Anthropogenic pollutions appear to have affected the presence and the intensity of DGGE bands at the stations receiving discharge of primarily treated sewage. The relative abundance of major bacterial species, calculated by the relative intensity of DGGE bands after PCR amplification, also indicated the effects of hydrological or seasonal variations and sewage discharges. For the first time, a systematic molecular fingerprinting analysis of the bacterioplankton community composition was carried out along the environmental and pollution gradient in a subtropical marine environment, and it suggests that hydrological conditions and anthropogenic pollutions altered the total bacterial community as well as the dominant bacterial groups. [source] Progress towards understanding the fate of plasmids in bacterial communitiesFEMS MICROBIOLOGY ECOLOGY, Issue 1 2008Frances R. Slater Abstract Plasmid-mediated horizontal gene transfer influences bacterial community structure and evolution. However, an understanding of the forces which dictate the fate of plasmids in bacterial populations remains elusive. This is in part due to the enormous diversity of plasmids, in terms of size, structure, transmission, evolutionary history and accessory phenotypes, coupled with the lack of a standard theoretical framework within which to investigate them. This review discusses how ecological factors, such as spatial structure and temporal fluctuations, shape both the population dynamics and the physical features of plasmids. Novel data indicate that larger plasmids are more likely to be harboured by hosts in complex environments. Plasmid size may therefore be determined by environmentally mediated fitness trade-offs. As the correlation between replicon size and complexity of environment is similar for plasmids and chromosomes, plasmids could be used as tractable tools to investigate the influence of ecological factors on chromosomes. Parallels are drawn between plasmids and bacterial facultative symbionts, including the evolution of some members of both groups to a more obligate relationship with their host. The similarity between the influences of ecological factors on plasmids and bacterial symbionts suggests that it may be appropriate to study plasmids within a classical ecological framework. [source] Spatial and temporal heterogeneity of the bacterial communities in stream epilithic biofilmsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Gavin Lear Abstract The spatial and temporal variability in bacterial communities within freshwater systems is poorly understood. The bacterial composition of stream epilithic biofilms across a range of different spatial and temporal scales both within and between streams and across the profile of individual stream rocks was characterised using a community DNA-fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA). The differences in bacterial community structure between two different streams were found to be greater than the spatial variability within each stream site, and were larger than the weekly temporal variation measured over a 10-week study period. Greater variations in bacterial community profiles were detected on different faces of individual stream rocks than between whole rocks sampled within a 9-m stream section. Stream temperature was found to be the most important determinant of bacterial community variability using distance-based redundancy analysis (dbRDA) of ARISA data, which may have broad implications for riparian zone management and ecological change as a consequence of global warming. The combination of ARISA with multivariate statistical methods and ordination, such as multidimensional scaling (MDS), permutational manova and RDA, provided rapid and effective methods for quantifying and visualising variation in bacterial community structure, and to identify potential drivers of ecological change. [source] Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewaterFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Changsoo Lee Abstract Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas -like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts. [source] Bacterial community analysis of shallow groundwater undergoing sequential anaerobic and aerobic chloroethene biotransformationFEMS MICROBIOLOGY ECOLOGY, Issue 2 2007Todd R. Miller Abstract At Department of Energy Site 300, beneficial hydrocarbon cocontaminants and favorable subsurface conditions facilitate sequential reductive dechlorination of trichloroethene (TCE) and rapid oxidation of the resultant cis- dichloroethene (cis -DCE) upon periodic oxygen influx. We assessed the geochemistry and microbial community of groundwater from across the site. Removal of cis -DCE was shown to coincide with oxygen influx in hydrocarbon-containing groundwater near the source area. Principal component analysis of contaminants and inorganic compounds showed that monitoring wells could be differentiated based upon concentrations of TCE, cis -DCE, and