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PubMed1987

Adaptation to and biodegradation of xenobiotic compounds by microbial communities from a pristine aquifer.

The ability of subsurface microbial communities to adapt to the biodegradation of xenobiotic compounds was examined in aquifer solids samples from a pristine aquifer. An increase in the rates of mineralization of radiolabeled substrates with exposure was used as an indication of adaptation. For some compounds, such as chlorobenzene and 1,2,4-trichlorobenzene, slight mineralization was observed but no adaptation was apparent during incubations of over 8 months. Other compounds demonstrated three patterns of response. For m-cresol, m-aminophenol, and aniline intermediate rates of biodegradation and a linear increase in the percent mineralized with time were observed. Phenol, p-chlorophenol, and ethylene dibromide were rapidly metabolized initially, with a nonlinear increase in the percent mineralized with time, indicating that the community was already adapted to the biodegradation of these compounds. Only p-nitrophenol demonstrated a typical adaptation response. In different samples of soil from the same layer in the aquifer, the adaptation period to p-nitrophenol varied from a few days to as long as 6 weeks. In most cases the concentration of xenobiotic added, over the range from a few nanograms to micrograms per gram, made no difference in the response. Most-probable-number counts demonstrated that adaptation is accompanied by an increase in specific degrader numbers. This study has shown that diverse patterns of response occur in the subsurface microbial community.

Aminophenols↗

PubMed2001

Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling.

Genetic profiling techniques of microbial communities based on PCR-amplified signature genes, such as denaturing gradient gel electrophoresis or single-strand-conformation polymorphism (SSCP) analysis, are normally done with PCR products of less than 500-bp. The most common target for diversity analysis, the small-subunit rRNA genes, however, are larger, and thus, only partial sequences can be analyzed. Here, we compared the results obtained by PCR targeting different variable (V) regions (V2 and V3, V4 and V5, and V6 to V8) of the bacterial 16S rRNA gene with primers hybridizing to evolutionarily conserved flanking regions. SSCP analysis of single-stranded PCR products generated from 13 different bacterial species showed fewer bands with products containing V4-V5 (average, 1.7 bands per organism) than with V2-V3 (2.2 bands) and V6-V8 (2.3 bands). We found that the additional bands (>1 per organism) were caused by intraspecies operon heterogeneities or by more than one conformation of the same sequence. Community profiles, generated by PCR-SSCP from bacterial-cell consortia extracted from rhizospheres of field-grown maize (Zea mays), were analyzed by cloning and sequencing of the dominant bands. A total of 48 sequences could be attributed to 34 different strains from 10 taxonomical groups. Independent of the primer pairs, we found proteobacteria (alpha, beta, and gamma subgroups) and members of the genus Paenibacillus (low G+C gram-positive) to be the dominant organisms. Other groups, however, were only detected with single primer pairs. This study gives an example of how much the selection of different variable regions combined with different specificities of the flanking "universal" primers can affect a PCR-based microbial community analysis.

Bacteria↗

PubMed2001

Spatial Patterns of Soil Microbial Communities in a Norway Spruce (Picea abies) Plantation.

The phospholipid fatty acid (PLFA) profiles of soil microbial communities were determined in relation to the patterns of tree cover in a mature Norway spruce plantation. Replicate samples of the surface organic layers were taken close to the trunk, at 1 m and at 2 m (under the edge of the canopy) beneath five trees. Samples were analyzed for standard PLFAs to assess the initial composition of the microbial communities. Replicate samples were then incubated under constant or fluctuating moisture conditions for 30 d to test the hypothesis that the patterns of microbial community structure (or its physiological state) might be determined by biophysical conditions under the tree canopies. The PLFA profiles near the trunks and at 2 m were similar, but samples taken 1 m from the bases of the trees contained lower concentrations of polyunsaturated (fungal) and monounsaturated PLFAs, and higher concentrations of saturated PLFAs. These differences in PLFA profiles were maintained during laboratory incubation under a regime of drying and wetting cycles, but there was some evidence of convergence in community structure under constant moisture conditions resulting from significant increases and decreases in specific bacterial PLFA concentrations. There were no effects of either moisture treatment on fungal PLFA concentrations. It is concluded that variation in the soil biophysical environment beneath the tree canopies resulted in the differentiation of spatially defined bacterial communities that were tolerant of moisture stress. The anomaly that differences in community structure were largest at an intermediate position of 1 m between the trunk and below the canopy edge was not explained but may relate to tree root distribution.

