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PubMed2006

Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes.

In an effort to better understand the factors contributing to patterns in freshwater bacterioplankton community composition and diversity, we coupled automated ribosomal intergenic spacer analysis (ARISA) to analysis of 16S ribosomal RNA (rRNA) gene sequences to follow the persistence patterns of 46 individual phylotypes over 3 years in Crystal Bog Lake. Additionally, we sought to identify linkages between the observed phylotype variations and known chemical and biological drivers. Sequencing of 16S rRNA genes obtained from the water column indicated the presence of phylotypes associated with the Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, TM7 and Verrucomicrobia phyla, as well as phylotypes with unknown affiliation. Employment of the 16S rRNA gene/ARISA method revealed that specific phylotypes varied independently of the entire bacterial community dynamics. Actinobacteria, which were present on greater than 95% of sampling dates, did not share the large temporal variability of the other identified phyla. Examination of phylotype relative abundance patterns (inferred using ARISA fragment relative fluorescence) revealed a strong correlation between the dominant phytoplankton succession and the relative abundance patterns of the majority of individual phylotypes. Further analysis revealed covariation among unique phylotypes, which formed several distinct bacterial assemblages correlated with particular phytoplankton communities. These data indicate the existence of unique persistence patterns for different common freshwater phylotypes, which may be linked to the presence of dominant phytoplankton species.

Bacteria↗
PubMed2003

Molecular characterization of the microbial community structure in two activated sludge systems for the advanced treatment of domestic effluents.

Although activated sludge systems with enhanced biological phosphorus removal (EBPR) represent state-of-the-art technology for phosphate removal from wastewater it is still unknown which species of bacteria are responsible for the EBPR process. The aim of this study was to compare the bacterial composition of activated sludge from two laboratory plants with different modes of operation, anoxic/oxic- (EBPR, no nitrification) and Phoredox-system (EBPR, nitrification and denitrification) with particular emphasis on microorganisms responsible for EBPR process. In addition to fluorescence in situ hybridization (FISH), we applied further rRNA-based molecular techniques like terminal restriction-fragment length polymorphism analysis and comparative 16S rDNA analysis to yield additional information and to verify the results from FISH analysis, like e.g. for the identification of polyphosphate accumulating organisms (PAO). Despite the different modes of operation only minor differences in the bacterial composition were detected by FISH analysis based on the probes used in this study. In contrast T-RFLP analysis yielded characteristic community fingerprints for each of the investigated plants and comparative 16S rDNA analysis indicated highly diverse microbial communities in both plants suggesting substantial differences in the microbial structure. The results obtained by FISH analysis with specific probes for PAOs support the presumption that not only one specific organism is responsible for the EBPR. In our case Tetrasphaera spp. dominated the PAO community, but other possible PAOs, like Microlunatus spp. and members of the Rhodocyclus group, were also detected.

Bacteria↗
PubMed2006

Effect of sheep urine deposition on the bacterial community structure in an acidic upland grassland soil.

The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.

Agrostis↗
PubMed2002

Microbial cellulose utilization: fundamentals and biotechnology.

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.

Bacteria↗
PubMed2004

Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods.

The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus appeared to dominate the communities in four of the five women. However, the community of one woman was dominated by Atopobium sp., whereas a second woman had appreciable numbers of Megasphaera sp., Atopobium sp. and Leptotrichia sp., none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to Lactobacillus crispatus, whereas the second group of two women had clones of Lactobacillus iners that were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.

Actinobacteria↗
PubMed2006

Characterizing a stable methane-utilizing mixed culture used in the synthesis of a high-quality biopolymer in an open system.

AIMS: To characterize a methane-utilizing poly-beta-hydroxybutyrate (PHB)-producing microbial community. METHODS AND RESULTS: Three different approaches based on microbiology, analytical chemistry and molecular biology were used to determine the composition of the mixed culture. The dominant species, Methylocystis sp. GB25, represents more than 86% of the total biomass. Seven accompanying bacterial species are present in the mixed culture of which two are methylotrophic bacteria and five are utilizers of complex carbon sources. Both these groups were found to be present at the same ratio with respect to each other. Results of fatty acid analysis and PCR-DGGE fingerprints reflect the stability of the mixed-culture composition in the open system during multiple continuous growth and polymer formation processes throughout a period of 29 months. The consistently high quality of the accumulated polymer further corroborates this finding. CONCLUSION: The methane-utilizing mixed culture has the potential of self-regulation resulting in a stable composition even under non-aseptic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: Avoiding the necessity of sterile conditions, as demonstrated in this paper, is an important step towards the development of a viable large-scale process for the production of PHB using cheap substrates like methane from natural or renewable sources. This is the first report characterizing a bacterial mixed culture being used for the biotechnological production of a high-value product in an open system.

