How to track the environment with fish

Clockwise from right – Juvenile Murray cod after calcein marking; Juvenile silver perch during the experiment; An adult golden perch. Credit: Zoe Doubleday

Clockwise from right – Juvenile Murray cod after calcein marking; Juvenile silver perch during the experiment; An adult golden perch. Credit: Zoe Doubleday

Following up on an earlier post about how hard body parts can be used to reconstruct environmental signatures, Dr Zoe Doubleday and her team have identified the relative contribution of water (that the fish are swimming in) and diet to otolith (fish ear bones) chemistry in freshwater fish. Now I know that this isn’t strictly a study about oceans, but the techniques and findings of this paper are extremely useful if you want to do this in the ocean as well! See her report below.

Otolith chemistry is used extensively around the world to address key questions relating to fish ecology and fisheries management, particularly in marine systems. Nevertheless, there is limited research on the relative contribution of water and food to elements within otoliths.
Using a controlled lab experiment, researchers at the University of Adelaide sought to address this gap by explicitly testing the relative contribution of water and food in three iconic Australian freshwater fish species — silver perch, golden perch and Murray cod.  Water was found to be the key, but not sole, contributor to otolith chemistry in all fish species. This research will improve interpretation of otolith chemistry data in freshwater fish and will help to build a more accurate picture of their movements and the environments they inhabit.
Read journal article here:

Atmospheric CO2 reaches 400 ppm

In May 2013 the National Oceanic and Atmospheric Administration in the USA reported that the atmospheric concentration of CO2 at one of their recording stations topped 400 ppm for the first time. The media surrounding this event seems to have been very much based around the event itself with little comment on what it may mean. I find this moderately disappointing because we can be moderately confident of one thing  – increased CO2 in the atmosphere means that more will dissolve into the ocean, which means an increase in ocean acidification (this is classical chemistry!).

Despite the recent efforts of some of the worlds best scientists, both here in Australia and overseas, we still have an incomplete picture of the likely biological and ecological effects of this ocean acidification. However, we can be fairly certain of two things:

1. Ocean acidification will have negative impacts on organisms which form calcareous structures like the shells of molluscs (see pictures below) and the skeletons of corals; and

2. We are becoming increasingly aware that the increase in CO2 as a resource will cause changes to systems that are dominated by primary producers like seagrass and algae (e.g. kelp), mostly for the worse (for a starting point you could look at my webpage, but contact me for more information if you want!).

Unfortunately, as we enter a time of uncertainty for science funding in Australia, we may not develop a complete understanding of the system-wide effects of ocean acidification until it’s too late.

The growing edge of a juvenile abalone under high atmospheric CO2 (ultra-high magnification). Photo: Owen Burnell

The growing edge of a juvenile abalone under high atmospheric CO2 (ultra-high magnification). Photo: Owen Burnell

The growing edge of a juvenile abalone under normal atmospheric CO2 (ultra-high magnification)

The growing edge of a juvenile abalone under normal atmospheric CO2 (ultra-high magnification)

Aquatic body parts reveal all

This post is written by guest blogger Dr Zoë Doubleday, who is a Post-doctoral Fellow in the Marine Biology Program at The University of Adelaide. She has a particular interest in the utilisation of hard calcified tissues found in aquatic organisms as tools for answering critical questions in aquatic ecology. What interests me about Zoe’s work is how you can apply the techniques below to understanding past environmental conditions in the ocean and what that can tell us about the future…..


When you look at a tree stump what do you see? That’s right, rings, rings radiating out from the center to the edge; rings that represent the growth history of the tree.  Aquatic species also have rings laid down like this, year after year, decade after decade, in all kinds of body parts.  Fish and squid ear bones, shark vertebrae, coral skeletons, marine mammal teeth, bivalve and gastropod shells, cuttlefish bones. . .and the list goes on.  The beauty of hard calcified tissues is that many form growth rings with a precise periodicity (e.g. daily or annual), providing a time-calibrated archive of biological and environmental information.  To extract information from these natural chronometers we can analyse their chemical composition (such as trace elements and isotopes) and examine their growth ring

The otolith (ear bone) of a Murray Cod showing annual growth rings. Photo: Zoe Doubleday

The otolith (ear bone) of a Murray Cod showing annual growth rings. Photo: Zoe Doubleday

patterns (such as number and width) in relation to the temporal context of ring formation.  From here we can examine both the biological history (e.g. age, growth, diet, and movement) and environmental history (e.g. temperature and salinity) of an individual from birth to death.  This type of data can additionally tell us two important things: how the environment is changing and what biological impact that environmental change is having.

