A Subtropical Estuary Habitat Description
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A Subtropical Estuary Habitat Description

An easy intro to one of the most important ecosystems in the world

A Subtropical Estuary Habitat Description
Ray Hennessy

An estuary is a partly enclosed body of water where freshwater and saltwater mix (such as where a river meets an ocean). Lagoons, sloughs, bays, and sounds are all estuaries. The most common type of estuary formed when glaciers melted 18,000 years ago and drowned river valleys. Chesapeake bay was formed this way. Other types of estuaries are bar-built meaning they occur between an offshore bar and the mainland such as the NC sounds, tectonic estuaries such as in San Francisco, and fjord estuaries where glaciers carve out valleys the sea then rushes into (Ward and Ward 2017). Estuaries are primarily found along passive margins and somewhat follows the distribution of mangroves, the dominant intertidal vegetation, and are found in environments with a 20-degree isotherm between January and June. Subtropical estuaries, in particular, are found north of the tropic of Cancer and south of the tropic of Capricorn and continue being found until the water reaches a winter low of 12°C. In Mozambique and East Australia, subtropical estuaries can be found as far south as 32° S. (Blaber 2000).

One of the most defining characteristics of an estuary is its salinity. A positive estuary, or a salt wedge, is river-dominated and has a distinct stratification wedge where saltwater meets freshwater. Chesapeake Bay and Pamlico Sound are salt wedge temperate estuaries and as such have lower salinities than other types of estuaries. A homogenous estuary is neutral and roughly midway between fresh and salt water in terms of salinity due to the complete mixing of the water and the evaporation rate equaling the freshwater inflow. The Gulf of Mexico is a homogenous subtropical estuary. A negative estuary, or an evaporate estuary, has the highest salinity of the estuary types due to the high evaporation rate of the water. This makes the surface water hyper saline so it then sinks to the bottom forming a bottom current. There’s also an intermittent estuary where the water is completely non-existent part of the year. The salinity in an estuary can vary up to 15 PSU in a single spot over the course of the year due to seasons, tides, freshwater input, evaporation, and water density.

Another typical characteristic of subtropical estuaries is the high turbidity from muddy substrate. This high turbidity helps camouflage the organisms that live there but oxygen cannot mix in sediments creating anoxic and hypoxic regions. Additionally, estuaries have a temperature gradient due to their semi-enclosed nature, have currents from both the ocean tide and the river flow, mix oxygen in non-sediment areas, and have waves with a smaller fetch than the ocean. Estuaries also have a “flushing time” which is the time it takes for all the water in the estuary to be exchanged with the nearby bodies of water (Ward and Ward 2017). Other notable characteristics are extensive intertidal areas, semi-diurnal or diurnal tides, water layering/mixing, sediment suspension/transport, extremely high productivity, high nutrients, nutrient exchange, and specially adapted organisms (ABPmer 2008).

Overall, estuaries have highly variable abiotic characteristics and thus the organisms that live there need to be specially adapted in order to cope with the variance. There are two primary groups of organisms that can be found in estuaries: stenohaline and euryhaline. Stenohaline organisms do not have a wide range of salt tolerance and can only be in the estuary for a short while. Stenohaline organisms come into the estuary to feed or to breed but do not live in the estuary because they aren’t adapted to the conditions. Euryhaline organisms, however, have a wide salt tolerance range. Most euryhaline’s are osmoconformers meaning they do not try to keep a constant internal osmolarity like osmoregulators, but rather match the osmolarity of the outside environment. This makes them better suited to the estuary conditions because they are not always expending energy trying to secrete/intake the proper amount of salt.

Estuaries have the highest diversity of biota of any other habitat, but most of their organic matter is allochthonously produced. Their algal primary productivity is very low, but this is okay because there aren’t many herbivores. Estuaries are primarily comprised of detrivores and omnivores. Manatees and dugongs are some of the only herbivorous species found in estuaries and they feed on seagrass. For the most part, however, the food web of the estuary relies on detritus and feces (Ward and Ward 2017).

