Donachie Lab

Introduction

The Department of Microbiology supports the university's strategic plan by offering courses and training opportunities that provide qualified microbiology majors for the State of Hawaiʻi and beyond. The number of majors in our undergraduate programs has doubled in recent years, and is expected to continue growing. Almost 10% of graduating College of Natural Sciences (CNS) majors are from Microbiology, and ~2000 majors in 11 degree programs use our courses.

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My courses

The main courses I teach are required by majors in the CNS Marine Biology program, and provide a background in the field for those aiming to pursue careers in this field or enter graduate school first. I designed and have taught since 2004 two courses, Marine Microbiology (MICR 401) and Marine Microbiology Laboratory (MICR 401L). Enrollment in both courses grew quickly from 10 and one, respectively, in Spring 2004, and by Spring 2015 had reached 74 and 51, respectively. I have taught both courses every spring, except in 2014, when I was on sabbatical. With the Marine Biology program's rapid growth, I elected to offer both courses every semester: some students might have just one opportunity each year to take the lab, so there's a better chance if its' offered every semester! Beyond that, we may not have the laboratory space in which to provide multiple laboratory sections that would be required in one semester. Feel free to contact me with any questions you may have, or to ask for a syllabus. For advice about your degree requirements and other academic issues, contact the Student Academic Success Center <https://www.hawaii.edu/natsci/advising/>

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Other courses

I have taught Advanced Marine Microbiology (MICR 652), and General Microbiology (MICR 130) and Microbiology Laboratory (MICR 140L); the latter are often taken by students aiming to enter different healthcare fields, e.g., Nursing, Dentistry, although I included microbial ecology and marine microbiology! With one other instructor I team-taught the Marine Biology Program’s capstone writing intensive, ‘Advanced Topics in Marine Biology’ (BIOL 404W); with two other instructors I taught undergraduate and graduate ethics courses (MICR 314, MICR 614). In summer 2011 I provided two students an ‘O’ designated MICR 499 course, in which they focused on presentation skills for public speaking. As our DNA sequencing capabilities grew, I led 12 students through a laboratory-based course in bacterial cultivations and genomics (Microbiological Problems, MICR 499). Each student worked with a different sample from around campus, or our archive, or that they collected. This Outreach College course resulted in one publication (Wan et al., 2015a).

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Training and research opportunities for undergraduates

My lab routinely provides training, and research and discovery opportunities for undergraduates through 'Microbiological Problems'  (MICR499) and the equivalent for Marine Biology majors (BIOL499). MICR499 is described as, "Directed research opportunities in a microbiology laboratory. Students learn and perform basic research techniques." Some students with no microbiology experience have taken pivotal roles in projects, or used their experience to develop their own proposals. I also encourage you to apply to the University of Hawai‘i at Mānoa Undergraduate Research Opportunities Program (UROP). Typical projects you may participate in include sequencing bacterial genomes, such as those of novel species we have cultivated, or helping formally describe new species (Zepeda et al., 2015; Wan et al., 2016a,b, 2017; Hayashi et al., 2018). We have hosted many '499', and UROP-funded students:

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Vanessa Zepeda (Marine Biology) required ‘499’ credit; she formally described a bacteria strain I isolated from a small pond on Southeast Island on Pearl and Hermes Atoll, in the Northwestern Hawaiian Islands 14 years earlier. We published a paper describing a new genus and species, Terasakiispira papahanaumokuakeensis (Zepeda et al., 2015). We also sequenced the strain's genome (Wan et al., 2016a). The genus was named to honor Prof. Yasuke Terasaki, a Japanese microbiologist, for his contributions to the study of spiral-shaped bacteria.

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Kazukuni Hayashi (Molecular Cell Biology) investigated ecological connectivity among sharks through their oral bacteria. One expects variation among individuals of the same shark species, but are specific bacteria consistently in any one species? Kazu prepared over 350 pure bacteria cultures from 139 individuals of 11 shark species, plus 10 water, and 2 hook samples. Cultures affiliated with 126 species in 55 genera in 3 Bacteria phyla and 2 classes. Of seven potentially novel species, Kazukuni formally described Rheinheimera salexigens sp. nov., and we sequenced the strain’s genome (Wan et al., 2016b; Hayasahi et al., 2018).

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Yan Nguyen and Jessica Thawley cultivated a new Piscirickettsia species during their MICR401L (laboratory). Alex Lee then prepared a draft of the strain's genome during his participation in our NSF-funded REU-Site (Wan et al., 2016c). 

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James Miller (UROP) cultivated a novel Luteimonas from coral mucus. We sequenced the strain’s genome, and will formally describe the new species (Wan et al., 2016d).

