Perazzolli Michele, Herrero Noemí, Sterck Lieven, Lenzi Luisa, Pellegrini Alberto, Puopolo Gerardo, Van de Peer Yves, Pertot Ilaria
Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige, Italy.
Present Address: Institute of Entomology, Biology Centre-The Czech Academy of Sciences, Branišovská 31/1160, České Budějovice, 37005, Czech Republic.
BMC Genomics. 2016 Oct 27;17(1):838. doi: 10.1186/s12864-016-3174-4.
Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms.
A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea.
This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.
土壤微生物是土壤肥力和植物健康的关键决定因素。土壤植物病原真菌是全球范围内造成作物损失的最重要原因之一。微生物生物防治剂作为控制植物病原土壤微生物的替代品已得到广泛研究，但它们之间的分子相互作用主要是在二元培养中进行表征，而未考虑土壤微生物群落。我们采用RNA测序方法来阐明土壤微生物群落对植物病原体及其生物防治剂的分子相互作用，以研究微生物激活的分子模式。
在可控条件下，将含有11种土壤微生物的简化土壤微宇宙与植物根病原体（蜜环菌）及其生物防治剂（绿色木霉）一起培养24小时。每个重复样本获得了超过4600万对末端读数，总共鉴定出28309个差异表达基因。通路分析揭示了土壤微生物对土壤基质的恶劣条件以及相互的微生物竞争/合作关系的复杂适应性。简化土壤微宇宙能特异性识别植物病原体及其生物防治剂：分别针对竞争性（绿色木霉）或非竞争性（蜜环菌）微生物激活防御反应机制和中性适应过程。此外，在同时存在蜜环菌和绿色木霉的简化土壤微宇宙中，抗性机制的激活占主导地位。绿色木霉的生物防治过程在简化土壤微宇宙培养期间就已被激活，可能是为了在竞争生态系统中占据生态位，并且引入蜜环菌并未进一步增强其生物防治过程。
这项工作是朝着理解土壤生态系统中植物病原体与生物防治剂之间分子相互作用迈出的又一步。对简化土壤微宇宙的全局转录分析揭示了土壤环境中的复杂代谢适应性以及对拮抗或中性入侵者的特异性反应。
