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Alfred Puhler - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach
Microbial Ecology, 2000Co-Authors: Stefan Weidner, Walter Arnold, Erko Stackebrandt, Alfred PuhlerAbstract:: The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences. Most sequences originated from members of the gamma-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the alpha-subclass was determined for 24.2% of the sequences. They were related to the genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several alpha-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related to beta-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms.
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phylogenetic analysis of bacterial communities associated with leaves of the seagrass halophila stipulacea by a culture independent small subunit rrna gene approach
Microbial Ecology, 2000Co-Authors: Stefan Weidner, Walter Arnold, Erko Stackebrandt, Alfred PuhlerAbstract:The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences. Most sequences originated from members of the gamma-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the alpha-subclass was determined for 24.2% of the sequences. They were related to the genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several alpha-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related to beta-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms.
Masahiro Yamamoto - One of the best experts on this subject based on the ideXlab platform.
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Sulfur metabolisms in epsilon- and Gamma-Proteobacteria in deep-sea hydrothermal fields.
Frontiers in Microbiology, 2011Co-Authors: Masahiro YamamotoAbstract:In deep-sea hydrothermal systems, super hot and reduced vent fluids from the subseafloor blend with cold and oxidized seawater. Very unique and dense ecosystems are formed within these environments. Many molecular ecological studies showed that chemoautotrophic epsilon- and Gamma-Proteobacteria are predominant primary producers in both free-living and symbiotic microbial communities in global deep-sea hydrothermal fields. Inorganic sulfur compounds are important substrates for the energy conservative metabolic pathways in these microorganisms. Recent genomic and metagenomic analyses and biochemical studies have contributed to the understanding of potential sulfur metabolic pathways for these chemoautotrophs. Epsilon-Proteobacteria use sulfur compounds for both electron-donors and -acceptors. On the other hand, Gamma-Proteobacteria utilize two different sulfur-oxidizing pathways. It is hypothesized that differences between the metabolic pathways used by these two predominant proteobacterial phyla are associated with different ecophysiological strategies; extending the energetically feasible habitats with versatile energy metabolisms in the epsilon-Proteobacteria and optimizing energy production rate and yield for relatively narrow habitable zones in the Gamma-Proteobacteria.
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Sulfur metabolisms in epsilon- and Gamma-Proteobacteria in deep-sea hydrothermal fields.
Frontiers in Microbiology, 2011Co-Authors: Masahiro Yamamoto, Ken TakaiAbstract:In deep-sea hydrothermal systems, super hot and reduced vent fluids from the subseafloor blend with cold and oxidized seawater. Very unique and dense ecosystems are formed within these environments. Many molecular ecological studies showed that chemoautotrophic epsilon- and Gamma-Proteobacteria are predominant primary producers in both free-living and symbiotic microbial communities in global deep-sea hydrothermal fields. Inorganic sulfur compounds are important substrates for the energy conservative metabolic pathways in these microorganisms. Recent genomic and metagenomic analyses and biochemical studies have contributed to the understanding of potential sulfur metabolic pathways for these chemoautotrophs. Epsilon-Proteobacteria use sulfur compounds for both electron-donors and -acceptors. On the other hand, Gamma-Proteobacteria utilize two different sulfur-oxidizing pathways. It is hypothesized that differences between the metabolic pathways used by these two predominant proteobacterial phyla are associated with different ecophysiological strategies; extending the energetically feasible habitats with versatile energy metabolisms in the epsilon-Proteobacteria and optimizing energy production rate and yield for relatively narrow habitable zones in the Gamma-Proteobacteria.
Rudolf I. Amann - One of the best experts on this subject based on the ideXlab platform.
