EMRI member Kim-Anh Lê Cao wins prestigious 2019 – 2022 Career Development Fellowship (CDF2) from the National Health and Medical Research Council (NHMRC) ‘Microbiome biomarkers of human disease: novel computational methods to facilitate therapeutic developments’, $483K.
The Environmental Microbiology Research Initiative (EMRI) is a research consortium that aims to explore how environmental microorganisms influence ecosystem and human health, change the chemistry of the planet, respond to the impacts of industrial contamination and climate change, and potentially yield new biotechnologies.
Environmental systems harbour complex microbial networks and interactions that reflect biological and geological co-evolution, including the impacts of the Anthropocene.
Only recently have the vastness, novelty and ingenuity of Earth’s microbiomes been revealed through advances in metagenomics and utilisation of multi-omics approaches.
Understanding the distribution, complexity and functionality of the planet’s largely uncultivated environmental microbes presents a new frontier of science.
EMRI is an interdisciplinary research initiative created to explore and make discoveries across this new frontier. EMRI involves five faculties at the University of Melbourne: Science; Engineering; Medicine, Dentistry and Health Sciences; Veterinary and Agricultural Sciences; and Arts.
EMRI RESEARCH PROGRAM
EMRI research is grouped into three interconnected themes of microbial resilience, microbial systems and microbial evolution. The three themes underpin the research program that will address five key research objectives:
- Contribute strategically to the growing global catalogue of environmental genomes and metagenomics datasets
- Understand key environmental factors that shape microbial communities
- Predict adaptations in microbial communities and their functionality under changing environmental conditions
- Identify novel metabolic/enzymatic pathways for nutrient cycling or contaminant remediation
- Use metagenomics to drive cultivation-based hypothesis-testing experiments and selective enrichment/species isolations.
International Conference Organising Committee Membership:
- Gordon Research Conference – Marine Molecular Ecology (Novel Insights into Marine Patterns and Processes) 14-19 July, 2019 Hong Kong. Madeleine van Oppen (organising chair) and Linda Blackall (vice chair).
- Microscale Ocean Biophysics 5.0. 10-16 January, 2019, Whistler, Canada. Douglas Brumley on the organising committee and invited speaker.EMRI Personel:
EMRI 2nd General Workshop held on 17th August, 2018.
- Dr Kim-Anh Lê Cao wins 2019-2022 Career Development Fellowship (CDF2) from the National Health and Medical Research Council (NHMRC) ‘Microbiome biomarkers of human disease: novel computational methods to facilitate therapeutic developments’, $483K.
- Prof Karen Day (Dean of the Faculty of Science) awarded the title of Redmond Barry Distinguished Professor for her outstanding leadership within the University’s professoriate.
- EMRI funds 2 PhD students (2018-2021) – Mr Francesco Ricci and Mr Heyu Lin.
- Prof Madeleine van Oppen wins Australian Research Council (ARC) Laureate Award for Engineering microbial symbionts that increase coral climate resilience (2019-2023; $3,011,916).
- Dr Douglas Brumley wins ARC Discovery Early Career Researcher Award for The mechanisms driving microbial navigation in marine systems (2018 – 2021; $348,575)
- Prof Jillian Banfield receives 2018 UK Microbiology Society Prize Medal.
- Prof Jillian Banfield elected as a Fellow of the Royal Society (FRS)
- EMRI scientists host 3 Uni Melbourne symposia (till August, 2018)
International Conference Presentations:
- The 17th International Symposium on Microbial Ecology Leipzig, Germany – Ms Katarina Damjanovic, Ms Giada Tortorelli, Mr Leon Hartman
- The 9th International Symbiosis Society Congress Corvallis, Oregon, USA – Ms Ashley Dungan, Ms Giada Tortorelli, Prof Linda Blackall
EMRI 1st General Workshop held on 11th July, 2017.
- Prof Jillian Banfield wins prestigious VM Goldschmidt Award from the Geochemical Society.