nitrate. Structurally similar communities were detected in groundwater from wells containing cis -DCE, high TCE, and low nitrate levels. Bacteria identified by sequencing 16S rRNA genes belonged to seven phylogenetic groups, including Alpha -, Beta -, Gamma - and Deltaproteobacteria, Nitrospira, Firmicutes and Cytophaga,Flexibacter,Bacteroidetes (CFB). Whereas members of the Burkholderiales and CFB group were abundant in all wells (104,109 16S rRNA gene copies L,1), quantitative PCR showed that Alphaproteobacteria were elevated (>106 L,1) only in wells containing hydrocarbon cocontaminants. The study shows that bacterial community structure is related to groundwater geochemistry and that Alphaproteobacteria are enriched in locales where cis -DCE removal occurs. [source] Soil parent material is a key determinant of the bacterial community structure in arable soilsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Andreas Ulrich Abstract The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes. [source] Seasonal and management influences on bacterial community structure in an upland grassland soilFEMS MICROBIOLOGY ECOLOGY, Issue 3 2005Nabla M. Kennedy Abstract Floristically diverse Nardo,Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement. [source] Effects of soil improvement treatments on bacterial community structure and soil processes in an upland grassland soilFEMS MICROBIOLOGY ECOLOGY, Issue 1 2003Neil D. Gray Abstract Temporal temperature gradient electrophoresis (TTGE) analysis of 16S rRNA gene fragments amplified with primers selective for eubacteria and ,-proteobacterial ammonia-oxidising bacteria (AOB) was used to analyse changes in bacterial and AOB community profiles of an upland pasture following soil improvement treatments (addition of sewage sludge and/or lime). Community structure was compared with changes in activity assessed by laboratory measurements of basal respiration and ammonia oxidation potentials, and with measurements of treatment- and time-related changes in soil characteristics. The predominant bacterial populations had a high degree of similarity under all treatment regimens, which was most pronounced early in the growing season. Most of the differences that occurred between soil samples with time could be accounted for by spatial and temporal variation; however, analysis of variance and cluster analysis of similarities between 16S rDNA TTGE profiles indicated that soil improvement treatments exerted some effect on community structure. Lime application had the greatest influence. The impact of soil improvement treatments on autotrophic ammonia oxidation was significant and sustained, especially in soils which had received sewage sludge and lime treatments in combination. However, despite obvious changes in soil characteristics, e.g. pH and soil nitrogen, increasing heterogeneity in the AOB community structure over time obscured the treatment effects observed at the beginning of the experiment. Nevertheless, time series analysis of AOB TTGE profiles indicated that the AOB community in improved soils was more dynamic than in control soils where populations were found to be relatively stable. These observations suggest that the AOB populations exhibited a degree of functional redundancy. [source] Comparison of DNA- and RNA-based bacterial community structures in soil exposed to 2,4-dichlorophenolJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2009L. Lillis Abstract Aims:, To examine the effect of the pollutant 2,4-dichlorophenol on DNA- and RNA-based bacterial communities in soil. Methods and Results:, Soil was exposed to 100 mg kg,1 of 2,4-dichlorophenol (2,4-DCP), and degradation was monitored over 35 days. DNA and RNA were coextracted, and terminal restriction fragment length polymorphism (T-RFLP) was used to report changes in bacterial communities in response to the presence of the chlorophenol. The phylogenetic composition of the soil during degradation was determined by creating a clone library of amplified 16S rRNA sequences from both DNA and reverse-transcribed RNA from exposed soil. Resulting clones were sequenced, and putative identities were assigned. Conclusions:, A significant difference between active (RNA-based) and total (DNA-based) bacterial community structure was observed for both T-RFLP and phylogenetic analyses in response to 2,4-DCP, with more pronounced changes seen in RNA-based communities. Phylogenetic analysis indicated the dominance of Proteobacteria in both profiles. Significance and Impact of the Study:, This study describes the response of soil bacterial communities to the addition of the xenobiotic compound 2,4-DCP, and highlights the importance of including RNA-based 16S rRNA analysis to complement any molecular study in a perturbed soil. [source] Bacterial community structure, compartmentalization and activity in a microbial fuel cellJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2006G.T. Kim Abstract Aims:, To characterize bacterial populations and their