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PubMed2002

Effects of resource supplies on the structure and function of microbial communities.

The supplies of nutrients, and their elemental stoichiometry, can have significant impacts upon the structure and function of microbial communities. This review focuses on the effects of nutrient supplies on the biodegradation of organic matter, and on the dynamics of host-pathogen interactions. Analyses of data from the literature suggest significant effects of nitrogen:phosphorus supply ratios on the microbial decomposition of organic matter, and it is argued that these stoichiometric effects may have important implications for the fate and fluxes of carbon in natural ecosystems. In addition, it is shown that the supplies of nitrogen and phosphorus to the host can strongly influence the outcome of infections in both terrestrial and aquatic plants, suggesting that resource availability and resource supply ratios potentially may have significant effects on the health of many plant communities.

Bacteria↗
PubMed1985

Examination of thermophilic methane-producing digesters by analysis of bacterial lipids.

Thermophilic methane-producing digesters were examined by the analysis of lipids to determine the microbial biomass, community structure, and nutritional status of the microbes within the digesters. The digesters received a daily feedstock of cattle feed and Bermuda grass, with some digesters receiving additional supplements of propionate, butyrate, or nitrate. Microbial biomass, measured as total extractable lipid phosphate, was decreased in slurries from digesters receiving continuous addition of the fermentation intermediates propionate or butyrate as compared with slurries from control digesters receiving the feedstock alone. In slurries from digesters that received continuous addition of nitrate, the microbial biomass was higher than in the slurries from control digesters. The control digesters had ca. 2.5 x 10 bacteria per g (dry weight) as determined from total extractable lipid phosphate. Shifts in microbial community structure were observed by analysis of ester-linked phospholipid fatty acids. Statistical analysis of the patterns of phospholipid fatty acids indicated that the digesters receiving different supplements could be distinguished from the control digester and from each other. Poly-beta-hydroxybutyric acid, an indicator of metabolic stress, was detected in slurries from all the digesters. Slurries from the nitrate-amended digester had the highest concentration of poly-beta-hydroxybutyric acid, whereas slurries from the propionate-amended digester had the lowest concentration. These chemical analyses offer a quantitative means to correlate shifts in microbial biomass, community structure, and nutritional status in complex fermentation systems to the production of a specific end product.

Journal Article↗
PubMed1998

Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities.

Abstract In this study, two different agricultural soils were investigated: one organic soil and one sandy soil, from Stend (south of Bergen), Norway. The sandy soil was a field frequently tilled and subjected to crop rotations. The organic soil was permanent grazing land, infrequently tilled. Our objective was to compare the diversity of the cultivable bacteria with the diversity of the total bacterial population in soil. About 200 bacteria, randomly isolated by standard procedures, were investigated. The diversity of the cultivable bacteria was described at phenotypic, phylogenetic, and genetic levels by applying phenotypical testing (Biolog) and molecular methods, such as amplified rDNA restriction analysis (ARDRA); hybridization to oligonucleotide probes; and REP-PCR. The total bacterial diversity was determined by reassociation analysis of DNA isolated from the bacterial fraction of environmental samples, combined with ARDRA and DGGE analysis. The relationship between the diversity of cultivated bacteria and the total bacteria was elucidated. Organic soil exhibited a higher diversity for all analyses performed than the sandy soil. Analysis of cultivable bacteria resulted in different resolution levels and revealed a high biodiversity within the population of cultured isolates. The difference between the two agricultural soils was significantly higher when the total bacterial population was analyzed than when the cultivable population was. Thus, analysis of microbial diversity must ultimately embrace the entire microbial community DNA, rather than DNA from cultivable bacteria.

Journal Article↗
PubMed2005

Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment.