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Characterization of bacterial communities from activated sludge: Culture-dependent numerical identification versus in situ identification using group- and genus-specific rRNA-targeted oligonucleotide probes
Microbial Ecology, 1996Co-Authors: Peter Kampfer, Judith Böhringer, M. Wagner, Claudia Beimfohr, Renate Erhart, Rudolf I. AmannAbstract:The structures of bacterial communities were studied in activated sludge samples obtained from the aerobic and anaerobic zones of a wastewater treatment plant showing enhanced phosphorous removal. Samples were analyzed by in situ hybridization with oligonucleotide probes complementary to selected regions of the 16S and 23S ribosomal RNA (rRNA) characteristic for defined phylogenetic entities (genera and larger groups). The microbial community structures revealed by molecular techniques were compared with the compositions of culturable bacterial communities, obtained from the characterization of 255 isolates from tryptone-soy (TS) agar and R2A agar. These isolates were characterized by 89 physiological tests and their cellular fatty acid patterns, and identified. Culture-dependent techniques indicated the following distribution: different Aeromonas spp. (2.7–8.3% on R2A agar; 45.0–63.7% on TS agar), Acinetobacter spp. (5.4–9.0% on R2A agar; 5.0–9.1% on TS agar), Pseudomonas spp. (up to 10% on R2A agar) and Shewanella putrefaciens (up to 3.0% on R2A agar), all members of the gamma subclass of Proteobacteria, were isolated most frequently. The relatively rare isolates of the beta subclass were identified as Acidovorax spp., Alcaligenes spp., and Comamonas spp., The Gram-positive bacteria (high DNA G+C) were assigned mainly to Arthrobacter spp., Microbacterium spp., and Mycobacterium phlei . In order to assess the in situ abundance of the most frequently isolated genus, Aeromonas , two rRNA-targeted oligonucleotide probes were developed. The two gamma proteobacterial genera Aeromonas and Acinetobacter constituted less than 5% of all bacteria. In situ, Proteobacteria belonging to the beta subclass and high G+C Gram-positive bacteria were dominant. From filamentous bacteria, Sphaerotilus spp. and Leptothrix spp. could be detected occasionally. In addition, one sample contained a high proportion of the morphologically distinct filaments of Microthrix parvicella . As for the genus Acinetobacter , the relative abundance of the most frequently Gamma-Proteobacterial genus Aeromonas was overestimated by the intrinsic selectivity of cultivation. Cultivation on nutrient-rich medium (TS-agar) especially supported an enhanced isolation of bacteria belonging to these two genera.
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characterization of bacterial communities from activated sludge culture dependent numerical identification versus in situ identification using group and genus specific rrna targeted oligonucleotide probes
Microbial Ecology, 1996Co-Authors: Judith Böhringer, Peter Kampfer, Claudia Beimfohr, Renate Erhart, Michael Wagner, Rudolf I. AmannAbstract:The structures of bacterial communities were studied in activated sludge samples obtained from the aerobic and anaerobic zones of a wastewater treatment plant showing enhanced phosphorous removal. Samples were analyzed by in situ hybridization with oligonucleotide probes complementary to selected regions of the 16S and 23S ribosomal RNA (rRNA) characteristic for defined phylogenetic entities (genera and larger groups). The microbial community structures revealed by molecular techniques were compared with the compositions of culturable bacterial communities, obtained from the characterization of 255 isolates from tryptone-soy (TS) agar and R2A agar. These isolates were characterized by 89 physiological tests and their cellular fatty acid patterns, and identified. Culture-dependent techniques indicated the following distribution: different Aeromonas spp. (2.7–8.3% on R2A agar; 45.0–63.7% on TS agar), Acinetobacter spp. (5.4–9.0% on R2A agar; 5.0–9.1% on TS agar), Pseudomonas spp. (up to 10% on R2A agar) and Shewanella putrefaciens (up to 3.0% on R2A agar), all members of the gamma subclass of Proteobacteria, were isolated most frequently. The relatively rare isolates of the beta subclass were identified as Acidovorax spp., Alcaligenes spp., and Comamonas spp., The Gram-positive bacteria (high DNA G+C) were assigned mainly to Arthrobacter spp., Microbacterium spp., and Mycobacterium phlei. In order to assess the in situ abundance of the most frequently isolated genus, Aeromonas, two rRNA-targeted oligonucleotide probes were developed. The two gamma proteobacterial genera Aeromonas and Acinetobacter constituted less than 5% of all bacteria. In situ, Proteobacteria belonging to the beta subclass and high G+C Gram-positive bacteria were dominant. From filamentous bacteria, Sphaerotilus spp. and Leptothrix spp. could be detected occasionally. In addition, one sample contained a high proportion of the morphologically distinct filaments of Microthrix parvicella.
