UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
UMR IRHS, INRA, Agrocampus Ouest, Université d'Angers, 49071, Beaucouzé, France.
Microbiome. 2019 Aug 30;7(1):125. doi: 10.1186/s40168-019-0736-0.
Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to identify microorganisms interacting with it. We used metabarcoding to characterize the microbiome associated with wheat residues placed outdoors, with and without preliminary Z. tritici inoculation, comparing the first set of residues in contact with the soil and a second set without contact with the soil, on four sampling dates in two consecutive years.
The diversity of the tested conditions, leading to the establishment of different microbial communities according to the origins of the constitutive taxa (plant only, or plant and soil), highlighted the effect of Z. tritici on the wheat residue microbiome. Several microorganisms were affected by Z. tritici infection, even after the disappearance of the pathogen. Linear discriminant analyses and ecological network analyses were combined to describe the communities affected by the infection. The number of fungi and bacteria promoted or inhibited by inoculation with Z. tritici decreased over time and was smaller for residues in contact with the soil. The interactions between the pathogen and other microorganisms appeared to be mostly indirect, despite the strong position of the pathogen as a keystone taxon in networks. Direct interactions with other members of the communities mostly involved fungi, including other wheat pathogens. Our results provide essential information about the alterations to the microbial community in wheat residues induced by the mere presence of a fungal pathogen, and vice versa. Species already described as beneficial or biocontrol agents were found to be affected by pathogen inoculation.
The strategy developed here can be viewed as a proof-of-concept focusing on crop residues as a particularly rich ecological compartment, with a high diversity of fungal and bacterial taxa originating from both the plant and soil compartments, and for Z. tritici-wheat as a model pathosystem. By revealing putative antagonistic interactions, this study paves the way for improving the biological control of residue-borne diseases.
小麦残体是导致小麦叶枯病流行的一个重要决定因素，因为它支持病原菌禾旋孢腔菌的有性繁殖。我们旨在研究这种真菌病原体感染对存在于小麦残体上的微生物群落的影响，并鉴定与之相互作用的微生物。我们使用宏条形码技术来描述在户外放置的小麦残体上的微生物组，这些残体分别经过禾旋孢腔菌的预先接种和未接种，比较了两年中四个采样日期的第一组与土壤接触的残体和第二组未与土壤接触的残体。
由于组成分类群的来源不同（仅来自植物，或来自植物和土壤），测试条件的多样性导致了不同微生物群落的建立，突出了禾旋孢腔菌对小麦残体微生物组的影响。即使在病原体消失后，一些微生物也受到了禾旋孢腔菌感染的影响。线性判别分析和生态网络分析相结合，描述了受感染影响的群落。接种禾旋孢腔菌后促进或抑制的真菌和细菌数量随时间减少，与土壤接触的残体数量减少。尽管病原菌作为网络中的关键分类群具有很强的地位，但病原菌与其他微生物之间的相互作用似乎大多是间接的。与群落其他成员的直接相互作用主要涉及真菌，包括其他小麦病原体。我们的研究结果提供了关于仅由真菌病原体存在引起的小麦残体微生物群落改变的重要信息，反之亦然。已经被描述为有益或生物防治剂的物种被发现受到病原体接种的影响。
这里开发的策略可以被视为一个概念验证，重点关注作为一个特别丰富的生态隔室的作物残体，具有来自植物和土壤隔室的高多样性的真菌和细菌分类群，以及禾旋孢腔菌-小麦作为一个模式病理系统。通过揭示潜在的拮抗相互作用，这项研究为改善对残体传播疾病的生物防治铺平了道路。
