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PubMed2006

Filter clogging in coarse pore filtration activated sludge process under high MLSS concentration.

Coarse pore filtration activated sludge process is a type of hybrid process in which the secondary settling tank of the conventional activated sludge process is replaced by non- woven and coarse pore filter modules. The filter has pores, which are irregular in shape, and much bigger than micro-filtration membrane pores in size. The objective of the study is to find out the effect of the microbial community structure on filter clogging in the coarse pore filtration activated sludge process under high MLSS concentration in aerobic and anoxic/aerobic (A/A) conditions. Filter clogging started from day 65 and 70 in the A/A and aerobic process, respectively, but it was more severe in the A/A process compared to that in the aerobic process. EPS contents of sludge did not change significantly during the operation in both processes, and did not have a crucial effect on the observed filter clogging. There was no strong evidence for direct effect of the type and number of metazoa on filter clogging. The main difference between aerobic sludge and A/A sludge during the filter clogging period was the relative abundance of filamentous bacteria. According to the obtained results, it can be concluded that a higher presence of filamentous bacteria could reduce the severity of filter clogging in a coarse pore filtration activated sludge process.

Bacteria, Aerobic↗

PubMed2025

A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities.

Accurate genome binning is essential for resolving microbial community structure and functional potential from metagenomic data. However, existing approaches-primarily reliant on tetranucleotide frequency (TNF) and abundance profiles-often perform sub-optimally in the face of complex community compositions, low-abundance taxa, and long-read sequencing datasets. To address these limitations, we present MBGCCA, a novel metagenomic binning framework that synergistically integrates graph neural networks (GNNs), contrastive learning, and information-theoretic regularization to enhance binning accuracy, robustness, and biological coherence. MBGCCA operates in two stages: (1) multimodal information integration, where TNF and abundance profiles are fused via a deep neural network trained using a multi-view contrastive loss, and (2) self-supervised graph representation learning, which leverages assembly graph topology to refine contig embeddings. The contrastive learning objective follows the InfoMax principle by maximizing mutual information across augmented views and modalities, encouraging the model to extract globally consistent and high-information representations. By aligning perturbed graph views while preserving topological structure, MBGCCA effectively captures both global genomic characteristics and local contig relationships. Comprehensive evaluations using both synthetic and real-world datasets-including wastewater and soil microbiomes-demonstrate that MBGCCA consistently outperforms state-of-the-art binning methods, particularly in challenging scenarios marked by sparse data and high community complexity. These results highlight the value of entropy-aware, topology-preserving learning for advancing metagenomic genome reconstruction.

canonical correlation analysis↗

PubMed2001

Population dynamics of anaerobic microbial consortia in thermophilic granular sludge in response to feed composition change.

A thermophilic UASB reactor was operated at 55 degrees C for greater than 470 days in order to investigate the effects of feed composition on the changes in microbial community structure where thermophilic granular sludge was used as the inoculum source. The feed compositions were changed with cultivation days; phase 1 (1-70 days), alcohol distillery wastewater; phase 2 (71-281 days), artificial acetate wastewater; phase 3 (282-474 days), artificial sucrose wastewater. During the first one month of each phase, the methanogenic activity and cell density of methanogens quantified by fluorescence in situ hybridization (FISH) drastically changed as a result of shift in feed composition. When artificial acetate wastewater was used as feed, retained granular sludge was partially disintegrated due to a decrease in the number of symbiotic bacterial community members: acetogens (acidogens) and hydrogenotrophic methanogens. In contrast, when the feed was shifted to sucrose (phase 3), granulation of biomass was promoted by a remarkable proliferation of the symbiotic community. The presence of hydrogen-utilizing methanogens and acetogens (acidogens) are shown to be effective for the enhancement of thermophilic granulation. The cell density of methanogens determined by FISH was strongly correlated with the methane-producing potential of the retained thermophilic granular sludge.

Acetates↗

PubMed2001

Study of microbial community of brewery-treating granular sludge by denaturing gradient gel electrophoresis of 16S rRNA gene.

