Category Archives: Technology for Ocean Science

Eavesdropping on an underwater world: Technology for Ocean Science

The ocean is not a quiet place.  Water can move rocks and sediment, even sufficiently to create underwater landslides.  Bivalves make clapping noises, fish make sounds during courtship, and cetaceans communicate with clicks and whistles, just to name a few.  And of course there is human activity – like shipping, drilling, and sonar, which all add to the sounds of the ocean.  There are many different reasons why we might want to hear these noises.  Thanks to acoustic monitoring technology we can.

There are many different types of acoustic monitoring equipment but you will tend to find one type of sensor at their heart – the hydrophone.  Hydrophones are microphones that can be dropped into the water and listens for sounds coming from any direction.  If you have been on a whale-watching boat you may very well have seen one of the crew drop one of these into the water.  With the hydrophone, the crew can hear a noisy whale and even work out their location.  In some places, hydrophones are anchored to the sea floor and float in the water column recording any sounds within their range, until their battery runs out and/or they are picked up again by boat.

Continue reading Eavesdropping on an underwater world: Technology for Ocean Science

Multi-tasking underwater

Often when I say to people I do underwater biodiversity/habitat surveys, they have an image of glorious tropical seas, great visibility, and general ohhing and ahhing at the beautiful marine critters. The reality is somewhat different (especially when you’re not in tropical waters!).

A small team of intrepid divers are currently undertaking maerl surveys at an offshore reef, just off the coast of Jersey (Channel Islands).  Maerl is a hard red seaweed, that forms little blobs.  It’s a super important habitat for our smaller ocean brethren, and super slow growing too.  On this particular survey, my job was to conduct a general habitat and species survey of the site, and keep hold of the SMB – basically and inflatable sausage attached to the end of the line you can see me holding that sits on the surface of the sea so we can be spotted.  You can see that the visibility wasn’t that great, but what you can’t see is the current that was trying to take me one direction, whilst the wind was pulling the SMB the other.  This is why I’m kneeling on the seabed so I could make some notes on the board I am holding, whilst also making sure I don’t let go of the SMB!

Image: Taken by Kevin McIlwee/Jersey Seasearch

Biodiversity in the high seas. We know it’s there but how do we quantify it?

When I was younger, the term “high seas” conjured up images of pirates, and big galleons, and sea monsters.  Perhaps a little less exciting to my younger self, the high seas are actually international waters – those that lie outside the Economic Exclusive Zone (EEZ) of any country (for a map of the world’s Economic Exclusive Zones, head over here).  The area of high seas is vast – comprising 58% of the ocean, so it’s not surprising that the high seas are full of life.  Just like inside EEZ’s, the high seas area heavily utilized by people, and just as in our own waters, marine biodiversity needs protection to ensure its long-term persistence.  Sounds good so far.  Leaving aside the political issues of managing human activity in international waters, there are problems for effective conservation – assessing where areas of significant biodiversity are to implement meaningful areas of protection.  Some of this is down to logistics – like the cost of sampling areas of the ocean far from land.  Some of this comes from the high mobility of marine species that are found in the high seas; if we see them here today, they are probably somewhere else next week.  Some of these critters are undergoing migrations, some change location depending on where in their life cycle they are, and some appear much more ‘free’ (though aren’t wandering around aimlessly).  If our knowledge gaps on marine biodiversity in coastal waters are big, they are vast when it comes to the high seas.  We need a plan, and we need it sooner than later.  And integral to that plan, argue Ei Fujioka and Patrick Halpin, both from Duke University, is a “publically accessible online framework that provides interactive tools to assess marine biodiversity from a variety of perspectives”.  There wasn’t one, so these guys set about setting a prototype up.

Ei and Patrick are no strangers to the mapping of marine critters, and already heavily involved in OBIS – a repository of marine mammal, seabird and sea turtle observations from across the globe.  Running for over 10 years, it has more than 2.9 million records for some 311 different species.  The data within it comes from a number of different sources, such as photographs, and tagging animals.  Some of the data gives on-off records of sightings, some tracks individual movements over a period of time.  This is a veritable treasure-trove of data, and some relates to the high-seas.  The next step is to pool all of this data together into something usable, something succinct, so that researchers – and indeed the public – can understand where our fellow marine critters like to hang out, where the areas of greatest biodiversity are.

There are actually many ways of measuring biodiversity.  The simplest is species richness – simply a count of the number of different species found in any given sample.   This does not take account of the relative abundance of each species – known as species evenness, so for this there are a number of different indices, each with its own formula for calculating diversity.  Alongside species richness, the researchers included 3 of these indices into the mapping – the Shannon-Wiener, the Simpson, and the Hulbert index.  This is quite handy.  With different ways of quantifying how much diversity, like-for-like comparisons can be more difficult.  Providing a range of indices allows the data to be used in more ways than if just a single index was provided, and crucially because all areas have the same indices, they can easily be compared on a like-for-like basis.

