Rhizosphere microorganism diversity associated to tomato in an agroecosystem from Valle de Guasave, Sinaloa, México

Abstract

Rhizosphere microorganism diversity associated to different plant species in Mexican soils has been understudied. Most of those studies have been done  using conventional microbiological techniques, which, although useful, present a limitation  their incapacity to detect unculturable microorganisms, which represent 95-99% of the total microorganisms in soils. The present work employs ribosomal DNA (rDNA) sequencing to overcome this limitation and to improve exploration of the diversity of culturable and non-culturable microorganisms associated to tomato (Solanum lycopersicum, L.) in an agroecosystem from Sinaloa. Genomic DNA from rhizospheric soil was extracted and a hypervariable region on the rDNA was amplified using universal oligonucletides directed to amplify prokaryotic and eukaryotic rDNA. Sequence analysis of 476 and 441 rDNA clones of prokaryotic and eukaryotic origin respectively showed the most abundant phyla. In Eukaryotes, they were Ascomycota (62.1%), Chlorophyta (17.6%) and Basidiomycota (11.4%). The most abundant prokaryotic phyla were Firmicutes (43%), Acidobacteria (17.2%) and Proteobacteria (11.6%). The present work represents, to the best of our knowledge, the most complete characterization of the microorganism diversity associated to tomato rhizosphere. The work discusses the role that species belonging to genuses from prokaryotic (Bacillus and Paenibacillus) or eukaryotic origin (Alternaria) may play in biological control of phytopathogens in the rhizosphere.