SEARCH · Search PubMed

Results for “microbial community composition”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources

PubMed2004

Respirometric activities of heterotrophic and nitrifying populations in aerobic granules developed at different substrate N/COD ratios.

Aerobic granules were successfully developed at substrate N/COD ratios ranging from 5/100 to 30/100 by weight. By measuring respective respirometric activities of heterotrophic, ammonia-oxidizing, and nitrite-oxidizing bacteria, it was found that the relative abundance of nitrifying bacteria over heterotrophs in aerobic granules was closely related to the substrate N/COD ratios. Results further showed that the populations of both ammonia and nitrite oxidizers were significantly enriched with the increase of the substrate N/COD ratio, while a decreasing trend of heterotrophic population was observed in the aerobic granules. These seem to indicate that high substrate N/COD ratio favors the selection of nitrifying bacteria in the aerobic granules, while the relative activity of nitrifying population against heterotrophic population evolved until a balance between two populations was reached in the aerobic granular sludge community. Moreover, cell elemental composition was correlated with the shift in microbial populations, e.g., the enriched nitrifying population in the aerobic granules resulted in a high cell nitrogen content normalized to cell carbon content. This study provides a good insight into microbial interaction in aerobic granules.

Aerobiosis↗

PubMed1985

X-ray microanalytic method for measurement of dry matter and elemental content of individual bacteria.

A method for the determination of dry matter and elemental content of individual bacterial cells is described. The method is based on energy-dispersive X-ray microanalysis in a transmission electron microscope. A theory for area correction of intensity is developed. Escherichia coli in the late exponential phase of growth and early stationary phase (glucose limited) had an average dry matter content of 278 and 154 fg/cell, respectively. Of the elements detected, sodium, magnesium, phosphorus, sulphur, chlorine, potassium, and calcium together made up 15 to 17% of the dry matter content. A phosphorus content of 4.2 to 5.4% of the dry matter was found in these cells. Volume measurements of air-dried cells gave an average of 1.20 to 1.25 micron3. These results emphasize that dry matter content and elemental composition can be measured directly on single cells from complex microbial communities.

Electron Probe Microanalysis↗

PubMed2005

The effect of raw milk microbial flora on the sensory characteristics of Salers-type cheeses.

The sensory characteristics of Salers Protected Denomination of Origin raw-milk cheeses are linked to the biochemical composition of the raw material (milk) and to the resultant microbial community. To evaluate the influence of the microbial community on sensory characteristics, Salers-type cheeses were manufactured with the same pasteurized milk, reinoculated with 3 different microbial communities from 3 different filtrates from microfiltered milks. Each cheese was subjected to microbial counts (on selective media), biochemical tests, and volatile and sensory component analyses at different times of ripening. Adding different microbial communities to specimens of the same (biochemically identical) pasteurized milk lead to different sensory characteristics of the cheeses. Cheeses with fresh cream, hazelnut, and caramel attributes were opposed to those with fermented cream, chemical, and garlic flavors. The aromatic compounds identified (esters, acids, alcohols, and aldehydes) in these cheeses were quite similar. Nevertheless, one milk was distinguished by a higher content of acetoin, and lower 2-butanone and 3-methylpentanone concentrations. Over the production period of 1 mo, the different cheeses were characterized by the same balance of the microbial population assessed by microbial counts on different media. This was associated with the stability of some sensory attributes describing these cheeses. Nevertheless, there was no linear correlation between microbial flora data and sensory characteristics as measured in this study.

Acetoin↗

PubMed2006

Ecological consequences of carbon substrate identity and diversity in a laboratory study.

