Revolutionising mass fish marking one otolith at a time

The use of farmed and restocked fish to supplement the worldwide human consumption of fish, recreational fishing stocks, and conservation efforts, is growing globally. But how well fish survive after release from hatcheries is still a mystery in many places. Hatcheries seldom mark or tag all fish prior to release, despite a range of mass-marking methods being available to mark farmed and restocked fish en masse. In a recent paper, Dr. Fletcher Warren-Myers and co-authors reviewed a range of thermal and chemical otolith (ear-bone) marking methods to assess their suitability as mass marking tools for hatchery-produced fish. These marking methods were compared in terms of (1) ease of application, (2) cost, (3) mark longevity, and (4) effects on fish welfare. His conclusion? Although some techniques will have limited use due to regulations, the majority of otolith mass marking techniques are simple, easy to apply, cost effective and highly suitable for long term monitoring of hatchery produced fish.

Feeling the heat: helping populations build thermal tolerance

Climate change is a major threat to biodiversity and important species on our planet. A potential solution to prevent vulnerable species from being lost is improving their thermal tolerances, making them better adapted to warmer temperatures and climates. University of Melbourne Masters student Kristal Sorby and co-authors tried to improve survival of individuals to extreme heat events within and across generations using a brine shrimp (Artemia franciscana) as a test animal. In combination with serotonin, methionine or neither, brine shrimp were exposed to ‘heat hardening’ over two generations and their thermal tolerances were recorded. While treatments did not increase their upper thermal limit, serotonin and methionine-treated shrimp outperformed control shrimp for thermal performance traits. Some effects were also present across generations, suggesting that heat hardening could provide resilience and stability in populations vulnerable to increasing temperatures.


Making a delousing treatment more fish-friendly

A cure should never be worse than the disease. In modern aquaculture, unfortunately that’s not always the case. When chemical treatments for parasites go wrong, they go very wrong, and cause mass mortalities of hundreds of thousands of fish.
One very common treatment to control external parasites is hydrogen peroxide baths. For salmon, the treatment is extremely toxic at warmer temperatures and can lead to fish deaths.
Kathy Overton, a Melbourne University Masters student invented a new method to make hydrogen peroxide treatment more fish friendly. By switching fish from warm ocean temperatures to cold treatment baths, Kathy showed the treatment was just as effective against the parasites and no deaths occurred. Once the industry takes up the new method, millions fewer fish will suffer each year.

Kathy Overton performing her experiment at the Institute of Marine Research, Norway.

Urchin Aquaculture Australia

Introducing Urchin Aquaculture Australia – a collaboration between The University of Melbourne, Deakin University, Southern Cross University and industry partner, AquaTrophic.

Sea urchin roe (‘uni’) is a prized delicacy in countries such as China and Japan. Uni is a particularly high value product, with a large export market in Japan worth around US $200 million annually. Increasing demand and reduced supply from collapsing wild fisheries are creating opportunities for commercial sea urchin culture in Australia to supply the Japanese market.

The aim of our AgriFutures Australia-funded research is to target major bottlenecks in sea urchin aquaculture industry development. Our current research focuses on two commercially-valuable sea urchin species: the collector urchin (Tripneustes gratilla) and the purple urchin (Heliocidaris erythrogramma).

To learn more, head to



Helping fish fight their own battles

A terrific article on the groundbreaking research of past PhD student Samantha Bui, which was recently published in the Journal of Zoology. Through a creative experiment, Sam and her colleagues worked out that fish have an inherent ability to use behaviour to deter parasites at the point of contact. Behaviour really is the first line of defence.

Her results are important for aquaculture – if the artificial environments fish farms create restrict the way fish display these natural defence behaviours, then they will be more susceptible to infection.

Know your enemy – understanding the movements of a devastating parasite to outsmart it

Sun Tzu’s ‘The Art of War’ tells us we must know our enemy if we hope to defeat it. In modern aquaculture, the greatest enemies are parasites that plague production and are a key part of many environmental effects. One of the worst parasites in salmon farming is a pesky amoeba that causes severe gill damage. As parasite outbreaks are extremely costly, the search is on for methods to reduce infection rates. One strategy is to reduce contact between salmon and the parasites in fish farms. But to do this, we must first know where these tiny parasites are and what drive their movements.

In a new study published in Aquaculture Environment Interactions this month, Dr Daniel Wright and colleagues from the University of Melbourne hunted for this marine parasite in Tasmanian salmon farms over 2 years. After taking over 300 separate water samples at farms and in their surrounds, there was no clear pattern between where the parasite was, depth in the ocean or the swimming depth of the fish.

Now we know our enemy, we have a better idea of which control methods will work and which won’t. For other parasites, control methods we developed that permanently change the swimming depth of fish swim are very successful. But they won’t work for this amoeba. We must now look for other possibilities to disconnect amoeba from salmon. These could include spreading fish densities more evenly at night with underwater lights and moving fish into brackish water that makes the amoeba leave the gills.


Rapid growth leads to hearing loss in farmed salmon

A new article led by Tormey Reimer, a Melbourne University Masters graduate, reveals that about half of farmed salmon are deaf due to accelerated growth in the aquaculture industry. Tormey and colleagues discovered that fast-growing fish were three times more likely to have ear bone deformities, leading to substantial hearing loss.
In this pursuit article, co-author Associate Professor Tim Dempster explains that these results “raise serious questions about the welfare of farmed fish” as the deformity is irreversible and becomes worse over time.

