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

This study aimed to assess microbial community diversity in recycled nutrient solutions used in soil-less glasshouse 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. Similarities of ITS regions with known species ranged from 95% to 100%. This artificial ecosystem was shown to be microbiologically diverse, since recovered isolate were close to 35 bacterial species, 11 oomycete species and 3 fungal species. Bacteria belonged almost exclusively to γ-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 pathogens, while other isolates could be protective bacteria such as Pseudomonas fluorescens. Oomycetes isolated mostly belonged 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 microorganism 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 avoiding plant disease spreading.