Journal Article↗

PubMed2002

The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach.

The composition of the microbial community present in the nitrifying-denitrifying activated sludge of an industrial wastewater treatment plant connected to a rendering facility was investigated by the full-cycle rRNA approach. After DNA extraction using three different methods, 94 almost full-length 16S rRNA gene clones were retrieved and analyzed phylogenetically. 59% of the clones were affiliated with the Proteobacteria and clustered with the beta- (29 clones), alpha- (24), and delta-class (2 clones), respectively. 15 clones grouped within the green nonsulfur (GNS) bacteria and 11 clones belonged to the Planctomycetes. The Verrucomicrobia, Acidobacteria, Nitrospira, Bacteroidetes, Firmicutes and Actinobacteria were each represented by one to five clones. Interestingly, the highest 'species richness' [measured as number of operational taxonomic units (OTUs)] was found within the alpha-class of Proteobacteria, followed by the Planctomycetes, the beta-class of Proteobacteria, and the GNS-bacteria. The microbial community composition of the activated sludge was determined quantitatively by using 36 group-, subgroup-, and OTU-specific rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH), confocal laser scanning microscopy and digital image analysis. 89% of all bacteria detectable by FISH with a bacterial probe set could be assigned to specific divisions. Consistent with the 16S rRNA gene library data, members of the beta-class of Proteobacteria dominated the microbial community and represented almost half of the biovolume of all bacteria detectable by FISH. Within the beta-class, 98% of the cells could be identified by the application of genus- or OTU-specific probes demonstrating a high in situ abundance of bacteria related to Zoogloea and Azoarcus sensu lato. Taken together, this study provides the first encompassing, high-resolution insight into the in situ composition of the microbial community present in a full-scale, industrial wastewater treatment plant.

Bacteria↗

PubMed2000

Sediment microbial community structure and mercury methylation in mercury-polluted Clear Lake, California.

Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure. Seasonal changes and changes potentially attributable to temperature regulation of bacterial membranes were detectable but were less important influences on sediment PLFA composition than were differences due to lake sampling location. Analysis of biomarker PLFAs characteristic of Desulfobacter and Desulfovibrio groups of sulfate-reducing bacteria suggests that Desulfobacter-like organisms are important mercury methylators in the sediments, especially in the Lower Arm of Clear Lake.

California↗

PubMed2001

Effects of temperature on biodegradation characteristics of organic pollutants and microbial community in a solid phase aerobic bioreactor treating high strength organic wastewater.

The BOD removal rate and microbial community structure in a solid phase aerobic bioreactor using polyvinyl alcohol gel particles as packing material for the treatment of high strength organic wastewater were investigated at various temperatures. The BOD removal rate in the bioreactor increased when the temperature increased from 20 degrees C to 30 degrees C, 40 degrees C, and 50 degrees C, but it decreased when the temperature increased from 50 degrees C to 60 degrees C. Higher temperature enhanced the endogenous respiration of microbes in the bioreactor. The microbial community structure in the bioreactor was analyzed with quinone profile. The experimental results showed that the microbial community structure in the bioreactor was significantly affected by temperature. The dominant quinone of the microbes inhabiting the bioreactor was ubiquinone-8 at 30 degrees C, but that at 50 degrees C and 60 degrees C was menaquinone-7. It was estimated that the thermophilic Bacillus having menaquinone-7 dominated in the bioreactor at higher temperature. The microbial diversity in the bioreactor varied with temperature.

