Hoffert Michael, Anderson Rika E, Reveillaud Julie, Murphy Leslie G, Stepanauskas Ramunas, Huber Julie A
Biology Department, Carleton College, Northfield, MN, United States.
Finch Therapeutics Group, Somerville, MA, United States.
Front Microbiol. 2021 Aug 20;12:714920. doi: 10.3389/fmicb.2021.714920. eCollection 2021.
Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
氢营养型产甲烷菌是普遍存在的化能自养古菌，栖息于全球分布的深海热液喷口生态系统以及岩石海底内相关的海底以下生态位，但对于它们如何在这些栖息地中适应和多样化却知之甚少。为了确定喷口处产甲烷菌种群内的基因组变异和选择压力，我们结合来自加勒比海开曼中脊两个地球化学特征不同的热液喷口区域的15个宏基因组和10个宏转录组，研究了5个单细胞扩增基因组（SAG）。我们观察到，在各个喷口位点，一些谱系及其转录本比其他谱系更为丰富，这表明谱系之间存在不同的适应性。每个样本中由SAG代表的谱系相对丰度与基于单拷贝通用基因的系统发育关系相匹配，与固氮和CRISPR/Cas免疫系统相关的基因是区分进化枝的基因之一。拥有这些基因的谱系比缺失该基因组区域的谱系丰度更低。总体而言，核苷酸变异模式表明，至少在本研究涵盖的栖息地和采样时间内，产甲烷菌的种群动态不受克隆扩张或选择性清除的控制。我们的研究结果共同表明，尽管特定的产甲烷菌谱系在这些栖息地中共存，但一些谱系比其他谱系更具竞争力，并且拥有辅助代谢功能并不一定在所有条件下都能在这些栖息地中提供适应性优势。这项工作突出了结合单细胞、宏基因组和宏转录组数据集来确定进化如何塑造热液喷口生态系统中微生物丰度和多样性的能力。
