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David M Karl - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic diversity of the bacterial community from a microbial mat at an active hydrothermal vent system loihi seamount hawaii
Applied and Environmental Microbiology, 1995Co-Authors: Craig L Moyer, Fred C Dobbs, David M KarlAbstract:The phylogenetic diversity of small-subunit rRNA genes associated with the domain Bacteria was examined (by using previously defined operational taxonomic units [C. L. Moyer, F.C. Dobbs, and D. M. Karl, Appl. Environ. Microbiol. 60:871-879, 1994]; those for Pele's Vents Bacteria are hereafter abbreviated PVB Otus) with samples from a microbial mat at an active, deep-sea hydrothermal vent system. A cluster of phylogenetically related PVB Otus (Otus 2, 3, 6, and 8) was closely affiliated with Thiovulum sp. contained within the epsilon subclass of the class Proteobacteria and accounted for 60.5% of the small-subunit rRNA bacterial clone library from Pele's Vents. A second, smaller cluster of PVB Otus (Otus 1 and 11) was closely affiliated with Xanthomonas sp., contained within the gamma subclass of the Proteobacteria and accounted for a total of 27.1% of the bacterial clone library. The remaining five PVB Otus each accounted for 2.1% of the clones recovered and were affiliated with the following phylogenetic groups: PVB OTU 5 was a member of the Alteromonas group; PVB OTU 12 was a member of the Colwellia assemblage; PVB OTU 4 was loosely determined to be a member of the Thiothrix group, with the endosymbiotic bacteria from Bathymodiolus thermophilus and Calyptogena magnifica as the nearest relatives; PVB OTU 10B was a member of the Myxobacterium group; and PVB OTU 9A was a member of the Paraphyletic assemblage, with the Octopus Spring microbial mat type K clone as the closest known relative.(ABSTRACT TRUNCATED AT 250 WORDS)
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estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16s rrna genes from a microbial mat at an active hydrothermal vent system loihi seamount hawaii
Applied and Environmental Microbiology, 1994Co-Authors: Craig L Moyer, Fred C Dobbs, David M KarlAbstract:PCR was used to amplify (eu)bacterial small-subunit (16S) rRNA genes from total-community genomic DNA. The source of total-community genomic DNA used for this culture-independent analysis was the microbial mats from a deep-sea, hydrothermal vent system, Pele9s Vents, located at Loihi Seamount, Hawaii. Oligonucleotides complementary to conserved regions in the 16S rRNA-encoding DNA (rDNA) of bacteria were used to direct the synthesis of PCR products, which were then subcloned by blunt-end ligation into phagemid vector pBluescript II. Restriction fragment length polymorphism patterns, created by using tandem tetrameric restriction endonucleases, revealed the presence of 12 groups of 16S rRNA genes representing discrete operational taxonomic units (Otus). The rank order abundance of these putative Otus was measured, and the two most abundant Otus accounted for 72.9% of all of the 16S rDNA clones. Among the remaining 27.1% of the 16S rDNA clones, none of the 10 Otus was represented by more than three individual clones. The cumulative OTU distribution for 48 bacterial 16S rDNA clones demonstrated that the majority of taxa represented in the clone library were detected, a result which we assume to be an estimate of the diversity of bacteria in the native hydrothermal vent habitat. 16S rDNA fingerprinting of individual clones belonging to particular Otus by using an oligonucleotide probe that binds to a universally conserved region of the 16S rDNA fragments was conducted to confirm OTU specificity and 16S rDNA identity. Images
Håvard Kauserud - One of the best experts on this subject based on the ideXlab platform.
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fungi ahoy diversity on marine wooden substrata in the high north
Fungal Ecology, 2014Co-Authors: Teppo Rama, Joseph W Spatafora, Jenni Norden, Marie L Davey, Geir Mathiassen, Håvard KauserudAbstract:Marine fungi are severely understudied in the polar regions. We used molecularly identi- fied cultures to study fungi inhabiting 50 intertidal and sea-floor logs along the North Norwegian coast. The aim was to explore the taxonomic and ecological diversity and to examine factors shaping the marine wood-inhabiting fungal communities. The 577 pure cultures analyzed clustered into 147 operational taxonomic units (Otus) based on 97% ITS sequence similarity. Ascomycota dominated, but Otus belonging to Basidiomycota, Mucoromycotina and Chytridiomycota were also isolated. Nine Otus could not be assigned to any fungal phylum. Almost half of the Otus were considered non-marine. The western and eastern part of the Norwegian Barents Sea coast hosted different communities. Geography, substratum and site level variables contributed to shaping these communities. We characterized a previously overlooked fungal community in a poorly studied area, discovered high diversity and report many taxa for the first time from the marine environment.
