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Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Melina Kerou Rafael Ponce-Toledo Rui Zhao Sophie S. Abby 1 Miho Hirai Hidetaka Nomaki Yoshihiro Takaki Takuro Nunoura Steffen Jørgensen Christa Schleper
1 TIMC-TrEE - Translational microbial Evolution and Engineering
TIMC - Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525
Abstract : Abstract Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales , of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.
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Soumis le : mardi 5 octobre 2021 - 11:32:18
Dernière modification le : mardi 19 octobre 2021 - 11:06:02

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Melina Kerou, Rafael Ponce-Toledo, Rui Zhao, Sophie S. Abby, Miho Hirai, et al.. Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages. ISME Journal, Nature Publishing Group, 2021, 15 (9), pp.2792-2808. ⟨10.1038/s41396-021-00962-6⟩. ⟨hal-03365290⟩

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