Of course no prototype is complete without a case study.  For this, Ei and Patrick chose the Sargasso Sea – a high seas gyre ecosystem in the mid-North Atlantic Ocean that is named after the floating mats of Sargassum – a brown seaweed that accumulate there.  Previous work by a number of different researchers has already indicated that the Sargasso Sea is a key are for biodiversity,  and the OBIS-SEAMAP data-house itself hold some 5,825 observation records, and 32 datasets for this area.  These records go from 1966 to 2013, making it possible to assess how biodiversity across the four indices (Hurlbert, Shannon, and Simpson, and species richness) has changed decadally (every 10 years).  The indices that took into account species abundance – that’s Hurlbert, Shannon, and Simpson – all pointed towards a decline in biodiversity since the 1960’s (excluding the 1980’s – they only had one record for that year, so assessment couldn’t really be done), with an increase in the 2010’s.  Species richness on the other hand was a bit more all over the place.  This may partly be down to ‘effort hours’ in collecting the data, which has a statistically significant impact on species richness scores, but not on the other 3 indices.  But crucially the case study has demonstrated that it is possible to bring together different datasets to produce some meaningful analysis, and present it in a format that is useful for the public and researchers alike.  This pooling together of data – particularly high quality data – is useful for all types of ecological study and conservation planning.  Where data is much sparser, just like on the high seas, pooling together is even more important.

Ei and Pat also note that the prototype is flexible, and can incorporate all sorts of different measures of biodiversity, tailored to achieving different goals and objectives, or answering questions to guide us in making good conservation decisions.  As a prototype, its pretty good.  Don’t forget the OBIS-SEAMAP is also publicly available, and free to use – so why not have a play yourself.

The original paper appears in the journal Endangered Species Research.  The researchers have paid for the paper to be made open access – you can access it here .

Image:  This little critter is a White backed Planes minutus.  They can be found living on the sargassum weed throughout the Sargasso Sea.  Credit Eric Heupel/Flickr (CC BY-NC-ND 2.0).

Secchi disk:  Simple technology for ocean science

We still have a lot to learn about the ocean.  Technology is helping us to uncover more and more about this blue planet, but not all technology needs to be complicated.  Some can be absurdly simple.

The Secchi disk doesn’t look like much – a black and white/all white disk attached to some rope, a measuring tape, or a pole, with a weight suspended underneath.  It’s not even complicated to use – just lower it into the water until you can’t see it anymore (the point known as the Secchi depth).  Excited?  No me neither.  But this simple technology tells us something important – the turbidity of the water at that particular point, at that particular time.  Turbidity is a measure of water clarity.  Particles in the water prevent light penetrating through the water column.  So the more particles there are, the less light can penetrate, and the more turbid it is.  Particles that restrict light can be almost anything – from silts and clays to plankton and other tiny critters.  Secchi disks in cruder forms (china plates!) have been around since the early 1800’s , but the actual disk itself was first developed and extensively used by Pietro Angelo Secchi – a priest and astronomer who undertook oceanographic research whilst aboard the papal yacht L’Immacolata Concezione.  There are of course more efficient and accurate ways to measure turbidity these days, but the Secchi disk is still in use.  Here are a couple of open access pieces for your enjoyment:

Building up a picture of the Baltic Sea
Because Secchi disks are ‘old school technology’ they have collected data on turbidity for a long time.  In some places – like the Baltic Sea – Secchi disks have been used repeatedly for a several years.  In this paper by Oer Sanden of Linkoping University and Bertil Jakansson of the Swedish Meteorological and Hydrological Institute compare the Secchi depths of two separate time periods – 1919 to 1939 and 1969 to 1991.  With this data, the researchers were able to get a grasp on the scale and magnitude of eutrophication (phytoplankton blooms as a result of increased nutrient) in the Baltic Sea.  Their analysis indicated that the Secchi depth was declining by an average of 0.05 meters per year, indicating that phytoplankton was indeed increasing, and thus turbidity decreasing.  The discussion is particularly interesting as the researchers explore the possible reasons why this decline would be seen.  You can access the paper here

Tying all the data together
Long term data is great.  The more long-term data we have, the more we can start to understand trends and patterns and determine long-terms changes.  One of the problems we have is tying together data collected using different techniques as the measurements may not necessarily be consistent – especially as newer technology is often much more accurate than older technologies.  In this paper by Daniel Boyce and colleagues from Dalhousie University, Secchi disk data is tied to satellite remote sensing and newer in-situ measuring data.  They can do this because the Secchi disk data is surprisingly robust.  As long as the researchers can determine the methodology used to collect Secchi depths, then the information is comparable.  This is great news because this team of researchers were able to create a “globally integrated chlorophyll time series extending 120 years into the past”.   Chloro-what-now you ask?  Chlorophyll in the ocean is an indicator of phytoplankton biomass – tiny free-floating one-celled ‘plants’ that float freely in the ocean.  Very cool.  See their paper here

