Coral Bleaching – Worse than we thought?

Last week’s episode of Blue Planet 2, Coral Reefs, highlighted the brilliance and importance of reef ecosystems, but also their fragility. I adored each story that was told in the episode – the hypnotic cuttlefish, clever clownfish, and horrifying Bobbit worm – but the scene that hit me hardest was the time-lapse footage of the coral bleaching event at the Great Barrier Reef. I’d, therefore, like to dedicate this post to the contemporary research being conducted along the Great Barrier Reef, and how technological advancements may help our scientific understanding of coral bleaching.

I’ve also been writing some posts for the University of Southampton – Exploring our Oceans blog regarding Blue Planet 2. Excited for the upcoming episodes? Read my latest post on what we can expect from episode 4, Big Blue!

With the current bleak outlook for corals, will in situ monitoring provide a greater understanding of bleaching events along the Great Barrier Reef?


Is this the future? – Increasing global thermal stress is causing mass coral bleaching events along the Great Barrier Reef. Wikipedia (CC BY).

Coral bleaching has recently been thrust into the spotlight of global media, with major concerns over the health of the Great Barrier Reef in particular. Coral bleaching is the expulsion of symbiotic algae by their coral polyp hosts, which typically occurs when the corals are subjected to sustained stressful environmental conditions, such as warming as a result of climate change. Coral reefs support more than a million marine species worldwide and an estimated 500 million people rely on coral reefs for their livelihoods via fishing and tourism, yet a sustained increase in global water temperatures has led to thermal stress and consequently bleaching across almost all coral reefs. The Great Barrier Reef is the largest reef system on the planet, with its structure visible from space, and thus has been central to bleaching event concerns. The publically documented decline of the famous reef has led to it becoming a ‘last chance’ tourism destination, with most tourists now visiting purely seeking an opportunity to experience the reef ‘before it’s gone’.

Last year (2016) was the hottest year on record to date, and consequently, the Great Barrier Reef suffered its worst ever mass bleaching event. A recent study that featured in the Journal of Operational Oceanography studied the observed coral bleaching patterns along the Great Barrier Reef during the 2015-2016 austral summer, using state of the art sensors installed across the reef to measure temperature and light conditions in real time. The in situ observations not only identified the environmental conditions that led to bleaching events but helped explain the changes in conditions across the Great Barrier Reef, to help scientists identify the vulnerable and at-risk areas.

In relation to this data, slight bleaching was predicted in the south of the Great Barrier Reef, moderate in central areas of the reef, and widespread to severe bleaching in the north; a prediction consistent with an initial survey. The recorded water temperatures also remained above the long-term mean well into the austral autumn, highlighting the persistence of the bleaching event. This finding also spells doom and gloom for the reef since coral communities can take up to twenty-five years to recover from bleaching events. Thus, the survival of the Great Barrier Reef relies on a halting of warming and would benefit from a shift in monitoring and conservation approaches.

Furthermore, the study compared the in situ sea surface temperature data to satellite data and found that due to issues such as cloud cover, the in situ data was more accurate than satellite observation, which tended to underestimate the severity of the environmental conditions that can cause bleaching. With satellite observation still the most common method of monitoring for bleaching risk, it is hoped that the in situ real-time data can be used to improve the accuracy of data from satellite observation.

In situ monitoring offers far greater insight into potential bleaching events, providing more accurate and reliable data than satellite observations, through a real-time view of the reef’s environmental parameters. The study emphasised the value and importance of in situ observations, which can allow daily measures of coral thermal stress and bleaching risks, thus providing a framework for understanding bleaching responses across the reef. These findings have huge implications for future reef monitoring and conservation opportunities, with a greater understanding of these processes enabling a more informed management framework for the Great Barrier Reef.


Temperature and light patterns at four reefs along the Great Barrier Reef during the 2015–2016 austral summer: understanding patterns of observed coral bleaching – Bainbridge, S. J. Journal of Operational Oceanography (2016).

How does climate change affect coral reefs? – National Ocean Service, NOAA (2016).

Great Barrier Reef sharply declines in north but signs coral recovering elsewhere – Slezak, M. The Guardian (2017).

Great Barrier Reef suffered worst bleaching on record in 2016, report finds – Griffith, H. BBC News (2016).

Great Barrier Reef survival relies on halting warming – BBC News (2017).

‘Last change’ tourists are flocking to see the Great Barrier Reef ‘before it’s gone’ – Piggot-McKellar, A. and McNamara, K. E. Business Insider (2016).

Two-thirds of Great Barrier Reef may be damaged beyond recovery – Clark, L. Wired (2017).


Blue Planet II

Blue Planet 2

“In 2001, The Blue Planet opened our eyes to the worlds beneath the waves. A generation on, new science and technology allow us to journey deeper than ever before, at the most crucial time in our oceans’ history.

Take a deep breath.” – Sir David Attenborough

The original The Blue Planet series, like many of my peers, inspired my passion for the ocean and marine life, prompting me to study and follow a career in Marine Biology. It, therefore, felt right to focus my next series of blog posts around the new Blue Planet II series, using this unique platform that the series is providing to raise awareness of contemporary marine research and relating innovative marine science to each episode.

My passion for marine science, sparked by The Blue Planet, has led me to focus my MSci dissertation project on a hydrothermal vent sea cucumber that is likely to be a new species to science. The experience of participating in the discovery of a new species from an ecosystem discovered merely 40 years ago, and working with a supervisor (Dr Jon Copley) whose research is featured in the new Blue Planet II series, is beyond exciting! Check out this behind-the-scenes video to get a glimpse of Dr Copley’s life aboard the Alucia whilst working on the Blue Planet II episode ‘The Deep‘, and my blog post Deep Sea Discoveries to find out more about my MSci project.

