Landscape of the Metaplasmidome of Deep-Sea Hydrothermal Vents located at Arctic Mid-Ocean Ridges in the Norwegian-Greenland Sea - Ecological Insights from Comparative Analysis of Plasmid Identification Tools

IF 3.5 3区 生物学 Q2 MICROBIOLOGY FEMS microbiology ecology Pub Date : 2024-09-12 DOI:10.1093/femsec/fiae124
Karol Ciuchcinski, Runar Stokke, Ida Helene Steen, Lukasz Dziewit
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Abstract

Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools - PlasX, GeNomad and PLASMe – on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multi-approach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analyzing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin-antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.
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挪威-格陵兰海北极洋中脊深海热液喷口的元质粒群景观--从质粒鉴定工具的比较分析中获得生态学启示
质粒是微生物适应和进化的关键驱动力之一。然而,它们的多样性及其在适应过程中的作用,尤其是在极端环境中的作用,在很大程度上仍未得到探索。在这项研究中,我们旨在鉴定、描述和比较从北极洋中脊深海热液喷口采集的样本中的质粒序列。为此,我们在这一独特生态系统的元基因组数据中使用了最近开发的三种质粒鉴定工具--PlasX、GeNomad 和 PLASMe,并对其进行了基准测试。迄今为止,这是首次在极端环境数据背景下对这些计算方法进行直接比较。质粒等位基因恢复后,我们进行了多方法分析,重点是识别每种工具数据集中的分类和功能偏差。接下来,我们采用了一种多数投票系统来识别高可信度的质粒等位基因,从而提高了研究结果的可靠性。通过分析共识质粒序列,我们深入了解了它们的多样性、生态作用和适应意义。在高置信度序列中,我们发现了大量的假单胞菌和弯曲杆菌,以及多种毒素-抗毒素系统。我们的发现确保了对质粒如何帮助塑造生活在热液喷口极端条件下的微生物群落有更深入的了解,从而有可能发现新的适应机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
FEMS microbiology ecology
FEMS microbiology ecology 生物-微生物学
CiteScore
7.50
自引率
2.40%
发文量
132
审稿时长
3 months
期刊介绍: FEMS Microbiology Ecology aims to ensure efficient publication of high-quality papers that are original and provide a significant contribution to the understanding of microbial ecology. The journal contains Research Articles and MiniReviews on fundamental aspects of the ecology of microorganisms in natural soil, aquatic and atmospheric habitats, including extreme environments, and in artificial or managed environments. Research papers on pure cultures and in the areas of plant pathology and medical, food or veterinary microbiology will be published where they provide valuable generic information on microbial ecology. Papers can deal with culturable and non-culturable forms of any type of microorganism: bacteria, archaea, filamentous fungi, yeasts, protozoa, cyanobacteria, algae or viruses. In addition, the journal will publish Perspectives, Current Opinion and Controversy Articles, Commentaries and Letters to the Editor on topical issues in microbial ecology. - Application of ecological theory to microbial ecology - Interactions and signalling between microorganisms and with plants and animals - Interactions between microorganisms and their physicochemical enviornment - Microbial aspects of biogeochemical cycles and processes - Microbial community ecology - Phylogenetic and functional diversity of microbial communities - Evolutionary biology of microorganisms
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