Another valuable attribute of calcified tissues is that they can hang around long after the organism has died.  This allows us to compare information derived from modern-day samples with information derived from historical (e.g. 19th and 20th Century), archeological and even paleontological samples.  Such comparisons are very powerful and can provide a rare and crucial insight into past biological baselines and what aquatic environments may have been like, say, prior to industrial-scale fishing or European colonization. This in turn can help us make a more realistic assessment of how much humans have impacted, and are impacting, the environment and about what environmental changes might happen in the future.

In the Marine Biology Program, we have a number of biochronologists working away on a range

Red Gurnard Perch (deep-water marine fish) ear bone with growth ring measurements. Photo: Gretchen Grammer

Red Gurnard Perch (deep-water marine fish) ear bone with growth ring measurements. Photo: Gretchen Grammer

of calcified tissues collected from freshwater to oceanic environments.  From here we are linking chemical and growth pattern data to various climatic and oceanographic variables, tracking movement patterns of individuals over large spatial and temporal scales, and seeing how biological indices, such as growth rate, age, and diet are changing.  However, there is still much to discover and uncover in calcified tissues and, in my opinion, is a mu ch underutilized resource of historical data, particularly in Australia.  As we continue to dig up long forgotten sample archives, find novel body parts with chronological properties, and work with constantly evolving analytical technology, who knows what we will find next…

Vertebra of Port Jackson Shark. Photo: Chris Izzo

Vertebra of Port Jackson Shark. Photo: Chris Izzo

The sins of the parents…..

Are not necessarily visited on the children, at least not with ocean acidification.Clownfish

There has been a lot of discussion over the last few years about the ability of plants and animals to adapt to ocean acidification. Some researchers are adamant that the rate of change is so fast that no animals will be able to adapt. A recent study by Miller et al. suggests that this may not be the case. In fact, they show that nature may just be a little more resilient than we give her credit for (or at least some species will be).

Professor Phil Munday and his team from James Cook University has been working on this concept for a while. The difficulty is that it is hard to raise multiple species of long-lived animals (or plants) in the lab to conduct these experiments. Miller et al. show that it’s worth trying. They exposed breeding pairs of cinnamon anemonefish to different levels of ocean acidification (OA) for two months before the breeding season. The astonishing thing is that their offspring weren’t negatively affected by this OA, whereas other juvenile fish coming from “normal” seawater were. What does this mean? That there was some sort of non-genetic adaptation within one generation!

We don’t know the underlying physiological mechanisms for this adaptation, or what other long-term trade-offs it may have (e.g. reduced reproductive output in the offspring?), but it is a promising outcome. Now all we need are more long-term, multi-generational research and we may begin to put a picture together on how our oceans will (or won’t) adapt to ocean acidification!

Disrupting synergies – making things not so bad.

Healthy forest of the kelp Ecklonia radiataI’ve posted on synergies between environmental stressors (what most people think of as pollution) before. Basically, a synergy is when the impact of the two stressors, say increased CO2 nd nutrients, is greater than the sum of their individual impacts. Once you recognise that synergies can occur, and are often much worse than we predict, the next question is can we do anything to stop them? The short answer is in most cases yes.

The way that synergies work means that, theoretically, if you remove one of the stressors then the “extra” impact should also be removed. In essence, if a synergy is 1 + 1 = 5, then removing 1 means that 1 + 0 = 1. When you’re talking about impacts to ecosystems that are essential to our GDP and way of life (not to mention that they have intrinsic value anyway) that is a really big consideration.

One of my Ph.D. students has just published a rather elegant study demonstrating it is possible to disrupt a synergy between CO2 and nutrients that has the potential to cause the loss of our kelp forest ecosystems. Basically, where CO2 and nutrients cause the synergistic growth of “weedy” species of algae you can remove the nutrients and remove the synergy. There is, however, a caveat. If you wait to remove the nutrients from the system then a large part of the impact will remain – things won’t go back to normal.

The thing that I like most about this outcome is that it provides useful information to the people who manage our coastal waters. If you are concerned that increasing concentrations of CO2 will have a negative impact in areas around major population centres then recycling and redirecting treated waste water away from the ocean, such as into industry or agriculture, can increase the resilience of marine systems. But, timing matters. Sooner is better.

Coral reef structures resistant to Ocean Acidification

Coral reefs are structurally complex and "cemented" together by Crustose Coralline Algae.

Coral reefs are structurally complex and “cemented” together by Crustose Coralline Algae.

Unlike some of the media coverage, I’m not saying that coral reefs will be resistant to ocean acidification, and I’m certainly not saying that corals will be. There is some good news for the gloom of ocean acidification. Yet, the devil is in the detail!