Microbial community composition and structure were characterized in marine sediments contaminated for >80 years with cadmium, copper, lead, and zinc. Four sampling sites that encompass a wide range of sediment metal loads were compared in a Norwegian fjord (Sorfjord). HCl-extractable metals and organic matter constantly decreased from the most contaminated site (S1) to the control site (S4). All sampling sites presented low polychlorinated biphenyl (PCB) concentrations (Sigma(7)PCB < 7.0 ng g [dry weight](-1)). The biomass ranged from 4.3 x 10(8) to 13.4 x 10(8) cells g (dry weight) of sediments(-1) and was not correlated to metal levels. Denaturing gradient gel electrophoresis indicated that diversity was not affected by the contamination. The majority of the partial 16S rRNA sequences obtained were classified in the gamma- and delta-Proteobacteria and in the Cytophaga-Flexibacter-Bacteroides (CFB) bacteria. Some sequences were closely related to other sequences from polluted marine sediments. The abundances of seven phylogenetic groups were determined by using fluorescent in situ hybridization (FISH). FISH was impaired in S1 by high levels of autofluorescing particles. For S2 to S4, the results indicated that the HCl-extractable Cu, Pb, and Zn were negatively correlated with the abundance of gamma-Proteobacteria and CFB bacteria. delta-Proteobacteria were not correlated with HCl-extractable metals. Bacteria of the Desulfosarcina-Desulfococcus group were detected in every site and represented 6 to 14% of the DAPI (4',6'-diamidino-2-phenylindole) counts. Although factors other than metals may explain the distribution observed, the information presented here may be useful in predicting long-term effects of heavy-metal contamination in the marine environment.

Colony Count, Microbial↗
PubMed2002

Histopathological methods for the investigation of microbial communities associated with disease lesions in reef corals.

AIMS: To determine the spatial structure of microbial communities associated with disease lesions of reef corals (Scleractinia). METHODS AND RESULTS: Agarose pre-embedding preserved the structure of the disease lesion and surrounding tissues prior to demineralization of the carbonate exoskeleton and embedding in resin. Fluorescence in situ hybridization (FISH) was used to localize bacteria in the lesions of various diseases. CONCLUSIONS: The techniques successfully preserved the in situ spatial structure of degenerated coral tissues. In one case (white plague disease), significant bacterial populations were found only in fragmented remnants of degenerated coral tissues at the lesion boundary that would not have been detected using conventional histopathological techniques. SIGNIFICANCE AND IMPACT OF THE STUDY: Determining the composition, spatial structure and dynamics of microbial communities within the disease lesions is necessary to understand the process of disease progression. The methods described may be applicable to a wide range of diseases involving necrotic lesion formation and requiring extensive tissue processing, such as skeleton demineralization.

Adaptation, Physiological↗
PubMed2006

Community structure and physiological characterization of microbial mats in Byers Peninsula, Livingston Island (South Shetland Islands, Antarctica).

The community structure and physiological characteristics of three microbial mat communities in Byers Peninsula (Livingston Island, South Shetland Islands, Antarctica) were compared. One of the mats was located at the edge of a stream and was dominated by diatoms (with a thin basal layer of oscillatorian cyanobacteria), whereas the other two mats, located over moist soil and the bottom of a pond, respectively, were dominated by cyanobacteria throughout their vertical profiles. The predominant xanthophyll was fucoxanthin in the stream mat and myxoxanthophyll in the cyanobacteria-dominated mats. The sheath pigment scytonemin was absent in the stream mat but present in the soil and pond mats. The stream mat showed significantly lower delta13C and higher delta15N values than the other two mats. Consistent with the delta15N values, N2 fixation was negligible in the stream mat. The soil mat was the physiologically most active community. It showed rates of photosynthesis three times higher than in the other mats, and had the highest rates of ammonium uptake, nitrate uptake and N2 fixation. These observations underscore the taxonomic and physiological diversity of microbial mat communities in the maritime Antarctic region.

Animals↗
PubMed2005

Larger islands house more bacterial taxa.

The power law that describes the relationship between species richness and area size is one of the few generalizations in ecology, but recent studies show that this relationship differs for microbes. We demonstrate that the natural bacterial communities inhabiting small aquatic islands (treeholes) do indeed follow the species-area law. The result requires a re-evaluation of the current understanding of how natural microbial communities operate and implies that analogous processes structure both microbial communities and communities of larger organisms.

Bacteria↗
PubMed2003

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities.

