Helpful Bacteria Promoted Tomato Growth and Shaped Root Soil Bacteria

Jenn Hoskins
15th July, 2025

Helpful Bacteria Promoted Tomato Growth and Shaped Root Soil Bacteria

Inoculation with Pseudomonas sp. F204 significantly altered the rhizosphere bacterial community composition of tomato plants, characterized by an increased relative abundance of the phylum Proteobacteria (a) and the enrichment of specific genera including Pseudomonas (b) compared to the control.

Image adapted from: Li et al. / CC BY (Source)

Key Findings

  • Researchers at Northeast Agricultural University discovered Pseudomonas sp. F204, a soil bacterium that effectively breaks down harmful plant DNA, which causes "soil sickness."
  • This beneficial bacterium not only degrades problematic DNA but also significantly promotes tomato plant growth and improves the microbial community around their roots
In agricultural systems, a phenomenon known as "soil sickness" can significantly hinder crop growth and reduce yields. This problem often arises when the same crop is grown repeatedly in the same soil, leading to a decline in plant health. Recent research has pointed to extracellular DNA (eDNA) as a key contributor to this issue. While eDNA is simply genetic material released from cells into their surroundings, its role in the environment is surprisingly complex and multifaceted. For instance, in bacteria, eDNA is not merely cellular debris; it's a vital component of structures called biofilms. Biofilms are communities of microbes encased in a self-produced matrix, often seen as the slimy layer on surfaces. Early work showed that adding an enzyme called DNAse, which breaks down DNA, caused Pseudomonas aeruginosa biofilms to disappear, highlighting eDNA's structural importance[2]. Beyond structure, eDNA helps bacteria stick to surfaces and even contributes to their resistance against antimicrobial treatments. It does this by binding to and blocking positively charged antimicrobials, and by triggering genetic responses that enhance resistance[2]. This widespread importance of eDNA in microbial communities is now well-established, with eDNA being actively secreted or released through controlled cell lysis[2][3]. However, the story of eDNA changes when we look at plants. Here, extracellular self-DNA (esDNA), the plant's own genetic material released from damaged or decaying cells, can act as a "Damage-Associated Molecular Pattern" (DAMP)[3][4]. DAMPs are internal danger signals that activate a plant's innate immune system, much like an alarm system. Studies have confirmed that esDNA can inhibit root growth and trigger the production of reactive oxygen species (ROS), which are stress signals, in plants like Arabidopsis and tomato[4]. This negative effect is mediated through a specific internal communication system known as the jasmonic acid (JA) signaling pathway, which also plays a role in plant defense against pathogens[4]. This understanding of esDNA as a plant autotoxin – a substance produced by the plant itself that becomes toxic to it – helps explain negative plant-soil feedback (PSF). Negative PSF occurs when a plant leaves behind residues in the soil that harm subsequent plants of the same species. Research has shown that the accumulation of plant self-DNA in the soil, particularly from decaying plant litter, is inversely related to plant biomass[5]. In other words, the more plant eDNA in the soil, the worse the plant grows. This accumulation of self-DNA can weaken a plant's root system, making it more vulnerable to soilborne pathogens[5]. Given eDNA's detrimental effects on plants, researchers at Northeast Agricultural University have been investigating ways to mitigate this "soil sickness"[1]. Their recent study focused on a novel approach: harnessing the power of specific soil microbes to degrade the problematic eDNA. The central problem they aimed to solve was how to alleviate the autotoxicity caused by eDNA accumulation in continuously cropped soils, thereby promoting plant growth. The team embarked on a comprehensive screening process, isolating over 600 different bacterial strains from various soil samples. Their goal was to identify strains with a strong capacity to break down eDNA. Among these, one particular strain, Pseudomonas sp. F204, stood out. Not only did it demonstrate the most potent eDNA-degrading ability, but it also possessed other beneficial traits for plants, such as the ability to solubilize phosphate (making it available for plant uptake), produce siderophores (compounds that help plants absorb iron), and generate indole-3-acetic acid (a plant hormone that promotes growth). To assess the practical impact of Pseudomonas sp. F204, the researchers conducted a pot experiment using tomato plants. They inoculated the soil with the selected bacterial strain and observed its effects on plant growth and the microbial community in the rhizosphere – the narrow zone of soil directly influenced by root secretions. The results were significant: inoculation with Pseudomonas sp. F204 substantially altered the structure and composition of the bacterial community in the tomato rhizosphere. Crucially, it also stimulated the growth of the tomato seedlings. This study from Northeast Agricultural University provides a compelling solution to the challenge of eDNA-induced soil sickness. By identifying and utilizing eDNA-degrading bacteria like Pseudomonas sp. F204, it demonstrates a biological strategy to counter the negative effects of accumulated plant self-DNA. While eDNA plays essential roles in other biological contexts, such as forming protective bacterial biofilms[2][3], its accumulation in agricultural soils can be detrimental to plant health, as highlighted by its function as a DAMP and its contribution to negative plant-soil feedback[4][5]. This research expands our understanding of eDNA's complex roles by showing how specific microbial interventions can manage its presence in the soil, turning a potential toxin into a manageable component of the soil ecosystem. It underscores the vital role of the soil microbial community in maintaining plant health and offers a promising avenue for improving crop yields in continuous cropping systems.

AgricultureEcologyPlant Science

References

Main Study

1) Pseudomonas sp. F204 Promoted Tomato Growth and Altered Rhizosphere Bacteria Community

Published 12th July, 2025

https://doi.org/10.1007/s00284-025-04278-y

Related Studies

2) The role of extracellular DNA in the establishment, maintenance and perpetuation of bacterial biofilms.

https://doi.org/10.3109/1040841X.2013.841639

3) The Role of DNA in the Extracellular Environment: A Focus on NETs, RETs and Biofilms.

https://doi.org/10.3389/fpls.2020.589837

4) Plant extracellular self-DNA inhibits growth and induces immunity via the jasmonate signaling pathway.

https://doi.org/10.1093/plphys/kiad195

5) Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA.

https://doi.org/10.1016/j.micres.2024.127634


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