By Renee J. Piccitto

Originally submitted to

College of Aviation

In Partial Fulfillment of PhD Thesis Requirements for

PhD in Aviation

Embry-Riddle Aeronautical University

College of Aviation – Worldwide

Department Chair

03 March 2018

Copyright: Renee Piccitto and The Marquis Group, Inc. and affiliates Planet Shark Divers, Marquis Media, Marquis Hosting and Diver’s Against Lupus and MS


This paper identifies an increasing local issue in South Florida, HAB’s, or harmful algal blooms, and how they have a negative and toxic impact on the local marine environment as well as humans. These environmental and habitat changes directly impact the marine apex predators, sharks. These changes aren’t limited to a single or one particular species, but multiple species. This paper identifies a viable solution in monitoring and possibly eliminating HAB’s. The solution is a combination of innovative technologies, autonomous biosensors and unmanned systems capable of flight and underwater propulsion.


Chondrichthyans are the group of cartilaginous fishes in which include rays, chimaeras, skates, and of course sharks. Sharks are complex organisms that are extremely diverse and unique among species within their class and order. Since sharks are so diverse, each species depends on a unique environment and ecosystem. Their dependency correlates to a behavioral product. Changes in a shark’s typical environment directly impact the behaviors in sharks.

Unmanned systems and autonomous biosensors can monitor environments to prevent risks. Technologies in both autonomous biosensors and unmanned systems capable of both aerial and marine use are explored as possible solutions to real-time monitoring and prevention of one marine environment risk, harmful algal blooms.

Different Shark Environments and Habitats

There are around 500 different identified species of sharks in our oceans. Each one of these species has a preferred environment from water temperature, depth, and even salinity. Some sharks can survive in brackish and even fresh water for a certain period. One of these species does inhabit Florida and other tropical and sub-tropical environments globally. The Bull shark Carcharhinus leucas, can survive in both freshwater and in salt water by taking control of their osmoregulatory process (Compagno, Dando and Fowler 2005, Pg. 299).

Osmoregulation is the ability of an organism to maintain a constant concentration of water in its body, even when the outside environment may cause it to lose or gain water (Evans, 2010). On a cellular level, a membrane separates the external and internal environment of any organism that depends on osmoregulation. This membrane allows substances, like water, to move (Shark Savers, 2018). The movement itself is at a cellular level, as well as the whole organism, meaning across the skin. According to Shark Savers, 2018, “In sharks, the normal mechanism of osmoregulation in a marine (salt) environment is the high concentration of urea and other biological solvents in their blood and the removal of excess salt from their bloodstream through urine. The former allows them to absorb water from their marine surroundings, while the latter rids them of the salt they continually absorb. These tasks are primarily controlled by the kidneys.” This means that sharks do not have control over this process. The Bull shark (Carcharhinus leucas), however, is extremely unique in that it can control this process. The Bull shark can adapt to different environments.

Habitats of sharks can differ greatly. Sharks of the intertidal zone inhabit the shallowest of environments. The intertidal zone is the area along the shore exposed at low tide. One unique shark that lives in the intertidal zone is the Epaulette shark Hemiscyllium ocellatum. The Epaulette shark also has a unique ability. This shark can live out of water, or with little oxygen for a period but shutting down its organs one by one. It uses its pectoral fins to crawl its way along.

Estuaries are quite common here in Florida. These are areas that are enclosed by land, and usually where fresh and salt water meet to form brackish water. Many estuaries are a part of a mangrove forest, where intertwined roots help protect juvenile fish and sharks, becoming a safe nursery protected from predators. The floors of estuaries are covered in seagrass that is extremely important to the overall environment and habitat. Florida seagrass species consist of Turtle Grass Thalassia testudinum, Manatee Grass Syringodium filiforme, Shoal Grass Halodule wrightii, Johnson’s Seagrass Halophila johnsonii (unique separate species found only in the Indian River Lagoon discovered by FAU’s Harbor Branch Oceanographic Institute in 1980), Paddle Grass Halophila decipiens, Star Grass Halophila engelmanni, and Widgeon Grass Ruppia maritima. Each species of seagrass supports different marine life from the smallest organisms to fish, turtles and manatees. Bull sharks Carcharhinus leucas and Lemon sharks Negaprion brevirostris are common sharks found in estuaries and rely on the unique habitat beneath.

Florida coastline consist of a lot of barrier islands and whether they are manmade or natural, these are important because they separate the mainland from a lagoon.

