Hydroponic lettuce producers face ongoing challenges in optimizing growth, nutrient efficiency and crop resilience in soilless systems.
A new study published in the International Journal of Molecular Sciences by researchers from the Institute for Advanced Learning and Research (IALR) reveals that a naturally occurring beneficial bacterium can significantly enhance lettuce growth while triggering coordinated changes in plant gene expression and root microbial communities. The findings offer a biological pathway to improve productivity in controlled environment agriculture without increasing chemical inputs.
The challenge
Hydroponic systems are central to controlled environment agriculture, allowing growers to produce high yields with limited land and water. However, maximizing plant performance in these systems can be difficult. Crops often experience physiological stress, nutrient imbalances and reduced resilience due to the absence of natural soil ecosystems.
As growers seek sustainable strategies to improve crop health and efficiency, interest has grown in plant growth-promoting bacteria that can function in hydroponic environments.
“Understanding how beneficial microbes work in hydroponic systems is critical for developing sustainable solutions that improve both productivity and plant health.” – Chuansheng Mei, Ph.D., Chief Scientist, IALR
The study
The study evaluated the effects of Pseudomonas psychrotolerans IALR632, a beneficial bacterial endophyte, on lettuce grown in a nutrient film technique hydroponic system. Researchers measured plant growth, analyzed changes in plant gene expression over time and examined shifts in the root bacterial microbiome.
Lettuce plants inoculated with IALR632 showed significant gains in shoot and root biomass, along with higher leaf greenness, compared to untreated controls. By 21 days after transplanting, treated plants exhibited improved overall vigor and biomass accumulation.
At the molecular level, RNA sequencing revealed extensive transcriptional reprogramming in inoculated plants. Thousands of genes were differentially expressed over the course of early growth, with notable increases in pathways related to cell wall remodeling, lipid metabolism, nitrogen assimilation, and nutrient uptake. Genes associated with ethylene signaling, a hormone pathway often linked to plant stress responses, were modulated in a way that suggests reduced stress signaling and improved growth efficiency.
“This study provides clear molecular evidence that beneficial endophytes can fundamentally reprogram plant physiology in hydroponic systems,” Mei said.
Building on endophyte research
This work builds on years of research by IALR’s Plant Endophyte Research Center, which houses a library of more than 2,000 characterized bacterial endophytes. These naturally occurring microbes have repeatedly demonstrated their ability to act as biostimulants, boosting plant growth and nutrient uptake, and as biocontrol agents, reducing disease pressure in crops such as lettuce, cucumber and strawberries.
Previous studies have shown selected endophytes can increase yields by 20% or more in controlled environments and improve crop resilience under stress.
“What’s particularly exciting is that we’re now connecting those growth benefits to specific changes in gene expression and microbial community structure. That kind of mechanistic understanding helps move these technologies closer to practical adoption.” – Scott Lowman, Ph.D., Vice President, Applied Research, IALR
Root microbiome insights
In addition to plant growth and gene expression, researchers analyzed the root-associated bacterial communities. Inoculation with IALR632 significantly reshaped the root microbiome, increasing microbial diversity and enriching bacterial groups linked to nutrient cycling and plant growth promotion.
Despite its strong effects, Pseudomonas itself remained a relatively minor component of the overall root microbiome, suggesting the bacterium exerts its influence by triggering broader microbial and physiological shifts rather than dominating the community.
“This finding highlights the complexity of plant–microbe interactions in hydroponic systems. A single beneficial organism can act as a catalyst for much larger ecological and physiological changes.” – Sajeewa Amaradasa, Ph.D, Senior Scientist, IALR
Why it matters
The results demonstrate that beneficial endophytic bacteria can enhance lettuce growth in hydroponic systems through coordinated effects on plant metabolism and root microbial communities. This biological approach offers growers a practical tool to improve productivity, nutrient efficiency and crop resilience without increasing reliance on synthetic chemicals.
The findings are especially relevant for indoor farms, vertical agriculture operations and other controlled environment systems seeking scalable, sustainable technologies.
Future research will focus on integrating beneficial microbes into commercial hydroponic practices, evaluating performance across additional crops, and exploring microbial consortia tailored to specific production environments.
The research team
- Chuansheng Mei, Ph.D., chief scientist, IALR
- Scott Lowman, Ph.D., vice president, applied research, IALR
- Sajeewa Amaradasa, Ph.D., senior scientist, IALR
- Robert Chretien, laboratory research associate, IALR
