Identifying microbial indicators of land-use change and determining their relevance for soil ecosystem services

Armbruster, Melanie and Ostle, Nick and Griffiths, Robert (2021) Identifying microbial indicators of land-use change and determining their relevance for soil ecosystem services. PhD thesis, Lancaster Environment Centre.

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Abstract

Microbial communities drive many soil ecosystem services and are heavily influenced by land use change and intensive agriculture. In order to manage land sustainably, there is a need to close critical knowledge gaps as to how management affects multiple soil services and their resilience to future change, and the functional importance of microbial communities in this complex system. While local studies revealed responses of biodiversity to land use, there is a need to study the landscape scale and synthesise findings in order to predict different soil, land use and climatic contexts. In this thesis, microbial indicators were determined for contrasting land use types and their relation with organic matter recovery tested. At the large scale, this relationship was confirmed in a restoration chronosequence of calcareous grasslands, which was limited to high pH soils and revealed consistent responses of distinct bacterial and fungal taxa (verrucomicrobial DA101 and Ca. Xiphinematobacter and alpha-Proteobacteria in low intensity, vs. ammonia-oxidising archaea and bacteria in cropland). These indicator taxa were confirmed in a mesocosm experiment, in which contrasting soil communities were transferred to a degraded long term bare fallow soil and their relative contribution to C related soil functions assessed across a pH gradient. While pH significantly changed extracellular enzyme activities, respiration and OM contents, all tested soil functions were independent of land use of the applied bacterial community, pointing us to a non-linear relationship between bacterial diversity and ecosystem functionality. In contrast, a survey of Conservation Agriculture field experiments which covered reduced tillage, cover cropping and manure application in 14 different farm systems, did not confirm the indicative meaning of these organisms and the effect of Site was stronger than any management change. Nevertheless, I found distinct communities depending on management intensity, with tillage having stronger implications than cover cropping or the addition of organic amendments. In synthesis, soil microbial communities were mainly driven by pH and site-dependent factors, but there were consistent indicators of recovered organic matter stocks and C related functions in high pH systems. Farming intensity simultaneously affected soil C contents and prokaryote and eukaryote communities, with an associated change in soil pH. Restoration of degraded soil functions which are related to carbon cycling via application or manipulation of distinct microbial communities is thus clearly pH-dependent and has to consider individual site-related factors. Further investigations considering other soil (pH) systems and managements are hence needed to confirm specific indicators and their relative contribution to soil health. With the help of modern soil functional assays as well as new isotopic, metagenomic and transcriptomic tools, new insights into the functional capacity of soils and their microbiomes will shed light on their resistance-resilience to land use and climate change.