- EMRI academics appointed (0.4 FTE) – Prof Jillian Banfield, Prof Linda Blackall.
- Dr Heroen Verbruggen, Prof Linda Blackall, Assoc Prof Kat Holt for Hybrid assembly of holobiont genomes in the coral skeleton ($19,971; seed funding from Univ Melbourne Computational Biology Research Initiative)
- Damjanovic K, Blackall LL, Webster NS, van Oppen MJH (2017) The contribution of microbial biotechnology to mitigating coral reef degradation. Microbial Biotechnology, doi:10.1111/1751-7915.12769.
- Prof Madeleine van Oppen featured on ABC Catalyst
- EMRI scientists host 7 Uni Melbourne symposia
- EMRI and Melbourne Integrative Genomics member Dr Kim-Anh Lê Cao has received a prestigious National Health and Medical Research Council Career Development Fellowship (2019-2022) – she will seek to develop new computational methods that can be used to determine which bacteria living in our bodies are effective biomarkers of disease.
- Prof James Prosser, University of Aberdeen, public seminar at Uni Melbourne: Harnessing soil microbiomes for agricultural production: transforming hype and hope into reality. Tuesday 4th September, 6pm.
- Careers in Computational Biology run by Computational Biology Research Initiative on Monday 17th September.
- EMRI member Prof Madeleine van Oppen wins prestigious ARC Laureate Award (2019-2023). “Postdoc in engineering of coral-associated prokaryotes to increase coral climate resilience”. See link: postdoc prokaryotes
- The University Melbourne, School of BioSciences posts events each week – here are the events for the week starting 20th August, 2018.
- The Victorian Branch of the Australian Society for Microbiology Food Microbiology Special Interest Group are holding a presentation night on “From Environment to Hosts – the diverse niches of bacteria” on Tuesday 21st August, 2018 at Swinburne University of Technology, Lecture Theatre ATC101, Advanced Technologies Centre, 441/401-451 Burwood Rd, Hawthorn, Vic 3122.
- EMRI member Dr Doug Brumley on the organising committee and an invited speaker of Microscale Ocean Biophysics 5.0, 10-16 January, 2019, Whistler, Canada.
Mr Francesco Ricci (2018-2021) (firstname.lastname@example.org)
- Supervisors: Dr Heroen Verbruggen, Prof Linda Blackall, Prof Michael Kühl (University of Copenhagen, Denmark).
- Project Title: Physicochemical micro-niches in the coral skeleton and their relation to the microbiome
- Brief Description: I investigate the micro-niches within the calcium carbonate skeleton of scleractinian (stony or hard) corals, using planar optode imaging to analyse their physicochemical properties and molecular techniques to characterise the associated microbiota.
Mr Heyu Lin (2018-2021).
- Supervisors: Dr. John Moreau, Assoc Prof Kat Holt
- Project Title: Investigating the potential for mercury methylation by marine micro aerophilic bacteria
- Brief Description: This project will employ culturing-based and culture-independent techniques to understand the mechanisms for microbial mercury methylation in aerobic marine water columns. We will be looking for new genes and pathways employed by marine bacteria to metabolize or resist anthropogenic mercury contamination, in order to investigate the role of bacteria in the marine biogeochemical mercury cycling.
EMRI Affiliated PhDs
- Supervisors: Dr. John Moreau, Prof. Jillian Banfield (Univ Melbourne, Univ California, Berkeley, USA)
- Project Title: Geomicrobiology of rare earth elements
- Description: The project aims to discover novel microbial compounds that liberate rare earth elements and phosphorus from minerals. By focusing on the interactions between soil microorganisms and lanthanide-phosphate minerals, this proposal seeks to understand how microbes break down these highly insoluble secondary minerals in the environment. Expected outcomes include new strategies for accessing phosphorus in depleted agricultural soils and recovering lanthanides from currently uneconomical mine tailings. This project will provide new knowledge of the microbially-controlled processes mediating the biogeochemical cycling of phosphorus and lanthanides in nature, for harnessing to improved land management and economical resource extraction.
