Dr Charles K. Lee

Charles Lee

Senior Lecturer

Qualifications: BSc (Life Science) Tsing-Hua Taiwan, PhD Waikato

About Charles

I am a microbial ecologist who utilises diverse technology-intensive approaches (e.g., genomics, molecular biology, drone-based remote sensing, and machine learning) to address basic and applied scientific challenges. My main interests are in extreme ecosystems such as Antarctica and geothermal environments, but I work on a wide range of habitats where my expertise can make an impact.

I co-lead Te Tumu Whakaora Taiao Environmental Research Institute with Tim Manukau, where our mission is to address longstanding challenges and new opportunities in environmental management and ecosystem degradation in Aotearoa and beyond. The ERI focuses on developing transformative and truly inter-disciplinary solutions that offer clear value and empower kaitiaki and policymakers; these solutions are built on mātauranga māori as well as technology-intensive and geospatially explicit frameworks that easily scale to meet specific challenges. We work closely with mana whenua to ensure that our efforts contribute to upskilling the next generation of kaitiaki so they can utilise cutting-edge research to achieve holistic environmental management goals.

🔬 My ORCID: 0000-0002-6562-4733

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Papers Taught

Research Supervised


  • Pollard, Georgia (in progress - chief supervisor Craig Cary): Molecular genetic analysis of zooplankton communities of the Ross Sea MPA: past, present and future projections.
  • Hamill, Carlin (in progress - chief supervisor Vic Arcus): Understanding enzyme evolution and allostery using Macromolecular Rate Theory
  • Abbaszadeh, Jaber (in progress): The global ecology of Deinococcaceae
  • Noble, Anya (in progress): The biogeography and functional roles of the Leptospermum scoparium (mānuka) phyllosphere microbiome
  • Cabria, Gamaliel Lysander (in progress): Intra-species genomic variation and gene flow in hydrogen-oxidizing bacteria
  • Monteiro, Maria (in progress - chief supervisor Craig Cary): Resolving functional resilience of microbial communities to climate-induced change in the McMurdo Dry Valleys of Antarctica
  • Wakerley, Georgia (in progress - chief supervisor Craig Cary): Human impact on the McMurdo Dry Valley soils of Antarctica: extending the limits of forensic DNA detection
  • Brandt, Shelly (2022 - chief supervisor Craig Cary): The effects of ocean acidification on microbial nutrient cycling and productivity in coastal marine sediments
  • Payyakkal Viswam, Jayadev (2016 - chief supervisor Ian McDonald): The role of the gut microbiome of the Huhu grub in lignocellulose breakdown

MSc (Research)

  • Prout, Bernadette (in progress): The microbiome of perennial ryegrass
  • Livne, Shir (in progress): The microbiome of colonial ascidians
  • Challis, Jacinda (2021): Effects of post-operative antibiotics in endoscopic sinus surgery
  • Ferris, Kelsey (2021): eDNA-based monitoring of freshwater mussel populations
  • Noble, Anya (2018): Environmental and biogeographical drivers of the Leptospermum scoparium (mānuka) phyllosphere microbiome
  • Hu, Xiaoxue (2017): Genetic tool to detect three New Zealand freshwater mussels (Echyridella menziesii, Echyridella aucklandica, Echyridella onekaka) in environmental DNA
  • Juwono, Joshua (2017): Enhancement of “flavours” through enzymatic release of glutamate

Undergraduate Research

  • Cooper, Helen (2021): The microbiome of seaweed-based bio-stimulant

Research Interests

My research focuses on utilising technology- and data-intensive techniques, such as (meta)genomics and remote sensing, to address critical challenges for exemplary ecosystems such as terrestrial Antarctica and geothermal habitats and focal species such as kākahi/kāeo (freshwater mussels) and mānuka. I have a track record of assembling experts across diverse disciplines (including mātauranga Māori and data science) and acquiring the necessary expertise and capabilities to answer transformative scientific questions using hypothesis-driven approaches.

I am an expert in the microbial ecology and microbial genomics of a wide range of unusual ecosystems, including terrestrial geothermal habitats and the Antarctic Dry Valleys. I also have active research projects on the microbiomes of plant-, animal-, and human-associated habitats. I have developed and validated a number of novel molecular techniques and bioinformatic analyses, particularly methodologies related to environmental DNA (eDNA).

I currently serve as the Co-Principal Investigator for the Antarctic Science Platform Project 3, a $10-million six-year effort to understand how Ross Sea Region ecosystems will respond to climate scenarios consistent with the Paris Agreement. My expertise and experience across divergent disciplines (e.g., molecular genetics, ecological modelling, remote sensing, machine learning) contribute to this flagship research programme integrating all major ecosystems present in the part of Antarctica under New Zealand's stewardship.

Recent Publications

  • Monteiro, M. R., Marshall, A. J., Hawes, I., Lee, C. K., McDonald, I. R., & Cary, S. C. (2022). Geochemically defined space-for-time transects successfully capture microbial dynamics along Lacustrine chronosequences in a Polar desert. Frontiers in Microbiology, 12. doi:10.3389/fmicb.2021.783767 Open Access version:

  • Vopel, K., Marshall, A., Brandt, S., Hartland, A., Lee, C. K., Cary, S. C., & Pilditch, C. A. (2021). Biogeochemical feedbacks to ocean acidification in a cohesive photosynthetic sediment. Scientific Reports, 11(1). doi:10.1038/s41598-021-02314-y Open Access version:

  • de Jesus, H. E., Carreira, R. S., Paiva, S. S. M., Massone, C., Enrich-Prast, A., Peixoto, R. S., . . . Rosado, A. S. (2021). Microbial succession under freeze–thaw events and its potential for hydrocarbon degradation in nutrient-amended antarctic soil. Microorganisms, 9(3), 1-16. doi:10.3390/microorganisms9030609

  • Bottos, E. M., Laughlin, D. C., Herbold, C. W., Lee, C. K., McDonald, I. R., & Cary, S. C. (2020). Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica. FEMS microbiology ecology, 96(5). doi:10.1093/femsec/fiaa042

Find more research publications by Charles Lee


Antarctica; Biochemistry; Biology; Biotechnology; Ecology; Environmental Biochemistry; Environmental Science and Technology; Microbiology; Molecular Biology

Contact Details

Email: [email protected]
Room: TRU.G.17
Phone: +64 7 838 4241