Soil properties in agricultural systems affect microbial genomic traits

Goodall, Tim ORCID: https://orcid.org/0000-0002-1526-4071; Busi, Susheel Bhanu ORCID: https://orcid.org/0000-0001-7559-3400; Griffiths, Robert I.; Jones, Briony ORCID: https://orcid.org/0000-0003-4428-583X; Pywell, Richard F. ORCID: https://orcid.org/0000-0001-6431-9959; Richards, Andrew; Nowakowski, Marek; Read, Daniel S. ORCID: https://orcid.org/0000-0001-8546-5154. 2025 Soil properties in agricultural systems affect microbial genomic traits. FEMS Microbes, 6, xtaf008. 11, pp. 10.1093/femsmc/xtaf008

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Official URL: https://doi.org/10.1093/femsmc/xtaf008

Abstract/Summary

Understanding the relationships between bacteria, their ecological and genomic traits, and their environment is important to elucidate microbial community dynamics and their roles in ecosystem functioning. Here, we examined the relationships between soil properties and bacterial traits within highly managed agricultural soil systems subjected to arable crop rotations or management as permanent grass. We assessed the bacterial communities using metabarcoding and assigned each amplicon trait scores for rRNA copy number, genome size, and guanine-cytosine (GC) content, which are classically associated with potential growth rates and specialization. We also calculated the niche breadth trait of each amplicon as a measure of social ubiquity within the examined samples. Within this soil system, we demonstrated that pH was the primary driver of bacterial traits. The weighted mean trait scores of the samples revealed that bacterial communities associated with soils at lower pH (<7) tended to have larger genomes (potential plasticity), have more rRNA (higher growth rate potential), and are more ubiquitous (have less niche specialization) than the bacterial communities from higher pH soils. Our findings highlight not only the association between pH and bacterial community composition but also the importance of pH in driving community functionality by directly influencing genomic and niche traits.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1093/femsmc/xtaf008
UKCEH and CEH Sections/Science Areas:	Biodiversity and Land Use (2025-) Environmental Pressures and Responses (2025-)
ISSN:	2633-6685
Additional Information:	Open Access paper - full text available via Official URL link.
NORA Subject Terms:	Agriculture and Soil Science
Related URLs:	https://zenodo.org/records/13912858
Date made live:	08 Jul 2025 08:34 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/539799

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1093/femsmc/xtaf008

UKCEH and CEH Sections/Science Areas:

Biodiversity and Land Use (2025-)
Environmental Pressures and Responses (2025-)

ISSN:

2633-6685

Additional Information:

Open Access paper - full text available via Official URL link.

NORA Subject Terms:

Agriculture and Soil Science