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Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields
Author(s) -
Kyselková Martina,
Almario Juliana,
Kopecký Jan,
SágováMarečková Markéta,
Haurat Jacqueline,
Muller Daniel,
Grundmann Geneviève L.,
MoënneLoccoz Yvan
Publication year - 2014
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12131
Subject(s) - biology , 16s ribosomal rna , ribosomal dna , horticulture , agronomy , bacteria , phylogenetics , gene , genetics
Summary Very few soil quality indicators include disease‐suppressiveness criteria. We assessed whether 64 16 S 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 A zospirillum , G luconacetobacter , S phingomonadaceae , P lanctomycetes , M ycoplasma , L actobacillus crispatus and T hermodesulforhabdus 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 A grobacterium , M ethylobacterium , O chrobactrum ) 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 16 S rRNA probes targeting diverse rhizobacteria can be useful as suppressiveness indicators under field conditions.