activities within a microbial fuel cell (MFC), using cultivation-independent and cultivation approaches. Methods and Results:, Electron microscopic observations showed that the fuel cell electrode had a microbial biofilm attached to its surface with loosely associated microbial clumps. Bacterial 16S rRNA gene libraries were constructed and analysed from each of four compartments within the fuel cell: the planktonic community; the membrane biofilm; bacterial clumps (BC) and the anode biofilm. Results showed that the bacterial community structure varied significantly between these compartments. It was observed that Gammaproteobacteria phylotypes were present at higher numbers within libraries from the BC and electrode biofilm compared with other parts of the fuel cell. Community structure of the MFC determined by analyses of bacterial 16S rRNA gene libraries and anaerobic cultivation showed excellent agreement with community profiles from denaturing gradient gel electrophoresis (DGGE) analysis. Conclusions:, Members of the family Enterobacteriaceae, such as Klebsiella sp. and Enterobacter sp. and other Gammaproteobacteria with Fe(III)-reducing and electrochemical activity had a significant potential for energy generation in this system. Significance and Impact of the Study:, This study has shown that electrochemically active bacteria can be enriched using an electrochemical fuel cell. [source] Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analysesJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2001A. Ogino Aims:,The objective of this study was to investigate the changes in the indigenous bacterial community structure for assessing the impact of biostimulation on spilled oil. Methods and Results:,Changes in the bacterial community structure were monitored by denaturing gradient gel electrophoresis (DGGE) and clone library methods based on 16S rRNA gene (rDNA) sequences. The results of DGGE, coupled with the use of the Shannon index and principal component analysis (PCA) and clone library analyses, were consistent. In the treated (fertilized) area, one operational taxonomic unit (OTU) became dominant during the fertilization period, and it was most closely related to Pseudomonas putida. Conclusions:,The bacterial community structure in the treated area was markedly different from that in the control (non-fertilized) area during the fertilization period, but in the two areas it became similar at 14 weeks after the end of fertilization. Significance and Impact of the Study:,The results suggest that the bacterial community structure was disrupted by the biostimulation treatment, but that it recovered immediately after the end of fertilization. [source] Long-term effects on the digestive tract of feeding large amounts of resistant starch: A study in pigsJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 11 2007Daniel Martínez-Puig Abstract The present study aimed to assess the digestive consequences of the long-term intake of two starches providing different amounts of resistant starch. Growing pigs were used as the animal model and meal-fed for 14 weeks on a diet containing a high amount of either raw potato starch (RPS) or corn starch (CS). Digestive adaptation was chronologically evaluated by measuring organic matter (OM), crude protein (CP), neutral detergent fibre (NDF) and starch digestibility. After 97 days, whole-tract digestibility of OM, CP and NDF was lower for RPS- compared to CS-fed pigs, whereas no differences were observed in faecal starch digestibility. In contrast, starch digestibility was reduced in the proximal compartments (ileum, caecum and proximal colon) of animals fed the RPS diet. The concentration of short-chain fatty acids (SCFAs; P < 0.05), and purine bases (PBs; P < 0.01) was also higher in distal colon and rectum of animals fed the RPS diet. Changes in bacterial community structure (dendogram analyses) were seen in the rectum. Biodiversity tends to increase more in RPS compared to CS fed animals (34.1 vs. 28.8; P = 0.07). Among SCFAs, the proportion of butyrate was two-fold higher in proximal colon digesta of RPS compared to CS fed pigs (0.20 vs. 0.11; P < 0.05). Increased butyrate formation in the colon reduced the number of apoptosis per crypt in the proximal colonic mucosa (0.38 vs. 0.62; P < 0.05). RPS fermentation reduced indices associated with damage to intestinal epithelial cells, such as crypt cell hyperproliferation and magnesium excretion. Long-term ingestion of RPS induces pronounced changes of the digestive tract and their microflora, modifying mineral absorption and colonic morphology for which health benefits are likely to be associated. Copyright © 2007 Society of Chemical Industry [source] Relative Abundance and Species Composition of Gram-Negative, Aerobic Bacteria Associated with the Gut of Juvenile White Shrimp Litopenaeus vannamei Reared in Oligotrophic Well Water and Eutrophic Pond WaterJOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 2 2000Shaun M. Moss Gut bacteria may