A new study from IBMCP (CSIC–UPV) reveals that agricultural biostimulants and controlled saline stress can significantly reshape the endophytic microbiome of lettuce and tomato. Published in Foods, the research shows these treatments boost microbial diversity and increase beneficial genera linked to plant health and potential probiotic effects. The findings open pathways to sustainable farming practices that enhance both crop resilience and consumer gut health.
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A study by the Institute of Molecular and Cell Biology of Plants (IBMCP) — a joint centre of the Spanish National Research Council (CSIC) and the Polytechnic University of Valencia (UPV) — has shown that biostimulants used in both organic and conventional agriculture, combined with controlled saline stress, significantly influence the microorganisms living inside the edible tissues of lettuce and tomato. These endophytic microbes, which are consumed alive when the vegetables are eaten raw, form part of the microbiota that ultimately reaches the human digestive system. The findings, published in Foods, point toward new strategies for improving the microbial quality of crops without relying solely on fertilisers or synthetic pesticides, while also supporting the production of foods that benefit consumer microbiota.
The study set out to examine how agricultural practices — including microbial biostimulants based on bacteria and fungi, as well as exposure to saline stress — shape the endophytic microbiome of lettuce and tomato. To do this, researchers conducted a greenhouse experiment at the Cajamar Foundation facilities in Paiporta (Valencia), growing plants in soil treated with a growth-promoting bacterium (Priestia megaterium) and a mycorrhizal fungus (Rhizophagus irregularis), which establishes a symbiotic relationship with plant roots to improve water and nutrient uptake. Both organisms are commonly used in organic and conventional farming. The trial also incorporated a non-microbial biostimulant, Calbio, developed at IBMCP in collaboration with the company Caldic, according to a press release.
Using advanced metagenomic sequencing techniques, which allow precise identification of microbial communities, the research team assessed how these treatments altered the composition and diversity of the endophytic microbiome and explored their potential implications for plant health and probiotic value.
“We have seen that the endophytic microbiome can be significantly altered by the use of these biostimulants and by saline stress,” summarizes Rosa Porcel, deputy director of the IBMCP and responsible for research. “Specifically, treatments with bacteria and salt increased the abundance of bacterial genera such as Pantoea, Stenotrophomonas and Massilia, which are associated with plant health and may have probiotic potential,” says the researcher.
The study found that the use of microbial biostimulants — widely applied in organic farming and increasingly adopted in conventional systems — as well as controlled saline stress, which is often viewed negatively in crop production, actually increased microbial diversity in the plants. These treatments also promoted the presence of microorganism groups linked to a healthy human gut microbiota.
“The change in the composition of the endophytome is very variable depending on the treatment,” Porcel says. “In some cases we have seen that the composition changes completely and in others between 20-40%.”
Benefits for Plants and Consumers
“The results open a path to design specific strategies to manipulate and improve the microbial community of crops, instead of relying solely on fertilizers or synthetic pesticides,” highlights the IBMCP researcher. This would have two fundamental advantages. On the one hand, to develop new agricultural practices allowed in the EU, aimed at enhancing beneficial microbial communities in crops and improving plant health and their resistance to environmental stress. “This has an impact on sustainable agriculture, based on reducing dependence on chemicals and promoting more ecological practices,” says Porcel.
But the final benefit would also be for the consumer, “since improving the microbiological quality of fruits and vegetables would strengthen their potential to contribute to better digestive health in those who consume them,” concludes Porcel. Thus, although more research should be carried out to confirm whether these changes have a positive effect on the intestinal microbiota and a better diet, the results are promising, the authors maintain.
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