Bacteria↗
PubMed1999

BIOCONTROL WITHIN THE CONTEXT OF SOIL MICROBIAL COMMUNITIES: A Substrate-Dependent Phenomenon.

Broad spectrum biological control of diseases caused by soilborne plant pathogens such as Pythium, Phytophthora, and Rhizoctonia solani requires the introduction into or presence of edaphic sources of organic nutrients in soil for sustenance of biocontrol agents. The decomposition level of organic matter critically affects the composition of bacterial taxa as well as the populations and activities of biocontrol agents. Competition, antibiosis, parasitism, and systemic induced resistance are all affected. Highly stabilized sources of Sphagnum peat consistently fail to support sustained biological control, even when inoculated with biocontrol agents. Composts, on the other hand, can serve as an ideal food base for biocontrol agents and offer an opportunity to introduce and establish specific biocontrol agents into soils, which in turn leads to sustained biological control based on the activities of microbial communities.

Journal Article↗
PubMed2006

Deep biosphere-related bacteria within the subsurface of tidal flat sediments.

Biogeochemical and microbiological processes in the upper sediment layers of tidal flats were analysed in many investigations, while deeper zones remained largely unexplored. Therefore, denaturant gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments along the depth profile of up to 5.5 m-long sediment cores was performed in comparison with lithological and geochemical parameters. The investigation revealed that different compartments of the sediment columns were characterized by specific microbial communities. These compartments were analysed by sequencing of 113 DGGE bands. The upper layers down to 160-200 cm were dominated by gamma- and delta-Proteobacteria representing more than 60% of the total number of phylotypes. Underneath, a striking shift in community composition was observed, as the Proteobacteria were replaced by Chloroflexi with more than 60% of all sequences. As sulfate was still available as an electron acceptor in these layers, the abundance of Chloroflexi might be promoted by the electron donor or the quality of the carbon source. The dominance of this group, previously known as green non-sulfur bacteria, indicates the presence of a typical deep-biosphere microbial community in relatively young subsurface sediments. Thus, tidal flats might offer a convenient possibility to study and understand certain aspects of the deep biosphere in general.

Bacteria↗
PubMedDate not supplied

[Microbiological and isotopic-geochemical investigations of meromictic lakes in Khakasia in winter].

Microbiological and isotopic-geochemical investigations of the brackish meromictic lakes Shira and Shunet were performed in the steppe region of Khakasia in winter. Measurements made with a submersed sensor demonstrated that one-meter ice transmits light in a quantity sufficient for oxygenic and anoxygenic photosynthesis. As in the summer season, in the community of phototrophic bacteria found in Lake Shira, the purple sulfur bacteria Amoebobacter purpureus dominated, whereas, in Lake Shunet, the green sulfur bacteria Pelodictyon luteolum were predominant. Photosynthetic production, measured using the radioisotopic method, was several times lower than that in summer. The rates of sulfate reduction and production and oxidation of methane in the water column and bottom sediments were also lower than those recorded in summer. The process of anaerobic methane oxidation in the sediments was an exception, being more intense in winter than in summer. The data from radioisotopic measurements of the rates of microbial processes correlate well with the results of determination of the isotopic composition of organic and mineral carbon (delta13C) and hydrogen sulfide and sulfate (delta34S) and suggest considerable seasonal variations in the activity of the microbial community in the water bodies investigated.

Bacteria↗
PubMed2006

Spatial scaling of microbial biodiversity.

A central goal in ecology is to understand the spatial scaling of biodiversity. Patterns in the spatial distribution of organisms provide important clues about the underlying mechanisms that structure ecological communities and are central to setting conservation priorities. Although microorganisms comprise much of Earth's biodiversity, little is known about their biodiversity scaling relationships relative to that for plants and animals. Here, we discuss current knowledge of microbial diversity at local and global scales. We focus on three spatial patterns: the distance-decay relationship (how community composition changes with geographic distance), the taxa-area relationship, and the local:global taxa richness ratio. Recent empirical analyses of these patterns for microorganisms suggest that there are biodiversity scaling rules common to all forms of life.

Animals↗
PubMed2006

Accurate phylogenetic classification of variable-length DNA fragments.

