Current and Past Research Projects
How Does Soil Microbiome History Influence Plant Responses to Environmental Stress?
As global climate change accelerates, drought is expected to become more frequent and severe worldwide. Microbial communities exhibit a remarkable capacity to adapt to environmental stresses. Stress-induced shifts can influence microbiome trajectory and alter host plant responses to future perturbations— known as microbiome legacy effects.
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Our findings show that soil microbiomes from historically dry climates can buffer the transcriptional responses of a native wild grass, eastern gamagrass, to subsequent drought. This buffering effect resulted in improved water use efficiency, transpiration, and altered root anatomy under drought conditions. However, the benefits provided by drought-adapted microbiomes did not extend to domesticated maize, suggesting that domesticated plants may not derive the same advantages from adapted soil microbiomes as wild species.
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Related preprint:
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What Genetic Factors Drive Microbial Adaptations to Environmental Stress?
We have isolated and identified over 970 bacterial and fungal isolates that can survive in the soil and as maize root endophytes. We sequence closely related Luteibacter genomes from this collection. Using a pangenome analysis we identified genes associated with strains from low-precipitation regions, compared to high-precipitation regions. To investigate our candidate genes' role in bacterial stress tolerance, we screened our strains using in vitro and in planta growth assays and are completing a genome-wide association study.
How Do Plant-Microbe Interactions Impact Plant Phenology & Development?
Plant phenology, the timing of annual plant life-cycle events, affects the fitness of the plant and the organisms that are dependent on it. In the context of agriculture, it can affect the potential yield, growing distribution range, and a crops adaptability to climate change.
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Evergreen perennial trees, like Citrus sinensis (sweet orange), retain leaves for years, allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This allowed us to separate phenological effects on the microbiome from impacts due to annual leaf maturation or senescence. We determined that host phenological stage is a main determinant of bacterial and fungal community composition across roots and leaves, but particularly the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal, likely from pollinators, were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades, suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction.
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Related publications:
- O’Brien, Ginnan, et al., 2021, American Journal of Botany
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How Does Microbe-Microbe Competition Shape Plant
Microbiome Assembly?
This project focused on observing how symbiotic bacteria influence the colonization of other native bacteria within the plant. Preliminary results show that some microbiome members regulate the colonization of other microbiome members and that physical niche selections may be driven more by competition rather than physical and biochemical differences between host compartments.
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We are utilizing a gnotobiotic plant system and a four-member synthetic microbial community.
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Can the Microbiome Be Harnessed for Plant Disease management?
The microbiome has the potential to interact with pathogens directly by promoting, impeding, or blocking colonization of the host, or indirectly by provoking a plant response, aiding in host nutrient acquisition, increasing plant growth capabilities, or transforming into secondary or opportunistic pathogens.
We developed a Citrus Huanglongbing (HLB) disease ecology model using high-throughput (HT) amplicon sequencing and multi-year field sampling. HLB is a devastating disease associated with a phloem-limited, unculturable, insect-vectored bacterium. We examined microbiome shifts across disease states and identified putative disease antagonists/facilitators. To deepen our understanding, we established a culture collection of citrus-associated bacteria and fungi, created a HT pipeline for discovering active microbial metabolites, and employed untargeted metabolomics to identify compounds with therapeutic potential against HLB.
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Related publications:
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- Ginnan et al. 2018, Phytobiomes
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- Ginnan et al. 2020, Phytobiomes
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- Xi, Deyett, Ginnan, et al., Phytobiomes
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- Aksenov, Blacutt, Ginnan, et al. accepted to Scientific Reports