Phd in marine microorganisms (Australia)

PhD Project: Microbial indicators for environmental stress & ecosystem health assessments

Supervisory Panel:
Dr Nicole Webster & Dr David Bourne (Australian Institute of Marine Science)
Dr Marcus Sheaves (James Cook University)

Marine microorganisms drive all globally important biogeochemical cycles, underpin the health of marine ecosystems, are the first biological responders to environmental perturbation and are therefore sensitive early indicators for ecosystem health and/or environmental stress. This 4 year PhD project will develop advanced computational and bioinformatics approaches to establish microbial baselines for the Great Barrier Reef (GBR) and to identify specific microbial indicator species / functions that are representative of 'healthy' coral reef states. Identification of microbial indicators would facilitate the development of early warning systems for cumulative stress associated with altered environmental conditions.

This project will explore how microbial composition, microbial function and microbial activity in coral reef sediments, seawater and dominant habitat forming taxa (corals, sponges, sea-grasses) varies under different environmental states. The candidate will bring together sequence datasets from parallel nodes of the project (based on the Great Barrier Reef, New South Wales and Western Australia) to develop quantitative indicator metrics that can implemented into decision frameworks and ecosystem models. A computational pipeline will be constructed to enable robust simultaneous analysis of 16S rRNA amplicon, metagenomic and metatranscriptomic sequence data (thereby coupling microbial composition, functional potential and activity). Advanced statistical analysis of the sequence output with the extensive environmental metadata (salinity/conductivity, temperature, chlorophyll a, turbidity and nutrients - collected in conjunction with the Integrated Marine Observing System (IMOS))
  will enable the first quantitative assessments of microbial changes with environmental conditions and facilitate the identification of microbial indicators for inclusion in management frameworks. The bioinformatics analysis and computational biology will be conducted in close collaboration with Assoc. Prof. Gene Tyson at the Australian Centre for Ecogenomics, who is a global leader in the development of bioinformatics workflows. The project is also part of a national program established with investment from Bioplatforms Australia.

The preferred applicant is expected to have completed a recognised undergraduate degree in science with a major in microbiology / marine biology / quantitative ecology / computational biology and have had exposure to courses in applied statistics, mathematics, bioinformatics, or ecological modelling.. Quantitative bioinformatics analyses are critical to achieving the project's primary objective of identifying microbial indicators of different environmental states.

To Apply: Please send a cover letter and CV to Dr Nicole Webster (n.webster@aims.gov.au) and Dr David Bourne (d.bourne@aims.gov.au)

Deadline for Applications is 30th May 2015.

Additional Details Available at: http://aims.jcu.edu.au/current-funding-opportunities.aspx