Investigations into soil microbiome stability in the face of agriculture and climate change related perturbations

Abstract

Soils and the vital ecosystem services performed by their indigenous microbiota are under increasing pressure from anthropogenic stresses and climate change. In an effort to understand how the provision of soil ecosystem services will evolve with such pressures, significant research has been undertaken into the stability of microbial community functioning and composition, in terms of resistance and resilience. The overall aim of this thesis was to contribute to such knowledge through investigation of the responses of soil microbial communities subjected to a variety of perturbations relevant in the context of agriculture and climate change. These include lime addition, slurry application and flooding, which were chosen to include representative disturbances commonly encountered by agrarian soil ecosystems. As metaproteomics represents a valuable tool for linking microbial phylogeny and function, the first step was to develop a method allowing for the co-extraction of DNA, RNA and proteins from soil samples. We then employed culture-independent techniques to investigate the microbial community composition in the face of the three perturbations. In addition, we assessed the functioning of the microbial communities by assessing rates of litter decomposition, potential nitrification and potential denitrification. While the lime product did not perform as hoped in terms of pH alteration, microbial communities responded strongly to the development of the barley plants with which they were associated. Slurry induced significant functional and compositional alterations in the microbial assemblage; while some functions were transiently affected, others remained altered 140 days post-application. While the soil microbiome was sensitive to flooding, it appeared remarkably resilient in terms of functioning. When the flooding perturbation was compounded by a preceding slurry application, improvements in resistance were seen in functional assays. In closing, a co-extraction method was developed which is easily employed for a number of sample types including soil. Additionally, we addressed certain hypotheses regarding microbial community stability while contributing to advancing knowledge in the field.