Current Projects
Contributions of the floral transmission pathway to early seed microbial community assembly
Co-investigator(s): Johan Leveau, Rachel Vannette
Seed-associated microbial communities are a source of microbial inoculum between plant generations. However, there is high variability in microbial communities between seeds due to multiple interacting ecological processes (e.g. host selection, dispersal), making it difficult to discern their effects and predict community assembly outcomes. We posit that a process-based approach focusing on the transmission pathway between flowers and developing seeds will provide new insight into the roles of selection and stochasticity during initial microbial community assembly in developing seeds. Using commercial watermelons (Citrullus lanatus), we are testing for floral transmission processes at multiple spatial scales. We are interested in the following questions:
Co-investigator(s): Johan Leveau, Rachel Vannette
Seed-associated microbial communities are a source of microbial inoculum between plant generations. However, there is high variability in microbial communities between seeds due to multiple interacting ecological processes (e.g. host selection, dispersal), making it difficult to discern their effects and predict community assembly outcomes. We posit that a process-based approach focusing on the transmission pathway between flowers and developing seeds will provide new insight into the roles of selection and stochasticity during initial microbial community assembly in developing seeds. Using commercial watermelons (Citrullus lanatus), we are testing for floral transmission processes at multiple spatial scales. We are interested in the following questions:
- What portion of microbial communities are shared between stigmas and seeds in commercial watermelon fields? What are their effects on seedling viability? (Collaboration with Dr. Matthieu Barret, Dr. Marie Simonin; contributions from Rudy Mahajan, Kacie Lui, Alex Velasco and Carina Lopez)
- How does pollination impact stigma and seed microbial communities? (Collaboration with Dr. Matthieu Barret and Dr. Marie Simonin; contributions from Karen Barragan and Carina Lopez)
- How do microbe-microbe interactions affect transmission from flowers to seeds? What are the relative contributions of these interactions and stochasticity during transmission of larger communities? (Contributions from Karen Barragan)
- Which microbial traits influence transmission from flowers to seeds? (Collaboration with Dr. Adam Deutschbauer and Dr. Matthieu Barret)
Optimizing methods for detecting seed microbes at various spatial scales
Seed microbiologists use a variety of methods to detect and describe microbial community composition and behavior (e.g. culturing, next generation sequencing, microscopy). However, these methods are often not standardized across plant systems or research questions, and detection of microbes can be challenging based on the spatial scale of interest. In this methods review, I seek to summarize the current techniques for detecting microbial communities in seeds, conceptual and technical challenges faced with these techniques, and potential solutions for future research.
If you are a seed microbiologist and interested in contributing to this work, please email me at [email protected] or fill out my survey on this topic here: LINK
Seed microbiologists use a variety of methods to detect and describe microbial community composition and behavior (e.g. culturing, next generation sequencing, microscopy). However, these methods are often not standardized across plant systems or research questions, and detection of microbes can be challenging based on the spatial scale of interest. In this methods review, I seek to summarize the current techniques for detecting microbial communities in seeds, conceptual and technical challenges faced with these techniques, and potential solutions for future research.
If you are a seed microbiologist and interested in contributing to this work, please email me at [email protected] or fill out my survey on this topic here: LINK
Effects of invasive plants on the bacterial communities of native wildflowers
Co-investigator: Rebecca Nelson
Co-investigator: Rebecca Nelson
Longitudinal profiling of the Citrus leaf microbiota
Co-investigator(s): Johan Leveau, Shruti Parikh
Co-investigator(s): Johan Leveau, Shruti Parikh
The aims of this project are to: 1) Prepare a dataset and scripts for teaching microbiome analysis methods in R to high school and undergraduate projects, and 2) to evaluate how the fungal and bacterial communities on Citrus leaves change over time.
Previous Projects
Association of fungal wood endophytes and disease response in Populus trichocarpa
Co-investigators: Michael Getz, Jared LeBoldus, Posy Busby
Co-investigators: Michael Getz, Jared LeBoldus, Posy Busby
The aim of this project was to characterize the fungal wood communities of Populus trichocarpa in healthy trees and those infected with Sphaerulina musiva.
The core seed mycobiota of Pseudotsuga menziesii var. menziesii across provenances in the Pacific Northwest, USA
Co-investigator: Posy Busby
Co-investigator: Posy Busby
Fungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. “Core” taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: (i) Seed mycobiome composition differed among seed provenances. (ii) Despite variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir: Trichoderma spp., Hormonema macrosporum, Mucor plumbeus, and Talaromyces rugulosus. Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival, and competition.
This work is published in Mycologia.
This work is published in Mycologia.
Characterizing the culturable seed microbiota of Populus trichocarpa
Co-investigators: Sabrina Heitmann, Edward Barge, George Newcombe, Mary Ridout, Posy Busby
Co-investigators: Sabrina Heitmann, Edward Barge, George Newcombe, Mary Ridout, Posy Busby
Plants harbor a diverse community of microbes, whose interactions with their host and each other can influence plant health and fitness. While microbiota in plant vegetative tissues has been extensively studied, less is known about members of the seed microbiota. We used culture-based surveys to identify bacteria and fungi found in the seeds of the model tree, Populus trichocarpa, collected from different sites. We found that individual P. trichocarpa seeds typically contained zero or one microbe, with common taxa including species of Cladosporium, Aureobasidium, Diaporthe, Alternaria, and Pseudomonas, a bacterium. Pseudomonas isolates were associated with seed mortality and were negatively associated with the occurrence of fungal isolates within Epicoccum, Alternaria, and Aureobasidium from the same seed. Next, we conducted an inoculation experiment with one of the isolated seed microbes, Pseudomonas syringae pv. syringae, and found that it reduced seed germination and increased seedling mortality for P. trichocarpa. Our findings highlight common fungi and bacteria in the seeds of P. trichocarpa, prompting further study of their functional consequences. Moreover, our study confirms that P. syringae pv. syringae is a seed pathogen of P. trichocarpa and is the first report that P. syringae pv. syringae is a lethal seedling pathogen of P. trichocarpa, allowing for future work on the pathogenicity of this bacterium in seedlings and potential antagonism with other seed microbes.
This work is published in MDPI Pathogens.
This work is published in MDPI Pathogens.