Principles of microbiome structure and their implications for climate change mitigation
Embargo Date
2027-03-19
OA Version
Citation
Abstract
Microorganisms assemble into diverse communities of various ecological structures across virtually all of Earth’s environments, where they drive biogeochemical processes that range from microscopic to climatic scales. While most studies of these communities, or microbiomes, have been traditionally focused on demographic surveys of what microbes reside where, there is increasing interest in gaining a more systematic perspective and identifying general principles that govern microbiome structure, i.e. the way in which the resident taxa or the functions enacted by those taxa are organized within a community. Uncovering these principles could enable unprecedented control over the ecological structure of microbiomes as well as their surrounding environments, paving the way to microbiome engineering. In this dissertation, I first reviewed the legacy of prior attempts at employing environmental microbiome engineering towards sustainability and climate change mitigation, including proposed approaches for overcoming outstanding challenges to its implementation. A promising approach consists of using directed evolution to design microbial communities as inocula to boost the carbon stabilization capacity of soils. Importantly, this avenue would require further research into the principles that govern the establishment of new microbial communities into existing ecosystems. Second, I used experimental and computational approaches to specifically address this last aspect of microbiome engineering, focusing on the question of whether different microbiomes states are, in principle, possible under a given environment. This study uncovered a novel principle of microbiome structure: that environmental metabolic complexity drives the taxonomic divergence of microbial communities, or how taxa differ between communities. This suggests that complex environments may be more susceptible to microbiome engineering since these environments can host a larger diversity of types of microbial communities, which may include communities with higher capacity than the resident one to perform climate change mitigating activities, for example. Finally, I expanded the previous analysis to explore how taxonomic divergence relates to functional divergence — an essential step to ensure that communities displaying distinct taxonomic composition in a given environment do not always converge to identical functions, which would reduce the impact of the engineering effort. To address this question, I developed a novel metric called functional response to understand what environments can host communities that vary in function. I then measured the functional response of microbial communities in natural microbial communities from an existing dataset and in synthetic communities from a newly generated dataset. Ultimately, these projects contribute to growing efforts to understand microbiome structure and inform engineering efforts to overcome challenges in microbially-regulated systems, such as with human disease and climate change.
Description
2025
License
Attribution 4.0 International