Chen Sheng-Chung, Weng Chieh-Yin, Lai Mei-Chin, Tamaki Hideyuki, Narihiro Takashi
Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
Mar Genomics. 2019 Oct;47:100673. doi: 10.1016/j.margen.2019.03.008. Epub 2019 Mar 30.
To date, the only methanoarchaea isolated directly from methane hydrate bearing sediments were Methanoculleus submarinus Nankai-1 and Methanoculleus sp. MH98A. Here, we provide the genome of Methanoculleus taiwanensis CYW4 isolated from the deep-sea subseafloor sediment at the Deformation Front offshore southwestern Taiwan, where methane hydrate deposits are likely located. Through comparative genomics analyses of nine Methanoculleus strains from various habitats, 2-3 coding genes for trehalose synthases were found in all nine Methanoculleus genomes, which were not detected in other methanogens and are therefore suggested as a signature of genus Methanoculleus among methane-producing archaea. In addition, the structural genes adjacent to trehalose synthase genes are comprised of the signaling module of Per-Arnt-Sim (PAS) domain-containing proteins, Hsp20 family proteins, arabinose efflux permeases and multiple surface proteins with fasciclin-like (FAS) repeat. This indicates that trehalose synthase gene clusters in Methanoculleus might play roles in the response to various stresses and regulate carbon storage and modification of surface proteins through accumulation of trehalose. The non-gas hydrate-associated Methanoculleus strains harbor carbon-monoxide dehydrogenase (cooS/acsA) genes, which are important for the conversion of acetate to methane at the step of CO oxidation/CO reduction in acetoclastic methanogens and further implies that these strains may be able to utilize CO for methanogenesis in their natural habitats. In addition, both genomes of M. bourgensis strains MS2 and MAB1 harbor highly abundant transposase genes, which may be disseminated from microbial communities in their habitats, sewage treatment plants and biogas reactors, which are breeding grounds for antibiotic resistance. Through comparative genomic analyses, we gained insight into understanding the life of strictly anaerobic methane-producing archaea in various habitats, especially in methane-based deep-sea ecosystems.
迄今为止，直接从含甲烷水合物沉积物中分离出的仅有的甲烷古菌是南海海底甲烷袋状菌（Methanoculleus submarinus）南开1号菌株和甲烷袋状菌属（Methanoculleus sp.）MH98A菌株。在此，我们提供了从台湾西南部近海变形前沿深海海底沉积物中分离出的台湾甲烷袋状菌（Methanoculleus taiwanensis）CYW4的基因组，该区域可能存在甲烷水合物矿床。通过对来自不同生境的9株甲烷袋状菌菌株进行比较基因组学分析，在所有9个甲烷袋状菌基因组中均发现了2 - 3个海藻糖合酶编码基因，而在其他产甲烷菌中未检测到这些基因，因此这些基因被认为是产甲烷古菌中甲烷袋状菌属的一个特征。此外，与海藻糖合酶基因相邻的结构基因由含Per-Arnt-Sim（PAS）结构域蛋白的信号模块、Hsp20家族蛋白、阿拉伯糖外排通透酶以及多个具有类成束蛋白（FAS）重复序列的表面蛋白组成。这表明甲烷袋状菌中的海藻糖合酶基因簇可能在应对各种胁迫中发挥作用，并通过海藻糖的积累来调节碳储存和表面蛋白的修饰。与天然气水合物无关的甲烷袋状菌菌株含有一氧化碳脱氢酶（cooS/acsA）基因，这对于乙酸裂解产甲烷菌在CO氧化/CO还原步骤中将乙酸转化为甲烷很重要，进一步表明这些菌株在其自然生境中可能能够利用CO进行甲烷生成。此外，布尔根甲烷袋状菌（M. bourgensis）菌株MS2和MAB1的基因组中都含有大量转座酶基因，这些基因可能从其生境、污水处理厂和沼气反应器中的微生物群落传播而来，而这些地方是抗生素抗性的滋生地。通过比较基因组学分析，我们深入了解了严格厌氧的产甲烷古菌在各种生境中的生活，尤其是在以甲烷为基础的深海生态系统中的生活。