With The Blue Planet series being so central to my discovery of and enthusiasm for marine biology, you can imagine my uncontainable excitement for the new series! Despite my ridiculously high expectations, two episodes in and Blue Planet II has absolutely exceeded them. The technology advancements required to capture such breathtaking footage is incredible; the wildlife filmmaking and production efforts are truly inspirational. It’s incredible that even after four years of studying marine biology, the ocean never fails to amaze me!

My future ambition is to embark on a career in science communication and to contribute to the research and production of future marine documentaries. It is becoming increasingly apparent that communicating science is just as important as conducting it. Documentary series’ such as Blue Planet II beautifully and intelligently visualise this notion by producing a form of marine science which is accessible to everyone and increasingly encouraging public engagement with our ocean.

The wonder of marine biology has consistently captivated my imagination throughout my degree, and is now immortalised by one of Britain’s most-watched television programmes. Here’s to the next generation of marine biologists who will inevitably be inspired by Sir David Attenborough’s narration of our blue planet, just as I was.

The Danger of Overlooking Biodiversity

Are the effects of biodiversity on ecosystem functioning being underestimated? – A synthesis on the current consensus of biodiversity importance.

Species extinctions are currently occurring at rates that greatly outpace those predicted from the fossil record1. It has been suggested that a sixth mass extinction (a period of intense species loss, whereby > 75% of species are lost within a geologically short time interval), may be either currently underway or on the near horizon1. This has prompted a surge in studies examining the effect of biodiversity on ecosystem functioning2. However, despite extensive research, the importance of biodiversity for ecosystem functioning, in terms of multifunctionality and compared to other factors of ecosystem change, remain contested and unclear.

The term ecosystem functioning incorporates ecosystem processes carried out by biota (bioturbation, decomposition, etc.), and fluxes of materials and energy (primary production, nutrient cycling, etc.). Bioturbation, for example, is the disturbance of sedimentary deposits by living organisms and plays an important role in sediment oxygen uptake3. Species diversity has long been theorised as a major determinant of ecosystem functioning4, with hundreds of studies, spanning a range of ecosystems5,6,7, demonstrating that high diversity systems are approximately twice as productive as monocultures4.

However, the importance of biodiversity for integrated ecosystem functioning remains unclear due to the majority of experimental analyses focussing on individual functions, as opposed to the many that appear in natural systems8. Thus, ecosystem multifunctionality is currently at the forefront of biodiversity-ecosystem function (BEF) research. Multifunctionality is the ability to maintain multiple ecosystem functions simultaneously9, and it suggests that the effect of biodiversity on ecosystem function becomes increasingly significant as more functions are considered8.

Soil communities, for example, are complex and highly diverse, so focussing BEF research on a singular group of organisms disregards the complex food webs in which soil organisms interact10. Agricultural and land-use intensification has reduced the biodiversity and altered the composition of soil communities, prompting an investigation into its effect on ecosystem functions10. Soil biodiversity loss was found to impair multiple ecosystem functions, such as decomposition and nutrient cycling, with the average response of all measured functions exhibiting a strong positive linear relationship with soil biodiversity10. This implies that biodiversity is critical to highly multifunctional ecosystems and that prior analyses may have significantly underestimated the fundamental importance of biodiversity, by focussing excessively on individual functions or organisms8.

As well as underground, species richness is also positively and significantly related to ecosystem multifunctionality above-ground and under-water9,11. This relationship was observed in drylands and is consistent with experimental results obtained from other terrestrial environments9. The preservation of plant diversity in drylands is crucial to mitigate the negative effects of desertification caused by climate change9. In the marine environment, a meta-analysis revealed that generally, changes to species richness tends to alter the functioning of marine ecosystems, with multiple species treatments enhancing ecosystem function, relative to monocultures11. For example, deep-sea ecosystem functioning has been shown to be exponentially related to biodiversity, across a wide range of deep-sea ecosystems6. Deep-sea ecosystems are the most extensive and represent the largest reservoir of biomass on Earth6, so it is vital to evaluate and understand the consequences of biodiversity loss in this system.


Figure 1: General trend of the biodiversity and ecosystem function (BEF) relationship, as summarised from several hundreds of BEF experiments, and the approaches required for further improvement of BEF understanding and importance.16

However, the majority of BEF studies have strongly relied upon controlled experiments to formulate their conclusions. For example, the very first BEF experiment – the ‘Ecotron’ – utilised a mesocosm approach, with sixteen chambers of identical environmental conditions and differing biodiversity levels, to determine the effect of biodiversity on primary production12. These experiments have substantially advanced our understanding of the relationship between biodiversity and ecosystem functioning, by revealing the underlying mechanisms of biodiversity dynamics13. Nevertheless, they have been subject to intense criticism14.

The controversy regarding the use of controlled experiments stems from the argument that they do not characterise the complexity of ecosystems, nor the large spatial and temporal scales experienced under natural environmental conditions. Their results are therefore argued not to be truly representative of natural conditions14, however, this view is widely refuted by BEF experts. The criticism that these experiments overestimate the importance of biodiversity in order to justify conservation policies, as argued by Thompson and Starzomski15, has also been largely overstated.

