通过单培养基生长和上清液检测预测细菌相互作用结果

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae045
Désirée A Schmitz, Tobias Wechsler, Ingrid Mignot, Rolf Kümmerli
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引用次数: 0

摘要

如何得出群落动态和稳定性的原理是微生物生态学的一个核心问题。自下而上的实验,即混合少量细菌物种的实验,已成为解决这一问题的流行方法。然而,由于共培养实验耗费大量人力,而且物种难以区分,因此实验设置通常受到限制。在这里,我们利用一个四种细菌群落来证明,单培养生长信息和分泌化合物诱导的抑制效应信息可以结合起来预测群落中的竞争等级顺序。具体来说,综合单培养生长参数可以建立初步的竞争排序,然后利用上清液检测的抑制效应对排序进行调整。虽然我们的程序适用于两种不同的培养基,但我们观察到不同培养基的物种排列顺序存在差异。然后,我们利用经验数据对计算机模拟进行了参数化,结果表明,高阶物种相互作用在很大程度上遵循了配对相互作用的动态预测,但有一个重要的例外。在高阶群落中,抑制性化合物的影响减弱了,因为它们的负面影响分散到了多个目标物种上。总之,我们制定了三条简单的规则,说明如何结合单培养生长数据和上清液检测数据来确定实验性四物种群落中的竞争性物种等级顺序。
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Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.

How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.

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