Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales

We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-IMRE50, which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-IMRE50 CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-IMRE50, further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.本研究报道了一株嗜温氢营养型产甲烷菌沼泽甲烷囊菌（Methanocella paludicola）的完整基因组序列，该菌株是甲烷囊菌目（Methanocellales）首次获得纯培养的代表菌株，而该目此前被认为是稻田甲烷排放中未培养的关键古菌类群。沼泽甲烷囊菌的基因组由一条长度为2957635 bp的环状单染色体组成，共包含3004个蛋白质编码序列（CDS）。研究鉴定出了产甲烷古菌已知多数功能相关的基因，例如完整的氢化酶组与产甲烷酶系。通过基因组特征分析明确了沼泽甲烷囊菌的混合营养生长特性，并通过后续的生长实验对该特性进行了验证。通过与此前报道的宏基因组重建菌株RC-IMRE50的基因组序列进行比较基因组分析，结果显示沼泽甲烷囊菌约70%的蛋白质编码序列与RC-IMRE50的蛋白质编码序列具有遗传相关性。这些具有相关性的蛋白质编码序列涵盖了氢营养型甲烷生成、不完全三羧酸（TCA）循环、同化性硫酸盐还原等相关基因。不过，两株甲烷囊菌目菌株的碳固定、固氮以及抗氧化系统相关的遗传组分存在差异。该差异可能与沼泽甲烷囊菌与RC-IMRE50之间的生理特性差异相关，进一步印证了甲烷囊菌目产甲烷菌的基因组与生理多样性。通过与此前已解析的产甲烷菌基因组进行比较基因组分析，结果表明从遗传组成来看，甲烷囊菌目产甲烷菌与甲烷八叠球菌目（Methanosarcinales）和甲烷微菌目（Methanomicrobiales）产甲烷菌具有全基因组水平的亲缘关系。同时，通过跨产甲烷菌物种的比较基因组分析，也从一个维度揭示了甲烷囊菌目产甲烷菌独特的进化历程。