The microbial community structure of granular sludge from an upflow anaerobic sludge blanket (UASB) reactor treating brewery effluent was studied by denaturing gradient gel electrophoresis (DGGE). Twelve major bands were observed in the DGGE fingerprint for the Bacteria domain and four bands for the Archaea domain. Of the bacterial bands observed, six were successfully purified and sequenced. Among them, three were related to the gram-positive low G + C group, one to the Delta subclass of the Proteobacteria, one to the Gamma subclass, and one to the Cytophaga group with no close related sequence. The 16S rRNA sequences of the four archaeal bands were closely associated with Methanosaeta concilii and Methanobacterium formicum.

Bacteria, Anaerobic↗

PubMed2002

Analysis of microbial community that performs enhanced biological phosphorus removal in activated sludge fed with acetate.

Enhanced biological phosphorus removal (EBPR) activated sludge was operated in a laboratory-scale sequencing batch reactor (SBR) fed with acetate as the sole carbon source. The microbial community of the sludge was analyzed using the polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) method for about 2 months of start-up period. As a result, the number of major bands decreased during the enrichment, indicating that the microbial community structure was getting simpler. Since the phosphate removal activity was maintained at a high level, the bacteria which still remained at the end can be considered as the important bacteria playing key roles in the present EBPR sludge, maybe polyphosphate accumulating organisms (PAOs). The dominant band in the last sample on the DGGE gel was excised and the DNA recovered from it was sequenced. The sequence was closely related to one of the putative PAOs group which Crocetti et al. (2000) and Hesselmann et al. (1999) have proposed. This PAOs group is closely related to the Rhodocyclus group (b-Proteobacteria). The fluorescence in situ hybridization (FISH) method with the probe specific for this PAOs group and the DAPI staining at a phosphate-probing concentration indirectly showed that these Rhodocyclus related bacteria really accumulated polyphosphate.

Acetates↗

PubMed2002

Quantifying the impact of wastewater micronutrient composition on in situ growth activity of Acinetobacter spp.

Batch growth studies with pure cultures of Acinetobacter johnsoniiT and Acinetobacter johnsonii strain 210 on various media formulations were used to examine the effects of micronutrient composition on the growth rate of microbial populations in wastewater treatment systems. On nutrient rich Luria-Bertani medium, both strains of A. johnsonii grew with a doubling time of approximately 30 min. On a defined, minimal medium with acetate as the sole carbon source, the doubling time of A. johnsoniiT was 9.62 h and the doubling time of strain 210a was 2.6 h. Using a synthetic wastewater as a growth medium, the type strain had a doubling time of 56 h and strain 210a had a doubling time of 9.62 h. The concentration and redox state of iron appeared to be the principle growth limiting factors with higher doubling times occurring in media containing ferric iron as compared to ferrous iron. Additionally, grab samples from batch growth experiments were analyzed with oligonucleotide hybridization probes targeting the mature 16S ribosomal RNA (rRNA) and precursor 16S rRNA of Acinetobacter spp. Results showed that the precursor 16S rRNA levels responded more rapidly and to a greater extent than total 16S rRNA levels to changes in the micronutrient composition of the growth media. Precursor 16S rRNA levels increased in both strains when overnight cultures were diluted with fresh media and when micronutrient supplements were added to growing cultures. Our results show that the micronutrient composition of the influent wastewater can have a significant impact on the microbial community structure in wastewater treatment systems.

Acinetobacter↗

PubMed2003

Molecular characterization of bacteria inhabiting a water distribution system simulator.

The objective of this study was to monitor the impact of chlorination and chloramination treatments on heterotrophic bacteria (HB) and ammonia-oxidizing bacteria (AOB) inhabiting a water distribution system simulator. HB densities decreased while AOB densities increased when chloramine was added. AOB densities decreased below detection limits after the disinfection treatment was switched back to chlorination. The presence of AOB was confirmed using a group-specific 16S rDNA-PCR method. 16S rDNA sequence analysis showed that most bacterial isolates from feed water, discharge water, and biofilm samples were alpha-Proteobacteria or beta-Proteobacteria. The latter bacterial groups were also numerically dominant among the sequences recovered from water and biofilm 16S rDNA clone libraries. The relative frequency of each culturable bacterial group was different for each sample examined. Denaturing gradient gel electrophoresis analysis of total community 16S rDNA genes showed notable differences between the microbial community structure of biofilm samples and feed water. The results of this study suggest that disinfection treatments could influence the type of bacterial community inhabiting water distribution systems.