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probing activated sludge with oligonucleotides specific for proteobacteria inadequacy of culture dependent methods for describing microbial community structure
Applied and Environmental Microbiology, 1993Co-Authors: Michael Wagner, Rudolf I. Amann, Hilde Lemmer, Karl-heinz SchleiferAbstract:Bacterial community structures in activated sludge samples from aeration tanks of a two-stage system with a high-load first stage and a low-load second stage were analyzed with oligonucleotide probes. The probes were complementary to conserved regions of the rRNA of the alpha, beta, and gamma subclasses of proteobacteria and of all bacteria. Group-specific cell counts were determined by in situ hybridization with fluorescent probe derivatives. Contributions of the proteobacterial subclasses to total bacterial rRNA were quantified by dot blot hybridization with digoxigenin-labeled oligonucleotides. The activated sludge samples were dominated by proteobacteria from the alpha, beta, or gamma subclass. These proteobacteria account for about 80% of all active bacteria found in the activated sludge. For both samples the community structures determined with molecular techniques were compared with the composition of the heterotrophic saprophyte flora isolated on nutrient-rich medium. Probes were used to rapidly classify the isolates and to directly monitor population shifts in nutrient-amended, activated sludge samples. The rich medium favored growth of gamma-subclass proteobacteria (e.g., enterobacteria) and selected against beta-subclass proteobacteria. The culture-dependent community structure analysis of activated sludge produced partial and heavily biased results. A more realistic view will be obtained by using in situ techniques. Images
Mikhail S Gelfand - One of the best experts on this subject based on the ideXlab platform.
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Taxon-specific regulation of SOS-response in Gamma-Proteobacteria
Molecular Biology, 2007Co-Authors: L. V. Sycheva, E. A. Permina, Mikhail S GelfandAbstract:: SOS-response system is a cascade of reactions induced by DNA damage in a cell. Genes participate in these reactions are regulated by the LexA protein binding to specific sequence in their upstream regions. The criterion for selection of genes putatively responsible for the SOS-response is the presence of such sequence. Genes with taxon-specific regulation in Enterobacteriales, Pasteurellales, Vibrionales, Pseudomonadales and Alteromonadales were analyzed using comparative genomic approaches. Some genes have conserved sites in regulatory region and suitable function, although their function in SOS-response has not been studied in experiment. The list of such genes includes mfd, which encodes a product repairing the mother chain in case of DNA damage-caused transcription stop; VC0082, which encodes a recombinase, and VP2449, responsible for xenobiotics resistance. Overall, this study characterized the content and evolution of the LexA regulon in Gamma-Proteobacteria are described here.
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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of Gamma-Proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).
BMC genomics, 2007Co-Authors: Dmitry A. Ravcheev, Andrey A Mironov, Anna Gerasimova, Mikhail S GelfandAbstract:Gamma-Proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription factors, Fnr, ArcA, NarL and NarP. However, in other Gamma-Proteobacteria the composition of global respiration regulators may be different. In this study we applied a comparative genomic approach to the analysis of three global regulatory systems, Fnr, ArcA and NarP. These systems were studied in available genomes containing these three regulators, but lacking NarL. So, we considered several representatives of Pasteurellaceae, Vibrionaceae and Yersinia spp. As a result, we identified new regulon members, functioning in respiration, central metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway, citrate cicle, metabolism of pyruvate and lactate), metabolism of carbohydrates and fatty acids, transcriptional regulation and transport, in particular: the ATP synthase operon atpIBEFHAGCD, Na+-exporting NADH dehydrogenase operon nqrABCDEF, the D-amino acids dehydrogenase operon dadAX. Using an extension of the comparative technique, we demonstrated taxon-specific changes in regulatory interactions and predicted taxon-specific regulatory cascades. A comparative genomic technique was applied to the analysis of global regulation of respiration in ten Gamma-Proteobacterial genomes. Three structurally different but functionally related regulatory systems were described. A correlation between the regulon size and the position of a transcription factor in regulatory cascades was observed: regulators with larger regulons tend to occupy top positions in the cascades. On the other hand, there is no obvious link to differences in the species' lifestyles and metabolic capabilities.