A three-year study in Pensacola Bay, Florida showed that the phytoplankton present were mostly less than 5 μm and that cyanobacteria abundance peaked in the summertime. The larger algae is mostly diatoms, specifically in genera Thalassiosira, Pennales and Cyclotella, as well as a fair number of chlorophytes, cryptophytes, and dinoflagellates. Zooplankton is most abundant in the summer with the most ubiquitous species being Acartia tonsa most of the year but Oithona sp. during summer when picophytoplankton also increases in abundance (Lores and Murrell 2004). Meanwhile, another study in Biscayne National Park, Florida found the most abundant seagrass to be Thalassia testudinum which was always present and covered 75% to 100% of the seagrass beds. Syringodium filiforme and Halodule wrightii were also present but sparsely and inconsistently across testing sites. Fish diversity in this area was much higher with 25 taxa observed. The three most abundant fish taxa in this subtropical estuary were sea bream ( Archosargus rhomboidalis ), pinfish ( Lagodon rhomboides ), grey snapper ( Lutjanus griseus ) and juvenile grunt species ( Haemulon sp .) (Bourque and Fourqurean 2013).

Bird species that frequent estuaries are wading birds such as Roseaste Spoonbills ( Ajaia ajaja ), Great Blue Herons ( Ardea herodias ), various other herons ( Egretta sp. ), Great Egrets ( Casmerodius albus ), and White Ibis ( Eudocimus albus ). Which birds feed when depends on the water level, with only the tallest species (the great blue heron) present all year, and both day and night. Other species are only found at certain times of the year, only during the day, only at night, or a combination (Powell 1987). Of the fish in estuaries, most of them do not spend their entire lives in the estuary but cluepids, gobies, engraulids, ambassids, artherinids, and syngathids do. While these are just a few common species, medium to large subtropical estuaries are home to 100-200 different species of fish as opposed temperate environments that only feature 20 species of fish and the indo-west Pacific has over 600 species recorded. By far the most common fish found in estuaries, though, are members of the mullet family ( Mugillidae ) (Blaber 2000).

Not all the species found in estuaries are supposed to be there. The U.S. congressional Office of Technology Assessment estimates that 2-8% of species are non-indigenous and 15% of these are harmful to their habitat. These species are introduced by human activity such as the introduction of Crassostrea gigas , the Pacific oyster to the estuary in San Francisco Bay. Most of the non-native species in estuaries are bacteria, dinoflagellates, crabs, and small fish released from ballasts of visiting ships. Essentially, there are 60-212 non-native species per estuary spanning a broad range of taxonomic and tropic groups. Chesapeake Bay has 116, Coos Bay has 60, the Great Lakes have 137, and San Francisco Bay has 212. Species that are non-native and cause significant problems for native species across worldwide estuaries are Carcinus maenas, Cyprinus carpio, Dreissena polymorpha, Hydrilla verticillata, Illyanassa obsoleta, Littorina littorea, Membranipora membranacea, Mnemiposis leidyi, Potamocorbula amurensis, Spartina anglica, Tritonia plebia, and Zostera japonica (Carlton et al. 1997).

Because of these non-native species and because of other human impacts such as habitat destruction, there are a lot of threatened and endangered species found in estuaries. Most of these are the larger animals such as all five species of sea turtle, manatees ( Trichechus manatus ), the american alligator ( Alligator mississipiensis ), and the american crocodile ( Crocodylus acutus ). Birds like the southern bald eagle ( Haliaetus leucocephalus ), the piping plover ( Charadrius melodus ), the wood stork ( Mycteria americana ), and the cape sable seaside sparrow ( Ammodramus maritima mirabilis ) (Florida Museum). In Chesapeake Bay, fish such as shad, menhaden, and striped bass are threatened, as are blue crabs and oysters (Chesapeake Bay Program). In the gulf, conchs and seagrasses are threatened. It is important to try and save these threatened species to help maintain the amazing diversity that estuaries have.