Plants return a wide range of carbon (C) substrates to the soil system. The decomposition rate of these substrates is determined by their chemical nature, yet few studies have examined the relative ecological role of specific substrates (i.e., substrate identity) or mixtures of substrates. Carbon substrate identity and diversity may alter soil chemistry and soil community composition, resulting in changes in belowground ecosystem functions such as decomposition and nutrient transfer, creating feedbacks that may affect plant growth and the aboveground community. A laboratory experiment was set up in which eight C substrates of varying chemical complexity were added to a base soil singly, in pairs, fours, or with all eight together every four days over a 92-day period. After 92 days these soils were analyzed for changes in chemistry, microbial community structure, and components of ecosystem functioning. The identity of the added C substrates significantly affected soil chemistry, microbial basal and substrate-induced respiration, and soil microbial community structure measured by either the catabolic response profile (CRP) technique or phospholipid fatty acid composition. These belowground changes strongly affected the ability of the soil microflora to decompose cellulose paper, probably because of differential effects of the C substrates on soil energy supplies and enzyme activities. The addition of C substrates to soils also reduced plant growth compared to the unamended control soil, but less so in soils amended with a tannin than those amended with other substrates. Carbon substrate diversity effects saturated at low diversity levels, tended to have neutral or negative effects on ecosystem functions, and depended strongly on which C substrates were added. It increased CRP compound use but had little effect on other measures of the soil microbial community. Overall, results showed that the chemical nature of C substrates added to soil, and sometimes their diversity, can affect the soil microbial community and soil chemistry, which subsequently affect other ecosystem processes such as decomposition and plant growth. The identity and diversity of substrates that plants add to soil may therefore have important consequences for both above- and belowground ecosystem functions.

Biodiversity↗

PubMed2026

Postpartum compositional changes in bovine calf nasal and dam vaginal microbiota and concurrent immune responses following prepartum betadine lavages.

As interest in bovine reproductive tract microbial communities increases, there remains limited information on how the insult of parturition influences postpartum dam reproductive microbiota and early-life microbial development. The objective of this study was to characterize postpartum changes in dam vaginal microbiota and neonatal calf nasal microbiota following transient prepartum disruption of the dam vaginal microbiota using betadine lavages (BLGs), and to evaluate concurrent systemic immune responses in dams and calves. Multiparous beef cows (n = 12) were randomly assigned to either BLG (n = 7) or control (CON; n = 5) 3 wk prior to the expected calving date, and dam vaginal swabs, calf nasal swabs, and blood were collected at 0 (+1), 15 (±1), 30 (±1), and 60 (±1) d postpartum. Samples from Angus cow-calf pairs (n = 12) underwent 16S rRNA gene sequencing with standard contamination controls and QIIME2 processing. Blood samples were analyzed using the D2Dx immunity assay to evaluate systemic humoral immune responses. Microbial alpha diversity (ANOVA), Bray-Curtis beta diversity (PERMANOVA), taxonomic composition (LEfSe), and D2Dx immune responses (repeated-measures mixed model) were analyzed (P < 0.05). In calves, treatment influenced nasal alpha diversity at d 0 (P = 0.03), while nasal beta diversity tended to differ at d 0 (P = 0.08); however, treatment effects were not detected at d 15, 30, or 60 for alpha diversity (P ≥ 0.76) or beta diversity (P ≥ 0.14). Calf nasal communities shifted over time (P = 0.001), with d 0 differing from d 15, 30, and 60, and beta diversity differing over time (P = 0.006). In dams, BLG did not alter vaginal alpha diversity (P ≥ 0.42) or beta diversity (P ≥ 0.14) over time, and time did not affect vaginal alpha diversity (P = 0.60) while vaginal beta diversity tended to shift over time (P = 0.06). Postpartum dam vaginal and calf nasal communities differed compositionally regardless of time (P < 0.05). Systemic immune responses, measured via D2Dx scores, fluctuated postpartum in dams (day effect: P < 0.001) and calves (day effect: P < 0.001), with BLG calves tending toward decreased immune response compared with CON (P = 0.08). Prepartum BLG minimally influenced neonatal nasal microbial diversity at birth and did not alter postpartum dam vaginal community structure, while calf nasal microbiota and D2Dx immune responses changed markedly over the first 60 d of life.

Animals↗

PubMed1998

Influence of trophic status on the toxic effects of a herbicide: A microcosm study

