2013 in Review

The WordPress.com stats helpers prepared a 2013 annual report for this blog.

Here’s an excerpt:

A San Francisco cable car holds 60 people. This blog was viewed about 3,200 times in 2013. If it were a cable car, it would take about 53 trips to carry that many people.

Click here to see the complete report.


ROV Data Collection

Michael Cohen prepares for a test run of his submersible ROV in the tidal portion of the Peconic River.

Michael Cohen prepares for a test run of his submersible ROV in the tidal portion of the Peconic River.

In 2012 Michael Cohen, graduate of URI, spent a summer on the tour boat collecting data with a YSI meter and recording first-hand observations of other abiotic factors in the Peconic Estuary. We have previously posted his graphs of our readings from the 2011 through 2013 tour boat seasons. In subsequent graduate work, Michael has most recently created a project proposal based on his experiences and developed around his engineering of a submersible ROV. The ROV will allow the user to observe the entire water column at each station and further correlate YSI data with the occurrence and abundance of marine life observed.

Adjusting flotation to accommodate differences in density found in the salt wedge.

Adjusting flotation to accommodate differences in density found in the salt wedge.

Michael prepares sand bags to modify his field trial.

Michael prepares sand bags to modify his field trial.

The ROV descends with a video feed and live capture of plankton.

The ROV descends with a video feed and live capture of plankton.

Michael Cohen, Project Leader
Marine Ecosystems Project Proposal

Effects of Water Quality on the Diversity of Plankton and Fish Species along the Peconic Estuary


Estuaries are environments where fresh water from rivers mixes with ocean water. They are characterized by water density and flow. The interactions of different water densities, rise and fall of the tide, and variations in river flow show complex patterns of water circulation in an estuary. This allows estuaries to be categorized by their circulation patterns. These circulation patterns lead towards an organized variability in water quality throughout an estuary.

Species that live in estuaries are adapted to tolerate salinity fluctuations. Salinity is known to be a critical factor in limiting the range of travel for marine species, however, there are many that are capable of rapid regulation and adjust to the changing osmotic stress of varying salinity. There are also species that are adapted to this environment by occupying the bottom waters, where salinity is greatest. They are able to penetrate an estuary farther upstream than species that occupy the surface, such as planktonic organisms.

Numerous studies have been conducted that show the effects of water quality on estuary species. Studies performed on the San Francisco Bay estuary hypothesized that seasonal and interannual fluctuations in estuarine phytoplankton biomass and primary production could be regulated jointly by direct physical efforts and trophic interactions (Alpine and Cloern, 1992). An observation on the South San Francisco Bay showed that estuarine phytoplankton biomass fluctuates because of variability fluctuations in tidal energy (Cloern, 1991). Another study suggested tidal flux at a particular location might have an effect on recruitment on estuary species that spawn offshore (Boehlert and Mundy, 1988). In the northern part of the estuary, the phytoplankton are in low biomass and dominated by microflagellates or freshwater diatoms in winter, and high biomass dominated by neritic diatoms in summer (Cloern et al., 1983). For the Chesapeake Bay, in the spring there is a high biomass of phytoplankton and zooplankton during times of high input of freshwater (Roman et al., 2005).

This proposal will study how water quality affects the diversity of plankton and fish species along the Peconic Estuary. Salinity is major contributor towards where a species can live and prosper, however this project will take into account the levels of dissolved oxygen and temperature measurements of the area to determine if other environmental factors influence species distribution. With the Peconic Estuary having the characteristics of a salt wedge estuary, it could have a significant affect on the richness and evenness of species at different locations and the salinity readings should be able to give an indication of its characteristics. The project also has the opportunity to educate the general public on how scientific research studies are conducted, the different equipments that are used, and give them some understanding about the constant changes that are occurring in the environment and how it can be monitored.