Ammonia↗

PubMed2003

[Effect of ecological organic fertilizer on tomato bacterial wilt and soil microbial diversities].

The effects of ecological organic fertilizer (EOF) on tomato bacterial wilt and soil microbial community were studied through field trial and fatty acid methyl esters (FAMEs) analysis. The results showed that the incidence rate of tomato bacterial wilt was 100% in continuous cropped soil, and significantly reduced to 39% and 50% when applying EOF at 1.0 kg.m-2 and 0.5 kg.m-2, respectively. There was no significant difference between two fertilization treatments. The fatty acid fingerprints of soil microbial community were greatly changed, and the relative contents of cyc17:0 cited as biomarker for GN bacteria, c18:2 w6 as biomarker for fungi and c16:1 11c as biomarker for arbuscular mycorrhizal (AM) fungi all increased when applying EOF. The minimum distance of cluster analysis was 1.08 between control and treatments of applying ecological organic fertilizer, and 0.70 between different fertilization treatments. Applying EOF could adjust soil microbial community structure, benefit for soil beneficial microbes, and develop stability and disease suppression of soil ecological system, and hence, improve soil quality.

Ecology↗

PubMed2004

Denaturing gradient gel electrophoresis analysis of bacterial populations in 5-stage biological nutrient removal process with step feed system for wastewater treatment.

Changes in the bacterial populations of a 5-stage biological nutrient removal (BNR) process, with a step feed system for wastewater treatment, were monitored by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA fragments. DGGE analysis indicated seasonal community changes were observed, however, community profiles of the total bacteria of each reactor showed only minor differences in the samples obtained from the same season. The number of major bands was higher in the summer samples, and decreased during the winter period, indicating that the microbial community structure became simpler at low temperatures. Since the nitrogen and phosphate removal efficiencies were highly maintained throughout the winter operation period, the bacteria which still remaining in the winter sample can be considered important, playing a key role in the present 5-stage BNR sludge. The prominent DGGE bands were excised, and sequenced to gain insight into the identities of the predominant bacterial populations present, and most were found to not be closely related to previously characterized bacteria. These data suggest the importance of culture-independent methods for the quality control of wastewater treatment.

Bacteria↗

PubMed2005

Effect of heavy metals on soil microbial activity and diversity in a reclaimed mining wasteland of red soil area.

The microbial biomass, basal respiration and substrate utilization pattern in copper mining wasteland of red soil area, southern China, were investigated. The results indicated that soil microflora were obviously different compared with that of the non-mine soil. Microbial biomass and basal respiration were negatively affected by the elevated heavy metal levels. Two important microbial ecophysiological parameters, namely, the ratio of microbial biomass C(Cmic)/organic C(Corg) and metabolic quotient(qCO2) were closely correlated to heavy metal stress. There was a significant decrease in the Cmic/Corg ratio and an increase in the metabolic quotient with increasing metal concentration. Multivariate analysis of Biolog data for sole carbon source utilization pattern demonstrated that heavy metal pollution had a significant impact on microbial community structure and functional diversity. All the results showed that soil microbiological parameters had great potential to become the early sensitive, effective and liable indicators of the stresses or perturbations in soils of mining ecosystems.

Analysis of Variance↗

PubMed2004

Basic features of biofilms--why are they difficult therapeutic targets?