Bacillus↗

PubMed2006

Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3.

The extent of soil microbial diversity is seen to be critical to the maintenance of soil health and quality. Different agricultural practices are able to affect soil microbial diversity and thus the level of suppressiveness of plant diseases. In a 4-year field experiment, we investigated the microbial diversity of soil under different agricultural regimes. We studied permanent grassland, grassland turned into arable land, long-term arable land and arable land turned into grassland. The diversity of microbial communities was described by using cultivation-based and cultivation-independent methods. Both types of methods revealed differences in the diversities of soil microbial communities between different treatments. The treatments with higher above-ground biodiversity generally maintained higher levels of microbial diversity. Moreover, a positive correlation between suppression of Rhizoctonia solani AG3 and microbial diversity was observed. Permanent (species-rich) grassland and grassland turned into maize stimulated higher microbial diversities and higher levels of suppressiveness of R. solani AG3 compared with the long-term arable land. Effects of agricultural practices on Bacillus and Pseudomonas communities were also observed and clear correlations between the levels of suppressiveness and the diversities of these bacterial groups were found. This study highlighted the importance of agricultural management regime for soil microbial community structure and diversity as well as the level of soil suppressiveness.

Agriculture↗

PubMed2006

Periphytic photosynthetic stimulation of extracellular enzyme activity in aquatic microbial communities associated with decaying typha litter.

We examined the effect of light on extracellular enzyme activities of periphytic/endogenous microbial assemblages associated with decomposing litter of an emergent macrophyte Typha angustifolia within a small inland wetland in southeastern Michigan. Standing-dead Typha leaf litter was collected, placed into floating wire mesh litter baskets, and submerged in a wetland pool. Enzyme saturation assays were conducted on three occasions following litter submergence (days 9, 28, and 44) to generate saturation curves for the individual enzymes tested and to examine potential differences in enzyme saturation kinetics during microbial colonization and development. Experimental light manipulations were conducted on two occasions during microbial development (days 10 and 29). Short-term (30 min) light exposure significantly increased extracellular beta-glucosidase activity of litter-associated microbial communities. Activities of beta-xylosidase and leucine-aminopeptidase were not stimulated, and stimulation of phosphatase activity was variable. The exact mechanism for increased enzyme activity remains unknown, but it may have been increased pH arising from periphytic algal photosynthesis. These results suggest that extracellular enzyme activity in microbial communities colonizing natural organic substrata may be influenced by light/photosynthesis, as has previously been demonstrated for periphyton communities grown on artificial, inert substrata. Thus, light/photosynthetic mediated stimulation of extracellular enzyme activities may be a common occurrence in microbial communities associated with natural decaying plant litter in wetlands and might engender diurnal patterns in other microbial decay processes (e.g., production, organic matter decomposition, and mineralization).

Bacteria↗

PubMed2006

Effects of naphthalene on microbial community composition in the Delaware estuary.

The effects of naphthalene on microbial communities in the bottom boundary layer of the Delaware Bay estuary were investigated in microcosms using denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) with oligonucleotide probes. Three days after the addition of naphthalene, rates of bacterial production and naphthalene mineralization were higher than in no-addition controls and than in cases where glucose was added. Analyses using both DGGE and FISH indicated that the bacterial community changed in response to the addition of naphthalene. FISH data indicated that a few major phylogenetic groups increased in response to the glucose addition and especially to the naphthalene addition. DGGE also demonstrated differences in community composition among treatments, with four phylotypes being unique to naphthalene-amended treatments and three of these having 16S rRNA genes similar to known hydrocarbon degraders. The bacterial community in the naphthalene-amended treatment was distinct from the communities in the glucose-amended treatment and in the no-addition control. These data suggest that polycyclic aromatic hydrocarbons may have large effects on microbial community structure in estuaries and probably on microbially mediated biogeochemical processes.