Sharks that seem to flourish in the sandy plains (the sandy, shallow area that makes up the continental shelf) feed on several different types of organisms like rays, small fish, and crustaceans. Great Hammerhead sharks Sphyrna mokarran are a shark that you will find here, preying on rays resting on the ocean floor.

Rocky Coasts can vary in depth, and in temperatures. So, the types of sharks that rely on this environment can range from Great White sharks Carcharodon carcharias, to Scalloped Hammerheads Sphyrna lewini to Basking sharks Cetorhinus maximus. Many sharks rely on the rocky coastline throughout their lifecycle.

Another habitat is the kelp forest. Cool and shallow waters, kelp forests can be home to another completely different variety of sharks. Leopard sharks ‎Triakis semifasciata and Sevengill sharks Notorynchus cepedianus can be found reliant on this type of environment.

One habitat that most are familiar with is the coral reef. Coral reefs are an important habitat of many organisms and are living themselves. Blacktip Reef sharks Carcharhinus melanopterus, Whitetip Reef sharks Triaenodon obesus and Caribbean Reef sharks Carcharhinus perezii are common apex predators among this environment.

The Pelagic Zone is home to many species. Common Thresher sharks Alopias vulpinus, Blue sharks Prionace glauca, Silky sharks Carcharhinus falciformis, Mako sharks Isurus oxyrinchus, Isurus paucus and Oceanic Whitetip sharks Carcharhinus longimanus are some of the most well-known species.

Most of the Florida environments, coral reefs and Pelagic zones are home to many requiem species such as the Reef sharks, Silkies, Lemons, Tigers, and Blues.

Deep sea sharks are some of the most unique sharks around. The Frilled shark Chlamydoselachus anguineus and the Goblin shark Mitsukurina owstoni are two of the most unique, and strange looking sharks.

One shark that has found the fountain of youth is the Greenland shark Somniosus microcephalus and lives in the polar region. Seas can drop as cold as 272 degrees Kelvin. Friend and Professor of Marine Ecology at the Arctic University of Norway, Dr. Kim Praebel has taken DNA from over 100 Greenland Sharks that are at least 300 years old. He plans to compare this DNA with other shark species to attempt to identify mutations that can stop cancer cells and fight off forms of virus and bacteria.

Dr. Praebel (2017) states, “we’re particularly interested in a family of genes called the major histocompatibility complex. The more combinations of gene mutations you have in this family, the stronger your immune system is, and we’re searching for particular combinations which are only found in Greenland sharks that live for hundreds of years.”

Dr. Praebel’s research will also help to identify the secrets to life longevity, Dr. Praebel may have found the fountain of youth in one of the most amazing sharks on the planet.

 Shark Eating Habits and Food Supply

Each of these environments or habitats differs in temperatures and organisms from the most microscopic to the largest of apex predators, the sharks. Sharks are also categorized by how they eat their food. Some sharks are known as ram sharks and others as suction sharks. Many sharks are a combination of both.

A pure ram-feeding shark would have a large, gaping mouth without exerting any energy. A good example of a pure ram-feeding shark would be a Basking shark Cetorhinus maximus since when it opens its mouth the water and food rushes in. The shark doesn’t do anything with its mouth other than open it. The Basking shark moves its body and that is it.

With a suction-feeder, the prey is inhaled. The spiny dogfish Squalus acanthias is somewhat a suction-feeder. A pure suction-feeding shark would be a Nurse shark Ginglymostoma cirratum or a Wobbegong Orectolobidae. With suction-feeding sharks, their mouths would work like a vacuum. These sharks don’t have to move their bodies to suck the prey in.

The ram suction index (RSI) was developed to quantify movements of predator and prey. Primarily the body and jaw movements are quantified in predators. Sharks can be categorized by their ram vs suction vs biting to feed.

Images courtesy of Norton and Brainerd, 1993



It is important to understand RSI, because each shark registers different through the index, and therefore all have different prey. Therefore, based on varying RSI, different habitats, and feeding habits, not all sharks have the same diet, and don’t all eat the same fish, so it is very important to understand what each shark’s diet is, and those fish and other marine organisms, what their diet consists of.

Behavioral Changes in Sharks

Sharks have strong short and long-term memory. They the ability to learn or solve problems, and therefore human interaction is among one of the most noticeable cause and concern in shark behavioral changes. For example, sharks have adapted and evolved to recognize the shape of a boat in heavily fishing areas and associate the shape of a boat with a food source, and thus will be attracted to it.

