Isotope tools scaling soil microbial ecology to biogeochemistry

Microorganisms influence the composition of the atmosphere, the cycling of elements within and through ecosystems, the functioning of agricultural ecosystems on which humans depend, and human health. Microorganisms are also the most metabolically flexible and the most taxonomically and evolutionarily diverse organisms on Earth. Yet deciphering how that diversity imprints on the processes they influence at larger scales has proven challenging, because of the overwhelming complexity of microbial communities, and because of the difficulty of quantifying how microbial taxa assimilate and transform elements in the environment. New approaches that blend traditions from microbial ecology and ecosystem science make it possible to explore how the diversity and physiology of microorganisms shape ecosystem biogeochemistry and how it responds to global environmental change. Quantitative stable isotope probing has revealed cases where ‘omics data scales to quantitative ecology and biogeochemistry. Lab and field warming experiments in tropical, temperate, boreal, and arctic ecosystems point to generalized relationships between microbial growth rates (measured using isotope-enabled omics) and carbon release from soil through respiration (measured at the whole-system scale using classic techniques). Phylogenetic signals describe these relationships, indicating the potential for grounding biogeochemistry within the evolutionary histories of the organisms involved. In a meta-analysis across 27 independent experiments, quantitative stable isotope probing also indicates the general importance of predatory bacterial taxa in microbiomes, a role that increases in response to resource pulses, and which may provide a trophic theoretical underpinning to processes like the soil priming effect. More generally, such approaches hold potential for linking microbial diversity to carbon and element cycling in ecosystems. Historically, the diversity, complexity, and intractability of microbial ecosystems has relegated their study to either a reductionist descriptive tradition in microbial ecology or to a simplistically quantitative one in ecosystem science. Yet, new ideas and tools are poised to push microbial ecology forward to a point where it can more meaningfully integrate with ecological fields at larger scales, from populations to ecosystems to the globe.