Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation.

Abstract

Microbially induced calcium carbonate precipitation (MICP) holds potential for soil stabilization and carbon sequestration efforts, with the overall efficiency of the process being a major determinant for its use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such processes remain poorly characterized. To address this gap, we interrogated a MICP-capable four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Bacillus toyonensis and a Microbacterium species), termed carbon storing consortium - A (CSC-A). Prior work shows that CSC-A yields carbonate at a higher quantity compared to the sum of carbonate individually produced by each member, suggesting MICP is driven by community dynamics. To that end we applied a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of specialization by B. toyonensis and Microbacterium, while metatranscriptomic perturbation was almost ten times greater in the absence of R. qinshengii than C.flaccumfaciens, suggesting that R. qingshengii is a keystone species when grown in urea, a molecule key to the MICP process. By comparing individual species' metabolomes to the metabolic profile of a shared well, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types and mapping them to the KEGG reactome highlighted over 20 different enriched pathways with reactions related to glutamate metabolism, succinate metabolism, and branched chain amino acid biosynthesis. As succinate metabolism was a major node in this network we applied laboratory assays to confirm that additional added succinate led to increased carbonate precipitation by CSC-A, a critical validation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortium to carbonate precipitation.