Under controlled experimental conditions, the dominant influence of individual species on ecosystem functioning is largely a consequence of the simplified environments and the single functional response variables considered. Thus, experiments on this level are more likely to have underestimated the importance of biodiversity on ecosystem functioning in natural settings, rather than overestimating it14. The reality is that the experimental evidence for BEF is generally consistent and represents a practical method for the study of biodiversity importance to ecosystem functioning.

Additionally, the effects of biodiversity loss on ecosystem functions, such as productivity and decomposition, are comparable to the effects of many other environmental changes2. For example, an intermediate species loss of 21-40% induced a decrease in primary production of 5-10%, comparable to that of climate warming and ultraviolet radiation. Higher levels of species loss (41-60%) induced effects rivalling those of ozone, acidification and elevated CO22. Thereby, the ecosystem consequences of changes in local biodiversity are as quantitatively significant, if not more significant, as the direct effects of environmental change stressors2; many of which have gained wide media coverage as major international concerns.

It is therefore imperative that the biodiversity of ecosystems be preserved to maintain effective ecosystem functioning. Future requirements primarily consist of improvement to the understanding of biodiversity loss impact, through taking observed experimental BEF relationships and linking ecosystem functions to the provisioning and regulating of ecosystem services16 (ecosystem functions on which human welfare depends17). This, in turn, will increase international interest and concern; therefore, expanding the focus of BEF research to better mimic real-world circumstances, and improve predictions through the development of models that scale experimental results to whole systems16 (Figure 1).

Biodiversity-loss mitigation strategies may also be incorporated into future BEF research, for example, through the use of assisted colonisation18. Assisted colonisation is the planned introduction of taxa to sites beyond their historical distribution range, with the principle that relocating species will help to restore ecosystem processes18. Despite wide discussion of the risks related to this method, including the possibility that the relocated taxa may have detrimental effects on native species19, ecologists have once again underestimated the potential benefits that species introductions may pose for the restoration of ecological functioning. It is therefore regarded that assisted colonisation may be a key adaptation strategy to restore ecological function18, though more research and experimental trials are required to develop a sufficient understanding of the potential consequences, and to confirm this19.

In conclusion, the accumulation of evidence that biodiversity loss will negatively affect ecosystem functioning is indeed a cause for global concern. It is therefore imperative not to overlook biodiversity as an important factor of ecosystem functioning, and thus methods for the mitigation of species loss must be addressed and pursued without delay.



1 Barnosky, A. D. et al. Nature. 471, 51-57 (2011).
2 Hooper, D. U. et al. Nature. 486, 105-109 (2012).
3 Solan, M. et al. Science. 306, 1177-1180 (2004).
4 Tilman, D. et al. Annu. Rev. Ecol. Evol. Syst. 45, 471-493 (2014).
5 Tilman, D. et al. Nature. 379, 718-720 (1996).
6 Danovaro, R. et al. Curr. Biol. 18, 1-8 (2008).
7 Mora, C. et al. PLoS Biol. 9, e10000606 (2011).
8 Lefcheck, J. S. et al. Nat. Commun. 6, 6936 (2015).
9 Maestre, F. T. et al. Science. 335, 214-218 (2012).
10 Wagg, C. et al. PNAS. 111, 5266-5270 (2014).
11 Gamfeldt, L. et al. OIKOS. 124, 252-265 (2015).
12 Naeem, S. et al. Nature. 368, 734-737 (1994).
13 Loreau, M. et al. Science. 294, 804-808 (2001).
14 Duffy, J. E. Front. Ecol. Environ. 7, 437-444 (2009).
15 Thompson, R. & Starzomski, B. M. Biodivers. Conserv. 16, 1359 (2007).
16 Cardinale, B. J. et al. Nature. 486, 59-67 (2012).
17 Luck, G. W. et al. Trends Ecol. Evolut. 18, 331-336 (2003).
18 Lunt, I. D. et al. Biol. Conserv. 157, 172-177 (2013).
19 Ricciardi, A. & Simberloff, D. TREE. 24, 248-253 (2009).


Carbon Capture and Storage – the future for emission mitigation?

It has been a busy few months at University with exams and deadlines, including my third-year (BSc) independent research project, hence my lack of blogging. This latest post will discuss this project, which explored the use of Autonomous Underwater Vehicle (AUV) habitat mapping as an approach for detecting change in the North Sea benthos, in relation to carbon capture and storage.

Introduction to Carbon Capture and Storage

Carbon capture and storage (CCS) is the process of separating carbon dioxide (CO2) from industrial or energy-related sources, and transporting it to a secure storage location for long-term isolation from the atmosphere (Metz et al., 2005). It has been presented as a viable solution for the mitigation of greenhouse gas emission and has the potential to reduce future world emissions from energy by 20% (Haszeldine, 2009). Thus, CCS could provide an alternative to a reduction in consumption of fossil fuels, which would ultimately cause a radical disruption to contemporary life (Chadwick et al., 2004; Monastersky, 2013). For more information, please see the Global CCS Institute.

Despite this, little is known about the environmental implications associated with CCS (Noble et al., 2012); thus, the aim of my research project was to assess the use of benthic imagery as a biological monitoring method for evidence of potential CO2 seepage impact at the Statoil Sleipner CCS field in the North Sea.

Data Acquisition and Analysis

Benthic images generated by an AUV (Autosub 6000 mission 66, deployed during the 77th voyage of RRS James Cook) were analysed for variability in shell cover. Recent studies have demonstrated that high concentrations of CO2 elicit a stress-induced surfacing response in benthic infauna, such as echinoderms and molluscs (Schade et al., 2016). Therefore for the purposes of this project, shell debris was considered an indicator of infaunal stress to assist in the location of CCS reservoir seepage. Benthic image analysis was automated via Matlab (R2016b), and a contour plot map of shell cover was produced, using coloured pixels as a proxy. Automated image analysis can be an effective tool for identifying change in the environment (Schoening et al., 2016), since it is a non-invasive technique that removes the concern of time-consuming manual quantification and thus, human error (Schoening et al., 2012).

