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PubMed1989

Comparison of effective toxicant biotransformation by autochthonous microorganisms and commercially available cultures in the in situ reclamation of abandoned industrial sites.

Biotransformation and biodegradation of polycyclic aromatic hydrocarbons by the subsurface autochthonous microflora collected from an abandoned petroleum refinery site was investigated. In addition, the inoculation of a commercially available blend of bacterial cultures, with known ability to degrade polycyclic aromatics, was evaluated. This supplemental addition of select microorganisms has been referred to by commercial interests as "bioaugmentation". Their biodegradative potential was evaluated using laboratory mesocosms (simulations) containing a predetermined optimal waste loading rate based on % oil and grease, mixed with predetermined optimal loading rates of clay and river silt materials. The waste consisted primarily of aliphatic and aromatic hydrocarbons found in buried sludges and abandoned lagoons. All mesocosms received nutrient amendment without additional energy sources. Experimental mesocosms were inoculated with adapted indigenous microflora and/or commercial strains. Microbial ATP, microbial diversity, and related enzyme assays were used to establish the detoxification efficiency of the experimental microflora. Quantitative toxicant concentrations and transformations were documented by GC/MS data. Information will be presented mainly on the kinetics of toxicant biotransformation processes to identify "bioaugmentation" contribution and relevancy in the recovery of abandoned polluted sites.

Bacteria↗

PubMed1983

Bacterial plasmids--an overview.

Resistance to antimicrobial substances and various factors contributing to pathogenicity are only some of the bacterial traits that can be determined by plasmid genes. Not all plasmids are involved with resistance, nor is all resistance to antimicrobials plasmid-mediated. Nevertheless, the impact of R-plasmids on the choice of antimicrobial therapy is substantial, especially in hospital and when dealing with certain community pathogens, such as Haemophilus influenzae. The discovery of transposition elements has helped us to understand the rapidity with which certain resistance determinants develop and become disseminated among diverse microbial species. Similarly, not all determinants of microbial pathogenicity are plasmid encoded and the genes for many toxins, cellular attachment pili, iron sequestration systems, etc. are found on the bacterial chromosomes. In Yersinia, pathogenicity is even more complex in that plasmid determinants play an essential role, but only in concert with chromosomal genes. The particularly significant features of such pathogenicity-determined plasmid-mediated genes is not that they are found on extrachromosomal elements, but that they may possess greater genetic mobility. Another consequence of the presence of virulence genes on bacterial plasmids is that it makes them easier to study by the newer techniques of microbial genetics and molecular biology.

Anti-Bacterial Agents↗

PubMed1999

Structural features of autoreactive TCR that determine the degree of degeneracy in peptide recognition.

Structural aspects of human TCRs that allow the activation of autoreactive T cells by diverse microbial peptides were examined using two human myelin basic protein (MBP)-specific T cell clones. The TCR sequences of these clones differed only in the N region of TCR-alpha and -beta since the clones had the same Valpha-Jalpha and Vbeta-Jbeta rearrangements. The two clones had a similar fine specificity for the MBP peptide, except for the P5 position of the peptide (lysine). In the crystal structure of the HLA-DR2/MBP peptide complex, P5 lysine is a prominent, solvent-exposed residue in the center of the DR2/MBP peptide surface. Five microbial peptides with conservative or nonconservative changes at the P5 position (lysine to arginine, serine, or proline) activated one of these clones. In contrast, the other clone was activated only by three of these peptides which had a conservative lysine to arginine change at P5. The degree of specificity/degeneracy in recognition of the P5 side chain was the key difference between these TCRs since the Escherichia coli/Haemophilus influenzae peptide stimulated both clones when the P5 position was substituted from serine to arginine. These results demonstrate that the complementarity-determining region 3 loops contribute to the degree of degeneracy in peptide recognition by human MBP-specific TCRs.

Amino Acid Sequence↗

PubMed2026

The Rhizosphere Microbiome: A Key Mediator of Crop Responses to Fertilization Strategies.

The rhizosphere microbiome, the plant's "second genome" is pivotal for crop nutrient acquisition, health, and stress responses. While fertilization ensures high agricultural yields, a key challenge is reshaping this microbiome to boost crop performance. This review synthesizes how mineral, organic, and bio-organic/microbial inoculant fertilizers affect rhizosphere microbial structure, diversity, and function. Long-term excessive mineral fertilizers (especially nitrogen) reduce microbial diversity, diminish beneficial groups (e.g., diazotrophs, PGPR), and disrupt microbial networks via soil acidification and altered root exudates, causing continuous cropping obstacles. In contrast, organic fertilizers improve soil microenvironments, maintaining high microbial diversity, enriching beneficial taxa (e.g., Proteobacteria, Actinobacteria), and enhancing community complexity. Bio-organic fertilizers/microbial inoculants "engineer" the microbiome by introducing exogenous beneficial microbes (e.g., Bacillus, Pseudomonas, AMF), directly promoting growth, suppressing diseases, and "reconditioning" indigenous beneficial communities. We also clarify how fertilization regulates plant-microbe dialog via root exudates and rhizosphere chemistry (e.g., pH, ion balance), discuss current challenges (causality, lab-to-field translation, genotype-microbiome-fertilization interactions), and outline future directions. Integrating rhizosphere microbiome management into fertilization is crucial for reducing chemical fertilizer reliance and advancing agricultural green transformation.

fertilization strategies microbial community assem↗

PubMed2005

The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil.

