Calderón-Osorno Melany, Rojas-Villalta Dorian, Lejzerowicz Franck, Cortés Jorge, Arias-Andres Maria, Rojas-Jimenez Keilor
Costa Rica National High Technology Center (CeNAT), Pavas, San José, 10108, Costa Rica.
Maestría académica en Biología con enfásis en genética y biología molecular, University of Costa Rica, San Pedro, San José, 11501-20260, Costa Rica.
Sci Rep. 2025 Jan 23;15(1):2959. doi: 10.1038/s41598-025-86098-5.
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.
质粒在促进基因交换和增强微生物群落适应性方面发挥着关键作用。尽管它们很重要，但环境质粒仍未得到充分研究，特别是那些存在于深海等脆弱且未被充分探索的生态系统中的质粒。在本文中，我们实施了一个生物信息学流程，以研究来自“塔拉号”和“马勒斯皮纳号”探险队的81个深海宏基因组中质粒群落（质粒组）的组成、多样性和功能属性，这些宏基因组样本采集自太平洋、大西洋和印度洋，深度范围为270至4005米。我们观察到深度与质粒特征之间存在关联，270 - 1000米范围（中层带样本）的质粒数量最多，质粒大小也最大。α-变形菌纲和γ-变形菌纲的质粒在各大洋中占主导地位，特别是在这个深度范围内，这里还展现出最高的物种多样性和代谢途径丰度，包括芳香化合物降解。令人惊讶的是，在深海生态系统中发现的抗生素抗性基因相对较少，大多数存在于中层带。这些包括β-内酰胺酶、抗杀菌剂和氨基糖苷类等类别。我们的研究还确定MOBP和MOBQ松弛酶家族在各个分类类别中普遍存在。这项研究强调了独立于染色体背景研究质粒组的重要性。我们对深海微生物生态学，尤其是其质粒组的了解有限，这就要求在采矿等人类活动中谨慎行事。此类活动可能会对这个基本上未被探索的生态系统产生不可预见的影响。
