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At least 19 recordsLinked to original sources
PubMed2025

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.

MOTIVATION: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes. RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. AVAILABILITY AND IMPLEMENTATION: Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.

Mice↗
PubMed1983

Degradation of chlorophenols by a defined mixed microbial community.

Synthetic sewage containing phenol, acetone, and alkanols plus 4-chlorophenol or a mixture of isomeric chlorophenols is completely degraded by a defined mixed culture with Pseudomonas sp. strain B13 as a chlorocatechol-dissimilating member of the community. Total degradation of the organic carbon was indicated by release of stoichiometric amounts of chloride and low content of dissolved organic carbon in the cell-free effluents. During adaptation to high loads of chlorophenols the initial meta-cleavage activity was completely replaced by ortho-cleavage activity of type I and II. In the fully acclimated culture, hybrid strains such as Alcaligenes sp. strain A7-2 were detected, which are more competitive than Pseudomonas sp. strain B13 with respect to chlorophenol degradation.

Alcaligenes↗
PubMed2026

Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.

BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications. RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance. CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.

Caragana↗
PubMed2002

A statistical procedure for the analysis of microbial communities based on phenotypic properties of isolates.

A novel statistical procedure for the analysis of microbial communities based on phenotypic properties of randomly collected isolates is presented and discussed. The procedure allows the representation of the microbial communities as a set of ellipses in a bidimensional graph. This representation is obtained by the following steps: (a) measurement of a set of binary phenotypic properties for n isolates belonging to k samples, each representing a different community; (b) repeated sampling by bootstrapping of the m samples, thus obtaining, for each community, i subsamples of j isolates; (c) calculation of the frequency of positive results for each test for each subsample; (d) calculation of the matrix of Euclidean distances between the k x i frequency vectors; (e) use of multidimensional scaling (MDS) to obtain a representation in two dimensions of the distance relationships between the frequency vectors; (f) plotting of the 95% confidence ellipses for the i frequency vectors of each of the k communities. By using both simple, synthetic microbial communities, and samples of lactic acid bacteria isolated from natural microbial communities (sourdoughs, compressed yeast, fermented sausages), it was demonstrated that the position and shape of the ellipses are clearly related to the composition of the community, while the relationship between the size of the ellipses and the phenotypical diversity of the community is less straightforward: while communities with very different diversity (measured with the Functional Evenness index and the mean taxonomic distance) had ellipses that were very different in size, there was no strict proportionality between the size of the ellipse and the diversity of the community. Nevertheless, the representation of microbial communities obtained by bootstrapping and multidimensional scaling appears to be superior to the more usual representation based on tabulation of the frequencies of isolates belonging to different clusters.

Animals↗
PubMed1983

Microcosm and experimental pond evaluation of microbial community response to synthetic oil contamination in freshwater sediments.

A multivariate approach was used to evaluate the significance of synthetic oil-induced perturbations in the functional activity of sediment microbial communities. Total viable cell densities, ATP-biomass, alkaline phosphatase and dehydrogenase activity, and mineralization rates of glucose, protein, oleic acid, starch, naphthalene, and phenanthrene were monitored on a periodic basis in microcosms and experimental ponds for 11 months, both before and after exposure to synthetic oil. All variables contributed to significant discrimination between sediment microbial responses in control communities and communities exposed to a gradient of synthetic oil contamination. At high synthetic oil concentrations (4,000 ml/12 m), a transient reduction in sediment ATP concentrations and increased rates of oleic acid mineralization were demonstrated within 1 week of exposure. These transient effects were followed within 1 month by a significant increase in rates of naphthalene and phenanthrene mineralization. After initial construction, both control and synthetic oil-exposed microbial communities demonstrated wide variability in community activity. All experimental microbial communities approached equilibrium and demonstrated good replication. However, synthetic oil perturbation was demonstrated by wide transient variability in community activity. This variability was primarily the result of the stimulation of polyaromatic hydrocarbon mineralization rates. In general, microcosms and pond communities demonstrated sufficient resiliency to recover from the effects of synthetic oil exposure within 3 months, although polyaromatic hydrocarbon mineralization rates remained significantly elevated.

Journal Article↗
PubMed2026

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.

BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom 3 improved the neutral detergent fiber degradation (NDFD) by 20.39% averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom 3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF, + 11.47%). Genomic analysis revealed that the SynCom 3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.

Animals↗
PubMed2026

Precisely designed keystone metabolites boost shrimp disease resistance by recruiting symbionts via the lipoxin A4-AP-1 pathway.

