Learn Marine Ecology: My Narrated PowerPoint Lectures

Due to the COVID-19 pandemic this spring I had to switch from conventional teaching to "online instruction" halfway through the semester at Florida Gulf Coast University. Online instruction is not as efficient, effective, or fun as conventional teaching, but it IS better than nothing. One bonus of producing recorded teaching materials is that I can make them available for free to interested members of the public. I have done this with the lectures for my Marine Ecology course "OCB4633C." This is a required course in the BS Marine Science program at colleges in the Florida State University system. I recorded the lectures by doing "voice overs" of my existing PowerPoint slideshow presentations, then converting the presentations to video and uploading them to YouTube. The voice over recording function in powerpoint also lets you use a "laser pointer" or "pen" tool to scribble on the slides as you talk, so I did a lot of that.

These presentations are not National Geographic quality, and some of them move a little slowly with an inordinate amount of "ums" and "ok, so"s. Also, they don't cover the entire semester's curriculum because I only started making them when the semester was half over. Furthermore, I did my coral reefs lecture early and out of order this year, so I've substituted another scientist's coral reef lecture video into that spot. If we're still locked down in the fall I'll record and post the rest of my lectures including my own take on coral reef ecology. Anyway, with those disclaimers done, here are the videos, in the order that I would normally present these topics to the students. Please let me know if you have any questions or comments, if you note mistakes or unclear segments, etc.


Estuaries


Seagrass, Saltmarsh, and Mangrove Ecosystems


Coral Reef Ecosystems (NOT MY LECTURE- This is distinguished professor Nancy Knowlton from UCSD)


Deep Sea Ecology


Foodwebs, Biodiversity, and Ecosystem Functions (this one is long with a lot of theory; casual watchers may want to skip or save for last)


Fisheries Ecology


Aquaculture (aka Fish Farming)


Disturbance Ecology


Pollution and Climate Change

Snorkeling spots in Lee County, Florida (Bonita Springs, etc.)

Snorkeling Estero Bay from the East side of the road at Bonita Beach Dog Park.


Folks who know I'm a marine biologist often ask me if I can recommend any good, nearby snorkeling spots. (Within the Naples / Bonita Springs / Estero / Fort Myers / Sanibel area.) The answer is YES I CAN- SORT OF.

The thing is, this part of Florida doesn't have any near-shore coral reefs, and the waters are often dark and murky from a combination of natural and man-made factors like stirred-up mud, tannins, and blooms of microscopic algae that feed off the high levels of nutrients in the water. So even where there IS cool underwater life to see, you often can't see it very well because of the poor water clarity. Having given those disclaimers to set expectations appropriately low, I have had some good snorkeling experiences around here, and I'll tell you where your best bets are to have some good experiences yourself.

General recommendations-

1. Best times are weekday mornings before there is much boat traffic to stir up the water. Boats can also run over you and chop you into little giblets of meat with their propellers. So you should bring a dive flag if you're going in an area that potentially has powerboats.

2. Best times are when it hasn't been too windy / wavy, because wind makes waves and waves stir up mud from the bottom that reduces the visibility. Winds less than 10 knots are usually OK. That said, you can get away with snorkeling when it's windier if the winds are OFFSHORE WINDS. That means winds blowing from the land out to sea. These will not make waves along the shoreline, so they won't stir up the water.

3. Tide (level and whether it's coming in or going out) matters. Particularly when you're near the mouth of the estuary, where there's a changing mix of fresher estuary water and saltier ocean water, you may get the best water clarity when the tide is coming in, bringing the more clear water from offshore in the Gulf of Mexico. However, if there have recently been a lot of waves in the Gulf of Mexico from West winds, the incoming tide won't help and it could actually be more clear further back into the estuary. Tide can also matter because some sites may be too shallow at low tide or too deep at high tide.

Specific sites-

Estero Bay- Estero Bay is a shallow, semi-enclosed body of water where fresh and salt water mix. It has some interesting sea bottom habitats including beds of seagrass and seaweed that often have snails, fish, sea urchins, anemones, crabs, and other organisms living in them. The trick is to find a seagrass bed accessible from shore, in an area where the water isn't too murky. I have had some luck going from the east side of the road at Bonita Beach Dog Park on Lovers Key.There's a shallow area with seagrass, and a deeper channel as you go south towards the New Pass bridge that has some oysters and other shells and often has interesting crabs, urchins, and fish like Mangrove Snappers and Sheepshead.

