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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 Microbial Diversity in the Rhizoplane of Oilseed Rape (Brassica napus cv. Westar) Employing Cultivation-Dependent and Cultivation-Independent Approaches.
Microbial ecology, 2001Co-Authors: Olaf Kaiser, Alfred Puhler, Werner SelbitschkaAbstract:The structure of the microbial rhizoplane community of the important crop plant oilseed rape was studied by using a culture-dependent as well as a culture-independent approach based on 16S rDNA amplification. After isolation of the microbial community from the rhizoplane of oilseed rape (Brassica napus cv. Westar), the collected suspension was divided into two parts. One part was used for cultivation of bacteria onto three different growth media to establish a culture collection. From the other part of the rhizoplane suspension, genomic DNA was isolated and purified. Thereafter, 16S rDNA was amplified by PCR and cloned to obtain a library of 16S rDNA genes representative for the bacterial communities of this habitat. Phylogenetic 16S rDNA sequence analysis of 103 clones of this library revealed considerable differences from the corresponding nucleotide sequences of 111 cultured bacteria. Whereas the 16S rDNA clone library was dominated by alpha -Proteobacteria and bacteria of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum (51% and 30%, respectively), less than 17% of the cultured bacteria belonged to these two groups. More than 64% of the cultivated isolates were allocated to the beta- and gamma -subclasses of the Proteobacteria, which were present in the clone library at about 14%. Most of the clones of the alpha -Proteobacteria of the library showed highest similarity to Bradyrhizobium sp. No such bacteria were found in the culture collection. Similarly, the second dominant group of the clone library comprising members of the CFB phylum was represented in the culture collection by a single isolate. The phylogenetic analysis of isolates of the culture collection clearly emphasized the need to use different growth media for recovery of rhizoplane bacteria. Whereas most of the alpha -Proteobacteria were recovered on complex medium, most of the beta -Proteobacteria were isolated onto minimal media. Our results demonstrate that the combined approach pursued in this paper is necessary to explore the biodiversity of bacterial rhizoplane communities.
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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.
Antonio Correia - One of the best experts on this subject based on the ideXlab platform.
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seasonal and spatial variability of free living bacterial community composition along an estuarine gradient ria de aveiro portugal
Estuarine Coastal and Shelf Science, 2006Co-Authors: Isabel Henriques, Artur Alves, Marta Tacao, Adelaide Almeida, ângela Cunha, Antonio CorreiaAbstract:We examined the dynamics of the free-living bacterial community in the Ria de Aveiro estuary (Portugal) using 16S rDNA PCRedenaturing gradient gel electrophoresis (DGGE). Samples were collected along the salinity gradient in April, July and October 2003 and January 2004. Analysis of DGGE profiles indicated that the compositional shifts within this community occurred between the brackish and freshwater sections. Those shifts were particularly evident in samples collected in April, October and January. Less pronounced changes were also detected along the salinity gradient in the marine and brackish sections. Seasonally driven changes in microbial community in this estuary also occur. Canonical correspondence analysis (CCA) revealed that salinity and temperature accounted for a significant amount of the variability in the bacterioplankton community composition (26%). Dominant phylotypes were identified either by direct sequencing or by cloning and sequencing DGGE bands. Analysis of DNA sequences revealed that the dominant bacterial groups changed from Bacteroidetes, Alpha-Proteobacteria and Gamma-proteobacteria in the marine-brackish section to Bacteroidetes, Beta-proteobacteria, Delta-proteobacteria and Epsilon-proteobacteria in the freshwater section of the estuary. 2006 Elsevier Ltd. All rights reserved.
Mark van der Giezen - One of the best experts on this subject based on the ideXlab platform.
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evolution of the isd11 iscs complex reveals a single α proteobacterial endosymbiosis for all eukaryotes
Molecular Biology and Evolution, 2006Co-Authors: Thomas A Richards, Mark van der GiezenAbstract:Giardia and Trichomonas are eukaryotes without standard mitochondria but contain mitochondrial-type alpha-proteobacterium-derived iron-sulfur cluster (ISC) assembly proteins, located to mitosomes in Giardia and hydrogenosomes in Trichomonas. Although these data suggest a single common endosymbiotic ancestry for mitochondria, mitosomes, and hydrogenosomes, separate origins are still being proposed. Here, we present a bioinformatic analysis of Isd11, a recently described essential component of the mitochondrial ISC assembly pathway. Isd11 is unique to eukaryotes but functions closely with the alpha-proteobacterium-derived cysteine desulfurase IscS. We demonstrate the presence of homologues of Isd11 in all 5 eukaryotic supergroups sampled, including hydrogenosomal and mitosomal lineages. The eukaryotic invention of Isd11 as a functional partner to IscS directly implies a single shared Alpha-Proteobacterial endosymbiotic ancestry for all eukaryotes. This pinpoints the Alpha-Proteobacterial endosymbiosis to before the last common ancestor of all eukaryotes without ambiguity.
