Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq)
Hydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput...
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Frontiers Media S.A.
2025-01-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1491488/full |
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| author | John E. Hinkle John E. Hinkle Jeffrey P. Chanton Molly A. Moynihan Molly A. Moynihan S. Emil Ruff S. Emil Ruff Andreas Teske |
| author_facet | John E. Hinkle John E. Hinkle Jeffrey P. Chanton Molly A. Moynihan Molly A. Moynihan S. Emil Ruff S. Emil Ruff Andreas Teske |
| author_sort | John E. Hinkle |
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| description | Hydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yielded promising results in analyses of microbial ecosystems, such as the human gut microbiome. In this study, LoopSeq is used to obtain near-full length (approximately 1,400–1,500 nucleotides) bacterial 16S rRNA gene sequences from hydrothermal sediments in Guaymas Basin. Based on these sequences, high-quality alignments and phylogenetic analyses provided new insights into previously unrecognized taxonomic diversity of sulfur-cycling microorganisms and their distribution along a lateral hydrothermal gradient. Detailed phylogenies for free-living and syntrophic sulfur-cycling bacterial lineages identified well-supported monophyletic clusters that have implications for the taxonomic classification of these groups. Particularly, we identify clusters within Candidatus Desulfofervidus that represent unexplored physiological and genomic diversity. In general, LoopSeq-derived 16S rRNA gene sequences aligned consistently with reference sequences in GenBank; however, chimeras were prevalent in sequences as affiliated with the thermophilic Candidatus Desulfofervidus and Thermodesulfobacterium, and in smaller numbers within the sulfur-oxidizing family Beggiatoaceae. Our analysis of sediments along a well-documented thermal and geochemical gradient show how lineages affiliated with different sulfur-cycling taxonomic groups persist throughout surficial hydrothermal sediments in the Guaymas Basin. |
| format | Article |
| id | doaj-art-de7bc97911294ee7886d54caef98bddc |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-de7bc97911294ee7886d54caef98bddc2025-01-07T10:47:07ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-01-011510.3389/fmicb.2024.14914881491488Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq)John E. Hinkle0John E. Hinkle1Jeffrey P. Chanton2Molly A. Moynihan3Molly A. Moynihan4S. Emil Ruff5S. Emil Ruff6Andreas Teske7Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, United StatesDepartment of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, United StatesDepartment of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, United StatesMarine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United StatesMarine Biological Laboratory, The Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United StatesMarine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United StatesMarine Biological Laboratory, The Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United StatesDepartment of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, United StatesHydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yielded promising results in analyses of microbial ecosystems, such as the human gut microbiome. In this study, LoopSeq is used to obtain near-full length (approximately 1,400–1,500 nucleotides) bacterial 16S rRNA gene sequences from hydrothermal sediments in Guaymas Basin. Based on these sequences, high-quality alignments and phylogenetic analyses provided new insights into previously unrecognized taxonomic diversity of sulfur-cycling microorganisms and their distribution along a lateral hydrothermal gradient. Detailed phylogenies for free-living and syntrophic sulfur-cycling bacterial lineages identified well-supported monophyletic clusters that have implications for the taxonomic classification of these groups. Particularly, we identify clusters within Candidatus Desulfofervidus that represent unexplored physiological and genomic diversity. In general, LoopSeq-derived 16S rRNA gene sequences aligned consistently with reference sequences in GenBank; however, chimeras were prevalent in sequences as affiliated with the thermophilic Candidatus Desulfofervidus and Thermodesulfobacterium, and in smaller numbers within the sulfur-oxidizing family Beggiatoaceae. Our analysis of sediments along a well-documented thermal and geochemical gradient show how lineages affiliated with different sulfur-cycling taxonomic groups persist throughout surficial hydrothermal sediments in the Guaymas Basin.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1491488/fullLoopSeq16S rRNAsulfur-cycling bacteriasulfur cycleGuaymas Basinhydrothermal sediments |
| spellingShingle | John E. Hinkle John E. Hinkle Jeffrey P. Chanton Molly A. Moynihan Molly A. Moynihan S. Emil Ruff S. Emil Ruff Andreas Teske Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq) Frontiers in Microbiology LoopSeq 16S rRNA sulfur-cycling bacteria sulfur cycle Guaymas Basin hydrothermal sediments |
| title | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq) |
| title_full | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq) |
| title_fullStr | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq) |
| title_full_unstemmed | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq) |
| title_short | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq) |
| title_sort | complex bacterial diversity of guaymas basin hydrothermal sediments revealed by synthetic long read sequencing loopseq |
| topic | LoopSeq 16S rRNA sulfur-cycling bacteria sulfur cycle Guaymas Basin hydrothermal sediments |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1491488/full |
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