Naturally derived microbial communities were developed in the laboratory under three nutrient regimes by manipulating phosphate and nitrate concentrations. Resulting communities differed in both functional and structural attributes. Low nutrient microcosms (0.05 mg N-NO3-/L + 0.01 mg P-PO4-3/L) showed the sharpest differences. Medium (0.5 mg N-NO3-/L + 0.1 mg P-PO4-3/L) and high (5.0 mg N-NO3-/L + 1.0 mg P-PO4-3/L) nutrient treatments differed in total algal biomass and algal community composition. After a 25-day acclimation period, a single dose of the herbicide diquat (3.5 mg/L) was added to test the response of the microbial communities to herbicide stress. Regardless of nutrient regime, diquat-dosed microcosms had decreased electron transport system activity (ETSA), an almost complete absence of cyanobacteria, and reduced gross photosynthesis (GP), respiration, and pH relative to undosed microcosms. Inorganic nutrients (PO4-3, NO3-) were released from the stressed algal communities, probably as a result of their altered metabolism. Alkaline phosphatase activity (APA), total microbial biomass (estimated as protein), algal biomass (estimated as chlorophyll), and relative abundance of green algal taxa proved highly insensitive to herbicide action. Nutrient treatments had a small influence on toxicant effects; the magnitude of the herbicide effects was comparable across nutrient levels. Only the capacity of recovery from the toxic stress was affected by trophic status. At the end of the study period, ETSA had recovered to control values in high nutrient microcosms but not in medium and low ones. Microcosm pH, and to a lesser extent GP, showed recovery under both high and medium nutrient treatments. Trophic status affected the diquat disappearance rate; the herbicide persisted longer in low nutrient microcosms than in high and medium nutrient ones. Differences in recovery capacity may stem from higher nutrient level microcosms reaching less toxic herbicide levels in a shorter period of time.

Journal Article↗

PubMed2003

[Characterization of several synthetic and environmental microbial samples by quantitative hybridization].

Limitations of traditional techniques based on selective enrichment and pure-culture isolation make it difficult to precisely characterize the natural microbial ecosystems. Molecular techniques are now being developed and used to address these limitations. Group-specific 16S rRNAs-targeted oligonucleotide probes of different phylogenetic levels are increasingly used to identify and quantify the microbial members in complex environmental samples. Two domain-specific probes were used in this study to elementarily characterize the defined mixtures of RNAs extracted from pure culture (synthetic samples) and a RNA sample obtained from landfill leachate (environmental sample). The results demonstrated that 16S rRNA quantitative hybridization provided an excellent estimation of domain level community composition of these samples, and thus, had a huge potential of usefulness in microbial ecology studies.

Ecology↗

PubMed2004

Are viruses driving microbial diversification and diversity?

Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.

Bacteria↗

PubMed2006

Microbial diversity in natural environments: focusing on fundamental questions.

Interactions with Gijs Kuenen and other Dutch scientists have led my lab to fundamental insights into the composition, structure and function of a hot spring cyanobacterial mat community that should influence our thinking about all microbial communities. By focusing on the distribution of molecular sequence variants of predominant mat phototrophs, we have discovered that small-scale sequence variation can be ecologically meaningful. By applying novel cultivation approaches, we have been able to obtain genetically relevant community members and thus to test the hypothesis that closely related sequence variants arose via adaptive evolutionary radiation. By applying the analytical tools of organic geochemistry we have gained insight into the metabolisms of major phototrophic members of the mat community as well as interactions between phototrophic guilds. These observations challenge traditional paradigms about prokaryotic species and cause us to consider evolutionary ecology theory as we develop genome-based methods for high-resolution analysis of the species-like fundamental units comprising microbial communities, and for investigating how such units coordinate the physiological activities within guilds of the community.

Autotrophic Processes↗

PubMed2001

Characterization of microbial community in an activated sludge process treating domestic wastewater using quinone profiles.

The dynamics of microbial community structure of activated sludges in a small-scale domestic wastewater treatment process were examined using a novel approach of quinone profiles. The composition and content of quinones in the activated sludges were analyzed monthly over a period of one year. More than 4 types of ubiquinones and 12 types of menaquinones were observed in the activated sludges, with the dominant quinones being ubiquinone (UQ)-8, menaquinone (MK)-7, followed by UQ-10, MK-8 and MK-6. The total quinone contents in the activated sludges varied from 0.93 to 2.68 mumol per gram of particle organic carbon. The molar ratio of ubiquinones to menaquinones (UK/MK) changed from 0.38 to 0.98, indicating that anaerobic bacteria dominated the microbial community of the activated sludges examined. The ratio of UQ/MK varied similar to that of dissolved oxygen in the bulk. The microbial diversity of the activated sludges calculated from the quinone compositions was 13.4-16.8. The diversity of menaquinones was much higher than that of ubiquinones, and increased slightly with increasing temperature. The microorganisms containing menaquinones appear to be sensitive to the change in temperature than those containing ubiquinones.

