Bacterial Shifts in Nutrient Solutions Flowing Through Biofilters Used in Tomato Soilless Culture


In soilless culture, slow filtration is used to eliminate plant pathogenic microorganisms from nutrient solutions. The present study focused on the characterization and the potential functions of microbial communities colonizing the nutrient solutions recycled on slow filters during a whole cultivation season of 7 months in a tomato growing system. Bacterial microflora colonizing the solutions before and after they flew through the columns were studied. Two filters were amended with Pseudomonas putida (P-filter) or Bacillus cereus strains (B-filter), and a third filter was a control (C-filter). Biological activation of filter unit through bacterial amendment enhanced very significantly filter efficacy against plant potential pathogens Pythium spp. and Fusarium oxysporum. However, numerous bacteria (103–104 CFU/mL) were detected in the effluent solutions. The community-level physiological profiling indicated a temporal shift of bacterial microflora, and the metabolism of nutrient solutions originally oriented towards carbohydrates progressively shifted towards degradation of amino acids and carboxylic acids over the 7-month period of experiment. Single-strand conformation polymorphism fingerprinting profiles showed that a shift between bacterial communities colonizing influent and effluent solutions of slow filters occurred. In comparison with influent, 16S rDNA sequencing revealed that phylotype diversity was low in the effluent of P- and C-filters, but no reduction was observed in the effluent of the B-filter. Suppressive potential of solutions filtered on a natural filter (C-filter), where the proportion of Proteobacteria (α- and β-) increased, whereas the proportion of uncultured candidate phyla rose in P- and B-filters, is discussed.

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This project was supported by the Regional Councils of Brittany and Pays de la Loire and by the French Ministry of Research.

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Correspondence to Patrice Rey.

Electronic supplementary material

Supplementary Table 1

Abundance of 16S–ribosomal RNA gene phylotypes in the clone libraries constructed from nutrient solutions sampled from influent and effluent of C-filter (iClib, eClib), B-filter (iBlib, eBlib) and P-filter (iPlib, ePlib). For each phylotype affiliation, the closest described relative from the GenBank database with its accession number (in brackets) and the percentage of similarity as given by the Blast program are provided. (DOCX 172 kb)

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Renault, D., Déniel, F., Vallance, J. et al. Bacterial Shifts in Nutrient Solutions Flowing Through Biofilters Used in Tomato Soilless Culture. Microb Ecol 76, 169–181 (2018).

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  • Bacterial communities
  • Soilless culture
  • Recirculating solutions
  • Single-strand conformation polymorphism
  • Community level physiological profiling