Feng Wenlu, Wan Xiaonan, Zhang Yiran, Quensen John, Williams Tom A, Thompson Michael, Streeter Matthew, Zhang Yang, Jiao Shuo, Wei Gehong, Zhu Yuanjun, Gu Jie, Tiedje James M, Qian Xun
Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Shaanxi 712100, China.
Department of Environmental Science, College of Natural Resources and Environment, Northwest A&F University, Shaanxi 712100, China.
Proc Natl Acad Sci U S A. 2025 Mar 25;122(12):e2424463122. doi: 10.1073/pnas.2424463122. Epub 2025 Mar 18.
The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.
深层地下土壤微生物群落包含大量尚未充分研究的系统发育多样性和代谢新奇性，这些群落的代谢能力和生态作用在很大程度上仍然未知。我们在深层土壤中观察到一个广泛且相对丰富的细菌门（CSP1 - 3），并评估了其系统发育、生态学、代谢和进化历史。基因组分析表明，CSP1 - 3的成员在原位积极复制，并广泛参与碳、氮和硫循环。我们确定了CSP1 - 3成员在贫营养深层土壤环境中的潜在适应特征，包括混合营养型生活方式、灵活的能量代谢和保守途径。CSP1 - 3的祖先可能起源于水生环境，随后定殖于表土，后来又定殖于深层土壤环境，主要的CSP1 - 3分支适应了这些不同的生态位。向陆地环境的转变与基因组扩张有关，包括水平获得一系列碳水化合物和能量代谢基因，并且在一个谱系中，获得了高亲和力末端氧化酶以支持微需氧生活方式。我们的结果突出了深层关键带中微生物的生态学和基因组进化。
