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

从环境样本中对细菌基因组进行测序，通常会发现相应菌株缺乏必要的生物合成基因。然而，细菌已经失去了产生氨基酸、维生素甚至核苷酸等关键代谢物的能力，它们是如何在已知这些化合物浓度极低的环境中生存的呢？最近提出的黑皇后假说解释了这些突变体的出现和持续存在，因为营养不良细菌通过利用其他细菌细胞产生的代谢物获得适应性利益。如果这是真的，这一过程将促进多种营养不良基因型的形成和细胞间代谢网络的建立，在这种网络中，单个细胞的存活依赖于其他群落成员产生的代谢物。为了验证这一想法，将使用先前建立的从27个不同的土壤微生物群落中分离出来的7000个细菌。这些菌株具有良好的基因特征（16SrRNA）和表型特征（代谢缺陷，运动性）。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实验测试黑色女王假说。具体来说，我们的目标是确定控制营养不良细菌基因型群落中代谢交叉摄食相互作用的建立和功能的生态和生理因素。此外，这一过程所产生的进化后果将被揭示。通过将土壤微观环境中精心控制的共培养实验与相互作用群体的微观和化学分析相结合，黑皇后假说的理论预测可以得到经验验证。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.