News and events
MQMarine workshop on ancient DNA
9 - 11 October, 2017
Assessing the potential of ancient DNA in marine sediments
Organisers: Dr Linda Armbrecht, Macquarie University, NSW
& A/Prof Leanne Armand, Australian National University, ACT
Macquarie University hosted a workshop to examine the potential for ancient DNA to illuminate the past, present and future of ocean-climate processes. The workshop was led by Dr Linda Armbrecht and attracted participants from around Australia as well as Japan and Switzerland. ARC Laureate Fellow Professor Alan Cooper (Australian Centre for Ancient DNA) opened the workshop and catalysed two and a half days of open discussion about advances in technology, limitations, pitfalls and potential opportunities. Advances in the fields of ancient DNA and forensics have a lot to offer researchers applying ‘omics techniques to understand living systems, including eDNA approaches for biosecurity. A/Prof Leanne Armand (ANU, Director ANZIC) outlined the unprecedented opportunity for 'biosphere frontier’ projects to participate in the IODP program, including upcoming voyages and accessing an existing repository of sediment samples.
A consensus emerged that there were significant opportunities to combine geobiology and ‘omics techniques, however, baseline data and experiments were required to establish the in situ rates of DNA degradation in different sediments, and use established techniques to verify the ancient versus living source of extracted DNA. Exploring the deep ocean seafloor has parallels with prospecting for life on distant planets. Contamination and ‘background DNA’ from living organisms in the sediment was a major concern that emerged repeatedly. We heard of the importance of rigorously identifying and eliminating the sources of contamination, even in contemporary DNA research. An outcome of the workshop was the establishment of a network to begin to coordinate research in efforts in this area. Participants are developing a paper ‘Are we contaminating the deep biosphere?’ to highlight the issues, from sample collection to informatics analyses, that will outline a pathway forward and catalyse collaboration in this emerging field of research.
Successful MQMarine workshop on 'Functional Traits'
26 - 27 September, 2017
Collection and analysis of marine species functional traits
Two main goals were identified for the workshop, find the important traits for defining functional groups and identify the appropriate statistical analyses. The first day of the workshop was dedicated to the underlying biology of the problem of using traits to identify functional groups of marine species. Dr Vidette McGregor of NIWA, New Zealand, presented an introduction to the problem on behalf of Dr Michelle Masi. This talk identified the underlying problem and set up important definitions to be used for the rest of the day. Dr Beth Fulton (CSIRO) talked about how functional groups are used for ecosystem models. She identified some of the important considerations to be made when creating functional groups for this purpose, and some of the key criteria of a good functional group. Prof. Mark Westoby, Macquarie University, gave an excellent presentation on how traits have been used in the plant literature for the past three decades. This talk helped participants to think more about the theory of the problem and identified some potential methods that could be used for this problem. The lunch-time seminar was a joint presentation from Prof Judi Hewitt (NIWA) and Dr Fabrice Stephenson (NIWA). The first workshop day finished with a presentation by Dr Matt Dunn (NIWA) who spoke of the issues of validation when creating functional groups or guilds from diet data. Several collaborative papers were discussed around these important issues for making functional groups.
The second workshop day focused on the statistics that can be used to create functional groups. Dr Roy Costilla (The University of Queensland) presented a potential solution to this problem – bi-clustering. Dr Cotilla’s talk identified the potential to utilise Bayes probabilities when creating functional groups, where the probability of a species belonging to a certain functional group can be included in the model, and updated with new information from traits. Prof Shirley Pledger (VUW) demonstrated some solutions to the problem that are currently available, as well as solutions that will become available once her new package ‘clustglm’ becomes available. The current solution utilised the package ‘FD’ in R that clusters species into functional groups using hierarchical clustering. Shirley’s new package, that utilises glm’s to cluster rows and columns, will be available next year. Dr Nokuthaba Sibanda (VUW) rounded off our statistics morning by discussing and demonstrating some of the potential validation procedures for evaluating the functional group fit. Her talk highlighted some of the issues with the current methods of evaluation for cluster analysis and she emphasised the need to evaluate multiple methods. Dr Asta Audzijonyte (University of Tasmania) finished our workshop with a lunch-time seminar with a very entertaining talk on the importance of including reproductive effort in the classification of fish to functional groups. Through simulation, Dr Audzijonyte showed that reproductive effort must be taken into account along with foraging effort and growth in order to gain a complete understanding of fish physiology. The information gained from this day will be tested and written into a manuscript that will be completed by December where it will be presented at SEEM in Queenstown, New Zealand.
