Tag Archives: St. Joseph Bay


The Historical Database Known as Trees (and a new video)

Rob Diaz de Villegas WFSU-TV

IGOR chip- human appreciation 150I like the idea of hiking cross country, unimpeded, for miles at a time.  Trails are great- and usually safer- but the idea that you can have space to literally walk off the beaten path is appealing.  A couple of hundred years ago, you could travel across the entire southeastern coastal plain in this manner.  This was a road paved by fire.  On this blog, we’ve covered how fire creates the pine flatwoods ecosystem with its widely spaced trees, and how and why mankind has had to replicate a process that had happened naturally.  But how do we know how often to burn, and at what time of year?  It would be convenient if we could ask someone who was around before the area was settled.  As it turns out, we can.

Trees have the answers in their rings.  We get a glimpse of this towards the end of the video above, but I wanted to take a closer look at how Dr. Jean Huffman was able to interpret the data locked within trees.

The photo to the right is a detail of a longleaf pine stump cross-section.  In it you can see that the rings alternate in shading between light and dark.  The light wood is early wood.  This is from the beginning of the growing season, typically spring, when a tree usually grows the fastest.  The growth in the summer and fall is darker, and is called late wood.  Winter is the dormant season.  So one light and one dark ring equal one year of growth for the tree.  You may also notice that some rings are wider than others.  Wide rings indicate a higher rainfall, and especially narrow rings indicate drought.  Knowing this, we can start building a master chronology.

A master chronology is made by comparing the relative width of rings in a series of trees. In this way rings in each tree can be dated exactly, even if there are occasional missing rings or false rings in an individual tree. The master chronology can be used to exactly date the rings in individual stumps.  Since longleaf pine is such a long-lived species, there is potentially hundreds of years’ worth of climatological data in its rings.  When you have data for many trees, you can build a reliable chronology that goes back before people started keeping records.  This is a dendrochronology (dendro= tree, chronology= matching events to specific dates based on historical records).

fire scarFinally, you match years in your chronology to fire scars (that’s a scar to the left).  Longleaf pine are a fire resistant species, and it takes a lot to kill the cambium and create a scar.  Because of this, Jean only created fire histories for periods when she had at least three “recorder” trees- enough to establish a pattern.

She determined that there were frequent fires in the area- every one to three years.  That’s enough to keep oak and other woody plants from encroaching on ground cover plants, including the many rare plants of the SJB State Buffer Preserve.  It was strange to just trample over the grass and palmettos in the managed area, and all of the gems potentially hidden underneath them.  It doesn’t exactly adhere to the “Leave no Trace” ethos.  But the reality is that all of it will burn and go away, and then grow back again, and again, and again…

The video features music by Pitx and Airtone.  Thanks to Dr. Jean Huffman for reviewing my text for accuracy.
Next on EcoAdventures North Florida, we’re going to a place where large chunks of land get swallowed up by the earth, and where a river goes underground.  Of course we mean Aucilla Sinks (Wednesday April 11 at 7:30 PM/ ET on WFSU-TV’s dimensions).
The carnivorous chapman's butterwort is listed as a threatened plant.  Dr. Alvin Chapman, an 19th century Apalachicola botanist, discovered many of the plant species in the Buffer.

At the Buffer Preserve, Rare Plants Are “In the Grass”

Rob Diaz de Villegas WFSU-TV
dimensions, March 21 at 7:30 PM/ ET on WFSU-TV: our latest EcoAdventure explores the Buffer Preserve in search of rare plants and one woman’s quest to learn the fire history of the area.
Explore our map!  Click enlarge on a photo to read additional information about each plant.

IGOR chip- human appreciation 150I want to apologize in advance to anyone who watches tomorrow’s EcoAdventure on dimensions and gets excited about seeing the Chapman’s rhododendron.  Aside from naturally occurring in only three North Florida counties, its peek blooming only lasts about two weeks.  This peek usually starts at the end of March and goes into April, so we had planned on shooting then.  This year’s mild winter changed our plans.  A couple of weeks ago, at the beginning of March, Dr. Jean Huffman wrote to tell me that they had exploded.  In fact, the first bush we saw once we got out there was already starting to whither.  We did find a group of bushes in full bloom, and it was worth the hike.  By the time our footage airs, those flowers might very well be gone.