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Figure 1: Examples of the benthic images taken by Autosub6000 in the North Sea. Figure 1a shows an area of high shell debris, and Figure 1b shows an area of low shell debris.

However, the use of coloured pixel as a proxy for shell cover was discovered to be inconsistent and unreliable. Comparison of the coloured pixel results produced in Matlab and visual analysis of shell debris (Figure 1) demonstrated that there were large inconsistencies in the method, with a number of false-positive results. For example, the coloured pixel results indicated that Figure 1a was an area of low shell debris, and that Figure 1b was an area of high shell debris, despite visual analysis indicating otherwise. The produced contour plot map was therefore likely to have incorrectly portrayed the shell cover of the benthos at the survey site.

Similar results have been observed in other studies aiming to simplify the time-consuming task of manual image analysis through autonomous methods. Kannappan et al. (2015) concluded that although automated analysis provides a more attractive option to manual processing, available automated detection of organism populations (scallops in this case) do not work well with noisy low-resolution images since they are likely to produce a significant number of false-positive results.

An alternative proxy discussed for the detection of shell cover variation was the quantification of seabed roughness through the use of a high resolution sidescan sonar-equipped AUV, where high roughness would be expected to indicate high shell cover (Jaramillo and Pawlak, 2011). This method may have proved more effective in identifying Figure 1a as an area of high shell cover, and Figure 1b as an area of low shell cover, and therefore should be investigated further during future studies.

The Efficiency of Biological Monitoring

Biological monitoring of CCS sites through benthic imagery does have the potential to be effective (Noble et al., 2012), and is necessary since public concern is largely focussed on the potential environmental impacts of CCS (Widdicombe, 2015). Despite this, biological indicators are far more difficult to quantify than chemical or physical ones. It is widely agreed that exposure to acidified seawater or sediment environments (due to an increase in CO2 concentrations), significantly alters the macrofaunal community structure, partially through surfacing behaviour of infaunal species (Thistle et al., 2005; Schade et al., 2016). However, variability in inter- and intra-species tolerances to CO2 means that the likelihood of species loss is determined by both phenology and ecology (Widdicombe, 2015), thus adding an extra dimension to the monitoring. Also, whilst surfacing behaviour is widely considered to be an indicator of infaunal stress, this is not necessarily limited to high sedimentary CO2 levels indicative of a CCS leakage (ECO2, 2015).

The best candidates for biological indicators of CCS leakage are those that can be mapped on a large scale by benthic imagery, for example, increased shell cover (as discussed in this project) or microbial mats on the sediment surface. Areas with a high indication of leakage could then be investigated further to determine the cause of this environmental variability, though care should be taken with the use of these indicators of CCS leakage since they are transient signals. However, it is also argued that biological responses are more ideally suited to monitoring the progress of a leakage for ecosystem recovery once it has been detected, rather than the locating of potential leak sites (Widdicombe, 2015).


The project concluded that a multidisciplinary approach to CCS monitoring, integrating biological, chemical and physical analyses, is likely to be the most effective method, and it is recommended that this is explored further in future studies (Hicks et al., 2015). Nonetheless, it is essential for future research directives to address determining a biological baseline for these indicators, to quantify the natural fluctuations so that unnatural variability can be differentiated and detected.

With increasing pressures on both oil and gas companies and governmental bodies for a reduction in fossil fuel emissions, the need for CCS development, and thus monitoring, is greater than ever. Biological monitoring through assessment of surficial shell cover provides a reasonable solution for the monitoring of CCS leakage sites. Nonetheless, caution is required with the use of biological indicators, AUV imaging technology, and the use of proxies for indicator parameterisation during automated image analysis. Discrepancies in the use of pixel colour as a proxy for shell cover and AUV survey programming do not, however, suggest that the use of benthic imagery is an ineffective method of monitoring potential CCS sites for evidence of CO2 seepage impact. These method limitations and their associated problems could be mitigated with future development and considerations.

“What a long neck you have!” “All the better to feed with…”

I have just come to the end of a Vertebrate Paleobiology module, so I thought I would share something that I have learned during its study – the evolution of gigantism and neck elongation in Sauropod Dinosaurs.


Sir David Attenborough lying next to the 8 foot-long femur (thigh bone) of a newly discovered Titanosaur (BBC, 2014). For more information, I highly recommend watching Attenborough and the Giant Dinosaur.

Sauropods are regarded as the largest terrestrial animals to have ever lived, with body lengths greater than 40 m, heights of more than 17 m, and estimated body masses of 50 to 80 tonnes(see above). Their gigantic size is thought to have been a definitive factor in their success, allowing them to dominate the ecosystem for more than 100 million years, from the Middle Jurassic to the end of the Cretaceous1. Along with gigantism, they were also able to evolve extremely long necks, three to four times the length of their bodies. But how and why did a group of dinosaurs derived from small, bipedal omnivores such as Panphagia2, achieve such gigantism and neck elongation?