A sand perch hanging out by a clump of oyster shells in the deeper channel part.




Another site at Estero Bay that sometimes works is the Big Carlos Pass beach access at the north end of Lovers Key. Big Carlos Pass is the biggest opening from Estero Bay into the Gulf of Mexico, and it sometimes has pretty clear water on an incoming tide. The bottom there is shelly, and there are some big pieces of rubble further out, like concrete pipes, that are covered with sponges, seaweed, and sometimes soft corals. Underneath the Big Carlos Pass bridge, around the pilings, there are piles of concrete blocks that often have reef fishes swimming around them. Just watch out for fishing lines and boats.



The ocean side of Lovers Key can also work for brave snorkelers if the tide is slack or outgoing and there are no waves. Near the entrance to Big Carlos Pass there is kind of a deep channel between shore and an offshore sandbar, and the sand is scoured away from the bottom there revealing rocks with urchins, seaweed, and sometimes big fish. You can swim really far out from shore and still in be in shallow water over the shifting sandbars. Watch out for boats, though.



San Carlos Bay- San Carlos Bay is the crossroads of several estuaries in the more northern part of Lee County. It's where the Caloosahatchee Estuary meets Matlacha Pass and Pine Island Sound. The toll bridge to Sanibel Island (the Sanibel Causeway) crosses San Carlos Bay and includes two man-made islands where you can pull off and park to snorkel or windsurf or picnic or whatever. Look at the area on Google Earth and pick a spot where you see dark, mottled patches near shore. Those are seagrass and seaweed beds with a mixed shelly / sandy bottom. Depending on which direction the wind is coming from, different sides of the different causeway islands may offer the best shelter from the wind and waves and the most clear water.



If you want to snorkel in a similar environment but don't want to pay the $7 toll for the Sanibel Causeway, you can pull off on the side of the road just before the causeway at San Carlos Bay beach.



Another interesting spot is Bunche Beach, which has a mix of seagrass, seaweed, sand, rock/shell and invertebrates like sponges.



Good luck exploring, and if you make any great snorkeling discoveries, please share them in the comments.

Hydrofoil flyby of buddy's OC1 canoe

My friend Matt is a good artist, and tech wizard who gets lots of cool water shots. The other day he caught this clip of us horsing around off Bonita Beach, FL.



If you want to see more of Matt's artistry, check out his ceramics studio webpage.

Hydrofoil Windsurf Session with Lots of Jibes

I'm getting better at jibing my hydrofoil windsurf without touching the water. SO FUN!

CERF Report 2019

I just got back from five days at the 2019 Coastal and Estuarine Research Federation (CERF) conference in Mobile, Alabama. https://www.cerf.science/cerf-2019

View of Mobile Bay from the hotel room

Fancy boat outside the Mobile convention center

Statistics workshop with collaborators after the meeting

I’ve gone to science conferences like this once or twice per year since the early 2000s when I was a graduate student at the Virginia Institute of Marine Science https://www.vims.edu. Conferences are a place to present your research with a poster or a talk, and to absorb and exchange ideas from others’ research. My usual conference is the Benthic Ecology Meeting (BEM https://www.bemsociety.org/), which is a get-together of marine biologists who specialize in sea-bottom life like seagrasses, corals, and shellfish. This was actually the first time I’ve been to a CERF meeting.

CERF overlaps a lot with BEM in terms of topics and attendees, with a couple of distinctions:

1. CERF includes more of what’s happening on land; in the “watersheds” that funnel freshwater and pollution into the ocean, and along the coastlines where marine and terrestrial ecosystems interact.
2. CERF has more focus on “applied research” as opposed to “basic research.” I.e., there is more focus on trying to understand and solve particular environmental problems.

My early-career research addressed a lot of basic issues like how grazers and predators, and biodiversity, per se, affect ecosystem processes. I’m still interested in those general topics, but my research since joining the faculty at Florida Gulf Coast University has been more “applied,” addressing particular environmental problems affecting seagrass beds and water quality in Southwest Florida. Going to this CERF conference, and schmoozing with other practitioners of both basic and applied research, was very helpful in inspiring me and giving me useful research ideas. I’ll briefly review some memorable things I picked up from the conference.