In the course of my travels, I had the opportunity to see several subtropical estuaries along the east coast of the United States. A characteristic that I noticed across the various types of estuaries we visited was the shallow water. Estuaries are very shallow for quite a bit longer than most continental shelves. The waves are smaller and more uniform, the seafloor is usually covered in seagrass fields, and the sediment is quite a bit softer and lighter than usual sand. Biota that I could see was mostly seagrass and crabs. When we seined, however, we were able to catch hundreds of fish, the biggest of which was a pipefish maybe four inches long. In the Cape Fear Estuary, we only caught three species of fish and only caught them near the pilings, which provided a nice habitat for them. 75% of the fish were Florida pompano ( Trachinotus carolinus ). This estuary lacked seagrass so far as I could tell and the waves, while they had the stereotypical smaller fetch of an estuary, were rough and frequent.

In Apalachicola bay, most of the fish we caught were pinfish ( Lagodon rhomboides ) though we also caught a lot of silversides ( Menidia menidia ). Using casting nets we also found a mullet ( Mugil cephalus ) and a half beak ( Hemiramphus brasiliensis ), which were quite a bit larger at maybe eight inches. We also caught a lot of pigfish ( Orthopristis chrysoptera ) and three different species of shrimp. Overall we saw 22 species in the bay, 15 of which were caught while seining (Figure 1). Of all the habitats we visited and seined, this estuary definitely had the most animal species diversity (H=1.584, 1-D=.7482). The water here was extremely calm with hardly noticeable waves reminiscent of those caused by boats in a lake. The sediment was very loose and easily kicked up such that walking through the water turned it from see-through to opaque in a matter of seconds. The seagrass began about ten to fifteen feet from shore and occurred in large patches extending horizontally. Most of the fish we saw and found stayed in and around this seagrass for the protection it offered and for the microbiota that grows on it.

The last estuary we visited was on the gulf side of Bahia Honda. Here the water was a little deeper and the seafloor almost entirely seagrass. The marine vegetation was the most diverse at this location with at least three types of seagrass and several species of alga. Where we were allowed to swim there were hardly any fish, likely due to the heavy amount of human traffic creating an unsuitable environment, however, there were some feather duster worms along the man-made jetty and two separate pods of a cetacean species (we could not determine if they were dolphin or porpoise) were seen crossing through the sound. The water here was pretty calm within the protected coves and a little rougher further out where the ocean currents coming around the island were affecting the water. The turbidity was typical of an estuarine system.

Estuaries are very important to the world’s ecosystems because they are nursery grounds for so many different species. Anthropogenic impacts on estuaries harm the entire food chain and affect many ecosystems beyond the estuary itself. One of the biggest anthropogenic impacts humans have is the destruction of seagrass beds. Though seagrass isn’t a food source for many organisms in an estuary, it is the only food source for animals such as manatees, dugongs, and green turtles is a home for animals such as sea horses and is very important in nutrient cycling. The destruction of seagrasses due to pandemic disease, boat propellers, coastal engineering, natural disasters, and global climate change has led to a permanent 29% loss of seagrass worldwide since 1879 which equates to nearly 51,000 square kilometers in 127 years (Calladine et al. 2007). If this continues, a great number of ecosystems will collapse and many species will go extinct. Restoration attempts have been underway since the mid-seventies but herbivores can hinder restoration progress by eating transplanted seagrasses before they have a chance to really establish themselves in their new environment (Bourque and Fourqurean 2013).

The conservation efforts to save the seagrass, in turn, help the conservation efforts aimed at saving manatees, dugongs, and green sea turtles from extinction. The two main factors of their endangerment are habitat destruction and direct injuries from boats/humans. Saving the seagrass helps mediate habitat destruction and spreading the word about how to avoid harming them with boats and other man-made devices has also helped. In fact, restoration efforts were successful enough that the West Indian Manatee has been reclassified from endangered to threatened (MacKenzie 2016). Maybe in time they won’t be in any danger at all.