Sauropod gigantism is largely thought to have evolved due to predation pressures3, although high C/N ratios available in plant foods during the Mesozoic is also likely to have been a factor4. Gigantism in sauropods was made possible by a number of key biological evolutionary innovations, such as a high body mass ratio (BMR), an avian-style respiratory system and the absence of food mastication (see figure below). The evolution of a long neck is thought to have allowed more efficient energy uptake and therefore greater BMR, by making food accessible that was out of reach for other herbivores2. The absence of mastication added to this through unrestricted food uptake rates2.

The avian-style respiratory system includes cross-current gas exchange and a voluminous, highly heterogeneous lung, both with great implications for gigantism in sauropods5. Extensive pneumaticity of the axial skeleton contributed to the evolution of both gigantism and neck elongation, allowing a lowered cost of breathing, reduced specific gravity, and the removal of excess body heat2. Cervical pneumaticity was, therefore, an important prerequisite for neck enlargement, and vertebral pneumaticity in other parts of the body is expected to have had a similar role in enabling gigantism6.


Comparison of the main biological properties that control upper limits of body size in terrestrial herbivores (Sander et al., 2008).

Long necks were able to evolve due to the small head, absence of mastication and pneumatic axial skeleton2. Despite this knowledge, there is continuing debate over the function and posture of these long necks. The conventional view on sauropod neck length states that high browsing was necessary to meet high energy demands1. This theory assumes that the long neck allowed sauropods to reach more nutritious foliage that other herbivores could not. There is evidence for high browsing in a number of species, including Euhelopus zdanskyi, suggesting that high browsing was worthwhile despite an increased metabolic rate7.

Despite this, some studies state that the evolution of neck elongation was driven by runaway sexual selection, and not over competition for foliage. This suggests that the sauropod neck was primarily a display organ1, although there is a lack of evidence for this and only a few studies have discussed such a function15.

There is much debate over whether sauropods held their giant necks horizontally or vertically. This is largely due to the physiological problems associated with long necks. For example, the hypertension required for vertical neck posture would have involved the sauropod expending half of its energy intake just to circulate blood8. Digital reconstructions by articulating the vertebrae with the zygapophyses in maximum contact show an inflexible neck9, yet these studies did not account for the presence of soft tissue, cartilage or intervertebral spacing. However, reconstructions of sauropod neck posture inferred from extant animals, like ostriches, show that there would have been enough flexibility at the neck base and neck-head junction to vertically extend and hold the neck10,11. Evidence strongly suggests that habitual neck posture varied between sauropod species, implying that feeding strategy varied too12. For example, Brachiosaurus has been reconstructed to have giraffe-like necks13, whereas Diplodocus is thought to have had a camel-like neck14.

The above evidence suggests that it was a combination of biological factors that led to the evolution of gigantism in sauropods, including an avian-style respiratory system and an elongated neck. I believe that the evolution of large body size and long necks were central to each other, with the long neck providing access to a greater food source with very little whole body movement required, and the large body size providing protection from predation for the vulnerable long neck. Understanding neck function has major implications on our understanding of sauropod foraging strategies, ecology and biomechanics. The current literature strongly suggests a foraging related function. Although sauropods were capable of vertical neck extension and flexibility, neck postures and foraging strategies varied interspecifically and intraspecifically.



1 Sander, P. M. et al. Science. 322, 200-201 (2008).
2 Sander, P. M. et al. Biol. Rev. 86, 117-155 (2011).
3  Clauss, M. in Biology of the Sauropod Dinosaurs: Understanding the Life of Giants (Klein, N. et al.) 3-10 (2011).
4 Wilkinson, D. M. et al. Funct. Ecol. 27, 131-135 (2013).
5 Perry, S. F. et al. J. Exp. Biol. 311A, 600-610 (2009).
6 Schwarz-Wings, D. et al. Proc. R. Soc. B. (2009).
7 Christian, A. Biol. Lett. 6, 823-825 (2010).
8 Seymour, R. S. Biol. Lett. 5, 317-319 (2009).
9 Stevens, K. A. et al. Science. 284, 798-800 (1999).
10 Taylor, M. P. et al. Acta. Palaeontol. Pol. 54, 213-220 (2009).
11 Cobley, M. J. et al. PLOS ONE. 8, e72187 (2013).
12 Christian, A. et al. in Biology of the Sauropod Dinosaurs: Understanding the Life of Giants (Klein, N. et al.) 251-259 (2011).
13 Christian, A. et al. Fossil Rec. 10, 38-49 (2007).
14 Dzemski, G. et al. J. Morphol. 268, 701-714 (2007).
15 Senter, P. J. Zool. 271, 45-53 (2006).

‘Biggest dinosaur ever’ discovered
Reconstructing the ‘world’s biggest dinosaur’

Deep Sea Discoveries

First of all, Happy New Year! Here’s to 2017 – a year (hopefully) filled with pioneering discoveries, innovative conservation and greater scientific outreach across the globe.


Fireworks at Southampton Docks – Bonfire Night 2016 (Photo by E. Thomas).

I am personally looking forward to 2017 to begin work on my extended research project or dissertation, as part of the MSci degree. I have the amazing opportunity of studying a potentially new species of holothurian (sea cucumber) found at the hydrothermal Longqi Vent Field on the South-West Indian Ridge, in 2011. The project will use the morphological and molecular characteristics of the specimen to determine whether this is a new species of deep-sea holothurian, or whether it is the same species as Chiridota hydrothermica – a species found at the South-East Pacific Rise hydrothermal vents, that was described in 2000 by Smirnov et al. Both will make extremely exciting research projects, either with the chance to describe a newly discovered species, or study the remarkably wide range of the Chiridota hydrothermica species (from Eastern Pacific Ocean vents to South-West Indian Ocean vents).