Enhanced rhizosphere degradation uses plants to stimulate the rhizosphere microbial community to degrade organic contaminants. We measured changes in microbial communities caused by the addition of two species of plants in a soil contaminated with 31,000 ppm of total petroleum hydrocarbons. Perennial ryegrass and/or alfalfa increased the number of rhizosphere bacteria in the hydrocarbon-contaminated soil. These plants also increased the number of bacteria capable of petroleum degradation as estimated by the most probable number (MPN) method. Eco-Biolog plates did not detect changes in metabolic diversity between bulk and rhizosphere samples but denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified partial 16S rDNA sequences indicated a shift in the bacterial community in the rhizosphere samples. Dice coefficient matrices derived from DGGE profiles showed similarities between the rhizospheres of alfalfa and perennial ryegrass/alfalfa mixture in the contaminated soil at week seven. Perennial ryegrass and perennial ryegrass/alfalfa mixture caused the greatest change in the rhizosphere bacterial community as determined by DGGE analysis. We concluded that plants altered the microbial population; these changes were plant-specific and could contribute to degradation of petroleum hydrocarbons in contaminated soil.

Bacteria↗

PubMed2006

[Soil microbial ecological process and microbial functional gene diversity].

Soil microbes in terrestrial ecosystem carry out a series of important ecological functions, such as geo-chemical cycling of elements, degradation of pollutants, and buffering to the acute changes of environment, etc. Soil microbial ecological function has a close relation with soil function, and the changes in the structure and composition of soil microbial populations can directly affect the realization of soil function. Through their produced enzymes, soil microbes take part in a series of metabolic activities, and the functional genes of coded enzymes are the functional markers of microbes. In recent ten years, molecular ecology focusing on the functional gene diversity has been developed rapidly, which gives us a new cut-in point to understand soil microbial ecological function from the point of functional gene. This paper reviewed the research advances in the functional gene diversity correlated to soil microbial ecological function, with the perspectives in this field discussed.

Bacteria↗

PubMed2006

Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats.

Hamelin Pool in Western Australia is one of the two major sites in the world with active marine stromatolite formation. Surrounded by living smooth and pustular mats, these ancient laminated structures are associated with cyanobacterial communities. Recent studies have identified a wide diversity of bacteria and archaea in this habitat. By understanding and evaluating the microbial diversity of this environment we can obtain insights into the formation of early life on Earth, as stromatolites have been dated in the geological record as far back as 3.5 billion years. Automated ribosomal intergenic spacer analysis (ARISA) patterns were shown to be a useful method to genetically discriminate halophilic archaea within this environment. Patterns of known halophilic archaea are consistent, by replicate analysis, and the halophilic strains isolated from stromatolites have novel intergenic spacer profiles. ARISA-PCR, performed directly on extracted DNA from different sample sites, provided significant insights into the extent of previous unknown diversity of halophilic archaea within this environment. Cloning and sequence analysis of the spacer regions obtained from stromatolites confirmed the novel and broad diversity of halophilic archaea in this environment.

Archaea↗

PubMed2001

Characterisation of the microbial 16S rDNA diversity of an aerobic phosphorus-removal ecosystem and monitoring of its transition to nitrate respiration.

The microbial community of a conventional anaerobic-aerobic sequencing batch reactor was investigated by cloning and sequencing bacterial 16S rDNA. The 92 16S rDNA sequences analysed ranged across 50 different operational taxonomic units (OTU). The majority of these sequences were not closely related to known species. They belonged to 12 different groups, but essentially to the Cytophagales and the Proteobacteria beta, which represented 38% and 17% of the retrieved sequences respectively. No OTU numerically outnumbered the others. However, similarities were observed with previous reports on molecular characterisation of phosphorus-accumulating ecosystems, suggesting an enrichment in microorganisms belonging to the Rhodocyclus group. Thereafter, the ability of this anaerobic-aerobic microbial community to accumulate phosphorus with nitrate as its energy source was investigated. The reactor was shifted from anaerobic-aerobic running conditions to anaerobic-anoxic conditions by injection of nitrate; and its microbial community was monitored by PCR-single strand conformation polymorphism (SSCP). The reactor maintained a good phosphorus accumulation and similar SSCP microbial community patterns for a period of 17 days, suggesting that the same microbial community was able to respire both oxygen and nitrate. However, this situation was unstable, since a breakdown in phosphorus accumulation occurred thereafter.

