Marine science roundup, 2nd November 2010

November 2nd, 2010

A real mixed-bag this week, our marine science highlights consider techniques for identifying viruses (or molecular quasi-species) and nanotech trackers to follow zooplankton. In conservation, we see progress on a new generation of bioreactors that promise to remove nitrogen from land runoff. In fisheries, even the best environmental practices at fish farms need improvement. In pollution, science of the gulf oil spill in the service of the law.

For those of you who worry about climate change, but feel they can’t do anything about it right now, we finish with the opportunity to transcribe the logs of British warships from the turn of the last century. The transcriptions will extend our baseline data about climate back in time over a wide area of the Earth’s surface, and so improve the qualty of our climatic forecasts.

Marine science

Computer, fish: The development of a new computer model of how fish swim, which models the hydrodynamic interactions between the water and the fishes body. Previously the effect of the moving water on the body of the fish was not considered, due to computational difficulties. ScienceDaily (Oct. 18, 2010)

An alternative to the family tree: We are all familiar with the ‘tree of life’ evolutionary model, with related species sitting close together, their ‘twigs’ having  split apart only ‘recently’ in evolutionary time. The tree is an OK model for eukaryotes, less so for bacteria, which have a liberal attitude to sharing genetic code, and seriously problematical for molecular quasi-species, such as viruses. This paper developes the Chinese Restraunt Process – a mathematical model – for characterising the relatedness of viruses. In the study it is used to compare HIV viruses infecting different patients, but this sort of quick and dirty identification process is likely to be important in studies of marine viruses, an area that we are only beginning to think about studying…
Prosperi MCF, De Luca A, Di Giambenedetto S, Bracciale L, Fabbiani M, et al. (2010) The Threshold Bootstrap Clustering: A New Approach to Find Families or Transmission Clusters within Molecular Quasispecies. PLoS ONE 5(10): e13619. doi:10.1371/journal.pone.0013619
There is more on the Chinese Restraunt Process from Wikipedia, though the paper has a pretty good description.

Trackers for zooplankton:  Zooplankton are amongst the smallest animals in the marine ecosystem, but they are very important. So, how do you go about tracking them? This paper uses quantum dots, nanometre scale lumps of semiconductor that posses characteristic flourescence patterns. Zooplankton tagged with the quantum dots can be followed in light or darkness, and show no changes in bahaviour to un-tagged animals. The advance will allow scientists to follow the migration of zooplankton through the water column.
Lard M, Bäckman J, Yakovleva M, Danielsson B, Hansson L-A (2010) Tracking the Small with the Smallest – Using Nanotechnology in Tracking Zooplankton. PLoS ONE 5(10): e13516. doi:10.1371/journal.pone.0013516

I didn’t know that … there are freshwater bryozoans! Familiar with horn-wrack that is washed up on many UK beaches,  I hadn’t realised that the bryozoan responsible has fresh-water cousins. Thesehave recently been busy in an artificial lake in the US producing an ‘alien space-pod’. Aparently fresh-water bryozoans are less diverse than their marine cousins, with about 50 species world-wide. (Bryozoans are filter feeders, and help to keep water bodies clean, so if you see them, they are no threat, on the contrary, they are an indicator of the health of the water body!). ScienceDaily (Nov. 1, 2010)

King crabs don’t like the cold: Only two species of king crab are found south of 60° latitude, adnd the coldest water they are found in is in the Ross Sea, at about 0.5°C. Increasing water temperatures may therefor extend the range of this voracious predator. ScienceDaily (Nov. 1, 2010)

Call for global marine monitor: The Partnership for Observation of the Global Oceans (POGO) is calling for the establishment of an integrated monitoring strategy. It is hoped that this will allow us to follow effects such as ocean acidification and habitat change more efficiently. ScienceDaily (Oct. 31, 2010)

Vanishing act: Scientists have identified some of the genes that permit bony fish such as flounder to change their skin colour and ‘disappear’. The so-called agouti genes are related to those involved with seasonal fur-colour changes seen in the arctic hare – though fish don’t have to shed their scales to change colour! ScienceDaily (Oct. 29, 2010)

