Microbes as a reflection of their environment – what do we know and where do we go from here? 

Soil is home to an almost-unfathomable abundance and diversity of microbes which together recycle nutrients, change soil structure, and release carbon and nitrogen back into the atmosphere in the form of the greenhouse gases carbon dioxide and nitrous oxide, among other things. Each of these functions is the result of the intricate interplay between these organisms as well as their physical and chemical environment, which together define who is there, what they do, and how fast they do it. For instance, sometimes microbes cooperate with one-another, acting synergistically to complete processes faster or more fully than they could individually, while other times – or even at the same time – they compete with one another, negatively affecting the abundance and activity of the other. 

But how and why is this the case? How often do microbes evolve to complete steps in greenhouse gas producing and removing pathways which are complementary to those in other microbes? Under what soil conditions are bacteria most individually and collectively resource-efficient? And when and where are the petabytes of sequencing data the scientific community has generated actually useful for disentangling how soil microbes interact with one-another and their environment?

A principle challenge to addressing these questions is that microbe-environment-microbe interplay occurs at a much smaller spatiotemporal scales than those at which we measure and are interested in the processes resulting from them. This impedes identification of the specific organisms and interactions which matter for these processes. Furthermore, despite a recent boom in the diversity of soil bacteria we have isolated and grown in the lab and ever-expanding availability of sequencing data, our understanding of their physiology is patchy, with in-depth detail for a select few model organisms and no or only superficial data for the majority of dominant organisms. My research program aims to address these dual challenges by combining large-scale sequencing datasets – which provide a grand overview of ecophysiological drivers but miss fine-scale interactions and interventions to redirect soil nutrient cycling – with detailed bacterial isolate physiology which enables in-depth responses of individual organisms to environmental drivers but outside of their biotic and usually abiotic context.

In my lecture, I will expand upon the theory which underpins my research, providing examples from my recent work of how these challenges can be addressed towards the ultimate goal of linking bacterial ecology and physiology to soil processes.