1. Genetic diversity within a single species can be very important, especially in seagrasses. In 2004, A. Randall Hughes et al. published a highly-influential paper showing that there were many different genetic strains within the eelgrass species (Zostera marina) in California. Hughes also showed that a genetically-mixed patch of eelgrass could resist and recover from environmental disturbances (like goose grazing) significantly better, than any one genetic strain alone. Fifteen years later, Hughes’ legacy was apparent at CERF in the numerous presentations on within-species genetic diversity effects in seagrass beds from all over the world.
2. “Living shorelines” are a growing, green revolution, even though most people don’t know what they are. Sea level rise, subsidence, and erosion are eating away at the coasts of the world, threatening both natural habitats and man-made coastal developments. The old way of dealing with this was by heavy-handed “coastal armoring” (seawalls, jetties, dikes, etc.), which tended to be expensive, bad for the environment, and prone to failure. The living shorelines approach uses natural protective elements like oyster reefs, mangroves, and saltmarsh grasses, in combination with man-made structural elements, to protect coasts in more natural, self-sustaining, and environmentally-beneficial ways. I saw talks showing how various living shoreline projects had reversed erosion, helped absorb nutrient pollution and carbon dioxide pollution, and created naturally-expanding habitats for birds, fish, and shellfish. Southwest Florida has hundreds of kilometers of eroding or unnaturally-armored canals and coasts that are prime candidates for living shoreline projects.
3. The global trend of seagrass decline from the mid 20^th century until now may have finally hit bottom and turned around into a recovery phase. However, this optimistic forecast is driven by a few, positive cases of recovery. Seagrasses continue to decline in many areas. Water quality seems to be a key factor differentiating the happy seagrass stories from the tragedies. Where water quality is naturally good, and/or there have been concerted efforts to improve water quality, seagrasses have spread and algae blooms have decreased. However, where pollution oversight has been lax, repeated harmful algal blooms and other water quality issues have devastated seagrass beds. Below is a rank of several important seagrass ecosystems in the eastern United States from most exciting recovery to most tragic decline in recent decades.
1. Virginia Coastal Bays- Exciting recovery! The shallow estuaries on the sparsely populated eastern side of the Delmarva peninsula are an ideal place for seagrass, with relatively little pollution. However, they lost all their seagrass in the 1930s due to a combination of hurricanes and disease, and they just had bare mud bottoms from then until the 1990s. It was hypothesized that “recruitment limitation” (a lack of seed supply) was the reason for the lack of natural recovery in the area. This hypothesis was tested in the late 1990s when Dr. Robert Orth’s group of VIMS scientists replanted some seagrass in one of the bays. To their joy, the seagrass rapidly expanded. Subsequent re-seeding efforts were even more successful. 20 years later, as Orth is retiring, he can be proud to have helped restore thousands of acres of seagrass, enhancing fish and waterfowl populations, improving water clarity, and furnishing the other wonderful “ecosystem services” that come with healthy seagrass beds.
2. Tampa Bay and Boston Harbor- Hard-Won Victories. In the late 20^th century, population growth in the Tampa Bay watershed led to severe nutrient pollution from wastewater and stormwater runoff. The nutrient pollution caused “eutrophication” – a chronic overgrowth of algae in the water and on the bottom. In these dark and murky waters, seagrasses perished for lack of light. Managers in the region got serious about upgrading wastewater treatment plants and stormwater infrastructure, and implementing stricter regulations on the sale and use of fertilizer. They started a multitude of projects, large and small, to reduce nutrient inputs. As one of their benchmarks for success they aimed to return seagrass beds to 1950s levels. Sure enough, nutrient levels in the water declined, which caused algae levels in the water to decline, which made the water clear enough for seagrass beds to rapidly expand. Tampa Bay recently surpassed the 1950s-based goal, and now has some of the clearest and fishiest water in generational memory. Another seagrass area in the USA that has a big urban population but has nevertheless made good progress in seagrass restoration is the Boston Harbor area. They made billion dollar investments in upgraded sewage treatment infrastructure, which translated into clearer harbor waters, regrowth of seagrass, and an invigorated city waterfront economy.