Murderous snails: Cone snails catch their prey by firing a hollow barb into them, and injecting venom. The snails have been known to attack swimmers – thankfully they don’t live in UK waters! ScienceDaily (Oct. 29, 2010)

Marine microbes taking the P: Marine bacteria in the Atlantic have many more copies of genes for phosphorus (P) uptake than their Pacific cousins. P is known to be a limiting nutrient in the Atlantic. Review in We Beasties, October 19, 2010

Listen up! Studies show that squid (Loligo pealii) can hear sounds up to a frequency of about 500 Hz. While this may help them avoid some predators, it cannot detect the high frequency echo-location chirps emitted by dolphins, so the role of hearing in squid is still a bit of a mystery. ScienceDaily (Oct. 15, 2010)

Coding the worm: A new technique has been developed for DNA barcoding fee living marine nematodes. The technique focuses on the Cytochrome CO1 area of the genome. The authors note the proviso that contamination with any extraneous genetic material makes identification problematic.
Derycke S, Vanaverbeke J, Rigaux A, Backeljau T, Moens T (2010) Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes. PLoS ONE 5(10): e13716. doi:10.1371/journal.pone.0013716


Marine conservation policy: Here it is proposed that information from the Census of Marine Life (CoML), a wide reaching marine study program that brought together many academic institutions from around the world, be used as a basis for determining future conservation policy for the high seas.
Williams MJ, Ausubel J, Poiner I, Garcia SM, Baker DJ, et al. (2010) Making Marine Life Count: A New Baseline for Policy. PLoS Biol 8(10): e1000531. doi:10.1371/journal.pbio.1000531

Bioreactors remove nitrogen: Nitrogen contamination from argricultural and urban runoff is a major threat to many coastal waters, where it can result in severe oxygen depletion, killing all of he animals in that body of water. As a result, any progress on the development of techniques for reducing nitrogen in the run-off from farmand is to be welcomed. This is a brief report on a workshop held at the University of Rhode Island claims that simple, inexpensive bioreactors may be up to the job. ScienceDaily (Nov. 1, 2010)

Global seagrass under threat: Seagrass is an important shallow-water habitat, as well as stabilising marine sediments from wave action. This study shows that while seagrass areas are declining it is not suffering as badly as some other endangered species. The authors note that without conservation efforts, however, the area of seagrass would be 20% smaller. ScienceDaily (Oct. 30, 2010) Author’s note: seagrass is now quite a rare sight in UK waters, having suffered a severe decline about a century ago, and never recovered.

Fungus endangers turtles: The eggs of Atlantic Loggerhead turtles laid at Cape Verde are suffering from a fungal infection that may put the species at increased risk. ScienceDaily (Oct. 31, 2010)

Chagos reserve: The largest marine reserve on the planet officially became a no-fishing zone at midnight on the 31st October 2010, when the last extant fishing licenses expired. Project Chagos, 1st November 2010.

One third of sharks and rays threatened: The exact level of threat to sharks and rays is subject to some speculation, as insufficient data exists for many species from which to make accurate population forecasts. This study is based on species for which adequate data does exist, but the conclusions from these statistics are broadened to cover all species of cartilaginous fish. This results in the conclusion that one third of all species of cartilaginous fishes may be in categories with cause for concern – vulnerable, endangered or critically endangered, as the defined by the IUCN Red List. ScienceDaily (Oct. 26, 2010)

Fisheries and exploitation

Fish farms are bad for the environment: Even the best aquaculture practices result in environmental degredation according to this new report. Farmed fish are an increasingly important source of seafood, as many natural fisheries are in steep decline. The problem is greatest in Asia, where fish farming is rapidly expanding, but environmental standards are poor. ScienceDaily (Oct. 28, 2010)
The ScienceDaily report is based on data acquired by the Global Aquaculture Performance Index (GAPI), which can be viewed in more detail at (Javascript required).

