Introduction
The American Society for Microbiology notes, “Several initiatives are underway or are being proposed that seek to inventory biota of the world. Although microorganisms are known to make up the bulk of the biota in both natural and managed ecosystems, they are mentioned only in passing in these initiatives.”
Research in my lab addresses questions such as: 1) Which microbes are in a particular system? 2) What are they doing, and how are they doing it? 3) Can we cultivate them, and if so, do they have potential uses in other fields?
We have collected samples from diverse terrestrial and marine sites, but also from 'urban' sites. The urban environment presents an incredible range of niches for microbes, and you may be surprised by what you can find... We thus investigate the diversity and role of microorganisms in the environment, and consider each of the Archaea, Bacteria, and Eucarya, either individually, or as communities.
Through these pages you can see the type of work we have done, the work we are doing, and what some of the
opportunities may be if you are an undergraduate looking for lab experience, or a potential graduate student looking for an MS or PhD project. For either of those, or if you have other questions, feel free to contact me.
Ongoing and previous projects are described under
'Research'. For details of the courses I teach or have taught,
look under 'Education and Outreach'. That section also
provides advice on opportunities in the lab, and how we
might help if you are a Science Fair student. There are
sections also for our publications, and for the people who
have been in the lab, who are in the lab, and for those we
collaborate with.
Looking for motile bacteria? You've come to the right place! I saw so many videos that people said were showing motile bacteria, but were only showing Brownian motion of non-motile bacteria, I just had to make my own! Here are motile, spiral cells of Terasakiispira papahanaumokuakeensis that we discovered and named (Zepeda et al., 2015) [Thanks to Dr. Daisuke Takagi in the Department of Mathematics at UHM for helping make the video.]
News
-
Students in a class I teach (SEA-PHAGES) named a phage that infects Arthrobacter globiformis B-2979(T). The phage's genome was sequenced and annotated.
Chong R, SEA-PHAGES students University of Hawai‘i at Mānoa, Donachie SP, Reed F, Porter M (2022) Genome sequence of Arthrobacter globiformis phage KeAlii from Hawai‘i. Microbiology Resource Announcements 11(8):e0043922. doi: 10.1128/mra.00439-22.
-
Rebecca Prescott, one of my previous PhD students, published a DNA-based analysis of Bacteria communities in Hawaiian lava caves and fumaroles on the island of Hawai‘i.
Prescott RD, Zamkovaya T, Donachie SP, Northup DE, Medley JJ, Monsalve N, Saw JH, Decho AW, Chain PSG, Boston PJ (2022) Islands within islands: bacterial phylogenetic structure and consortia in Hawaiian lava caves and fumaroles. Front Microbiol 13:934708. doi: 10.3389/fmicb.2022.934708
-
A paper I'd been thinking of writing for years, since the term 'microbiome' became popular for just about anything pertaining to microbes, was published in Diversity. A nice joint effort with Dr. Marguerite Butler and her graduate students, Claire Fraser and Ethan Hill, at the University of Hawai‘i at Mānoa.
Donachie SP, Fraser CJ, Hill EC, Butler MA (2021) The Problem with ‘Microbiome’. Diversity 13:138. https://doi.org/10.3390/d13040138
-
Kazukuni Hayashi's paper in which he described Rheinheimera salexigens sp. nov., isolated from a fishing hook, was published (Hayasahi et al., 2018). We also sequenced the strain’s genome (Wan et al., 2016). Kazu' was a Molecular Cell Biology major who isolated the new species during his UROP-funded investigation of the bacteria on sharks' teeth!
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, Hayashi K, Anderson J, Donachie SP (2016) 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
-
A novel cultivated Ichthyosporean we provided featured in a paper from Inaki Ruiz-Trillo's lab (Grau-Bové et al., 2017). Read more here.
Grau-Bové X, Torruella G, Donachie SP, Suga H, Leonard G, Richards TA, Ruiz-Trillo I (2017) Dynamics of genomic innovation in the unicellular ancestry of animals. eLife 2017;6:e26036 doi: 10.7554/eLife.26036