Chiridota hydrothermica at the Rehu Marka site (South East Pacific Rise), at a depth of 2578 m (Smirnov et al., 2000).

My prospective supervisor, Dr Jon Copley, recently co-authored a paper on the ecology and biogeography of the new species found at the Longqi Vent Field (Copley et al., 2016). The discovery of six new species at the site (including the comically named Hoff Crab), has led to widespread recognition from a number of popular science outlets, including BBC News, Natural History Museum, Live Science and IFLScience. Although these six species have been confirmed as newly discovered, most specimens collected by the mission have not been formally described, including the holothurian mentioned above.


A sample of photographs taken at the Longqi Vent Field during the first Remotely Operated Vehicle (ROV) dives in 2011, showing the differing morphologies of the active hydrothermal vent chimneys observed (Copley et al., 2016).

It was previously thought that there was little or no life in the deep sea due to the lack of photosynthetic energy, but the discovery of unique ecosystems at hydrothermal vents has changed this perception. Life is able to thrive at these sites (despite their toxicity) due to the high thermal and chemical energy produced by the vents, allowing chemoautotrophic bacteria to populate the area. This chemosynthesis, in turn, supports a diverse range of organisms across a number of invertebrate phyla. Hydrothermal vents are even hypothesised to hold the key to the origin of life (Martin et al., 2008).


For more information, please visit the following sites:

Deep Sea Hydrothermal Vents: Redefining the Requirements for Life

Exciting new creatures discovered on ocean floor



Tagging of Top Pacific Predators – the Key to Conservation

A News and Views Article in the style of Nature:


“Without an aggressive effort to zone and effectively manage these resources, the predator populations they support will decline and the biodiversity of this open-ocean wilderness will be irreplaceably lost.” – Block et al., 2011.

Apex predators play a vital role within ecosystem functioning in the North Pacific Ocean through top-down ecological structuring, and thus the importance of understanding their extensive migration patterns cannot be overlooked. Predators face an increasing number of anthropogenic threats including overexploitation of resources by fisheries and human-induced environmental change, influencing their spatiotemporal distribution within the North Pacific. Block et al.1 used an extensive data set of 4,306 electronic tags in 23 different species (from the Tagging of Top Pacific Predators, Census of Marine Life programme2), spanning almost a decade (2000-2009), to examine seasonal and annual distribution, reveal migratory behaviour, and inform population assessments of predators within the North Pacific basin. For many of the seven predator congener guilds tagged (sharks, tunas, albatrosses, shear-waters, sea turtles, pinnipeds and rorqual whales), population assessments are either non-existent or very rare, highlighting the importance of this long-term observational study.

Within the North Pacific, there are two main biological hotspots– the California Current Large Marine Ecosystem (CCLME) and the North Pacific Transition Zone (NPTZ) – both of which are extremely important marine predator ecosystems (Figure 1). Tagged predators showed fidelity to the cool and productive CCLME, with some species migrating there annually over great distances (>2000 km), either from the west, central, or south Pacific, and some undertaking seasonally recurring north-south migrations within CCLME. NPTZ serves as an east-west migration and foraging corridor between CCLME and various other productive systems, such as the Eastern Pacific Islands and Subtropical Gyre. Block et al.1 have demonstrated that the attraction of CCLME is consistent with the high primary productivity and, as such, high biomass of basal prey found there. This has been observed previously, with marine predators recognising that prey congregate at regions of high productivity, consistent with oceanographical processes3. Both CCLME and NPTZ can therefore be regarded as predictable foraging regions for top marine predators.

Block et al.1 assessed the factors that affect the migration pathways of predators, such as ocean processes, species-specific thermal tolerances, and shifts in prey distributions. Generally, species would occupy the smaller region of cooler, nutrient-rich waters of northern latitudes over the large region of warmer, oligotrophic waters of lower latitudes, with the data showing a strong positive relationship between sea-surface temperature (SST), chlorophyll a, and predator incidence. This suggests that seasonal warming due to climate change could trigger northward migration of populations to more suitable habitats.

Ectotherms, are mainly restricted by their thermotolerance, with colder, northern waters of CCLME limiting their cardiac function and therefore preventing their exploitation of the more productive environment. Endotherm migration, on the other hand, is more constrained by prey availability meaning they are more likely to exploit the most productive regions of CCLME. This is indicative that predator distribution is controlled by a trade-off of these factors, to exploit the environment to the greatest ability.


Figure 1: Map showing the CCLME (dashed line) and NPTZ (dotted line), as well as the dominant oceanic features of the North Pacific1.

Niche partitioning was also observed between species of the same guild. In-situ data showed how congeneric species had differing habitat use to effectively partition marine resources within the same environment. Many of these observations were consistent with SST ranges, cardiac performances and physiological specialisations.

The importance of this study stems from the great loss in predator biodiversity worldwide and its implications. Removal of predators from the pelagic system has a high impact on trophic dynamics, for example, the decline of shark and tuna species in the Atlantic Ocean has caused a near-ecological extinction of demersal fish like cod1. Over 50 million tonnes of sharks and tunas were removed from the Pacific by commercial fisheries in under 60 years (1950-2004), and bycatch mortality from the same fisheries has decimated sea bird and turtle populations4. In fact, the biomass of some species is only 36% of the biomass predicted in the absence of fisheries4. Top-down forcing is not a new concept to the North Pacific, with the decline of rorqual whales altering the preferred prey of orcas to pinnipeds, effectively causing the collapse of the food web5.