Metagenome studies have retrieved vast amounts of sequence data from a variety of environments leading to new discoveries and insights into the uncultured microbial world. Except for very simple communities, the encountered diversity has made fragment assembly and the subsequent analysis a challenging problem. A taxonomic characterization of metagenomic fragments is required for a deeper understanding of shotgun-sequenced microbial communities, but success has mostly been limited to sequences containing phylogenetic marker genes. Here we present PhyloPythia, a composition-based classifier that combines higher-level generic clades from a set of 340 completed genomes with sample-derived population models. Extensive analyses on synthetic and real metagenome data sets showed that PhyloPythia allows the accurate classification of most sequence fragments across all considered taxonomic ranks, even for unknown organisms. The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments >or=1 kb with high specificity.

Animals↗
PubMed2003

Scanning transmission X-ray, laser scanning, and transmission electron microscopy mapping of the exopolymeric matrix of microbial biofilms.

Confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and soft X-ray scanning transmission X-ray microscopy (STXM) were used to map the distribution of macromolecular subcomponents (e.g., polysaccharides, proteins, lipids, and nucleic acids) of biofilm cells and matrix. The biofilms were developed from river water supplemented with methanol, and although they comprised a complex microbial community, the biofilms were dominated by heterotrophic bacteria. TEM provided the highest-resolution structural imaging, CLSM provided detailed compositional information when used in conjunction with molecular probes, and STXM provided compositional mapping of macromolecule distributions without the addition of probes. By examining exactly the same region of a sample with combinations of these techniques (STXM with CLSM and STXM with TEM), we demonstrate that this combination of multimicroscopy analysis can be used to create a detailed correlative map of biofilm structure and composition. We are using these correlative techniques to improve our understanding of the biochemical basis for biofilm organization and to assist studies intended to investigate and optimize biofilms for environmental remediation applications.

Bacteria↗
PubMedDate not supplied

Soil ciliate species richness and abundance associated with the rhizosphere of different subtropical plant species.

Soil protozoa, and ciliates in particular, represent a microbial group abundant in the rhizosphere with an influential role on nutrient cycling. Under laboratory conditions, ciliates regulate the size and the composition of bacterial communities, and appear to stimulate ammonification and nitrification. In spite of their important ecological role, our understanding about the factors that control their diversity and abundance in natural forest ecosystems is still rudimentary. Plant species-specific interactions have been demonstrated between plants and soil bacteria and mycorrhizal fungi, due in part to the release of phytohormones and C- and N-rich exudates. We tested the hypothesis that the rhizosphere environments of different plant species also influence the species richness and abundance of soil ciliates. Plant effect, soil pH, moisture content, microbial biomass C, and inorganic nitrogen were measured among five plant species to determine the best predictor variables for soil ciliate species richness and total abundance in a subtropical moist forest in Puerto Rico. Based on an analysis of variance, we rejected the hypothesis that there was a plant species-specific effect on soil ciliates, unlike other microbial groups mentioned above. Using multiple regression analysis, we demonstrated that the flush of total inorganic nitrogen was the best predictor variable for both species richness and abundance of ciliates.

Animals↗
PubMedDate not supplied

[Studies on the growth and reproduction of bacterial communities on structural materials of the international space station].

Probability of microbial growth and reproduction on the ISS interior and equipment materials varying in chemical composition was studied with the strains of Bacillus subtilis, Staphylococcus epidermidis, Staphylococcus saprophyticus, Pseudomonas putida etc. sampled from the ISS environment. Controls were ground reference strains of same bacterial species. Based on our results, some of the microorganisms are able to survive and proliferate on structural materials; the ability was greater in space isolates as compared with their ground analogs. The greatest ability to grow and proliferate on materials was demonstrated by Bacillus subtilis.

Bacillus subtilis↗
PubMed1981

Effects of pharmaceutical wastes on microbial populations in surface waters at the puerto rico dump site in the atlantic ocean.

A series of cruises during 1979 and 1980 to the pharmaceutical dump site located 64 km north of Arecibo, Puerto Rico, in the Atlantic Ocean, was carried out to evaluate effects of wastes on the ecology of the microflora of surface waters of the dump site. In addition to bacteriological monitoring of the waste plume created by the release of wastes from the disposal barge, stations along a series of transects, extending north from coastal waters through and beyond the dump site, were sampled. Largest numbers of culturable bacteria on marine agar were found at stations closest to shore and in the vicinity of the dump site. Bacteria recovered on marine agar were predominantly Vibrio and Aeromonas spp., with the relative abundance of these organisms decreasing as gram-positive organisms (staphylococci, micrococci, and bacilli) became dominant in areas immediately affected by waste dumping. Total numbers of bacteria (determined by acridine orange direct counts [AODC]), which were relatively stable throughout the region, and a direct estimate of viable cells (DVC), i.e., those cells responsive to additions of yeast extract and nalidixic acid, were determined by acridine orange staining and epifluorescence microscopy. Heterotrophic bacterial activity, measured by the uptake (V(max)) of C-labeled amino acids, declined relative to distance from land. Increases in specific activity indices (DVC/AODC and V(max)/AODC) were observed near the dump site. The composite results of this study, i.e., increased specific activities (determined by two methods), increased numbers of culturable marine bacteria, and marked alteration of the taxonomic composition of the culturable bacterial community in waters within and surrounding the Puerto Rico dump site, indicate demonstrable changes in the marine microbial community in the region used for waste disposal.