Bacteria↗

PubMed2003

Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater.

A set of microcosm experiments was performed to assess different bioremediation strategies, i.e., biostimulation and bioaugmentation, for groundwater contaminated with chlorobenzenes. The biodegradative potential was stimulated either by the supply of electron acceptors (air, (NO3-), to increase the activity of the indigenous bacterial community, or by the addition of aerobic chlorobenzene-degrading bacteria (Pseudomonas putida GJ31, Pseudomonas aeruginosa RHO1, Pseudomonas putida F1deltaCC). Experiments were performed with natural groundwater of the aquifer of Bitterfeld, which had been contaminated with 1,2-dichlorobenzene (1,2-DCB), 1,4-dichlorobenzene (1,4-DCB), and chlorobenzene (CB). The microcosms consisted of airtight glass bottles with 800 mL of natural groundwater and were incubated under in situ temperature (13 degrees C). Behavior of the introduced strains within the indigenous bacterial community was monitored by fluorescent in situ hybridization (FISH) with species-specific oligonucleotides. Dynamics of the indigenous community and the introduced strains within the microcosms were followed by single-strand conformation polymorphism (SSCP) analysis of 16S rDNA amplicons obtained from total DNA of the microbial community. An indigenous biodegradation potential under aerobic as well as anaerobic denitrifying conditions was observed accompanied by fast and specific changes in the natural bacterial community composition. Augmentation with P. aeruginosa RHO1 did not enhance bio-degradation. In contrast, both P. putida GJ31 as well as P. putida F1deltaCC were capable of growing in groundwater, even in the presence of the natural microbial community, and thereby stimulating chlorobenzene depletion. P. putida GJ31 disappeared when the xenobiotics were depleted and P. putida F1deltaCC persisted even in the absence of CB. Detailed statistical analyses revealed that community dynamics of the groundwater microbiota were highly reproducible but specific to the introduced strain, its inoculum size, and the imposed physicochemical conditions. These findings could contribute to the design of better in situ bioremediation strategies for contaminated groundwater.

Bacteria, Aerobic↗

PubMed2005

Environments shape the nucleotide composition of genomes.

To test the impact of environments on genome evolution, we analysed the relative abundance of the nucleotides guanine and cytosine ('GC content') of large numbers of sequences from four distinct environmental samples (ocean surface water, farm soil, an acidophilic mine drainage biofilm and deep-sea whale carcasses). We show that the GC content of complex microbial communities seems to be globally and actively influenced by the environment. The observed nucleotide compositions cannot be easily explained by distinct phylogenetic origins of the species in the environments; the genomic GC content may change faster than was previously thought, and is also reflected in the amino-acid composition of the proteins in these habitats.

Amino Acids↗

PubMed2006

Microbial degradation and impact of Bracken toxin ptaquiloside on microbial communities in soil.

The carcinogenic and toxic ptaquiloside (PTA) is a major secondary metabolite in Bracken fern (Pteridium aquilinum (L.) Kuhn) and was hypothesized to influence microbial communities in soil below Bracken stands. Soil and Bracken tissue were sampled at field sites in Denmark (DK) and New Zealand (NZ). PTA contents of 2.1 +/- 0.5 mg g(-1) and 37.0 +/- 8.7 mg g(-1) tissue were measured in Bracken fronds from DK and NZ, respectively. In the two soils the PTA levels were similar (0-5 microg g(-1) soil); a decrease with depth could be discerned in the deeper B and C horizons of the DK soil (weak acid sandy Spodosol), but not in the NZ soil (weak acid loamy Entisol). In the DK soil PTA turnover was predominantly due to microbial degradation (biodegradation); chemical hydrolysis was occurring mainly in the uppermost A horizon where pH was very low (3.4). Microbial activity (basal respiration) and growth ([3H]leucine incorporation assay) increased after PTA exposure, indicating that the Bracken toxin served as a C substrate for the organotrophic microorganisms. On the other hand, there was no apparent impact of PTA on community size as measured by substrate-induced respiration or composition as indicated by community-level physiological profiles. Our results demonstrate that PTA stimulates microbial activity and that microorganisms play a predominant role for rapid PTA degradation in Bracken-impacted soils.

Biodegradation, Environmental↗

PubMed1981

Simulation of the rat intestinal ecosystem using a two-stage continuous culture system.

