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

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(12)

Published: March 18, 2025

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, the capabilities ecological roles these communities remain largely unknown. We observed widespread relatively abundant bacterial phylum (CSP1-3) in soils evaluated its phylogeny, ecology, metabolism, evolutionary history. Genome analysis indicated that members CSP1-3 were actively replicating situ widely involved carbon, nitrogen, sulfur cycles. identified potential adaptive traits for oligotrophic environments, including mixotrophic lifestyle, flexible energy metabolisms, conservation pathways. ancestor likely originated an aquatic environment, subsequently colonizing topsoil and, later, with major clades adapted to each distinct niches. transition into terrestrial environment was associated genome expansion, horizontal acquisition range genes carbohydrate metabolism one lineage, high-affinity terminal oxidases support microaerophilic lifestyle. Our results highlight ecology evolution microbes Critical Zone.

Language: Английский

The dynamic history of prokaryotic phyla: discovery, diversity and division

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2024, Volume and Issue: 74(9)

Published: Sept. 9, 2024

Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, concept phylum has evolved from a group sharing common phenotypes to organisms ancestry, with modern taxonomy based on phylogenetic classifications drawn macromolecular sequences. Phyla came as surprising latecomers formalities nomenclature in 2021. Since then names have been validly published for 46 phyla, replacing some established neologisms, prompting criticism debate within scientific community. Molecular barcoding enabled analysis microbial ecosystems without cultivation, leading identification candidate divisions (or phyla) diverse environments. The introduction metagenome-assembled genomes marked significant advance identifying classifying uncultured lumper–splitter dichotomy led disagreements, experts cautioning against pressure create profusion new phyla prominent databases adopting conservative stance. Candidatus designation widely used provide provisional status taxa, named under this convention now clearly surpassing those names. Genome Taxonomy Database (GTDB) offered stable, standardized normalized taxonomic ranks, which both lumping splitting pre-existing GTDB framework introduced unwieldy alphanumeric placeholder labels, recent publication over 100 user-friendly Latinate unnamed Most remain ‘known unknowns’, limited knowledge their genomic diversity, ecological roles, or Whether still reflect evolutionary partitions across life remains an area active debate. However, practical importance microbiome analyses, particularly clinical research. Despite potential diminishing returns discovery biodiversity, offer extensive research opportunities microbiologists foreseeable future.

Language: Английский