Dr Kim Marie Handley

PhD, Environmental Geochemistry and Geomicrobiology, University of Manchester, UK

Profile Image
Senior Lecturer


Following the completion of my PhD at the University of Manchester in 2008 I was a postdoctoral scholar at the University of California, Berkeley (2008-2012) where I used proteogenomic techniques to study microbial community interactions in the terrestrial subsurface. I then undertook a second postdoctoral research position at the University of Chicago and Argonne National Laboratory (2012-2015) where I studied the physiology and distribution of uncultivated microbial communities in marine, terrestrial and built environments using environmental genomics. In 2015 I returned to New Zealand to take up a Rutherford Discovery Fellowship at the University of Auckland.

Research | Current

My group studies the metabolism and lifestyles of microbial communities, their impact on environment or host, and their roles in biogeochemical cycling. A large part of our research aims to understand microbial processes in aquatic environments, such as streams, estuaries and aquifers using genomic techniques. Examples of our research include:

  • Application and development of approaches in environmental genomics to elucidate microbial ecosystems, e.g. from stream-to-sea (funded by Genomics Aotearoa)
  • The biogeochemical role of microbial communities in anthropogenically perturbed coastal marine environments (supported by a Rutherford Discovery Fellowship).
  • The formation of toxin-producing cyanobacterial biofilms in streams (with Dr. Susie Wood, Cawthron Institute, Nelson, NZ)
  • The metabolic capacity of groundwater communities (collaboration with GNS and ESR funded by an MBIE Smart Ideas Grant)
  • The metabolic role of marine fish gut microbiomes (collaboration with PIs Profs Kendall Clements, SBS, and Lindsey White, AUT, funded by an MBIE Endeavour Fund grant)
  • The physiology and evolution of bacterial sponge symbionts (collaboration with PI Dr. Laura Steindler, University of Haifa, Israel)

Postdoctoral Researchers (current):

  • Dr David Waite (Environmental microbial genomics)
  • Dr Camen Astudillo-Garcia (Environmental microbial genomics)

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)
  • Cesar Facimoto (PhD candidate)
  • Alessandro Pisaniello (Co-supervised PhD candidate, Clements Lab)
  • Victor Gambarini (Co-supervised PhD candidate, Lear Lab)
  • Syrie Hermans (Co-supervised PhD candidate, Lear Lab)
  • Giselle Wong (Co-supervised PhD candidate, Taylor Lab)

Past students:

  • 2019 - Claire Delecrin (Intern, University of Bordeaux)
  • 2018 - Pierre Mathray (Intern, Lyon Catholic University)
  • 2017 - Chanenath Sriaporn (BSc Hons)
  • 2017 - Agathe Couturier (Intern, Lyon Catholic University)
  • 2016 - Redmond Mortimer (BSc Hons)


2014 Rutherford Discovery Fellow, Royal Society of NZ

Areas of expertise

  • Microbiology
  • Genomics
  • Biogeochemistry

Selected publications and creative works (Research Outputs)

  • Tee, H. S., Waite, D., Payne, L., Middleditch, M., Wood, S., & Handley, K. M. (2020). Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium. The ISME journal10.1038/s41396-020-0676-5
  • Sriaporn, C., Campbell, K. A., Millan, M., Ruff, S. W., Van Kranendonk, M. J., & Handley, K. M. (2020). Stromatolitic digitate sinters form under wide-ranging physicochemical conditions with diverse hot spring microbial communities. Geobiology10.1111/gbi.12395
    Other University of Auckland co-authors: Kathleen Campbell
  • Burgsdorf, I., Handley, K. M., Bar-Shalom, R., Erwin, P. M., & Steindler, L. (2019). Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. mSystems, 4 (4).10.1128/mSystems.00057-19
    URL: http://hdl.handle.net/2292/49524
  • Handley, K. M. (2019). Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers. mSystems, 4 (3).10.1128/mSystems.00153-19
    URL: http://hdl.handle.net/2292/49523
  • 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


Contact details

Primary office location

Level 2, Room 252
New Zealand

Web links