Data_Sheet_1_Response of Tomato Rhizosphere Bacteria to Root-Knot Nematodes, Fenamiphos and Sampling Time Shows Differential Effects on Low Level Taxa.PDF

A factorial taxonomic metabarcoding study was carried out to determine the effect of root-knot nematodes (Meloidogyne incognita, RKN) and the nematocide fenamiphos on the rhizosphere microbiome of tomato. Plants inoculated (or not) with RKN second-stage juveniles (J2), and treated (or not) with the nematocide, were tested in a 6 months greenhouse assay using a RKN-free soil proceeding from an organic crop. Rhizosphere soil was sampled at J2 inoculation, 3 months later (before the second nematocidal treatment), and again after 3 months. At each sampling, the RNAs were extracted and the 16S rRNA V4 regions sequenced with a Next Generation Sequencing (NGS) protocol. Changes in bacteria metagenomic profiles showed an effect of the treatments applied, with different representations of taxa in samples receiving nematodes and fenamiphos, at the two sampling times. In general, a tendence was observed toward an increase number of OTUs at 6 months, in all treatments. β-Proteobacteria were the most abundant class, for all treatments and times. When compared to soil before transplanting, the presence of tomato roots increased frequency of Actinobacteria and Thermoleophilia, reducing abundance of Solibacteres. At lowest taxonomic levels the samples clustered in groups congruent with the treatments applied, with OTUs differentially represented in relation to RKN and/or fenamiphos applications. Bacillus, Corynebacterium, Streptococcus, and Staphylococcus were more represented at 6 months in samples inoculated with RKN. The nematodes with the nematocide application increased the emergence of rare OTUs or reduced/enhanced the abundance of other taxa, from different lineages.

本研究采用析因设计分类学宏条形码（metabarcoding）技术，探究根结线虫（Meloidogyne incognita，简称RKN）与杀线虫剂克线磷（fenamiphos）对番茄根际微生物组的影响。本试验采用源自有机种植体系的无根结线虫土壤，设置接种/不接种RKN二龄幼虫（J2）、施用/不施用该杀线虫剂的四组处理，开展为期6个月的温室培养试验。分别于RKN二龄幼虫接种时、接种后3个月（第二次杀线虫剂施用前）及再培养3个月后三个时间点采集根际土壤样本。每个采样时间点均提取RNA，采用下一代测序（Next Generation Sequencing，NGS）技术对16S rRNA的V4可变区进行测序。细菌宏基因组谱的变化显示，施加的处理对其存在显著影响；两个采样时间点下，接种根结线虫与施用克线磷的样本中类群的相对丰度均存在显著差异。总体而言，所有处理组在试验进行至6个月时，操作分类单元（Operational Taxonomic Unit，OTU）的数量均呈现上升趋势。在所有处理组与采样时间点中，β-变形菌纲（β-Proteobacteria）均为丰度最高的类群。与移栽前的初始土壤相比，番茄根系的定植显著提升了放线菌门（Actinobacteria）与热孢菌纲（Thermoleophilia）的相对频率，同时降低了溶杆菌纲（Solibacteres）的丰度。在最低分类学层级上，样本的聚类结果与施加的处理组完全匹配，且部分OTU的相对丰度与RKN接种及/或克线磷施用存在显著关联。接种根结线虫的样本在试验进行至6个月时，芽孢杆菌属（Bacillus）、棒状杆菌属（Corynebacterium）、链球菌属（Streptococcus）与葡萄球菌属（Staphylococcus）的相对丰度显著升高。同时接种根结线虫并施用克线磷的处理，既可促进稀有OTU的出现，也可上调或下调不同进化分支类群的丰度。