The Long Island Aquarium is located along the scenic Peconic River in Riverhead. The Aquarium is home to The Riverhead Foundation for Marine Research and Preservation, New York’s only authorized marine mammal and sea turtle rescue and rehabilitation center. Themed around the “Lost City of Atlantis,” it blends science and nature with myth to create an informative and entertaining environment for visitors. It offers a variety of experiences, from fascinating marine life exhibits to Aquatic Adventures and educational programs. Their goal is to capture the visitors’ imaginations and emphasize the importance of marine life and environmental preservation. They aim to provide an interactive and exciting educational experience.

With the corporation provided by the staff of the Long Island Aquarium’s Explorer Tour Boat and equipment, the desirable test sites will be accessible. The measurements of water quality can be collected along with noting the richness of fish and plankton species at both sites. In return for the aid and access, a presentation will be made to educate visitors on the purpose of the project and the importance of it. In addition to that, the presentation will also describe how the equipment is used for this project and in the scientific community. After the diversity indices tables and water quality graphs are made, they can be posted on Blue Ocean Institute’s Next Wave in the Peconic Estuary blog to allow the educational community and the general public to gain an understanding of ecosystem diversity. The goals of the Blue Ocean Institute are to understand how the ocean is changing and what changes mean for wildlife and people. It also provides scientific information so interested people with a limited scientific background can understand it.

Materials and Methods

To determine how the salt wedge characteristics affect the diversity of species, certain materials and methods will be needed to gather the appropriate data. The materials that will be used in the project include a ROV, plankton net, magnifying glass, YSI meter, seine net, and the computer program Microsoft Excel. The aquarium will provide the YSI meter and seine net. The seine net is already being used as a tool to gather fish to show visitors what type of species can be found in the area. Educators and interns involved in the “data collection assistant” internship offered by the aquarium operate the YSI meter. The project leader will provide the ROV, plankton net, and magnifying glass. The ROV and plankton net are homemade and designed to be used together.

The ROV’s frame is made out of 2 inch PVC piping and fittings. It is structured to house the electronics (control relays, wiring, camera system, and lights). The typical homemade ROV has frame structures which are box-shaped and separate housings for the electronics which are placed on the frame. The frame is glued together with PVC cement and the edges sealed with marine sealant to prevent leaks. At the back end of the ROV, the power wires, control wires, and Ethernet cable are threaded through a PVC rubber pipe cap and then sealed with hot glue, marine epoxy, and marine sealant. The three windows for the camera and two lights were created with a PVC trap adapter with Plexiglas and sealed using the same three sealants as the pipe cap, with the addition of electrical tape. The electrical tape is used to seal small leaks but allow access to the lights and camera.

The frame structure is built to have an upper and lower compartment. The upper compartment houses the electronics while the lower compartment acts as ballast to add negative buoyancy to the ROV. Due to the amount of air the 2-inch pipes can hold, the ballast compartments are filled with wet play sand (the type used in children’s sandboxes). The reason for using wet sand is because, even though the sand alone fills up the ballast compartment to its fullest, the interstitial space between the sand contains air. Carefully filling the ballasts with water to the point where all the sand is damp allows for the appropriate negative buoyancy to be added, achieving a slightly positively buoyant ROV. Small sand baggies are placed inside open spaces in the upper compartment for additional weight.

The thrusters are four 500 GPH Johnson Pump Cartridge Bilge Pump. Two are for vertical movement and two for horizontal movement. The two that are used for horizontal movement are placed on the back end and parallel to one another on top of the ROV ballasts so it can be moved similarly to that of a tank. The vertical thrusters are centered in the middle of the ROV. The thrusters are held in place on the PVC pipe using hose clamps that are epoxy and hot glued together. The propellers for propulsion come from model airplanes. The sizes for the horizontal (larger) and vertical (smaller) thrusters are different in order to fit the ROV design while still allowing for enough thrust for movement. The wiring for the controller, control relays, and lighting is designed to have minimal numbers of wires running between the controller and the ROV. The set-up for the camera system uses video baluns, a 75-foot Ethernet cable, portable DVD player, and a mini-security camera. The control, power wires (both slightly longer then 50 feet), and Ethernet cable are threaded though a 50 foot tether sleeve with Styrofoam floats zip-tied to it to allow for positive buoyancy. Their own 12-volt battery powers the camera system and ROV. The plankton net is based on an educational design set, but modified to fit this ROV.

