Healthy, Surviving, Dying: Tracking the Microbiome Through Rapid ʻŌhiʻa Death
Rosemary Gillespie, Professor
Environmental Science, Policy and Management
Applications for Fall 2026 are closed for this project.
This project addresses dynamics of plant microbial communities under disease pressure through the study of Rapid ʻŌhiʻa Death (ROD) in Hawaiʻi. ROD is caused by two fungal pathogens, Ceratocystis lukuohia and C huliohia, which co- occur on Hawaiʻi Island. Fieldwork was conducted across an altitudinal gradient (from 100 to 1,800 m above sea level), substrate age, and five different sites on
Hawaiʻi Island (Keauʻohana, Nānāwale, Honuaʻula, ʻŌlaʻa, and the Hilo Watershed). Tree sampling captured a gradient of health conditions (i.e. healthy, surviving, symptomatic, and dead) to test whether the ʻōhiʻa-associated
microbiome (fungal and bacterial, across wood and root tissues) differs systematically with disease status, and whether surviving trees carry a distinctive microbial signature indicative of resistance. The work integrates prior
characterization of microbial communities associated with ambrosia beetle vectors
of Ceratocystis. Fieldwork, paired with amplicon sequencing (ITS1, ITS2, 16S) and community ecology analyses, will produce a systematic account of how ROD reshapes the ʻōhiʻa holobiont, with direct relevance to conservation and restoration decision-making.
Role: Undergraduates involved in this project will contribute to research on plant
microbiome of M. polymorpha affected by ROD. Students will be trained generally in
molecular lab techniques, with a primary focus on Next-Generation Sequencing
(NGS) library preparation. DNA has already been extracted from field-collected
samples (wood and root) and is ready for downstream processing. The student's
main responsibility will be preparing amplicon sequencing libraries (ITS1, ITS2,
16S) for Illumina sequencing, including PCR amplification, cleanup, quantification,
and pooling. Students will gain hands-on experience with core molecular biology
techniques and an introduction to the workflow connecting wet-lab sequencing prep to downstream bioinformatic analysis of microbial community data.
By the end of this experience, students will be able to:
Perform PCR amplification
-Conduct DNA library prep for NGS sequencing
-Understand the principles of amplicon-based NGS (ITS/16S) and how each library design relates to downstream taxonomic and community analyses
-Apply careful laboratory practices essential to reproducible molecular work
-Describe how wet-lab sequencing preparation connects to bioinformatic analysis of microbial community data for evolutionary ecology relevant research-
-Gain foundational exposure to the broader research context of plant-
microbiome interactions,
Qualifications: Students should have completed or be currently enrolled in at least one semester of undergraduate coursework in the biological sciences (e.g. Biology 1B) and should have an interest in evolutionary biology, ecology and/or island biology.
Day-to-day supervisor for this project: Edoardo Scali, PhD Candidate
Hours: to be negotiated
Biological & Health Sciences Environmental Issues