Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui
The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extrac...
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| Format: | Article |
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MDPI AG
2022-07-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/7/1395 |
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| author | Qi Liu Zichen He Takeshi Naganuma Ryosuke Nakai Luz María Rodríguez Rafael Carreño Franco Urbani |
| author_facet | Qi Liu Zichen He Takeshi Naganuma Ryosuke Nakai Luz María Rodríguez Rafael Carreño Franco Urbani |
| author_sort | Qi Liu |
| collection | DOAJ |
| description | The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extracted from three speleothems of two types, i.e., one soft whitish mushroom-like speleothem and two hard blackish coral-like speleothems. The extracted DNAs were amplified for sequencing the V3–V4 region of the bacterial 16S rRNA gene by MiSeq. A total of 210,309 valid reads were obtained and clustered into 3184 phylotypes or operational taxonomic units (OTUs). The OTUs from the soft whitish speleothem were mostly affiliated with <i>Acidobacteriota</i>, <i>Pseudomonadota</i> (formerly, <i>Proteobacteria</i>), and <i>Chloroflexota,</i> with the OTUs ascribed to <i>Nitrospirota</i> being found specifically in this speleothem. The OTUs from the hard blackish speleothems were similar to each other and were mostly affiliated with <i>Pseudomonadota</i>, <i>Acidobacteriota,</i> and <i>Actinomycetota</i> (formerly, <i>Actinobacteria</i>). These OTU compositions were generally consistent with those reported for limestone and silicate caves. The OTUs were further used to infer metabolic features by using the PICRUSt bioinformatic tool, and membrane transport and amino acid metabolism were noticeably featured. These and other featured metabolisms may influence the pH microenvironment and, consequently, the formation, weathering, and re-deposition of silicate speleothems. |
| first_indexed | 2024-03-09T06:10:04Z |
| format | Article |
| id | doaj.art-15b132af4ba04f509b353a78994176e7 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T06:10:04Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj.art-15b132af4ba04f509b353a78994176e72023-12-03T11:59:10ZengMDPI AGMicroorganisms2076-26072022-07-01107139510.3390/microorganisms10071395Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield TepuiQi Liu0Zichen He1Takeshi Naganuma2Ryosuke Nakai3Luz María Rodríguez4Rafael Carreño5Franco Urbani6Graduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, JapanGraduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, JapanGraduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, JapanBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, JapanVenezuelan Society of Speleology, Apartado 47.334, Caracas 1041-A, VenezuelaVenezuelan Society of Speleology, Apartado 47.334, Caracas 1041-A, VenezuelaVenezuelan Society of Speleology, Apartado 47.334, Caracas 1041-A, VenezuelaThe diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extracted from three speleothems of two types, i.e., one soft whitish mushroom-like speleothem and two hard blackish coral-like speleothems. The extracted DNAs were amplified for sequencing the V3–V4 region of the bacterial 16S rRNA gene by MiSeq. A total of 210,309 valid reads were obtained and clustered into 3184 phylotypes or operational taxonomic units (OTUs). The OTUs from the soft whitish speleothem were mostly affiliated with <i>Acidobacteriota</i>, <i>Pseudomonadota</i> (formerly, <i>Proteobacteria</i>), and <i>Chloroflexota,</i> with the OTUs ascribed to <i>Nitrospirota</i> being found specifically in this speleothem. The OTUs from the hard blackish speleothems were similar to each other and were mostly affiliated with <i>Pseudomonadota</i>, <i>Acidobacteriota,</i> and <i>Actinomycetota</i> (formerly, <i>Actinobacteria</i>). These OTU compositions were generally consistent with those reported for limestone and silicate caves. The OTUs were further used to infer metabolic features by using the PICRUSt bioinformatic tool, and membrane transport and amino acid metabolism were noticeably featured. These and other featured metabolisms may influence the pH microenvironment and, consequently, the formation, weathering, and re-deposition of silicate speleothems.https://www.mdpi.com/2076-2607/10/7/1395Guiana Highlandsopal-Abacterial diversityOTUmicrobiome |
| spellingShingle | Qi Liu Zichen He Takeshi Naganuma Ryosuke Nakai Luz María Rodríguez Rafael Carreño Franco Urbani Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui Microorganisms Guiana Highlands opal-A bacterial diversity OTU microbiome |
| title | Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui |
| title_full | Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui |
| title_fullStr | Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui |
| title_full_unstemmed | Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui |
| title_short | Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui |
| title_sort | phylotypic diversity of bacteria associated with speleothems of a silicate cave in a guiana shield tepui |
| topic | Guiana Highlands opal-A bacterial diversity OTU microbiome |
| url | https://www.mdpi.com/2076-2607/10/7/1395 |
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