Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.
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DOI：
10.1371/journal.pcbi.1004986
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发表时间：
2016-06
影响因子：
4.3
通讯作者：
Kost C
中科院分区：
文献类型：
--
作者：
Germerodt S;Bohl K;Lück A;Pande S;Schröter A;Kaleta C;Schuster S;Kost C
细菌群落在分类学上高度多样，但维持这种多样性的机制仍然知之甚少。我们假设，专性和相互交换的代谢产物，是非常常见的细菌细胞，可以稳定不同的基因型内的微生物群落。为了测试这一点，我们开发了一种元胞自动机来模拟六种经验表征的基因型之间的相互作用，这些基因型在产生氨基酸的能力和倾向上不同。通过系统地改变内在的（即效益成本比）和外在的参数（即代谢物扩散水平，环境氨基酸的可用性），我们表明，专性交叉喂养的必需代谢物是在广泛的条件下选择。在空间结构化的环境中，交叉饲养者之间的积极分类导致合作集群的形成，这限制了非生产营养缺陷型的利用，但允许它们在集群的外围持续存在。引人注目的是，交叉饲养有助于维持种群内的基因型多样性，而向环境补充氨基酸则可以消除专性相互作用，并有利于营养缺陷型细胞，从而比代谢自主的原养型细胞节省了氨基酸生产成本。总之，我们的研究结果表明，空间结构化的环境和有限的营养物质的可用性应该促进代谢相互作用的演变，这可以帮助保持天然微生物种群内的基因型多样性。天然细菌群落通常物种丰富，并且这些群落中的细菌细胞经常彼此交换代谢产物。然而，专性代谢相互作用是否以及在多大程度上有助于维持所观察到的细菌多样性尚不清楚。在这项研究中，我们通过计算来解决这个问题，通过模拟六种不同细菌菌株的种群，这些菌株在从环境中获得氨基酸的需求以及释放其他氨基酸的倾向方面有所不同。通过系统地改变关键变量，如代谢产物生产的成本，代谢产物在环境中扩散的速度，以及环境中的氨基酸可用性，我们表明，在广泛的生物现实条件下，必需氨基酸的合作交换是进化稳定的。特别是在空间结构的环境中，如细菌生物膜，以及代谢产物生产的适度成本有利于代谢相互作用。最后，我们的工作确定专性代谢相互作用作为一个强大的生态机制，以保持不同的细菌基因型与微生物群落。
Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio) and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability), we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters’ periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations. Natural bacterial communities are usually very species-rich and bacterial cells within these communities often exchange metabolites with each other. Whether and to which extent obligate metabolic interactions can contribute to maintaining the observed bacterial diversity, however, is not known. In this study, we address this question computationally, by simulating populations of six different bacterial strains that differ in their requirement to obtain amino acids from the environment as well as their propensity to release other amino acids. By systematically varying key variables such as the cost of metabolite production, the speed with which metabolites diffuse in the environment, as well as the amino acid availability in the environment, we show that a cooperative exchange of essential amino acids is evolutionary stable over a broad range of biologically realistic conditions. In particular spatially structured environments, such as bacterial biofilms, and moderate costs of metabolite production favored metabolic interactions. Finally, our work identifies obligate metabolic interactions as a powerful ecological mechanism to maintain different bacterial genotypes with microbial communities.