Bekris Fotios, Vasileiadis Sotirios, Papadopoulou Elena, Samaras Anastasios, Testempasis Stefanos, Gkizi Danae, Tavlaki Georgia, Tzima Aliki, Paplomatas Epaminondas, Markakis Emmanuel, Karaoglanidis George, Papadopoulou Kalliope K, Karpouzas Dimitrios G
Laboratory of Plant and Environmental Biotechnology, Viopolis, Department of Biochemistry and Biotechnology, University of Thessaly, 41500, Larissa, Greece.
Plant Pathology Laboratory, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
Environ Microbiome. 2021 Dec 4;16(1):23. doi: 10.1186/s40793-021-00390-1.
Grapevine trunk diseases (GTDs) is a disease complex caused by wood pathogenic fungi belonging to genera like Phaeomoniella, Phaeoacremonium, Fomitiporia, Eutypa and members of the family Botryosphaeriaceae. However, the co-occurrence of these fungi in symptomatic and asymptomatic vines at equivalent abundances has questioned their role in GTDs. Hence, we still lack a good understanding of the fungi involved in GTDs, their interactions and the factors controlling their assemblage in vines. We determined the fungal and bacterial microbiome in wood tissues of asymptomatic and symptomatic vines of three main Greek cultivars (Agiorgitiko, Xinomavro, Vidiano), each cultivated in geographically distinct viticultural zones, using amplicon sequencing.
We noted that cultivar/biogeography (lumped factor) was the strongest determinant of the wood fungal microbiome (p < 0.001, 22.7%), while GTD symptoms condition had a weaker but still significant effect (p < 0.001, 3.5%), being prominent only in the cultivar Xinomavro. Several fungal Amplicon Sequence Variants (ASVs), reported as GTD-associated pathogens like Kalmusia variispora, Fomitiporia spp., and Phaemoniella chlamydosporα (most dominant in our study), were positively correlated with symptomatic vines in a cultivar/viticultural zone dependent manner. Random Forest analysis pointed to P. chlamydosporα, K. variispora, A. alternata and Cladosporium sp., as highly accurate predictors of symptomatic vines (0% error rate). The wood bacterial microbiome showed similar patterns, with biogeography/cultivar being the main determinant (p < 0.001, 25.5%) of its composition, followed by the GTD status of vines (p < 0.001, 5.2%). Differential abundance analysis revealed a universal positive correlation (p < 0.001) of Bacillus and Streptomyces ASVs with asymptomatic vines. Network analysis identified a significant negative co-occurrence network between these bacterial genera and Phaemoniella, Phaeoacrominum and Seimatosporium. These results point to a plant beneficial interaction between Bacillus/Streptomyces and GTD pathogens.
Our study (a) provides evidence that GTD symptomatic plants support a wood fungal microbiome, showing cultivar and biogeography-dependent patterns, that could be used as a proxy to distinguish between healthy and diseased vines, (b) points to strong interactions between the bacterial and fungal wood microbiome in asymptomatic vines that should be further pursued in the quest for discovery of novel biocontrol agents.
葡萄树干病害（GTDs）是一种由木本致病真菌引起的病害复合体，这些真菌属于诸如拟茎点霉属、拟顶孢霉属、木层孔菌属、顶囊壳属以及葡萄座腔菌科的成员。然而，这些真菌在有症状和无症状葡萄藤中以相当的丰度共同出现，这对它们在GTDs中的作用提出了质疑。因此，我们仍然缺乏对参与GTDs的真菌、它们之间的相互作用以及控制它们在葡萄藤中组合的因素的充分理解。我们使用扩增子测序确定了希腊三个主要品种（阿吉奥吉提科、希诺玛弗洛、维迪亚诺）的无症状和有症状葡萄藤木质组织中的真菌和细菌微生物群，每个品种种植在地理上不同的葡萄种植区。
我们注意到品种/生物地理学（综合因素）是木质部真菌微生物群的最强决定因素（p < 0.001，22.7%），而GTD症状状况的影响较弱但仍显著（p < 0.001，3.5%），仅在希诺玛弗洛品种中较为突出。一些被报道为与GTD相关病原体的真菌扩增子序列变体（ASVs），如多变卡尔穆菌、木层孔菌属物种和厚垣拟茎点霉（在我们的研究中最占优势）以品种/葡萄种植区依赖的方式与有症状的葡萄藤呈正相关。随机森林分析指出，厚垣拟茎点霉、多变卡尔穆菌、链格孢和枝孢属是有症状葡萄藤的高度准确预测因子（错误率为0%）。木质部细菌微生物群表现出类似的模式，生物地理学/品种是其组成的主要决定因素（p < 0.001，25.5%），其次是葡萄藤的GTD状态（p < 0.001，5.2%）。差异丰度分析揭示了芽孢杆菌和链霉菌ASVs与无症状葡萄藤之间普遍存在正相关（p < 0.001）。网络分析确定了这些细菌属与拟茎点霉属、拟顶孢霉属和拟盘多毛孢属之间存在显著的负共现网络。这些结果表明芽孢杆菌/链霉菌与GTD病原体之间存在对植物有益的相互作用。
我们的研究（a）提供了证据，表明GTD有症状的植物支持一种木质部真菌微生物群，呈现出品种和生物地理学依赖的模式，可作为区分健康和患病葡萄藤的代理指标，（b）指出无症状葡萄藤中细菌和真菌木质部微生物群之间存在强烈的相互作用，在寻求发现新型生物防治剂的过程中应进一步研究。