The carnivorous chapman's butterwort is listed as a threatened plant. Dr. Alvin Chapman, an 19th century Apalachicola botanist, discovered many of the plant species you can see in the Buffer.

That’s the bad news.  The good news is, many of the other rare flowering plants in the Saint Joseph Bay State Buffer Preserve will start blooming soon.  In a lot of ways, finding and photographing rare plants is as difficult as finding and photographing rare birds.  Especially when our seasons go screwy.  And unlike the Chapman’s rhododendron, many of the rare plants in the Buffer are hiding in tall grasses.  The Buffer is home to 21 rare plant species, and it’s the only place where the Chapman’s rhododendron is protected on public land (Correction: there is a small population at Camp Blanding, north of Gainesville).

I thought I’d share some photos of the plants we saw.  If you look at the map above, you can see an approximation of where we saw each of them.  You can see in the satellite image that the photos of the rare plants are located where the tree cover is lighter.  This goes back to, once again, controlled burning and its role in clearing out woody growth between longleaf pines.  When those shrubs get pushed back to where lightning-caused fire had once naturally confined them, grasses and herbaceous plants sprout up (and the animals that eat them return to the flatwoods).  If you’re in the Buffer, look for where the trees are spaced apart and grasses fill the ground.  It’s in those grasses that you’ll find some interesting characters.

I also included some photos of the bay section of the Preserve.  This is how I first encountered the Buffer, shooting salt marsh footage in conjunction with Randall Hughes’ research in SJB (click up in the Salt Marsh menu for more info on that).  There are plenty of birds, crabs, and predatory snails to see if you wade out into the sand flats and marshes by the visitor center.

Thanks to my production assistant, Alex Saunders, who brought his nice camera and took the plant photos in the map.

Dude, where’s my water?

Rob Diaz de Villegas WFSU-TV

IGOR chip- human appreciation 150

St. Joe Bay is really jumping in the summer. People are everywhere; scalloping, fishing, kayaking and snorkeling. The people are mostly gone in the autumn, as they head back to work and school, and the weather is a little cooler. With less people to scare them off, you see more blue crabs, stingrays, and sharks swimming closer to the shore. It’s my favorite time of year to get footage there. When winter rolls around, the only people out on the water either have to be because they’re working (like Randall and her crew), or they’re just hardcore ecowarriors. It can make for difficult paddling in the winter (though this December is much milder than last year, when we shot this footage).

Super-low tide in St. Joe Bay.

The difficulty doesn’t so much stem from the cold, though it can get cold (especially for a native Floridian who thinks Massachusetts beach water is too chilly in July). The real challenge is the wind and the tides. It makes for a surreal landscape.  It’s mostly devoid of living animals, at least on the surface, but that north wind does push some interesting seagrass bed denizens onto the marsh with the seagrass wrack.

As I noted earlier, it has been milder this year.  Hopefully that holds for our next few EcoAdventure shoots, which include trips down the Wacissa and St. Marks rivers.  And I’ve already started planning some of next year’s shoots as well, so stay tuned!

Dan and Debbie VanVleet, who we interviewed in the video, are the proprietors of Happy Ours Kayak and Canoe Outfitter.
The music in the video was by Bruce H. McCosar.

A long time in the making

Dr. Randall Hughes FSU Coastal & Marine Lab

IGOR chip- biodiversity 150

As I mentioned in my last update, we have been working to set up a new marsh experiment in St. Joe Bay. The goal of the experiment is to see whether the genetic diversity of marsh cordgrass (Spartina alterniflora) affects how quickly or abundantly the plants grow, or influences the number of fiddler crabs, grasshoppers, snails, and other critters (like Ibis??) that call the plants home. But what is genetic diversity, exactly, and why do we think it may be important?


A flock of Ibis resting among our experimental marsh plots.

