Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics

Malik, Ashish A.; Thomson, Bruce C.; Whiteley, Andrew S.; Bailey, Mark; Griffiths, Robert I. ORCID: https://orcid.org/0000-0002-3341-4547. 2017 Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics. mBio, 8 (4), e00799-17. 13, pp. https://doi.org/10.1128/mBio.00799-17

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Abstract/Summary

Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where “low-pH” is ~pH 4.3 and “high-pH” is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1128/mBio.00799-17
UKCEH and CEH Sections/Science Areas:	Acreman Directors, SCs
ISSN:	2150-7511
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper - full text available via Official URL link.
Additional Keywords:	ecophysiology, metagenomics, soil microbiology
NORA Subject Terms:	Agriculture and Soil Science Biology and Microbiology
Date made live:	06 Sep 2017 10:37 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/517729

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