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different bacterial communities in ectomycorrhizae and surrounding soil
Scientific Reports, 2013Co-Authors: Ramiro Logares, Rakel Blaalid, Ingrid Bakke, Tor Carlsen, Rune Halvorsen, Anne-brit Kolstø, Ole Andreas Økstad, Håvard KauserudAbstract:Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (Otus) was found in plant roots (3,571 Otus) and surrounding soil (3,476 Otus). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and Otus unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the Otus, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis.
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changes in the root associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing
Molecular Ecology, 2012Co-Authors: Rakel Blaalid, Tor Carlsen, Rune Halvorsen, Surendra Kumar, Karl I Ugland, Giovanni Fontana, Håvard KauserudAbstract:We investigated changes in the root-associated fungal communities associated with the ectomycorrhizal herb Bistorta vivipara along a primary succession gradient using 454 amplicon sequencing. Our main objective was to assess the degree of variation in fungal richness and community composition as vegetation cover increases along the chronosequence. Sixty root systems of B. vivipara were sampled in vegetation zones delimited by dated moraines in front of a retreating glacier in Norway. We extracted DNA from rinsed root systems, amplified the ITS1 region using fungal-specific primers and analysed the amplicons using 454 sequencing. Between 437 and 5063 sequences were obtained from each root system. Clustering analyses using a 98.5% sequence similarity cut-off yielded a total of 470 operational taxonomic units (Otus), excluding singletons. Between eight and 41 fungal Otus were detected within each root system. Already in the first stage of succession, a high fungal diversity was present in the B. vivipara root systems. Total number of Otus increased significantly along the gradient towards climax vegetation, but the average number of Otus per root system stayed unchanged. There was a high patchiness in distribution of fungal Otus across root systems, indicating that stochastic processes to a large extent structure the fungal communities. However, time since deglaciation had impact on the fungal community structure, as a systematic shift in the community composition was observed along the chronosequence. Ectomycorrhizal basidiomycetes were the dominant fungi in the roots of B. vivipara, when it comes to both number of Otus and number of sequences.
Mark Morrison - One of the best experts on this subject based on the ideXlab platform.
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status of the phylogenetic diversity census of ruminal microbiomes
FEMS Microbiology Ecology, 2011Co-Authors: Minseok Kim, Mark MorrisonAbstract:In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (Otus) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 Otus), Bacteroidetes (1610 Otus) and Proteobacteria (226 Otus) were the most predominant. These bacterial sequences were grouped into more than 3500 Otus at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level Otus in phylum Euryarchaeota. Although clustered into 670 genus-level Otus, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At least 78218 bacterial and 24480 archaeal sequences would be needed to reach 99.9% coverage. The results of this study may serve as a framework to assess the significance of individual populations to rumen functions and to guide future studies to identify the alpha and global diversity of ruminal microbiomes.
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A meta-analysis of the microbial diversity observed in anaerobic digesters.
Bioresource Technology, 2011Co-Authors: Michael C. Nelson, Mark MorrisonAbstract:In this study, the collective microbial diversity in anaerobic digesters was examined using a meta-analysis approach. All 16S rRNA gene sequences recovered from anaerobic digesters available in public databases were retrieved and subjected to phylogenetic and statistical analyses. As of May 2010, 16,519 bacterial and 2869 archaeal sequences were found in GenBank. The bacterial sequences were assigned to 5926 operational taxonomic units (Otus, based on ≥ 97% sequence identity) representing 28 known bacterial phyla, with Proteobacteria (1590 Otus), Firmicutes (1352 Otus), Bacteroidetes (705 Otus), and Chloroflexi (693 Otus) being predominant. Archaeal sequences were assigned to 296 Otus, primarily Methanosaeta and the uncharacterized WSA2 group. Nearly 60% of all sequences could not be classified to any established genus. Rarefaction analysis indicates that approximately 60% of bacterial and 90% of archaeal diversity in anaerobic digesters has been sampled. This analysis of the global bacterial and archaeal diversity in AD systems can guide future studies to further examine the microbial diversity involved in AD and development of comprehensive analytical tools.
