PNNL

The Science

Researchers do not fully understand how microbial species in soil interact to drive important functions such as organic matter composition and persistence, plant growth promotion, or soil stabilization and biocementation. One process that can affect all these desired outcomes is the formation of the mineral calcium carbonate (CaCO₃) in soil. While scientists have a detailed understanding of how individual species form calcium carbonate, how communities of microbes interact to form this mineral is less clear. Because microbes exist in community settings in all ecosystems, understanding how these communities operate is key to driving new biotechnology solutions.  

To address this problem, Pacific Northwest National Laboratory (PNNL) researchers supported by the Predictive Phenomics Initiative developed a community of bacterial species isolated from field soil in California, referred to as CSC-A. One member of CSC-A, a Rhodococcus, produced the majority of the CaCO₃. However, other members also played significant roles in the overall CaCO₃ produced by CSC-A, even when initial genomic and phenotypic analysis of each individual species suggested otherwise. The amount of CaCO₃ produced was enhanced (>20 percent) when all species were cultivated together as one system. Loss of members, even those with no direct role in CaCO₃ production, led to a 30–50 percent reduction in CaCO₃. Fully mapping how interactions drive outcomes required taking a community-level view of the system through integrated multi-omics analysis.

The Impact

This work demonstrates that interactions within the community, as much as any single process expressed by an individual species, are critical to driving phenotypes of interest. These results also highlight the species in the community that likely have critical roles in the process, helping researchers harness the right members for an even more productive community. In addition to the knowledge outcomes, CSC-A will serve as a platform for future work aimed at understanding community interactions and processes. Researchers can dissect the interactions that drive calcium carbonate production and either apply the community to the soil as a probiotic or use the knowledge gained from analysis of CSC-A to target similar species in the native soil microbiome directly to boost a carbonate production phenotype. The knowledge gained and model communities built will help facilitate microbial solutions across the bioeconomy. This will also help researchers develop a holistic understanding of overall microbiome behavior and how such behavior is a combinatorial outcome of genome-encoded traits, interactions, and predictable phenotypic responses. The intermediate complexity of the CSC-A system (<10 species) and the wide ranging -omics and phenotypic data already collected in an AI-ready manner position this project to enable Department of Energy goals based on using AI to scale the biotechnology revolution.

Summary

Recently, there has been a focus on using soil microbes to form calcium carbonate minerals for a variety of bioeconomy relevant applications. While the specific molecular processes involved in calcium carbonate formation induced by microbes are known, there is still much to learn about how community interactions, emergent processes that are distinct from the roles of individual members, may drive the formation of carbonate. To answer these questions, PNNL researchers describe the development and application of a community of soil microbes (CSC-A). Growth assays show that only a subset of CSC-A members produce calcium carbonate with one member, Rhodococcus, producing the majority of the product. However, the complete CSC-A produces significantly higher amounts (>20 percent) of calcium carbonate compared to the sum total produced by each member species when cultivated individually, indicating that the microbial species are more productive when they work together. This discovery is important for future explorations of scientific questions about the molecular interactions surrounding carbonate mineral formation in soil and other processes of interest.

Contact

Ryan McClure, Ryan.McClure@pnnl.gov, Pacific Northwest National Laboratory

Funding

The research described in this paper is part of the Predictive Phenomics Initiative at PNNL and conducted under the Laboratory Directed Research and Development Program. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under Contract No. DE-AC05-76RL01830.