Acinetobacter↗

PubMed2006

Identification of prevalent microbial communities in a municipal solid waste landfill.

To identify the microbial communities in Istanbul, Odayeri Municipal Solid Waste Landfill, leachate samples were collected from different sections at different stabilization phases. In identification of microbial communities in leachate samples, molecular techniques such as FISH, DGGE and cloning based on 16S rRNA and mcrA genes were used. As the chemical and microbiological compositions of the samples were compared, obvious correlations were found between the stability of the landfill section and abundance of active methanogens. On the other hand, there were considerable differences between acidogenic and mature leachate samples in DGGE profiles of archaeal and bacterial 16S rRNA genes. Moreover, in acidogenic leachate samples having BOD5/COD ratio of about 0.5 acetate utilizing Methanosarcina and Methanosaeta species were intensively detected in FISH. Although only very few H2-utilizing methanogens were identified with FISH analysis, most of the clones isolated from mature leachate samples clustered within H2-utilizing Methanobacteriales and Methanomicrobiales according to phylogenetic analysis of 16S rRNA and mcrA clones, respectively.

Archaea↗

PubMed1983

Adaptation of natural microbial communities to degradation of xenobiotic compounds: effects of concentration, exposure time, inoculum, and chemical structure.

Adaptation of microbial communities to faster degradation of xenobiotic compounds after exposure to the compound was studied in ecocores. Radiolabeled test compounds were added to cores that contained natural water and sediment. Adaptation was detected by comparing mineralization rates or disappearance of a parent compound in preexposed and unexposed cores. Microbial communities in preexposed cores from a number of freshwater sampling sites adapted to degrade p-nitrophenol faster; communities from estuarine or marine sites did not show any increase in rates of degradation as a result of preexposure. Adaptation was maximal after 2 weeks and was not detectable after 6 weeks. A threshold concentration of 10 ppb (10 ng/ml) was observed; below this concentration no adaptation was detected. With concentrations of 20 to 100 ppb (20 to 100 ng/ml), the biodegradation rates in preexposed cores were much higher than the rates in control cores and were proportional to the concentration of the test compound. In addition, trifluralin, 2,4-dichlorophenoxyacetic acid, and p-cresol were tested to determine whether preexposure affected subsequent biodegradation. Microbial communities did not adapt to trifluralin. Adaptation to 2,4-dichlorophenoxyacetic acid was similar to adaptation to nitrophenol. p-Cresol was mineralized rapidly in both preexposed and unexposed communities.

Journal Article↗

PubMed2006

Testing for differentiation of microbial communities using phylogenetic methods: accounting for uncertainty of phylogenetic inference and character state mapping.

Comparative analyses of microbial communities increasingly involve the assay of 16S rRNA (or other gene) sequences from environmental DNA. Determining whether the composition of two or more communities differ in their phylogenetic composition involves testing for covariation between phylogeny and community type. This approach requires estimating the phylogenetic relationships among all sampled sequences and assessing whether the distribution of sequences among communities differs from the null expectation that sequences are randomly distributed. One method developed for implementing the phylogeny-based test of differentiation, referred to as the Phylogenetic test, relies on a single estimate of the phylogeny. However, for most data sets, many alternative phylogenetic trees provide statistically equivalent descriptions of the data. Because the actual phylogeny is unknown, phylogenetic tests of differentiation among microbial communities must account for phylogenetic uncertainty. In this article, we evaluate bootstrapping and Bayesian phylogenetic methods when implementing the Phylogenetic test using parsimony to map character states, and we investigate the effects of character mapping uncertainty by using a Bayesian approach to stochastically map character states on trees. Our approaches incorporate uncertainty into the tests of two closely related null hypotheses: (1) populations are panmictic, and (2) identical communities existed in both environments over the course of evolutionary history. We use two data sets previously implemented in tests for community differentiation: nitrite reductase genes sampled from marsh and upland soils and 16S rDNA sequences sampled from the human mouth and gut. We show that accounting for phylogenetic and mapping uncertainties can drastically affect results when implementing the Phylogenetic test. Accounting for phylogenetic and character mapping uncertainty provides a more conservative and robust test of covariation between phylogeny and environment when comparing microbial communities using DNA sequences.