3. Chesapeake Bay- Finally turning the corner? Chesapeake Bay is a huge estuary spanning multiple states, with a watershed area that extends into even more states. The watershed includes many, heavily populated areas, as well as many areas of intensive agriculture, which makes reducing pollution to the bay a huge organizational challenge. The federally-funded Chesapeake Bay Program has been tracking bay health and implementing nutrient-reduction and habitat restoration projects in the area for years. There have been some ups and downs, with climate variation (extreme wet and dry, hot and cold years, etc.) often throwing a wrench in the works. But now, finally, it seems that a signal of recovery is emerging through the noise. Seagrasses in the bay are doing a bit better, though they still have a way to go before they meet the restoration goal. It’s time to seize that momentum and double down on restoration to make sure the positive trend continues and stabilizes. One encouraging thing to think about is the developing synergy between different types of habitat restoration effort in the bay. For example, restoring oyster beds along shorelines and channels in the bay increases the bay’s filter feeding capacity, which improves water clarity and can indirectly benefit seagrasses.
4. Florida Bay- Still Dicey. Florida Bay is the shallow expanse of water between the Everglades and the Florida Keys. It has relatively little nutrient pollution because of its unpopulated surroundings and the fact that most of the freshwater that enters it has been filtered through the extensive wetlands of the Everglades. The seagrass beds in Florida Bay are some of the largest in the world. However, Florida Bay periodically suffers from massive seagrass dieoffs related to hypersalinity (excessive saltiness). These hypersalinity events are worse now that much of the freshwater flow of the Everglades has been diverted for human uses. After a seagrass dieoff in Florida Bay there are after-shocks that can lead to more seagrass dieoffs. For example, dead and rotting seagrass releases nutrients into the water that fuel dense algal blooms. Furthermore, the lack of seagrass allows mud to be stirred up from the bottom by wind waves. The resultant plumes of dark, murky water kill more seagrass and other sea-bottom life, such as sponges, which are important filter feeders and habitat-providers. Everglades restoration projects are supposed to eventually deliver more freshwater to Florida Bay and reduce the hypersalinity events. Unfortunately, restoration progress is slow, and held up by contentious debates about things like how low the nutrient levels in the freshwater must be to prevent damage to the Everglades and the Bay. In the meantime, Florida Bay seagrasses die whenever there is a drought exacerbated by the unnaturally low freshwater flow.
5. Southwest Florida (Lee and Collier County)- Missing the recovery train. At the CERF meeting there was an ironic juxtaposition between my gloomy talk about “collapsing” ecosystems in SW Florida, and the talk that immediately followed mine, which was a sunny one about “recovering” ecosystems in SW Florida. Really we were both right; we were just talking about different parts of SW Florida. The other guy was talking about the northerly part of SW Florida that includes Tampa Bay but not Lee and Collier County, and I was talking about the southerly part of SW Florida that includes Lee and Collier County but not Tampa Bay. Anyway, seagrasses in my study areas are dying due to a combination of water quantity issues and water quality issues. The water quantity issues are well-known and related to artificial discharges from Lake Okeechobee to the Caloosahatchee River, which did not historically connect to the Lake. High discharges make the water of the Caloosahatchee Estuary and other connected estuaries too fresh for most seagrasses to survive, and also deliver dark, tannic waters, high nutrients, and sometimes harmful algae blooms to the estuaries and Gulf of Mexico. However, at other times the Caloosahatchee River flow is withheld for human uses and saltwater creeps abnormally far upstream, killing freshwater plants. While we have been obsessed with our bipolar water quantity problem and its complex solutions (which involve expensive changes to clean Okeechobee water and send more of it south into the Everglades again), we have been developing an equally serious water QUALITY problem that is more local in origin. I.e., sprawling development related to the ballooning population of SW Florida, in combination with weak regulations on both urban and agricultural nutrient sources, have led to rampant eutrophication of SW Florida’s estuaries. Our water is becoming too murky for seagrasses to grow, even at shallow depths, and gunky seaweeds are taking over formerly seagrassy places like Estero Bay. Furthermore, we have become the epicenter of a variety of recurring harmful