Understanding the genomics and specialised metabolites of the biopesticidal bacterium Burkholderia ambifaria

利用微生物和植物之间的有益互动，可以通过减少化学农药和化肥的使用，提高作物产量，为粮食安全提供多种解决方案。伯克霍尔德氏菌是一种革兰氏阴性环境细菌，已被用作天然生物技术制剂，用于污染物生物修复和植物病原菌的生物防治。它们大量出现在包括玉米和水稻在内的主要作物物种的根部。伯克霍尔德氏菌编码的途径可以固定大气中的氮，并产生抗菌代谢产物，杀死一系列植物病原体(细菌、真菌和线虫)。然而，在植物相互作用中最有益的途径还没有被系统地定义。伯克霍尔德氏菌基因组(8+Mb)包含多个大的染色体复制子。最小的第三条染色体(&gt；1Mb；c3)可以被删除，减弱毒力但保持根际适应性不变，开启了染色体工程作为利用伯克霍尔德氏菌生物技术潜力的一种手段。瞄准。博士将定义伯克霍尔德氏菌和参与保护和促进生长的根际相互作用的植物遗传途径，总体目标是将最有益的细菌途径工程到合成的c3上。目标1(1年级)。利用拟南芥模型筛选促进生长和植物保护的伯克霍尔德氏菌菌株。作为BBSRC抗生素发现基因组挖掘的一部分，多个伯克霍尔德氏菌生防菌株正在进行基因组测序(EM，2014-17)。PHD将对这些菌株进行遗传学表征(EM轮换)，并建立拟南芥生长促进分析(JM轮换)，以确定最具生物活性的伯克霍尔德氏菌。将建立一种拟南芥保护试验(MG轮换)，以确定细菌病原体Xanthomonas是如何在根际被Burkholderia杀死的，使用一系列防御和激素突变来提供机制洞察。目标2(2-3年级)。用后基因组方法探索促进生长和植物保护的分子基础。在有益的相互作用期间，Burkholderia和拟南芥中发生的全球基因表达将使用RNA-seq来确定，定义了参与这些过程的潜在转录网络(EM和JM实验室之间的跨学科轮换)。目标3(3-4年级)。合成工程伯克霍尔德氏菌c3以编码特定的生长促进和病原菌控制功能。从全球基因表达分析中确定的选定路径将被工程改造到合成的第三条染色体上。它们将在c3突变背景下进行重新测试，确定哪些有益途径在分离中仍然有效，最终致力于产生一种复合伯克霍尔德氏菌复制子，用于作物保护和植物生长促进，可用于环境适应的伯克霍尔德氏菌。

Harnessing beneficial interactions between microorganisms and plants can provide multiple solutions to food security by reducing chemical pesticide and fertilizer use, and improving crop yields. Burkholderia are Gram-negative, environmental bacteria that have been used as natural biotechnological agents for pollutant bioremediation and biological control of plant pathogens. They occur in high numbers at the roots of major crop species including maize and rice. Burkholderia encode pathways that can fix atmospheric nitrogen and produce antimicrobial metabolites that kill a range of plant pathogens (bacteria, fungi and nematodes). However, the pathways that are most beneficial in plant interactions have not been systematically defined. The Burkholderia genome (8+ Mb) contains multiple large chromosomal replicons. The smallest, third chromosome (> 1Mb; c3) can be deleted, attenuating virulence but leaving rhizosphere fitness intact, opening up chromosome engineering as a means to harness Burkholderia's biotechnological potential. Aim. The PhD will define the Burkholderia and plant genetic pathways involved in protective and growth promoting rhizosphere interactions, with an overall goal to engineer the most beneficial bacterial pathways onto a synthetic c3. Objective 1 (Year 1). Screening Burkholderia strains for growth promotion and plant protection using Arabidopsis models. Multiple Burkholderia biocontrol strains are being genome sequenced as part of BBSRC antibiotic discovery genome mining (EM, 2014-17). The PhD will genetically characterise these strains (EM rotation) and establish Arabidopsis growth promotion assays (JM rotation), to identify the most bioactive Burkholderia. An Arabidopsis protection assay will be established (MG rotation) to determine how the bacterial pathogen, Xanthomonas is killed at the rhizosphere by Burkholderia, using a range of defence and hormone mutants to provide mechanistic insight. Objective 2 (Year 2-3). Exploring the molecular basis for growth promotion and plant protection using post-genomic approaches. Global gene expression occurring in both Burkholderia and Arabidopsis during beneficial interactions will be determined using RNA-seq, defining the underlying transcriptional networks engaged in these processes (interdisciplinary rotations between EM and JM labs). Objective 3 (Year 3-4). Synthetically engineer the Burkholderia c3 to encode specific growth promotion and pathogen control functions. Selected pathways identified from the global gene expression analysis will be engineered onto a synthetic third chromosome. They will be re-tested in a c3 mutant background, establishing which beneficial pathways remain effective in isolation, ultimately working towards the goal of producing a composite Burkholderia replicon for crop protection and plant growth promotion that can be utilized in environmentally adapted Burkholderia's.