Unknown to most people, Crustose Coralline Algae (known in the field as CCA to stop us tripping over the long name) are the pink algae which cement together the matrix of coral reefs the world over, effectively solidifying the structure that we know as “coral” reefs. These CCAs also form a dense, concrete like ridge on the exposed side of most reefs, protecting the more fragile corals from destructive wave energy. So, from a reef perspective they are very important.

Until now, most of the research into the future of CCAs under ocean acidification has demonstrated that they are likely to dissolve (e.g. Tropical species and temperate species). However, some colleagues and I have recently discovered two important things about these CCAs, (1) that they contain dolomite, a rather robust mineral that most people associate with mountains in Italy; and (2) that dolomite is quite resistant to pH which we are expecting in the world’s oceans in the next 100 years (link to the paper here).

What does this mean? Unfortunately it doesn’t mean that the world’s coral reefs are going to be saved from ocean acidification by dolomite-rich CCA. By all accounts the corals are still in trouble (though I still have my hopes for more adaptive capacity than we give them credit for!). However, there is some hope, because these CCA are likely to maintain their structure and thus continue to protect reefs from damage by waves.

A systems perspective of the future


Experiments show that some clownfish may not be able to smell their predators in the future

To understand how complex ecosystems function, and how things will change if we push them too hard (and we’re constantly pushing!), we humans need to break them down into simple parts. I’m not going to tell you that we shouldn’t do this, because we need to start somewhere, and I’ve certainly done it myself. Where we go wrong, however, is by not putting the parts back together again to try and understand how the entire system may work, ultimately giving us a very simple view of how the world works. But, every now and then we are reminded in stunning detail how failing to build up again will provide us with the wrong information.

My research group recently had one of these stunning moments when we were visited by Prof. Phil Munday from James Cook University. His research is primarily concerned with how ocean acidification will impact on fish and their various roles in the functioning of ecosystems. Basically, he shattered our thoughts about ocean acidification by teaching us that 1 + 1 does not equal 2!

In an elegant series of experiments, Phil’s research group has shown that if you look at the separate responses of predatory fish and their prey to ocean acidification you may not accurately predict the outcomes. For example, under near-future ocean acidification, clownfish (Amphiprion percula) are unable to recognise the smell of their predators. Even worse, some species of fish became almost suicidal, being attracted to the smell of their predator!

If you were to take this on face value you would think that these results mean that small fish are going to have increased mortality under future ocean conditions. However, Phil has shown that it’s not that straight forward because when predatory fish are also exposed to ocean acidification their prey preference can change; preferred prey under current conditions are the less preferred prey under future conditions.

What does this tell us? Apart from the fact that some fish are going to get lucky, I think the big point here is that we cannot simply add up the results of a number of simple experiments looking at individual system components and identify what will happen to systems overall. Just like unexpected synergies among different stressors, we can’t assume that adding up the components will be enough. It’s time to take a more system-oriented approach where we can!

Geoengineering – can we really fix it?

Crustose Coralline Algae growing on the rock under a juvenile kelp (Ecklonia radiata). CCA can cover up to 80% of the rock surface in the temperate waters of Australia and is essential for the settlement of many species.
Photo: Dr Andrew Irving.

A student emailed me yesterday to request a letter that I wrote to the editors of Science a couple of years ago (“Honing the geoengineering strategy“). At the time, I was incensed by talk that we could stop global warming by dumping tonnes of sulphur into the atmosphere (which has a cooling effect) or a range of other “engineering” solutions. There is a series of excellent reports published by the UK Royal Society on the topic for anyone who is interested.

It wasn’t the ridiculous nature of these suggestions that got my attention though. I was more concerned by two things:

1. Anything that we do other than cutting carbon emissions is only buying time and I believe will only give us a false sense of security; and

2. The disregard that many geoengineering solutions have for the other effects of pumping millions of tonnes of CO2 into the atmosphere (but note, not all geoengineering fits into this category – something I will post on later).

Yes, there is warming, but from an ocean’s perspective there is also Ocean Acidification. Whether you believe in “Climate Change” or not, ocean acidification is happening and will continue to happen – its basic chemistry. As carbon dioxide dissolves into seawater it forms carbonic acid, which in turn reduces the pH of the water. Now, the ocean won’t become acidic like the acid you find in car batteries, but this increased acidity does reduce the amount of carbonate in the water. This carbonate is essential for all of the organisms that form hard structures from calcium carbonate, including everything from corals to snails to crustose coralline algae.