Get Involved!
Because the Secchi disk is so simple, it is a prime candidate for citizen science research.  Dr Richard Kirby of the Plymouth University Marine Institute is just one of many scientists around the world concerned with reports that in some areas oceanic plankton is declining, particularly as temperatures increase.  To get a better handle on what’s happening at a global scale, Richard is asking help from boat owners.  All you need to do is make your own Secchi disk, download a free app, and follow some very simple instructions.  Read more about this project – including how you can get involved and make your own disk – at Plymouth University’s  page here

Image:  Dr Richard Kirby from Plymouth University demonstrates that the Secchi disk is so simple, even a scientist can use one.  Credit:  Image made available via the media pack.

What lies beneath: Technology for Ocean Science

That’s a pretty intriguing image isn’t it.  What you can see is a map of the seafloor of the Piscataqua River inlet, which lies on the New Hampshire/Maine border in America.  Mapping the sea floor has a whole host of benefits.  It can tell us not only the topography of the sea floor, but what it is composed of.  For science and conservation, mapping can help us understand things like water movement, or figure out where different habitats are – important information if we want to make sure we use our marine environment with minimal impact.  We can even see items of historical and archaeological interest – like wrecks.  For industry, mapping is useful for aggregate extraction and fisheries.  Knowing the layout of the sea floor is also important for things like laying undersea cables for telephones or power.  There is a safety aspect too.  Accurate mapping of underwater hazards can help reduce the risk of collision.  There are a whole host of different technologies that are now used to map the sea floor.  Here is a quick overview of just one of them.

Airborne laser scanning ALS – essentially mounting LiDAR (Light Detection and Ranging) equipment onto an aeroplane with a GPS and flying it over the area you want to map – has been used for some time to map the terrestrial environment, but it has also – with some slight modifications – proved useful for mapping the seabed.  Unlike for the land, mapping the seabed requires two laser – an infrared one which reflects back from the surface from the water, and a green one which can penetrate through the water and reflects back from the seabed.  Calculating the difference in time it takes for these two lasers to reflect back to the sensors reveals how far down the seabed at any given point is.  What type of surface (say hard rocks, soft sediment, or even a kelp forest) the green laser reflects off can affect the intensity of the signal.  LiDAR operators are able to use these differences as well as the depth information to work out what sort of habitat is under the waves.  Sticking this sort of system on an aeroplane as some huge advantages.  You can cover huge areas in a relatively short period of time, the data it produces is seamless, and crucially it can map areas that may be too dangerous or difficult for a boat-based system to access.  This sort of system does have its limitations though – how far down the green laser can go.  LiDAR is only useful for shallow waters – if conditions are excellent down to around 50 meters depth.  If the waters are unclear – there is a lot of sediment, rough sea state, or even a substantial amount of plankton then the lasers ability to penetrate the water is reduced.  For this reason, LiDAR manufacturers will often relate the depth their equipment can reach to the amount of turbidity in an area – something called a Secchi depth… but more on that in a later post.

LiDAR has been used to improve our understanding of the marine environment and the critters that like to live there.  Here are just three open access pieces of science that have used this technology:

Mapping Coral Reefs
Coral reefs are highly complex structures found in shallow waters – perfect candidates for LiDAR mapping.  David Zawada and John Brock from the US Geological Survey used LiDAR to map an area of reef along the northern Florida Keys.  They managed to get a really good level of detail enabling them to make a number of suppositions about how different parts of the reef have formed – and continue to change.

Research into undersea waves
James Churnside at NOAA used LiDAR technology to measure undersea waves (yes – under the sea!) in the West Sound, Orcas Island in Washington.  James has done a fantastic short (4 ½ minute) film explaining his work .
How much fish in the Bight?
Another one from James Churnside.  This time, LiDAR was used to work out the density of sardines in the Southern California Bight.  How?  Well the sardines are reflective too.


Image:  Created by Larry Mayer of the University of New Hampshire.  Acquired from the WHOI + Oceaus magazine (

Drones & Dugongs:

Drones.  When you read that word, you first thoughts probably jump to war.  Drones in war are highly controversial.  These unmanned craft can be controlled either by an operator on the ground some distance away from the drone itself, or autonomously by a computer.  Whilst drones make it safer for a country to launch an attack, there are concerns over their use, such as the lack of accountability when these drones injure and kill civilians.  What we don’t hear so much about is the other uses of Drones.  Drones can be incredibly useful for both science and conservation efforts – especially when we are dealing with hard-to-reach or wide ranging animals.  As a bonus they may also prove to be cost effective.