Craig L Moyer - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic diversity of the bacterial community from a microbial mat at an active hydrothermal vent system loihi seamount hawaii
Applied and Environmental Microbiology, 1995Co-Authors: Craig L Moyer, Fred C Dobbs, David M KarlAbstract:The phylogenetic diversity of small-subunit rRNA genes associated with the domain Bacteria was examined (by using previously defined operational taxonomic units [C. L. Moyer, F.C. Dobbs, and D. M. Karl, Appl. Environ. Microbiol. 60:871-879, 1994]; those for Pele's Vents Bacteria are hereafter abbreviated PVB Otus) with samples from a microbial mat at an active, deep-sea hydrothermal vent system. A cluster of phylogenetically related PVB Otus (Otus 2, 3, 6, and 8) was closely affiliated with Thiovulum sp. contained within the epsilon subclass of the class Proteobacteria and accounted for 60.5% of the small-subunit rRNA bacterial clone library from Pele's Vents. A second, smaller cluster of PVB Otus (Otus 1 and 11) was closely affiliated with Xanthomonas sp., contained within the gamma subclass of the Proteobacteria and accounted for a total of 27.1% of the bacterial clone library. The remaining five PVB Otus each accounted for 2.1% of the clones recovered and were affiliated with the following phylogenetic groups: PVB OTU 5 was a member of the Alteromonas group; PVB OTU 12 was a member of the Colwellia assemblage; PVB OTU 4 was loosely determined to be a member of the Thiothrix group, with the endosymbiotic bacteria from Bathymodiolus thermophilus and Calyptogena magnifica as the nearest relatives; PVB OTU 10B was a member of the Myxobacterium group; and PVB OTU 9A was a member of the Paraphyletic assemblage, with the Octopus Spring microbial mat type K clone as the closest known relative.(ABSTRACT TRUNCATED AT 250 WORDS)
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estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16s rrna genes from a microbial mat at an active hydrothermal vent system loihi seamount hawaii
Applied and Environmental Microbiology, 1994Co-Authors: Craig L Moyer, Fred C Dobbs, David M KarlAbstract:PCR was used to amplify (eu)bacterial small-subunit (16S) rRNA genes from total-community genomic DNA. The source of total-community genomic DNA used for this culture-independent analysis was the microbial mats from a deep-sea, hydrothermal vent system, Pele9s Vents, located at Loihi Seamount, Hawaii. Oligonucleotides complementary to conserved regions in the 16S rRNA-encoding DNA (rDNA) of bacteria were used to direct the synthesis of PCR products, which were then subcloned by blunt-end ligation into phagemid vector pBluescript II. Restriction fragment length polymorphism patterns, created by using tandem tetrameric restriction endonucleases, revealed the presence of 12 groups of 16S rRNA genes representing discrete operational taxonomic units (Otus). The rank order abundance of these putative Otus was measured, and the two most abundant Otus accounted for 72.9% of all of the 16S rDNA clones. Among the remaining 27.1% of the 16S rDNA clones, none of the 10 Otus was represented by more than three individual clones. The cumulative OTU distribution for 48 bacterial 16S rDNA clones demonstrated that the majority of taxa represented in the clone library were detected, a result which we assume to be an estimate of the diversity of bacteria in the native hydrothermal vent habitat. 16S rDNA fingerprinting of individual clones belonging to particular Otus by using an oligonucleotide probe that binds to a universally conserved region of the 16S rDNA fragments was conducted to confirm OTU specificity and 16S rDNA identity. Images
Ramon Rossello-mora - One of the best experts on this subject based on the ideXlab platform.