I’m sure that everyone reading this will have heard about the corals, but who really cares about coralline algae (or CCAs as we term them)? In fact, do you know what they are? (the pink algae covering the rock in the picture above). Though they may be humble, thousands of species rely on them. In tropical systems they form a hard reef crest to protect corals from waves. In temperate kelp forests they are essential for the settlement of species like abalone, which are not only important to the ecosystem but support multi-million dollar fishing industries.

So, not only does the talk of geoengineering provide us with a false sense of security about our ability to treat the symptoms of climate change, but the discussion often disregards the multifaceted problems that are caused by excess carbon in our atmosphere. Ultimately, the only way to fix the problem is to treat the cause – reduce our reliance on carbon based sources of fuel.


Other excellent blogs on Ocean Acidification:

Australian and New Zealand Ocean Acidification Project

Common synergies


Algal turfs (brown fuzzy stuff) are overgrowing the hard corals at high CO2 concentrations near volcanic vents – a good “natural” experiment. Note also that the seagrass (green, long leaves) are also doing well – a subject for another post.

We frequently hear about “climate change” in the media these days. How could you avoid it? If you do a search of the scientific literature there are thousands of publications a year on the topic. When thinking about the worlds oceans, the most common things that we hear about are ocean warming or ocean acidification (aka. the “evil twin” of warming). Do you notice somthing about this statement? We hear about warming OR acidification. But is this a realistic scenario?

We as scientists commonly break things down into their components and try to understand them one at a time. This is understandable, because the best way to comprehend the functioning of amazingly complex systems is to break them down their component parts and then put them back together again. In this case, however, we are just starting to understand that by breaking things down to individual conditions, either temperature or acidification, we may be missing the most important part of the study. My research group started to realise this in 2009 when we discovered that, when increased in combination, carbon dioxide and nutrients had a massive effect on the growth of “weedy” species of algae which can help to maintain the loss of kelp forests (download the paper here). In hindsight, this result should not be so surprising – both carbon and nitrogen are resources which the algae use to grow. Isn’t hindsight a wonderful thing?

What was surprising is that when carbon dioxide was elevated in the absence of nutrients these algae didn’t respond by grow faster. In fact, they didn’t respond at all to the increased availability of carbon. This means that CO2 and nutrients cause a synergistic response in these algae – where the response to the combined conditions is greater than the sum of responses to the individual conditions (see here for a good review on the topic).

What now worries us is that increasing availability of carbon in the oceans will happen with ocean warming – these are not either/or conditions. Indeed, the first warning shots were fired when we discovered that these same “weedy” turf algae showed the same synergistic growth in response to combined CO2 and warming (see our results published here). We can do something about nutrient pollution (something I will post on in the near future), but CO2 and warming are inherently linked. I think it is time to not talk about warming or acidification but rather to discuss them in tandem.

Report card on Australia’s oceans

I love being a scientist. It can be the most self-indulgent of careers and I feel lucky to live in a society that allows me the freedom to pursue ideas and information. I have the opportunity to explore ideas about how humans interact with our oceans, how we do bad things to them, and most importantly to me, try to figure out how to help them recover. The first step is gathering this information so that people can access it.

While scientists often disagree on things (a very important part of the job), getting a group of scientists together on a problem can truly help to pull together a massive amount of information very rapidly. In this spirit, the “Marine Climate Change Impacts and Adaptation Report Card (Australia)” was released last week. I am lucky enough to have been involved with two of the chapters, observed impacts of Ocean Acidification and observed impacts on marine Macroalgae. Unfortunately, I’d have to say that things aren’t looking good. We are only at the leading edge of some of the changes we are going to see over the next 100 years and some of the observed changes are already bad.

An example that most people wouldn’t know about (because you can’t see it from the surface) is the shift in the distribution of some algae. Algae, aren’t they just the “seaweeds” that we see washed up on the beach? Well, yes, but before they get to the beach they are the foundation of many food webs of the ocean; if they are lost then so are the ecosystems that they support. I must be honest here, when we started this project I didn’t actually expect to find anything to have happened yet, but it has. We have documented substantial southward shifts of entire assemblages of these algae on both the east and west coasts of Australia.Why? The waters of both coasts have warmed rapidly over the past 50 years. In fact, the Leeuwin Current was so strong this year with warming and El Nino that it pushed well into South Australia (see here for a Sea Surface Temperature image from IMOS). Not unheard of, but becoming stronger and more common.

Are we in danger of losing our iconic kelp forests? If so, what will happen to the ecosystems that they support (including 100’s of millions of dollars worth of fisheries)? Only time will tell, but I sincerely hope we can figure out a way to help them…..

The present…..










The future?