Bacteria, Aerobic↗

PubMed2026

Landscape of retron diversity across the SPIRE microbial metagenome resource reveals candidate novel type XI-like lineages.

Retrons are bacterial genetic elements encoding a specialized reverse transcriptase (RT) that synthesizes multicopy single-stranded DNA and are increasingly recognized as components of bacterial anti-phage defense systems. However, their diversity and ecological distribution across large-scale genomic resources remain poorly characterized. Here, we surveyed retron RTs across the SPIRE representative metagenome collection, a non-redundant, species-level data set spanning diverse microbial habitats. Using a curated panel of type-specific hidden Markov models, we identified retrons representing all canonical types together with additional divergent lineages. Retron distribution showed strong taxonomic and ecological structuring, with some groups restricted to specific bacterial phyla, whereas others were broadly distributed across environmental categories. Systematic novelty assessment identified two candidate type XI-like lineages, TXI_C2like and TXI_noncan_h, characterized by protease-independent architectures and distinct accessory modules associated with WYL- and DnaB_C-containing proteins, respectively. De novo covariance-based analyses further identified candidate msr/msd-like non-coding RNA structures in both lineages, supporting conservation of the canonical RT-ncRNA organizational framework despite extensive sequence divergence. Together, these findings expand the known diversity of retron systems and identify type XI-like retrons as a dynamic and previously underexplored evolutionary group.IMPORTANCERetrons are bacterial genetic elements that are increasingly exploited as programmable tools for genome editing, molecular recording, and biosensing in addition to their natural role in anti-phage defense. Despite this growing biotechnological interest, the true diversity of retrons across the bacterial world has remained largely unmapped. By mining a resource of over 100,000 processed microbial metagenomes, we uncovered thousands of retron sequences spanning known types as well as previously unrecognized lineages and found that their distribution is strongly shaped by both bacterial taxonomy and ecological niche. Among these, we identified two candidate new lineages related to type XI retrons that lack the protease domain typical of this group but instead carry distinct accessory proteins, expanding the known architectural diversity of these systems. These findings broaden the catalog of retron diversity available for functional characterization and biotechnological engineering and provide a framework for prioritizing candidate lineages for future experimental validation.

effectors↗

PubMed2003

Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine.

Distribution and phylogenetic diversity of microbial communities in hot, deep underground environments in the Hishikari epithermal gold mine, southern part of Kyushu, Japan, were evaluated using molecular phylogenetic analyses. Samples included drilled cores such as andesitic volcanic rock (0.95-1.78 Ma) and the oceanic sedimentary basement rock of Shimanto-Supergroup (100 Ma), as well as geothermal hot aquifer waters directly collected from two different sites: AW-site (71.5 degrees C, pH 6.19) and XW-site (85.0 degrees C, pH 6.80) at a depth of 350 mbls (meters below land surface). Based on PCR-amplified 16S rRNA gene clone analysis, the microbial communities in the drilled cores and the hot aquifer water from the XW-site consisted largely of the 16S rRNA gene sequences, closely related to the sequences often found in marine environments, while the aquifer water from the AW-site contained 16S rRNA gene sequences representing members of Aquificales, thermophilic methanotrophs within the gamma-subdivision of the Proteobacteria and uncultivated strains within the beta-subdivision of Proteobacteria. The cultivable microbial community detected by enrichment cultivation analysis largely matched that detected by the culture-independent molecular analysis.

Bacteria↗

PubMed2001

Upstream-independent ribosomal RNA amplification analysis (URA): a new approach to characterizing the diversity of natural microbial communities.

Here, we propose an advanced method for recently developed fingerprinting strategies to analyse microbial populations by direct detection of 16S rRNA sequences occurring in natural habitats. The differential display (DD) technique, which is widely used to analyse for eukaryotic gene expression, was optimized to assess bacterial rRNA diversity in environmental samples. Double-stranded cDNAs of rRNAs were synthesized without a forward primer digested with endonuclease and ligated with a double-stranded adapter. The fragments obtained were then amplified using an adapter-specific extended primer and a 16S rDNA universal reverse primer pair displayed by electrophoresis on a polyacrylamide gel. We validated this approach by characterization of a microbial community colonizing a geothermal (48 degrees C) vent system located close to the eruption zone of the south-east crater of the Mount Etna volcano, Sicily. Analysis of the patterns of abundant 16S rRNA revealed a considerable diversity of metabolically active bacteria phylogenetically clustering within the Crenarchaeota, Cyanobacteria, Firmicutes, Planctomycetales and Thermus divisions. Two sequence phylotypes were affiliated with uncultivated representatives of the recently described candidate division OP10 from a Yellowstone hot spring.

