Updates on Microbes, Greenhouses, and Hydroponics

The tiny world of microbes just got a lot bigger, and 2025 is set to bring groundbreaking advancements to everyday growing practices. From inoculants and biologicals to beneficial microbes and even pathogens, the year ahead is all about embracing microbial innovation in greenhouses and hydroponics.

Explore these research highlights, each showcasing the incredible role of the microbiome in shaping sustainable agriculture.

1. The Greenhouse Phyllosphere Microbiome and Bumblebees as Vectors

• Title: The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites
• Year Published: 2022
• Publication: American Society for Microbiology: Microbiology Spectrum
• Research Institutions: University of Antwerp (Belgium) and Research Centre Hoogstraten (Belgium)
• Key Findings:
  • Investigated the phyllosphere microbiome of greenhouse-grown tomatoes and strawberries.
  • Discovered low diversity and abundance of bacterial communities, with notable variations over time and space.
  • Highlighted the role of bumblebees and predatory mites as vectors for bacteria in greenhouse environments.
  • Emphasized the need to understand microbial transport dynamics to improve greenhouse crop health.

Summary:

Dr. Marie Legein and her team at the University of Antwerp explored the often-overlooked microbe ecosystems within hydroponic greenhouses. They found that bumblebees and predatory mites don’t just help plants by pollinating or eating pests—they also carry bacteria with them. By identifying Snodgrasella and Gilliamella on both plants and bees, the team uncovered a new connection between pollination and microbial diversity. This breakthrough emphasizes the potential of biological interactions to enrich greenhouse microbiomes and boost plant health.

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2. How Microbes Live in Hydroponic Greenhouses with Hairy Root Disease

• Title: Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease
• Year Published: 2021
• Publication: Oxford University Press: FEMS Microbiology Ecology
• Research Institutions: KU Leuven (Belgium) and Research Centre Hoogstraten (Belgium)
• Key Findings:
  • Investigated bacterial communities in the rockwool substrate of tomato plants grown in hydroponic greenhouses, comparing healthy and Hairy Root Disease-infested environments.
  • Found that bacterial diversity was higher in HRD-infested greenhouses compared to healthy ones.
  • Paenibacillus, a genus with potential biocontrol properties, was more abundant in healthy greenhouses.
  • Identified rhizogenic Agrobacterium as the pathogen causing HRD and found it prevalent in infested greenhouses.
  • The study suggests that maintaining a higher Paenibacillus to Agrobacterium ratio could reduce Hairy Root Disease risk.

Summary:

Dr. Pablo Vargas and the team at KU Leuven took on the challenge of understanding the dynamics of microbes in hydroponic tomato greenhouses. By studying the bacteria in rockwool, they uncovered a tug-of-war between beneficial microbes like Paenibacillus and rhizogenic Agrobacterium, the cause of Hairy Root Disease. Their research highlighted the importance of microbial balance: greenhouses with a higher ratio of Paenibacillus were healthier and more productive. This points to new ways of using beneficial bacteria to address plant diseases and improve hydroponic farming practices.

3. Hydroponic Rockwool, Microbes, and Root Microbiome

• Title: The Hydroponic Rockwool Root Microbiome: Under Control or Underutilized?
• Year Published: 2023
• Publication: MDPI: Microorganisms
• Research Institutions: University of New England (Australia) and Western Sydney University (Australia)
• Key Findings:
  • Reviewed the microbial ecology of hydroponic rockwool systems and their potential to improve crop outcomes.
  • Found that the root microbiome in rockwool is shaped by plants’ organic exudates but has lower diversity compared to soil systems.
  • Demonstrated that hydroponic systems offer opportunities to actively steer the root microbiome for better disease control and plant growth.
  • Identified beneficial microbes like Trichoderma and Pseudomonas with potential for biocontrol and plant growth promotion.
  • Suggested that limited microbial diversity might hinder resilience to disturbances, but strategic microbiome management could address this.

Summary:

Dr. Phil Thomas and the team at the University of New England explored the fascinating dynamics of the hydroponic microbes in rockwool and roots. Unlike soil, rockwool provides a clean slate where plants cultivate their microbial partners from scratch. The team uncovered opportunities to harness beneficial microbes for disease control and crop steering, noting that microbes like Trichoderma and Pseudomonas could play vital roles. Their research highlights the untapped potential of microbiome management in hydroponic systems, offering growers new ways to enhance plant health and yield.

4. Hydroponic Greenhouses and Water Microbes

• Title: Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches
• Year Published: 2020
• Publication: Frontiers in Microbiology
• Research Institutions: Université de Brest (France)
• Key Findings:
  • Investigated the microbiota of water in hydroponic tomato greenhouses, focusing on its diversity and functionality.
  • Found that microbial communities varied significantly based on storage conditions (rainwater vs. groundwater) and greenhouse locations.
  • Open-tank storage promoted the growth of aerobic chemoheterotrophic bacteria, such as Sphingomonadaceae and Hyphomicrobiaceae.
  • Groundwater directly pumped from wells exhibited the lowest microbial diversity but had higher proportions of bacteria involved in nitrogen cycling.
  • Biofiltration systems reduced pathogen loads, such as Pythium spp. and Fusarium oxysporum, while maintaining microbial diversity.

