Streptomyces bacteria: Antibiotic production in the wheat endosphere

植物利用光合作用将空气中的二氧化碳转化为葡萄糖作为食物。然而，高达40%的碳从它们的根部释放到土壤中，这似乎是一种从周围土壤中吸引有益细菌的机制。细菌利用根系分泌物作为食物，这有助于植物组装健康的微生物组。其中一些微生物保护植物免受疾病的侵害，另一些微生物帮助它们从土壤中获得重要的营养物质。因此，根部微生物组对植物健康至关重要，但数百年来的作物育种选择了具有更多谷物的更大植物等性状，而可能忽略了对微生物组的（未知）影响。现在人们越来越感兴趣的是操纵小麦等作物的微生物组，使它们更能抵抗疾病和干旱和盐碱等非生物胁迫。小麦是约40亿人的主食作物，也是世界上最重要的作物之一，因此，如果我们要支持不断增长的世界人口，提高产量至关重要。我们的项目集中在一种叫做链霉菌的土壤细菌上。约600种已知的链霉菌产生大量的次级代谢产物，这些次级代谢产物占所有已知抗生素的一半。它们很容易从土壤中分离出来，但也与植物根系形成稳定的相互作用，并且可以在各种不同植物的根际和内圈中定殖。我们已经发现它们在小麦根内很丰富，并且一些菌株可以保护小麦免受真菌疾病的侵害，例如可能导致毁灭性作物损失的全蚀病。对于这些菌株之一，我们已经确定了负责这种抗真菌活性的分子和基因，并表明当我们向生长培养基中加入吲哚3乙酸（一种存在于小麦根分泌物中的植物激素）时，它会增加两倍。在这个建议中，我们的目标是更详细地研究土壤中的定居，产生抗生素的链霉菌细菌在小麦根中的定植。我们将对我们从小麦植株中分离的10种菌株的基因组进行测序，这些菌株在琼脂平板上抑制全蚀真菌，鉴定这些菌株产生的抗真菌剂，并确定它们是否可以保护小麦植株免受全蚀病的侵害。我们还将试图发现小麦根系分泌物中的哪些分子可以喂养这些细菌并打开它们的次级代谢产物的生产。由于链霉菌细菌形成的孢子可以干燥和储存很长一段时间，我们有兴趣开发含有这些孢子的小麦种子涂层，使细菌生长到发芽小麦植物的根部，并保护它们免受疾病的侵害。我们还将测试VII型分泌系统在这些菌株的根定殖中的作用，因为我们有初步证据表明，该系统有助于它们在小麦根定殖中胜过其他细菌。我们的最终目标是开发链霉菌作为种子包衣，以保护小麦植物免受真菌病害的侵害，并从小麦根系分泌物中发现我们可以用来在体外启动次生代谢产物生产的分子，因为我们知道它们编码的90%的次生代谢产物不是在实验室条件下产生的。这可以帮助我们从这些细菌中发现新的有用分子。

Plants use photosynthesis to fix carbon dioxide from the air into glucose which they use as food. However, up to 40% of the carbon they fix is released into the soil from their roots and this appears to be a mechanism to attract beneficial bacteria from the surrounding soil. The bacteria use the root exudates as food and this helps the plants assemble a healthy microbiome. Some of these microbes protect the plants against disease and others help them get important nutrients from the soil. The root microbiome is therefore essential for plant health, but crop breeding over hundreds of years has selected traits such as bigger plants with more grain while perhaps neglecting the (unknown) effects on the microbiome. There is now growing interest in manipulating the microbiomes of crop plants such as wheat to make them more resistant to disease and to abiotic stresses like drought and salinity. Wheat is a staple crop for about 4 billion people and one of the most important crops in the world so increasing yields is essential if we are to support a growing world population. Our project focuses on a genus of soil bacteria called Streptomyces. The ~600 known species of Streptomyces make numerous secondary metabolites, and these account for half of all the known antibiotics. They are easy to isolate from soil but also form stable interactions with plant roots and can colonise the rhizosphere and endosphere of a wide range of different plants. We have found they are abundant inside wheat roots and that some strains can protect wheat against fungal diseases such as Take-all which can cause devastating crop losses. For one of these strains we have identified the molecules and genes responsible for this antifungal activity and shown it is increased two-fold when we add indole 3 acetic acid, a plant hormone present in wheat root exudates, to the growth medium. In this proposal we aim to look in more detail at the colonisation of wheat roots by soil dwelling, antibiotic-producing Streptomyces bacteria. We will sequence the genomes of 10 strains we have isolated from wheat plants which inhibit the take-all fungus on agar plates, identify the antifungals made by these strains and determine if they can protect wheat plants against take-all disease. We will also try to discover which molecules in wheat root exudates can feed these bacteria and switch on their production of secondary metabolites. Since Streptomyces bacteria form spores which can be dried and stored for long periods, we are interested in developing wheat seed coatings containing these spores so the bacteria grow into the roots of germinating wheat plants and protect them against disease. We will also test the role of the type VII secretion system in root colonisation by these strains since we have preliminary evidence that this system helps them outcompete other bacteria for wheat root colonisation. Our ultimate aim is to develop streptomycetes as seed coatings to protect wheat plants against fungal disease and to discover molecules from wheat root exudates that we can use to switch on secondary metabolite production in vitro because we know that 90% of the secondary metabolites they encode are not made under laboratory conditions. This could help us discover new and useful molecules from these bacteria.