Data from: Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments

Assays to accurately estimate relative fitness of bacteria growing in
multistrain communities can advance our understanding of how selection
shapes diversity within a lineage. Here, we present a variant of the
“evolve and resequence” approach both to estimate relative fitness and to
identify genetic variants responsible for fitness variation of symbiotic
bacteria in free-living and host environments. We demonstrate the utility
of this approach by characterizing selection by two plant hosts and in two
free-living environments (sterilized soil and liquid media) acting on
synthetic communities of the facultatively symbiotic bacterium Ensifer
meliloti. We find (i) selection that hosts exert on rhizobial communities
depends on competition among strains, (ii) selection is stronger inside
hosts than in either free-living environment, and (iii) a positive
host-dependent relationship between relative strain fitness in multistrain
communities and host benefits provided by strains in single-strain
experiments. The greatest changes in allele frequencies in response to
plant hosts are in genes associated with motility, regulation of nitrogen
fixation, and host/rhizobia signaling. The approach we present provides a
powerful complement to experimental evolution and forward genetic screens
for characterizing selection in bacterial populations, identifying gene
function, and surveying the functional importance of naturally occurring
genomic variation.

能够精准估算多菌株群落中生长细菌相对适应度的实验方法，可推动我们对选择如何塑造谱系内多样性的认知。本研究提出一种改良版的“进化重测序（evolve and resequence）”方法，可同时估算相对适应度，并识别自由生活与宿主环境中共生细菌适应度差异相关的遗传变异。我们以两种植物宿主、两种自由生活环境（灭菌土壤与液体培养基）为研究对象，作用于兼性共生细菌苜蓿根瘤菌（Ensifer meliloti）的人工合成群落，以此验证该方法的实用性。本研究发现：（1）宿主对根瘤菌群落施加的选择压力取决于菌株间的竞争；（2）宿主内部的选择强度高于任一自由生活环境；（3）多菌株群落中菌株相对适应度与单菌株实验中菌株为宿主带来的收益之间，存在依赖于宿主的正相关关系。在响应植物宿主的选择压力时，等位基因频率变化最显著的基因，主要与运动性、固氮调控以及宿主-根瘤菌信号通路相关。本研究提出的方法，可作为实验进化与正向遗传筛选的有力补充，用于表征细菌种群中的选择压力、鉴定基因功能，以及评估自然存在的基因组变异的功能重要性。