Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition.
Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition.
复制标题
DOI：
10.7554/elife.71900
复制
发表时间：
2021-12-31
期刊：
影响因子：
7.7
通讯作者：
Truman AW
中科院分区：
文献类型：
--
作者：
Pacheco-Moreno A;Stefanato FL;Ford JJ;Trippel C;Uszkoreit S;Ferrafiat L;Grenga L;Dickens R;Kelly N;Kingdon AD;Ambrosetti L;Nepogodiev SA;Findlay KC;Cheema J;Trick M;Chandra G;Tomalin G;Malone JG;Truman AW
农业土壤中有多种微生物，可以与植物形成有益的关系，包括抑制植物病原体。假单胞菌属是土壤和根际最丰富的细菌属之一，在促进植物健康方面发挥着重要作用。然而，这种有益活动的遗传决定因素仅被部分理解。在这里，我们对商业马铃薯田的荧光假单胞菌群体进行了遗传和表型表征，在那里我们发现了特殊代谢物生物合成与马铃薯病原体疥疮链霉菌和疫霉拮抗之间的强相关性。遗传和化学分析发现，氰化氢和环脂肽是抑制疥疮的关键代谢物，这在植物生物防治实验中得到了支持。我们表明，单个马铃薯田包含一个巨大的多样化和动态的假单胞菌群，其产生专门代谢物的能力是由植物定植和确定的环境输入塑造的。马铃薯赤霉病和枯萎病是造成重大作物损失的两种主要病害。它们分别是由疥疮链霉菌和一种被称为疫霉的卵菌（一种真菌状生物）引起的。与这些致病微生物的斗争可能涉及作物管理技术——例如，确保农田得到良好的灌溉有助于防止疥疮。利用生物防治剂还可以在尊重环境的同时提供控制疾病的方法。生物防治细菌，如假单胞菌，可以产生抑制疥疮链球菌和感染假单胞菌的化合物。然而，这些分子的身份和灌溉如何影响假单胞菌的数量仍然未知。为了研究这些问题，Pacheco-Moreno等人从一块商业马铃薯田取样并分离出数百株假单胞菌菌株，仔细检查了其中69株的基因组。根据是否能控制疥疮生长来比较菌株的遗传信息，发现环状脂肽是控制疥疮和疟原虫生长的关键。是否灌溉田地对形成假单胞菌种群的菌株也有很大影响。弄清楚假单胞菌是如何阻断疾病的，可以加快对生物防治剂的研究。Pacheco-Moreno等人开发的方法可以根据其遗传特征帮助预测哪些菌株可能最有效。类似的实验也适用于植物和疾病的其他组合。
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.