title: Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields.
abstract: Very few soil quality indicators include disease-suppressiveness criteria. We assessed whether 64 16S rRNA microarray probes whose signals correlated with tobacco black root rot suppressiveness in greenhouse analysis could also discriminate suppressive from conducive soils under field conditions. Rhizobacterial communities of tobacco and wheat sampled in 2 years from four farmers' fields of contrasted suppressiveness status were compared. The 64 previously identified indicator probes correctly classified 72% of 29 field samples, with nine probes for Azospirillum, Gluconacetobacter, Sphingomonadaceae, Planctomycetes, Mycoplasma, Lactobacillus crispatus and Thermodesulforhabdus providing the best prediction. The whole probe set (1033 probes) revealed strong effects of plant, field location and year on rhizobacterial community composition, and a smaller (7% variance) but significant effect of soil suppressiveness status. Seventeen additional probes correlating with suppressiveness status in the field (noticeably for Agrobacterium, Methylobacterium, Ochrobactrum) were selected, and combined with the nine others, they improved correct sample classification from 72% to 79% (100% tobacco and 63% wheat samples). Pseudomonas probes were not informative in the field, even those targeting biocontrol pseudomonads producing 2,4-diacetylphloroglucinol, nor was quantitative polymerase chain reaction for 2,4-diacetylphloroglucinol-synthesis gene phlD. This study shows that a subset of 16S rRNA probes targeting diverse rhizobacteria can be useful as suppressiveness indicators under field conditions.
authors.affiliation: Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, Ecologie Microbienne, UMR5557, Villeurbanne, France; Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology, České Budějovice, Czech Republic.
authors.forename: Martina
authors.initials: M
authors.lastname: Kyselková
authors.forename: Juliana
authors.initials: J
authors.lastname: Almario
authors.forename: Jan
authors.initials: J
authors.lastname: Kopecký
authors.forename: Markéta
authors.initials: M
authors.lastname: Ságová-Marečková
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Haurat
authors.forename: Daniel
authors.initials: D
authors.lastname: Muller
authors.forename: Geneviève L
authors.initials: GL
authors.lastname: Grundmann
authors.forename: Yvan
authors.initials: Y
authors.lastname: Moënne-Loccoz
mesh_terms: D058448:Biota; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000517:prevention & control*; D018517:Plant Roots / Q000254:growth & development*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D014026:Nicotiana / Q000254:growth & development*
chemical_list: D012336:RNA, Ribosomal, 16S