MQMarine member Peter Karuso sailing on RV Investigator!
Prof Peter Karuso (CBMS) will be taking part on voyage IN2017_V05 on the CSIRO's RV Investigatorfrom October 11 to November 11. Embarkation is in Broome and disembarking in Perth.
The project aims to correlate fluorescence in deep water sponges with the presence of symbiotic cyanobacteria or algae. By converting blue to red light, the sponge could aid photosynthesis in deeper water in return for organic nitrogen and carbon from the cyanobacteria.
With a focus on sponges and other benthic invertebrates, collections will also be made as part of developing a natural products library, based on Australian biodiversity held in CBMS at Macquarie University. The focus of this collection is on fluorescent sponges and corals collected from sled tows from 10 m to over 400 m depths. Multicomponent analysis will require fluorescence, chlorophyll content, water clarity, latitude, water temperature and depth. On board fluorescence and absorption readings will be made possible by the kind donation of a BMG CLARIOstar fluorescence plate reader by James Balmer from BMG Labtech.
SIMS Emerald Dinner
The annual Emerald Dinner wil be on 26th October at the highly acclaimed Sergeants Mess on the foreshore of Chowder Bay, Mosman. The Emerald Dinner celebrates SIMS' efforts and achievements in research, education and outreach and funds raised are used to support the vital work that SIMS undertakes.
This year, you will have the opportunity to meet with and hear from our guest speaker Professor Matthew England. A world expert in global scale ocean circulation and its influence on regional climates, Professor England was recently awarded the 2017 prestigious Tinker-Muse Prize for science and policy in Antarctica. The prize citation acknowledged Professor England’s “rare ability to translate global issues to local impacts, in an engaging and accessible way for the public.
5 spots available for workshop on Science Communication
Research Enrichment Program (REP) Masterclass: "Making your science matter: Linking science with action to improve the world"
We all want to feel like our research matters… but it is sometimes hard to know how to make it relevant to people and institutions beyond academia. How can we best make our science understood, appreciated, and perhaps even acted upon by policy-makers? These are the kinds of questions we will delve into. Inspired by the book “Escape from the Ivory Tower” by Nancy Baron, this short course will help you improve your ability to design and communicate your science to benefit the world at large.
When: Tuesday 24 October 2017, 2 - 4 pm
Facilitators: Dr. Elizabeth Madin, Macquarie University Dr. Emily Darling, Wildlife Conservation Society Dr. Marah Hardt, Future of Fish Prof. Lesley Hughes, Macquarie University
Register here to reserve your spot! Participant numbers will be capped (first-in secures a place).
Great seminar by Michal Kowalewski
Thanks to Michal for a fantastic talk on
"Evolutionary History of Prey: 600 million Years of Predator-Prey Interactions in Earth’s Oceans"
last Friday, and to everyone who joined us!
If you did not get the chance to talk to Michal but you have questions, please let us know so that we can put you in touch!
Thanks to Dr Laetitia Gunton for a great seminar!
Laetitia just finished her PhD on deep-sea polychaete worms in the Whittard Canyon (NE Atlantic) and gave a great talk as part of our June Social Friday. Thanks to everyone who came along and let us know if you would like us to put you in touch with Laetitia!
09 May 2017Do you have a topic in mind that you would love to hold a workshop about and gather all the national and international experts in ...
