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Andrew J. Weightman - One of the best experts on this subject based on the ideXlab platform.
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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new degenerate cytophaga flexibacter bacteroides specific 16s ribosomal dna targeted oligonucleotide probes reveal high bacterial diversity in river taff Epilithon
Applied and Environmental Microbiology, 2002Co-Authors: Louise A Osullivan, Andrew J. Weightman, John C. FryAbstract:River microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. In this study the bacterial diversity of River Taff Epilithon in South Wales was investigated. A 16S ribosomal DNA (rDNA) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. The Epilithon was found to be very diverse, with an estimated 59.6% of the bacterial populations not accounted for by these clones. Members of the Cytophaga-Flexibacter-Bacteroides division (CFBs) were most abundant in the library, representing 25% of clones, followed by members of the subdivision of the division Proteobacteria (-Proteobacteria), -Proteobacteria, gram-positive bacteria, Cyanobacteria, AŸ-Proteobacteria, -Proteobacteria, and the Prosthecobacter group. This study concentrated on the epilithic CFB populations, and a new set of degenerate 16S rDNA probes was developed to enhance their detection, namely, CFB560, CFB562, and CFB376. The commonly used probe CF319a/b may frequently lead to the underestimation of CFB populations in environmental studies, because it does not fully detect members of the division. CFB560 had exact matches to 95.6% of CFBs listed in the Ribosomal Database Project (release 8.0) small-subunit phylogenetic trees, compared to 60% for CF319a/b. The CFB probes detected 66 of 347 Epilithon TAF clones, and 60 of these were partially sequenced. They affiliated with the RDP-designated groups Cytophaga, Sphingobacterium, Lewinella, and Cytophaga aurantiaca. CFB560 and CF319a/b detected 94% (62 of 66) and 48.5% (32 of 66) of clones, respectively, and therefore CFB560 is recommended for future use. Probe design in this study illustrated that multiple degenerate positions can greatly increase target range without adversely effecting specificity or experimental performance.
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gene transfer in the aquatic environment persistence and mobilization of the catabolic recombinant plasmid pd10 in the Epilithon
Microbiology, 1994Co-Authors: Katja E Hill, John C. Fry, Andrew J. WeightmanAbstract:This study investigated mobilization and persistence of the recombinant, catabolic plasmid pD10 in laboratory microcosms by natural mobilizing plasmids, recently isolated from epilithic bacteria by exogenous isolation in Pseudomonas putida, as opposed to their isolation in the strains in which they occur in situ. Initial experiments in simple, beaker microcosms were used to optimize conditions for selection of the donor, recipient and transconjugant populations. Studies in a recirculating stream microcosm showed that donor, P. putida KT2440(pD10, pQKH6), and recipient, P. putida UWC6, populations, although declining with time, were able to survive for three weeks and that colonization and survival was predominantly in the Epilithon of the microcosm rather than in the liquid phase. Transconjugants UWC6(pD10, pQKH6) were also isolated from Epilithon, showing that plasmid pD10 had been mobilized by plasmid pQKH6. The donor strain was able to survive at 100-fold greater numbers than the recipient, but transconjugants were not isolated after day 15. Separate inoculation of the donor and recipient strains into the microcosm showed that they were able to colonize other stones, where transconjugants then arose as a direct result of plasmid transfer within the Epilithon. A catechol 2,3-dioxygenase gene, tdnC, was used to facilitate identification of donors and transconjugants. Preliminary laboratory matings showed that pD10 transferred to indigenous epilithic strains identified as Pseudomonas fluorescens, P. chlororaphis and P. aureofaciens. These results suggest that in the absence of selection, mobilization of introduced recombinant genes encoded by pD10 occurs at easily detectable frequencies, even in an oligotrophic environment.
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isolation and screening of plasmids from the Epilithon which mobilize recombinant plasmid pd10
Applied and Environmental Microbiology, 1992Co-Authors: Katja E Hill, Andrew J. Weightman, John C. FryAbstract:This study examined the potential of bacteria from river Epilithon to mobilize a recombinant catabolic plasmid, pD10, encoding 3-chlorobenzoate degradation and kanamycin resistance. Fifty-four mobilizing plasmids were exogenously isolated by triparental matings between strains of Pseudomonas putida and epilithic bacteria from the River Taff (South Wales, United Kingdom). Frequencies for mobilization ranged from 1.7 x 10(-8) to 4.5 x 10(-3) per recipient at 20 degrees C. The sizes of the mobilizing plasmids isolated ranged from 40 kb to over 200 kb, and 19 of 54 were found to encode mercury resistance. Plasmid-encoded resistance to tetracycline and streptomycin was also found but not resistance to UV light or various heavy metals. Eight plasmids of epilithic bacteria, analyzed by comparing restriction fragmentation patterns, showed significant differences between those isolated from different independent matings. Optimal temperatures for mobilization of pD10 were between 15 and 25 degrees C. Four mercury resistance plasmids were found to be broad host range, transferring mercury resistance and mobilizing pD10 readily to representative species of beta- and gamma-purple bacteria. In general, frequencies of pD10 mobilization by plasmids of epilithic bacteria were 2 to 3 orders of magnitude lower than conjugal transfer frequencies. Thus, there is a high potential for exchange of recombinant genes introduced into the Epilithon by mobilization between a variety of bacterial species.
Louise A Osullivan - One of the best experts on this subject based on the ideXlab platform.
