Molecular Identification of Microbial Communities in the Recycled Nutrient Solution of a Tomato Glasshouse Soil-Less Culture

Abstract

This study aimed to assess microbial community diversity in recycled nutrient solutions used in soil-less glass- house cultivation of tomato. One hundred bacterial strains, twenty oomycetes and 6 fungi were isolated and identified through genomic DNA isolation, PCR amplification of the ribosomal DNA region and database interrogations. Similari- ties of ITS regions with known species ranged from 95% to 100%. This artificial ecosystem was shown to be microbio- logically diverse, since recovered isolate were close to 35 bacterial species, 11 oomycete species and 3 fungal species. Bacteria belonged almost exclusively to � -Proteobacteria and Firmicutes, with most represented genera being Bacillus, Acinetobacter, Klebsiella and Serratia. A few bacterial sequences grouped with clones similar to plant and human patho- gens, while other isolates could be protective bacteria such as Pseudomonas fluorescens. Oomycetes isolated mostly be- longed to the genus Pythium (19 isolates) and were phylogenetically related to common cosmopolitan soil inhabitants or phytopathogenic Pythium species. The six fungal isolates were in 2 genera, Rhizopus and Caesia; Rhizopus isolates were closely related to the post harvest pathogen Rhizopus stolonifer. This original work adds to the efforts of assessing micro- organism diversity in recycled nutrient solutions commonly used in glasshouse vegetable production; microbial diversity was high and included potential plant pathogens. This study demonstrated the existence of a wide cultivable microbial community in the nutrient solution before recycling and recirculation and supported the necessity for disinfecting nutrient solutions used in soil-less cultivation systems, during the recycling process, in order to ensure crop sanitation and avoid- ing plant disease spreading.