algae blooms, some of them very dangerous to humans and other animals, and all of them related at least in part to our nutrient pollution. I asked one of the Tampa Bay restoration scientists what folks in “true SW Florida” could do to emulate Tampa Bay’s story of improving water quality and seagrass. He said, simply, “Start doing projects.” I think that’s excellent advice. It’s going to take lots of small and large nutrient-reduction projects to fix our water quality problem, so let’s start now and try to build momentum. While we’re doing little restoration things in our yards and communities, we can ask our leaders for big sewage system upgrades to “tertiary treatment with coupled nitrification-denitrification,” which removes most of the harmful nutrients and is what Tampa has, for the most part.
6. Indian River Lagoon- Paradise Lost. There’s one major seagrass system in Florida that is doing even worse than SW Florida, and that is the Indian River Lagoon (IRL)- a long, narrow estuary that runs parallel to the coast from Palm Beach to Cape Canaveral. The IRL is significant as the most biologically diverse estuary in the United States, because it spans from the temperate zone to the tropics and has a blend of species from both zones. A lot of those species depend directly or indirectly on the seven species of seagrasses found in the IRL. Up until 2011 the seagrasses and water clarity were slowly declining as a result of nutrient loading from human population growth in the areas around the IRL, combined with water quantity and salinity problems related to various canal systems and water diversions. But in 2011 the shit really hit the fan with a so-called “superbloom” of phytoplankton. The plankton darkened the waters and wiped out a majority of the IRL’s seagrass beds. Since then there have been all kinds of other nasty phytoplankton blooms alternating with nasty seaweed blooms, fish kills related to low oxygen, and even a super duper bloom in 2016 that was bigger than the original super bloom. It’s going to take a lot of nutrient reduction work, including septic to sewer conversions, new regulations on agriculture and suburban fertilizer use, wetland restoration, and other projects to restore the IRL. Needless to say, stricter limits on growth and sprawl are also desperately needed in the IRL watershed, as they are in SW Florida’s watersheds.  PS- Another Florida East Coast estuary that I’ll lump in with the IRL is Biscayne Bay, the high salinity estuary off of South Miami. It recently lost almost all its seagrasses as the culmination of decades of chronic nutrient loading and declining water quality. To preserve delicate ecosystems like seagrasses and reefs next door to a heavily populated area takes a serious investment in nutrient reduction infrastructure and regulation. Boston and Tampa did it fairly well, but SW Florida and SE Florida have dragged their feet to dire effect.
4. Climate change effects are showing up all over the place. A lot of research was presented on climate change impacts such as warming, sea level rise, and species range shifts. One of the sea level rise impacts examined was the shift of coastal forests to saltmarshes as saline water inundates roots. There were also tons of studies of the expansion of the black mangrove (Avicennia germinans) northward into former saltmarsh habitats. If the trend continues mangroves will eventually replace most of the saltmarshes along the Gulf of Mexico coastline. Seagrasses are also undergoing species range shifts. For example, in North Carolina where the temperate seagrass Zostera marina is at the southern end of its range and the tropical seagrass Halodule wrightii is at the northern end of its range, the ratio of the two coexisting species is shifting in favor of the tropical one. My own research colleagues presented data from turtlegrass (Thalassia testudinum) beds from Panama to Bermuda, which suggested that the intensity of grazing by tropical grazers is increasing in some areas, possibly due to warming.
5. Academia is a mixed bag. This is something I got from talking to a lot people I hadn’t seen since graduate school. Some were happy with their current lot, others were very frustrated. It seems that academic institutional cultures and pressures vary a lot from place to place. Some of my peers are flourishing in professional and supportive environments, while others are changing jobs in angst or leaving academia entirely due to shitty work environments. One of the stresses that some institutions seem to handle better than others is the teaching – research tradeoff. Expecting faculty to do a lot of both doesn’t seem to work well, and institutions transitioning from more teaching oriented to more research oriented sometimes jerk their faculty back and forth a lot through this process. I realized I’m pretty lucky to have landed at FGCU, where the teaching-research balance suits me pretty well.

