Dr Kim Marie Handley

PhD, Environmental Geochemistry and Geomicrobiology, Manchester, UK

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Senior Research Fellow


I am an environmental microbiologist with a background in geochemistry and expertise in microbial community genomics. My research focuses on understanding the metabolism of microbial communities and their role in biogeochemical cycling in aqueous sedimentary environments. I completed my PhD at the University of Manchester in 2008 where I studied microbial respiratory diversity in hydrothermal marine sediment. My postdoctoral training was undertaken at the University of California, Berkeley, for which I studied microbial community interactions in the terrestrial subsurface utilizing proteogenomics techniques. From 2012 to 2015, I was a research scientist at the University of Chicago and Argonne National Laboratory. There, I employed genomics to study the physiology and distribution of uncultivated microbial communities in marine, terrestrial and human environments.

Research | Current

  • The biogeochemical role of microbial communities in anthropogenically perturbed coastal marine environments (supported by a Royal Society of NZ Rutherford Discovery Fellowship).
  • Microbial response to the Gulf of Mexico Deepwater Horizon oil spill in seafloor sediments (in conjunction with Dr. Jack Gilbert, University of Chicago/Argonne National Laboratory, and Dr. Janet Jansson, Pacific Northwest National Laboratory)
  • The formation of toxin-producing Phormidium biofilms in streams (with Dr. Susie Wood, Cawthron Institute, Nelson, NZ)
  • The physiology and evolution of bacterial sponge symbionts (in collaboration with Dr. Laura Steindler, University of Haifa, Israel)

Teaching | Current

Introduction to Bioinformatics 301; Marine Ecology 333; Genome Bioinformatics and Systems Biology 703

Postgraduate supervision

Current students:

  • Katie Worrallo (PhD candidate)
  • Jian Boey (PhD candidate)
  • Chanenath Sriaporn (PhD candidate)
  • Olivia Mosley (PhD candidate)
  • Emilie Gios (PhD candidate)
  • Syrie Hermans (PhD candidate - co-supervisor)

Past students:

  • 2016 - Redmond Mortimer (BSc Hons)


Rutherford Discovery Fellow

Areas of expertise

  • Microbiology
  • Biogeochemistry
  • Genomics

Selected publications and creative works (Research Outputs)

  • Handley, K. M., Piceno, Y. M., Hu, P., Tom, L. M., Mason, O. U., Andersen, G. L., ... Gilbert, J. A. (2017). Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. The ISME Journal, 11 (11), 2569-2583. 10.1038/ismej.2017.110
    URL: http://hdl.handle.net/2292/36805
  • Lear, G., Lau, K., Perchec, A. M., Buckley, H. L., Case, B. S., Neale, M., ... Lewis, G. (2017). Following Rapoport's Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes. Environmental Microbiology, 19 (8), 3152-3162. 10.1111/1462-2920.13797
    URL: http://hdl.handle.net/2292/36806
    Other University of Auckland co-authors: Gavin Lear, Gillian Lewis
  • Lax, S., Sangwan, N., Smith, D., Larsen, P., Handley, K. M., Richardson, M., ... Defazio, J. (2017). Bacterial colonization and succession in a newly opened hospital. Science Translational Medicine, 9 (391)10.1126/scitranslmed.aah6500
    URL: http://hdl.handle.net/2292/36158
  • Brewer, T. E., Handley, K. M., Carini, P., Gilbert, J. A., & Fierer, N. (2016). Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’. Nature Microbiology, 2.10.1038/nmicrobiol.2016.198
    URL: http://hdl.handle.net/2292/31344
  • Joye, S., Kleindienst, S., Gilbert, J. A., Handley, K., Weisenhorn, P., Overholt, W. A., & Kostka, J. E. (2016). Responses of Microbial Communities to Hydrocarbon Exposures. Oceanography, 29 (3), 136-149. 10.5670/oceanog.2016.78
    URL: http://hdl.handle.net/2292/31348
  • Lin, X., Handley, K. M., Gilbert, J. A., & Kostka, J. E. (2015). Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. The ISME journal, 9 (12), 2740-2744. 10.1038/ismej.2015.77
    URL: http://hdl.handle.net/2292/28139
  • Burgsdorf, I., Slaby, B. M., Handley, K. M., Haber, M., Blom, J., Marshall, C. W., ... Steindler, L. (2015). Lifestyle evolution in cyanobacterial symbionts of sponges. mBio, 6 (3).10.1128/mBio.00391-15
    URL: http://hdl.handle.net/2292/27477
  • Handley, K. M., Wrighton, K. C., Miller, C. S., Wilkins, M. J., Kantor, R. S., Thomas, B. C., ... Banfield, J. F. (2015). Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environmental microbiology, 17 (3), 622-636. 10.1111/1462-2920.12467
    URL: http://hdl.handle.net/2292/27475


Contact details

Primary office location

Level 3, Room 348B
New Zealand

Web links