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Search for Alternative RNA Secondary Structures Regulating Expression of Bacterial Genes
Molecular Biology, 2003Co-Authors: E. V. Lyubetskaya, Mikhail S Gelfand, L. A. Leont'ev, Vassily A. LyubetskyAbstract:Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence. Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and Gamma-Proteobacteria. The attenuators of these operons are predicted for genomes of some poorly known Gamma-Proteobacteria including Shewanella putrefaciens, attenuators of the tryptophan operon in some alpha-proteobacteria are also predicted.
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Purine regulon of Gamma-Proteobacteria: a detailed description
Russian Journal of Genetics, 2002Co-Authors: Dmitry A. Ravcheev, Mikhail S Gelfand, Andrey A Mironov, A. B. RakhmaninovaAbstract:The structure of the purine regulon was studied by a comparative genomic approach in seven genomes of Gamma-Proteobacteria: Escherichia coli, Salmonella typhimurium, Yersinia pestis, Haemophilus influenzae, Pasteurella multocida, Actinobacillus actinomycetemcomitans , and Vibrio cholerae. The palindro- mic binding site of the purine repressor (consensus ACGCAAACGTTTGCGT) is fairly well conserved upstream genes encoding enzymes that participate in the synthesis of inosine monophosphate from phosphori- bozylpyrophosphate and in transfer of one-carbon units, and also upstream of some transport protein genes. These genes may be regarded as the main part of the purine regulon. In terms of physiology, the regulation of the purC and gcvTHP/folD genes seems to be especially important, because the PurR site was found upstream nonorthologous but functionally replaceable genes. However, the PurR site is poorly conserved upstream orthologs of some genes belonging to the E. coli purine regulon, such as genes involved in general nitrogen metabolism, biosynthesis of pyrimidines, and synthesis of AMP and GMP from IMP, and also upstream of the purine repressor gene. It is predicted that purine regulons of the examined bacteria include the following genes: upp participating in synthesis of pyrimidines; uraA encoding an uracil transporter gene; serA involved in serine biosynthesis; folD responsible for the conversion of N5,N10-methenyl tetrahydrofolate into N10-formyltet- rahydrofolate; rpiA involved in ribose metabolism; and genes with an unknown function ( yhhQ and ydiK ). The PurR site was shown to have different structure in different genomes. Thus, the tendency for a decline of the conservatism of site positions 2 and 15 was observed in genomes of bacteria belonging to the Pasteurellaceae and Vibrionaceae groups.
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Comparative analysis of FUR regulons in Gamma-Proteobacteria.
Nucleic acids research, 2001Co-Authors: Ekaterina M. Panina, Andrey A Mironov, Mikhail S GelfandAbstract:Iron is an essential element for the survival and pathogenesis of bacteria. The strict control of iron homeostasis is mediated by the FUR repressor, which is highly conserved among various bacterial species. Here we apply the comparative genomics approach to analyze candidate Fur-binding sites in the genomes of Escherichia coli (K12 and O157:H7), Salmonella typhi, Yersinia pestis and Vibrio cholerae. We describe a number of new loci encoding siderophore biosynthesis and transport proteins. A new regulator of iron-acquisition systems was found in S.typhi. We predict FUR regulation for several virulence systems. We also predict FUR regulation for the chemotaxis system of V.cholerae that is probably involved in the process of pathogenesis.
Stefan Weidner - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach
Microbial Ecology, 2000Co-Authors: Stefan Weidner, Walter Arnold, Erko Stackebrandt, Alfred PuhlerAbstract:: The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences. Most sequences originated from members of the gamma-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the alpha-subclass was determined for 24.2% of the sequences. They were related to the genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several alpha-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related to beta-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms.
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phylogenetic analysis of bacterial communities associated with leaves of the seagrass halophila stipulacea by a culture independent small subunit rrna gene approach
Microbial Ecology, 2000Co-Authors: Stefan Weidner, Walter Arnold, Erko Stackebrandt, Alfred PuhlerAbstract:The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences. Most sequences originated from members of the gamma-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the alpha-subclass was determined for 24.2% of the sequences. They were related to the genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several alpha-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related to beta-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms.