- Supervisors: Dr. Jay Black, Dr. John Moreau, Dr. Andre Mu
- Project Title: Understanding microbial responses to supercritical CO2 stress, and the implications for CO2 geosequestration
- Description: In this research, we will use a high-pressure and temperature experimental apparatus to simulate geological conditions at 1-2 km below the Earth’s surface, where supercritical carbon dioxide will be stored in large plumes that may trigger microbial metabolic responses with consequence for aquifer geochemistry and mineralogy. Specifically, we are interested in the viability of microbial biofilms that might help trap or limit the migration of subsurface supercritical carbon dioxide plumes.
- Supervisors: Dr. Mathew Watts, Dr. John Moreau, Dr. Berin Boughton
- Project title: Determining microbial community structure and metabolic pathway changes in a thiocyanate biodegradation system under environmental perturbations
- Description: This project will examine how bioreactor microbial communities self-structure and metabolise thiocyanate and intermediation breakdown products during thiocyanate bioremediation of mining wastewater. We are particularly interested in resolving the species-dependent metabolic “handoffs” of nitrogen, sulfur and carbon, with broader implications for these biogeochemical cycles in both industrial-scale bioremediation systems and natural aqueous environments.
Ms Ashley Dungan (2017-2020) (email@example.com)
- Supervisors: Prof Linda Blackall, Prof Madeleine van Oppen
- Project Title: The exploration of bacterial probiotics in the model organism Exaiptasia pallida to increase climate resilience in corals
- Brief Description: The goal of my research is to develop a probiotic to mitigate the effects of thermal stress in E. pallida by understanding the phenotypic and genetic traits of their symbiotic bacteria and how these bacteria might neutralize toxic reactive oxygen species. I use pure culturing techniques, fluorescence in situ hybridisation, whole genome sequencing, metabarcoding, and physiological assessment of the anemone host to answer my questions.
Ms Katarina Damjanovic (2015-2019) (firstname.lastname@example.org)
- Supervisors: Prof. Linda Blackall, Prof. Madeleine van Oppen
- Project Title: Manipulating prokaryotic symbionts to enhance coral tolerance to stress
- Brief Description: This project consists in exploring the feasibility of manipulating the coral prokaryotic microbiome by targeted exposures into the laboratory and gaining insights into the transmission mode of bacteria and Symbiodinium in corals with different reproductive strategies.
Miss Giada Tortorelli (2017-2020) (email@example.com)
- Supervisors: Prof Geoff McFadden, Prof Madeleine van Oppen, Prof Simon Davy (Victoria University of Wellington, New Zealand)
- Project title: Dissecting the symbiotic partnership between algae and animals that powers coral reefs
- Brief description: I am interested in the really initial steps during the establishment of symbiosis between Cnidaria and Symbiodinium. My main aim is to dissect the inter-partner molecular signalling that allows recognition between host and photosymbionts in the setup of symbiosis.
Mr Leon Hartman (2016-2020) (firstname.lastname@example.org)
- Supervisors: Prof Linda Blackall, Prof Madeleine van Oppen, Prof Damien Hicks (Swinburne University of Technology)
- Project Title: Manipulation of prokaryotic communities in the coral model organism: Exaiptasia pallida
- Brief Description: We are establishing Australia’s first cultures of the coral model organism, E. pallida, and characterising its prokaryotic communities. Having access to this model and its baseline microbiome data will facilitate investigation of coral bleaching mitigation strategies, particularly inoculation with probiotic bacteria, which is the focus of my work.
