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.]
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 project I contributed to during my sabbatical in the Matsunaga, Takeyama and Tanaka laboratory in Tokyo University of Agriculture and Technology, Koganei, Japan, was published (Arakaki et al., 2017).
Arakaki A, Nakata S, Tokuhisa T, Ogawa Y, Sato K, Sonoi T, Donachie SP, Matsunaga T (2017) Quantitative and time-course analysis of microbial degradation of 1H,1H,2H,2H,8H,8H-perfluorododecanol in activated sludge. Applied Microbiology and Biotechnology 101:8259-8266. doi: 10.1007/s00253-017-8538-4.
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
A paper I contributed to in my colleague's (Prof. Tung Hoang) lab was published. This describes single-cell transcriptomes in Pseudomonas aeruginosa at different points in a biofilm (Heacock-Kang et al., 2017).
Heacock-Kang Y, Sun Z, Zarzycki-Siek J, McMillan I, Norris M, Bluhm A, Cabanas D, Fogen D, Vo H, Donachie SP, Borlee B, Sibley C, Lewenza S, Schurr M, Schweizer H, Hoang T (2017) Spatial transcriptomes within the Pseudomonas aeruginosa biofilm architecture. Molecular Microbiology 106:976–985.