The influence of depth on the global deep-sea plasmidome
Abstract Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we impl...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-025-86098-5 |
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| author | Melany Calderón-Osorno Dorian Rojas-Villalta Franck Lejzerowicz Jorge Cortés Maria Arias-Andres Keilor Rojas-Jimenez |
| author_facet | Melany Calderón-Osorno Dorian Rojas-Villalta Franck Lejzerowicz Jorge Cortés Maria Arias-Andres Keilor Rojas-Jimenez |
| author_sort | Melany Calderón-Osorno |
| collection | DOAJ |
| description | Abstract Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270–1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea’s microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem. |
| format | Article |
| id | doaj-art-bf9ec2aeb749470692ba371f85fdf735 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-bf9ec2aeb749470692ba371f85fdf7352025-01-26T12:32:34ZengNature PortfolioScientific Reports2045-23222025-01-0115111110.1038/s41598-025-86098-5The influence of depth on the global deep-sea plasmidomeMelany Calderón-Osorno0Dorian Rojas-Villalta1Franck Lejzerowicz2Jorge Cortés3Maria Arias-Andres4Keilor Rojas-Jimenez5Costa Rica National High Technology Center (CeNAT)Costa Rica National High Technology Center (CeNAT)Section for Aquatic Biology and Toxicology, University of OsloCentro de Investigación en Ciencias del Mar y Limnología (CIMAR), University of Costa RicaCentral American Institute for Studies on Toxic Substances, Universidad NacionalBiology School, University of Costa RicaAbstract Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270–1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea’s microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.https://doi.org/10.1038/s41598-025-86098-5PlasmidsMetagenomicsDeep-seaGenetic exchangeAdaptive traits |
| spellingShingle | Melany Calderón-Osorno Dorian Rojas-Villalta Franck Lejzerowicz Jorge Cortés Maria Arias-Andres Keilor Rojas-Jimenez The influence of depth on the global deep-sea plasmidome Scientific Reports Plasmids Metagenomics Deep-sea Genetic exchange Adaptive traits |
| title | The influence of depth on the global deep-sea plasmidome |
| title_full | The influence of depth on the global deep-sea plasmidome |
| title_fullStr | The influence of depth on the global deep-sea plasmidome |
| title_full_unstemmed | The influence of depth on the global deep-sea plasmidome |
| title_short | The influence of depth on the global deep-sea plasmidome |
| title_sort | influence of depth on the global deep sea plasmidome |
| topic | Plasmids Metagenomics Deep-sea Genetic exchange Adaptive traits |
| url | https://doi.org/10.1038/s41598-025-86098-5 |
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