22-BBSRC/NSF-BIO: Community-dependent CRISPR-cas evolution and robust community function

Rationally designed synthetic microbial communities offer an exciting avenue to decipher basic rules of microbial organization and engineer novel microbial solutions to pressing applied challenges. Yet, the robustness of synthetic microbiomes to environmental perturbations remains relatively untested. A major class of microbiome perturbation stems from assault by molecular parasites such as bacteriophage viruses (phages).
Individual species commonly evolve resistance to phages by modifying or entirely deleting the surface receptor used by the phage, but this can have substantial impacts on the functional capacities and species interactions of the bacterium, due to the importance of surface factors in mediating environmental interactions. In a synthetic community perspective, evolved surface factor modifications in response to phage exposure risk damaging the functional capacities of the community. Bacteria can also evolve resistance to phages via their 'adaptive immunity' mechanism, known as CRISPR-Cas, which leave the functional capacity of the cell intact, yet this pathway of acquired resistance is rarely seen in a lab setting. The paucity of lab CRISPR-Cas evolution (lack of spacer acquisition in response to phage exposure) presents a challenge to our understanding of CRISPR-Cas as a primary mechanism of acquired resistance.
We hypothesize that CRISPR-Cas immunity acquisition is an emergent property of intra- and inter-specific cell-cell signaling mechanisms (Aim 1) and community-dependent fitness costs (Aim 2), which together promote robust community functioning. We further hypothesize that the regulatory (Aim 1) and eco-evolutionary (Aim 2) impacts of phage exposure on community performance are predictable, given information on species interactions and available mechanisms of phage resistance.

Rationally designed synthetic microbial communities offer an exciting avenue to decipher basic rules of microbial organization and engineer novel microbial solutions to pressing applied challenges. Yet, the robustness of synthetic microbiomes to environmental perturbations remains relatively untested. A major class of perturbation stems from assault by molecular parasites such as bacteriophage viruses (phages). Individual species commonly evolve resistance to phages by modifying or entirely deleting the surface receptor used by the phage, but this can have substantial impacts on the functional capacities and species interactions of the bacterium, due to the importance of surface factors in mediating environmental interactions. In a synthetic microbiome perspective, evolved surface factor modifications in response to phage exposure risk damaging the functional capacities of the community. Bacteria can also evolve resistance to phages via their 'adaptive immunity' mechanism, known as CRISPR-Cas, which leave the functional capacity of the cell intact, yet this pathway of acquired resistance is rarely seen in a lab setting. Accordingly, there is a critical need to determine the mechanisms promoting CRISPR-Cas adaptive immunity, in order to design robust synthetic microbiomes. In light of our pilot data, we hypothesize that CRISPR-Cas immunity acquisition is an emergent property of specific community features that promote robust community functioning. We hypothesize that phage exposure on community performance are predictable via mathematical modeling, given information on species interactions and available mechanisms of phage resistance.