Bacteria↗

PubMedDate not supplied

[The homeostasis of the microbial communities in soils polluted by heavy metals].

Homeostatic potentialities of microbial communities in soils contaminated with heavy metals have been studied. To estimate the effect of contaminants on the soil microflora it was proposed to use the indices characterizing homeostasis of microbial community: microorganism survivability in contaminated soil and the period of restoration of their number, sensitivity to certain contaminants. In the model experiments on dark-grey podzolized soil it was shown that contamination with heavy metals (Cu2+, Cd2+, Sr2+, Pb2+, Hg2+) in the doses of 2 and 4 maximum permissible concentrations provokes a short-term inhibition of microorganisms development after which their number restores. Introduction of the mixture of metals evokes more intensive inhibition and extends the period of microorganism number restoration as compared with the effect of certain metals in the same doses.

Colony Count, Microbial↗

PubMed1991

Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization.

The BLOLOG redox technology based on tetrazolium dye reduction as an indicator of sole-carbon-source utilization was evaluated as a rapid, community-level method to characterize and classify heterotrophic microbial communities. Direct incubation of whole environmental samples (aquatic, soil, and rhizosphere) in BIOLOG plates containing 95 separate carbon sources produced community-dependent patterns of sole-carbon-source utilization. Principal-component analysis of color responses quantified from digitized images of plates revealed distinctive patterns among microbial habitats and spatial gradients within soil and estuarine sites. Correlation of the original carbon source variables to the principal components gives a functional basis to distinctions among communities. Intensive spatial and temporal analysis of microbial communities with this technique can produce ecologically relevant classifications of heterotrophic microbial communities.

Journal Article↗

PubMed2005

Impacts of chelate-assisted phytoremediation on microbial community composition in the rhizosphere of a copper accumulator and non-accumulator.

Chelate-assisted phytoremediation has been proposed as an effective tool for the extraction of heavy metals from soil by plants. However, side effects of the addition of chelate to soil microbial community are usually neglected. We studied the potential effects of chelate (glucose and citric acid) amendment on phytoextraction of copper and microbial community composition in soil under laboratory conditions. A copper (Cu) accumulator, Elsholtzia splendens, and a non-accumulator, Trifolium repens, were grown on a sandy loam soil containing 317 mg kg(-1) Cu. Microbial community compositions were analyzed by using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The results showed that the biomass of E. splendens grown with the chelate did not differ from that of the control. Addition of citric acid decreased the biomass of T. repens in comparison to that of glucose treatment. Application of glucose or citric acid significantly increased the extractable Cu concentration in planted and unplanted soils. Concentrations of Cu in the shoots of E. splendens were 2.6, 1.9 and 2.9 times of those of T. repens under no chelate, citric acid and glucose treatments, respectively. PCR-DGGE fingerprint analysis revealed that there were negative correlations between bacteria diversity and NH4NO3 extractable Cu under glucose or citric acid treatment. It was indicated the amendment of glucose to the plant T. repens increased the bacteria diversity in soil as compared to that in soils of non-chelate treatment. The above results indicated chelate addition facilitated phytoremediation of soil Cu and did not have a negative effect on microbial community.

Biodegradation, Environmental↗

PubMed2005

Microbial communities associated with skeletal tumors on Porites compressa.

