Exploring how species interactions shape adaptive evolution in soil microbial communities

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Agricultural soil microbial communities provide vital ecosystem services such as providing nutrients to crops, protection against pathogens, breaking down toxic heavy metals and carbon storage. However, these communities are increasingly faced with harsh environmental conditions imposed by human activity - such as intensive use of pesticides, increased salinity from rising sea levels, and antibiotic run-off from pig farms. While experiments in vitro reveal that microbes can rapidly evolve resistance to such stressors, such studies are limited to a single species evolving in the presence of a single stressor in a highly artificial laboratory environment. In a complex natural community, however, evolutionary responses may be impeded because adapting to the presence of other competing species is more important than adapting to the environment. The ability of microbes to persist in the face of anthropogenic stress has clear consequences for maintaining ecosystem functions that rely on stable and efficient microbial communities. My proposed research will use real-time experimental evolution of soil microbial communities, to test if and how species interactions in complex soil microbial communities influence evolutionary responses to a stressful environment. I will focus on stressors highly relevant to agriculture: a broad-spectrum azole fungicide, antibiotic run-off from pig farms and increasing salinity and temperatures driven by climate change. Since environmental stressors are commonly encountered in combination, I will test the impact of these stressors individually and in combination.This research will be conducted at the Institute of Integrative Biology at the University of Liverpool, a member of the UK Russell Group with cutting-edge research in the fields of evolutionary biology, ecology and microbiology. State-of-the-art technologies such as 16s rRNA, internal transcribed spacer (ITS) metagenomics and whole genome sequencing will complement this research, supported by the Centre for Genomic Research at Liverpool. I will employ the MicroResp system to measure CO2 production by evolved microbes, thus highlighting the link between evolutionary adaptation and microbial ecosystem functioning (collaborating with Dr Emma Sayer, Lancaster University). My proposed research will yield insights into if and how evolutionary responses to agricultural stress occur in natural soil communities. Such questions are particularly relevant as we face challenges such as climate change and growing threats from agricultural pests, while simultaneously needing to feed over 9 billion people worldwide by 2050. This research will meet challenges associated with the BBSRC strategic priority 'Bioscience for sustainable agriculture and food', by gaining fundamental insights into the role of microbial evolutionary adaptation in an intense agricultural setting. Such fundamental understanding will inform future research that aims to harnass and manipulate microbial communties for efficient, environmentally friendly, food production. The need for fundamental, causal, microbiome research is highlighted by BBSRC prioritising Integrative Microbiome Research as a responsive mode priority in 2019.