Locally here in Jupiter, Florida the local Lemon shark (Negaprion brevirostris) population (as well as the nurse sharks and some tiger sharks) exhibits noticeable changes. Over the past 7 years about 20 Lemon sharks have been studied (visual identification) and show behavioral changes, adaptations and evolution based on human feeding interaction with divers and fisherman. Natural Lemon shark temperament and feeding behavior is patient and gentile. Jupiter Lemon sharks identify the sound of a boat engine and the shape of a boat with their food source. These sharks aren’t timid or patient and seem a bit more aggressive than other Lemon sharks. One famous Jupiter Lemon shark named “Miss Snooty” (Named by local photographer Alan C. Egan) is usually the first in line. She can be identified by the damage on the side of her jaw due to her lack of fear of boats and fishing vessels.  So, although loved by locals alike, locals are the cause of her injuries based on interaction. Over the years, she has been touched and rubbed by so many locals that she has become accustomed to humans touching her.

The White Shark clans that frequent and live around the East Coast of the UAS are born off of Long Island, New York (confirmed discovery credited to OCEARCH in 2016), increasing and contributing to the number of juvenile white sharks specifically in the Northeast coast of the USA, but all along the East Coast stretching from South Florida to Maine. One clue was that these sharks seemed to act differently than other White Sharks, apparently more aggressive towards humans. In all species, juvenile sharks exhibit different behaviors than adult sharks naturally because they are still learning and understanding what their actual prey is. These sharks were energetically learning, a completely natural behavior for juveniles So, what would cause an adult shark to exhibit different and extreme behavioral changes?

 Local Impacts: The Problem

In 2012, the East Coast of South Florida experienced an anomaly. An area spanning from Daytona Beach down to Jensen Beach and Stuart Florida (including the Fun Coast, The Space Coast and the Treasure Coast) experienced a record breaking number of shark attacks since 2000. According to Space Coast Daily (2013) and the University of Florida (2013), of the 26 total shark bites in Florida (27 according to The Florida Museum, 2017) eight were recorded off the Space Coast. The International Shark Attack File has some useful information by species, decade, time of day.

The years following 2012 have seen similar statistics, but this is an important year and some time should be spent on understanding why.

Researchers thought sea turtles had something to do with it. During 2012 (FWC, 2012), sea turtles began to lay their eggs almost a month earlier than they usually do. It was thought that maybe since the sea turtles were coming early that this disrupted typical Tiger Shark behavior. There is a problem with this theory though because the attacks in 2012 were not just Tiger Sharks.

One leading scientist, Associate Professor of Biology, Dr. Daniel Huber of the University of Tampa is a leading expert in the biomechanics of feeding and locomotion in chondrichthyans. Dr. Huber will use his research to help improve the health of captive animals and reduce the dependence of aquariums on wild animals (UT, 2018).

This means that Dr. Huber is an expert in identifying species by bite forces and bite marks. In When Sharks Attack, Episode 1, Season 1 (2013), a television special on National Geographic, Dr. Huber confirms that these attacks were not all the same species. And not all sharks depend on sea turtles as a part of their diet, so this couldn’t be a behavioral change because of the early nesting.

The cause of the rapid and uncharacteristic behavior in multiple shark species during this time was a result of an HAB or harmful algae bloom, specifically brown algae in the Indian River Lagoon. “The Brown Tide” as it was fittingly named carried harmful bacteria that killed multiple seagrass species and organisms, as well as blocked sunlight which inhibited seagrass growth (Brown Tide, 2012). This severely impacted the local sharks and their diet.

One recent issue (2016) locally to us here in Martin County, Florida, but received international attention, has been that of the polluted Indian River Lagoon due mostly to agricultural runoff (Waymer and Berman, 2016). Runoff from agricultural land can carry large amounts of nitrogen, phosphorus, and sediment. Excess nitrogen and phosphorus can cause harmful algal blooms, or HAB’s in waterways that can be toxic to humans, livestock, and fish. Sediment can clog fish gills, smother plants and can reduce light penetration in the water. Without light, aquatic plants on the river bed cannot survive. Aquatic plants are important for commercial and recreational fishing as they provide a habitat and food source for fish. HAB’s are a major global concern as well because they can cause other environmental damage, major health concerns for people and animals, and economic losses. In algal blooms, researchers look for the presence of toxic phytoplankton.

Green algae, or cyanophyta, cyanobacteria was responsible for the problems in the Indian River Lagoon in 2016, along with brown algae, although not as severe as the case in 2012. Here are a variety of cyanobacteria to be concerned about in Indiana. They include Cylindrospermopsis spp., Microcystis spp., Anabaena spp., Aphanizomenon spp., and Pseudoanabaena spp. The specific algae responsible was Microcystis aeruginosa (Florida Atlantic University’s Harbor Branch Oceanographic Institute, 2016). The fact that two devastating outbreaks occurred within a five-year period cannot be ignored.

In 2012 the Treasure coast experienced a wave of extremely uncommon shark attacks that were a direct cause of the harmful algae blooms. The algal harmful blooms impacted the seagrass, effecting the fish population, which resulted in irregular behavior in several different species of sharks. In addition, HAB’s can make humans extremely sick and in some cases a result has been death. So, as you can see reducing agricultural runoff, reducing HAB’s and monitoring the waterways is extremely important for many reasons.

Solutions: Customized Unmanned Systems and Sensors

Typically, researchers would rely on tedious manual monitoring and lab bases analysis to test for HAB’s. Again, these are extremely time-consuming. Manual processes that can become extremely expensive. One common method is light microscopy, or LM. It is important to note that real-time data is required, so if too much time has passed, or mistakes were made along in the process, then the data must be re-collected and tested again, by qualified individuals.

According to McPartlin, Loftus, Crawley, Silke, Murphy, and O’Kennedy (2017) of Dublin City University’s School of Biotechnology, huge efforts around biosensors, and the development of nucleic acid-based methods such as ribosomal RNA (rRNA ) or DNA (r DNA) over the past five years. This has led to the development of the ALGADEC system developed by Dierck-Horn (McPartlin, Loftus, Crawley, Silke, Murphy, and O’Kennedy, 2017). ALGADEC is a semi-automated rRNA biosensor. It detects Alexandium minutum, one type of HAS or harmful algal species, and potentially able to detect 14 others.



Pasternak, Greenman and Ieropoulos (2017) developed a sensor system completely autonomous and self-powered that continuously, in real-time, monitors water quality based on oxygen demand. With several modifications, a system like this could be used to identify an HAB risk before the bloom occurs. Below are some images of how this system looks. Read their finding further for the full research and science behind the system.



A new system combining ALGADEC, and Pasternak, Greenman and Ieropoulos’ sensor system could result in a monitoring solution here locally.

One area of interest is in amphibious drones or unmanned vehicles capable of both aerial and water for a very important reason. One of the most interesting applications today is that of pollution control. In China, there are drones that can release chemicals that in polluted areas will reduce PM2.5.

Innovative research in drones and unmanned systems could be part of the solution. An unmanned system can be designed to carry a payload of autonomous biosensors as well as thermal, optical and video sensors. The unmanned system will have the ability to take off from land or water, propel under water, and land in the water or terrain. The system will have the ability to be submersed in water and propel itself. This will give researchers the ability to drop an autonomous biosensor in a remote location of waterways being studied or watched. The biosensor will be able to be monitored in real-time remotely, and then collected by the unmanned system later.

This will give researchers new ways of monitoring all of the many intertwined canals and waterways that make up South Florida’s East Coast. In addition, water testing kits can be fitted onto these special unmanned systems. The ability to be aerial or underwater will allow for more efficient means for monitoring and combating runoff all the way from the source to the coast.

Autonomous and in situ monitoring of algae and their associated marine biotoxins is a concept that is emerging rapidly. Such systems, which are now becoming commercially available, allow for real-time or near-real-time monitoring of algae and their toxins at the site of an ongoing bloom or early in the process of bloom initiation and the relaying of this information to the relevant authorities. They can be deployed on stationary moorings or potentially on autonomous underwater vehicles (AUVs). One example is the Imaging Flow Cytobot (IFCB; McLane Research Laboratories, Inc., East Falmouth, MA, USA), which combines high-resolution video imagery with flow cytometry to allow the autonomous in situ classification of marine algae to species level. Another example is the Environmental Sample Processor (ESP) developed by the                 Monterey Bay Aquarium Research Institute(MBARI) and collaborators at the National Oceanic and Atmospheric Administration (NOAA), which has been deployed in

Monterey Bay, CA, USA, for the detection of both Pseudo-nitzschia species and the neurotoxin domoic acid (DA) produced by some of these organisms. The robotic ESP system, also available from McLane Research Laboratories, Inc., allows the autonomous sub-surface detection of the toxin and algae using enzyme-linked immunosorbent assay (ELISA) and DNA probe arrays, respectively.

Other ESPs have been deployed in the Gulf of Maine to monitor levels of Alexandrium species and paralytic shellfish poisoning (PSP) toxin levels (Suddleson, 2011). This project will determine the feasibility and the economic advantage of deploying remote, autonomous sensors for harmful algal species (NOAA, 2013).