Shrimp disease spreads: White spot syndrome virus (WSSV) effects a variety of farmed shrimp in Asia, including giant tiger prawns (Penaeus monodon) and the sushi staple P. japonicus. The disease was first documented in the early 1990’s, since which time it has become more virulent, causing death more quickly in its host, and increasing the financial cost of infection. The change in virulence is reflected in changes in the virus’ DNA, which has reduced in size as it specialises in killing its hosts. This paper reviews the evolutionary history of the virus, and compares it to mathematical models of genetic optimisation. The model indicates that the virus did not radiate out from a central inception point, but extended its geographical range in a series of random hops, almost certainly the result of commercial transport of the disease with stock or equipment.
Zwart MP, Dieu BTM, Hemerik L, Vlak JM (2010) Evolutionary Trajectory of White Spot Syndrome Virus (WSSV) Genome Shrinkage during Spread in Asia. PLoS ONE 5(10): e13400. doi:10.1371/journal.pone.0013400

Mis-selling food: A review of how some companies ‘green wash’ food to make it sound ethical, and encourage comsumers to buy it. Largely focussed on the US market. Deep Sea News, October 25th, 2010
Fish selling practices in the UK are carefully monitored by the National MCS, who rank supermarkets by how ethically they source their fish.

Fish oil doesn’t stop Alzheimers: The wishful thinking that fish oils could slow the development of Alzheimer’s disease has been knocked on the head by this study, which showed no effect. Whilst earlier studies have shown an effect, this study was the first to employ a randomised controlled trial, and indicates that fish-oil supplements are of no benefit to people suffering mild to moderate forms of the disease. ScienceDaily (Nov. 2, 2010)


Research into plover populations to provide ammunition for litigation: The effects of the Deepwater Horizon oilspill on piping plovers, a species that has been listed as threatened, are to be monitored. The primary aim of the study is to provide evidence for litigation, though researchers hope that the data collected will also help restoration efforts. ScienceDaily (Oct. 27, 2010)

Chandeleur Islands about to disappear: Lack of sediment from the Mississippi seems to be the main cause of the loss of these islands, which used to form an important barrier between the delta cities and hte Gulf of Mexico. Sediment supplies have dried up due to cannalisation of the river, though there have been recent attempts to se-supply them artificially. The islands were an important barrier to oil from the Deepwater Horizon, and the effect of the cleanup operation on the erosion problem is the main subject of this report. ScienceDaily (Oct. 29, 2010)

Access to samples problem: Marine scientists in the Gulf area are still having problems accessing samples taken after the Deepwater Horizon spill. Deep Sea News, October 31st, 2010

Deep reefs OK: Preliminary studies on deep sea reefs close to the spill indicate that the coral commnities appear to have been unaffected by the spill. There are, however, more reports of oil coating deep sea sediments, and long plumes of oxygen depleted water up to 50 miles from the well head. Deep Sea News, October 26th, 2010

Burial mounds: Claims that there have been recent fish kills around Grand Isle, Louisiana.

BP claims spill overkill: In an attempt to recover some of its reputation, Bob Dudley, the CEO of BP, claims that stories from the time of the oil spill were ‘scaremongering’. BP has suffered criticism that it had aculture that put cost saving before safety, and is currently selling assets to raise $30 billion to cover the cost of the spill. Not much of a cost saving there then. York Times, October 25, 2010

Compensation call: Tourist beaches that were not hit by the Gulf Oil spill are still calling for compensation, claiming that people stayed away because of the bad press… Deep Sea News broadens the debate to whether or not scientists or institutions not bordering the gulf should receive funds for studying the spill… Deep Sea News, October 25th, 2010

Climate change

Narwhals test the temperature: Narwhals in Baffin Bay have been tagged with sensors that record water temperatures, probing the waters of the arctic to a depth of over 1.7km during their dives! This low-cost survey shows that water temperatures over the last two years have been 1°C above their historic averages. ScienceDaily (Oct. 30, 2010)

Baked Alaska? An overview of the arctic ecosystem in 2010. ScienceDaily (Oct. 22, 2010)

WW1 Weather: This BBC report (13 October 2010) on the activities of volunteers who are transcribing hand written records from the British Fleet from around the time of the first world war. The records provide valuable climatic data from around the world, helping us understand climate at a wider scale over the last century, and better predict how it might change over the next. You can get involved at: Old Weather

Posted in Conservation, Marine science update, Science