Sanitization of hydroponic farming facilities in Singapore: what, why, and how

Abstract

This study performed microbial analysis of nutrient film technique (NFT) hydroponic systems on three indoor farms in Singapore (the "what"). To justify the necessity of sanitizing hydroponic systems, strong biofilm-forming bacteria were isolated from the facility and investigated for their influence on Salmonella colonization on polyvinyl chloride (PVC) coupons in hydroponic nutrient solutions (the "why"). Finally, sanitization solutions were evaluated with both laboratory-scale and field-scale tests (the "how"). As a result, the microbiome composition in NFT systems was found to be highly farm specific. The strong biofilm formers Corynebacterium tuberculostearicum C2 and Pseudoxanthomonas mexicana C3 were found to facilitate the attachment and colonization of Salmonella on PVC coupons. When forming dual-species biofilms, the presence of C2 and C3 also significantly promoted the growth of Salmonella (P < 0.05). Compared with hydrogen peroxide (H₂O₂) and sodium percarbonate (SPC), sodium hypochlorite (NaOCl) exhibited superior efficacy in biofilm removal. At 50 ppm, NaOCl reduced the Salmonella Typhimurium, C2, and C3 counts to <1 log CFU/cm² within 12 h, whereas neither 3% H₂O₂ nor 1% SPC achieved this effect. In operational hydroponic systems, the concentration of NaOCl needed to achieve biofilm elimination increased to 500 ppm, likely due to the presence of organic matter accumulated during crop cultivation and the greater persistence of naturally formed multispecies biofilms. Sanitization using 500 ppm NaOCl for 12 h did not impede subsequent plant growth, but chlorination byproduct chlorate was detected at high levels in the hydroponic solution and in plants in the sanitized systems without rinsing.

Importance: This study's significance lies first in its elucidation of the necessity of sanitizing hydroponic farming systems. The microbiome in hydroponic systems, although mostly nonpathogenic, might serve as a hotbed for pathogen colonization and thus pose a risk for food safety. We thus explored sanitization solutions with both laboratory-scale and field-scale tests. Of the three tested sanitizers, NaOCl was the most effective and economical option, whereas one must note the vital importance of rinsing the hydroponic systems after sanitization with NaOCl.

Keywords: Salmonella; biofilms; hydroponics; sanitization; sodium hypochlorite.

Fig 1

The key microbial analysis results of NFT hydroponic systems at three commercial indoor farms in Singapore. (a) The microbial loads in different components of NFT systems. Values denoted with different letters are significantly different (P < 0.05). For each data point, 10 samples were collected from each farm (n = 30). (b) The illustration of the NFT systems. (c) The bacteria phyla identified by 16S rDNA sequencing (>1%) from selected samples. (d) Microbiome compositional difference (beta diversity) based on the bacterial composition analysis. Unweighted UniFrac (left, presence of taxa), weighted UniFrac (middle, presence and relative abundance of taxa), and Bray-Curtis (right, presence and relative abundance of taxa) distances are visualized by principal coordinate analysis plots.

Fig 2

Screening of strong biofilm formers from the interior surfaces of hydroponic systems. (a) Biofilm-forming capability and Gram-staining results of the 10 bacterial isolates. The results are based on the average of triplicates. (b) and (c) Single nucleotide polymorphis (SNP) trees based on the maximum likelihood method illustrating the phylogenetic relationships between C2 and C3 and closely related members of the same genus, respectively. The numbers represent bootstrap values. The red IDs represent human clinical isolates, the blue IDs represent environmental isolates, and the black IDs represent strains of unknown origin.

Fig 3

Experimental setups and results showing the effectiveness of C. tuberculostearicum C2 and P. mexicana C3 on the colonization of Salmonella on PVC coupons. (a) Adherence and colonization of S. Brunei on preexisting C. tuberculostearicum C2 and P. mexicana C3 biofilms. Each value is the average of triplicates from three independent experiments. The error bars indicate the standard deviations (SDs). The dotted line represents the limit of detection. Panels a–d show the significance of Salmonella enumeration at different time points on C2- or C3-preformed biofilms, respectively. (b) Salmonella [on xylose lysine deoxycholate (XLD) plates] and total bacteria counts [on tryptone soya agar (TSA) plates] from single- and dual-species biofilms. Each value is the average of triplicates from three independent experiments. The error bars indicate the SDs. *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001, respectively.

Fig 4

Experimental setup and results of the sanitization of S. Typhimurium, C. tuberculostearicum C2, and P. mexicana C3 biofilms grown on PVC coupons. Each value (Log CFU/cm² ± SD) is the average of triplicates from three independent experiments. N.d., not detected, <1 log CFU/cm².