Sean Swift

Position

PhD Student - Marine Biology

Biography

I had a non-linear path to marine biology. I was born on Maui and grew up in upcountry Kula. Spent a lot of time cruising around the forest and the beach. I think that taught me how to move around in natural spaces and pay attention to things. In 8th grade, I moved to New York City, which obviously changed my perspective on the world in a lot of ways. The city forces you to deal with many many people in a very small space. For college, I went to a small liberal arts school called Bard College at Simon's Rock in Western Massachusetts. I may be biased, but I'm a big fan of liberal arts education. I was free to take courses in political theory and anthropology alongside biology and organic chemistry. I did not take any marine science at all. I did, however, develop an interest in mycology, microbiology, and how humans interact with the natural world. I like microbiology because it’s highly technical and quasi-magical. I like mycology because hunting weird ephemeral fruiting bodies in a quiet forest and then leisurely keying them out with your friends is just a fantastic way to spend a day. While I was in undergrad, I also started working as a landscaper, and I think that shaped me too. There are certain practical aspects of getting work done that I think are better learned outside of academia. After graduating, I knew I wanted to come back to Hawaiʻi and had vague notions of pursuing a career in science or conservation. I volunteered with a graduate student at UH-Hilo working on mushroom biogeography in the Kipuka up on Saddle Road. His advisor, Dr. Brian Perry, took me on as a M.S. student at California State University, East Bay, where he had funding for me to do fieldwork in Hawaiʻi. The M.S. built a critical foundation for me in terms of actually doing research. Afterwards, I wasn't sure if I wanted to pursue a PhD. Instead, I worked as a lab technician and lab manager for Dr. Nicole Hynson at UH Mānoa. In retrospect, this was a great call. I earned some money, got involved in local projects, and I met so many people that are still important mentors to me today. One of those people was Dr. Craig Nelson, who's lab I joined as a PhD student in 2021. I love being in the Nelson lab. I am incredibly excited to be working on microbial biogeochemistry and metabolomics in marine, freshwater, and terrestrial systems. I'm having a great time trying to balance the PhD with caring for my deadly cute son Rafael. 

Research Interests

Researchers are often pushed towards specialization, but I have always felt like a generalist and, honestly, I have trouble focusing on one thing for too long. Early on, I was interested in microbial bioremediation of contaminants, in particular chlorinated organic compounds, like PCBs. Landscaping and courses in geography got me interested in ecological restoration. My M.S. advisor was an alpha taxonomist and evolutionary biologist and my project in his lab focused on fungal endophytic symbionts of plants. That work got me thinking about things like island biogeography, phylogenetics, and symbiosis. On the technical side of things, I've done a lot of high-throughput amplicon sequencing, which means I’ve spent a lot of time doing statistical programming to investigate ecological patterns in environmental microbiology. Right now, I am particularly interested in how microbes do organic chemistry. This entails understanding something about the distribution of microbial taxa and pairing their observed traits with their genetic capacity. I am enthusiastically learning untargeted LC-MS/MS techniques that enable us to generate profiles of thousands of organic compounds. Basically, I want to know how microbes eat different organic compounds and also how they might use them to communicate with host organisms, like terrestrial plants, algae, and coral. Lastly, it’s a trope that anyone who uses linux will tell you, and I am not bucking the trend. My commitment to linux has led me to engage with a lot of interesting technical puzzles that come up when working with metagenomic and metabolomic data. 

Education

B.A. Environmental Studies & Political Studies Bard College at Simon's Rock 2012

M.Sc. Biology California State University, East Bay 2016

Publications

Darcy, J., Amend, A., Swift, S., Sommers, P., & Lozupone, C. (2022). specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data. Environmental Microbiome, 17(1). 10.1186/s40793-022-00426-0

Thompson, L., Swift, S., Egan, C., Yogi, D., Chapin, T., & Hynson, N. (2022). Traits and tradeoffs among non-native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape. Molecular Ecology, 31(15), 4176–4187. 10.1111/mec.16564

Amend, A., Swift, S., Darcy, J., Belcaid, M., Nelson, C., Buchanan, J., Cetraro, N., Fraiola, K., Frank, K., Kajihara, K., McDermot, T., McFall-Ngai, M., Medeiros, M., Mora, C., Nakayama, K., Nguyen, N., Rollins, R., Sadowski, P., Sparagon, W., . . . Hynson, N. A. (2022). A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes. Proceedings of the National Academy of Sciences, 119(33). 10.1073/pnas.2204146119

Kacie T Kajihara, Egan, P., Swift, S., Wall, C., Muir, C., Hynson, N. (2022) Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured. New Phytologist. 10.1111/nph.18058

Koko, Jerry H., Swift, S., Hynson, N. (2021). Hawaiian Island Endemic and Indigenous Plant Species Have Higher Mycorrhizal Incidence Than the Global Average. American journal of botany. Early view. 10.1002/ajb2.1731

Egan, C. P., Koko, J., Muir, C., Zahn, G., Swift, S., Amend, A.; Hynson, N. (2021). Restoration of the mycobiome of the endangered Hawaiian mint Phyllostegia kaalaensis increases its resistance to a common powdery mildew. Fungal Ecology, 52. 10.1016/j.funeco.2021.101070

Darcy, J., Swift, S., Cobian, G., Zahn, G., Perry, B., & Amend, A. (2019). Fungal communities living within leaves of Native Hawaiian dicots are structured by landscape-scale variables as well as by host plants. Molecular Ecology. 29(16), 3102-3115. 10.1101/640029

Wall, C. B., Egan, C. P., Swift, S., & Hynson, N. A. (2020). Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests. Molecular Ecology. Early view. 10.1111/mec.15624

Swift, S., Munroe, S., Im, C., Tipton, L., & Hynson, N. A. (2018). Remote tropical island colonization does not preclude symbiotic specialists: New evidence of mycorrhizal specificity across the geographic distribution of the Hawaiian endemic orchid Anoectochilus sandvicensis. Annals of Botany, 123(4), 657- 666. 10.1093/aob/mcy198