Beam Jacob P, Becraft Eric D, Brown Julia M, Schulz Frederik, Jarett Jessica K, Bezuidt Oliver, Poulton Nicole J, Clark Kayla, Dunfield Peter F, Ravin Nikolai V, Spear John R, Hedlund Brian P, Kormas Konstantinos A, Sievert Stefan M, Elshahed Mostafa S, Barton Hazel A, Stott Matthew B, Eisen Jonathan A, Moser Duane P, Onstott Tullis C, Woyke Tanja, Stepanauskas Ramunas
Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.
Department of Energy Joint Genome Institute, Berkeley, CA, United States.
Front Microbiol. 2020 Aug 17;11:1848. doi: 10.3389/fmicb.2020.01848. eCollection 2020.
Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell-cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
最近的发现表明，候选超群“Patescibacteria”和“DPANN”在细菌和古菌的系统发育多样性中占很大比例。据推测，它们的小基因组和有限的编码潜力是对专性共生生活方式的祖先适应性。为了验证这一假设，我们对来自全球46个分布于地表和地下的野外样本中的4829个细菌和古菌个体细胞进行了细胞间关联、基因组和系统发育分析。这证实了“Patescibacteria”和“DPANN”在地下环境中的普遍性和丰度、它们基因组和细胞的小尺寸，以及它们的基因内容与其他细菌和古菌的差异。我们的分析表明，在所研究的地下环境中，大多数“Patescibacteria”和“DPANN”不会与其他微生物形成特定的物理关联。这些数据还表明，它们不寻常的基因组特征和普遍的营养缺陷可能是缺乏呼吸作用的祖先最小细胞能量转导机制的结果，因此仅依靠发酵来保存能量。
