Identifying the role of nodule endophytes in shaping nitrogen fixation effectiveness

无效根瘤在农业领域很常见，并限制了生物固氮在农业中的广泛使用。使根瘤有效的因素是多种因素的产物，从根瘤菌固有的固氮能力到它们与宿主的兼容性。其他与根相关的微生物如何影响根瘤功能还没有得到彻底的研究。在第一个资助期，我们发现：1)虽然不同种类和不同土壤接种物的莲花根瘤以根瘤菌为主，但其多样性和确切组成差异很大；ii)根瘤组成在很大程度上取决于接种物，但寄主的基因型和健康状况也有贡献；iii)伯氏乳杆菌比其他莲花植物更混杂，这可能导致无效根瘤的形成；iv)健康的伯氏乳杆菌根瘤富含假单胞菌，以及v)共分离的根瘤内生菌以宿主特有的方式促进生长。在第二个资助期，我们的目标是阐明根瘤内生真菌如何通过与根瘤菌和寄主的相互作用来影响根瘤功能。为了研究这一点，我们将应用一种基于灵知生菌系统中合成微生物群落重建的简化论方法。在一项包括微生物学、计算生物学和遗传学的跨学科研究中，我们将i)鉴定和表征促进有效根瘤形成的根瘤内生菌，以及ii)寻找根瘤内生菌促进寄主特异性生长的遗传决定因素。这个跨学科和协作的项目将帮助我们了解有效根瘤的形成，以便在未来我们可以改进农业实践，以避免建立无效的根瘤共生体。

Ineffective nodules are common in agricultural fields and constitute a limitation to the widespread use of biological nitrogen fixation in agriculture. What makes a nodule effective is the product of multiple factors, from the inherent capacity of rhizobia to fix nitrogen, to their compatibility with the host. How other root associated microbes impact nodule function has not been thoroughly investigated. In the first funding period we have shown that i) although Lotus nodules from different species and soil inoculums are dominated by Rhizobiales bacteria, the diversity and exact composition can vary greatly, ii) nodule composition largely depends on the inoculum, but the host genotype and health status also contribute, iii) L. burttii is more promiscuous than other Lotus plants, which can lead to the formation of ineffective nodules, iv) healthy L. burttii nodules are enriched in Pseudomonas, and v) co-isolated nodule endophytes promote growth in a host specific manner. In the second funding period we aim to elucidate how nodule endophytes impact nodule function through interactions with rhizobia and the host. To investigate this, we will apply a reductionist approach based on the reconstruction of synthetic microbial communities in gnotobiotic systems. In an interdisciplinary study including microbiology, computational biology and genetics we will i) identify and characterise nodule endophytes promoting formation of effective nodules and ii) find the genetic determinants underlaying host specific growth promotion by nodule endophytes. This interdisciplinary and collaborative project will help us understand the formation of effective nodules so in the future we can improve agricultural practices to avoid the establishment of ineffective root nodule symbioses.