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Environmental metagenomics

Micro-organisms are a major component of the environment – determining their role therefore means understanding their impact on environmental health. A better understanding of New Zealand’s microbial ecosystem has major opportunities for our environmental, primary production and health research.

A powerful way of studying microorganisms is by direct sampling of their DNA from the environment. Metagenomics, the study of the genetic material recovered directly from environmental samples, allows sets of complete or partial genomes to be produced from complex DNA mixtures derived from the different microbial species inhabiting an environment.

NZ river landscape

While metagenomics is a rapidly growing research approach, there is limited capacity in New Zealand for utilising metagenomic technologies and applying them to environmental management. This project aims to fill a technology and capability gap, developing national capabilities in genomics to contribute to improved environmental monitoring approaches.

The researchers will produce high quality genomes of single organisms from microbial communities with different levels of species complexity using a range of up-to-date DNA sequencing technologies. The aim is to work towards developing monitoring tools that will be applicable in even very complex microbial ecosystems.

The project will generate a high quality database of these mixed genomes collected from a stream. This can then be used to determine the stream’s genetic potential and implications for its chemical state and health.

This project brings together researchers from three Universities, two Crown Research Institutes and the Cawthron Institute. One postdoc, linked to our postdoc community through the bioinformatics infrastructure, and one PhD student are employed to build capability.


  • Tools to analyse partial or complete genome sequences from multi-genome mixtures
  • Tools to better understand the relationship between biology and environment
  • Increased capacity in metagenomics analysis and implementation
  • Effective co-operation between GA partners and stakeholders
  • Use proven methods and emerging ideas into new technologies in metagenome assembly

Metagenomics summer school


  • Dr Kim Handley (University of Auckland) – lead researcher
  • Dr Gavin Lear (University of Auckland)
  • Bevan Weir (Manaaki Whenua - Landcare Research)
  • Louise Weaver (ESR)
  • Dr Matt Stott (Canterbury University)
  • Charles Lee (University of Waikato)
  • Dr Susie Wood (Cawthron)
  • Dr Michael Hoggard (University of Auckland)
  • Hwee Sze Tee (University of Auckland)
  • Carmen Astudillo-Garcia (University of Auckland)
  • Chanenath Sriaporn (University of Auckland)

  • Jian Shen Boey (University of Auckland)


Strategies for successful cyanobacterial proliferation in freshwater
S Wood, HS Tee, KM Handley
Nature Research Microbiology Community, May 2020

Tools for successful proliferation: Diverse strategies of nutrient acquisition by a benthic cyanobacterium
HS Tee, D Waite, L Payne, M Middleditch, S Wood, KM Handley
The ISME Journal, 14, 2020,

Determining microbial roles in ecosystem function: Redefining microbial food webs and transcending kingdom barriers
KM Handley
mSystems 4(3), e00153-19, 2019, doi:10.1128/mSystems.00153-19

Bioinformatics resources on Genomics Aotearoa GitHub: