Supp_Tab2 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.

驱动本地适应的强烈歧化选择，常被用以解释微生物生态系统中细菌的惊人多样性。然而，自然界中细菌克隆株特化至不同生态位的实例却极为少见。本研究旨在探究假单胞菌（Pseudomonads）及其近缘菌株的自然分离株，在跨时空尺度下对其生存土壤环境的本地适应程度。尽管多数分离株在多数环境中生长状况良好，但研究发现呈斑块状分布的低质量环境，会推动菌株发生特化。与微生物适应相关的实验进化研究不同，在本次采样的分离株与环境中，时间维度上的适应强度高于空间维度。对两个生长季的适合度进行时移分析后发现，预适应（preadaptation）的作用强度远超预期。这种看似未来适应的模式，可能由这些环境中未知的非生物特性、噬菌体（phages）、细菌竞争者，或是生态位释放（ecological niche release）的通用机制所导致，值得后续开展进一步研究。