Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacterial Serratia proteamaculans and Serratia plymuthica. Rhizoctonia solani AG-3 Rhs1AP

Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. To understand the functional response of the fungal phytopathogen Rhizoctonia solani to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had fold values exceeding 8x and for further analyses this cut-off value was used. Functional classification of DEGs revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. In conclusion, it was found out that most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere. Overall design: Transcriptome profiling of fungal hyphae from treatments challenged with the bacteria and from control treatments containing only the fungus were generated by deep sequencing, in triplicate, by using Illumina® TruSeq.

加深对根际（rhizosphere）细菌-真菌互作的理解，有助于将细菌成功开发为植物真菌病害的生物防治制剂，为可持续农业中的化学农药提供替代方案。为明确植物病原真菌立枯丝核菌（Rhizoctonia solani）对不同细菌的功能响应，并阐明该真菌所利用的分子机制属于普遍应激反应还是更为特异性的应答，我们利用RNA测序（RNA-seq），分析了与沙雷氏菌属（Serratia）S4和AS13菌株互作过程中，立枯丝核菌Rhs1AP融合群3（AG-3）的全转录组表达谱。转录组分析结果显示，在与沙雷氏菌互作期间，该真菌约10%的转录本发生了差异表达。S4和AS13特异性的差异表达基因（differentially expressed genes, DEG）数量分别为866个和292个，而两个处理组中共有的差异表达基因则有1035个。分别有460个和242个基因的表达倍数差异超过8倍，后续分析均采用该阈值作为筛选标准。对差异表达基因进行功能归类分析后发现，该真菌的基因表达整体发生了显著改变，涉及异生物质降解、毒素与抗氧化产物合成、能量代谢、碳水化合物与脂质代谢以及菌丝重排等相关基因均受到转录调控。综上，本研究发现，在两种沙雷氏菌分离株处理下，大部分基因的表达调控模式一致，但也存在部分菌株特异性的应答反应。本研究的结果可为后续生物防治相关研究以及根际细菌-真菌互作的深入探索提供有益参考。实验设计：本研究通过Illumina® TruSeq建库试剂盒进行深度测序，设置三组生物学重复，分别对细菌处理组与仅含真菌的对照组的真菌菌丝进行转录组测序分析。