Justin Shaffer, Ph.D.

(research, teaching, outreach)

I am a broadly trained plant and microbial ecologist with expertise in lichenology, mycology, plant pathology, and community ecology. My research interests are centered on host-microbe interactions, particularly those involving bacteria and fungi, and seek to elucidate the roles of such microbes in driving community-wide patterns, influencing host fitness, and/or impacting ecosystem services.

I obtained my Ph.D. in Plant Pathology and Microbiology from the University of Arizona in Tucson, in August 2017. My dissertation work focused on the evolutionary relationships, and effects on host fitness and ecology of bacteria that inhabit the living tissues of plant-associated fungi. In addition to revealing their widespread abundance, diversity, and close relationships to known free-living bacteria, my work showed that these endohyphal bacteria can influence the outcome of plant-fungus interactions, namely seed survival and germination.

I was raised in California where I learned to appreciate the outdoors. I fell in love with nature and science through courses in high school and community college, and exploration of wildlife in my backyard and at state and national parks. Living in southern California, I became fascinated with links between human society and the environment.

I pursued human-environment interactions at the University of California, Santa Cruz, where I obtained a Bachelors of Arts in Environmental Studies. There, my interests grew to focus on plant pathology and tropical forest ecology, and specifically aspects concerning plant community succession and the role of plant-associated microbes, particularly fungi, in shaping such ecological processes. I completed an undergraduate thesis project that explored the potential for common corticolous macrolichens to indirectly protect their woody plant hosts from cosmopolitan, pathogenic fungi. In familiarizing myself with the lichens of California, I quickly fell in love with lichens, and fungi in general – their beautiful morphologies and cryptic ecologies, and decided to pursue a career focused on mycology and host-microbe interactions.

In October 2018 I joined Prof. Rob Knight’s group in the School of Medicine at the University of California, San Diego, as a postdoctoral fellow with support from UCSD’s Institutional Research and Academic Career Development Award (IRACDA) . Although I am involved in several ongoing projects, including the Earth Microbiome Project (EMP), a major goal of mine is to progress development of molecular methods to elucidate interactions in complex and diverse host-associated microbial communities, including nucleic acid extraction and sequencing library preparation methods. In addition, I am interested in how we can best recover microbial genomes from metagenomic data, in part by using third-generation sequencing technologies in parallel with state-of-the-art assembly methods.

Alongside my research with the Knight group, I am actively involved in science education research, student mentoring, and the development and implementation of pedagogical techniques to increase the retention and success of underrepresented groups in STEM education and research. As an IRACDA fellow, one of my goals looking forward is to develop an education-research program surrounding microbial ecology with which to engage undergraduate and graduate students.