Gaboyer Frédéric, Burgaud Gaëtan, Alain Karine
CNRS, Centre de Biophysique Moléculaire, Imagerie Spectroscopie et Chimie du Vivant rue Charles Sadron Orléans, FR 45071 Cedex2, France.
Université de Brest, UEB, Laboratoire Universitaire de Biodiversité et d'Écologie Microbienne EA 3882n IFR 148 SFR ScInBioS, ESIAB, Plouzané, France.
FEMS Microbiol Ecol. 2015 May;91(5). doi: 10.1093/femsec/fiv029. Epub 2015 Mar 19.
Subseafloor sediments represent a large reservoir of organic matter and are inhabited by microbial groups of the three domains of life. Besides impacting the planetary geochemical cycles, the subsurface biosphere remains poorly understood, notably questions related to possible metabolic pathways and selective advantages that may be deployed by buried microorganisms (sporulation, response to stress, dormancy). In order to better understand physiological potentials and possible lifestyles of subseafloor microbial communities, we analyzed two metagenomes from subseafloor sediments collected at 31 mbsf (meters below the sea floor) and 136 mbsf in the Canterbury Basin. Metagenomic phylogenetic and functional diversities were very similar. Phylogenetic diversity was mostly represented by Chloroflexi, Firmicutes and Proteobacteria for Bacteria and by Thaumarchaeota and Euryarchaeota for Archaea. Predicted anaerobic metabolisms encompassed fermentation, methanogenesis and utilization of fatty acids, aromatic and halogenated substrates. Potential processes that may confer selective advantages for subsurface microorganisms included sporulation, detoxication equipment or osmolyte accumulation. Annotation of genomic fragments described the metabolic versatility of Chloroflexi, Miscellaneous Crenarchaeotic Group and Euryarchaeota and showed frequent recombination events within subsurface taxa. This study confirmed that the subseafloor habitat is unique compared to other habitats at the (meta)-genomic level and described physiological potential of still uncultured groups.
海底以下沉积物是大量有机物质的储存库，并且生活着生命三域的微生物群体。除了影响全球地球化学循环外，地下生物圈仍然知之甚少，尤其是与埋藏微生物可能采用的代谢途径和选择优势（孢子形成、应激反应、休眠）相关的问题。为了更好地了解海底以下微生物群落的生理潜力和可能的生活方式，我们分析了来自坎特伯雷盆地海底以下31米（海底以下米数）和136米沉积物的两个宏基因组。宏基因组的系统发育和功能多样性非常相似。细菌的系统发育多样性主要由绿弯菌门、厚壁菌门和变形菌门代表，古菌的系统发育多样性主要由奇古菌门和广古菌门代表。预测的厌氧代谢包括发酵、甲烷生成以及脂肪酸、芳香族和卤化底物的利用。可能赋予地下微生物选择优势的潜在过程包括孢子形成、解毒机制或渗透溶质积累。基因组片段的注释描述了绿弯菌门、杂项泉古菌组和广古菌门的代谢多功能性，并显示了地下类群内频繁的重组事件。这项研究证实，在（宏）基因组水平上，海底以下栖息地与其他栖息地相比是独特的，并描述了仍未培养的类群的生理潜力。