Summary:

Dr. Adeline Picot and the team at Université de Brest explored the hidden world of water microbes in hydroponic greenhouses. They discovered that water storage methods shape microbial communities: open tanks encouraged bacteria that thrive in oxygen-rich environments, while groundwater harbored microbes involved in nutrient cycling. By introducing biofiltration, the team demonstrated a way to reduce plant pathogens without harming beneficial microbes. Their work reveals how managing water microbiota can enhance greenhouse sustainability and disease prevention.

5. Hydroponic Plants Dictate Root Microbe Composition

• Title: Plants Dictate Root Microbial Composition in Hydroponics and Aquaponics
• Year Published: 2022
• Publication: Frontiers in Microbiology
• Research Institutions: University of Gothenburg (Sweden) and Wageningen University & Research (Netherlands)
• Key Findings:
  • Demonstrated that under hydroponic and aquaponic conditions, plants have a stronger influence on shaping their rhizosphere microbial community than external sources like water.
  • Found that lettuce (Lactuca sativa) cultivated in soil-less systems can select microbial taxa aligned with their needs, regardless of upstream microbial communities.
  • Showed that sterilization of water and media had less impact on microbial composition compared to plant-driven selection.
  • Highlighted the role of beneficial microbes like Bacillus amyloliquefaciens in supporting plant health under hydroponic conditions.

Summary:

Dr. Victor Lobanov and the team at the University of Gothenburg explored how plants shape their own microbial communities in soil-less systems. By growing lettuce in hydroponics and aquaponics, they discovered that plants act as gatekeepers, selecting specific microbes to form their rhizosphere communities. Even when upstream water or media were sterilized, the plants determined which microbes thrived near their roots. This research reveals how plants, not just their environments, drive microbial diversity in hydroponic farming, paving the way for targeted microbiome management to enhance crop productivity.

6. The Microbes, Hydroponic Lettuce and Phytophthora

• Title: Unveiling the Microbiome of Hydroponically Cultivated Lettuce: Impact of Phytophthora cryptogea Infection on Plant-Associated Microorganisms
• Year Published: 2024
• Publication: Oxford University Press: FEMS Microbiology Ecology
• Research Institutions: KU Leuven (Belgium)
• Key Findings:
  • Investigated the impact of the oomycete pathogen Phytophthora cryptogea on the microbiomes of hydroponically grown lettuce in three greenhouses.
  • Found significant shifts in bacterial communities between healthy and infected plants, particularly in the rhizosphere.
  • Identified an increase in the abundance of Pseudomonas and Flavobacterium in symptomatic plants, suggesting a potential role in disease dynamics or plant responses.
  • Highlighted the importance of bacterial diversity in the rhizosphere for plant health and resistance to pathogens.
  • Emphasized the need for further exploration of Pseudomonas and Flavobacterium spp. as potential biocontrol organisms for managing Phytophthora cryptogea.

Summary:

Dr. Liese Vlasselaer and the team at KU Leuven delved into the microbial dynamics of hydroponic lettuce, focusing on how infection by Phytophthora cryptogea reshapes the plant’s microbiome. They discovered that infected plants attracted higher numbers of beneficial bacteria like Pseudomonas and Flavobacterium, which could play a role in mitigating disease effects. This fascinating “cry-for-help” response by plants demonstrates how microbiomes adapt under stress, paving the way for new biocontrol strategies to protect hydroponic crops against devastating pathogens.

Conclusion: Harnessing the Power of Microbes in Greenhouse and Hydroponic Systems

The six studies reviewed here underscore the pivotal role that microbiomes play in shaping the future of sustainable agriculture. From understanding how pollinators like bumblebees and mites carry beneficial bacteria, to revealing the dynamic microbial shifts in hydroponic systems, these findings highlight the complex yet powerful relationships between plants, microbes, and their environments. You can learn more about microbes in hydroponics in this blog.

Across diverse studies, researchers have shown how plants influence their microbial communities, often selecting microbes that enhance growth or combat disease. Beneficial genera like Paenibacillus, Pseudomonas, and Flavobacterium consistently emerge as key players, offering insights into biocontrol and plant health promotion. At the same time, advances in filtration and water microbiota management reveal practical ways to suppress pathogens like Phytophthora and Agrobacterium without compromising microbial diversity.

Together, these breakthroughs point to a transformative approach to agriculture where microbial ecosystems are actively managed and optimized. By steering microbiomes in hydroponic and greenhouse systems, growers can improve disease resistance, nutrient uptake, and overall crop resilience. As we move forward, integrating these findings into everyday growing practices promises a future of healthier plants, reduced chemical reliance, and more sustainable farming.

The microbial revolution has only just begun, and these studies provide a glimpse of the potential waiting to be unlocked in 2025 and beyond.

Disclaimer

The information we present in this blog is based on collating published peer-reviewed scientific literature, and sources we think are reliable. This is by no means an exhaustive review of pathogens. This blog gives a small glimpse of what is known about pathogens. We encourage growers to do more research on the pathogens concerning their crops and hydroponic systems. We are not plant pathologists; thus, the information presented should not be used as professional advice to treat pathogens or operate your system.

David Santos is the CMO of Healthy Hydroponics InnoTech