Table_1_Xylella fastidiosa Infection Reshapes Microbial Composition and Network Associations in the Xylem of Almond Trees.docx

Xylella fastidiosa represents a major threat to important crops worldwide including almond, citrus, grapevine, and olives. Nowadays, there are no efficient control measures for X. fastidiosa, and the use of preventive measures and host resistance represent the most practical disease management strategies. Research on vessel-associated microorganisms is gaining special interest as an innate natural defense of plants to cope against infection by xylem-inhabiting pathogens. The objective of this research has been to characterize, by next-generation sequencing (NGS) analysis, the microbial communities residing in the xylem sap of almond trees affected by almond leaf scorch disease (ALSD) in a recent X. fastidiosa outbreak occurring in Alicante province, Spain. We also determined community composition changes and network associations occurring between xylem-inhabiting microbial communities and X. fastidiosa. For that, a total of 91 trees with or without ALSD symptoms were selected from a total of eight representative orchards located in five municipalities within the X. fastidiosa-demarcated area. X. fastidiosa infection in each tree was verified by quantitative polymerase chain reaction (qPCR) analysis, with 54% of the trees being tested X. fastidiosa-positive. Globally, Xylella (27.4%), Sphingomonas (13.9%), and Hymenobacter (12.7%) were the most abundant bacterial genera, whereas Diplodia (30.18%), a member of the family Didymellaceae (10.7%), and Aureobasidium (9.9%) were the most predominant fungal taxa. Furthermore, principal coordinate analysis (PCoA) of Bray–Curtis and weighted UniFrac distances differentiated almond xylem bacterial communities mainly according to X. fastidiosa infection, in contrast to fungal community structure that was not closely related to the presence of the pathogen. Similar results were obtained when X. fastidiosa reads were removed from the bacterial data set although the effect was less pronounced. Co-occurrence network analysis revealed negative associations among four amplicon sequence variants (ASVs) assigned to X. fastidiosa with different bacterial ASVs belonging to 1174-901-12, Abditibacterium, Sphingomonas, Methylobacterium–Methylorubrum, Modestobacter, Xylophilus, and a non-identified member of the family Solirubrobacteraceae. Determination of the close-fitting associations between xylem-inhabiting microorganisms and X. fastidiosa may help to reveal specific microbial players associated with the suppression of ALSD under high X. fastidiosa inoculum pressure. These identified microorganisms would be good candidates to be tested in planta, to produce almond plants more resilient to X. fastidiosa infection when inoculated by endotherapy, contributing to suppress ALSD.

Xylella fastidiosa 作为全球重要农作物（包括杏仁、柑橘、葡萄树和橄榄）的主要威胁，其影响范围广泛。目前，针对 X. fastidiosa 的控制措施尚无高效手段，因此采取预防措施和寄主抗性成为最实际的疾病管理策略。对与导管相伴的微生物的研究日益受到关注，因为这些微生物构成了植物对抗木质部病原体侵染的天然防御机制。本研究旨在通过下一代测序（NGS）分析，对近期在西班牙阿利坎特省爆发的 X. fastidiosa 疫情中受杏仁叶枯病（ALSD）影响的杏仁树木质部汁液中居住的微生物群落进行特征描述。同时，我们还确定了木质部居住微生物群落与 X. fastidiosa 之间的群落组成变化和网络关联。为此，从 X. fastidiosa 疫情划定的区域内五个市镇中的八个代表性果园中选取了91棵具有或无 ALSD 症状的树木，其中54%的树木经定量聚合酶链反应（qPCR）分析证实为 X. fastidiosa 阳性。在全球范围内，Xylella（27.4%）、Sphingomonas（13.9%）和 Hymenobacter（12.7%）是最丰富的细菌属，而 Diplodia（30.18%），属 Didymellaceae 科（10.7%），以及 Aureobasidium（9.9%）是最主要的真菌类群。此外，基于 Bray-Curtis 和加权 UniFrac 距离的主坐标分析（PCoA）主要根据 X. fastidiosa 感染区分了杏仁木质部细菌群落，而真菌群落结构则与病原体的存在没有密切关联。当从细菌数据集中移除 X. fastidiosa 读取序列时，也获得了相似的结果，尽管影响较小。共现网络分析揭示了 X. fastidiosa 的四个扩增子序列变异体（ASVs）与属于 1174-901-12、Abditibacterium、Sphingomonas、Methylobacterium-Methylorubrum、Modestobacter、Xylophilus 以及 Solirubrobacteraceae 科的非鉴定成员等不同细菌 ASVs 之间的负关联。确定木质部居住微生物与 X. fastidiosa 之间的紧密关联有助于揭示与抑制 ALSD 相关的特定微生物参与者。这些已鉴定的微生物将是植栽实验的良好候选者，以测试其在通过内疗法接种 X. fastidiosa 后，对杏仁树提高抗感染力的潜力，从而有助于抑制 ALSD。