Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity

A - Papers appearing in refereed journals

Neal, A. L., Hughes, D. J., Clark, I. M., Jansson, J. K. and Hirsch, P. R. 2021. Microbiome Aggregated Traits and Assembly are More Sensitive to Soil Management than Diversity. mSystems. 6 (3), pp. e01056-20. https://doi.org/10.1128/mSystems.01056-20

AuthorsNeal, A. L., Hughes, D. J., Clark, I. M., Jansson, J. K. and Hirsch, P. R.
Abstract

How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic disturbance of the magnitude of organic carbon inputs with acute effects of physical disturbance by tillage. We show that because of the variety of ways it can be assessed, biodiversity – here based on microbial small subunit ribosomal RNA genes – does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with ribosomal RNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea and fungi do not share a common response to land management change and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately.

KeywordsSoil; Microbiome; Diversity; Community aggregated traits; Community assembly soil; Agriculture; Tillage
Year of Publication2021
JournalmSystems
Journal citation6 (3), pp. e01056-20
Digital Object Identifier (DOI)https://doi.org/10.1128/mSystems.01056-20
Web address (URL)https://doi.org/10.1128/mSystems.01056-20
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Natural Environment Research Council
Funder project or codeS2N - Soil to Nutrition - Work package 1 (WP1) - Optimising nutrient flows and pools in the soil-plant-biota system
The Rothamsted Long Term Experiments [2017-2022]
NE/N018125/1 LTS-M ASSIST
Publisher's version
Accepted author manuscript
Supplemental file
Output statusPublished
Publication dates
Online27 May 2021
Publication process dates
Accepted29 Jan 2021
PublisherAmerican Society for Microbiology
ISSN2379-5077

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