Earbones from the same farmed Atlantic salmon. The left is normal, while the right has 90 per cent vaterite deformation. Picture: Tormey Reimer

Escapes from aquaculture – what a technical standard can do

The recent dramatic images of the breakdown of an Atlantic salmon farm on the Pacific coast of the U.S. are startling. Square steel cages in a tangled mess with the fate of the 305000 fish they contained as yet uncertain. Some have been recovered from the cages, some will have escaped. Norway suffered a similar spate of escapes due to whole cage or farm breakdown over a decade ago. Norway still suffers escapes from salmon farms, but farm or whole cage breakdown has disappeared from the causes of escape. How did they fix it?

From 2009-2012, the European Union’s Prevent Escape project led by Tim Dempster (now with the Sustainable Aquaculture Laboratory at the University of Melbourne) delved deep into the causes and consequences of escapes from aquaculture, with the purpose of identifying how we could better stop escapes.

As part of the project’s work, a detailed analysis of escapes in Norway’s Atlantic salmon production revealed that after the Norwegian technical standard (NS 9415) for the proper design, dimensioning and operation of sea-cage farms was implemented in 2006, the total number of reported escaped Atlantic salmon declined dramatically, despite the total number of salmon held in sea-cages increasing by greater than 50% during this period (Jensen, Dempster et al. 2010; Aquaculture Environment Interactions).

What did the introduction of the technical standard do? Well, it encodes the type of technology (cages, mooring systems etc.) that can be used at farming sites depending upon the maximum forces those sites experience in a once-in-50-year storm or severe weather event. Prior to the technical standards introduction in Norway, big escapes happened due to the breakdown of cage structures and mooring systems. The technical standard basically eliminated complete farm failure as a cause of escape.

Based on the success of this measure, the Prevent Escape project recommended that policy-makers worldwide introduce a technical standard for sea-cage aquaculture equipment coupled with an independent mechanism to enforce the standard. We were pleased to see that Scotland followed with a new technical standard in 2015, yet other producing nations are still lagging behind on this key mechanism to prevent escapes.

It leads us to ask the question, if the U.S. had introduced a legislated technical standard that reflected best practice and drew upon the long success of the Norwegian technical standard, would this massive escape ever have occurred?

PhD project with $10000 per year top-up scholarship available

The future of aquaculture: how will fish cope with an offshore life?

A PhD project is available to investigate the behaviour and welfare of farmed salmon in new and emerging fish farm designs, principally for offshore and exposed locations. The project is a collaboration between the Sustainable Aquaculture Lab at the University of Melbourne ( and the Institute of Marine Research, Norway ( The student will be based in the School of BioSciences at the University of Melbourne, while experimental work will occur at the Institute of Marine Research’s state-of-the-art aquaculture research facility near Bergen, Norway, and in the field at commercial farms around the scenic fjords of western Norway.

There has been much debate regarding the salmon industry’s footprint in coastal waters. Part of the debate has revolved around whether farms should move to more exposed or offshore locations, where many of the problematic interactions with coastal environments and communities might diminish. A myriad of new fish farming concepts are now being proposed and implemented to tackle this challenge.

Offshore and exposed production system types have design aspects that alter the environmental conditions and behavioural context for fish relative to standard farms. Understanding these new production environments and their challenges for fish is key to success. Existing evidence suggests that several parameters critical for production will differ, including current flows, fish swimming speeds, school structure, dissolved oxygen levels, and fish buoyancy levels.

The PhD project will develop knowledge of the behaviour and welfare of salmon in new production systems. We will use a range of equipment to study fish farming environments and fish behaviours, including individual fish tags, echo sounders, and camera systems. Experiments will be conducted in research facilities and salmon farms that are testing new technologies.

The student will need to obtain an Australian Government Research Training Program Scholarship (…) for a PhD at the University of Melbourne. A first class honours or Masters is essential to qualify. A $10 000 per year top-up scholarship will be available in addition. Experience working with fish or in marine environments is desirable, but not essential. The student must be prepared to spend 2-3 months per year in Norway for experiments. The project starting date is flexible.

Expressions of interest (with CV attached) are welcome at any time until the position is filled. For further information contact Assoc. Prof. Tim Dempster (

Can we “program” fish by modifying their environment during early development to improve performance?

Salmon farmers want fish to be healthier, faster growing and to produce flesh of the highest quality at harvest. Unlike livestock, fish spawn eggs into the water, so that eggs, alevin and other stages of early development are fully exposed to a range of different factors which occur in the natural or aquaculture environment. A number of important processes and systems develop and become functional during these early stages of development (eg. the immune system, musculature, stress response axis etc).

We know that some external factors, like water temperature, can affect these developmental processes (for instance, higher temperatures resulting in higher incidences of spinal and jaw deformities). Some such factors are known to change the “epigenome”, areas outside of the genome that can have lasting affects throughout development on the rate of gene transcription. But what if we could manipulate the environment in which the animal is immersed to optimise and tailor development to produce a faster growing, healthier fish of exceptional quality?

In a new paper published in Scientific Reports, a team of Scientists from Nofima in Norway, including Associate Professor Nick Robinson from Melbourne University, have investigated how low temperatures and oxygen deprivation can program the Atlantic salmon embryo and post-hatch larvae to affect performance of the fish in later life. Low temperature and oxygen deprivation during these developmental phases were found to modify the epigenome, so that gene expression was regulated in a way that affected the subsequent growth performance of fish for 35 days after they were put out to the sea in cages. Fish that were treated with such mild chronic stresses both during embryonic and post-hatch larvae stages grew faster than unstressed fish, or fish that were treated at just the embryonic or just the post-hatch larvae stage.

The findings support the general notion that tighter regulation of factors in the water surrounding the fish during these early developmental phases could be utilised in a way to program the animal for improved performance in the aquaculture environment.

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