UC Berkeley

The exchange of metabolites among members of microbial communities enables the catabolism of complex substrates and supports the growth of auxotrophic microbes. Many microbes depend on other organisms in their environment for the biosynthesis of essential metabolites such as corrinoids. Corrinoids are cobalt-containing tetrapyrroles that function as cofactors for enzymes that facilitate carbon skeleton rearrangements, methyl group transfers, and reductive dehalogenation. Members of all three domains of life use corrinoid cofactors, yet the complete biosynthesis of corrinoids, which requires approximately 30 enzymatic steps, is performed only by a subset of prokaryotes. Bioinformatic analyses show that while 76% of bacterial genomes contain corrinoid-dependent enzymes, only 39% of these contain the complete corrinoid biosynthesis pathway. As such, corrinoid cross-feeding is crucial for functionally integrated microbial communities.

Corrinoids are identified by the structure of their lower axial ligand, which can be a benzimidazole, purine, or phenolic compound. Corrinoids with different lower ligands do not function equivalently as cofactors. Given the diversity of corrinoid structures, microbes that require exogenous corrinoids must have mechanisms to acquire the specific corrinoids that function as cofactors for their corrinoid-dependent enzymes. However, the variety of corrinoids that can serve as cofactors for any one organism, the means by which microbes acquire specific corrinoids, and the diversity of corrinoids present in microbial communities have not been well studied.

In the first chapter, I summarize the strategies employed by corrinoid-dependent bacteria for fulfilling their corrinoid requirements and provide background on corrinoid structure, function, and biosynthesis.

Chapter 2 details my work examining the range of corrinoids that function as cofactors for the organohalide-respiring bacterium Dehalococcoides mccartyi, which has an obligate requirement for exogenously supplied corrinoids. D. mccartyi plays an important role in the bioremediation of chlorinated solvents in the environment, a process that relies on corrinoid-dependent enzymes. Together with my collaborators Shan Yi, Yujie Men, and Lisa Alvarez-Cohen, I showed that D. mccartyi can only use specific corrinoids containing benzimidazole lower ligands, but is capable of remodeling other corrinoids by lower ligand replacement when provided a functional benzimidazole base.

While Chapter 2 focuses on corrinoid metabolism in D. mccartyi in pure culture, my experiments presented in Chapter 3 focus on examining corrinoid cross-feeding in microbial communities containing D. mccartyi. Using a liquid chromatography-tandem mass spectroscopy method developed with my collaborators, I identified the specific corrinoids and free lower ligands present in microbial communities containing D. mccartyi, examined the contributions of different phylogenetic groups to the community corrinoid profile, and provided evidence that D. mccartyi engages in corrinoid remodeling in its natural environment. These findings provide novel insights into the roles played by different phylogenetic groups in corrinoid production and corrinoid cross-feeding within microbial communities, and may also have implications for optimizing chlorinated solvent bioremediation.

As a parallel to my work on how corrinoid cross-feeding supports the growth of D. mccartyi in a microbial community, and the strategies that D. mccartyi uses to obtain functional corrinoid cofactors, in Chapter 4, I explore how the cross-feeding of tetrapyrrole precursors allows microbes with an incomplete corrinoid biosynthesis pathway to fulfill their corrinoid requirements. Using a comparative genomics analysis, I identified 39 bacteria that lack genes required for the production of the universal tetrapyrrole precursors including 5-aminolevulinic acid (ALA), the first steps required for corrinoid biosynthesis, despite having otherwise complete corrinoid biosynthesis pathways. I tested the ability of three putative ALA auxotrophs to scavenge ALA from the growth medium and showed that in the presence of ALA, all three were capable of corrinoid production. My work showed that all 39 tetrapyrrole precursor auxotrophs are animal host-associated, raising the question of whether host-produced tetrapyrrole precursors might be scavenged by corrinoid-producing members of the microbiota.

The results of the experiments presented in this work provide insights into the array of strategies that microorganisms employ in acquiring essential nutrients from the environment. Better understanding of corrinoid production, modification, and utilization in microbial communities will aid in the exploration of how nutrient exchange shapes these communities, and the ecological roles played by individual community members.