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At least 127 records · Page 7Linked to original sources
PubMed2004

Effects of the pesticides captan, deltamethrin, isoproturon, and pirimicarb on the microbial community of a freshwater sediment.

In three microcosm experiments, we exposed microbial communities of a natural sediment to environmentally relevant concentrations of the fungicide captan, the herbicide isoproturon, and the insecticides deltamethrin and pirimicarb. Exposure concentrations were estimated negligible concentrations (NCs), maximum permissible concentrations (MPCs), and 100 times MPC (100MPC). Experimental endpoints were microbial community respiration and biomass, bacterial activity, and denitrification. All four pesticides inhibited bacterial activity by 20 to 24% at MPC, which corresponded to concentrations in the range of microg/kg dry-weight sediment. Treatments with deltamethrin and isoproturon showed inhibiting effects on bacterial activity at NC exposures. Surprisingly, for captan, deltamethrin, and isoproturon, this inhibiting effect was not observed at 100MPC treatments. Microbial biomass was negatively effected in MPC treatments with deltamethrin and in NC treatments with isoproturon. The tested pesticides did not affect community respiration and denitrification rates. These results show that exposure to the tested pesticides may induce toxic responses in sediment microbial communities at concentrations that are predicted to be environmentally safe.

Bacteria↗
PubMed2026

Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.

Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterized the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss as CO2 after 4 weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term 'bioplastisphere' to denote the distinctive microbial communities associated with biodegradable plastics.

Seawater↗
PubMed2004

[Effects of different organic materials and their composting levels on soil microbial community].

In this paper, a pot experiment with tomato and different organic material amendment was installed in a greenhouse, and the diversity of soil microbial communities and their utilization pattern of amine, amino acid, carbohydrate, carboxylic acid, polymer and miscellaneous were assessed by Biolog method at 60 days after amendment. The results showed that organic material amendment could improve soil microbial community diversity. Fresh distiller grain amendment was a little bit better than its 10 days composting, and the composting level of cow manure had a significant positive or negative effect on the microbial diversity. Among the six carbon sources, the utilization of carbohydrate by soil microbial communities was the highest, and the microbial communities in soils amended with distiller grain had a significantly higher utilization of polymer, relative to those in soils amended with cow manure.

Carbon↗
PubMed2003

Sedimentary microbial community dynamics in a regulated stream: East Fork of the Little Miami River, Ohio.

A field study was conducted in the Lower East Fork of the Little Miami River, a regulated stream in Clermont county, Ohio, to determine how changes in streamflow, water temperature and photo-period affect sediment microbial community structure. Surface sediment cores were collected from sampling stations spanning 60 river kilometers three to four times per year between October 1996 and October 1999. During the final year of the field study, water temperature, water depth, conductivity, total suspended solids, dissolved organic carbon, instantaneous streamflow velocity, sediment grain size and sediment organic matter were determined. Total microbial biomass was measured using the phospholipid phosphate technique (PLP) and ranged between 2 and 134 nmol PLP * g(-1) dry weight sediment with a mean of 25 nmol PLP * g(-1). Microbial community structure was determined using the phospholipid fatty acid analysis and indicated seasonal shifts in sedimentary microbial community composition. January to June sedimentary microbial biomass was predominately prokaryotic (60% +/- 2), whereas microeukaryotes dominated samples collected during the late summer (55% +/- 2.4) and fall (60% +/- 2). These changes were correlated with stream discharge and water temperature. Microbial community structure varied spatially about a reservoir with prokaryotic biomass dominant at upstream stations and eukaryotic biomass dominant at downstream stations. These findings reveal that sedimentary microbial communities in streams are dynamic responding to the seasonal variation of environmental factors.

Ecosystem↗
PubMedDate not supplied

[Patterns of formation of microbial communities of alluvial soils in the selenga estuary].