Another anthropogenic impact on estuaries is river modification. As mentioned before, most estuaries occur where a freshwater river meets the ocean creating a mixed salinity region. As a result, any change in nutrients, sediments, or flow of the river due to man-made things or pollution will affect the make-up of the estuary. For example there is a large “dead zone” in the Gulf of Mexico on the Louisiana shelf where the water is hypoxic and covered in algal blooms. This region is a result of the Mississippi river becoming more nutrient rich and then emptying into the Gulf. Similar problems have been noted in the estuaries near the Nile river, the Yangtze river, and the Baltic sea. Additionally, droughts reduce freshwater inflow to the estuary and result in a rise in salinity, which can drastically alter biota ratios in the estuary. While droughts can be a result of natural weather patterns, man-made structures like dams and levies, can also cause river droughts that affect the estuary. Ironically, many conservation efforts made to improve health of the rivers upstream can cause irreversible damage to the ecosystems like estuaries downstream. Phytoplankton in estuaries relies on a certain level of nitrogen and phosphorous from the river to flourish. Too much or too little due to runoff or protection, alters this phytoplankton diversity and biomass (Booe 2017).

Currently most conservation efforts are being aimed at preserving the land and shape of estuaries by halting or reducing habitat destruction. As well as the loss of seagrass meadows mentioned above, dredging, mangrove clearing, and saltmarsh reclamation also impact estuarine landscapes causing detrimental effects to the organisms that live there. One way scientists would like to amend this is to make fine-detailed maps of all coastal waterways to create the landscape composition data needed to aid in the restoration and protection of terrestrial and aquatic species in and around estuaries. Currently coastline mapping and coral reef mapping are the most common and have been effective in habitat maintenance and research. In 2005, Cameron et al. suggested techniques for mapping estuaries with enough resolution and detail to be helpful to conservation scientists. Their method was sound and worked well and took about 35 days to map more than 48,000 hectares with a 0.774 accuracy (k=.695). Inaccurate mapping occurred from confusing sand/mud in the aerial photos and confusing type of vegetative cover (patchy or contiguous) from photos. The end result, however, is a thematic mapping technique that can be used by anyone in the field for research (Cameron et al. 2005).

Eutrophication and nutrification are two other common problems in estuaries. Eutrophication is the input of nutrients that cause light-blocking algal blooms. The lack of light hinders primary producers and causes a break down in the food chain. Nutrification is the input of nutrients that causes hypoxic or anoxic areas where toxic algal blooms flourish killing surrounding organisms.

According to NOAA, in the last hundred years, the world has lost millions of acres of estuaries. From 1996 to 2000, 13% of the estuaries worldwide went from “good” water quality to “poor” water quality. In 1972, Congress passed the National Estuarine Research Reserve System (NERRS), which protects and preserves more than one million acres of estuary within the United States. In 2000, the Estuary Restoration Act was passed in an attempt to rescue habitats that could not be properly protected. This act makes restoration of estuarine habitats a priority. The goal was to restore one million acres by 2010 (NOAA 2008). In 2010, the act was revised to reflect global changes in climate and sea level rise and boost effectiveness. The success of restoration, according to the revised act, relies on ecosystem approach, sustainable design, coordination and collaboration, innovative technology, and adaptive management and maintenance. They also laid out guidelines for monitoring data and tracking projects. The new action plan was published in 2013 and was set for a five-year goal (NOAA 2013). A new plan is expected within the next year or two.

Global climatic shifts are becoming more and more of a problem to marine habitats, especially estuaries. Climate change is driven by several factors including changes in sea level, changes in precipitation patterns which changes freshwater, nutrient, and sediment delivery to estuaries, rises in ocean temperature, changes in global currents, increased frequency and intensity of storms, and increased carbon dioxide levels in the atmosphere. These factors each affect the estuaries in a unique and alarming ways. The rise in sea level and the increase in storms pose a threat to estuary shorelines and sediment composition/levels. Changes in timing and amounts of freshwater, nutrients, and sediment delivery to the estuary as a result of changes in storms and sea level will affect estuarine productivity, which in turn will affect the productivity and diversity of other ecosystems. Meanwhile, rises in water temperature in combination with the change in freshwater delivery will change estuarine stratification and eutrophication, which will change residence time of species in the estuary. Rising temperatures are also expected to cause species to shift more poleward towards ocean temperatures more suited to their physiology, which will change the makeup of estuaries and other habitats globally. All of these climatic changes and variability effect and are effected by other negative ecosystem stresses, including anthropogenic impacts, such as pollution, harvesting, habitat destruction, invasive species, resource depletions, and natural disasters (Boesch 2002).

