2020 Interdisciplinary PhD Scholarships

ABOUT THE PROGRAM

The Environmental Microbiology Research Initiative (EMRI) is a research collaboration that investigates the complex microbial networks, or microbiomes, which form a critical component of Earth’s environmental systems. Leading researchers across a range of disciplines have converged with the common goal of understanding the dynamics, structure, function and resilience of microbial consortia.

Two (2) fully funded Strategic Research Training Program (SRTP) Scholarships are available for students to undertake a PhD in a novel, interdisciplinary field.
Applications close on Friday October 16 at 5pm. Late applications will not be accepted. Results will be announced in late October or early November.
Total fee remission and living allowance of $31,200 per year pro rata (2020 full-time rate).
The successful students must accept and complete their enrolment by December 2020.

ELIGIBILITY

Students must adhere to the following eligibility conditions:

Applications are encouraged from a range of disciplines, including but not limited to, microbiology, microbial ecology, mathematics, statistics, physics, chemistry, bioinformatics, engineering, etc. Applicants will be assessed on their track record and the fit with a proposed interdisciplinary research project (see below).
Applicants must be Australian/New Zealand citizens or Australian Permanent Residents.
The following minimum entry requirements must be met: https://study.unimelb.edu.au/how-to-apply/graduate-research/domestic-applications/entry-requirements.

HOW TO APPLY

Complete the online application form here, and upload the relevant documents. Before you apply, you must:

Nominate one or more of the advertised projects (see below) and speak to the named potential supervisor(s). You must receive written approval (by email) that this supervisor is willing to supervise you if your application is successful. Print this email as a PDF for upload.
Have your academic transcript or statement of results ready to upload.
Have your CV ready to upload.
Have a brief statement detailing why you would like to be part of the Scholarship Program and your career aspirations and future plans (limit 300 words). Save the statement as a PDF for uploading to the application form.
Gather the contact details of two academic referees.
For further information, please contact Dr. Douglas Brumley (d.brumley@unimelb.edu.au) or Prof. Linda Blackall (linda.blackall@unimelb.edu.au).

PROJECTS AND SUPERVISORS

There are four possible projects that can be undertaken as part of this Scholarship Program (see summaries below). Please contact the named supervisors directly to discuss details of the project.

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Down the Drain: Bioinformatics-based approaches to enhance our understanding of water-based microbial communities

Understanding and managing simple microbial communities is something we have done well in the past (e.g. in food production). The advent of low-cost, high-throughput, DNA sequencing means that we are able to understand much more complex microbial communities with a strong expectation that these communities can be managed. This project will be part of the ongoing work that enables us to better manage the water systems associated with urban environments.DNA sequencing is increasingly being used to detect microbial flora in water.

This project will interact with projects generating sequence data at The Environmental and Public Health Microbiology Laboratory. The project will use these data and many other public sequence data resources to enhance our understanding of links between microbial flora in the various water systems in an urban context. Given this context and as a general overview for the project, bioinformatics-based approaches will be used to detect and understand persistence of a variety of pathogens and/or antimicrobial resistance gene markers. Candidates should have a background in Microbiology and Bioinformatics and a willingness to work across disciplines. Please feel free to contact me to discuss potential projects in more detail.

Supervisors: Dr Dieter Bulach (dieter.bulach@unimelb.edu.au; The Doherty Institute, The University of Melbourne), Dr Rebekah Henry & Assoc Professor David McCarthy (Environmental and Public Health Microbiology Laboratory, Monash University).
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The role of endosymbionts in the ability of insect pests to respond to climate change

Aphids are serious agricultural pests in Australia that cause damage estimated at $723m pa. With climate change leading to increasing temperatures globally, understanding the impact of temperature on pest insects is crucial for their management. Aphids carry essential endosymbiotic bacteria called Buchnera which are vulnerable to high temperatures. However, relatively little is known about how temperature shifts affect aphids and their endosymbionts in the long-term, or their potential to adapt to increasing temperatures.

This interdisciplinary project combining expertise in entomology, climate change modelling and environmental microbiology will explore how endosymbionts influence the ability of aphid pests to respond to climate change. The successful applicant should have a background in any of these areas and preferably some basic molecular skills. The candidate will first assess the impact of increased temperatures on multiple aphid species and their endosymbionts. Then, by manipulating endosymbionts, the candidate will evaluate their role in climate change adaptation and make predictions about their impact on future risk of agricultural pests through modelling. This PhD should lead to high-quality academic research outputs and practical applications for pest management.

Supervisors: Dr. Perran Stott-Ross, University of Melbourne (perran.ross@unimelb.edu.au), Dr. Belinda van Heerwaarden, University of Melbourne – (belinda.vanheerwaarden@unimelb.edu.au).
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Machine Learning for metagenome binning

Metagenomics makes use of shotgun sequencing of environmental samples (e.g. water, air, soil) to identify the biodiversity and functional roles of microbiota, many of which are yet unknown to science. Metagenomic binning, the grouping of assembled contigs into bins corresponding to species-specific genomes, is a key step required to gain insight into the biodiversity, genomic repertoire and functional roles of individual microbial species. Current methods separate contigs into bins based on base composition (GC%, k-mer frequency) and coverage (abundance) profiles. These tools have proven beneficial, but there is significant potential for improvement, especially to assign short contigs and separate closely related species.

This project aims to develop sophisticated metagenome binning tools that integrate multiple sources of evidence, combining traditional approaches based on k-mer composition and coverage with several innovative elements, including phylogenetic affinities, assembly graphs and lineage-specific marker genes. You will design improved clustering and classification algorithms based in machine learning (supervised and unsupervised learning) to generate the finest resolution and purest MAGs.

Supervisors: Saman Halgamuge (Engineering), Kshitij Tandon and Heroen Verbruggen (BioSciences). For more details please contact Heroen Verbruggen (heroen@unimelb.edu.au) or visit here.
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Recruitment, resilience and dynamics of coral microbiomes

The collective action of microbial consortia underpins the functioning of corals. At the heart of this are symbiotic partnerships and metabolic interactions among bacteria, algae and coral tissue. Despite advances in the accuracy and breadth of sequencing data, fine-scale spatial processes are routinely overlooked, and the physical mechanisms underpinning the establishment and functioning of the coral microbiome remain vastly unexplored. This project will take a micro-scale approach, investigating the dynamic interactions between core microorganisms responsible for coral health.

Using a multidisciplinary method involving microbiology, high-speed video-microscopy, and biophysical modelling, the successful student will:

1. Determine the physical/chemical factors involved in the recruitment of bacteria from the water column.
2. Elucidate how bacteria transition from planktonic cells to intracellular symbionts.
3. Investigate how the overall phenotype and fitness of the coral depends on the microbial community structure.

Taken together, this will provide a transformative view of the establishment and maintenance of coral microbiomes, and their resilience in changing ecosystems. The successful applicant will have a background in either life sciences (e.g. microbiology, microbial ecology) OR physical sciences (e.g. mathematics, physics), and will be supervised and mentored by an interdisciplinary team between University of Melbourne and University of Technology Sydney.

Supervisors: Dr. Douglas Brumley (d.brumley@unimelb.edu.au), Prof. Linda Blackall (linda.blackall@unimelb.edu.au), Dr. Jean-Baptiste Raina (Jean-Baptiste.Raina@uts.edu.au) for more information.

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