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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new degenerate cytophaga flexibacter bacteroides specific 16s ribosomal dna targeted oligonucleotide probes reveal high bacterial diversity in river taff Epilithon
Applied and Environmental Microbiology, 2002Co-Authors: Louise A Osullivan, Andrew J. Weightman, John C. FryAbstract:River microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. In this study the bacterial diversity of River Taff Epilithon in South Wales was investigated. A 16S ribosomal DNA (rDNA) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. The Epilithon was found to be very diverse, with an estimated 59.6% of the bacterial populations not accounted for by these clones. Members of the Cytophaga-Flexibacter-Bacteroides division (CFBs) were most abundant in the library, representing 25% of clones, followed by members of the subdivision of the division Proteobacteria (-Proteobacteria), -Proteobacteria, gram-positive bacteria, Cyanobacteria, AŸ-Proteobacteria, -Proteobacteria, and the Prosthecobacter group. This study concentrated on the epilithic CFB populations, and a new set of degenerate 16S rDNA probes was developed to enhance their detection, namely, CFB560, CFB562, and CFB376. The commonly used probe CF319a/b may frequently lead to the underestimation of CFB populations in environmental studies, because it does not fully detect members of the division. CFB560 had exact matches to 95.6% of CFBs listed in the Ribosomal Database Project (release 8.0) small-subunit phylogenetic trees, compared to 60% for CF319a/b. The CFB probes detected 66 of 347 Epilithon TAF clones, and 60 of these were partially sequenced. They affiliated with the RDP-designated groups Cytophaga, Sphingobacterium, Lewinella, and Cytophaga aurantiaca. CFB560 and CF319a/b detected 94% (62 of 66) and 48.5% (32 of 66) of clones, respectively, and therefore CFB560 is recommended for future use. Probe design in this study illustrated that multiple degenerate positions can greatly increase target range without adversely effecting specificity or experimental performance.
Gavin J. Humphreys - One of the best experts on this subject based on the ideXlab platform.
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
Joachim Rinna - One of the best experts on this subject based on the ideXlab platform.
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
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culturable phylogenetic diversity of the phylum bacteroidetes from river Epilithon and coastal water and description of novel members of the family flavobacteriaceae Epilithonimonas tenax gen nov sp nov and persicivirga xylanidelens gen nov sp nov
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Louise A Osullivan, Joachim Rinna, Gavin J. Humphreys, Andrew J. WeightmanAbstract:Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river Epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river Epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T).
Haydee Pizarro - One of the best experts on this subject based on the ideXlab platform.
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Algal structure of the littoral Epilithon in lentic water bodies at Hope Bay, Antarctic Peninsula
Polar Biology, 2006Co-Authors: Stella Maris Bonaventura, Luz Allende, A. Vinocur, Haydee PizarroAbstract:We studied the composition and density of the algae of the littoral Epilithon and the taxa turnover in nine lentic water bodies at Hope Bay, Antarctic Peninsula, during summer 2002. At each site we measured the main physical and chemical variables, and took epilithic samples for the algal analysis. Two composed samples (one for qualitative and one for quantitative analysis) were taken randomly about 1 m away from the shore-line of each sampling site. The morphology of the algal mats could be included in the ‘moat and pond type’ in which Cyanobacteria are well represented. A total of 69 algal taxa were recorded in the whole study area. Chlorophyceae showed the highest taxa richness (33%), followed by Cyanobacteria (29%), Bacillariophyceae (26%), Chrysophyceae (10%), and Tribophyceae (2%). As a result of the redundancy analysis performed, we found that the number, composition, and density of taxa in the water bodies at Hope Bay were strongly influenced by nitrate and suspended solids concentrations and by the distance from the sea. The geographical trend in taxa turnover within Hope Bay was explained by elements from the combination of the metapopulation dynamics and the continuum theories, which are related to dispersal limitation and environmental heterogeneity, respectively.
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littoral Epilithon of lentic water bodies at hope bay antarctic peninsula biomass variables in relation to environmental conditions
Hydrobiologia, 2004Co-Authors: Haydee Pizarro, Luz Allende, Stella Maris BonaventuraAbstract:We studied the structural characteristics of the littoral Epilithon in nine lentic water bodies at Hope Bay, Antarctic Peninsula, during summer 2002. At each site we measured the main physical and chemical variables and took epilithic samples for the analysis of dry weigh, ash, ash-free dry weight and chlorophyll a concentration. Distance from the sea of each water body was also considered. One site was selected for sampling lakes and ponds, except for Boeckella lake, where two sampling sites (A and B) were selected due to the heterogeneity of its littoral zone. Three stones for chlorophyll a analysis and another three to estimate dry weight, ash and ash-free dry weight, were taken randomly about 1 m away from the shore-line of each sampling site. Measurements of physical and chemical characteristics were obtained similarly. Water samples for chemical analysis were taken sub-superficially. Lakatos’s system of classification and the Autotrophic Index were used to make functional inferences about the epilithic communities. Two PCA analyses were made to classify the water bodies according to environmental features and epilithic variables. In the latter, major patterns in data of Epilithon were subsequently interpreted based on environmental data using external validation. Pingui pond, located in the middle of the penguin rookery, was considered as a passive sample in both PCA analyses due to its extreme characteristics. Limnological features of the studied water bodies were similar to those of other Maritime Antarctic lakes. According to the Lakatos’s index, 60% of the sampled lakes had high epilithic mass and a same proportion showed an inorganic type of Epilithon The fact that 40% of the water bodies were autotrophic confirmed the importance of benthos as primary producer. According to environmental features, the well-defined groups of lakes emerged from the PCA were mainly determined by distance from the sea, pH, conductivity and salinity, and corresponded to the principal hydrological basins found in the region. Based on the results of the second PCA, littoral Epilithon was affected by nitrate concentration and conductivity. In this ordination, water bodies from the same hydrological basin were separated probably as a result of a very complex inter-play of factors with a site-specific response to particular microhabitat characteristics.