Predicting the emergence of host-adapted bacterial phytopathogens

预测适应宿主的细菌植物病原体的出现

• 批准号: BB/T010746/1
• 负责人: Richard Harrison
• 金额: $ 185.87万
• 依托单位: National Institute of Agricultural Botany
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FT010746%2F1
• 关键词: Predicting; emergence; host; adapted; bacterial

Bacterial phytopathogens are hard to control and therefore pose a high risk to crop production and the wider natural environment. In order to mitigate that risk, we propose multidisciplinary research into the tempo at which and the mechanism by which bacteria adapt to hosts. Our findings will support new developments in disease management and control strategies. The host range of a pathogen encompasses all the species it can successfully infect and colonise. It is hypothesised that plant species outside this range mount an effective non-host resistance response, preventing colonisation. Plant pathologists traditionally define some pathogens as having a wide host range (generalists) whilst others are limited to one or a few hosts (specialists), although a continuum between these two life strategies probably exists. Our work focuses on the ubiquitous bacterial species complex Pseudomonas syringae (Ps), lineages of which are pathogens of over 300 different plant species. At least eight lineages of Ps are known to cause bacterial canker of cherry trees including the recognised pathogens Ps pv. morsprunorum and Ps pv. syringae. From our preliminary work, sampling from the leaf and shoot surface across cherry orchards around the UK, we have shown that there are large regional variations in Ps populations. We have found that, in addition to the known pathogens, many additional lineages of Pseudomonas (which have the potential to be pathogenic) are present on non-diseased cherry leaves and such strains are extremely widespread across orchards and regions. These epiphytic (surface) populations of pseudomonads may either be donors or repositories of bacterial genes predicted to have a key role in host adaptation to Prunus. We have shown that there is significant variation in resistance to canker within cherry cultivars and also between genotypes of wild cherry. What we do not know is whether or not the epiphytic populations of Ps are similar or variable between cultivated and wild cherry hosts, or if there is a flow of bacterial strains between wild and cultivated cherry. In this multidisciplinary research proposal, we will extend our initial experiments to study the ecological niches occupied by Ps. Using repeated sampling and genome sequencing of isolates from cultivated crops and surrounding plant species, we will determine if epiphytic Ps populations, some of which contain known pathogens, are stable over time and space. In controlled field experiments we will also ask whether agronomic interventions, such as nitrogen rates and polytunnel covering of crops also play a role in shaping bacterial populations. Our previous work has shown that key genes have been transferred between Pseudomonas lineages by phages and plasmids. In order to explore the molecular factors that may affect virulence and lead to new disease outbreaks, we will carry out tests to determine whether epiphytic lineages have 'pathogenic potential' and study the mechanisms of host range expansion through a range of directed evolution experiments. Our analysis will include controlled assessment of gene exchange between bacteria through phage infection. Finally, we will explore whether machine learning approaches can predict the host range of a Pseudomonas isolate with any degree of certainty from its genome sequence alone- a feat that is currently impossible with our current knowledge base, without direct pathogenicity testing upon a host. These predictions will be tested and validated using existing datasets but also on new datasets gathered as part of this work.

细菌性植物病原体难以控制，因此对作物生产和更广泛的自然环境构成高风险。为了减轻这种风险，我们建议对细菌适应宿主的速度和机制进行多学科研究。我们的发现将支持疾病管理和控制策略的新发展。病原体的宿主范围包括它能成功感染和定植的所有物种。据推测，在这个范围之外的植物物种会产生有效的非寄主抗性反应，从而阻止定植。植物病理学家传统上将一些病原体定义为具有广泛的寄主范围（通才），而其他病原体则局限于一个或几个寄主（专才），尽管这两种生命策略之间可能存在连续统一体。我们的工作重点是无处不在的细菌种类复杂的丁香假单胞菌（Ps），其谱系是超过300种不同植物的病原体。至少有八种已知的Ps谱系可以引起樱桃树的细菌性溃疡病，包括公认的病原体Ps pv。morsprunorum和pspv。两。从我们的初步工作中，从英国各地的樱桃园的叶子和茎表面取样，我们已经表明，Ps种群存在很大的区域差异。我们发现，除了已知的病原体外，在未患病的樱桃叶片上还存在许多额外的假单胞菌谱系（具有致病性的潜力），这些菌株在果园和地区非常普遍。这些假单胞菌的附生（表面）群体可能是细菌基因的供体或储存库，预计在寄主适应李子的过程中起关键作用。我们已经证明，樱桃品种之间以及野生樱桃基因型之间对溃疡病的抗性存在显著差异。我们不知道的是，Ps的附生种群在栽培和野生樱桃宿主之间是否相似或不同，或者在野生和栽培樱桃之间是否存在菌株流动。在这个多学科的研究计划中，我们将扩展我们最初的实验来研究Ps所占据的生态位。通过对栽培作物和周围植物物种分离物的重复采样和基因组测序，我们将确定附生Ps群体是否随时间和空间的变化而稳定，其中一些含有已知的病原体。在受控的田间实验中，我们还将询问农艺干预措施，如氮肥用量和作物的多洞覆盖，是否也在塑造细菌种群方面发挥作用。我们以前的工作表明，关键基因已经通过噬菌体和质粒在假单胞菌谱系之间转移。为了探索可能影响毒力并导致新疾病爆发的分子因素，我们将开展测试，以确定附生谱系是否具有“致病潜力”，并通过一系列定向进化实验研究宿主范围扩大的机制。我们的分析将包括通过噬菌体感染控制细菌之间基因交换的评估。最后，我们将探索机器学习方法是否可以仅从其基因组序列中预测假单胞菌分离的宿主范围，并且具有一定程度的确定性-这一壮举目前在我们现有的知识库中是不可能的，没有对宿主进行直接的致病性测试。这些预测将使用现有数据集进行测试和验证，但也将使用作为本工作一部分收集的新数据集进行测试和验证。

项目成果

Genetic dissection of the tissue-specific roles of type III effectors and phytotoxins in the pathogenicity of Pseudomonas syringae pv. syringae to cherry

III 型效应子和植物毒素在丁香假单胞菌致病性中的组织特异性作用的基因剖析。

• DOI: 10.1101/2024.02.06.578989
• 发表时间: 2024
• 作者: Vadillo-Dieguez A

Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface.

• DOI: 10.1111/nph.18573
• 发表时间: 2023-02
• 期刊: NEW PHYTOLOGIST
• 影响因子: 9.4
• 作者: Hulin, Michelle T.;Rabiey, Mojgan;Zeng, Ziyue;Dieguez, Andrea Vadillo;Bellamy, Sophia;Swift, Phoebe;Mansfield, John W.;Jackson, Robert W.;Harrison, Richard J.
• 通讯作者: Harrison, Richard J.