Rhizosphere microorganisms associated to tomato in an agroecosystem from Guasave Valley, Sinaloa, Mexico

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 present an important limitation due to 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 194 and 384 rDNA clones of prokaryotic and eukaryotic origin respectively showed that for eukaryotes, the most abundant phylum was Ascomycota (59%), followed by Chlorophyta (21%) and Basidiomycota (12%), while for Prokaryotes, the phylum Firmicutes (45%) was the most abundant followed by Proteobacteria (14.7%) and Gemmatimonadetes (13.1%). This contribution represents the most complete characterization of the microorganism diversity associated to tomato rhizosphere. The work discusses the role that species belonging to genera from prokaryotic (Bacillus and Paenibacillus) or eukaryotic origin (Alternaria) identified on this work, could play in the rhizosphere of tomato and the biological control of phytopathogens in this species.