Using these materials will assist in gathering data of plankton and fish abundance at two locations in the estuary. The first location is right behind the aquarium, roughly 1.5 miles upstream (site A). The second location is in Flanders Bay and in the vicinity of Hubbard County Park (site B). Site B a common spot where the tour boat goes to perform seine net catches and gather specimens on a remote beach. At both sites, surface and bottom water quality readings (temperature, oxygen, and salinity) will be taken using the YSI meter. At site A, the ROV’s camera system will be use to determine the abundance of fish by counting the number of fish viewed on a portable DVD player located on the surface. The plankton net will will assist in determining the plankton abundance, with a magnifying glass to identify the species caught. At site B, the ROV will be used for the same purposes as at site A for determining plankton abundance, but a seine net will be used to determine the abundance of fish. The reasons for the different fish abundance methods is because site A’s depth is too great to perform a seine net catch, and a seine net should be more accurate then using a TV screen and camera.

Once the daily abundance and water quality data has been collected, diversity indices will be used to determine the diversity of the population and any correlation between the quantified diversity values and the graphed water quality readings. The diversity indices that will be used include the Shannon Weiner index, Simpson’s Diversity index, and Morisita’s index. The Shannon Wiener index uses richness and evenness to indicate the species diversity of an area. The higher the calculated values indicate a high diversity for that area. The higher value also an indicator of lower competition between species. The Simpson’s Diversity Index expresses the probability that two individuals drawn from the community at random will be from same species. The higher the calculated value, the lower the diversity of the area. The Morisita’s Index quantifies the degree of overlap between two arrays of species from two areas. Low calculated values means that there is no similarity between the two areas. High values indicate a strong similarity of diversity. The reason for using multiple indices is to have enough information to support the hypothesis of how water quality affects the diversity of species.

Additional data that will be collected includes the current moon phase of that day and if the tide is flooding or ebbing. Data will be collected on days when an internist or project leader will be on the boat using the equipment and during the season when the tour boat is active (May-September). The data collected by the internists will be sent to the project leader via email for review and organization. The data and indices equations will be put into a Microsoft Excel program and the combination of water quality graphs and indices table will help to determine to what extent water quality has on the diversity of species in the area.

Expected Results

What can be generally expected from the data collected is a greater diversity of marine species at Site B then at Site A because of the greater salinity. The Shannon Weiner index and Simpson’s Diversity index should also indicate that the diversity is greater at Site B. However, it can also be expected that because of the ever-changing tidal ranges, the diversity at Site A will fluctuate depending the gravitational force between the sun and moon. The calculated index value for Site A should not be greater then the diversity at Site B. The reason for recording the moon phases of that day and tidal movements is to have additional information to support the hypothesis. An example of a situation for when this could happen is during a Full moon when the tidal ranges are highest, leading towards the diversity values for both sites as nearly equal. The Morisita’s index will determine to what degree the diversity at both sites are similar or different and will support the values calculated by the other indices. If the Morista’s index values are high, it indicates a similarity between the two locations. The values for the Shannon Weiner and Simpson’s indices should also indicate a similar level of diversity.


Alpine A and Cloern J (1992). Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary. Limnol. Oceanogr. 37(5): 946-955.
Boehlert G and Mundy B (1988). Roles of Behavioral and Physical Factors in Larval and Juvenile Fish Recruitment to Estuarine Nursery Areas. American Fish Society Symposium 3: 51-67.
Cloern J, Alpine A, Cole B, Wong R, Arthur J, and Ball M (1983). River Discharge Controls Phytoplankton Dynamics in the Northern San Francisco Bay Estuary. Estuarine, Coastal and Shelf Science 16: 415-429.
Cloern J (1991). Tidal stirring and phytoplankton bloom dynamics in an estuary. Journal of Marine Research 49: 203-221.
Roman M, Zhang X, McGillard C, and Boicourt W (2005). Seasonal and annual variability in the spatial patterns of plankton biomass in Chesapeake Bay. Limnol. Oceanogr. 50(2): 480-492.