DEAN OF SCIENCE
Karen Day, Dean, Faculty of Science
John Moreau, School of Earth Sciences
Jill Banfield, School of Earth Sciences
Malcolm McConville, Department of Biochemistry and Molecular Biology, Bio21 Institute
Linda Blackall, School of BioSciences and School of Earth Sciences
Robyn Sloggett, Grimwade Centre
Jizheng (Jim) He, Agriculture and Food, Faculty of Veterinary and Agricultural Sciences
Andrew Western, Department of Infrastructure Engineering, Melbourne School of Engineering
Sammy Bedoui, Department of Microbiology and Immunology, School of Biomedical Sciences
Andrew Brooks, Department of Microbiology and Immunology, School of Biomedical Sciences
Douglas Brumley, School of Mathematics and Statistics
Deli Chen, Agriculture and Food, Faculty of Veterinary and Agricultural Sciences
Stuart Dashper, Melbourne Dental School
Mark Davies, Department of Microbiology and Immunology, School of Biomedical Sciences
Zoe Dyson, Department of Biochemistry and Molecular Biology, Bio21 Institute
Sally Gras, Chemical and Biomolecular Engineering, Melbourne School of Engineering
Ralf Haese, School of Earth Sciences
Eric Hanssen, Bio21 Institute
Ary Hoffman, School of BioSciences, Bio21 Institute
Kathryn Holt, Department of Biochemistry and Molecular Biology, Bio21 Institute
Ben Howden, Molecular Diagnostics Unit, Doherty Institute
Kate Howell, Agriculture and Food, Faculty of Veterinary and Agricultural Sciences
Alexander Idnurm, School of BioSciences
Alex Johnson, School of BioSciences
Stephan Kaiser, Administration Support, Department of Microbiology and Immunology, School of Biomedical Sciences
Caroline Kyi, Grimwade Centre
Kim-Anh Le Cao, School of Mathematics and Statistics
Michael McCarthy, School of BioSciences
Andre Mu, Doherty Institute
Hayley Newton, Department of Microbiology and Immunology, School of Biomedical Sciences
Laura Parry, School of BioSciences
Ute Roessner, School of BioSciences
Robyn Schofield, School of Earth Sciences
Anne Steinemann, Department of Infrastructure Engineering, Melbourne School of Engineering
Geoff Stevens, Chemical and Biomolecular Engineering, Melbourne School of Engineering
Michael Stewardson, Department of Infrastructure Engineering, Melbourne School of Engineering
Timothy Stinear, Department of Microbiology and Immunology, School of Biomedical Sciences
Dick Strugnell, Chancellery (PVC-GR) and Department of Microbiology and Immunology, School of Biomedical Sciences
Stephen Swearer, School of BioSciences
Madeleine van Oppen, School of BioSciences
Heroen Verbruggen, School of BioSciences
Peter Vesk, School of BioSciences
Karena Waller, Department of Microbiology and Immunology, School of Biomedical Sciences
Michelle Ward, Administration and Support, Faculty of Science
Mathew Watts, School of Earth Sciences
Tony Weatherley, School of Ecosystem and Forest Sciences
Andrew Western, Department of Infrastructure Engineering, Melbourne School of Engineering
Bioremediation of mine wastes
Gold mining produces toxic heavy metals and other chemical waste products.
Some environmental microorganisms can biodegrade these contaminants into less harmful or non-toxic substances.
The Moreau Geomicrobiology Lab applies both cultivation-based and molecular biology approaches to developing new biotechnologies for mitigating mining impacts on soil and groundwater
Geomicrobiology and biogeochemistry of mercury methylation
The Moreau Geomicrobiology Lab studies the processes by which certain microorganisms convert toxic ionic mercury (Hg2+) into the more toxic organometallic compound, methylmercury (CH3Hg+).
This process occurs in aqueous environments from riverine sediments to the open ocean, but the mechanisms and triggers for microbial mercury methylation are still poorly understood.
Manipulation of microbes to assist coral adaptation to climate change
Our group is called the Marine Microbial Symbiosis group. We explore how corals interact with their associated microbial communities, and attempt to augment the capacity of corals to tolerate stress by manipulating these communities. Our research aims to support development of novel coral reef restoration approaches.
