Dr Kim Marie Handley

PhD, Environmental Geochemistry and Geomicrobiology, Manchester, UK

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Senior Research Fellow


As an environmental microbiologist, my research aim is to understand the metabolism and lifestyles of natural microbial communities, and their role in biogeochemical cycling. Much of my group's work focuses on studying microbial processes in aqueous environments, such as in estuarine sediments, streams and aquifers. I completed my PhD at the University of Manchester in 2008 on microbial respiratory diversity in hydrothermal marine sediment. This was followed by postdoctoral research at the University of California, Berkeley (2008 to 2012), studying microbial community interactions in the terrestrial subsurface using proteogenomic techniques, and at the University of Chicago and Argonne National Laboratory (2012 to 2015), studying the physiology and distribution of uncultivated microbial communities in marine, terrestrial and human environments using environmental genomics. I took up my current position at the University of Auckland in mid 2015 as a Royal Society of NZ Rutherford Discovery Fellow.

Research | Current

  • The biogeochemical role of microbial communities in anthropogenically perturbed coastal marine environments (supported by a Royal Society of NZ Rutherford Discovery Fellowship).
  • The formation of toxin-producing Phormidium biofilms in streams (with Dr. Susie Wood, Cawthron Institute, Nelson, NZ)
  • The metabolic capacity of groundwater communities (collaboration with GNS and ESR supported by an MBIE Smart Ideas Grant)
  • Environmental metagenomics and stream microbial ecology (Genomics Aotearoa)
  • 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:

  • Hwee Sze Tee (PhD candidate)
  • Katie Worrallo (PhD candidate)
  • Jian Boey (PhD candidate)
  • Chanenath Sriaporn (PhD candidate)
  • Olivia Mosley (PhD candidate)
  • Emilie Gios (PhD candidate)
  • Syrie Hermans (Co-supervisor - PhD candidate, Lear Lab)
  • Giselle Wong (Co-supervisor - PhD candidate, Taylor Lab)
  • Pierre Mathray (Intern, Lyon Catholic University)

Past students:

  • 2016 - Redmond Mortimer (BSc Hons)
  • 2016 - Agathe Couturier (Intern, Lyon Catholic University)


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

COMMERCE A - Bldg 114
Level 1, Room 121
New Zealand

Web links