Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq).
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| Formato: | Artículo científico |
| Lenguaje: | en |
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Frontiers in microbiology
2024
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| author | Hinkle, John E Chanton, Jeffrey P Moynihan, Molly A Ruff, S Emil Teske, Andreas |
| author_facet | Hinkle, John E Chanton, Jeffrey P Moynihan, Molly A Ruff, S Emil Teske, Andreas Hinkle, John E Chanton, Jeffrey P Moynihan, Molly A Ruff, S Emil Teske, Andreas |
| collection | PubMed - marine biology |
| contents | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). Hinkle, John E Chanton, Jeffrey P Moynihan, Molly A Ruff, S Emil Teske, Andreas 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 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 Desulfofervidus and , and in smaller numbers within the sulfur-oxidizing family . 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 | Artículo científico |
| id | pubmed_39839103 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | Frontiers in microbiology |
| record_format | pubmed |
| spellingShingle | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). Hinkle, John E Chanton, Jeffrey P Moynihan, Molly A Ruff, S Emil Teske, Andreas Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). Hinkle, John E Chanton, Jeffrey P Moynihan, Molly A Ruff, S Emil Teske, Andreas 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 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 Desulfofervidus and , and in smaller numbers within the sulfur-oxidizing family . 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. |
| title | Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). |
| url | https://pubmed.ncbi.nlm.nih.gov/39839103/ |