contribute significantly to the growth and survival of cultured shrimp, although little is known about factors that affect bacterial community structure in shrimp guts. The objective of this study was to determine the abundance and species composition of gut bacteria in juvenile white shrimp Litopenaeus vannamei reared in two different environments. Eight 120-L tanks were stocked at a density of 8 shrimphank. Two treatments were tested for 10 d and consisted of tanks receiving flow-through water from one of two sources: 1) well water pumped from a sea-water aquifer (Well treatment), and 2) pond water pumped from an intensive shrimp pond (Pond treatment). Shrimp mid- and hindguts were excised on days 1, 3, 6, and 10 for enumeration of gram-negative, aerobic bacteria by quantifying colony-forming units (CFU) using standard microbiological plating techniques. Identification of bacterial isolates was made using the Biologa® GN Microplate system. Bacterial numbers were significantly greater (P > 0.05) in Well shrimp than in Pond shrimp on days 1 and 3. Following day 3, a decrease in bacterial numbers occurred in the Well shrimp, and no significant differences between treatments were observed on days 6 or 10. Guts from Well shrimp were dominated by Vibrio and Aero-monas, and these two genera accounted for 80,851 of the bacteria on each sampling day. Guts from Pond shrimp exhibited a greater bacterial diversity and were dominated by Vibrio, Aeromonas, and Pseudomonas. Flavobacterium were identified in the guts of Pond shrimp on days 3 and 10, but were not identified in any of the Well shrimp. A greater understanding of gut bacteria-shrimp interactions could lead to increased production and profitability for shrimp farmers through the development of more cost-effective feeds and novel disease control strategies. [source] rpoB -PCR amplified gene and temporal temperature gradient gel electrophoresis: a rapid tool to analyse bacterial strains representative of cold-smoked salmon microfloraLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2004S. Giacomazzi Abstract Aim:, To evaluate rpoB gene as a biomarker of microbial biodiversity associated to cold-smoked salmon by a novel nested-polymerase chain reaction/temporal temperature gradient gel electrophoresis (PCR/TTGE) technique applied on pure cultures of reference strains. Methods and Results:, DNA obtained from pure cultures of reference strains was used in a succession of a first PCR amplification of rpoB fragment with degenerated nonclamped primers and a nested-PCR with nondegenerated clamped primers. PCR products were then applied on a TTGE gel in order to analyse strains profile. High quantity of nested-PCR products were obtained for each tested strain and TTGE profiles showed a good separation between the different reference bacteria and an easy way to associate one band to one species. Conclusion:, The nested-PCR/TTGE technique used in this study is a promising way of investigating bacterial community structure of cold-smoked salmon or other food matrix. Significance and Impact of the Study:, Because of its single copy state leading to single band profiles in TTGE, rpoB constitute a good potential molecular marker for further development of cold-smoked salmon biodiversity analysis. [source] Microbial colonisation of artificial and deep-sea sediments in the Arctic OceanMARINE ECOLOGY, Issue 4 2009Corinna Kanzog Abstract Although environmental factors such as grain size and organic carbon content may influence the distribution of microbes in marine sediments, there has been little experimental study of the topic to date. To investigate how those sediment variables affect microbial colonisation under in situ conditions, deep-sea sediments and artificial sediments (glass beads, sands) were incubated in the Arctic deep sea at 2500 m water depth with or without chitin, one of the most important carbon polymers in marine environments. Microbial abundance, biomass, chitobiase activity and changes in community structure were monitored after 7 days and 1 year. In control sediments without chitin addition, no significant changes in microbial abundance, biomass and activity were observed after 1 year. In the presence of chitin, however, considerable increases in these parameters were recorded in all three sediment types tested. Regardless of chitin addition, natural deep-sea sediments were always associated with higher values of microbial abundance, biomass and activity compared with artificial sediments. Sediment type was always found to be the most significant factor explaining variation in enzymatic activity and bacterial community structure as compared to the effects of chitin amount, incubation time, and changes in cell number or biomass. Overall, this is the first in situ study that has addressed the effects of multiple factors and their interactions on abundance, biomass, activity and community structure of microbial communities in the deep Arctic Ocean. [source] | ||||||||||||||||||||||||||||