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甲烷营养型 ANME-1 古菌的进化多样性及其广泛的病毒组。

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.

机构信息

MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany.

Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.

出版信息

Nat Microbiol. 2023 Feb;8(2):231-245. doi: 10.1038/s41564-022-01297-4. Epub 2023 Jan 19.

DOI:10.1038/s41564-022-01297-4
PMID:36658397
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9894754/
Abstract

'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.

摘要

“甲烷八叠球菌目”（ANME-1）是负责深海沉积物中厌氧甲烷氧化的一个具有分类学级别的古菌目。ANME-1 的多样性、生态和进化仍然知之甚少。在这项研究中，我们使用深海热液样本的宏基因组学来扩展 ANME-1 的多样性，并揭示病毒-宿主动态的影响。系统发育分析揭示了一个深分支、嗜热的家族，“甲烷热螺旋菌科”，与短链烷烃氧化菌密切相关。全球系统发育和近乎完整的基因组表明，ANME-1 内的产氢代谢是一种古老的特征，它是垂直遗传的，但在谱系多样化过程中不同程度地丢失了。宏基因组学还揭示了迄今为止仅针对 ANME-1 古菌的 16 种未描述的病毒科，这些病毒科具有独特的结构和复制特征。广阔的 ANME-1 病毒组包含一个代谢基因库，通过病毒介导的基因置换，这些基因可以影响宿主的生态和进化。我们的研究结果表明，厌氧甲烷和短链烷烃氧化菌之间存在一个连续的进化过程，并强调了病毒对甲烷驱动的生态系统动态和进化的影响。

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