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Microbial Genomics logo Microbial Genomics

Volume 11, Issue 1

An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Open Access

Abstract

Members of the phylum inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes , , and were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes and showed preferences to non-soil habitats. However, while specific preferences were observed, most lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of the . The observed lack of strong habitat specialization and habitat-transition-driven lineage evolution in the suggest ready cross-colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of as a major component in soil microbiomes post-ecosystem disturbance events or during pedogenesis.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acidobacteria , comparative genomics , metagenomics , niche colonization and soil
Funding
This study was supported by the:
  • National Institute of Health (Award 1P20GM152333-01)
    • Principal Award Recipient: MostafaS. Elshahed
  • National Science Foundation (Award 2016423)
    • Principal Award Recipient: NohaH Youssef
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-01-29
2026-04-16

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An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota
M Gen 11, 001344 (2025); https://doi.org/10.1099/mgen.0.001344
/content/journal/mgen/10.1099/mgen.0.001344
/content/journal/mgen/10.1099/mgen.0.001344
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