The purpose of this paper is to review the basic features of biofilms associated with human infections and summarize why such biofilms are resistant to antimicrobial agents. The formation of most biofilms involves adherence of bacteria to a conditioned surface, growth and division of the attached bacteria, synthesis of a polymeric slime matrix, formation of a structured microbial community, and incorporation of other micro-organisms into the microbial mass. The transition of bacteria from free-floating (planktonic) to biofilm environments involves extensive up-regulation of genes associated with adherence. Micro-organisms in established biofilms engage in complex integrated activities involving activation and deactivation of genes that promote the survival of bacteria within the biofilm community. Mechanisms of the increased resistance of biofilm bacteria to antimicrobial agents may involve: (1) neutralization or consumption of the drug, (2) failure of the drug to completely penetrate the biofilm, (3) inability of the drug to affect metabolically inactive bacteria, and (4) presence of drug-resistant bacteria within biofilms.

Biofilms↗

PubMed1994

Community structure of a microbial mat: the phylogenetic dimension.

Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

Bacteria↗

PubMed2003

Molecular characterization of community structures and sulfur metabolism within microbial streamers in Japanese hot springs.

Community structures of submerged microbial slime streamers (SMSS) in sulfide-containing hot springs at 72 to 80 degrees C at Nakabusa and Yumata, Japan, were investigated by molecular analysis based on the 16S rRNA gene. The SMSS were classified into two consortia; consortium I occurred at lower levels of sulfide in the hot springs (less than 0.1 mM), and consortium II dominated when the sulfide levels were higher (more than 0.1 mM). The dominant cell morphotypes in consortium I were filamentous and small rod-shaped cells. The filamentous cells hybridized with fluorescent oligonucleotide probes for the domain Bacteria, the domain Archaea, and the family Aquificaceae: Our analysis of the denaturing gradient gel electrophoresis (DGGE) bands by using reverse transcription (RT)-PCR amplification with two primer sets (Eub341-F with the GC clamp and Univ907R for the Bacteria and Eub341-F with the GC clamp and Arch915R) indicated that dominant bands were phylogenetically related to microbes in the genus Aquifex: On the other hand, consortium II was dominated by long, small, rod-shaped cells, which hybridized with the oligonucleotide probe S-*-Tdes-0830-a-A-20 developed in this study for the majority of as-yet-uncultivated microbes in the class Thermodesulfobacteria: The dominant DGGE band obtained by PCR and RT-PCR was affiliated with the genus Sulfurihydrogenibium: Moreover, our analysis of dissimilatory sulfite reductase (DSR) gene sequences retrieved from both consortia revealed a high frequency of DSR genes corresponding to the DSR of Thermodesulfobacteria-like microorganisms. Using both sulfide monitoring and (35)SO(4)(2-) tracer experiments, we observed microbial sulfide production and consumption by SMSS, suggesting that there is in situ sulfide production by as-yet-uncultivated Thermodesulfobacteria-like microbes and there is in situ sulfide consumption by Sulfurihydrogenibium-like microbes within the SMSS in the Nakabusa and Yumata hot springs.

Ecosystem↗

PubMedDate not supplied

[Structure and function of microbial communities in soil from the southern Taiga].

General regularities in the structure of the microbial communities of southern taiga soil ecosystems and taxonomic differences between the microbial communities of soils with different hydrothermal characteristics are discussed with reference to the main types of soils of the Central State Forest Biosphere Reserve.

Bacteria↗

PubMed2006

Structural and functional responses of a sewage microbial community to dilution-induced reductions in diversity.

The relationship between functional redundancy and microbial community structure-diversity was examined using laboratory incubations to ensure constant environmental conditions. Serial dilutions of a sewage microbial community were prepared, used to inoculate sterile sewage, and maintained in batch culture. Probability suggests that dilution of the initial community should remove rare organism types, creating mixtures of cells differing in diversity. Regrowth of the diluted mixtures generated communities similar in abundance but differing in community structure and relative diversity (as determined using two DNA fingerprinting techniques and dilution-to-extinction analysis of community-level physiological profiles). The in situ function of each regrown community was examined by monitoring the short-term uptake of five different (14)C-labeled compounds (glucose, acetate, citrate, palmitic acid, and an amino acid mixture). No significant differences were detected between treatments in either the rate of uptake of a substrate or the efficiency with which each community assimilated each compound. The fact that the activity of the original community was the same as that of a community regrown from an inoculum containing fewer that 100 cells (10(-6) dilution) indicates that functional redundancy was quite high in this system. For each organism type eliminated during the dilution process, at least one of the remaining types was able to provide the same function at the same level as the lost one. Further research is necessary to determine what impact this functional redundancy may have on overall ecosystem function and stability.