Microbial communities of alluvial soils in the facies on islands in the Selenga estuary and near Stepnoi Dvorets and Istomino Settlements were studied. The distribution of the CFU-dominant microorganisms (Bacillus and Pseudomonas + Arthrobacter) has been revealed in the studied island soils. In addition, actinomycetes Streptomyces were found among the dominants in soils of the near-terrace floodplain. The quantitative distribution of microorganisms across soil layers was demonstrated. The effect of ecological factors in formation of microbial communities on the islands and central floodplain regions was revealed.

Gram-Positive Bacteria↗
PubMed1989

Acute copper and cupric ion toxicity in an estuarine microbial community.

Copper was acutely toxic to the estuarine microbial community of Middle Marshes, N.C. Under ambient water quality conditions, 10 mug of added total copper [Cu(II)] liter reduced the CFU bacterial abundance by up to 60% and inhibited the amino acid turnover rate (AATR) by as much as 30%. Copper toxicity, however, was a quantitative function of free cupric ion (Cu) activity that was not directly related to Cu(II) or ligand-bound copper. By using a nitrilotriacetic acid-cupric ion buffer to control pCu (-log Cu activity), it was found that an in situ pCu of 10.1 was bactericidal, reducing the CFU by 60%, but inhibited the AATR by only about 10%. A bacterial bioassay that was used to estimate the pCu in Cu(II)-treated Middle Marshes samples indicated that less than 0.5% of added Cu(II) was in the free cupric ion form. CFU was a more sensitive indicator of low-level copper stress than was AATR. When tested at different times, native microbial community responses to acute cupric ion stress were quantitatively quite similar even when there were large differences in bacterial abundances and in situ metabolic rates. Variations were observed in response to Cu(II) treatments at different times, but these were likely due to differences in water quality, which would quantitatively influence the distribution of copper complexes that were present. Asymptotic response curves suggest that some degree of copper resistance exists in this community. At a pCu of 8, more than 2 orders of magnitude above the minimum inhibitory level, the CFU was still 5 to 10% and the AATR was about 3% of the control values.

Journal Article↗
PubMed2004

Succession of aquatic microbial communities as a result of the water quality variations in continuous water.

The changes of structural and functional parameters of aquatic microbial communities in continuous water on campus of Tsinghua University, China are investigated, by polyurethane foam unit (PFU) method. The measured compositions of the communities include alga, protozoa, and some metazoa (such as rotifers). The measured indicators of water quality include water temperature, pH value, dissolved oxygen (DO), potassium permanganate index (COD(Mn)), total nitrogen (TN), total phosphorus (TP) and chlorophyll-a (Chla). The trophic level, expressed by the trophic level indices (TLIc), is assessed with analytic hierarchy process and principal component analysis (AHP-PCA) method. The changing trends of the structural and functional parameters of aquatic microbial communities, such as Margalef index of diversity (D), Shannon-weaver index of diversity (H), Heterotropy index (HI), number of species when the colonization gets equilibrium (S(eq)), colonizing speed constant (G) and time spent when 90 percent of S(eq) colonized in PFU (T(80%)), are also analyzed. The experimental results showed the succession of aquatic microbial communities along the water flow is consistent with the water quality changes, so the parameters of microbial community can reflect the changes of water quality from the ecological view.

Animals↗
PubMed2006

Microbial community responses associated with the development of oomycete plant pathogens on tomato roots in soilless growing systems.