Red tide house of horrors in SW Florida, Halloween 2019

Last year we had an unprecedentedly bad run of harmful algae blooms in Florida, fueled by rampant nutrient pollution. (See my July 2018 post.) The most widespread of those HABs was a nightmarish Karenia brevis bloom that that affected every shore of the Florida peninsula but was worst in my area, Southwest Florida. After killing scores of dolphins, sea turtles, birds, and manatees, and literally tons of fish and invertebrates, the bloom finally dissipated over the winter. Following that, we had a relatively dry 2019, and a less than usual amount of regulated discharge from Lake Okeechobee to SW Florida's Caloosahatchee River. Folks crossed their fingers that the algae nightmare was gone. But marine biologists and other careful observers knew that nutrient pollution was still flooding into our waterways in the form of poorly managed agriculture, chemical-soaked urban/suburban landscapes, badly maintained stormwater ponds, overloaded sewage and septic systems, etc.

Though the coastal waters looked fairly clear for much of the spring and summer, if you stuck your head under the water you'd see the signs of trouble. The bottom was covered in piles of macroalgae (seaweed) and stringy billows of filamentous cyanobacteria. These bottom-dwelling algae were feasting on nutrients released from decaying organic matter, submarine groundwater discharge, and other sources. The thing about nutrients is that they never really go away- they just cycle through different forms as they slowly move through the environment. If the cycle is in balance, fine. But when we keep adding extra nutrients to the cycle, the excess grows cumulatively, year on year, and the harmful algae blooms grow stronger with each return. The only solution is major reduction in man-made nutrient loading (much less fertilizer, much better sewage treatment, etc.), combined with major increase in nutrient removal (through the protection and enhancement of vegetated habitats like wetlands that absorb nutrients and take them out of circulation).

The sadness of our recurring red tide situation was emphasized to me today by what I saw, smelled, and felt when doing fieldwork for an oyster restoration project in Naples Bay. Red tide concentrations were high enough in the bay to be clearly visible as a maroon haze in the water, and dead fish were floating belly-up everywhere. (High concentrations were also measured quantitatively in the area, as indicated on https://myfwc.com/research/redtide/statewide/) Yet, at the Naples City Dock marina there were no warning signs or anything posted, and patrons at "The Dock" restaurant were dining inches from the dead fish and toxic algae, apparently completely in the dark about its health risks. I didn't have much choice about getting in the water because it's my job as a marine biologist, but it seemed absurd to me that people would be paying to put themselves in that environment.



The immediate symptoms of exposure to red tide toxins are obvious. Exposure to the aerosolized toxins (e.g., from boat wakes or breaking waves) causes coughing, burning eyes, headaches, etc. Exposure to higher concentrations of toxins through contaminated seafood is worse, resulting in neurotoxic shellfish poisoning. However, what troubles me more is the less-known long term effects of red tide toxin exposure. Last year after the big blooms I got the longest-lasting and worst cough/bronchitis I've ever had. I would wake up in the middle of night every night with terrifying, suffocating coughing fits. I'm not just a crybaby hypochondriac who makes shit like this up, either. This really happened to me. Also, just about everybody I know who was around the water a lot last year had similar respiratory complaints. So I'm inclined to think that red tide exposure is a lot more dangerous than our state's cavalier attitude about posting warning signs and such leads residents and tourists to believe.

PS- Some particular actions that would reduce harmful algae blooms in Naples Bay, and which we should strongly lobby our leaders to take, are:
1) stricter and better-enforced fertilizer rules for both agriculture and urban/suburban environments,
2) better management of the canals and stormwater ponds that feed into Naples Bay; i.e., stop killing the beneficial wetland plants with mowing and poisoning,
3) pony up the cash for septic to sewer conversions and upgrade the capacity and treatment level of wastewater plants,
4) moratorium on new development in wetland and shoreline areas,
5) reintroduce "living shoreline" elements like mangroves and oysters along developed waterfronts to filter nutrients and algae out of the water,
6) re-route the drainage expansions that increased the watershed area of Naples Bay from 10 sq miles to 130 sq miles so that it's not overloaded with more freshwater and pollution than the ecosystem can handle.

Just a picture of a guy windfoiling

The other day my photographer buddy Greg and I were doing wind-powered hydrofoil things in Estero Bay and Greg took this good picture with his GoPro camera. It's me with a 4.7 sail on an old Exocet formula board equipped with a Slingshot Hoverglide FWind1 with 76 cm Infinity wing. The wind is in the 10-15 knots range.



Greg took the picture while balancing on his tiny 6'6" SUP board with a GoFoil Maliko 280 hydrofoil, which he has been riding with a 5.0 Duotone handheld wing. Greg is rapidly improving on that setup, which I can testify is not that easy to use- especially not in light, shifty, or gusty wind, where the self-supporting stability and precise control of a windsurf sail is nice to have.