Dugongs (Dugong dugonare) fairly hefty marine mammals found across coastal waters of east Africa and the Western Pacific.  Feeding almost wholly on seagrass, and occasionally algae, these critters have been known to live up to 73 years old.  Whilst the IUCN Red List places dugongs in the ‘vulnerable’ category (the lowest of the ‘threatened with extinction categories’), dugong have been subject to a long history of human exploitation and many of the populations that once existed are now gone.  The largest population is found in Australia, with a range stretching from Shark Bay in Western Australia to Moreton Bay in Queensland.  The dugongs are faced with several threats, primarily gill netting, human settlement, agricultural pollution, and subsistence hunting.  Monitoring this population is important for implementing effective management, but the problem facing all researchers and conservationists looking at the remaining populations is that they aren’t all that easily accessible.  Even within Australia, only the ‘Urban Queensland’ section of the range has been studied and monitored to any depth.  As we move into the Northern Territories and Western Australia, we know less and less about the dugongs and the particular threats they face in those zones, nor how many there are in different places so effective catch limits for sustainable fishing can be implemented.

Surveying these populations by air is the quickest and simplest solution, but the problems with surveying are many.  First there is the cost.  Planes, pilots, accommodation, training is not cheap.  Then, once you have all that in place, if the weather turns sour, or the sea is too rough to be able to see into it, then you can’t do the survey.  Even with a plane, some sites are just too far from an airfield to realistically be surveyed in any detail with the small survey craft.  Then there’s the risk of misidentification of both the animal and the exact location.  And believe it or not, there is also a safety concern.  Some 11 marine mammal researchers have reportedly been killed in plane crashes undergoing aerial surveys.  You can see why Amanda Hodgson from Murdoch University and colleagues from CSIRO and the Australian Marine Mammal Centre decided to give drones a try instead.

The researchers focused their trial on one area in particular – Shark Bay located on the north-western tip of Australia.  Using a ScanEagle UAV, a digital SLR camera was attached, and then flew the drone over 1.3 square kilometres seven times, and at different altitude.  The drone was able to capture some 6,243 images which were analysed for dugongs, and assessed for sea state, turbidity, and sun glitter.  What they found was quite positive, with 95% of the dugongs sighted were classed as unmistakably dugong.  It seems that the images from the drones weren’t heavily impacted by the altitude the drone flew at, and sun glitter could largely be compensated for by overlapping the images that were taken at fixed intervals.  Turbidity and sea state may still reduce positive identification, but not to the same extent as using surveyors on board an aircraft.  And as a boon, the risk of double counting was heavily reduced, with individuals being identified and removed from further count.  The researchers were also able to successfully ID a whole host of other species in Shark Bay – particularly dolphins and turtles.  Having a permanent record of these images means they could be shared among different interest groups, reducing the costs of needing multiple fly-overs, or multiple surveyors on an aircraft.  It also seems that using drones is more environmentally friendly.  A standard aircraft used for these dugong surveys in Australia uses some 75 – 90 L of fuel an hour.  The drone needed just 330ml of fuel an hour.  The researchers were even able to view the SLR screen from their ground base in real time – handy for confirming that the images were indeed being captured in situ.

One of the downsides of this technology was the time it took for the researchers to analyse the images after they had obtained them.  From this relatively small survey area, the drone generated some 6243 images that had to be manually checked.  In future, it may be possible to develop some software to identify species from aerial photographs.  Developing this sort of software isn’t that straight forward for the marine environment because there are all sorts of factors that can alter the clarity of the image, such as light, white caps, and changes in the sea floor.  Here, the human eye might be a little better.

The next step for researching the use of these drones is to directly compare it to a manned aerial survey to make sure that the drone is able to at least pick up the same proportion of dugongs from an image as human eyes in the sky can, but so far the technology looks very promising.

The paper is published in the open access journal _PLoS ONE – you can access it here

Image: A Dugong near Marsa Alam (Egypt).  Credit Julien Willem/Wikimedia (CC BY-SA 3.0)

Wealthy backers support scientific efforts to explore deep seas

 There’s still so much of the ocean to explore and learn about, especially when it comes to the deep-sea.  But getting money fund research is getting harder and harder.

Take a look at the research vessel Falkor below.  Its owned by the Schmidt Ocean Institute in Palo Alto, California…an organisation made possible by Eric Schmidt and his wife of Google fame.  This is just one example of a number of wealthy folk who are ploughing some of their money into scientific research.

You can read more about these seemingly unlikely science funders in this article by Mark Schrope of the Washington Post

Image: The RV Falkor’s crew are treated to a viewing of dolphins.   Credit:Credit: Schmidt Ocean Institute/Mark Schrope (image available via the Schmidt Ocean Institute media use gallery)