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Evolution of the Isd11–IscS Complex Reveals a Single α-Proteobacterial Endosymbiosis for All Eukaryotes
Molecular Biology and Evolution, 2006Co-Authors: Thomas A Richards, Mark van der GiezenAbstract:Giardia and Trichomonas are eukaryotes without standard mitochondria but contain mitochondrial-type alpha-proteobacterium-derived iron-sulfur cluster (ISC) assembly proteins, located to mitosomes in Giardia and hydrogenosomes in Trichomonas. Although these data suggest a single common endosymbiotic ancestry for mitochondria, mitosomes, and hydrogenosomes, separate origins are still being proposed. Here, we present a bioinformatic analysis of Isd11, a recently described essential component of the mitochondrial ISC assembly pathway. Isd11 is unique to eukaryotes but functions closely with the alpha-proteobacterium-derived cysteine desulfurase IscS. We demonstrate the presence of homologues of Isd11 in all 5 eukaryotic supergroups sampled, including hydrogenosomal and mitosomal lineages. The eukaryotic invention of Isd11 as a functional partner to IscS directly implies a single shared Alpha-Proteobacterial endosymbiotic ancestry for all eukaryotes. This pinpoints the Alpha-Proteobacterial endosymbiosis to before the last common ancestor of all eukaryotes without ambiguity.
David L Kirchman - One of the best experts on this subject based on the ideXlab platform.
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Contribution of major bacterial groups to bacterial biomass production along a salinity gradient in the South China Sea
Aquatic Microbial Ecology, 2006Co-Authors: Yao Zhang, Matthew T. Cottrell, Nianzhi Jiao, David L KirchmanAbstract:Bacterial abundance and assimilation of 3 H-leucine were examined using a combination of microautoradiography and fluorescent in situ hybridization (Micro-FISH) to determine the bacterioplankton community structure and estimate the contribution of major bacterial groups to total bacterial biomass production (leucine incorporation) from the Pearl River mouth to the open water area in the South China Sea. Alpha-, beta-, gamma-proteobacteria and the Cytophaga-Flavo- bacterium cluster differed substantially in their relative abundance and contribution to leucine assim- ilation along the salinity gradient. The contribution of major bacterial groups to leucine assimilation was closely associated with their relative abundance in the communities. Alpha-Proteobacteria were the dominant group in the high-salinity water in terms of abundance and 3 H-leucine assimilation, whereas beta-proteobacteria were more important in fresh water. At all stations, gamma-proteobac- teria were a minor component, but the Cytophaga-Flavobacterium cluster was always a significant component in both marine and freshwater systems. The relative abundance of bacterial groups explained the variation in 3 H-leucine assimilation by the major bacterial groups to a great extent. At the singlebacterial group level, a statistically significant correlation between abundance and leucine- uptake activity was observed for beta-proteobacteria, suggesting that the relative abundance of beta- proteobacteria in bacterioplankton communities was controlled by growth-related processes. In general, the numerical dominance of the major phylogenetic groups and their contribution to total bacterial biomass production varied consistently along the salinity gradient in the South China Sea.
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Aerobic anoxygenic photosynthesis genes and operons in uncultured bacteria in the Delaware River.
Environmental Microbiology, 2005Co-Authors: Lisa A. Waidner, David L KirchmanAbstract:Summary Photosynthesis genes and operons of aerobic anoxygenic photosynthetic (AAP) bacteria have been examined in a variety of marine habitats, but genomic information about freshwater AAP bacteria is lacking. The goal of this study was to examine photosynthesis genes of AAP bacteria in the Delaware River. In a fosmid library, we found two clones bearing photosynthesis gene clusters with unique gene content and organization. Both clones contained 37 open reading frames, with most of those genes encoding known AAP bacterial proteins. The genes in one fosmid were most closely related to those of AAP bacteria in the Rhodobacter genus. The genes of the other clone were related to those of freshwater beta-proteobacteria. Both clones contained the acsF gene, which is required for aerobic bacteriochlorophyll synthesis, suggesting that these bacteria are not anaerobes. The beta-proteobacterial fosmid has the puf operon B-A-L-M-C and is the first example of an uncultured bacterium with this operon structure. The alpha-3-proteobacterial fosmid has a rare gene order (Q-B-A-L-M-X), previously observed only in the Rhodobacter genus. Phylogenetic analyses of photosynthesis genes revealed a possible freshwater cluster of AAP beta-proteobacteria. The data from both Delaware River clones suggest there are groups of freshwater or estuarine AAP bacteria distinct from those found in marine environments.
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Growth rate of the major phylogenetic bacterial groups in the Delaware estuary
Limnology and Oceanography, 2004Co-Authors: Taichi Yokokawa, Matthew T. Cottrell, Toshi Nagata, David L KirchmanAbstract:The phylogenetic composition of bacterial communities varies along the salinity gradient of estuaries, one notable pattern being the prevalence of alpha- and beta-proteobacteria in salt- and freshwater regions, respectively. We tested the hypothesis that bottom-up forces (substrate supply) control these and other changes in bacterial community composition in the Delaware estuary. We measured the biomass and growth rate of four major phylogenetic groups of bacterioplankton (alpha-, beta-, and gamma-proteobacteria and the Cytophaga-Flavobacter cluster) in low- and high-salinity regions of the estuary by the dilution culture approach combined with fluorescent in situ hybridization with rRNA-targeted probes. Group-specific growth rates were highly variable depending on location and season and could far exceed (up to nearly fourfold) the growth rates of total bacteria. The phylogenetic groups that exhibited the highest growth rates included alpha- and gamma-proteobacteria at both low- and high-salinity stations and betaproteobacteria at a low-salinity station. These data help to explain the high abundance of beta-proteobacteria in the freshwater region, but bottom up controls appear to account only partly for the variability in bacterial communities. The relationship between production and biomass suggested that bacterial communities at the low-salinity site were controlled by substrate supply, whereas bacterial mortality appeared to be more important at the high-salinity site. Our data demonstrate that group-specific growth rates are useful parameters for examining the competitive advantages of individual groups and the mode of regulation of bacterial communities in estuarine environments.
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.
