Collaborative Research: MIM: Defining the rules governing microbiome interactions critical for providing key ecosystem functions using a model diazotroph community

Single-celled microbes are the unseen engines that drive most ecosystems on planet Earth. While there is growing appreciation that non-random microbial associations can provide a collective advantage to individual cells, our understanding of the origins, function and maintenance of these interactions is limited. To address this knowledge gap, the project team proposes to use the environmentally important, colony-forming cyanobacterium Trichodesmium and its associated microbiome as a model system to define the rules that allow this microbial association to exist consistently and thrive throughout the global oceans.

The research team will quantify the interactions governing the microbiome by integrating state-of-the-art techniques from multiple disciplines. This work will develop a pipeline for identifying microbial interactions and exchanges that are critical for microbiome stability and function that can be applied to other systems in the biological and geological sciences.

As Trichodesmium is a keystone source of nitrogen to the ocean, data from this project will be essential for predicting oceanic primary production and providing a lab-tested framework for investigating the rules that govern microbiome interactions more generally. In addition to these discipline-level broader impacts, this work will train multiple Ph.D. and undergraduate students at both institutions and develop a new course designed to increase underrepresented group involvement in microbiome research.

The new undergraduate course, METAgenomic Global Environmental Microbiology (META-GEM), will integrate data from the project and include microbiology training, bioinformatics workshops, mentoring from all project faculty and a student-centric, three-day weekend symposium at the Wrigley Marine Sciences Center on Catalina Island. Involved students will gain firsthand research experience and will make lasting connections with developing and seasoned scientists.

This project aims to translate ocean wide Trichodesmium and specific bacterial taxa co-occurrence data into defined facultative microbial interactions in this globally important community. Because there is evidence that Trichodesmium selects its microbiome by excreting specific metabolites, the goal of defining relationships is tractable, timely, and transformative for general understanding of microbial interactions in natural communities.

Recent metagenomic work on trans-Atlantic Trichodesmium colonies has shown that the Trichodesmium microbiome consists of a non-random, distinct group of mostly Alphaproteobacteria and Bacteroidia with a biologically novel clade of the former consistently co-occurring. Herein the research team will apply holistic ‘omic approaches, machine learning algorithms, high-throughput culturing techniques, and numerical models to natural microbiomes and to USC Trichodesmium Culture Collection strains in axenic and mixed laboratory experiments to test three hypotheses.

Specifically, the team hypothesizes that biotic interactions influence Trichodesmium by: (i) increasing fitness through the coevolution of a non-random, partially dissociable epibiotic community that allows ‘division of labor’; (ii) enhancing nitrogen and carbon recycling within the community and thus altering nitrogen and carbon fluxes to the broader ecosystem; and (iii) stabilizing the community such that niche-overlapping opportunists are kept ‘in check’ - however, this stabilizing effect can be disrupted upon environmental change.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.