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Research Project: Enhancing Crop Resilience to Biotic and Abiotic Stress Through Understanding the Microbiome and Immune Signaling Mechanisms

Location: Plant Gene Expression Center

Title: Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Author
item ALVAREZ-APONTE, ZOILA - University Of California Berkeley
item GOVINDARAJU, ALEKHYA - University Of California Berkeley
item HALLBERG, ZACHARY - University Of California Berkeley
item NICOLAS, ALEXA - University Of California Berkeley
item GREEN, MYKA - University Of California Berkeley
item MOK, KENNY - University Of California Berkeley
item FONSECA-GARCIA, CITLALI - University Of California Berkeley
item Coleman-Derr, Devin
item BRODIE, EOIN - University Of California Berkeley
item CARLSON, HANS - Lawrence Berkeley National Laboratory
item TAGA, MICHIKO - University Of California Berkeley

Submitted to: Journal of the International Society for Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2024
Publication Date: 4/22/2024
Citation: Alvarez-Aponte, Z., Govindaraju, A., Hallberg, Z., Nicolas, A., Green, M., Mok, K.C., Fonseca-Garcia, C., Coleman-Derr, D.A., Brodie, E.L., Carlson, H.K., Taga, M.E. 2024. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. Journal of the International Society for Microbial Ecology. Article wrae068. https://doi.org/10.1093/ismejo/wrae068.
DOI: https://doi.org/10.1093/ismejo/wrae068

Interpretive Summary: Microbes in nature form ecological networks that are shaped by metabolic interactions. Interactions between bacteria can affect the community at many levels, and disruptions to certain interactions can greatly impact community structure and function. Thus, disentangling microbial interactions is crucial for generating a predictive understanding about how nutritional interactions can influence a community, and in turn the environment in which the community resides. Here, we focus on corrinoids (the vitamin B12 family of cofactors) as model shared nutrients to investigate ecological roles of bacteria that impact metabolic interactions. We evaluated corrinoid production and dependence phenotypes in representatives of the soil microbiota by building and characterizing a taxonomically diverse collection of 161 bacterial isolates. We found evidence of compatibility between corrinoid producers and dependent bacteria, and explore phylogenetic patterns amongst the distribution of these two classes of activity within the bacterial kingdom.

Technical Abstract: In this study, we took a reductionist approach to investigate nutrient production and dependence by focusing on corrinoids as a representative class of shared metabolites. We have extracted and purified four non-commercially available corrinoids to investigate the impact of corrinoid structure on bacterial growth and isolation from a California grassland soil. This soil community contains an abundance of predicted dependents (approximately 400 out of 500 analyzed metagenome-assembled genomes [MAGs]), with nearly all the remaining MAGs classified as producers. Consistent with these computational predictions, we found producers, dependents, and independents among our diverse collection of 161 bacterial isolates. Upon characterizing the corrinoid requirements of dependent isolates and corrinoid biosynthesis by producers, we found that the corrinoid synthesized by producers is compatible with the corrinoid requirements of all dependents in the collection. Further, corrinoids are released from cells in a subset of producers at levels that exceed the requirements of dependents in culture by up to 6,000-fold. These results provide an ecological framework for understanding nutritional interactions in soil through the lens of corrinoids.