Kyselková Martina, Kopecký Jan, Frapolli Michele, Défago Geneviève, Ságová-Marecková Markéta, Grundmann Geneviève L, Moënne-Loccoz Yvan
Université de Lyon, Lyon, France.
ISME J. 2009 Oct;3(10):1127-38. doi: 10.1038/ismej.2009.61. Epub 2009 Jun 25.
Work on soils suppressive to Thielaviopsis basicola-mediated tobacco black root rot has focused on antagonistic pseudomonads to date. The role of non-Pseudomonas rhizosphere populations has been neglected, and whether they differ in black root rot-suppressive versus -conducive soils is unknown. To assess this possibility, tobacco was grown in a suppressive and a conducive soil of similar physicochemical properties, and rhizobacterial community composition was compared using a 16S rRNA taxonomic microarray. The microarray contains 1033 probes and targets 19 bacterial phyla. Among them, 398 probes were designed for Proteobacteria, Firmicutes, Actinomycetes, Cyanobacteria and Bacteroidetes genera/species known to include strains relevant for plant protection or plant growth promotion. Hierarchical clustering as well as principal component analysis of microarray data discriminated clearly between black root rot-suppressive and -conducive soils. In contrast, T. basicola inoculation had no impact on rhizobacterial community composition. In addition to fluorescent Pseudomonas, the taxa Azospirillum, Gluconacetobacter, Burkholderia, Comamonas and Sphingomonadaceae, which are known to comprise strains with plant-beneficial properties, were more prevalent in the suppressive soil. Mycobacterium, Bradyrhizobium, Rhodobacteraceae, Rhodospirillum and others were more prevalent in the conducive soil. For selected taxa, microarray results were largely corroborated by quantitative PCR and cloning/sequencing. In conclusion, this work identified novel bacterial taxa that could serve as indicators of disease suppressiveness in soil-quality assessments, and it extends the range of bacterial taxa hypothesized to participate in black root rot suppression.
迄今为止，针对抑制根串珠霉介导的烟草黑根腐病的土壤研究主要集中在拮抗假单胞菌上。非假单胞菌根际菌群的作用一直被忽视，而且它们在抑制黑根腐病的土壤和利于发病的土壤中是否存在差异尚不清楚。为了评估这种可能性，将烟草种植在理化性质相似的抑制性土壤和利于发病的土壤中，并使用16S rRNA分类微阵列比较根际细菌群落组成。该微阵列包含1033个探针，可靶向19个细菌门。其中，398个探针是针对变形菌门、厚壁菌门、放线菌门、蓝细菌门和拟杆菌门中已知包含与植物保护或植物生长促进相关菌株的属/种设计的。微阵列数据的层次聚类以及主成分分析清楚地区分了抑制黑根腐病的土壤和利于发病的土壤。相比之下，接种根串珠霉对根际细菌群落组成没有影响。除荧光假单胞菌外，已知包含具有植物有益特性菌株的固氮螺菌属、葡糖醋杆菌属、伯克霍尔德菌属、丛毛单胞菌属和鞘脂单胞菌科在抑制性土壤中更为普遍。分枝杆菌属、慢生根瘤菌属、红杆菌科、红螺菌属等在利于发病的土壤中更为普遍。对于选定的分类群，微阵列结果在很大程度上得到了定量PCR和克隆/测序的证实。总之，这项研究确定了新的细菌分类群，这些分类群可作为土壤质量评估中疾病抑制性的指标，并扩展了假设参与抑制黑根腐病的细菌分类群范围。
