Interactions between strains govern the eco-evolutionary dynamics of microbial communities.
Interactions between strains govern the eco-evolutionary dynamics of microbial communities.
复制标题
DOI：
10.7554/elife.74987
复制
发表时间：
2022-02-04
期刊：
影响因子：
7.7
通讯作者：
Cordero OX
中科院分区：
文献类型：
--
作者：
Goyal A;Bittleston LS;Leventhal GE;Lu L;Cordero OX
基因组数据显示，同一物种的基因型变体，即菌株，共存，并在天然微生物群落中丰富。然而，目前尚不清楚菌株是否在生态学上是等同的，以及在什么样的特征遗传距离下它们可能表现出不同的相互作用和动态。在这里，我们通过在实验室中追踪猪笼草中10种分类多样的微生物群落300多代来解决这个问题。使用宏基因组测序，我们重建他们的动态随着时间的推移和跨尺度，从遥远的门密切相关的基因型。我们发现，大多数菌株是不生态等效的，并表现出不同的动态模式，往往是显着更相关的菌株从另一个物种比自己的。虽然即使是一个单一的突变可以影响实验室菌株，平均而言，天然菌株通常在其动态解耦超过100个碱基对的遗传距离。使用数学消费者资源模型，我们表明，这些分类模式自然出现的社区成员之间的生态相互作用，但只有当相互作用是粗粒度的菌株，而不是物种的水平。最后，通过分析菌株之间的基因组差异，我们确定了主要的功能枢纽，如转运蛋白，调节剂和碳水化合物分解代谢酶，这可能是菌株特异性相互作用的基础。我们的工作表明，自然群落中的精细尺度遗传差异可以通过菌株之间生态相互作用的快速多样化来创造和稳定。
Genomic data has revealed that genotypic variants of the same species, that is, strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, and at what characteristic genetic distance they might exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 taxonomically diverse microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that most strains are not ecologically equivalent and exhibit distinct dynamical patterns, often being significantly more correlated with strains from another species than their own. Although even a single mutation can affect laboratory strains, on average, natural strains typically decouple in their dynamics beyond a genetic distance of 100 base pairs. Using mathematical consumer-resource models, we show that these taxonomic patterns emerge naturally from ecological interactions between community members, but only if the interactions are coarse-grained at the level of strains, not species. Finally, by analyzing genomic differences between strains, we identify major functional hubs such as transporters, regulators, and carbohydrate-catabolizing enzymes, which might be the basis for strain-specific interactions. Our work suggests that fine-scale genetic differences in natural communities could be created and stabilized via the rapid diversification of ecological interactions between strains.