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four (13)C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the (13)C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-(13)C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by (13)C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram+ biomarkers showed more incorporation of SOM-C than did Gram- biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More (13)C (from both simple and recalcitrant sources) was incorporated into the Gram- biomarkers than Gram+ biomarkers despite the fact that the Gram+ group generally comprised a greater portion of the bacterial biomass than did markers for the Gram- group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.

Benzaldehydes↗
PubMed2026

Decoding microbial metabolic complementarity from individual traits to community structuring.

A fundamental challenge in microbiome research lies in elucidating the functional capacity of microbial communities through community membership and genomic data. As community structuring and emergent functional traits are determined by bacterial community metabolic networks, it is important to gain insights into the principles that govern bacteria-bacteria interactions. Here, we applied an integrative framework linking individual strain-level traits to community structuring in a simplified synthetic bacterial community (SSC8) that promotes the growth of ungrafted watermelon. By combining mono- and coculture assays with genome-scale metabolic modeling and metabolomic profiling of spent media, we characterized directional interactions and resource dependencies among community members. Our findings show that positive interactions dominated the community network, accounting for 55% of all pairwise combinations, indicating a high prevalence of growth-promoting effects among strains. Genome-scale metabolic modeling showed that functional divergence among strains enhanced the potential for metabolic complementarity as phylogenetic distance increased. Integrating metabolic modeling with metabolomics further suggested that Pseudomonas azotifigens Q6 not only benefited from all other community members, but also exhibited mutualistic interactions with the other three strains, with metabolite exchange involving compounds such as L-lysine and L-cysteine. Pseudomonas azotifigens Q6 acted as an important driver of community composition by affecting the abundance of several other consortium members in vitro. These findings highlight the role of metabolic complementarity in driving community structuring by promoting selective persistence of specific strains. Our work provides mechanistic insights into microbial interaction networks in vitro and offers a conceptual foundation for the rational design of functionally robust and plant-beneficial microbiomes.

Bacteria↗
PubMed2006

Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5.

The genetic structure of bacterial and fungal communities was characterized in the rhizosphere of Medicago truncatula Gaertn. cv. Jemalong line J5 at five developmental stages (three vegetative and two reproductive stages), and in three compartments (bulk soil, rhizosphere soil and root tissues). The genetic structure of microbial communities was determined by cultivation-independent methods using directly extracted DNA that was characterized by automated ribosomal intergenic spacer analysis (ARISA). Principal component analyses (PCA) indicate that, for all developmental stages, the genetic structure of microbial communities differed significantly by compartment, with a major shift in the community in root tissues corresponding to the most intimate compartment with the plant. Differences were also recorded during plant development, the most significant being observed during the transition between vegetative and reproductive stages. Throughout this period, plants were shown to establish the highest level of symbiotic association (mycorrhization, nodulation) with arbuscular mycorrhizal fungi and Rhizobia. During the reproductive stages, the dynamics of the genetic structure differed between bacterial and fungal communities. At the last reproductive stage, the genetic structure of bacterial communities became close to that recorded during the first vegetative stages, suggesting a resilience phenomenon, whereas the genetic structure of fungal communities remained different from the vegetative stages and also from the early reproductive stages, suggesting a persistence of the rhizosphere effect.

Bacteria↗
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↗
PubMed1999

Dilution/extinction of community phenotypic characters to estimate relative structural diversity in mixed communities.

Recent interest in microbial diversity has led to increased emphasis on the development of appropriate techniques. Structural diversity encompasses the number and distribution of separate or interacting biological entities responsible for a given function within the overall set of functions of a community. This study evaluated an approach for estimating the relative degree of structural diversity in heterotrophic microbial communities by dilution to extinction of community phenotypic traits. Serial dilutions of environmental samples (rhizosphere, stream) were tested for community phenotypic traits (i.e. carbon source respiration). The non-linear relationship between the number of positive responses (i.e. functional richness or R) and inoculum density in each sample dilution (I) fit the simple rectangular hyperbola model, allowing estimation of the maximal richness (R(max)) and the inoculum density at half-maximal richness (K(I)). The later term appears to be useful in assessing relative structural diversity as evidenced by significantly higher values for communities with higher predicted species diversity. The examination of community functional characteristics across a series of dilutions, particularly in conjunction with other techniques, may be a useful approach for the study of microbial diversity and related ecological parameters such as niche width and metabolic redundancy.

