1. health and fitness

Potential PhD project outlines for 2015 AIMS@JCU Cohort:
Topic
Supervisors
Pre-requisite
quantitative skills
Other prerequisites
Implement “microbialization scores” associated
with coral reefs for local and regional scale
assessment of ecosystem impacts. The
microbialization score represents the percentage
of the combined fish and microbial predicted
metabolic rate that is microbial. Previous studies
show strong positive correlations between reef
microbialization scores and human impacts. The
microbialization score is a powerful metric for
assessing the level of human impact a reef
system is experiencing . Ccurrently scoring is
based on fish metabolic rates, but we propose to
expand the correlative value and potential
applications for assessing within reef coral
resilience. By combining the assessment of
microbial productivity with already established
coral health indicators, such as lipid content and
photosynthetic potential, the resilience of
colony- and reef-scale coral communities can be
established. This can provide a rapid
environmental assessment of stress impacts on
coral communities and provide a measure for
determining the health status of coral reefs over
immediate and long-term spatial scales.
Prof. Bette Willis (JCU)
bette.willis@jcu.edu.au
- Honours or
Masters degree in
either:
(1)molecular
biology, with a
strong interest and
some background
in microbiology, or
(2) biology, with a
strong ecology
background.- a high aptitude
for and interest in
mathematical and
statistical
modelling.
- at least one
course in
biological
statistics would
be beneficial
Dr David Bourne, AIMS
d.bourne@aims.gov.au
Dr Kathy Morrow (AIMS)
k.morrow@aims.gov.au
Quantitative
skills to be
developed
during project
- Experimental
design and
biostatistics
- Predictive
model fitting
- Ecological
numerical
modelling
Quantitative
outcomes of the
project
Bring together
the approaches
from the cellular
level (microbial,
gene expression,
energetics,
metabolomics)
with the
integrated
monitoring
approaches and
then formulate
into useable
predictive tools
through
modelling.
Topic
Supervisors
Pre-requisite
quantitative skills
Microbial and Molecular Biomarkers of Coral
Health.
The persistence of coral-dominated reef
ecosystems in a changing world relies heavily on
the ability of hard corals to maintain their health
in the face of acute and chronic environmental
stress. However, we still have a poor
understanding of many fundamental aspects of
coral health and the drivers of change in this
condition in space and time. This project will
provide an improved and integrated
understanding of how gene expression,
nutritional physiology, and microbial symbionts
associated with corals are affected by different
environmental pressures. The project will use
this information to develop quantitative and
qualitative models that reveal the significance of
coral health on the desired attributes of ‘stress
tolerance’, ‘growth’, ‘fecundity’, ‘survival’ and
‘disease susceptibility’. It will also provide the
baseline information for developing biomarkers
that are linked to bioindicators to assess health
condition of reefs in space and time.
Dr Line Bay (AIMS)
l.bay@aims.gov.au
- Honours or
Masters degree in
either:
(1)molecular
biology or ecology,
with a strong
interest and some
background in
microbiology, or
virology (2)
biology, with a
strong ecology
background.- a high aptitude
for and interest in
mathematical and
statistical
modelling.
Dr David Bourne (AIMS)
d.bourne@aims.gov.au
Dr David Francis (AIMS)
d.francis@aims.gov.au
Prof. Bette Willis (JCU)
bette.willis@jcu.edu.au
Other prerequisites
Quantitative
skills to be
developed
during project
- Experimental
design and
biostatistics
- Predictive
model fitting
- Ecological
numerical
modelling
Quantitative
outcomes of the
project
Bring together
the approaches
from the cellular
level (microbial,
gene expression,
energetics,
metabolomics)
to develop
informative
indicators of
stress and fitness
of the coral
holobiont and
subsequently
integrate into
useable
predictive tools
through
modelling.
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)
th
Deadline for Applications is 30 May 2015.
Additional Details Available at: http://aims.jcu.edu.au/current-funding-opportunities.aspx