Data_Sheet_1_Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective.zip

Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant’s ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant’s response to viral disease, which may be microbially mediated.

生物胁迫（biotic stresses），如植物病毒，例如棉花曲叶病毒（cotton leaf curl virus, CLCuV），可改变植物根际与叶际相关的微生物多样性。该系统中存在复杂的生态动态过程，每一类微生物均参与众多生物与非生物互作，进而决定植物生态系统应对病害时的稳定性。解析这类互作网络是一项极具挑战性的任务。当前微生物组的推断研究尚处于起步阶段，常受限于底层分析假设以及测序深度方面的局限。此外，在用于识别网络中关键微生物类群的全网络统计指标方面，目前尚未形成统一共识。
本研究依托网络科学（network science）领域的最新进展，包括近期发表的整合影响力视图（Integrated View of Influence, IVI）等多项中心性测度指标，对棉花曲叶病（cotton leaf curl disease, CLCuD）感病、部分耐受及抗病棉花品种的根际与叶际微生物网络中的关键节点展开系统剖析。
研究结果表明，抗棉花曲叶病的树棉（Gossypium arboreum）拥有比例相当的群落关键种，这有助于其抵御生态压力。在抗病品种中，叶际聚集了最具影响力的微生物节点；而在感病品种中，这类节点则富集于根际。
基于枢纽度得分（hubness score）、传播得分（spreading score）以及IVI值，FDH-228（抗病）品种的前10位群落关键物种包括动孢囊菌属（Actinokineospora）、科恩杆菌属（Cohnella）、热芽孢杆菌属（Thermobacillus）、梭菌属（Clostridium）、脱硫产甲烷菌属（Desulfofarcimen）以及菌株MDD-D21。
在PFV-1（部分耐受）品种中，迷踪菌门（Elusimicrobia）、Clostridium-sensu-stricto_12、候选门Woesebacteria（Candidatus woesebacteria）以及戴尔菌属（Dyella）被鉴定为最具影响力的微生物节点。
在PFV-2（感病）品种中，其群落关键物种被鉴定为乔治菌属（Georginia）、涅斯捷连科氏菌属（Nesterenkonia）、Elusimicrobia MVP-88、解纤维梭菌属（Acetivibrio）、Tepedisphaerales目、螯球菌属（Chelatococcus）、亚硝化螺菌属（Nitrosospira）以及菌株RCP2-54。
本研究的这一思路解析了染病与健康植株对病毒病害的响应机制，该响应可能由微生物介导。