ArticleProceedings of the National Academy of Sciences of the United States of America2025
Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- Microbial niches at the One Health interface: linking environmental factors, biomes, and disease dynamics.Frontiers in microbiology · 2026Review
- Microbial Evolution and Systematics: Archaea and Bacteria.Progress in molecular and subcellular biology · 2026Review
- Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Polyphasic taxonomy and genome mining ofCurrent research in microbial sciences · 2025Article
- Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.ISME communications · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
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