To investigate the ecological mechanisms governing the community structure of the gut microbial ecosystem, we have attempted to simulate the rat gut ecosystem in vitro using a two-stage continuous culture. Extensive sampling of the rat hindgut has established a set of criteria with which the in vitro system may be compared. This paper discusses one of the criteria, the community composition and structure in vivo and in vitro. The experiments indicated that a gut microbial ecosystem could be satisfactorily mimicked in vitro. This was achieved using a two-stage continuous culture employing differential selection of species between the two stages on the basis of pH differences combined with cell recycling between stages.

Animals↗

PubMed2002

Microbial population dynamics in laboratory-scale activated sludge reactors.

As a first step in understanding nonlinear dynamics in activated sludge systems, two laboratory-scale sequencing batch reactors were operated under identical conditions and changes in their microbial communities were followed through microscopic examination, macroscopic observation, and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene segments from the prokaryotic community. Two experiments were performed. The first used activated sludge from a local wastewater treatment plant to start the replicate reactors. The second used the biomass from the first experiment as a source by intermixing the two and equally redistributing the biomass into the two replicate reactors. For both experiments, the two reactors behaved fairly similarly and had similar microbial communities for a period of 60 days following start-up. Beyond that, the microbial communities in the two reactors in the first experiment diverged in composition, while those in the second experiment remained fairly similar. This suggests that the degree of change occurring in replicate reactors depends upon the severity of perturbation to which they are exposed. The DGGE data showed that the bacterial communities in both experiments were highly dynamic, even though the system performance of the replicate reactors were very similar, suggesting that dynamics within the prokaryotic community is not necessarily reflected in system performance. Moreover, a significant finding from this study is that replicate activated sludge systems are not identical, although they can be very similar if started appropriately.

Bacteria↗

PubMedDate not supplied

[Soil biological activity in the Chernye Zemli, Kalmykia, inhabited by gerbils Meriones tamariscinus and M. meridianus].

The influence of tamarisk (Meriones tamariscinus) and midday (M. meridianus) gerbils on soil biological activity in the Chernye Zemli, Kalmykia, was studied. Nitrogen fixation, denitrification, and CO2 emission were measured in soil samples from different parts of gerbil burrows. Functional biodiversity of the microbial community was evaluated using multisubstrate testing and comparison of bacterial group composition in samples from gerbil burrows. The impact of gerbils on soil biological activity was mediated by the changes in the group composition of microorganisms.

Animals↗

PubMed2006

Structure of virioplankton in the Charente Estuary (France): transmission electron microscopy versus pulsed field gel electrophoresis.

Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 +/- 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 +/- 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.

Capsid↗

PubMed2005

Bacterial community dynamics during in-situ bioremediation of petroleum waste sludge in landfarming sites.

In-situ bioremediation of petroleum waste sludge in landfarming sites of Motor Oil Hellas (petroleum refinery) was studied by monitoring the changes of the petroleum composition of the waste sludge, as well as the changes in the structure of the microbial community, for a time period of 14 months. The analyses indicated an enhanced degradation of the petroleum hydrocarbons in the landfarming areas. A depletion of n-alkanes of approximately 75-100% was obtained. Marked changes of the microbial communities of the landfarms occurred concomitantly with the degradation of the petroleum hydrocarbons. The results obtained from terminal restriction fragment length polymorphism (T-RFLP) analysis of polymerase chain reaction (PCR) amplified 16S rRNA genes demonstrated that bacteria originating from the refinery waste sludge and newly selected bacteria dominated the soil bacterial community during the period of the highest degradation activity. However, the diversity of the microbial community was decreased with increased degradation of the petroleum hydrocarbons contained in the landfarms. T-RFLP fingerprints of bacteria of the genera Enterobacter and Ochrobactrum were detected in the landfarmed soil over the entire treatment period of 14 months. In contrast, the genus Alcaligenes appeared in significant numbers only within the 10 month old landfarmed soil. Genes encoding catechol 2,3-dioxygenase (subfamily I.2.A) were detected only in DNA of the untreated refinery waste sludge. However, none of the genes known to encode the enzymes alkane hydroxylase AlkB, catechol 2,3-dioxygenase (subfamily I.2.A) and naphthalene dioxygenase nahAc could be detected in DNA of the landfarmed soils.

Biodegradation, Environmental↗