Testing the black queen hypothesis in communities of soil-living bacteria

从环境样本中对细菌的基因组进行测序通常会发现相应的菌株缺乏必需的生物合成基因。然而，已经失去了产生氨基酸、维生素甚至核苷酸等关键代谢物能力的细菌如何在已知含有极低浓度这些化合物的环境中生存？最近提出的黑皇后假说解释了这些突变体的出现和持久性，营养缺陷型细菌通过利用其他细菌细胞产生的代谢产物获得适应性益处。如果这是真的，这个过程应该促进多重营养缺陷型基因型的形成和细胞间代谢网络的建立，其中单个细胞的生存依赖于其他群落成员产生的代谢产物。为了验证这一想法，将使用先前建立的从27个不同土壤微生物群落中分离出的7,000种细菌。这些菌株的基因型（16 SrRNA）和表型（代谢营养缺陷型，运动性）的特点。利用这一宝贵的资源，本项目的主要目标是在土壤细菌群落中通过实验验证黑皇后假说。具体来说，我们的目标是确定生态和生理因素，管理的建立和功能的代谢交叉喂养的相互作用的营养缺陷型细菌基因型的社区内。此外，这一过程所产生的进化后果也将被揭开。通过在土壤微宇宙中进行精心控制的共培养实验，并结合对相互作用的聚生体的微观和化学分析，可以从经验上验证黑皇后假说的理论预测。这项工作的结果将为塑造天然微生物群落结构和功能的力量提供基本的新见解。

Sequencing the genomes of bacteria from environmental samples commonly reveals that the corresponding strains lack essential biosynthetic genes. However, how do bacteria, which have lost the ability to produce key metabolites such as amino acids, vitamins, or even nucleotides, survive in environments that are well known to contain very low concentrations of these compounds? The recently proposed black queen hypothesis explains the emergence and persistence of these mutants by adaptive benefits auxotrophic bacteria gain by utilizing metabolites that are produced by other bacterial cells. If true, this process should facilitate the formation of multiply auxotrophic genotypes and the establishment of intercellular metabolic networks, in which the survival of individual cells rests upon the metabolites that are produced by other community members. To test this idea, a previously established collection of 7,000 bacteria will be used that have been isolated from 27 different soil microbial communities. These strains have been genotypically (16SrRNA) and phenotypically (metabolic auxotrophies, motility) well characterized. Taking advantage of this valuable resource, the main goal of this project is to experimentally test the black queen hypothesis in communities of soil-dwelling bacteria. Specifically, we aim at identifying the ecological and physiological factors that govern the establishment and functioning of metabolic cross-feeding interactions within communities of auxotrophic bacterial genotypes. In addition, the evolutionary consequences resulting from this process will be unravelled. By combining carefully controlled coculture experiments in soil microcosms with microscopic and chemical analyses of the interacting consortia, theoretical predictions made by the black queen hypothesis can be empirically verified. The results of this work will provide fundamental new insights into the forces that shape the structure and functioning of natural microbial communities.