Biodiversity↗

PubMed2000

Molecular techniques for determining microbial diversity and community structure in natural environments.

The ability to quantify the number and kinds of microorganisms within a community is fundamental to the understanding of the structure and function of an ecosystem. The simple morphology of most microbes provides few clues for their identification and physiological traits are often ambiguous. In addition, many organisms resist cultivation, which is essential to their characterization. Recombinant DNA techniques have provided a means whereby many of the obstacles associated with cultivation and description can be overcome and subsequently has allowed many new insights into the complexity of natural microbial communities. Molecular approaches based on 16S ribosomal RNA (rRNA) sequence analysis allow direct investigation of the community structure, diversity, and phylogeny of microorganisms in almost any environment, while quantification of the individual types of microorganisms or entire microbial communities may be addressed by nucleic acid hybridization techniques. Furthermore, the use of fluorescently labeled population-specific rRNA probes allows microscopic examination of individual cells in complex microbial assemblages as well as their interactions in situ. In this review, we discuss strategies for characterizing microbial communities without the need for cultivation.

DNA, Ribosomal↗

PubMed2006

Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats.

Diazotrophic community structure in microbial mats from Guerrero Negro (GN), Baja California, Mexico, was studied using polymerase chain reaction amplification of the nifH gene and a newly developed nifH oligonucleotide microarray. Ninety-six oligonucleotide probes designed for nifH sequences from cultivated isolates and the environment were printed on glass microarrays. Phylogenetic analysis showed that the probes represented all of the main nifH clusters. Specificity was tested by (i) evaluation of cross hybridization using individual targets, and (ii) comparison of the observed hybridization signals and those predicted from the sequences cloned from microbial mats. Signal intensity had a positive relationship with target concentration and the percentage identity between probe and target. Under moderate stringency and high target concentration, specificity of the probes varied from 77% to 100% with the individual targets tested. At the end of a 7-month long nutrient manipulation experiment in GN microbial mats, no expression of nitrogen fixation under nitrogen loading was detected, although a diverse community of diazotrophs was detected. The diversity in diazotrophic population present was higher than in the population expressing the nifH gene, and there were taxa specific differences in response to nutrients. The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment.

Bacteria↗

PubMed2000

Structure of a Natural Microbial Community in a Nitroaromatic Contaminated Groundwater Is Altered during Biodegradation of Extrinsic, but Not Intrinsic Substrates.

A BSTRACTThis study demonstrates microbial community changes over time in a nitroaromatic-contaminated groundwater upon amendment with hydrocarbons previously unknown to the microbial community (extrinsic) and hydrocarbons previously known to the microbial community (intrinsic). Sealed flasks, shaken and incubated at 25 degrees C, containing contaminated groundwater and salts were amended twice with extrinsic hydrocarbons including phenol, benzoic acid, and naphthalene, and intrinsic hydrocarbons including 2,4-dinitrotoluene (2,4-DNT) and para-nitrotoluene ( p-NT). Microbial growth, biodegradation, and community structure changes measured by random amplified polymorphic DNA (RAPD) and quantitative PCR (qPCR) targeting catechol-2,3-dioxygenase (C23O) genes were monitored over time. All amended substrates were biodegraded after both substrate amendments except for 2,4-DNT, which was only partially degraded after the second amendment. Unique microbial communities were developed in flasks amended with phenol, benzoic acid, and naphthalene. However, in the flasks amended with intrinsic hydrocarbons the microbial community remained similar to the unamended control flasks. The relative amount of C23O genes detected by qPCR correlated with the biodegradation of phenol and naphthalene but not with 2,4-DNT. The results showed that a selection for microorganisms capable of catabolizing extrinsic hydrocarbons naturally and initially present in the nitroaromatic-contaminated groundwater occurred. However, growth-linked biodegradation of added intrinsic hydrocarbons was not selective.

Journal Article↗