Electronic tag studies, such as Block et al.1, can help mitigate the anthropogenic risks that predators face, for example, monitoring cetacean movement can identify high-use areas and coordinate policy accordingly, and thus aid the recovery of the population by decreasing ship-strikes and noise pollution. If top predators exploit their environment in predictable ways, as this study suggests, their populations can be monitored and protected through spatial management conservation, hence the implications of this study are unparalleled.

The applications of these data are limitless, with possibilities for influencing government legislation, informing fishery protocols, and inspiring future research and cross-border conservation zones. Improved understanding of the spatiotemporal distribution of predators by pelagic fisheries could reduce bycatch in critical habitats, such as CCLME and NPTZ, for example by time-area closures. The decade’s worth of information on cross-boundary movements of predators between Mexican, US, and Canadian waters provides a baseline for an international conservation scheme for CCLME. Nonetheless, this remains a contentious topic due to reluctance from fisheries and governments to adapt their management protocols, meaning that more scientific evidence is required to make such an impact.

Future research directives include assessing the true impact of top predator biodiversity loss on trophic levels, how the shifts in predator abundance among latitudes could be used as a proxy for climate and ecosystem change, and applying similar methodology elsewhere in marine species richness zones, such as Southeast Asia. The influence of climate change on species movement is important, as previous studies have predicted a change of up to 35% in core habitat for some species6. A substantial northward displacement of biodiversity across the North Pacific could inhibit the recovery of some species populations already experiencing stress6.

Block et al.1 utilised sound methodology, gathering extensive data with differing precisions of tracking technologies being accounted for, and normalisation schemes applied to account for the variation in sample size of different taxa. Additionally, a lack of spatial skew in the data confirmed the observed density patterns were not driven by tag deployment locations. Despite this, the authors use ambiguous language, implying that further research is needed to ascertain their conclusions.

Although this study alone could not trigger the creation of an international management scheme for CCLME7, it has provided the foundation for such through international policy vehicles like UNESCO Marine World Heritage8.

  1. Block, B. A. et al. Nature. 475, 86-90 (2011).
  2. Yarincik, K. & O’Dor, R. Mar. 69, 201-208 (2005).
  3. Palacios, D. M. et al. Deep-Sea Res. II. 53, 250-269 (2006).
  4. Sibert, J. et al. Science. 314, 1883-1776 (2006).
  5. Springer, A. M. et al. PNAS. 100, 12223-12228 (2003).
  6. Hazen, E. L. et al. Nat. Clim. Chang. 3, 234-238 (2013).
  7. Wood, L. J. et al. Oryx. 42, 340-351 (2008).
  8. Meskell, L. Quart. 87, 217-243 (2014).

ORCA – an unforgettable internship

During the course of the summer, I undertook an internship with ORCA (Organisation Cetacea) – a whale and dolphin conservation charity based in Portsmouth. I was lucky enough to find this internship through the University of Southampton’s Excel Internships scheme, which is a great resource in supporting and helping students find relevant and paid work experience. My role with ORCA as Community Wildlife Assistant, reporting directly to Anna Bunney (Community Wildlife Officer), was mainly focussed around supporting the Your Seas (People & Port) educational programme, which aims to raise awareness of whale and dolphin conservation, especially on a local level.

I am a firm believer that conservation begins with education, and that by providing a better understanding of the importance of our oceans, society is more likely to participate in the future of its protection. This is especially relevant to younger generations – I was inspired to follow a career in marine biology when I was nine years old following a trip to the Great Barrier Reef. But it’s not always necessary to travel so far to find that inspiration, as the marine life found right on our doorstep in the UK and Europe is some of the best in the world, especially in terms of cetaceans (whales, dolphins and porpoises). This is one of the messages that ORCA convey at schools, events and on board passenger ferries/cruise ships.


Inspiring the next generation of cetacean conservationists

As Community Wildlife Assistant my main role was educating in schools, where I gave interactive presentations as part of a Wonderful Whales Workshop initiative. Since ORCA is a charity based in Southern England, it is not always possible to visit non-local schools as often requested by teachers, students and parents alike. Therefore, I produced a ‘teacher’s pack’ to enable the expansion of the programme, by providing the resources needed for teachers or ORCA volunteers to present the same workshop around the UK. The pack is currently being finalised, and I will update this blog when it is publicly available.

ORCA uses partnerships with passenger ferries, freight ships and cruise liners to conduct frequent marine mammal surveys around the UK, Europe and across the Atlantic. These vessels take identical routes for each voyage, making their crossings ideal scientific transects. By conducting these frequent surveys, ORCA has created a database of marine mammal sightings, as well as effort data, available to scientists around the world, making it an invaluable resource.


Looking out for whales and dolphins as Community Wildlife Assistant aboard the Pont-Aven

As Community Wildlife Assistant, I was fortunate enough to join a group of biology A-level students aboard the Brittany Ferries ship, the Pont Aven, for an educational trip across the Bay of Biscay to Santander, Spain. The Bay of Biscay is one of the best places to see cetaceans on earth, with sightings ranging from rorqual whales to beaked whales to toothed whales and dolphins. In fact, over a third of the 87 cetacean species can be seen in UK and European waters! The Bay of Biscay is so popular due to the range of habitats available, including deep-sea canyons, the abyssal plain and the continental shelf.