AIMS: To determine the spread of different oomycete pathogens in hydroponic, soilless tomato growing systems and their impact on established microbial communities, as baseline studies prior to future introduction of microbial inoculants for disease suppression. METHODS AND RESULTS: The oomycete pathogens, Pythium group F, Pythium aphanidermatum and Phytophthora cryptogea, were introduced into small-scale recirculating tomato growing systems containing rockwool 6 weeks after set-up when roots were well-established. Two weeks later, half of the systems were switched over to run-to-waste. Pythium aphanidermatum spreads the fastest, Pythium group F the slowest and Ph. cryptogea was intermediate in its spread. The switch to run-to-waste had no effect on pathogen recovery. Microbial communities, monitored by dilution plating, were well-established at the first sampling, 6 weeks after set-up and although differences in community levels were found between experiments, changes during any one experiment were small, generally less than 1 log10 CFU g(-1) for bacteria. Pathogen introduction increased microbial community levels in roots but the switch to run-to-waste had no effect. Analysis of bacterial communities through amplification of a fragment of the 16S rRNA gene and DGGE profiling showed that different communities were established within each pathogen experiment and that different communities were established on roots, rockwool and in nutrient solutions. However, no significant changes in microbial profiles were found over time in any experiment. CONCLUSIONS: In these systems, the microbial communities were well-established 6 weeks after set-up and were resistant to biological and physical perturbation. SIGNIFICANCE AND IMPACT OF THE STUDY: The implication for microbial inoculation of such systems for disease suppression is that the micro-organisms would either have to be introduced very early during the set-up of the system or be able to replace an established but variable community.

DNA, Fungal↗
PubMed2007

In vitro and in vivo effects of hydrolysates from conglycinin on intestinal microbial community of mice after Escherichia coli infection.

AIMS: To detect the effect of pepsin-hydrolysate conglycinin (PTC) on the growth of Escherichia coli O(138)in vitro, and investigate the effect of PTC on intestinal microbial community of mice after E. coli infection. METHODS AND RESULTS: Serial dilution method was used to detect the antibacterial activity of PTC in 96-well cell-cultivated plates. Fifty-five KM mice were randomly assigned to five groups: normal, feeding-E. coli control, HCl-full hydrolysis of conglycinin, conglycinin and PTC. Orally administrated with hydrolysates from conglycinin for 21 days, each mouse was fed with 2 x 10(8) CFU ml(-1) of E. coli O(138) on the 22nd day. The mice activities were monitored and polymerase chain reaction-denaturing gradient gel electrophoresis was used to analyse the microbial community in mice faeces. The results showed that PTC could inhibit growth of E. coli O(138) at nitrogen concentrations of more than 520 mg l(-1). There was high similarity of intestinal microbial community in mice between PTC and normal groups. CONCLUSION: PTC inhibits growth of E. coli O(138), keeps mice healthy following oral administration of E. coli infection and maintains a balanced active microbial community in their gastrointestinal tract. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrated the antibacterial activity of PTC against E. coli and its ability to maintain healthy intestinal microbial community in mice even after they were infected with E. coli. This observation is significant in the application of PTC to prevent gastrointestinal diseases caused by E. coli and unbalanced intestinal microflora.

Animals↗
PubMed1997

Ecofunctional enzymes of microbial communities in ground water.

Biolog technology was initially developed as a rapid, broad spectrum method for the biochemical identification of clinical microorganisms. Demand and creative application of this technology has resulted in the development of Biolog plates for Gram-negative and Gram-positive bacteria, for yeast and Lactobacillus sp. Microbial ecologists have extended the use of these plates from the identification of pure culture isolates to a tool for quantifying the metabolic patterns of mixed cultures, consortia and entire microbial communities. Patterns that develop on Biolog microplates are a result of the oxidation of the substrates by microorganisms in the inoculum and the subsequent reduction of the tetrazolium dye to form a color in response to detectable reactions. Depending upon the functional enzymes present in the isolate or community one of a possible 4 x 10(28) patterns can be expressed. The patterns were used to distinguish the physiological ecology of various microbial communities present in remediated groundwater. The data indicate that one can observe differences in the microbial community among treatments of bioventing, 1% and 4% methane injection, and pulse injection of air, methane and nutrients both between and among wells. The investigation indicates that Biolog technology is a useful parameter to measure the physiological response of the microbial community to perturbation and allows one to design enhancement techniques to further the degradation of selected recalcitrant and toxic chemicals. Further it allows one to evaluate the recovery of the microbial subsurface ecosystem after the perturbations have ceased. We propose the term 'ecofunctional enzymes' (EFE) as the most descriptive and useful term for the Biolog plate patterns generated by microbial communities. We offer this designation and provide ecological application in an attempt to standardize the terminology for this relatively new and unique technology.

