Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
Nat Commun. 2020 Oct 30;11(1):5490. doi: 10.1038/s41467-020-19200-2.
Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.
嗜盐菌（以下简称 Haloarchaea）是主要的需氧嗜盐微生物，据认为它们是由厌氧产甲烷菌进化而来的。这种显著的转变极有可能涉及大量细菌基因的涌入。这是否涉及到一次大规模的转移事件还是逐渐的基因转移，目前仍存在争议。为了解决这个问题，需要研究来自产甲烷菌到嗜盐菌中间阶段的基因组。在这里，我们介绍了五种这样的海洋第四组古菌（Hikarchaeia）的近乎完整的基因组，它们是 Haloarchaea 最接近的已知亲属。将它们纳入基因树感知祖先重建中，揭示了一个已经失去大量基因的中间阶段，包括几乎所有与甲烷生成和伍德-吕恩达尔途径相关的基因。相比之下，最后一个 Haloarchaea 共同祖先获得了大量基因，并扩展了其需氧呼吸和耐盐/耐紫外线基因库。我们的研究结果表明，复杂和渐进的增益和损失模式塑造了产甲烷菌到嗜盐菌的转变。