09 May 2017NMSC met face-to-face in Canberra on 23 March and our meeting report is now available....
31st Mar 2017 4:00pmDirect from Antarctica - an overview of the Sabrina Seafloor Survey on the RV Investigator. By Leanne Armand, Amaranta Focardi, Va...
7th Apr 2017 3:00pmLearn more about Antarctic in a warmer world: Investigating past Antarctic climates from geological drill cores.When: 07 Apr...
2016 Successes and News
Read about Dominic McAfees Endeavour Award experience overseas!
Last month I returned from a six month research fellowship at the University of Hong Kong’s SWIRE Institute of Marine Science (SWIMS), funded by an Endeavour Australia Cheung Kong Research Fellowship. In stark contrast to the vertigo-inducing vertical concrete jungle, for which Hong Kong is famed, SWIMS is situated at the other extreme of the island. The facility lies at the end of a mostly uninhabited, jungle-clad Peninsula, 40 minutes walk from the nearest bus stop. With the laboratories at the water’s edge looking out at the South China Sea, it is a dramatic setting and one of Hong Kong’s most beautiful spots. Yet turn your head north and you will see the twinkling lights of Kowloon, one of the most densely populated areas in the world, with the evidence of human excess plain to see as debris on the shore. The ceaseless traffic of container ships and relentless fishing fleets busy each night emphasise the extreme pressure this marine environment is under. It’s quite a site, and really quite environmentally sobering.
Despite this intense environmental pressure Hong Kong has a very rich marine biodiversity. It is a magnificent setting to study marine processes with a variety of spatial and temporal environmental gradients, provided by the extreme seasonal variation in temperature, humidity and rainfall. Similar to the east-meets-west cultural clash on land, temperate ocean currents deliver species to Hong Kong waters from the North through winter, while warm tropical currents from the southeast predominate in summer. Certainly on the rocky shoreline there is a rich biodiversity of organisms employing a range of behavioural and physiological approaches to deal with the 54 oC temperature range that the rocky intertidal experiences annually. Investigation of these physiological mechanisms was a major theme in my host supervisor’s lab (Prof Gray Williams), with ocean acidification and marine pollution the other two major themes at SWIMS. Historically, pure ecological research has not been on the agenda in this region, but the times are a changin’ and Hong Kong’s first comprehensive marine biodiversity survey is currently underway.
For me it was a very productive research experience, conducting two original experiments. The first assessed how the interaction strength between oysters and their associated biodiversity changed with the onset of summer on Hong Kong rocky shorelines. This was the first comprehensive survey of biodiversity living among Hong Kong oyster habitat, and will form part of Hong Kong’s biodiversity survey. The second was conducted when I wasn’t melting on the rocky shore; in the seawater aquarium facility at SWIMS. I built an artificial rocky shore habitat that I exposed to different climatic regimes, allowing me to investigate how the orientation and density of oyster habitat will influence the amount of heat stress associated invertebrates will experience as temperatures rise. Long story short, as the climate gets hotter, size (vertical relief) really does matter when trying to beat the heat.
Indeed this was an incredible experience for which I feel extremely privileged. One of the lasting impressions will be the regular sharing beers around a large dinner table of SWIMS colleagues with the number of nationalities represented typically in the high teens. Never a dull moment. The other impression is how resilient life is given the intense pressure we exert upon it, and how darn lucky we are to live in the Australia with the opportunity to learn from the rest of the world.
Key to Unravelling the Onset of the Antarctic Circumpolar Current on the RV Investigator
by Michael Farmer & Harry West (MRes year 1 students in Earth and Planetary Sciences)
Sunrise on the back deck – one of the perks of the 2am-2pm shift.