Journal Article↗
PubMed1995

Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics.

Because the human gut microbiota can play a major role in host health, there is currently some interest in the manipulation of the composition of the gut flora towards a potentially more remedial community. Attempts have been made to increase bacterial groups such as Bifidobacterium and Lactobacillus that are perceived as exerting health-promoting properties. Probiotics, defined as microbial food supplements that beneficially affect the host by improving its intestinal microbial balance, have been used to change the composition of colonic microbiota. However, such changes may be transient, and the implantation of exogenous bacteria therefore becomes limited. In contrast, prebiotics are nondigestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of one or a limited number of bacterial species already resident in the colon, and thus attempt to improve host health. Intake of prebiotics can significantly modulate the colonic microbiota by increasing the number of specific bacteria and thus changing the composition of the microbiota. Nondigestible oligosaccharides in general, and fructooligosaccharides in particular, are prebiotics. They have been shown to stimulate the growth of endogenous bifidobacteria, which, after a short feeding period, become predominant in human feces. Moreover, these prebiotics modulate lipid metabolism, most likely via fermentation products. By combining the rationale of pro- and prebiotics, the concept of synbiotics is proposed to characterize some colonic foods with interesting nutritional properties that make these compounds candidates for classification as health-enhancing functional food ingredients.

Bacteria↗
PubMed2005

Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem.

The geochemical energy budgets for high-temperature microbial ecosystems such as occur at Yellowstone National Park have been unclear. To address the relative contributions of different geochemistries to the energy demands of these ecosystems, we draw together three lines of inference. We studied the phylogenetic compositions of high-temperature (>70 degrees C) communities in Yellowstone hot springs with distinct chemistries, conducted parallel chemical analyses, and carried out thermodynamic modeling. Results of extensive molecular analyses, taken with previous results, show that most microbial biomass in these systems, as reflected by rRNA gene abundance, is comprised of organisms of the kinds that derive energy for primary productivity from the oxidation of molecular hydrogen, H2. The apparent dominance by H2-metabolizing organisms indicates that H2 is the main source of energy for primary production in the Yellowstone high-temperature ecosystem. Hydrogen concentrations in the hot springs were measured and found to range up to >300 nM, consistent with this hypothesis. Thermodynamic modeling with environmental concentrations of potential energy sources also is consistent with the proposed microaerophilic, hydrogen-based energy economy for this geothermal ecosystem, even in the presence of high concentrations of sulfide.

Archaea↗
PubMed2005

Isoflavones and functional foods alter the dominant intestinal microbiota in postmenopausal women.

Dietary phytoestrogens, such as isoflavones, are used as food additives to prevent menopause-related disorders. In addition to other factors, their bioavailability strongly depends on the activity of intestinal bacteria but the underlying interactions remain poorly understood. A randomized, double-blind, placebo-controlled study was undertaken with 39 postmenopausal women to characterize changes in the dominant microbial communities of the intestinal tract after 2 mo of isoflavone supplementation with and without pro- or prebiotic. The diversity and composition of the dominant microbiota were analyzed by temporal temperature-gradient gel electrophoresis (TTGE) and fluorescent in situ hybridization. Isoflavones alone stimulated dominant microorganisms of the Clostridium coccoides-Eubacterium rectale cluster, Lactobacillus-Enterococcus group, Faecalibacterium prausnitzii subgroup, and Bifidobacterium genus. The stimulation of the Clostridium coccoides-Eubacterium rectale cluster depended on the women's equol excretion and was transient, with the exception of a prolonged bifidogenic effect. Lasting changes in the diversity of the dominant species were also observed. The probiotic strain supplied could be detected by TTGE during its passage through the intestinal tract, and ingestion of fructooligosaccharides triggered a marked and specific bifidogenic effect. In conclusion, this is the first human study that shows changes in the diversity and composition of dominant bacterial communities in response to dietary supplementation with hormone-related compounds combined with functional foods.

Aged↗