TrEnD Bioinformatics 2019The trace and environmental DNA (TrEnD) lab is specialised in using degraded and ancient DNA to answer a number of biological questions. The significance of this research spans the areas of health, conservation, forensics, biosecurity, biodiversity, fisheries management and archaeology. We use NGS technologies and Bioinformatics to study a variety of fields. Projects in TrEnD in 2019 that utilised Magnus/Zeus CPU time were: - Several Chevron funded projects on biosecurity and ballast water (ongoing monitoring of Gorgon and Wheatstone infrastructure, oil/gas infrastructure baseline surveys, biosecurity risk of vessel movements) - Biosecurity work funded by Dept of Fisheries - Biosecurity work funded by Biosecurity QLD - Collaborative research with AIMS and Illumina describing biodiversity from seawater while at sea on a research vessel - Collaborative research with CSIRO on developing metabarcoding methodology - University funded projects to educate postgraduate students and provide eDNA metabarcoding data for a range of diet surveys (University of St. Andrews - penguin diet, University of Melbourne – small mammal diet, Edith Cowan University – fox diet). - An ARC Linkage project on isolating DNA from seawater - Microbial profiling as a member of WAHMCC. - An ARC funded Linkage project on Coral adaptation - An NHMRC projects (project on Ticks) - An NSF project on the Arctic - Biodiversity surveys in the Gulf of Carpentaria - Long term monitoring of marine vertebrates at the mouth of two rivers in Brazil - An eDNA survey of the Fortescue river and tributaries - An eDNA survey of subterranean habitats on Barrow Island - An eDNA biodiversity survey of marine species present at a marine seawall site in Queensland - Analysis of benthic infauna samples collected from an inshore location near Port Hedland - Oyster reef restoration study in NSW - Multiple ARC funded projects on restoration monitoring - Monitoring of urban bee diet - Industry funded projects on eDNA monitoring of terrestrial biodiversity
Principal investigatorMichael Bunce firstname.lastname@example.org
Area of scienceAncient DNA (aDNA), Biological Sciences, Coral, Environmental DNA (eDNA), Geosciences, Microbiome
Systems usedMagnus, Zeus, Nimbus, Managed Storage
Applications usedA wide range of applications were used for bioinformatic analysis including, BLAST, VELVET, RAXML, MrBayes, STRUCTURE, BEAST, USEARCH, DADA2, LULU, ADAPTER Removal, GHAP, STACKS
Many of the projects in the TrEnD activities address the national strategic priority; living in a changing environment. As a community we are more aware than ever of the impacts we have made, and are having, on our environment.
Using DNA preserved in fossil bones, seawater, sediments, ice cores, faecal material (and other substrates) a key outcome of this program is to provide perspective on biodiversity and humanity’s role in shaping it. Best-practice restoration, management and conservation can only be achieved if we understand what it is we are trying to restore and conserve.
In the TrEnD lab we generated a lot of Next-generation DNA sequencing data. We employed Pawsey resources to analyse various data in the following general areas.
(1) OTU generation and blast searching
(2) de novo assemblies
(3) Phylogeny and population Structure
List of Publications
Takahashi, M., DiBattista, J. D., Jarman, S., Newman, S.J., Wakefield C.B., Harvey, E., Bunce, M. (2020). Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding. Scientific Report. Doi: https://doi.org/10.1038/s41598-020-60779-9
Van der Heyde, M., Bunce, M., Wardell-Johnson, G., Fernandes, K., White, N.E., Nevill, P. Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding. (2020). Mol Ecol Resour. 00:1–14. https://doi.org/10.1111/1755-0998.13148
West, K. M., Stat, M., Harvey, E. S., Skepper, C. L., DiBattista, J. D., Richards, Z. T., … & Bunce, M. (2020). eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem. Molecular Ecology.
Alexander, J. B., Bunce, M., White, N., Wilkinson, S. P., Adam, A. A. S., Berry, T., et al. (2019). Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding. Coral Reefs. doi:10.1007/s00338-019-01875-9.
Mattia Saccò, Alison Blyth, Philip W Bateman, Quan Hua, Debashish Mazumder, Nicole White, William F Humphreys, Alex Laini, Christian Griebler, Kliti Grice (2019) New light in the dark – a proposed multidisciplinary framework for studying functional ecology of groundwater fauna. Science of the Total Environment, Vol 660, 963-977.
Nicole E White, Michelle T Gizik, Andrew D Austin, Glenn I Moore, William F Humphreys, Jason Alexander, Michael Bunce (in press) Detection of rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implication for threatened species management in subterranean environments. Hydrobiologia.
Saccò, Mattia; Blyth, Alison J.; Humphreys, William F.; Cooper, Steve; Austin, Andrew D.; Hyde, Josephine; Kuhl, Alison; Mazumder, Debashish; Hua, Quan; Smith, Colin; White, Nicole; Grice, Kliti (under review) Refining trophic dynamics through multi-factor Bayesian mixing models: a case study of subterranean beetles. Journal of Ecology and Evolution.