In August, we travelled 300km south-east of Hobart on board the RV Investigator for a 5-day trip to the Cascade Seamount on the East Tasman Plateau. The proposal team was led by Joanne Whittaker (UTAS) and included Nathan Daczko (Earth and Planetary Sciences). The goal of the research is to resolve questions relating to the subsidence history of the plateau, the current interpretation of ODP site 1172 and ultimately link these to the onset of the Antarctic Circumpolar Current. Over the five days, samples were collected successfully from six dredges, piston, gravity and Kasten cores, multiple CTD profiles and ongoing bathymetric mapping. Being part of the science team, our main role was to characterise and identify the dredge samples (>750 kg). The cores weren’t opened on the ship. The rocks and cores collected will be used to constrain their age of formation and the nature of the crust and palaeo-environment during the opening of the Tasman Seaway. Overall, good weather, good food and lots of samples resulted in an amazing experience for two MRes students.
Trying to get the sample out of the only successful Kasten corer proved to be a difficult task.
Helping to carry the heavy metal cylinders of the piston corer that protect the PVC encased sediment.
Two Macquarie scientists recognised in Antarctic research ‘wikibomb’
On 24 August the Scientific Committee on Antarctic Research (SCAR) celebrated the achievement of adding 170 women to Wikipedia for their contributions to research in Antarctica. SCAR had invited the community to nominate influential female Antarctic researchers, past and present, in an international effort to increase the presence of female scientists on Wikipedia.
Two Macquarie researchers from the Department of Biological Sciences were recognised: Dr Leanne Armand, for her contributions to marine phytoplankton and palaeoceanography; and Honorary Fellow Dr Patricia Selkirk, who specialises in plant biology and ecology, and is a former recipient of the Australian Antarctic Medal.
Read the full article here.
Macquarie’s Dr Leanne Armand (right) with Geoscience Australia colleagues Dr Alix Post and Dr Jodie Smith, at the SCAR Open Science Conference in Kuala Lumpur. Photo: C Carson, Geoscience Australia.
MQ Marine Grant Success
A/Prof Nathan Daczko, Joanne Whittaker, Rebecca Carey, Howie Scher and Jacqueline Halpin have been successful in attracting ANZIC special post-cruise analytical funding to conduct their study "East Tasman Plateau – key to unravelling the onset of the Antarctic Circumpolar Current: IODP drill site 1172, Leg 189". The team was awarded $20,000, congratulations!
Citizen science oceanography project with Chief Scientist Martin Ostrowski received recognition at highest level!
The White House Office of Science and Technology unveiled The National Microbiome Initiative, which aims to further advance microbiome science in all its varied forms. IndigoVexpeditions outreach officer Rachelle Jensen was there to outline the case for citizen oceanography for ocean health monitoring. Read all about these fantastic news here.
Dr Linda Armbrecht was accepted as one of very few participant to travel to Antarctica this winter for an Early Career Scientists Advanced Training Program in “Biological Adaptations to Environmental Change”. The program is fully sponsored by the US National Science Foundation and will start from Chile, where the participants will board a US research vessel to head to Palmer Station in Antarctica for 6 weeks.
Dr Linda Armbrecht talks at Women in Science Symposium 2016 at the Australian National Maritime Museum
Linda Armbrecht was invited to speak about marine science and her research at the Women in Science Symposium on this year’s International Women in Science Day. The event was organised by the Australian National Maritime Museum in partnership with the University of New South Wales, and was a great success in encouraging high school girls to look beyond the lab coats and to see the possibilities for careers in science. You can follow the event here.
2015 Successes and News
Dorrit Jacob (EPS) promoted to Professor!
TOAST bioinformatics Sydney coming up March 2016!
The Joint Academic Micobiology Series (JAMS) invites to The Omics Analysis Sydney Tutorial (TOAST) 2016! And at the same time, Jon Zehr will be visiting Sydney! Jon is an inspiring marine microbiologist, have a look at his lab's research here.