Bacteria↗
PubMed2006

Microbial community composition and function across an arctic tundra landscape.

Arctic landscapes are characterized by a diversity of ecosystems, which differ in plant species composition, litter biochemistry, and biogeochemical cycling rates. Tundra ecosystems differing in plant composition should contain compositionally and functionally distinct microbial communities that differentially transform dissolved organic matter as it moves downslope from dry, upland to wet, lowland tundra. To test this idea, we studied soil microbial communities in upland tussock, stream-side birch-willow, and lakeside wet sedge tundra in arctic Alaska, USA. These are a series of ecosystems that differ in topographic position, plant composition, and soil drainage. Phospholipid fatty acid (PLFA) analyses, coupled with compound-specific 13C isotope tracing, were used to quantify microbial community composition and function; we also assayed the activity of extracellular enzymes involved in cellulose, chitin, and lignin degradation. Surface soil from each tundra ecosystem was labeled with 13C-cellobiose,13C-N-acetylglucosamine, or 13C-vanillin. After a five-day incubation, we followed the movement of 13C into bacterial and fungal PLFAs, microbial respiration, dissolved organic carbon, and soil organic matter. Microbial community composition and function were distinct among tundra ecosystems, with tussock tundra containing a significantly greater abundance and activity of soil fungi. Although the majority of 13C-labeled substrates rapidly moved into soil organic matter in all tundra soils (i.e., 50-90% of applied 13C), microbial respiration of labeled substrates in wet sedge tundra soil was lower than in tussock and birch-willow tundra; approximately 8% of 13C-cellobiose and approximately 5% of 13C-vanillin was respired in wet sedge soil vs. 26-38% of 13C-cellobiose and 18-21% of 13C-vanillin in the other tundra ecosystems. Despite these differences, wet sedge tundra exhibited the greatest extracellular enzyme activity. Topographic variation in plant litter biochemistry and soil drainage shape the metabolic capability of soil microbial communities, which, in turn, influence the chemical composition of dissolved organic matter across the arctic tundra landscape.

Animals↗
PubMed2000

Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems.

This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of approximately 0.5 to approximately 1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. "Ferroplasma" spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength. Leptospirillum spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured Leptospirillum sp. dominated. Sulfobacillus spp. were detected as a prominent inhabitant in warmer ( approximately 43 degrees C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.

Bacteria↗
PubMed2005

Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis (DGGE).

To study the structure of microbial communities in the biological hydrogen production reactor and determine the ecological function of hydrogen producing bacteria, anaerobic sludge was obtained from the continuous stirred tank reactor (CSTR) in different periods of time, and the diversity and dynamics of microbial communities were investigated by denaturing gradient gel electrophoresis (DGGE). The results of DGGE demonstrated that an obvious shift of microbial population happened from the beginning of star-up to the 28th day, and the ethanol type fermentation was established. After 28 days the structure of microbial community became stable, and the climax community was formed. Comparative analysis of 16S rDNA sequences from reamplifying and sequencing the prominent bands indicated that the dominant population belonged to low G+C Gram-positive bacteria (Clostridium sp. and Ethanologenbacterium sp.), beta-proteobacteria (Acidovorax sp.), gamma-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacterium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase of Ethanologenbacterium sp., Clostridium sp. and uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fermentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types of Clostridium sp. Acidovorax sp., Kluyvera sp., and Bacteroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was dependent on both hydrogen producing bacteria and other populations. It implied that the co-metabolism of microbial community played a great role of biohydrogen production in the reactors.

Bacteroides↗
PubMed2001

Monitoring of the microbial community of a sequencing batch reactor bioaugmented to improve its phosphorus removal capabilities.