BACKGROUND: Gut metabolites and symbionts are indispensable for host health, yet the precise identification of keystone metabolites and construction of synthetic microbial communities (SynComs) to enhance disease resistance remains limited. RESULTS: Using Litopenaeus vannamei as a model, we identified pyruvic acid and DL-glutamine (1:2) as keystone metabolites by borrowing the microbial ecology principles of bio-indicators and driver taxa. Dietary supplementation with these metabolites sufficiently protected shrimp from white feces syndrome (WFS). Multi-omics analyses demonstrated that keystone metabolites exerted positive effects by enriching beneficial Ruegeria lacuscaerulensis, Bacillus subtilis and Nioella nitratireducens, strengthening the gut network stability, and enhancing shrimp immunity, which collectively potentiated WFS resistance. The recruited three strains were consumers and producers of the two keystone metabolites, and discriminative strains between healthy and diseased shrimp across global datasets. A SynCom constructed from the three strains (4:3:2) replicated the efficacy of keystone metabolites. Both keystone metabolites and SynCom elevated shrimp gut and hepatopancreas lipoxin A4 (LXA4) levels, which suppressed the pro-inflammatory transcription factor AP-1, as validated by in vivo inhibition assay. CONCLUSIONS: Our findings demonstrate that precisely designed keystone metabolites enhance shrimp disease resistance through the recruitment of key symbionts-LXA4-AP-1 axis. The rationally designed keystone metabolites and SynCom are compelling biocontrol solutions in improving host disease resistance. Video Abstract.

Animals↗
PubMed2026

Rhizosphere Dialogue: Microorganisms Mediated by Root Exudates Alleviate Drought Stress in Grasses.

Drought stress threatens the ecological functions and economic value of grasses, posing a major challenge to their sustainable production. Plants co-evolve with rhizosphere microbial communities, sometimes described as the plant's second genome, that can contribute to drought adaptation. Drought alters root architecture, hormonal and redox regulation and belowground carbon allocation, thereby modifying the quantity and composition of root exudation and reshaping the rhizosphere environment. This review uses the rhizosphere dialogue as an integrative framework to link these plant responses with microbial recruitment and subsequent feedback to the host. We summarise three linked stages of this dialogue: drought-induced changes in root exudation; microbial recruitment and colonisation through chemotaxis, attachment, biofilm formation, and root colonisation; and microbiome-mediated feedback that improves plant water relations, hormonal and redox homoeostasis, nutrient acquisition, and root function. We highlight microbial extracellular polymeric substances, 1-aminocyclopropane-1-carboxylate deaminase, and microbial volatile organic compounds as key mediators of drought alleviation. We then discuss how this framework may inform rational synthetic microbial community (SynCom) design, microbiome-informed breeding, artificial intelligence and machine-learning assisted strain prioritisation, rhizosphere legacy effects, and real-time monitoring. Future work should distinguish active exudate-mediated recruitment from drought-driven environmental filtering and integrate multi-omics, plant genetics, functional validation, and multi-location field trials to determine whether rhizosphere dialogue can become a predictive framework for climate-resilient grass production.

drought stress↗
PubMed2006

Sheep-urine-induced changes in soil microbial community structure.

Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.

Animals↗
PubMed2026

From dysbiosis to resilience: Microbiome engineering for sustainable shrimp aquaculture.

The intensification of shrimp aquaculture has increased exposure to disease, environmental perturbations, and antimicrobial pressure, making microbial stability increasingly relevant to sustainable production. Microbiome stability-encompassing resistance to disturbance and resilience of functional recovery-provides an ecological framework for understanding how shrimp and culture-environment microbial communities respond to intensive farming. This review examines the transition from microbial homeostasis to dysbiosis and evaluates how microbiome engineering could redirect disrupted communities towards resilient states. Evidence is integrated across the intestine, hepatopancreas, rearing water, sediment and biofloc to assess how host genetics, ontogeny, diet, culture conditions, antibiotics and pollutants shape microbiome assembly and destabilization. Disease-associated changes in acute hepatopancreatic necrosis disease, white faeces syndrome, Enterocytozoon hepatopenaei infection, and white spot syndrome virus infection are critically evaluated, with explicit separation of associations, pathogen-induced dysbiosis, and community-level causality. Established and emerging interventions-including probiotics, prebiotics, synbiotics, functional diets, biofloc management, phages, postbiotics, microbiota transplantation and synthetic microbial communities-are assessed according to their capacity to modify microbial function, persistence and recovery rather than taxonomic change alone. We further examine how multi-omics, microbiome-informed breeding, and environmental monitoring could support biomarker development, predictive decision support and context-specific intervention. We argue that progress requires a shift from taxonomic description to function-guided engineering, from endpoint comparisons to direct measurement of resilience, and from laboratory efficacy to reproducible farm-scale validation. Overall, microbiome management may contribute to more disease-resilient and sustainable shrimp production, provided that its effectiveness can be validated under commercial farming conditions.

