Exploring how species interactions shape adaptive evolution in soil microbial communities

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.

Understanding how microbial communities evolve and function is one of this century's greatest challenges. Microbial communities are highly diverse and complex, yet this same complexity makes it extremely challenging to understand how a community might respond and adapt to a changing environment. Experiments using simple 2-species communities have shown that species interactions can constrain evolutionary responses to the environment, yet we have little idea about how selection operates within communities in more realistic, natural settings.
A better understanding of microbial community function is of particular pertinence to agriculture, where soil microbial communities are increasingly faced with multiple harsh anthropogenic stressors such as intense pesticide application. I will use experimental evolution to test how species interactions in complex soil microbial communities shape evolutionary responses to multiple anthropogenic stressors: azole pesticides, fluoroquinolone antibiotics and increased salinity and temperatures driven by climate change.

Specific Objectives:
Obj. 1: Determine whether interactions with the microbial community shape the evolutionary response of P. fluorescens to anthropogenic agricultural stressors

Obj. 2: Understand how a multistressor environment influences P. fluorescens adaptation to a changing climate (increasing temperature), and how this is in turn shaped by species interactions with the natural community

Obj. 3: Show how the genetic response to selection in P. fluorescens varies with increasing multidimensionality of selection

I will complement real-time experimental evolution of microbial communities with state-of-the-art methods such as 16s rRNA, ITS metagenomics, whole genome sequencing and MicroResp. This research will yield causal, fundamental insights into microbial community dynamics, informing future research into harnassing microbial communties for efficient, environmentally friendly crop production.

I expect that the scientific outcomes from this research will have economic and societal benefits for a number of stakeholders related to agriculture, policy, academia, and members of the public. I will take a three-tiered approach towards dissemination: Dissemination for Awareness (communicating to those who I would like to be aware of my research), Dissemination for Understanding (communicating to those who will be directly affected by my research) and Dissemination for Action (communicating to those in a position to bring about change). A full research dissemination plan can be found in the Pathways to Impact attachment.

Dissemination for awareness (General public)

I anticipate that the general public will be interested in my research for two major reasons. Firstly, the public is beginning to realise the important role of microbial communities in our daily life, due to intense media coverage on topics such as the role of the microbiome in human health. Secondly, the public is becoming more aware of the threat of species extinction due to habitat loss driven in part by intensive agriculture (e.g. recent news coverage from the United Nations report showing that 1 million species could face extinction in the near future).

Results from this work could increase environmental awareness of the public and enable them to act as informed citizens. In particular, this work will reveal how intensive agricultural practices may be harmful for microbial community diversity (metagenomic sequencing in Obj. 1 and Obj. 2), as well as impede the ability of individual species to adapt to climate change (Phenotypic results from Obj 1. and Obj. 2). This may encourage the public to make more environmentally conscious food choices, e.g. buying organic produce.

Dissemination for Understanding (Academics)

Characterizing microbial communities in situ can yield interesting correlations between soil microbial communities and ecosystem function, but to explain these correlations requires an understanding of community ecology and evolution. Hence, it is at the interface of microbiology and eco-evolutionary research where scientific breakthroughs can be expected.

For example, new insights into how species interactions shape evolutionary trajectories will be of interest to evolutionary biologists (phenotypic data from Obj 1 and Obj 2). Microbiologists will be interested in causal experiments investigating how microbial community composition and diversity is shaped by anthropogenic stress (metagenomic data from Obj 1 and Obj 2). Molecular changes and horizontal gene transfer events identified in Obj. 3 will be relevant for molecular biologists. Results from this fellowship may also go on to inform future research into the development of novel diagnostics which rely on the repeatability of resistance mechanisms (Obj. 3).

Dissemination for Action (Policy makers, agricultural sectors, farmers)

Results generated by this research will be communicated to policy makers and those working in agricultural sectors who are in a position to bring about change. Our current intensive agricultural practices are depleting soil microbiome diversity, altering composition and reducing crop yield. Hence, novel ways of improving the health of our soils are required, especially given that we will need to feed over 9 billion people worldwide by 2050. Moreover, it is now clear that resistance is an evolutionary process, and a greater understanding of the evolutionary mechanisms involved in natural ecosystems can inform pesticide resistance risk assessment and management strategies. Beyond the life of this research, it is expected that the fundamental insights into microbial community dynamics will inform future research that aims to manipulate and harnass natural soil communities for efficient and environmentally friendly crop production.