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Environmental metagenomics

Environmental microbiomes, from virus to eukaryote

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 are producing 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 is already generating a high quality database of genomes from stream and estuarine environments and links with projects studying other aquatic systems. Genomes include those of simple viruses, prokaryotes (bacteria and archaea) and more complex microbial eukaryotes. This genetic data will be used to determine the stream’s metabolic potential (capacity to transform chemical species and pollutants such as nitrate) and implications for the health of the aquatic ecosystem.

This project brings together researchers from four Universities and the Cawthron Institute. Two postdocs, linked to our postdoc community through the bioinformatics infrastructure, and one research assistant are employed to build capability.

Outcomes

  • Guidelines for virome genome identification and annota
  • Guidelines for eukaryote metagenomics
  • Tools for recovering challenging prokaryotic genomes
     

Metagenomics summer school

Team

  • Dr Kim Handley (University of Auckland) – lead researcher
  • Dr Gavin Lear (University of Auckland)
  • Dr Jemma Geogehan (University of Otago)
  • Professor Murray Cox (Massey University)
  • Maui Hudson (University of Waikato)
  • Dr Michael Hoggard (University of Auckland)
  • Hwee Sze Tee (University of Auckland)
  • Chanenath Sriaporn (University of Auckland)
  • Jian Shen Boey (University of Auckland)

Publications

Genomic adaptations enabling Acidithiobacillus distribution across wide ranging hot spring temperatures and pHs.2021 
Sriaporn C, Campbell KA, Van Kranendonk MJ, Handley KM. 
Microbiome. 9, 135. https://doi.org/10.1186/s40168-021-01090-1

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, https://doi.org/10.1038/s41396-020-0676-5

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: