HOME >> SeaCAMEL Home >> Science Modules >> Module 6
Background:
Fig.1. A school of schoolmasters (Lutjanus apodus), lurking near the roof of Aquarius. The habitat is home to huge numbers of fishes. This last classroom module will census fish use of the habitat using a visual and video survey. We will also attempt to image the habitat and its fishes using side scan sonar deployed from oceanography’s latest tool, an Autonomous Underwater Vehicle.
Aquarius is a marvelous platform for in situ science. From it, scientist aquanauts can put in full working days out on the reef and accomplish in days what might take months diving from the surface. One common observation by the aquanauts is how much they feel like they are in an aquarium when they are back inside the habitat! Fishes peer in every port hole, and aquanauts venturing outside day, or night, are struck by how the habitat is home to hundreds or sometimes thousands of fishes. Aquarius is an amazing artificial reef.
Artificial reefs are just that: made by humans, not part of the natural environment. However, increasingly we are inserting these structures deliberately into a host of marine environments, in part to combat coastal degradation of natural reefs. In the Chesapeake Bay, the common oyster (Crassostrea virginica) used to form huge shoals. Calculations made by Dr. Roger Newell and others show that entire Bay was filtered every 3 days by the resident oysters, living on reefs. Today, disease, overharvesting, and habitat degradation have taken their toll, and the reefs are a shadow of their former selves. Yet states bordering the Bay, including Virginia, are experimenting with creating artificial reefs to encourage the growth of oysters. The results have been mixed. It is hard to mimic all of the characteristics possessed by a reef made by oysters, many of which are necessary for the settlement and growth of the juvenile stages.
Similarly, coral reefs are under assault world-wide, as we learned in Module 3, and there is interest in speeding recovery of reefs disturbed by humans by constructing structures, or sinking objects, to provide a home to corals (which then attract other organisms. including fishes). Aquarius itself is a big structure, with lots of surface area for sessile organisms like sponges, bivalves, polychaetes, corals and their allies, and other invertebrates, to settle on and live. Its three dimensional aspects are also very important, as this provides an environment conducive to fishes. Both predators and prey can take advantage of the nooks and crannies in and around the habitat to hide or hunt.
We will investigate Aquarius as an artificial reef for fishes. We will conduct at visual/video transect around the habitat from bow to stern, and port to starboard. During our explorations, we will make gross estimates of the numbers of the common species or guilds (for example we may lump all the snappers together) on a sector by sector basis. The area around the habitat will be divided into the following sectors: sand plain underneath Aquarius, bow port side, stern port side, bow starboard side, stern starboard side. We will ascertain the direction of the tidal current passing over the habitat at the start of the transect, as this may influence the fish distribution and abundance. (We will also post video snippets for you to make more quantitative estimates after the module. See Quantitative exercise #2 below).
Species we are likely to see include several kinds of grunts, angelfishes, barracuda, nurse sharks, rays, parrotfishes, wrasses, and groupers. We will also be on the lookout for actual predation events, cleaning stations where fishes gather to have their parasites removed by cleaner shrimps, aggressive displays, and mating behavior often seen in the vicinity of the habitat. And just for fun, like the Christmas Bird Count, that many bird watchers participate in every year, we will see how many different kinds of fishes in total we see during our hour visit around the habitat. One of our aquanauts inside Aquarius, will keep a running total for us.
<<< Fig. 2. Fetch1 AUV, operated by the Virginia Institute of Marine Science. The AUV is equipped with high frequency (600 kHz) side scan sonar, CTD, u/w video, altimeter, and dissolved oxygen and pH sensors. Weather permitting, the surface team of VIMS graduate students led by Dr. Daniel Jones, National Oceanograhy Centre (Uk) CASEE fellow, will deploy operate and recover this free-swimming robot.
Weather permitting, we will also deploy oceanography’s newest tools, a free-swimming robot names Fetch1 (Fig. 2). Free-swimming, untethered robots are called Autonomous Underwater Vehicles (AUVs). Fetch1 has been to Conch Reef previously. surveying water quality (Fig. 3) and the benthic environment (see movies in the Multimedia section). Because AUVs move rapidly through the ocean, they can help oceanographers observe the ocean quickly enough to see short-term changes. Already AUVs have made significant discoveries in ocean science including how krill behave under the ice in the Antarctic, how fishes utilize essential habitats, how geological activity affects hydrothermal vents in the deeper ocean, and how complex the water chemistry can be in environments like reefs.
Fig. 3. Fetch1 AUV discovers unexpected lowered oxygen in a coherent structure over Conch Reef while conducting benthic surveys (photomosaic lower right). This lowered oxygen results from respiration of the nearby reef making plumes that travel out over the seagrass bed where these data were taken (see FetchSeaGrass movies below).
Recently, Dr. Patterson and his colleagues have been using the Fetch1 AUV to count fishes and other creatures in the water column. To do this, they use a high frequency side scan sonar made by Marine Sonic Technology, a company located not far from VIMS. Side scan sonar listens to the echoes from high frequency acoustic pulses it emits, and creates a 2D view of objects on and above the seafloor. This sonar produces the crispest images in the industry. They are so rich in detail that the VIMS team recently trained the robot to recognized fishes down to the species level, and even were able to train the robot to recognized blue crabs (Callinectes sapidus) and jellyfishes (moon jellies - Aurelia aurita and sea nettles - Chrysoara quinquecirrha) in the Chesapeake Bay (Fig. 4). A patent was recently issued to the College of William & Mary (see Reading) to use a software program called a neural network to automatically recognize the images seen on a side scan sonar record, much the same way a human operator can identify objects from their appearance. In 2005, Fetch1 went to the Antarctic and became the first AUV to image krill simultaneously on its underwater video and side scan sonar. AUVs will become increasingly important in counting fishes in marine habitats in the future. They are much less expensive to operate than an acoutically quieted ship (so the fish don’t run away) with a scientific echosounder,the current standard in non-invasive stock assessment.
Fig. 4. High frequency side scan sonar images demonstrating detail seen, allowing taxon level recognition of water column targets. A. Blue crab (Callinectes sapidus) in swimming pool. B. Blue crab up off bottom swimming in York River. C. Crab pot and sea nettle (Chrysaora quinquecirrha) in tidal creek of York River (sea nettle is immediately to right of letter C). D. Sea nettles, York River, showing oral arms. E. Cross section of moon jelly (Aurelia aurita) in pool. F. Moon jellies in York River. G. Sand tiger shark (Odontapsis taurus) - showing spinal cord. H. Menhaden (Brevoortia tyrannus) school in York River. Images not to same scale.
What students will see during the show:
We hope this classroom will be a visual treat. In addition to the fish census, and interesting fish behaviors we will see, we hope to fly the Fetch1 AUV past Aquarius several times. We also will attempt something that hasn’t been done before, remote control of an AUV over the Internet. Michael Crockett, a senior at Gloucester High School in Virginia, and a former intern with Dr. Patterson, will attempt to take control of the Fetch1 AUV from 1200 miles away. His computer at his high school will communicate with a server at the Aquarius shore base, which will then connect to the wireless LAN in the Life Support Buoy that floats directly above Aquarius. The surface team of VIMS graduate students and Sea Grant advisory service teacher Chris Petrone, will relinquish control of the Fetch1 AUV, waiting at the surface, to Michael in VA. If all goes well, he will send programming commands to the robot and have it execute a flyby of the habitat. We hope to get the aquanauts perspective of it from underwater, as filmed by our cnematographer, D.J. Roller.
Learning outcomes:
At the end of the module, students will have learned the following:
1. What aspects of an artificial reef, a structure like Aquarius, attract organisms and allow the creation of a local food web.
2. How fishes utilize space on a coral reef around a structure like Aquarius in a manner reflective of their ecology.
3. How AUV technology can perform measurements of water chemistry and conduct fisheries stock assessment using sensors of various kinds.
4. How high frequency side scan sonar works to make an image of objects on the seafloor or in the water column.
5. How scientists conduct estimates of fish distribution and abundance using direct visual observations or by reviewing underwater video.
Quantitative exercises:
1. Habitat complexity. Aquarius is a big structure, but how much effective living space does it add, per unit area of seafloor, relative to the nearby coral reef? When assessing habitat complexity, scientists take into account the three dimensional structure of the habitat. One method they use is the chain estimate of the surface relief. A chain of known length is draped over the reef. The linear distance between the ends is measured by a taught line. The ratio of the chain length to the linear separation of the ends provides a measure of habitat complexity (and is similar to a mathematical object called a fractal often using to assess spatial complexity). While we can’t easily perform a chain measurement around the habitat, we can make some computations of a similar nature. Using the information on the Aquarius web site about the habitat, estimate the total surface are of the habitat itself, the wet porch, and the quadropod upon which it sits. Then figure out the approximate footprint or shadow area directly under the habitat. Calculate the ratio of habitat area/footprint area. In many coral environments, the chain measurement yields a ratio close to 1.6. If the habitat complexity measured using the chain method is the same in all directions, then the surface area ‘bonus ratio’ (relative to a flat surface) provided by the threedimensional nature of the coral reef, should approach 1.6 x 1.6 = 2.56. In other words, the coral reef has an area 2.56 times greater than that of a flat bottom. Assuming the nearby reef has a typical reef habitat complexity, how does Aquarius’s ‘surface complexity’ compare to the nearby reef, where the 2.56 value may hold?
2. Fish ecology. During the module, the aquanauts performed a video transect from the bow to the stern of Aquarius, and from port to starboard across the habitat. Video clips from this transect will be posted later on the web site. Using your favorite media viewer, make your own visual estimate of fish distribution and abundance around the habitat. While there are hundreds of fish species in the Caribbean, you need not be a fish identification expert to discover something new. Some suggestions: concentrate on a single species, for example, barracuda, or the schoolmaster snapper, and estimate how many fish you see in particular sectors of the habitat. (Use the same sectors that the aquanauts use, described above in the Background). Make a map of the habitat divided into sectors, and as you watch the video clips, count how many fish you see. How does your distribution look? How might it change by species? Does the tidal current have an influence? (Obviously, if you find an upstream/downstream difference, we would have to repeat the measurements again, when the tide was flowing the other way, to be sure of our result.)
Reading:
DeLoach, N. 1999. Reef Fish Behavior: Florida, Caribbean, Bahamas. New World Publications, 306 pp. - An excellent overview of the wonderfully complex behavior of many of the 500 species of fishes found on reefs in the Caribbean basin. Available at Amazon.com.
Humann, P., and N. DeLoach. 1994. Reef Fish Identification: Florida, Caribbean, Bahamas (2nd Ed.). New World Publications, 406 pp. - A very practical, beautifully executed field guide. Available at Amazon.com.
Patterson, M.R., D.F. Doolittle, Z-u. Rahman, and R.S. Mann. 2007. Method for identification and quantification of biological sonar targets in liquid medium. US Patent 7,221,621. - A recently issued patent on how to use neural networks to automatically recognize fish species using side scan sonar from an AUV (available at
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=
1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d
=PTXT&s1=7221621&OS=7221621&RS=7221621)
Patterson, M.R., and J.H. Sias. 1999. Modular Autonomous Underwater Vehicle System. U.S. Patent No. 5,995,882. 8 Claims, 17 Drawing Sheets. - The original description of the Fetch AUV hardware and software architecture. (available at
http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p
=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=19&f=G&l=50&co1=
AND&d=PTXT&s1=5995882&OS=5995882&RS=5995882)
Multimedia:
Movie of the Fetch1 Autonomous Underwater Vehicle sampling the water column not far from Aquarius. This kind of maneuver is called a ‘yo-yo’. When you combine a ‘yo-yo’ maneuver with ‘mowing the lawn’, an AUV can rapidly obtain a 3D view of what the ocean is doing.
Movie of a view from the nose camera on the Fetch1 AUV as it follows the terrain a set height above the bottom near Conch Reef. Right hand image has been cleaned up with the Retinex algorithm courtesy of Truview, Dr. Zia Rahman (http://www.truview.com/). Watch for the juvenile sea turtle!
Web Resources:
A video showing an artificial reef restoration using coral colonies in the Philippines, an area that has suffered a lot of reef destruction. (http://www.youtube.com/watch?v=aypw9KQZVEM) Part of ongoing efforts at coral reef conservation by the Coral Reef Alliance (http://www.coralreefalliance.org/)
Web site illustrating the Global Coral Reef Alliance (GCRA)’s efforts at reef restoration by creating artificial reefs using an innovative approach to rapidly creating suitable substrate for attachment of juvenile corals. The technique involves low-level electrical currents causing deposition of minerals on structural materials directly from the seawater. These minerals are acceptable for a host of coral, invertebrate, and algal species for settlement.
(http://www.globalcoral.org/Biorock%20%20Mineral%20
Accretion%20Technology%20for%20Reef%20Restoration.html) [Note GCRA is a different organization that the Coral Reef Alliance mentioned above.]
A dive to the Spiegel Grove, a 510’ long US Navy vessel sunk off the Florida coast to make one of the largest single artificial reefs on the planet.
(http://www.youtube.com/watch?v=i70tuO6ArDM)
Although not tropical, oyster reefs in the Chesapeake Bay have undergone severe degradation over the past 100 years. Efforts have been underway at the state, federal, and private level to try and build artificial reefs to help bring back a commercially viable fishery. This web site shows some of the practical concerns that go into siting an artificial reef (http://www.vims.edu/mollusc/oyrestatlas/oramaptoc.htm). For a review of the importance of oysters and the reefs they can form to the functioning of the Bay, visit the educator-friendly web site:
(http://www.vims.edu/mollusc/education/vortex.html).
How practicing fish biologists quickly key into what type of fish they are seeing:
http://www.agrra.org/background/fishback.html