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Other new species cultivated by other students are on the bench, including those cultivated by participants in our NSF-funded Research Experiences for Undergraduates (REU) Site (with co-PI Dr. Stephanie Kraft-Terry, and several mentors). [NSF Award Number 1560491]  Talk with me about such '499' and UROP opportunities, and if we can agree on the scope and schedule, I will provide the CRN and enter an override for you.

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Literature cited

Hayashi K, Busse H-J, Golke J, Anderson J, Wan X, Hou S, Chain PSG, Prescott RD, Donachie SP (2018) Rheinheimera salexigens, sp. nov., from a fishing hook off O‘ahu, Hawai‘i, and emended description of the genus Rheinheimera. International Journal of Systematic and Evolutionary Microbiology 68:35-41 doi: 10.1099/ijsem.0.002412

Wan X, Hou S, Phan N, Malone Moss JS, Donachie SP, Alam M (2015) Draft genome sequence of Pantoea anthophila strain 11-2 from hypersaline Lake Laysan, Hawai'i. Genome Announcements 3(3):e00321-15. doi: 10.1128/genomeA.00321-15

Wan X, Dasilveira L, Hou S, Saito JA, Donachie SP (2016a) Draft genome sequence of Terasakiispira papahanaumokuakeensis PH27AT, a spiral bacterium from the Northwestern Hawaiian Islands. Genome Announcements 4(5):e01166-16; doi: 10.1128/genomeA.01166-16

Wan X, Hou S, Hayashi K, Anderson J, Donachie SP (2016b) Genome sequence of Rheinheimera salexigens from a fishing hook off O‘ahu, Hawai‘i. Genome Announcements 4(6): e01390-16. doi: 10.1128/genomeA.01390-16

Wan X, Lee AJ, Hou S, Ushijima B, Nguyen YP, Thawley JA, Donachie SP (2016c) Draft genome sequence of Piscirickettsia litoralis, isolated from seawater. Genome Announcements 4(6), e01252–16. http://doi.org/10.1128/genomeA.01252-16

Wan X, Miller JM, Rowley SJ, Hou S, Donachie SP (2016d) Draft genome sequence of a novel Luteimonas sp. from coral mucus. Genome Announcements 4(6):e01228-16. doi: 10.1128/genomeA.01228-16

Zepeda VK, Busse H-J, Golke J, Saw J, Alam M, Donachie SP (2015) Terasakiispira papahanaumokuakeensis gen. nov., sp. nov., a Gammaproteobacteria from Pearl and Hermes Atoll, Northwestern Hawaiian Islands. International Journal of Systematic and Evolutionary Microbiology 65:3609-3617 doi: 10.1099/ijsem.0.000438

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Science Fair

My lab’ has hosted middle and high school students as part of their Science Fair projects:

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• Iris Kuo (‘Iolani School) discovered Flavobacterium akiainvivens during her Science Fair work in my lab’ (Kuo et al., 2013). We published a draft of the genome sequence of the species, too (Wan et al., 2015). The same species has been a candidate for Hawaii's ‘State Microbe'. Iris received a silver award (2nd place) at the Pacific Symposium for Science and Sustainability in 2011, reached the 2nd round of the national Junior Science and Humanities Symposium in 2012, and won a scholarship and research money for Washington University at St. Louis.

• Zoe Oda and Olivia Laus (Stevenson Middle School) in 2015, as they investigated how bread prepared with different preservatives succumbed to ‘mold’ over time. Their project was judged the best microbiology project in their school, and was the only one in their science class to advance to the regional competition.

• Makristina Villoso and Fritzie Acob (Waipahu High School AP Biology and Directed Studies in Scientific Research classes) in 2015, for their independent STEM research project. Both visited my lab’ to investigate how Spirulina commercially available in tablet form affected a range of bacteria.

• Jenna Kim, Ying Qi Li and Raina Nagamine (Stevenson Middle School) in 2016, as they investigated the effects of antibacterial agents on a meat-cutting board, after cutting raw meat.

• Summer Royal (Stevenson Middle School) in 2016, as she investigated the effects of liquid treatments on head louse eggs. Summer advanced to the top eight of the state-level competition, and won 1st place in the State’s Junior Division for “Bye Bye lice! So long eggs!”

• Suk Wen Ruan and Ahaena Kidder (Stevenson Middle School) in 2017, as they investigated mechanisms to remove bacteria from stream water.

 

Literature cited

Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SP (2013) Flavobacterium akiainvivens sp. nov., from decaying Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium. International Journal of Systematic and Evolutionary Microbiology 63:3280-3286 doi: 10.1099/ijs.0.047217-0

Wan X, Hou S, Saito J, Kaneshiro KY, Donachie SP (2015) Genome sequence of Flavobacterium akiainvivens IK-1T, from decaying Wikstroemia oahuensis, an endemic Hawaiian shrub. Genome Announcements 3(5):e01222-15. doi:10.1128/genomeA.01222-15