Research Overview
Plant-associated microbiota can strongly influence plant responses to stress, yet their effects vary across hosts and environments. We still do not understand how environmental history and microbial traits shape community assembly and function, or how host traits modify these processes. My research asks how environmental history, microbial interactions, and host biology jointly determine microbiota functions and plant performance under stress.
Overall, I seek to improve prediction of plant–microbiome outcomes while identifying microbial functions, management strategies, and host traits that can be leveraged to improve plant health and resilience.
Environmental History
How does environmental history shape microbial variation and future responses?
Environmental history can leave lasting legacy effects or memory that influence how microbial communities respond to future conditions. Using soils spanning a natural precipitation gradient, I found that historical water availability shaped microbial composition, activity, and genetic variation, with effects that persisted through subsequent experimental drought. These microbial legacies also altered plant drought responses in a host-dependent manner. I am resolving these community-level patterns at the population scale using wild Luteibacter isolates from semi-arid and humid environments. Together, this work asks how long-term environmental conditions generate microbial genetic and physiological variation and when those differences scale to changes in ecological interactions, community function, and host phenotype.
Related work:
Ginnan, NA, et al. 2025, Nature Microbiology.
https://doi.org/10.1038/s41564-025-02148-8
Ginnan, NA, et al. 2026, BioRxiv (pre-print).
https://doi.org/10.64898/2026.09.27.754828
Microbial Traits & Interactions
How do microbial traits and interactions scale to community function?
Microbiota functions emerge from interactions among organisms, not simply from the presence of individual microbial traits. I use cultured bacterial collections, gnotobiotic plant systems, microbial genetics, and synthetic communities to determine why some microorganisms successfully establish and function within plant-associated communities while others do not. My work has identified resource competition, including competition for iron, as one mechanism influencing microbial establishment and has generated large experimental resources for testing these processes. These include ZeaMiC, a defined collection representing diverse maize root-associated bacteria. I aim to identify when microbial traits predict community form and function.
Related work:
Garrell A*, Ginnan NA*, Swift J*, et al. 2026, BioRxiv (pre-print).
https://doi.org/10.64898/2026.03.23.713778
De Anda NI, Ginnan NA, & Roper MC. In preparation
Blacutt A, Ginnan NA, et al. 2020, AEM
https://doi.org/10.1128/AEM.02883-19
Host Biology
Why do microbiota produce different outcomes across plant hosts and environments?
Plant hosts create distinct physical and chemical environments that recruit or select for specific microbial taxa and modify microbial activity. Across citrus, maize, and eastern gamagrass, my research has shown that host species, developmental stage, physiology, and environmental conditions can restructure plant-associated microbiota with consequences for the host plant. For example, the same dry-history microbial communities that improved drought responses in eastern gamagrass did not benefit maize. In citrus, both plant phenology and orchard management altered root and rhizosphere communities. My research now asks which host traits explain this context dependence and how root structure, physiology, and chemistry interact with microbial traits to shape community function.
Related work:
O’Brien, Ginnan, et al. 2021, American Journal of Botany
https://doi.org/10.1002/ajb2.1743
Ginnan et al., 2022, mBio
https://journals.asm.org/doi/10.1128/mbio.00343-22
Ginnan, NA, et al. 2025, Nature Microbiology.
https://doi.org/10.1038/s41564-025-02148-8
Ginnan et al., 2026, ISME Communications
https://doi.org/10.1093/ismeco/ycag248
Ginnan, NA, et al., In preparation
Plant Health & Disease
When can microbiome functions be harnessed to improve plant health?
Plant-associated microorganisms can strongly influence disease and plant performance, yet beneficial effects observed in controlled experiments often fail to translate consistently across hosts or environments. My doctoral work used citrus Huanglongbing to investigate microbial and metabolic changes associated with disease and to identify microorganisms capable of pathogen inhibition. I built a collection of more than 300 citrus-associated microbes and helped develop approaches for screening microbial antagonism and candidate antimicrobial metabolites. This work led to a broader question that continues to shape my program: what determines whether a potentially beneficial microbial trait actually functions within a plant and its resident community?
Related work:
Ginnan NA, et al. 2018, Phytobiomes
https://doi.org/10.1094/PBIOMES-08-17-0032-A
Ginnan NA, et al. 2020, Phytobiomes
https://doi.org/10.1094/PBIOMES-04-20-0027-R
Xi, Deyett, Ginnan, et al., 2023, Phytobiomes
https://doi.org/10.3389%2Ffmicb.2023.1100590
Blacutt A, Ginnan NA, et al. 2020, AEM
https://doi.org/10.1128/AEM.02883-19
Aksenov, Blacutt, Ginnan, et al. 2024, Scientific Reports
One Health Microbiome Science
How can microbiome science connect health across organisms and environments?
Microbiomes connect the health of organisms and environments across traditional disciplinary boundaries. I extend my plant microbiome expertise through collaborative One Health research, training, and program development spanning agriculture, human and animal health, food science, and environmental microbiology.
Related work:
The Holobiont Biology Network [Bordenstein SR#, Gilbert TP, Ginnan NA, et al.] 2024, Science
https://doi.org/10.1126/science.ado2152
Ginnan NA, et al. 2025, mBio
https://doi.org/10.1128/mbio.03147-24
Ginnan NA, et al. In preparation.