Fin whales (3), common dolphins (153), orcas and sunfish were sighted during what was deemed a ‘quiet crossing’ of the Bay, whilst I was on board the Pont-Aven. It was thought that the Bay was so quiet due to the presence of orcas, a species known to drive other cetaceans away. The Pont-Aven also crossed over the continental shelf near north-west France during the night, an area renowned for its variety of cetacean sightings, due to its close proximity to shallow waters and the abyssal plain. This is another possible explanation for the shortage of sightings. It is typical that the day after my departure from the Pont-Aven, over 2000 animals were sighted including harbour porpoises; common, striped and bottlenose dolphins; minke, pilot and fin whales.


Common dolphins (mothers and calves) in the Bay of Biscay. Photograph by ORCA Facebook.

OceanWatch, another of ORCA’s projects, involves training bridge crew on how to spot cetaceans and record their sightings. This initiative trains crews from a number of different vessels and companies to record their sightings over a period of nine days, known as ORCA OceanWatch week. I participated in training the bridge crew of P&O cruise ships, the Aurora and the Oriana. During OceanWatch 2015, nearly 2000 sightings from 16 different species were recorded. I will update this post once data from OceanWatch 2016 are published.

My experience of working with ORCA was extremely rewarding and I look forward to volunteering with them in the future.

If you would like to get involved with any of ORCA’s projects or for more information on whale and dolphin conservation, please click the links below.


Species and Sightings

Your Seas (People & Port)


Falmouth Oceanography Field Course

For the last 10 years, marine biology and oceanography students at the University of Southampton have travelled to Falmouth to undertake a two-week intensive field course. This course gives students the opportunity to explore and study the Fal Estuary Special Area of Conservation (SAC), whilst applying the numerous oceanographical skills acquired during the first two years of the BSc and MSci programs.


Group 11 from the Falmouth 2016 field course.
Left to right: Lara, Kimi, Elin, Calvin, Abbie, Sarah, Jo, Ryan and Ed.

The opportunity to partake in hands-on oceanographic fieldwork was extremely rewarding, with opportunities to study the physical, chemical and biological aspects of the Fal Estuary and surrounding areas.

There were four research opportunities – review of the system’s offshore dynamics aboard the RV Callista; estuarine oceanography research aboard the RV Bill Conway; review and mapping of the benthic habitat at a chosen location within the Fal Estuary aboard Xplorer; and a short oceanographical time-series at the King Harry pontoon station. The aim of the course was to create a scientific web page, in groups, detailing the methods and results of each of the four research stations. These websites are publicly available online, subsequent to their publishing, and can be viewed here.

The oceanographical equipment used during the field course included side scan sonar, Van Veen grabs, Niskin bottles on a CTD rosette, ADCP’s, light sensors and flow meters. Biological samples of phytoplankton and zooplankton were taken and analysed in labs at Falmouth Marine School, as well as water samples preserved for quantifying parameters such as nitrate, phosphate, silicon and dissolved oxygen concentrations.

Deployment of equipment at the King Harry pontoon (left) and aboard Xplorer (right).

An in-depth individual report on a topic of choice will be submitted during the third year of the BSc and MSci degrees, using data collected during the last ten years of study in the Fal estuary system. My report detailed the short, mid and long-term temporal variability in offshore physical and biological structure in the Western English Channel.

Continuation of study in the Fal estuary is ecologically important due to the maerl and seagrass beds located in the system, and the uncertain future of the SAC status due to the recent Brexit vote.

The Regenerative Brittlestar

Amphiura filiformis

The brittlestar – Amphiura filiformis.
Photograph by Judith Oakley (

Amphiura filiformis is a benthic brittlestar species, discovered by O. F. Müller in 1776.  It is an infaunal Echinoderm, belonging to the class Ophiuroidea, which inhabits sandy and muddy sediments in the North Sea and North Atlantic ocean. A.filiformis feeds on plankton through active and passive suspension feeding, and detritus through deposit feeding. Varying in size annually, this species tends to reach its maximum size in August when it reaches sexual maturity.

A.filiformis has an important benthic ecological role, due to its species-sediment and interspecies interactions. It has evolved many physiological, morphological and behavioural adaptations for life in the benthos, and is a sign of a healthy benthic community according to its stage three classification in the Pearson-Rosenberg model of succession.

A recent university assessment required the creation of a group video presentation on the ecological role of a benthic species.

Ecological role – Elin Thomas:
“Amphiura filiformis has an important ecological role since it provides a link between the benthic and pelagic environments, especially in the North Sea where there are large populations of the species. It also provides an insight into benthic succession. Solan et al. (2004) found that A.filiformis has a disproportionately strong impact on bioturbation in Galway Bay since it is large, highly mobile, and consistently one of the most abundant species in the area. Therefore, the effect of extinction on bioturbation largely depends on whether A.filiformis survives the event or not. Wood et al. (2009) described how A.filiformis plays a key role in sediment nutrient cycling by irrigating and mixing the sediment. They demonstrated that as A.filiformis activity increased, the sediment release of nitrate and uptake of phosphate also increased. It has also been observed that A.filiformis populations have been increasing in abundance in the North Sea. This is thought to be due to eutrophication increasing the food supply and the decline in flatfish predator populations due to overfishing. As well as A.fililformis affecting the environment, the physical arrangement of the environment also influences the species. For example, A.filiformis responds to the tidal cycle by feeding at mid-tide when the current speed makes feeding most efficient.”

Duineveld et al. (1987) Neth J Sea Res 21(4): 317-329
Solan et al. (2004) Science 306: 1177-1180
Solan & Kennedy (2002) Mar Ecol Prog Ser 228: 179-191
Uthicke et al. (2009) Ecol Monogr 79(1): 3-24
Wood et al. (2009) Biogeosciences 6: 2015-2024