According to According to McPartlin, Loftus, Crawley, Silke, Murphy, and O’Kennedy (2017), another technology platform that could revolutionize HAB monitoring is that of AUVs. These unmanned systems currently could autonomously provide spatial and temporal information on algal pigment distributions that can be useful for HAB monitoring but provide no data on the species or toxin present. To address this shortcoming, scientists are currently developing a redesigned ESP that will fit within the payload of an AUV and thus enable measurements of algal and toxin concentrations on this mobile platform, which is something as yet unavailable to marine scientists and coastal managers. This could allow an advanced understanding of HAB occurrences, their frequency and their causes, and may potentially allow the enhanced prediction and protection of public health as well as economic interests in the future.

Professor Don Anderson of Woods Hole Oceanographic Institution is at the forefront of innovative research. His lecture at Harbor Branch Institute at FAU on March 28, 2018: New Applications of Autonomous Biosensors in Harmful Algal Bloom (Red Tide) Research and Monitoring shows promising results. His lecture can be watch streaming through FAU. He is leading this research in the United States. Anderson states that these autonomous sensors have advanced and progressed from th size of a canoe, to the size of a soccer ball. In addition, since the development in understanding their growth habits, research will allow us in the future to even prevent blooms from occurring. Unfortunately, environmental lobbyists here locally are preventing the advancement of research with criticism. Lobbyists are preventing the advancement of their own cause.

Biosensors and visual sensor imagery is essential as we identified above, but another type of sensor is extremely important to develop a full solution and that is infrared technology. Infrared thermography allows another layer of surface visual observation that can collect radiometric data that cannot be seen through our visual spectrum. The FLIR Lepton or Tau core are both extremely small and lightweight, as well as the visual Session core by GoPro. Both can easily be fitted into a system with waterproof housing, without adding too much additional weight to the biosensor payload. A combination of Wi-Fi and Bluetooth technologies can be used to transmit the data remotely.

As identified above, the technology for monitoring the risks of HAB is available today. Designing and customizing an unmanned system to carry this type of payload would be the next step.

The first unmanned quadcopter that can both fly in air, swim, take off and land on both solid terrain and in water has been recently designed and developed by a team at Rutgers University, funded and additional research contributed by the Navy (Maia, Soni, and Grias, 2015). It is fittingly named the NAVIATOR.

According to the NAVIATOR team on the project, the key to the success of this quad in multi terrains is the dual propellers rotating in opposite directions. This allows the NAVIATOR to take off and land on both land as well as in water and propel itself under the water.



The NAVIATOR is capable of three functions according to the team: seamless transition from air to water, multi propulsion (air and water), and the ability to fulfil requirements of lift and thrust for flight, and thrust and neutral buoyancy in water (Maia, Soni, and Diez-Garias, 2015).



In the above image, Maia, Soni and Diez-Garias (2015) outline the formulas used in the design on the NAVIATOR. The problem lies in the scalability and ability to carry payload that is useful. With the right funding in place, we propose we can re-design this system that can carry a payload autonomous biosensor. Above is a glance at some of their research. Read their full research for full information.

Another quadcopter available retail to the public is under $3,000.00 and can take off and land in water and on land (it cannot swim) is fitted with a gimbal for cameras. It is called the SwellPro Waterproof Splash Drone (version 3).

With technologies available now, NAVIATOR or a similar system can be re-designed to carry the autonomous biosensor payload. The proposed name is Aerial and Underwater Algae Detection System AUADS

Other Environmental Concerns

There are several other environmental concerns that most people know about, such as the bleaching of coral reefs, changes in water temperature and changes in salinity. There was a case known in Hawaii where microwave effected the health of Hawaii’s coral. This created murky water for a period of time, and in murky water, sharks depend on their lateral line instead of vision. Causing a string of rare and unintentional shark attacks.

Another area of impact is trash, waste and plastics that are being deposited into our oceans. These are all very important concerns, but since most people are unaware of HAB’s and how they can severely negatively impact our waters and oceans, it is extremely important we bring awareness and education in any way we can. Prevention is vital, so further research and development into technologies that can support prevention can have a positive result.


 Since sharks are so diverse, each species depends on a unique environment and ecosystem. Their dependency correlates to a behavioral product. Changes in a shark’s typical environment directly impact the behaviors in sharks. Technologies in both autonomous biosensors and unmanned systems capable of both aerial and marine use are a viable solution to real-time monitoring and prevention of one marine environment risk, harmful algal blooms. With the right funding in place, new research and design can commence.


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