Journal Article↗
PubMed1994

The structure and function of microbial communities in recirculating hydroponic systems.

Strategies to control the microbial community associated with plant growth systems need to be based on a fundamental understanding of the factors which structure and regulate the community. Spatial and temporal patterns in the abundance and production rate of microorganisms in hydroponic systems containing wheat were examined to evaluate how root-derived carbon is processed. The relevance of results to monitoring and control strategies is discussed.

Bacteria↗
PubMed2006

Phylogenetic clustering and overdispersion in bacterial communities.

Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.

Bacteria↗
PubMed2005

The influence of soil pollution on soil microbial biomass and nematode community structure in Navoiy Industrial Park, Uzbekistan.

The effects of ammonium-rich and heavy-metal air pollution produced by the industrial enterprises at Navoiy (Uzbekistan) on soil free-living nematodes and microbial population activities was investigated in soil samples collected in a 5-km radius surrounding the industrial enterprises. At each location (n=4), soil samples were collected from the upper layer (0-10 cm) for determination of soil moisture (SM), total organic carbon (C(org)), total soluble nitrogen (TSN), soil electrical conductivity (EC) and cations (Ca(2+), K(+), Na(+)). Heavy metals (As, Cu, Pb, Zn), soil basal respiration (BR), microbial biomass (C(mic)) and nematode populations were determined. The highest level of TSN was found near the industrial enterprises, with 23.8 and 24.0 mg/kg at NavoiAzot and NavoiGRES, respectively. Soil sample pH was found to be weakly alkaline, with levels ranging between 7.9 and 8.1. Mean soil moisture content varied from 0.75% to 0.93% of the wet weight, without any significant differences between the sampling stations. The heavy metals As, Cu, Pb and Zn were accumulated in the upper soil layer. A significant difference was found between soil heavy-metal content for Cu (p<0.0005) and As (p<0.02). Basal respiration and microbial coefficient (C(mic)/C(org)) were found to be significantly negatively correlated with Cu and As soil content. A significantly positive correlation was found between the Cd concentration and the metabolic quotient (qCO(2)) (p<0.003). No significant correlation was observed between the soil microbial population and total soluble nitrogen. Furthermore, the qCO(2), which is a known ecophysiological index for the soil microbial population, was found to be correlated with the total number of nematodes in general and with the bacteriovore-feeding group in particular. No significant correlation was observed between the soil microbial population and total soluble nitrogen.

Animals↗
PubMed2006

Influence of freeze-thaw stress on the structure and function of microbial communities and denitrifying populations in soil.

Microbial N2O release during the course of thawing of soil was investigated in model experiment focusing on denitrification, since freeze-thaw has been shown to cause significant physical and biological changes in soil, including a surge of N2O and CO2. The origin of these is still controversially discussed. The increase in denitrification after thawing may be attributed to the diffusion of organic substrates newly available to denitrifiers from disrupted soil aggregates, leading to an increase in microbial activity. Laboratory experiments with upper soil layer of a grassland were conducted in microcosms for real-time gas measurements during the entire phase of freeze and thaw. Shifts in microbial communities were evident on resolution of 16S and 18S rRNA genes and transcripts by denaturing gradient gel electrophoresis (DGGE). Microbial expression profiles were compared by RNA-arbitrarily primed PCR technique and subsequent resolution of amplified products on acrylamide gels. Differences in expression levels of periplasmic nitrate reductase gene (napA) and cytochrome cd1 nitrite reductase (nirS) were observed by most-probable-number-reverse transcription-PCR, with higher levels of expression occurring just after thawing began, followed by a decrease. napA and nirS DGGE profiles showed no change in banding patterns with fingerprints derived from DNA, whereas those derived from cDNA showed a clear succession of denitrifying bacteria, with the most complex pattern being observed at the end of the N2O surge. This study provides insight into the structural community changes and expression dynamics of denitrifiers as a result of freeze-thaw stress. Also, the results presented here support the belief that the gas fluxes observed during thawing is a result of freezing initiated high microbial activity.

Bacteria↗