Supp_Tab3 from Temporal patterns of local adaptation in soil Pseudomonads

Strong divergent selection leading to local adaptation is often invoked to explain the staggering diversity of bacteria in microbial ecosystems. However, examples of specialization by bacterial clones to alternative niches in nature are rare. Here, we investigate the extent of local adaptation in natural isolates of Pseudomonads and their relatives to their soil environments across both space and time. Though most isolates grew well in most environments, patchily distributed low-quality environments were found to drive specialization. In contrast with experimental evolution work on microbial adaptation, temporal adaptation was stronger than spatial adaptation among the isolates and environments we sampled. Time-shift analysis of fitness across two seasons of growth revealed an unexpectedly strong effect of preadaptation. This pattern of apparent future adaptation may be caused by unknown abiotic properties of these environments, phages, bacterial competitors or general mechanisms of ecological niche release, and warrants future study.

介导局部适应（local adaptation）的强烈歧化选择，常被用以阐释微生物生态系统中细菌的惊人多样性。然而，自然界中细菌克隆（bacterial clones）特化至不同生态位（alternative niches）的案例却极为稀少。本研究针对假单胞菌属（Pseudomonads）及其近缘类群的天然分离株，探究其在跨时空尺度下对土壤环境的局部适应程度。尽管多数分离株在多数环境中均可良好生长，但研究发现呈斑块状分布的低质量生境会推动特化进程。与微生物适应相关的实验进化（experimental evolution）研究结论不同，在所采样的分离株与环境类群中，时间尺度适应效应显著强于空间尺度适应效应。针对两季生长周期的适合度（fitness）开展时移分析（time-shift analysis），结果显示预适应（preadaptation）的作用强度远超预期。这种看似未来预适应的模式，可能由这些生境未知的非生物特性、噬菌体（phages）、细菌竞争者（bacterial competitors）或生态位释放（ecological niche release）的通用机制所引发，有待后续研究深入探索。