Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments
Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this stu...
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ftpubmed:oai:pubmedcentral.nih.gov:4096408 2023-05-15T15:10:38+02:00 Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments Li, Chongping Lai, Qiliang Li, Guizhen Liu, Yang Sun, Fengqin Shao, Zongze 2014-07-14 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096408 http://www.ncbi.nlm.nih.gov/pubmed/25019154 https://doi.org/10.1371/journal.pone.0101394 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/25019154 http://dx.doi.org/10.1371/journal.pone.0101394 This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2014 ftpubmed https://doi.org/10.1371/journal.pone.0101394 2014-07-20T00:58:49Z Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus. Text Arctic Arctic Ocean PubMed Central (PMC) Arctic Arctic Ocean Gata ENVELOPE(-19.702,-19.702,63.540,63.540) Pacific PLoS ONE 9 7 e101394 |
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Research Article Li, Chongping Lai, Qiliang Li, Guizhen Liu, Yang Sun, Fengqin Shao, Zongze Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments |
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Research Article |
description |
Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus. |
format |
Text |
author |
Li, Chongping Lai, Qiliang Li, Guizhen Liu, Yang Sun, Fengqin Shao, Zongze |
author_facet |
Li, Chongping Lai, Qiliang Li, Guizhen Liu, Yang Sun, Fengqin Shao, Zongze |
author_sort |
Li, Chongping |
title |
Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments |
title_short |
Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments |
title_full |
Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments |
title_fullStr |
Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments |
title_full_unstemmed |
Multilocus Sequence Analysis for the Assessment of Phylogenetic Diversity and Biogeography in Hyphomonas Bacteria from Diverse Marine Environments |
title_sort |
multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments |
publisher |
Public Library of Science |
publishDate |
2014 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096408 http://www.ncbi.nlm.nih.gov/pubmed/25019154 https://doi.org/10.1371/journal.pone.0101394 |
long_lat |
ENVELOPE(-19.702,-19.702,63.540,63.540) |
geographic |
Arctic Arctic Ocean Gata Pacific |
geographic_facet |
Arctic Arctic Ocean Gata Pacific |
genre |
Arctic Arctic Ocean |
genre_facet |
Arctic Arctic Ocean |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/25019154 http://dx.doi.org/10.1371/journal.pone.0101394 |
op_rights |
This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0101394 |
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PLoS ONE |
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9 |
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7 |
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e101394 |
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1766341619754205184 |