Engineering myxobacterial super-predators to fight crop disease

植物病原微生物（phytopathogens）在全球范围内造成巨大的经济损失，威胁粮食安全。例如，仅在美国，每年就有超过10亿美元的马铃薯作物损失。为了减少收获前浪费和提高粮食安全，迫切需要通过清除植物病原体来防治作物病害。黏菌等掠食性细菌有可能被用作生物防治剂，因为它们可以捕食植物病原体，从而减少作物病害并促进植物生长。粘杆菌能够捕食范围广泛的被捕食微生物，包括致病菌和真菌。虽然所有的黏菌分离物都有广泛的猎物范围，但偶尔菌株对特定猎物表现出不同寻常的有效掠食性活动。这种增强的掠食活性与菌株系统发育无关，这表明负责增强掠食活性的基因是水平遗传而不是垂直遗传的。这一设想得到了基因组测序的支持，该测序显示黏菌菌株具有小的“核心基因组”——每个菌株都拥有的基因。然而，大多数基因来自“辅助基因组”，这在很大程度上是单个菌株独有的。基因组之间的这种可变性可以用来确定负责特定猎物捕食的基因。当捕食基因被确定后，就有可能在菌株之间移植它们，以产生对特定猎物的捕食活动增加的“超级捕食者”菌株，或者对一系列猎物的捕食活动范围更广。超级捕食菌株将有利于作为农业接种剂，因为它们比环境菌株能够更好地杀死植物病原体。这个学生项目将测试一个假设，即移植特定猎物的捕食基因可以用来改变黏菌捕食者的捕食范围，增强它们保护作物免受疾病侵害和提高作物产量的能力。为了验证这一假设，比较基因组学将用于鉴定黏菌中特定猎物的捕食基因。捕食基因将在菌株之间移植，以增加对多种病原体的捕食活性。我们将重点关注新基因和那些编码消化酶/毒素的基因，而不是那些导致抗菌化合物产生的基因。我们还将设计超级捕食者，以减少对PGPRs（促进植物生长的根瘤菌）的捕食活动。这种经过改造的“超级捕食者”保护作物免受疾病侵害和促进植物生长的能力将在植物中得到评估。在此之前，我们分离了80株Corallococcus spp.，一种掠夺性粘菌属。其中大约一半的菌株现在已经进行了基因组测序，这表明它们是高度个体的，具有较大的附属基因组。菌株还对一组被捕食微生物（包括致病菌和真菌）表现出不同的捕食活动模式，表明这些菌株中存在/不存在猎物特异性捕食基因。该课程是遗传学、微生物学、植物生物学和生物信息学之间的交叉课程，旨在向学生介绍不断扩展的方法。项目团队将提供基因组分析、基因工程、微生物技术、基因表达测量、植物病理学分析和生物信息学/计算方法等现代方法的全面培训。管理人员还将提供培训，学习如何使用先进的计算基础设施进行基因组分析，例如IBERS内可用的高性能计算集群，以及通过威尔士超级计算。这些技能对生命和医学科学问题的适用性，使它们成为“一般的”跨学科。

Plant pathogenic microbes (phytopathogens) cause huge economic losses and threaten food security globally. For example, Ralstonia solanacearum alone causes more than $1 billion worth of potato crop losses each year in just the USA. To reduce pre-harvest wastage and increase food security, there is an urgent need to fight crop disease by targeting the removal of phytopathogens. Predatory bacteria such as myxobacteria have the potential to be used as biocontrol agents for this purpose, as they can prey upon phytopathogens, thereby reducing crop disease and promoting plant growth.Myxobacteria are able to prey upon a broad range of prey microbes, including pathogenic bacteria and fungi. While all myxobacterial isolates have a broad prey range, occasional strains exhibit unusually effective predatory activity against specific prey. Such enhanced predatory activity does not correlate with strain phylogeny, which suggests that the genes responsible for enhanced predatory activity have been inherited horizontally rather than vertically.This scenario is supported by genome sequencing, which shows that myxobacterial strains have small 'core genomes' - genes which every strain possesses. However, the majority of genes come from the 'accessory genome', which is largely unique to individual strains. Such variability between genomes can be exploited to identify the genes responsible for predation of specific prey. When predation genes have been identified, it is then possible to transplant them between strains, to generate 'super-predator' strains with increased predatory activity against particular prey, or with a broader activity against a range of prey. Super-predator strains would be advantageous for use as agricultural inoculants, as they would be better able to kill phytopathogens than environmental strains.This studentship will test the hypothesis that transplantation of prey-specific predation genes can be used to alter the prey-range of myxobacterial predators, enhancing their ability to protect crops from disease and increasing crop yields.To test this hypothesis, comparative genomics will be used to identify prey-specific predation genes in myxobacteria. Predation genes will be transplanted between strains to increase predatory activity against multiple pathogens. We will focus on novel genes and those which encode digestive enzymes/toxins rather than those which cause the production of antimicrobial compounds. We will also engineer super-predators to have reduced predatory activity against PGPRs (plant growth promoting rhizobacteria). The ability of the engineered 'super-predator to protect crops from disease and to promote plant growth will then be assessed in planta.Previously, we isolated >80 strains of Corallococcus spp., a genus of predatory myxobacteria. Around half of those strains have now been genome-sequenced, which showed that they are highly individual with large accessory genomes. Strains also exhibited diverse patterns of predatory activity against a panel of prey microbes (including pathogenic bacteria and fungi), indicating the presence/absence of prey-specific predation gene in those strains.This studentship lies at the interface between genetics, microbiology, plant biology and bioinformatics, and has been designed to gently introduce the student to an ever-expanding range of methods. The project team will provide full training in modern methods of genomic analysis, genetic engineering, microbiological techniques, gene expression measurements, plant pathology assays and bioinformatics/computational methods. Training will also be provided by the supervisors in the use of advanced computational infrastructures for genomic analyses, such as the high performance computing clusters available within IBERS, and via Supercomputing Wales. The applicability of these skills to problems across the life and medical sciences, make them 'generically' cross-disciplinary.