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Data_Sheet_3_Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.XLSX
2018Co-Authors: Xiangning Bai, Jing Yang, Dong Jin, Sara Díaz Moyá, Yanwen Xiong, Ramon Rossello-moraAbstract:The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with the application of the operational phylogenetic unit (OPU) approach, has been used to analyze the fecal microbial composition of the high-altitude and herbivorous Tibetan antelopes. The fecal samples of the antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, the largest depopulated zone in Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute mountain sickness. In total, 104 antelope fecal samples were enrolled in this study, and were clustered into 61,258 operational taxonomic units (Otus) at an identity of 98.7% and affiliated with 757 OPUs, including 144 known species, 256 potentially new species, 103 potentially higher taxa within known lineages. In addition, 254 comprised sequences not affiliating with any known family, and the closest relatives were unclassified lineages of existing orders or classes. A total of 42 out of 757 OPUs conformed to the core fecal microbiome, of which four major lineages, namely, un-cultured Ruminococcaceae, Lachnospiraceae, Akkermansia, and Christensenellaceae were associated with human health or longevity. The current study reveals that the fecal core microbiome of antelope is mainly composited of uncultured bacteria. The most abundant core taxa, namely, uncultured Ruminococcaceae, uncultured Akkermansia, uncultured Bacteroides, uncultured Christensenellaceae, uncultured Mollicutes, and uncultured Lachnospiraceae, may represent new bacterial candidates at high taxa levels, and several may have beneficial roles in health promotion or anti-intestinal dysbiosis. These organisms should be further isolated and evaluated for potential effect on human health and longevity.
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Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau
Frontiers Media S.A., 2018Co-Authors: Xiangning Bai, Jing Yang, Dong Jin, Sara Díaz Moyá, Yanwen Xiong, Ramon Rossello-moraAbstract:The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with the application of the operational phylogenetic unit (OPU) approach, has been used to analyze the fecal microbial composition of the high-altitude and herbivorous Tibetan antelopes. The fecal samples of the antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, the largest depopulated zone in Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute mountain sickness. In total, 104 antelope fecal samples were enrolled in this study, and were clustered into 61,258 operational taxonomic units (Otus) at an identity of 98.7% and affiliated with 757 OPUs, including 144 known species, 256 potentially new species, 103 potentially higher taxa within known lineages. In addition, 254 comprised sequences not affiliating with any known family, and the closest relatives were unclassified lineages of existing orders or classes. A total of 42 out of 757 OPUs conformed to the core fecal microbiome, of which four major lineages, namely, un-cultured Ruminococcaceae, Lachnospiraceae, Akkermansia, and Christensenellaceae were associated with human health or longevity. The current study reveals that the fecal core microbiome of antelope is mainly composited of uncultured bacteria. The most abundant core taxa, namely, uncultured Ruminococcaceae, uncultured Akkermansia, uncultured Bacteroides, uncultured Christensenellaceae, uncultured Mollicutes, and uncultured Lachnospiraceae, may represent new bacterial candidates at high taxa levels, and several may have beneficial roles in health promotion or anti-intestinal dysbiosis. These organisms should be further isolated and evaluated for potential effect on human health and longevity
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Data_Sheet_1_Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.PDF
2018Co-Authors: Xiangning Bai, Jing Yang, Dong Jin, Sara Díaz Moyá, Yanwen Xiong, Ramon Rossello-moraAbstract:The metataxonomic approach combining 16S rRNA gene amplicon sequencing using the PacBio Technology with the application of the operational phylogenetic unit (OPU) approach, has been used to analyze the fecal microbial composition of the high-altitude and herbivorous Tibetan antelopes. The fecal samples of the antelope were collected in Hoh Xil National Nature Reserve, at an altitude over 4500 m, the largest depopulated zone in Qinghai-Tibetan Plateau, China, where non-native animals or humans may experience life-threatening acute mountain sickness. In total, 104 antelope fecal samples were enrolled in this study, and were clustered into 61,258 operational taxonomic units (Otus) at an identity of 98.7% and affiliated with 757 OPUs, including 144 known species, 256 potentially new species, 103 potentially higher taxa within known lineages. In addition, 254 comprised sequences not affiliating with any known family, and the closest relatives were unclassified lineages of existing orders or classes. A total of 42 out of 757 OPUs conformed to the core fecal microbiome, of which four major lineages, namely, un-cultured Ruminococcaceae, Lachnospiraceae, Akkermansia, and Christensenellaceae were associated with human health or longevity. The current study reveals that the fecal core microbiome of antelope is mainly composited of uncultured bacteria. The most abundant core taxa, namely, uncultured Ruminococcaceae, uncultured Akkermansia, uncultured Bacteroides, uncultured Christensenellaceae, uncultured Mollicutes, and uncultured Lachnospiraceae, may represent new bacterial candidates at high taxa levels, and several may have beneficial roles in health promotion or anti-intestinal dysbiosis. These organisms should be further isolated and evaluated for potential effect on human health and longevity.
