Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale
Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale
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DOI：
10.1111/1462-2920.14467
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发表时间：
2018-12-01
影响因子：
5.1
通讯作者：
Wrighton, Kelly C.
中科院分区：
文献类型：
--
作者：
Borton, Mikayla A.;Daly, Rebecca A.;Wrighton, Kelly C.
美国约60%的天然气产量来自非常规储层的水力压裂，如页岩或富含有机物的泥晶岩。随着时间的推移，这一过程为这些储层中的耐盐微生物接种并富集，从而形成一个含盐生态系统，其中包括产生甲烷的古细菌。在这里，我们调查了非常规储层中产甲烷菌的生物地理，并报告了通过宏基因组学采样从每个水力压裂的非常规储层中回收的嗜盐甲烷菌属成员。我们提供了三个分离基因组的首次基因组测序，以及两个宏基因组组装基因组（MAGs）。利用其他六个先前测序的分离基因组和mag，我们对代表该属的11个基因组进行了比较分析。这项基因组研究揭示了地表和地下衍生基因组之间的差异，这些差异与每种环境中遇到的限制是一致的。从同一井中恢复的分离基因组之间也发现了基因型差异，表明密切相关菌株之间存在生态位分配。这些基因组底物利用预测随后被生理调查证实。在嗜盐甲烷菌的CRISPR-Cas系统中观察到精细尺度的微多样性，来自不同地理位置的非常规储层的基因组共享针对相同病毒群体的间隔。这些发现对提高非常规水力压裂储层生物甲烷产量的增产策略具有重要意义。
About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.