Dysbiosis↗
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↗
PubMed1979

Effect of concentration of organic chemicals on their biodegradation by natural microbial communities.

The effect of concentration on the biodegradation of synthetic organic chemicals by natural microbial communities was investigated by adding individual C-labeled organic compounds to stream water at various initial concentrations and measuring the formation of CO(2). The rate of degradation of p-chlorobenzoate and chloroacetate at initial concentrations of 47 pg/ml to 47 mug/ml fell markedly with lower initial concentrations, although half or more of the compound was converted to CO(2) in 8 days or less. On the other hand, little mineralization of 2,4-dichlorophenoxyacetate and 1-naphthyl-N-methylcarbamate, or the naphthol formed from the latter, occurred when these compounds were present at initial concentrations of 2 to 3 ng/ml or less, although 60% or more of the chemical initially present at higher concentrations was converted to CO(2) in 6 days. It is concluded that laboratory tests of biodegradation involving chemical concentrations greater than those in nature may not correctly assess the rate of biodegradation in natural ecosystems and that low substrate concentration may be important in limiting biodegradation in natural waters.

Journal Article↗
PubMed2026

PGPR inoculation and growth enhancement of crops cultivated in hydroponic systems.

Plant growth-promoting rhizobacteria (PGPR) are ubiquitous rhizosphere microorganisms that promote plant health through various mechanisms. Although the study of PGPR inoculants in soil has been done for ages, their application in hydroponic systems has received relatively limited attention. This review identifies PGPR inoculants that are commonly used in hydroponics, methods of application, and their effects on plant growth and nutrient use efficiency. Literature shows that PGPR inoculants improve plant performance in controlled hydroponic systems through the production of growth-stimulating substances, nitrogen fixation, and improved nutrient acquisition. However, the plant growth responses are highly variable depending on the composition of nutrient solutions, environmental factors, crop and microbe species, and the type of hydroponic system. The review identifies various challenges of PGPR inoculation in hydroponic systems and future research directions to address the current gaps. Generally, the productivity of hydroponic systems can be enhanced through advanced inoculation strategies and the development of suitable carrier materials to improve inoculant survival, viability, and functions. Emphasis should also be placed on designing system-specific microbial consortia and Synthetic communities that are tailored to the unique ecological conditions of hydroponic systems.

Hydroponics↗
PubMed2025

In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.

Understanding plant-microbe interactions is vital for developing sustainable agricultural practices and mitigating the consequences of climate change on food security. Plant-microbe interactions can improve nutrient acquisition, reduce dependency on chemical fertilizers, affect plant health, growth, and yield, and impact plants' resistance to biotic and abiotic stresses. These interactions are largely driven by metabolic exchanges and can thus be understood through metabolic network modelling. Recent developments in genomics, metagenomics, phenotyping, and synthetic biology now enable researchers to harness the potential of metabolic modelling at the genome scale. Here, we review studies that utilize genome-scale metabolic modelling to study plant-microbe interactions in symbiotic, pathogenic, and microbial community systems. This review catalogues how metabolic modelling has advanced our understanding of the plant host and its associated microorganisms as a holobiont. We showcase how these models can contextualize heterogeneous datasets and serve as valuable tools to dissect and quantify underlying mechanisms. Finally, we consider studies that employ metabolic models as a testbed for in silico design of synthetic microbial communities with predefined traits. We conclude by discussing broader implications of the presented studies, future perspectives, and outstanding challenges.

Plants↗
PubMed2025

Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.

Many microbial communities in nature are complex, with hundreds of coexisting strains and the resources they consume. We currently lack the ability to assemble and manipulate such communities in a predictable manner in the lab. Here, we take a first step in this direction by introducing and studying a simplified consumer resource model of such complex communities in serial dilution experiments. The main assumption of our model is that during the growth phase of the cycle, strains share resources and produce metabolic byproducts in proportion to their average abundances and strain-specific consumption/production fluxes. We fit the model to describe serial dilution experiments in hCom2, a defined synthetic human gut microbiome with a steady-state diversity of 63 species growing on a rich media, using consumption and production fluxes inferred from metabolomics experiments. The model predicts serial dilution dynamics reasonably well, with a correlation coefficient between predicted and observed strain abundances as high as 0.8. We applied our model to: (i) calculate steady-state abundances of leave-one-out communities and use these results to infer the interaction network between strains; (ii) explore direct and indirect interactions between strains and resources by increasing concentrations of individual resources and monitoring changes in strain abundances; (iii) construct a resource supplementation protocol to maximally equalize steady-state strain abundances.

