Dr Kim Marie Handley

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

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Senior Lecturer


Kim Handley is a microbiologist with a focus on genomics and ecology. She completed her PhD at the University of Manchester in the UK, and undertook her postdoctoral research at the University of California, Berkeley, followed by the University of Chicago (with a join appointment at Argonne National Laboratory). In 2015 she returned to New Zealand to take up a Rutherford Discovery Fellowship at the University of Auckland.

Research | Current

Her 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 this research aims to understand microbial processes in aquatic environments, such as streams, estuaries and aquifers using genomic techniques. Examples of current research include determining:

  • New or effective approaches in environmental genomics to study microbial ecosystems using a stream-to-sea model system (part of Genomics Aotearoa) (github resources in meta/genomics)
  • Microbial genetic adaptations to environmental stressors, including salt, pH and temperature (as part of Genomics Aotearoa and in collaboration with Profs Kathleen Campbell, SoE UoA and Martin Van Kranendonk, UNSW Sydney)
  • The character and metabolic capacity of groundwater communities (funded by an MBIE Smart Ideas Grant - collaboration with colleagues at ESR and GNS)
  • The role of microbial communities in nutrient cycling in anthropogenically perturbed coastal marine environments (funded by a Rutherford Discovery Fellowship)
  • The genetic mechanisms that enable cyanobacteria to proliferate in rivers, and that distinguish toxin and non-toxin producing populations (collaboration with Dr. Susie Wood, Cawthron Institute)
  • The metabolic role of microbial communities in the nutrition of herbivorous fish (collaboration with Profs Kendall Clements, SBS UoA, 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)

Current postdoctoral researchers:

  • Dr Micheal Hoggard
  • Dr Carmen Astudillo-Garcia

Current students:

  • Hwee Sze Tee (PhD candidate)
  • Katie Worrallo (PhD candidate)
  • Jian Boey (PhD candidate)
  • Chanenath (Kitty) 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 lab members:

  • 2018-2020 - Dr David Waite (postdoctoral researcher)
  • 2020 - Dr Syrie Hermans (co-supervised PhD student, Lear Lab)
  • 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)

Teaching | Current


2014 Rutherford Discovery Fellow, Royal Society of New Zealand/Te Apārangi (2015-2020)


Science Leadership Team - Genomics Aotearoa (GA)

GA-NeSI-UoA Metagenomics Summer School Organiser (see MSS materials)

Areas of expertise

  • Microbiology
  • Genomics
  • Biogeochemistry

Selected publications and creative works (Research Outputs)

As of 29 October 2020 there will be no automatic updating of 'selected publications and creative works' from Research Outputs. Please continue to keep your Research Outputs profile up to date.
  • 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. Geobiology, 18 (5), 619-640. 10.1111/gbi.12395
    Other University of Auckland co-authors: Kathleen Campbell
  • 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 journal, 14 (8), 2164-2178. 10.1038/s41396-020-0676-5
    Other University of Auckland co-authors: David Waite, Martin Middleditch
  • 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
  • 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
  • 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
    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
  • 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


Contact details

Primary office location

Level 2, Room 252
New Zealand

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