Evolutionary and ecological feedbacks across tripartite interactions in the rhizobial community

许多生物体参与共生;与另一个物种的亲密伙伴关系，可以对双方都有利。然而，这些关系并不是孤立发生的，而是嵌入在相互作用的物种网络中，这可以塑造共生伙伴关系的演变。固氮细菌（根瘤菌）和豆类（如豌豆和豆类）之间的关系可以说是共生关系中最重要的经济例子之一。根瘤菌从空气中吸收氮并将其转化为植物可以利用的形式。这是与植物交换，以换取养分和庇护所的专门器官称为根瘤。通过为植物提供氮供应，这些细菌有效地充当“生物肥料”，减少了对豆类以及与它们一起生长的非豆类作物施用昂贵且对环境有害的化肥的需求。然而，根瘤菌不仅与它们的植物宿主相互作用。当根瘤菌不生活在植物的根瘤中时，根瘤菌自由地生活在土壤中，与存在于土壤中的各种微生物群落相互作用。所有土壤微生物群落的关键成员是温带细菌，即感染细菌的病毒。这些病毒可以对其细菌宿主产生广泛和各种影响。一方面，它们可以是拮抗性的，杀死它们的宿主，以产生更多的病毒颗粒，继续感染新的细胞。然而，令人惊讶的是，这些病毒也可以是有益的。在感染细菌细胞时，它们往往不会繁殖以制造更多的病毒颗粒，而是将自己的DNA整合到细菌基因组中，使细菌能够获得新的基因，并有效地成为细菌可以用来对抗竞争对手的病毒武器。因此，根瘤菌与豆科植物宿主和温带植物之间存在两种重要的、截然不同的相互作用。这些独立的相互作用将对细菌种群施加不同的选择压力，因此可能对彼此产生重要影响。本项目将解开这种温带噬菌体-根瘤菌-豆科植物的关系，以了解这三方群落是如何形成的，以及如何被其组成成分的相互作用所形成的。本项目将联合收割机研究与自然和半自然群落的研究相结合，使用高度受控的实验室实验。实验室实验允许假设被直接测试，并且由于细菌中的世代的高更替，细菌-噬菌体协同进化被真实的时间观察到。同时，在“野外”或将自然群落带入实验室进行的实验展示了真实的群落是如何结构和行为的。结合这些方法提供了一个强大的方式来探索这些复杂的相互作用。这项工作将提供第一次全面检查的作用，温和的根瘤菌种群。随着全球粮食需求的增加，了解什么塑造了共生微生物（如根瘤菌）的生态和进化将变得越来越重要。因此，这项工作将为探索更广泛的微生物群落在这些过程中发挥什么作用奠定基础。这将导致未来的工作，研究我们如何将这些经验教训应用于可持续农业实践。例如，通过使用温带植物来提高生物肥料的有效性。

Many organisms engage in symbioses; intimate partnerships with another species that can be mutually beneficial to both partners. However, these relationships do not occur in isolation, but are embedded within a network of interacting species, which can shape the evolution of symbiotic partnerships. The relationship between nitrogen-fixing bacteria (rhizobia) and legumes (e.g. peas and beans) is arguably one of the most economically important examples of symbiosis. Rhizobia take nitrogen from the air and convert it into a form that plants can use. This is exchanged with the plant in return for nutrients and shelter in specialized organs called root nodules. By providing the plant with a supply of nitrogen these bacteria effectively act as 'biofertilisers', reducing the need for expensive and environmentally damaging applications of chemical fertiliser to legumes as well as the non-legume crops grown alongside them. Rhizobia do not only interact with their plant hosts however. When not living in the plant's root nodules, rhizobia live freely in the soil, interacting with the diverse microbial community that exists there. Key members of all soil microbe communities are the temperate phages, viruses that infect bacteria. These viruses can have widespread and various effects on their bacterial hosts. On the one hand they can be antagonistic, killing their host in order to produce more viral particles that will go on to infect new cells. Surprisingly however these viruses can also be beneficial. Every so often, upon infecting a bacterial cell, rather than reproducing to make more viral particles, they will integrate their own DNA into the bacterial genome, giving the bacteria access to novel genes and effectively becoming viral weapons that bacteria can use against their competitors. Rhizobia therefore engage in two important and highly contrasting interactions, with their legume hosts and with temperate phages. These separate interactions will place different selection pressures on the bacterial population and consequently are likely to have important implications for one another. This project will unpick this temperate phage - rhizobia - legume relationship in order to understand how this tripartite community shapes, and is shaped by, its constituent interactions.This project will combine studies using highly controlled lab experiments with studies of natural and semi-natural communities. Lab experiments allow hypotheses to be directly tested and, due to the high turnover of generations in bacteria, bacteria-phage coevolution to be observed in real time. Meanwhile, experiments conducted in the 'wild' or by bringing natural communities into the lab demonstrate how real communities are structured and behave. In combination these approaches offer a powerful way of exploring these complex interactions. This work will provide the first comprehensive examination of the role of temperate phages in rhizobial populations. With the rise in global food demand, understanding what shapes the ecology and evolution of symbiotic microbes such as rhizobia will be increasingly important. This work will therefore lay the foundation for exploring what roles the wider microbial community plays in these processes. This will lead to future work examining how we can apply these lessons to sustainable agricultural practices. For example, by using temperate phages to enhance the effectiveness of biofertilisers.