Coral tumors are atypical skeletal forms found on coral reefs worldwide. Here we present an analysis of the microbial communities associated with skeletal tumors on the coral Porites compressa. Microbial growth rates on both healthy and tumorous P. compressa were decoupled from the surrounding water column. Microbial communities associated with tumorous colonies had a significantly faster growth rate than those associated with healthy P. compressa. The microbial community associated with the tumors contained more culturable Vibrio spp. and could utilize more carbon sources than the microbes associated with healthy colonies. Presence of tumors affected the composition and dynamics of the microbial population associated with the entire colony.

Animals↗

PubMed2006

Seasonal variations in sugar contents and microbial community in a ryegrass soil.

The relationship among sugar concentrations, microbial community and physical variables (precipitation and soil temperature) was investigated in a ryegrass soil from January 2004 to January 2005. Mono- and disaccharide sugars were extracted using a mixture of dichloromethane and methanol and analyzed as their TMS derivatives by GC-MS. Changes in microbial community were assessed using phospholipid and neutral lipid fatty acids (PLFA and NLFA, respectively) analysis. The results of a one-year study showed that the seasonal variability of sugar contents found in the soil samples is mainly related to biomass or nutritional status of the fungal community. The increase in sucrose and fructose exudation by plant roots in the beginning of the growing season (early spring) may be responsible for the highest fungal biomass amount (PLFAs) observed in this study. Fungal storage lipid abundances (NLFAs) peaked in summer, during the same period that the highest concentrations of mannitol and trehalose were detected. This is consistent with these two sugars being stress-induced fungal metabolites, produced due to the low soil moisture observed during this season. In contrast, bacterial community growth seems to be more dependent on plant substrate than on physical variables, since the strongest decrease in bacterial biomass amounts (PLFAs) was found after cutting of the ryegrass field in early July.

Biomass↗

PubMed1997

Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups.

Two hundred ninety-seven bacteria carrying plasmids that range in size from 5 to 250 kb were identified from more than 1,000 aerobic heterotrophic bacteria isolated from coastal California marine sediments. While some isolates contained numerous (three to five) small (5- to 10-kb) plasmids, the majority of the natural isolates typically contained one large (40- to 100-kb) plasmid. By the method of plasmid isolation used in this study, the frequency of plasmid incidence ranged from 24 to 28% depending on the samples examined. Diversity of the plasmids occurring in the marine sediment bacterial populations was examined at the molecular level by hybridization with 14 different DNA probes specific for the incompatibility and replication (inc/rep) regions of a number of well-characterized plasmid incompatibility groups (repB/O, FIA, FII, FIB, HI1, HI2, I1, L/M, X, N, P, Q, W, and U). Interestingly, we found no DNA homology between the plasmids isolated from the culturable bacterial population of marine sediments and the replicon probes specific for numerous incompatibility groups developed by Couturier et al. (M. F. Couturier, F. Bex, P. L. Bergquist, and W. K. Maas, Microbiol. Rev. 52:375-395, 1988). Our findings suggest that plasmids in marine sediment microbial communities contain novel, as-yet-uncharacterized, incompatibility and replication regions and that the present replicon typing system, based primarily on plasmids derived from clinical isolates, may not be representative of the plasmid diversity occurring in some marine environments. Since the vast majority of marine bacteria are not culturable under laboratory conditions, we also screened microbial community DNA for the presence of broad- and narrow-host-range plasmid replication sequences. Although the replication origin of the conjugally promiscuous broad-host-range plasmid RK2 (incP) was not detectable in any of the plasmid-containing culturable marine isolates, DNA extracted from the microbial community and amplified by PCR yielded a positive signal for RK2 oriV replication sequences. The strength of the signal suggests the presence of a low level of the incP replicon within the marine microbial community. In contrast, replication sequences specific for the narrow-host-range plasmid F were not detectable in DNA extracted from marine sediment microbial communities. With the possible exception of mercuric chloride, phenotypic analysis of the 297 plasmid-bearing isolates did not demonstrate a correlation between plasmid content and antibiotic or heavy metal resistance traits.

Basidiomycota↗