We will inform you as soon as registrations are open! Until then, here is some preliminary information on the workshop:
Microbiology is undergoing a revolution bought about by advances in next-generation DNA sequencing technology. Researchers are now required to understand an array of bioinformatics principles and tools to interpret the vast amounts of data being generated. Presented by leading Australian & international researchers, TOAST is a 2-day event aimed at postgraduate students and early career postdocs providing in-depth hands on tutorials focusing on:
- Hands on tutorial: analysing 16S rRNA amplicon data using the QIIME pipeline (www.qiime.org).
- Online demonstration of common tools in comparative microbial genomics.
- Current Advances in Metagenomic analysis.
64bit laptop with 2GB RAM
Installation of VirtualBox
Bring your brain (and a laptop)
What are the minimum computer requirements?
A 64bit computer with a minimum of 2GB of memory and VirtualBox installed.
Where can I down load VirtualBox for my computer system?
Downloads for supported OSes are found here: https://www.virtualbox.org/wiki/Downloads
Where can I contact the organiser with any questions?
Please email: email@example.com
Leanne Armand (Biology) and Kelsie Dadd (Earth and Planetary Sciences) on the CSIRO Blog!
Read all about Leanne's and Kelsie's adventures on board the RV Investigator here.
Student and ECR Travel Scholarships 2016 from NCCARF!
The National Adaptation Network for Natural Ecosystems is offering four travel scholarships valued at $500 for students, early career researchers or practitioners to attend conference events in 2016.Read more!
Two ARC Discovery Project Successes for MQMarine Researchers!
Associate Professor Ian Goodwin; Dr Michael O'Leary; Dr Shari Gallop; Professor Jerry Mitrovica
The project is designed to contribute to answering important questions in climate change: Which polar ice sheets are the most vulnerable to warming? How fast will sea levels rise? What will be the impact on global coasts during the 21st century? The response of polar ice sheets to modest increases in global temperature and the rate of future sea-level rise remains highly uncertain. The project plans to examine the retreat of the polar ice sheets during the last warm interglacial period and the sea-level record archived in the Australian coastal sediments and morphology. It plans to use this unique sea-level signal to fingerprint the ice sheets that contributed the excess meltwater to the oceans and to map the configuration of the southern Australian coast under higher sea levels than present.
Dr Dorrit Jacob; Professor Stephen Eggins; Dr Richard Wirth
Biomineralization pathways in marine calcifyers
Shells and skeletons of marine organisms are important archives of past environmental change. Their reliability
relies on understanding their formation, which differs significantly from inorganic carbonate. This project will
combine innovative nano-analytical and aquaculture methods to develop new mechanism-based models that
improve the reliability of paleoclimate reconstructions and provide new insight into how increasing ocean
temperatures and acidification affect our marine resources.
IODP Award to MQ!
Macquarie University are part of a major consortia of 13 Australian universities, CSIRO and Geoscience Australia who were awarded a $10M ARC Lief grant to continue Australia’s participation in the International Ocean Discovery Program (IODP) for 5 years (2016-2020). The Director of the MQ Marine Research Centre, Prof. Simon George, is the CI from Macquarie University on this grant, which in addition to the $2M pa from ARC, also includes $875K pa from the partner organisations. These funds will enable at least two Australians to sail on each IODP cruise, and provides access to post-cruise funding for Macquarie University’s marine researchers. In the past six years, scientists from Macquarie University have participated in four marine expeditions and several more shore-based research programs.
ANZIC Funding Success!
Stefan Loehr (along with Martin Kennedy, Simon George and Bruce Schaefer) were awarded special ANZIC post-cruise analytical funding in Oct 2015 for a study “Constraining the impact of benthic meiofaunal activity on organic carbon burial in ancient oxygen-depleted sedimentary environments" [using material from ODP Leg 160]” Huiyuan Xu, Earth and Planetary Sciences, has started working on the project already!
Martin’s new paper published!
Read about microbial biogeography in the Indian Ocean in Martin Ostrowski’s hot-off-the-press article in Nature Scientific reports.