More Gyre News

"The face of climate change is shoreline erosion."  C. Safina

“The face of climate change is shoreline erosion.” C. Safina

On our tours of the Peconic Estuary, our observation of growing ocean-borne debris problems such as the Great Pacific Garbage Patch often surprises visitors who are unaware of the human-made phenomenon in the North Pacific Gyre. However, the concentration of plastic debris in ocean waters is closer to home in the appearances of a brew of trouble in the North Atlantic Gyre: http://phys.org/news190569673.html#nRlv

We are marking one year since Hurricane Sandy blasted our Long Island and New Jersey shores. These photos capture a view of yet another source of floating debris. With every flooding storm, not only silt, rock and sediment pour into our waterways, but also the remnants of flood destruction from human habitations.

After the storm, high energy waves continue to uproot hardened shoreline structures.

After the storm, high energy waves continue to uproot hardened shoreline structures.

Father and son explore parts of a bulkheading and boardwalk left after the storm.

Father and son explore parts of a bulkheading and boardwalk left after Hurricane Sandy.

Red Tide in Flanders Bay

Red Tide in Flanders Bay, August 31, 2013.  Photo by Sarah Sandler.

Red Tide in Flanders Bay, August 31, 2013. Photo by Sarah Sandler.

One of our daily journeys across Flanders Bay nine years ago revealed a concentration of a red algae suspended near the surface of the estuary waters, so dense and wide-spread as to produce a visual effect of bands of reddish-colored water, distinctly patterning the surface of the bay from our distance perspective to a closer view under the pontoons of our tour boat as it sped along cutting across the bands in our path. We took a sample and brought it to Long Island Aquarium’s senior aquarist, Todd Gardner, for identification. Under the microscope, what appeared was a spiral chain of four cells with a flagellum. It was the dinoflagellate Cochlodinium polykrikoides, known in blooms around the world as Red Tide. Fortunately, this is not the same red alga organism that produces a neurotoxin that can kill large mammals through ingestion or aspiration. However, we learned subsequently through the work of Stony Brook SoMAS Professor, Dr. Chris Gobler, that blooms of C. polykrikoides have impacted NY waters with very disturbing outcomes of “complete mortality of captive finfish … as well as caged and wild shellfish.” (Gobler, C., “The cause, effects, dynamics, and distribution of Cochlodinium polykrikoides blooms and cells in the Peconic Estuary, Suffolk County, NY”, p.2)

Furthermore, this red tide appears toxic to other phytoplankton and zooplankton, as well as the different life stages of many fish, hard clams, oysters and bay scallops, and is able to grow rapidly in varied nutrient conditions. In 2008 and 2009, local fishermen and aquaculturists reported losses of harvest during red tide blooms; closer examination of effected species, exposed to concentrations of Cochlodinium, revealed loss of gill function directly related to the density of the algae.

As our tour boat season closes this October 2013, we have once again experienced red tide in Flanders Bay and recognize it now as an annual event that challenges the local fishing industry, perhaps with as grave repercussions on the productivity of these waters as felt with earlier assaults of brown tide (Aureococcus anophagefferens) in the Peconic Estuary and other bay systems surrounding Long Island. Although thought to be rare prior to this century, Cochlodinium blooms now occur annually and globally in estuaries that provide nursery habitat, food energy, and shelter for 70% of marine life that humans harvest from Earth’s one great Ocean.

Submitted by Ann Haskell, Blue Ocean Institute marine educator


Introducing the New Southampton Marine Science Center!

