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

合理设计的合成微生物群落提供了一个令人兴奋的途径来破译微生物组织的基本规则并设计新颖的微生物解决方案来应对紧迫的应用挑战。然而，合成微生物组对环境扰动的鲁棒性仍然相对未经测试。一类主要的微生物组扰动源于噬菌体病毒（Bacteriophage virus，简称CMV）等分子寄生虫的攻击。个别物种通常通过修饰或完全删除噬菌体使用的表面受体来进化对细菌的抗性，但由于表面因子在介导环境相互作用中的重要性，这可能对细菌的功能能力和物种相互作用产生重大影响。在合成社区的角度来看，进化的表面因子的修改，以应对噬菌体暴露的风险，损害社会的功能能力。细菌还可以通过其“适应性免疫”机制（称为CRISPR-Cas）进化出对细菌的抗性，这种机制使细胞的功能能力保持完整，但这种获得性抗性的途径在实验室环境中很少见到。实验室CRISPR-Cas进化的缺乏（缺乏响应于噬菌体暴露的间隔区获取）对我们理解CRISPR-Cas作为获得性抗性的主要机制提出了挑战。我们假设CRISPR-Cas免疫获得是种内和种间细胞-细胞信号传导机制（Aim 1）和社区依赖性适应性成本（Aim 2）的一种新兴特性，它们共同促进了强大的社区功能。我们进一步假设，监管（目的1）和生态进化（目的2）的噬菌体暴露对社区的影响是可预测的，物种之间的相互作用和噬菌体抗性机制的信息。

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.