Bacteria↗

PubMed2003

[Introduction and progress of molecular microbial ecology].

Molecular microbial ecology is an interdisciplinary field of molecular biological techniques and microbial ecology, which deals with microbial population, diversity, function, and relationships between microorganisms and biotic and abotic environments in microbial ecosystem. All the progress in molecular microbial ecology, especially in microbial diversity, phylogeny and communities of some microoganisms, indicate the renovation in traditional microbial ecology by the introduction of molecular techniques and strategies. This article reviewed the ideation, development, key domains, main methods and the future hot fields in molecular microbial ecology.

Ecology↗

PubMed2004

The effect of an acute copper exposure on the diversity of a microbial community in North Sea sediments as revealed by DGGE analysis--the importance of the protocol.

The aim of the work was to investigate whether the marine bacterial communities in a North Sea sediment with background metal concentrations were affected by an acute copper exposure and if a commonly used molecular technique, denaturing gradient gel electrophoresis (DGGE), was robust enough to investigate the community changes. Sediments (n = 6) were placed in small microcosms and spiked with copper (50 microg/l). Controls were left untreated. After 12 days, bioavailable copper increased up to a factor 2.5 in the sediments. Plate counts and chitinase activity measurements have suggested limited effects of copper on growth rate and cell metabolism. To test the robustness of DGGE three different protocols were used. The three protocols lead to different conclusions. As a whole, it seems that copper had no immediate effect on the genetic diversity of the community. However, copper-sensitive bacterial populations were detected by one of the DGGE protocols. It is concluded that the DGGE approach is a valuable tool to investigate the effect of pollutants on microbial communities only if various DGGE protocols are compared.

Bacteria↗

PubMed2004

Are viruses driving microbial diversification and diversity?

Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.

Bacteria↗

PubMed2002

Strain diversity within a microbial collection.

Random subsets of a modest-sized microbial collection have been examined for culture redundancy, initially by morphology, both to the naked eye and microscopically, of cultures grown on a variety of agar-based solid media. Subsequent analysis, by simple TLC, of the extractable metabolites produced by morphologically similar cultures grown in submerged shaken fermentation was carried out. Apparent duplicate cultures were further examined on Biolog SF-P MicroPlates for differentiation. The results were subjected to a statistical analysis and the contribution of each stage in the process to resolving culture uniqueness was noted. A statistical extrapolation of the results, from the subsets of each culture type, to the total for that type within the entire collection, with 95% confidence limits, is presented. Morphological comparison, on four different agar media, gives a significant underestimation of the metabolic diversity of the collection. The weighted mean from the three types of cultures indicate that the expected content of the collection is approximately 93% unique strains.

Actinobacteria↗

PubMedDate not supplied

Siderophores: diverse roles in microbial and human physiology.

Siderophores, defined as high affinity iron(III) ion transport agents, and their cognate membrane-bound receptor complexes, occur in the enteric bacteria Escherichia coli and Salmonella typhimurium. The total system is tightly regulated by iron repression. The transport properties of the specific siderophores enterobactin and ferrichrome (which is not made by these particular enteric bacteria) have been examined in detail. In E. coli the outer membrane receptor for ferrichrome is programmed by the tonA gene; the receptor also serves as the binding site for T1, T5, phi80, albomycin and colicin M. Similarly, in S. typhimurium phage ES18, ferrichrome and albomycin compete for the genetic equivalent of the tonA locus. The ability of ascorbic acid to protect against atherosclerosis as well as rhinovirus infection in humans may be related to the role of the vitamin in iron metabolism. Deferrisiderophores are clinically useful in the treatment of acute and chronic iron poisoning but, on the other hand, they could constitute a natural hazard by transporting actinides, such as 239Pu, through the food chain.

Arteriosclerosis↗

PubMed1995

Diversity of anaerobic microbial processes in chlorobenzoate degradation: nitrate, iron, sulfate and carbonate as electron acceptors.

The utilization of monochlorobenzoate isomers (2-, 3- and 4-chlorobenzoate) by anaerobic microbial consortia in River Nile sediments was systematically evaluated under denitrifying, Fe-reducing, sulfidogenic and methanogenic conditions. Loss of all three chlorobenzoates was noted in denitrifying cultures; furthermore, the initial utilization of chlorobenzoates was fastest under denitrifying conditions. Loss of 3-chlorobenzoate was seen under all four reducing conditions and the degradation of chlorobenzoates was coupled stoichiometrically to NO3- loss, Fe2+ production, SO4(2-) loss or CH4 production, indicating that the chlorobenzoates were oxidized to CO2. To our knowledge, this is the first observation of halogenated aromatic degradation coupled to Fe reduction.

Bacteria, Anaerobic↗

PubMed2006

Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote.

The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents.

Archaea↗