Corky root severity, root knot nematode galling and microbial communities in soil, rhizosphere and rhizoplane in organic and conventional greenhouse compartments

• Tomato corky root was initially more severe in a conventional vs. organic greenhouse.
• Root knot nematode galling was also more severe in the conv. vs. org. greenhouse.
• Corky root was negatively correlated with soil C and N, O2 uptake rate, and yield.
• Corky root suppression was associated with certain DNA bands distinguished by DGGE.
• Rhizoplane microbes were largely subsets of those in rhizosphere and bulk soil.

Organic and conventional greenhouse compartments were set up to compare tomato production, disease development and microbial communities in two systems side by side. After one year, the organic greenhouse was split into two sections: one where straw was added to the soil (to reduce soil nitrogen) and the other without straw. This paper reports on naturally emerging corky root (CR) disease and root knot nematode (RKN) galling in the second and third years of the experiment. CR increased over the years in all systems, but earlier in the conventional system, so that there were significant differences between the two organic versus the conventional systems in the second year but not anymore in the third year. RKN galling became apparent in the third year, particularly in the conventional system and rarely in the organic systems. CR severity was significantly negatively correlated with dissolved organic carbon content, total carbon, nitrogen concentrations and oxygen uptake rate in soil, and with tomato yield. RKN galling was too rare to be related to any variables. CR severity classes were significantly separated based on selected operational taxonomic units (OTUs) or phylotypes of 16S rDNA for bacteria and actinomycetes and of 18S rDNA ITS for fungi detected by denaturing gradient gel electrophoresis (DGGE). Microbial communities in the rhizoplane were largely subsets of those in the rhizosphere and bulk soil, but the distributions of OTUs over different habitats were similar for the conventional and recently converted organic systems. These results may stimulate research into selection of microbial communities from one habitat into neighboring ones to support the hypothesis of microbial cycling in ecosystems.