Our lab research focuses on investigating the structure and function of bacteria in the phytobiome and their impact on plant health. We are particularly interested in understanding the mechanisms underlying the microbe-microbe and host-microbe interactions leading to increased resilience
plants against biotic and abiotic stresses.
Profiling of marker genes and high throughput metagenome sequencing have improved our understanding of the composition of microbial communities in the rhizosphere and plant environment. As a result, small consortia of microbes known as synthetic microbial communities (SynComs) can be engineered to mimic the observed structure and function of natural conditions. Recently, we showed that engineering SynComs should take into consideration multiple attributes, including desirable plant phenotypes and microbial traits (Martins et al. 2023) (Fig. 1).
Collapsible text for fig. 1: The figure shows three tomato plants in the left column. The top plant illustrates dysbiosis in diseased tomatoes. The middle plant shows changes in root exudation, representing a chemical “cry for help.” The bottom plant shows recovery to a healthy state due to the recruitment of beneficial soil microbes. This shift to eubiosis is associated with soil microbiome abundance and connectivity within phytobiome networks. These complex networks influence plant phenotypes and microbial traits. Application of synthetic microbial communities (SynComs) can enhance plant immune system priming (ISP), microbe-triggered immunity (MTI), microbial volatile organic compound (mVOC) production, secondary metabolite release, and biofilm formation.
Figure 1. Roadmap to engineering a successful synthetic microbial community (SynCom).
Using desired plant phenotype (e.g., disease resistance) and operational taxonomic unit (OTU) network analysis (PhONA) coupled with the core microbiome can improve the prediction of successful SynComs. In our recent study, Pasche et al. 2025 identified 36 significant OTUs strongly associated with the log odds probability, as determined by logistic regression analysis of decreased disease resistance in plants infected with Meloidogyne enterolobii (Fig. 2).
Figure 2. Nodes in the network are color-coded according to the corresponding phylum of the OTU, while node size reflects its relative abundance. The width of edges signifies the strength of the probability coefficient, with solid lines indicating positive associations. Additionally, a bolded font and node indicate members of the core microbiome. Venn diagram displaying number of OTUs of soil types and experiment found and the core microbiome between them at a 0.001 relative abundance detection limit and a 50% prevalence.
Collapsible text for fig. 2: The left figure shows that operational taxonomic unit network analysis is influenced by multiple factors. The right figure shows that agricultural and native soils share 101 core microbiome members, while high and standard inoculation treatments have 30 and 17 unique microbiome members, respectively.
Just as the human gut microbiome is colonized by a variety of microbes, so too is the rhizosphere of plants. An imbalance in this microbial community,
known as dysbiosis, can have a negative impact on plant health.
Ketehouli et al. 2024 observed that dysbiosis in the rhizosphere led to plants being more susceptible to a foliar pathogen Xanthomonas perforans (Xp) (Fig. 3).
This study highlights the vital role that beneficial rhizosphere microbes play in disease resistance, even against foliar pathogens.
Collapsible text for fig. 3: The top figure shows two tomato plants: one treated with streptomycin in the soil and the other with water as a control. After 24 hours, both plants were inoculated with the foliar pathogen Xanthomonas. The bottom figure shows that after two weeks, plants with streptomycin-treated rhizospheres exhibited higher disease severity than the control group.
Figure 3. Antibiotic application (streptomycin 0.6 g L-1) to plants' rhizosphere led to dysbiosis or "imbalanced" microbial community (A) and more disease development caused by Xanthomonas perforans (Xp) (B).
Our lab is also interested in investigating anthropogenic changes in the environment that interfere with plant-microbe interactions. In this study conducted by Pasche et al. (2023) we demonstrated that by planting Paspalum notatum to cover the soil between tomato cultivations in Years 1 and 2, a shift in the soil microbial structure was observed along with changes in the soil physical-chemical proprieties, ultimately leading to healthier plants (reduction of infections of plant-parasitic nematode Meloidogyne enterolobii) (Fig. 4).
Figure 4. Soil microbiome and physical-chemical proprieties changes between years 1 and 2 led to a reduction of infection by the plant-parasitic nematode.
Collapsible text for fig. 4: Top panel: Diseased tomato roots with galls are shown initially; after planting bahiagrass as a cover crop, soil nutrients, organic matter, and pH improve, resulting in healthy, gall-free tomato roots in the second year. Bottom panel: Heat maps and PCoA plots for Years 1 and 2 illustrate shifts in soil microbial community composition over time.
Outreach
Our research program integrates education by incorporating outreach activities, such as:
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USDA-NIFA (award n°: 2022-68015-36721)
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USDA-OREI (award n°: 2022-51300-37888)
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USDA-NIFA (award n°: 2021-68013-33758)
Figure 5. Top right: “Plants Get Sick Too!” workshop for K-12 teachers from Title I schools, where most of the students are eligible for the federal free and reduced-price meal program. Bottom right: Gained knowledge assessed through self-assessment in pre- and post-surveys (y-axis). The x-axis shows questions asked in the surveys (e.g.: Teachers were asked before and after the workshop to rate their confidence on a scale of 1 to 10 in teaching the topics of plant pathology: bacteriology, nematology, mycology, etc.). All activities conducted in this research were approved by the Institutional Review Board (service survey number: IRB202300828).
(Photo used by teachers’ permission).
Full publication: Pasche et al. 2024. Seeding Success: The “Plants Get Sick Too!” Workshop Nurtures Teacher Knowledge in Plant Pathology. Plant Health Instructor, doi.org/10.1094/PHI-O-2023-11-0011
Collapsible text for fig. 5: Top: Dr. Martins engaging participants during the workshop. Bottom: Pre- and post-survey self-assessments showing mean knowledge gains across questions.