Gastrointestinal Microbiome↗
PubMed2005

Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater.

Membrane-coupled bioreactors (MBRs) offer substantial benefits compared to conventional reactor designs for biological wastewater treatment. MBR treatment efficiency, however, has not been optimized because the effects of the MBR on process microbiology are poorly understood. In this study, the structure and function of the microbial communities growing in MBRs fed simple synthetic wastewater were investigated. In four starch-fed MBRs, the bacterial community substantially increased its alpha-glucosidase affinity (>1000-fold), while the leucine aminopeptidase and heptanoate esterase affinities increased slightly (<40-fold) or remained relatively constant. Concomitant to these physiological adaptations, shifts in the bacterial community structure in two of the starch-fed MBRs were detected by PCR-DGGE. Four of the bacterial populations detected by PCR-DGGE were isolated and exhibited specific growth rates in batch culture ranging from 0.009 to 0.22 h(-1). Our results suggest that bacterial communities growing under increasingly stringent nutrient limitation adapt their enzyme activities primarily for the nutrients provided, but that there is also a more subtle response not linked to the substrates included in the feed medium. Our research also demonstrates that MBRs can support relatively complex bacterial communities even on simple feed media.

Adaptation, Physiological↗
PubMed2026

Unveiling phthalate esters biodegradation from microbial community to Pseudarthrobacter scleromae HL-1: Kinetics, genomic insights, pathways, toxicity assessment and environmental remediation.

Phthalate esters (PAEs) are ubiquitous synthetic plasticizer pollutants posing severe ecological and human health risks. This study compared microbial community structures and dibutyl phthalate (DBP) degradation kinetics of two consortia: 7-day enriched MC1 (50&#x202f;mg/L DBP) and 6-cycle acclimated MC7 (50-1000&#x202f;mg/L DBP), demonstrating directional DBP stress selection generated a low-diversity, highly specialized degradative community with a 25.4&#x202f;mg/L/h maximum degradation rate (Vmax), 1.68-fold higher than MC1. Four dominant DBP-degrading strains were isolated from MC7; Pseudarthrobacter scleromae HL-1 showed the highest efficiency with 17.1&#x202f;mg/L/h Vmax and complete 500&#x202f;mg/L DBP removal within 72&#x202f;h, broad substrate spectrum, and strong adaptability after optimization. Whole-genome sequencing and GC-MS/MS elucidated a dual-parallel DBP mineralization pathway, first reported in Pseudarthrobacter, integrating ester hydrolysis and side-chain &#x3b2;-oxidation. ECOSAR and Chlorella vulgaris bioassays confirmed progressive toxicity attenuation, with >&#x202f;99% relative toxicity reduction after 72&#x202f;h and no toxic intermediate accumulation. Natural lake water trials with trace background PAEs showed HL-1 successfully colonized aquatic environments, reshaped indigenous communities into synergistic degradative consortia, and achieved 99.2% DBP removal in 84&#x202f;h. This work provides comprehensive insights into PAE biodegradation mechanisms from community to single strain and highlights HL-1 as a promising candidate for remediating PAE-polluted aquatic ecosystems.

Genomic analysis↗
PubMed2006

Analysis of bacterial community structure in the natural circulation system wastewater bioreactor by using a 16S rRNA gene clone library.

A variety of physical and chemical parameters are routinely monitored during operation of the Natural Circulation System, a wastewater purification bioreactor in which only natural materials and no synthetic chemicals are used. However, the microbial community structures existing in the Natural Circulation System have not been well characterized. Thus, bacterial community structure and composition in this system were studied using clone library analysis of 16S ribosomal RNA genes amplified using PCR with universal bacterial primer sets. The PCR products were then subcloned into the pGEM-T vector. Each unique restriction fragment length polymorphism pattern, created by using two pairs of restriction endonucleases, was designated as an operational taxonomic unit (OTU). The Natural Circulation System comprises five tanks, the second and third of which play a major role in the bioreactor. Clone library pro-files and principal component analysis revealed differences in the bacterial community structures of the second (anaerobic chamber) and the third (aerobic chamber) tanks. However, the beta-proteobacteria, Bacteroidetes/ Chlorobi and gamma-proteobacteria groups were dominant in both tanks. Bacterial composition was more complex in the second tank (107 OTUs) than in the third tank (68 OTUs). Of a total of 154 OTUs in the clone libraries, only 21 were common to the two tanks. The results obtained in this study should provide important information for future research into and management of the Natural Circulation System wastewater bioreactor.

Bacteria↗