Spartina is a clonal plant, which means that a single “individual” or clone made up of many stems can dominate a large area (low diversity), or there can be lots of different individuals mixed together (high diversity). In our surveys of marshes in the northern Gulf of Mexico, we find that there can be as few as 1 and as many as 10 clones in an area of marsh about the size of a hula-hoop. You may notice that our experimental plots are about that same size, though we used irrigation tubing rather than actual hula-hoops (not as fun, but more practical and less expensive!). We’re testing whether the differences in genetic diversity (1 vs. 10 clones) that we see in natural marshes has any influence on the marsh community.

A single experimental plot of Spartina that is 1m in diameter.

But why genetic diversity? We know from experiments by other researchers that Spartina clones grown individually differ in height, how many stems they have, and other characteristics. These same plant traits affect the critters that live in and among the plants – for example, periwinkle snails preferentially climb on the tallest plants. Because different animals may be looking for different plant traits, then having greater diversity (genetic and trait) may lead to a greater number of animal species that live in that patch of marsh. Or, a single clone may be the “best”, leading to higher numbers of animals in lower diversity areas.


A view of the existing marsh behind our experiment.

As my title alludes, this experiment has taken a long time to come to fruition, in large part because it’s impossible to look at any 2 stems in a marsh and know for certain whether they’re the same individual or not. Unlike some clonal plants such as strawberries, where there are multiple berries connected by a single above-ground “runner”, Spartina has runners (aka, rhizomes) that connect stems of the same genetic individual under the ground, making it difficult to tell which stems are connected to which. We have 2 ways to get around this problem: (1) we use small snippets of DNA (analyzed in the lab) to tell clones apart, and (2) we start with single stems that we know are different clones and then grow them separately in the greenhouse until we have lots of stems of each different clone. It’s this latter part that has delayed this experiment – it has taken much tender loving care from Robyn over the last 2 years to get our Spartina clones to grow in the greenhouse to the point that we have enough of each clone (36 small flowerpots of each, to be exact) to plant in our experiment.


Emily and Robyn work to remove existing rhizome material from around the plot edges.

But plant we finally did! With lots of help from members of the Hughes and Kimbro labs, we got all the sand in the experimental plots sieved (to remove any existing root material) and all the plants in the ground the Thursday and Friday before Thanksgiving.


Team Hug-bro (Hughes and Kimbro) helping sieve sand!



Meagan and Randall get the easy job - planting the plants.

Now we get to wait and see (and take data) whether Spartina genetic diversity matters for the marsh plant or animal community. There won’t be any quick answers – the experiment will run for at least 2 years – but we’ll be sure to keep you up-to-date!

Randall’s research is funded by the National Science Foundation.

Tricks or Treats? And more on the effects of predators in marshes.

Dr. David Kimbro FSU Coastal & Marine Lab

IGOR chip_ predators_NCE 150Unlike most of the experiments that I’ve conducted up to this point in my career, the oyster experiment from this past summer does not contain a lot of data that can be analyzed quickly.

For example, predator effects on the survivorship of oysters can be quickly determined by simply counting the number of living as well as dead oysters and then by analyzing how survivorship changes across our 3 experimental treatments (i.e., cages with oysters only; cages with mudcrabs and oysters; cages with predators, mudcrabs, and oysters).  But this simple type of data tells us an incomplete story, because we are also interested in whether predators affected oyster filtration behavior and whether these behavioral effects led to differences in oyster traits (e.g., muscle mass) and ultimately the oyster’s influence on sediment characteristics.  If you recall, oyster filter-feeding and waste excretion can sometimes create sediment conditions that promote the removal of excess nitrogen from the system (i.e., denitrification)


As we are currently learning, getting the latter type of data after the experiment involves multiple time-consuming and tedious steps such as measuring the length and weight of each oyster, shucking it, scooping out and weighing the muscle tissue, drying the muscle tissue for 48 hours, and re-weighing the muscle tissue (read more about this process here).

After repeating all of these steps for nearly 4,000 individual oysters, we can subtract the wet and dry tissue masses to assess whether oysters were generally:

(a) all shell…“Yikes! Lot’s of predators around so I’ll devote all of my energy into thickening my shell”

(b) all meat…“Smells relaxing here, so why bother thickening my shell”

(c) or a mix of the two.

