Soilless farming system design can determine microbial growth, impact on crops

UNIVERSITY PARK, Pa. — Vegetable production from soilless farming — a method of growing plants in a nutrient-rich solution rather than traditional soil — is significant, according to the U.S. Department of Agriculture (USDA), with more than half of tomatoes, cucumbers and lettuce grown using hydroponics. This fast-growing segment of modern agriculture addresses water scarcity, land limitations and food security, but microbial management remains a challenge, according to a team of researchers at Penn State. The team conducted a study of bacteria in five soilless farming systems and found that hydroponic system design strongly affects microbes in nutrient solution, the growing cycle strongly affects microbial community structure, each system may require different microbial management strategies and leaf contamination is less affected than water microbes.

The researchers experimentally grew the leafy vegetable bok choy to test if and how the different soilless farming system designs affect microbial growth, as well as whether microbial differences impact the plant, which could affect food safety. They published their findings today (Aug. 4) in Applied and Environmental Microbiology.

The U.S. soilless system food market is a rapidly expanding, multimillion-dollar sector with a market size projected to exceed $6 billion in 2026, noted study co-author Francesco Di Gioia, associate professor of vegetable crop science in the College of Agricultural Sciences. Soilless farming systems are playing a major role in the market for premium, local produce such as tomatoes, leafy greens and herbs, he said. For that reason, the findings of this research are essential.

“Microbial management is a significant challenge in soilless farming, acting as a double-edged sword that can either introduce hazards and increase food safety risks or enhance plant health,” said study senior author Jasna Kovac, Lester Earl and Veronica Dorothy Foehr Huck and J. Lloyd Huck Chair in Microbiomes in Food Safety and associate professor of food science. “If introduced into the system, pathogens can spread through recirculating nutrient solutions, making active management of the microbiome a potential tool for their control.”

The five types of soilless growing systems the researchers compared included: deep water culture — in which the roots sit directly in oxygenated nutrient water; Kratky — passive hydroponics with no pumps; nutrient film technique — a thin stream of nutrient solution flows over roots; ebb and flow — in which the roots are periodically flooded and drained; and drip irrigation — where the nutrient solution drips onto the roots. The drip irrigation system had the highest bacterial counts.

They looked at microbes in two places. First, the researchers measured concentration of bacteria in the nutrient solution feeding the plants. They also looked at which bacteria were present using 16S rRNA gene sequencing, a technique that identifies bacteria by sequencing a gene common to all bacteria. Second, they measured bacterial counts directly on the leaves to assess whether bacteria from nutrient solution transmit to leaves.

“In soilless farming, the microbial community can affect plant growth, nutrient cycling, disease suppression, food safety and crop yield,” said Kovac. “Some microbes are beneficial; some are harmful. Understanding the microbial ecology could help improve soilless farming food safety and productivity, reduce contamination risk and allow the design of safer systems.”

The team, led by study first author Auja Bywater, dual-title doctoral degree student in food science and international agriculture and development, reported that system design influenced bacterial levels and the composition of the microbiome — the community of microorganisms including bacteria, viruses and fungi — that live in the nutrient solution. Microbiome load and composition also varied among growing cycles, although some bacterial groups always were present, suggesting that they are well adapted to soilless farming environments. The team also found that higher pH of nutrient solution was associated with reduced bacterial counts.

Differences in microbial load and composition may carry food safety implications, however the question of whether systems supporting higher microbial loads provide more favorable conditions for survival and persistence of foodborne pathogens, if introduced, remains unanswered, Bywater explained. Even though the bacterial load in nutrient solution differed among systems, bacterial counts on bok choy leaves were similar across all systems.

“This suggests that the microbiome in the water did not directly translate to contamination on leaves,” she said.

These results — showing that the systems really do play a big part in bacterial load, as well as what type of bacteria are present — are important for the industry, Bywater pointed out. Follow-up research on microbiomes in soilless farming systems might influence future regulations governing hydroponics production, she added.

“There's a lot of talk in the industry right now about how these systems should be regulated. Our finding that microbial load and dynamics varied by system and growth cycle highlight considerations for regulation and demonstrate the need for further investigation of how survival and persistence of foodborne pathogens is influenced by system design and practices. There's still a lot that we don't know. This study brings up many questions for future research," Bywater said.

Contributing to the research were Aline Novaski Seffrin, doctoral degree candidate in agricultural and environmental plant science, and Jordan Bisanz, assistant professor of biochemistry and molecular biology, Dorothy Foehr and J. Lloyd Huck Early Career Chair in Host-Microbiome Interactions contributed to the research. This research was supported by the services of the One Health Microbiome Center Colab.

This research was supported by the Pennsylvania Department of Agriculture grant C940001528, the U.S. Department of Agriculture's National Institute of Food and Agriculture and Hatch Appropriation under Project PEN04853 and Accession 7005519, and the Multistate project 4666, the Lester Earl and Veronica Casida Career Development Endowment at Penn State, and the Huck Chair in Microbiomes in Food Safety from Penn State’s Huck Institutes of the Life Sciences. This content is solely the responsibility of the authors and does not necessarily represent the views of the funders.