The acclimatisation of an activated sludge to enhanced biological phosphorus removal conditions was followed after and without bioaugmentation with a low amount of phosphorus-accumulating sludge. Phosphorus removal yields were monitored by conventional analytical methods and microbial communities evolutions were followed by a finger printing molecular technique (PCR-SSCP). While the benefit of the bioaugmentation seems real at the level of the reactor parameters, bioaugmentation speeded up the installation of good and stable phosphorus removal yield, the establishment of the inoculated microbial community in the bioaugmented reactor is still unclear. Both the bioaugmented and the control microbial communities evolved in a similar way to end up with apparently comparable populations. At the time of the experiment, the results suggest that the microbial community inoculated for the bioaugmentation did not establish in the reactor but compensated for phosphorus accumulation until the acclimatisation of an endogenous microbial community arose.

Biodegradation, Environmental↗
PubMed2006

UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context.

BACKGROUND: Moving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial ecology and community assembly. Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses. RESULTS: We introduce UniFrac, a web application available at http://bmf.colorado.edu/unifrac, that allows several phylogenetic tests for differences among communities to be easily applied and interpreted. We demonstrate the use of UniFrac to cluster multiple environments, and to test which environments are significantly different. We show that analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities. CONCLUSION: UniFrac provides easy access to powerful multivariate techniques for comparing microbial communities in a phylogenetic context. We thus expect that it will provide a completely new picture of many microbial interactions and processes in both environmental and medical contexts.

Bacteria↗
PubMed2002

Composition and physiological profiling of sprout-associated microbial communities.

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.

Brassica↗
PubMed2004

Effect of pyocyanin on a crude-oil-degrading microbial community.

Pseudomonas aeruginosa is an n-alkane degrader that is frequently isolated from petroleum-contaminated sites and produces factors that enhance its competitiveness and survival in many environments. In this study, one such factor, pyocyanin, has been detected in an oil-degrading culture containing P. aeruginosa and is a redox-active compound capable of inhibiting microbial growth. To examine the effects of pyocyanin further, an oil-degrading culture was grown with and without 9.5 microM pyocyanin and microbial community structure and oil degradation were monitored for 50 days. Denaturing gradient gel electrophoresis (DGGE) analysis of cultures revealed a decrease in the microbial community diversity in the pyocyanin-amended cultures compared to that of the unamended cultures. Two members of the microbial community in pure culture exhibited intermediate and high sensitivities to pyocyanin corresponding to intermediate and low levels of activity for the antioxidant enzymes catalase and superoxide dismutase, respectively. Another member of the community that remained constant in the DGGE gels over the 50-day culture incubation period exhibited no sensitivity to pyocyanin, corresponding to a high level of catalase and superoxide dismutase when examined in pure culture. Pyocyanin also affected the overall degradation of the crude oil. At 50 days, the culture without pyocyanin had decreased polycyclic aromatic hydrocarbons compared to the pyocyanin-amended culture, with a specific reduction in the degradation of dibenzothiophenes, naphthalenes, and C(29) and C(30) hopanes. This study demonstrated that pyocyanin influenced the diversity of the microbial community and suggests the importance of understanding how interspecies interactions influence the degradation capability of a microbial community.

Bacteria↗
PubMed2006

A dynamic programming algorithm for binning microbial community profiles.

MOTIVATION: A number of community profiling approaches have been widely used to study the microbial community composition and its variations in environmental ecology. Automated Ribosomal Intergenic Spacer Analysis (ARISA) is one such technique. ARISA has been used to study microbial communities using 16S-23S rRNA intergenic spacer length heterogeneity at different times and places. Owing to errors in sampling, random mutations in PCR amplification, and probably mostly variations in readings from the equipment used to analyze fragment sizes, the data read directly from the fragment analyzer should not be used for down stream statistical analysis. No optimal data preprocessing methods are available. A commonly used approach is to bin the reading lengths of the 16S-23S intergenic spacer. We have developed a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling location and time. RESULTS: In a test example from an ocean time series sampling program, data preprocessing identified several outliers which upon re-examination were found to be because of systematic errors. Clustering analysis of the ARISA from different times based on the dynamic programming algorithm binned data revealed important features of the biodiversity of the microbial communities.

Algorithms↗