Introducing the New Southampton Marine Science Center!

Feedback from Inspired Teachers

Pulling the Seine Net

Teachers report that our Blue Ocean Institute Explorer tour boat presentation and experiential learning activities engage their students’ attention, effectively involve students in essential curriculum materials, and keep a balance between education and entertainment – all important features of the partnership aims of Blue Ocean Institute and Long Island Aquarium.

The naturalist was so accommodating to our needs … really outstanding in every way … provided a safe and informative experience … she was fantastic! Knowledgeable and personable and very interactive!

The educator was fantastic at pointing out the relevance of the river and its importance to the ecology of the area. She was wonderful at engaging the students. They loved seeing the organisms. This really helps sum up the concepts through the year.

We loved how the children could touch and see everything up close … really enjoyed the opportunity to explore and wade the waters at the beach ….

It was wonderful, age appropriate, and had lots of hands-on learning.

The naturalist understands our age group and gears her program seamlessly to their interests and knowledge base.

Our three to six year olds were strongly impressed!

It was a wonderful tour. Every year it’s a little different, depending on the water and weather conditions.

My students were thrilled to see firsthand what they studied, and they understood the nomenclature.

My students were engaged and enjoyed the day!

School groups range from pre-Kindergarten through college classes, as well as adult groups seeking an informal education experience. Furthermore, our team of educators offers customized experiences for groups with special needs and various learning styles – home-schooled students, English Language learners, and groups who need specific activities for unique curricula.

Local college students studying a Marine Habitat Ecology course heard two in-class lectures from Blue Ocean Institute scientists on sustainability. On their boat trip, we extended their experiences with information about estuaries, field study including surveys of estuary water measurements and beach zones, and an oyster-seeding activity over hard-bottom in Flanders Bay.

English for Speakers of Other Languages students participated in an Oceans summer program in their classroom and then explored the estuary with BOI educators, building new vocabulary through the classification of plants and animals and using technology and hands-on activities to connect Ocean Literacy concepts and new language with their experiences. Besides achieving their educational objectives, these students were inspired with hope, as well as a sense of achievement and connectedness in their new environment.

Article contributed by Blue Ocean Institute Marine Educator, Ann Haskell

Juvenile Horseshoe Crab Molts

Molting juvenile horseshoe crab

Juvenile horseshoe crabs molt sixteen times throughout the first ten years. Then they remain in the last, harder shell for the rest of their lives. It is thought that the female may molt one year longer than the male, since their body size is up to three times larger than males. Other than size, the other obvious morphological difference between males and females is the adaptation of the clasper claw on the front legs of the male, which allow the male to hook on to the back of the female’s shell when it’s time to mate. Juveniles do not show this adaptation before the final molt.

September 2, 2013

Thank you so much, Blue Ocean Institute, for the wonderful time I had on the boat. I was so lucky to be able to experience something so extraordinary. I learned so much and made amazing experiences and memories of the marine life and also the people. The other crew members were so nice and helpful and we had so much fun as a team. I really hope I can come back next year and help out. I’m going to miss this a lot! Thank you again for such a memorable summer and for all the great support.
Charlotte Schmidt

Today’s Observations

Air temp: 75 degrees F
Sky conditions: overcast
Wind speed: 8-12 mph, gentle breeze
Wind direction: SE
Tide: outgoing

What we caught (12:00 boat tour):
Beach: mud snails, fiddler crabs (no males), hermit crabs
Net: mud snails, striped killies, a lot of moon jellies and comb jellies
Crab trap: spider crabs, 1 blue claw crab, codium fragile, whelks
Blue claw crab trap: 1 blue claw crab

What we caught (2:00 boat tour):
Beach: hermit crabs, mud snails, 3 baby horseshoe crabs, fiddler crabs (males and females)
Net: silver sides, striped killies, sheepshead minnows
Crab trap: spider crabs, whelks

Contributed by BOI Intern Charlotte Schmidt