Subtropical estuaries are very important to the worldwide ecosystems because of their high productivity, high diversity, and their role in nutrient cycling. They are in great danger due to climate change, habitat destruction, and pollution but restoration and conservation efforts are underway to preserve these estuaries for generations to come.

Works Cited

ABP Marine Environmental Research (ABPmer). 2008. Understanding and managing change in estuaries. Estuary guide chapter 3. Department for Environment Food and Rural Affairs.

Blaber, Stephen J. M. 2000. Tropical Estuarine Fishes: Ecology, Exploration, and Conservation. Blackwell Science: Oxford. 1-4; 40-49.

Boesch, Donald F., Buddemeier, Robert W., Burkett, Virginia, Cayan, Daniel R., Field, John C., Fogarty, Michael, Harwell, Mark A., Howarth, Robert W., Mason, Curt, Reed, Denise J, Royer, Thomas C., Sallenger, Asbury H., Scavia, Donald, Titus, James G. 2002. Climate change impacts on U.S. coastal and marine ecosystems. Estuaries and Coasts. 25(2): 149-164.

Booe, Tyra, Davis, Stephen E., Dorado, Samuel, Lucchese, Allyson E.B., McInnes, Allison S., Pinckney, James L., Preischel, Hannah, Quigg, Antonietta, Roelke, Daniel L., Shepard, Alicia, Steichen, Jamie, Windham, Rachel. 2017. Towards an Understanding of the Interactions between Freshwater Inflows and Phytoplankton Communities in a Subtropical Estuary in the Gulf of Mexico. PLoS ONE. 10(7): e0130931

Bourque, Amanda S., Fourqurean, James W. 2013. Variability in herbivory in subtropical seagrass ecosystems and implications for seagrass transplanting. Journal of Experimental Marine Biology and Ecology. 445: 29-37

Calladine, Ainsley, Carruthers, Tim J.B., Dennison, William C., Duarte, Carlos M., Fourqurean, James W., Heck Jr., Kenneth L., Hughes, A. Randall, Kendrick, Gary A., Kenworthy, W. Judson, Olyarnik, Suzanne, Orth, Robert J., Short, Frederick T., Waycott, Michelle, Williams, Susan L. 2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. PNAS. 106(3):12377-12381.

Cameron, Bronwyn E., Loneragan, Neil R., Skilleter, Greg A., Zharikov, Yuri. 2005. Mapping and characterizing subtropical estuarine landscapes using aerial photography and GIS for potential application in wildlife conservation and management. Biological Conservation. 125(1):87-100.

Carlton, James T., Grosholz, Edwin D., Hines, Anson H., Ruiz, Gregory M. Global invasions of marine and estuarine habitats by non-indigenous species: mechanisms, extent, and consequences. American Zoology. 37: 621-632.

Chesapeake Bay Program. Learn the Issues. chesapeakbay.net Florida Museum. Threatened and Endangered Species. University of Florida. http://www.floridamuseum.ufl.edu/southflorida/habi...

Lores, Emile M., Murrell, Michael C. 2004. Phytoplankton and zooplankton seasonal dynamics in a subtropical estuary: importance of cyanobacteria. Journal of Plankton Research. 26(3): 371-382.

MacKenzie, Tom. 2016. U.S. Fish and Wildlife Service to Reclassify West Indian Manatee from Endangered to Threatened. Conserving the Nature of America. U.S. Fish and Wildlife Service. .

NOAA Ocean and Service Education. 2008. The future: managing, protecting, and restoring estuaries. U.S. Department of Commerce: National Oceanic and Atmospheric Administration. http://oceanservice.noaa.gov/education/kits/estuaries/estuaries11_future.html

NOAA. 2013. Estuary Restoration Act: Estuary Habitat Restoration Strategy. https://www.fws.gov/coastal/pdfs/EstuaryHabitatRes...

Powell, George V.N. 1987. Habitat use by wading birds in a subtropical estuary: implications of hydrography. The Auk. 104: 740-749.

Ward, Jennifer Rhode, Ward, Landon. 2017. Lecture Packet, Marine Biology. UNCA. 16-19.

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