Submitted to: Food Control
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2025
Publication Date: 2/27/2025
Citation: Gu, G., Zhou, B., Yang, Y., Nou, X., Millner, P.D., Zhang, B., Luo, Y. 2025. Microbial profiles of baby spinach produced hydroponically in controlled environment agriculture and from soil-based open field production practice. Food Control. https://doi.org/10.1016/j.foodcont.2025.111198.
DOI: https://doi.org/10.1016/j.foodcont.2025.111198

Interpretive Summary: Hydroponic system represents a novel alternative to traditional soil-based farm practice. While the microbial profile of leafy greens grown in soil has been well documented, the same information for the leafy greens grown hydroponically in controlled environment agriculture (CEA) is scarce. In this study, a team of USDA scientists investigated the bacterial and fungal profiles of ready-to-eat baby spinach grown hydroponically and in soil-based systems. Although the overall total culturable microbial populations are similar on spinach from both growing systems, substantial distinctions were revealed in spinach microbiome profiles. Pseudomonas was the dominant bacteria identified on the products from soil-based systems, while the cyanobacterial genus Synechocystis was most abundant in hydroponically grown spinach sampled in our studies. Findings provide important insights into how cultivation environments influence the microbial composition of a widely consumed leafy green and will benefit both consumers and producers.

Technical Abstract: Consumption of fresh leafy greens grown hydroponically in controlled environmental agriculture (CEA) has been rapidly increasing. However, no information is currently available regarding the microbial profiles of CEA leafy greens grown hydroponically (GH) on the market compared to those grown in soil (GS) via traditional open field production. In this study, packaged ready-to-eat baby spinach, including both GH and GS products, was sampled from three occasions at retail stores in the Mid-Atlantic region. Aerobic bacterial count (AC) and yeast and mold (YM) populations were determined. Microbiome was analyzed via high throughput 16S rRNA gene and ITS amplicon sequencing for comparison of bacterial and fungal communities, respectively. The AC (4.8-6.2 log CFU/g) and YM (2.0-3.8 log CFU/g) vary from trial to trial, but they are generally comparable between GH and GS. However, significant difference was observed on microbial community between GH and GS products. The dominant microbes on GS baby spinach were bacterial genus of Pseudomonas (average relative abundance: 70.08 %) and fungal genus Cystofilobasidium (52.89 %). The most abundant bacteria identified on GH baby spinach was a Cyanobacteria genus Synechocystis (25.32 %), and the major fungal genera were Penicillium (22.33 %) and Cladosporium (15.37 %). In general, alpha diversities of both bacterial and fungal communities on GH baby spinach were higher than GS samples (p<0.05). To our knowledge, this is the first report of Cyanobacteria presence in RTE baby spinach. Findings may point out new research regarding the potential interaction of Cyanobacteria with foodborne human pathogens and spoilage microorganism, and the impact on food safety, quality, and shelf life. Information is also useful for the understanding of blue-green algae in GH environment and transfer to leafy greens grown hydroponically.