Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

• 成果类型: Article
• 署名作者: 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
• 署名单位: Northwest A&F University - China; Northwest A&F University - China; Northwest A&F University - China; Michigan State University; University of Bristol; Iowa State University; University of Iowa; Northwest A&F University - China; Chinese Academy of Sciences; Institute of Soil & Water Conservation (ISWC), CAS; Northwest A&F University - China
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11984
• DOI: 10.1073/pnas.2424463122
• 发表日期: 2025-03-25
• 关键词: genome size; alignment; bacteria; tool; subsurface; algorithm; GROWTH; MODEL

摘要

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.