We use the sea anemone Exaiptasia pallida as a model animal, and focus on the role of prokaryotes and the algal symbiont Symbiodinium. The approaches used to manipulate microbial communities include use of probiotics, experimental evolution and genetic engineering.
Recent publication: Damjanovic K, Blackall LL, Webster NS, van Oppen MJH (2017) The contribution of microbial biotechnology to mitigating coral reef degradation. Microbial Biotechnology, doi:10.1111/1751-7915.12769.
Microbiologically influenced corrosion
Accelerated low water corrosion (ALWC) is a type of microbiologically influenced corrosion that substantially increases damage to metal structures in seawater around the low tide level. ALWC is a costly global issue.
We hypothesise that the functional features of microbes, including their propensity to attach to metal surfaces and their metabolic pathways, facilitate ALWC. We aim to identify the microbes in ALWC tubercles with the aim of better understanding this phenomenon.
Contact: Linda Blackall
Microbial fluid dynamics
Fluid mechanics at the microscale governs a myriad of physical, chemical and biological processes in the environment.
We apply advanced video-microscopy and microfluidic techniques to directly visualise dynamic processes at the single cell level, from the collective beating of cilia to the active search behaviour of motile bacteria.
These results will uniquely inform the development of mathematical models with far-reaching ecological insights.
Contact: Douglas Brumley
Evolutionary Diversification of Marine Algae
Research in the lab focuses on the evolutionary diversification of marine algae, using molecular phylogenetics to explore their diversification and answer specific questions about their evolution. We focus on a range of topics in algal biology, including geographic modes of speciation, evolution of niches through geological time, paleontology, the emergence of important cellular and physiological innovations and the genetic changes underlying such innovations. Bioinformatics and phylogenetics take a central position in our approach to these research questions. We also carry out systematic research, asking how molecular and morphometric data can complement one another in algal species delimitation.
Contact: Heroen Verbruggen
COMBINE RNA-seq Workshop register by 19th Sept
Details: What: Melbourne RNA-Seq Workshop Date: 26th-27th September Registration closes: 5 pm, 19th September Venue: Seminar Room 2, WEHI (1G Royal Parade, Parkville VIC 3051, Australia) Registration: www.abacbs.org/rnaseq-analysis-in-r#!event-register/2018/9/26/rna-seq-analysis-in-r Course materials: combine-australia.github.io/2018-09-26-RNAseq-Melbourne/ The COMBINE Melbourne Team are offering a two-day Introduction to RNA-seq workshop on 26th-27th September in Melbourne. In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential …News
Prof Karen Day (Dean of Science) named Redmond Barry Distinguished Professor
Prof Karen Day (Dean of the Faculty of Science) awarded the title of Redmond Barry Distinguished Professor for her outstanding leadership within the University’s professoriate.News
Kim-Anh Lê Cao wins prestigious Career Development Fellowship from the NHMRC
EMRI member Kim-Anh Lê Cao wins prestigious 2019-2022 Career Development Fellowship (CDF2) from the National Health and Medical Research Council (NHMRC) ‘Microbiome biomarkers of human disease: novel computational methods to facilitate therapeutic developments’, $483K. This new CDF2 follows on from Kim-Anh's previous 2015-2019 NHMRC Career Development Fellowship (CDF1) on ‘Development of statistical methodologies and application to clinical cancer studies’News
Dr Doug Brumley on organising committee of Microscale Ocean Biophysics 5.0, 1-16 January, 2019, Whistler, Canada
EMRI member Dr Doug Brumley on the organising committee of Microscale Ocean Biophysics 5.0, 10-16 January, 2019, Whistler, Canada.News
Prof James Prosser, University of Aberdeen: Harnessing soil microbiomes for agricultural production: transforming hype and hope into reality. Tuesday 4th September, 6pm.