For the next two months, I will resemble a kid with a full Halloween bag of candy who cannot wait to look inside his bag to see whether it’s full of tricks (nonsensical data) or some tasty treats (nice clean and interesting data patterns)!  I’ll happily share the answer with you as soon as we get all the data in order.

Because of this delay, let’s explore some new research of mine that examined how predators affect prey traits in local marshes and why it matters.


There are two main ingredients to this story:

(a) tides (high versus low) dictate how often and how long predators like blue crabs visit marshes to feast on tasty prey.

(b) prey are not hapless victims; like you and me, they will avoid risky situations.

attach.msc1In Spartina alterniflora systems, periwinkle snails (prey) munch on dead plant material (detritus) lying on the ground or fungus growing on the Spartina leaves that hover over the ground.  Actually, according to Dr. B. Silliman at the University of Florida, these snails farm fungus by slicing open the Spartina leaves, which are then colonized by a fungal infection.  If snails fungal farm too much, then the plant will eventually become stressed and die.

So, I wondered if the fear of predators might control the intensity of this fungal farming and plant damage.

For instance, when the tide floods the marsh, snails race (pretty darn fast for a snail!) up plants to avoid the influx of hungry predators such as the blue crab.

After thinking about this image for a while, I wondered whether water full of predator cues might enhance fungal farming by causing the snail to remain away from the risky ground even during low tide.  Eventually, the snail would get hungry and need to eat, right?  Hence, my hypothesis about enhanced fungal farming due to predator cues.   I also wondered how much of this dynamic might depend on the schedule of the tide.

Before delving into how I answered these questions, you are probably wondering whether this nuance really matters in such a complicated world.  Fair enough, and so did I.

Addressing this doubt, I looked all around our coastline for any confirmatory signs and found that Spartina was less productive and had a lot more snail-farming scars along shorelines subjected to a diurnal tidal schedule (12 hours flood and 12 hours ebb each day) when compared to shorelines subjected to a mixed semidiurnal schedule (2 low tides interspersed among 2 high tides that are each 6 hours).  Even cooler, this pattern occurred despite there being equal numbers of snails and predators along both shorelines; obviously density or consumption effects are not driving this pattern.


Ok, with this observation, I felt more confident in carrying out a pretty crazy laboratory experiment to see if my hypothesis might provide an explanation.


Enter Bobby Henderson.  This skilled wizard constructed a system that allowed me to manipulate tides within tanks and therefore mimic natural marsh systems; well, at least more so than does a system of buckets that ignore the tides.


Within each row of tide (blue or red), I randomly assigned each tank a particular predator treatment.  These treatments allowed me to dictate not only whether predators were present but whether they could consume & frighten snails versus just frightening them:

-Spartina only

-Spartina and snails

-Spartina, snails, and crown conch (predator)

-Spartina, snails, blue crab (predator)

-Spartina, snails, crown conch and blue crab (multiple predators)

-Spartina, snails, cue of crown conch (non-lethal predator)

-Spartina, snails, cue of blue crab (non-lethal predator)

-Spartina, snails, cues of crown conch and blue crab (non-lethal multiple predators)

attach.msc6After a few weeks, I found out the following:

(1) Predators caused snails to ascend Spartina regardless of tide and predator identity.  In other words, any predator cue and tide did the job in terms of scaring the dickens out of snails.

(2) Regardless of tide, blue crabs ate a lot more snails than did the slow moving crown conch and together they ate even more.  This ain’t rocket science!

(3) In this refuge from the predators, snails in the diurnal tide wacked away at the marsh while snails in the mixed tide had no effect on the marsh.


Whoa…the tidal schedule totally dictated whether predator cues indirectly benefitted or harmed Spartina through their direct effects on snail predator-avoidance and farming behavior.  And, this matches the observations in nature… pretty cool story about how the same assemblage of predator and prey can dance to a different tune when put in a slightly different environment.  This study will soon be published in the journal Ecology.  But until its publication, you can check out a more formal summary of this study here.

If this sort of thing happens just along a relatively small portion of our coastline, I can’t wait to see what comes of our data from the oyster experiment, which was conducted over 1,000 km.

Till next time,


David’s research is funded by the National Science Foundation.