Gilmore Sean P, Henske John K, Sexton Jessica A, Solomon Kevin V, Seppälä Susanna, Yoo Justin I, Huyett Lauren M, Pressman Abe, Cogan James Z, Kivenson Veronika, Peng Xuefeng, Tan YerPeng, Valentine David L, O'Malley Michelle A
Department of Chemical Engineering, University of California, Santa Barbara, California, USA.
Present Address: Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.
BMC Genomics. 2017 Aug 21;18(1):639. doi: 10.1186/s12864-017-4036-4.
The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications.
Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi.
Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO and formate are common electron carriers in microbial communities.
古菌产甲烷菌的代谢驱动甲烷释放到环境中，对于理解全球碳循环至关重要。与其他形式的呼吸作用相比，产甲烷作用在极低的还原电位下进行，因此对许多厌氧环境至关重要。利用或改变产甲烷菌的代谢有可能缓解全球变暖，甚至可用于能源应用。
在此，我们报告了分离出的产甲烷菌布氏甲烷杆菌、洞穴甲烷八叠球菌、兔甲烷球菌和微小甲烷微菌的基因组草图序列。这些厌氧产甲烷古菌代表了一组多样的分离株，能够进行甲基营养型、乙酸裂解型和氢营养型产甲烷作用。基因组的组装和分析使得能够简单快速地重建这四种产甲烷菌的代谢。将直系同源基因簇（COG）蛋白的分布与来自RefSeq数据库的基因组样本进行比较，揭示了所有测序产甲烷菌基因组组成中能量守恒的趋势。对预测的膜蛋白和转运蛋白的进一步分析区分了产甲烷过程中使用的不同能量守恒方法，例如洞穴甲烷八叠球菌中的化学渗透偶联以及布氏甲烷杆菌和兔甲烷球菌中与化学渗透偶联相关的电子歧化。
产甲烷菌占据独特的生态位，在厌氧环境中作为末端电子受体，其基因组显示出向能量守恒的显著转变。本文报道的基于基因组重建的代谢对多样的厌氧群落具有重要意义，并导致了此前未单独报道过的底物利用方式的提出，例如布氏甲烷杆菌中的甲酸和甲醇代谢以及兔甲烷球菌中的一氧化碳代谢。新提出的底物为解读产甲烷菌在自然群落中的行为奠定了重要基础，因为一氧化碳和甲酸是微生物群落中常见的电子载体。