Public Lecture: Professor James Prosser, Chair in Molecular and Cell Biology at the School of Biological Sciences, University of Aberdeen, will present a seminar "Harnessing soil microbiomics for agricultural production: transforming hype and hope into reality." Please join us for pre-seminar refreshments at the venue, from 5.00pm - 6.00pm. Tuesday 4 September, 6.00pm, Theatre 1 (B103), Building 379, 207 Bouverie Street. For …News
Careers in Computational Biology Workshop – 17th September
ATTENTION: ALL STUDENTS, POSTDOCS & EMCRs The Computational Biology Research Initiative (CBRI) would like to invite you to participate in the Careers in Computational Biology Workshop to be held on Monday 17th September, 11am-2pm. The workshop will be divided into two parts: 1. A career advice session with guest presenters from across the Parkville precinct with experience working in industry, government and academia; and 2. A CV feedback session, where workshop participants will have …News
2019 Gordon Research Conference – Marine Molecular Ecology
Program uploaded for 2019 Gordon Research Conference on Marine Molecular Ecology (Novel Insights into Marine Patterns and Processes) - July 14-19, 2019 at The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, CN. EMRI scientists Madeleine van Oppen (organising chair) and Linda Blackall (vice chair).News
Australian Society for Microbiology presentation “From environment to hosts – the diverse niches of bacteria” – 21st August, 6.30pm
The ASM Victorian Branch and ASM Food Microbiology SIG are pleased to present “From environment to hosts – the diverse niches of bacteria”. Presenters: Dr Nuwan Ruwani – Biodiversity of culturable microbiota in refrigerated raw milk Dr Snehal Jadhav – Application of Omics in Food Safety Dr Caitlin Cooper – Differences in colonization of Salmonella enterica serovar Sofia in broiler chickens …News
Australian Microbial Ecology Conference 2019, Perth (save the date 11-13 Feb, 2019)
The Australian Microbial Ecology (AusME2019) meeting will be held at the University of Western Australia, Perth, WA. AusME2019 is a single stream, 2.5 day conference with half days devoted to 4 broad microbiome systems (aquatic, terrestrial, symbiotic and engineered environments) and a fifth microbial ecology toolbox session. Each conference day will start with a presentation delivered by a Plenary Speaker. Each half …News
Microbial Ecology in Melbourne (Aust Society for Microbiology sponsored meeting) 27th September 14:00-17:30
What: Microbial Ecology in Melbourne (2 ECR speakers, 4 PhD speakers; afternoon tea, post meeting informal social) When: 27th September, 2018 from 14:00-17:30 Where: La Trobe city campus, 360 Collins Street , Melbourne (Room: 360C-2.10). Why: Promote communication/collaboration for microbial ecologists How: Sponsor: Australian Society for Microbiology Organisers: Dr Chris Greening (Monash); Assoc Prof Ashley Franks (La Trobe Uni); Prof Linda Blackall (University of Melbourne) Cost: …News
Dr Christina Kellogg, USGS (2018 Rudi Lemberg Travelling Fellow). Seminar “Microbial Diversity of Deep-Sea Corals”, Monday 22nd October at 10:00-11:00am, Turner Theatre, BioSciences 2 building, University of Melbourne
Dr Christina Kellogg, United States Geological Survey (USGS) is the 2018 Rudi Lemberg Travelling Fellow. She will deliver a presentation entitled "Microbial Diversity of Deep-Sea Corals". Monday 22nd October at 10:00-11:00am in Turner Theatre, BioSciences 2 building, University of Melbourne. About the speaker Dr. Christina Kellogg, United States Geological Survey (USGS), is an international leader in coral microbial ecology. She has been working …News
EMRI member Prof Madeleine van Oppen wins prestigious ARC Laureate Fellowship (2019-2023)
Engineering microbes that increase coral climate resilience An exciting proposal by Professor Madeleine van Oppen facilitated the award of a 2018 ARC Laureate Fellowship. Professor van Oppen’s program will seek to bioengineer the microalgae and bacteria that are integral to coral tissue, giving them characteristics that make them more resilient to climate change. Coral reefs around the world are being lost …News