Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics

• DOI: 10.1128/mbio.00799-17
• Publication Date: 2017-07-06T00:10:13Z
• Authors: Ashish A. Malik; Bruce C. Thomson; Andrew S. Whiteley; Mark Bailey; Robert I. Griffiths
• Keywords: Edaphic

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 eight geographically distributed soils at opposing ends a landscape gradient (where "low-pH" is ~pH 4.3 and "high-pH" 8.3) evaluated differences with respect functionally annotated genes. First, in diversity between the two categories were assessed alpha (mean sample richness) gamma (total richness pooled for each category). Low-pH soils, also exhibiting higher organic matter moisture, consistently had lower diversity, but this was not apparent assessments diversity. However, coherent changes relative abundances genes low- high-pH identified; strong multivariate clustering samples according independent geography. Assessment indicator revealed that acidic organic-rich possessed greater abundance cation efflux pumps, C N direct fixation systems, fermentation pathways, indicating adaptations both acidity anaerobiosis. Conversely, more transporter-mediated mechanisms substrate acquisition. These findings highlight distinctive physiological required bacteria survive various nutrient availability edaphic conditions generally indicate versatility gene annotations may be constrained by taxonomy.IMPORTANCE Over set spanning Britain, widely reported reductions low found accompanied significant consistent related observed, characteristic differential ecological acquisition strategies mineral low-pH anaerobic soils. Our assessment encapsulates limits temperate climates identifies key pathways serve as indicators element cycling storage processes other systems. end, make available data identifying different soils; well raw sequences, which given geographic scale our sampling should value future studies assessing novel genetic wide range attributes.