All posts by Randall

About Randall

Dr. Randall Hughes is an ecologist and marine biologist focusing on the causes and consequences of species and genetic diversity in coastal systems. She has conducted experimental work on plants and animals in seagrasses, salt marshes, oyster reefs, and kelp forests. The common thread throughout these activities is a long-standing interest in generating information that can enhance the effectiveness of conservation and management decisions.

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.

The making of an experiment

Dr. Randall Hughes FSU Coastal & Marine Lab

“Wow, quite the set-up! I am jealous of that space!

“…As a side question, how did you pump the cue water to all your tubs, a peristaltic pump? Was it just gravity? Seems like quite the complicated set-up.”

Excerpts from a comment on Randall’s September 28th post, Scared Hungry.  Read the whole comment here.

IGOR chip- employment 150This recent comment by John Carroll made me realize that there are a lot of unsung heroes at the lab that don’t typically get credit for the essential work that they do to facilitate our research. So here is a ‘behind-the-scenes’ look at setting up an experiment:

1. The idea. This is the main part that I can take credit for, though even then an idea usually stems not simply from my brain, but from a paper I’ve read, a conversation with a colleague or student, or an observation in the field.

2. The infrastructure. Each experiment has its own specifics, but in my research there are generally 3 main requirements:


The "small" deck, used by David and me for mesocosm experiments with snails, crabs, plants, oysters - you name it!

a. Space. FSUCML has numerous tanks and related facilities for use in research (Visit the Lab site here.). Of course, I often have specific needs or desires, and thus my first step is usually to speak to Mary Balthrop, our Associate Director, and then to Dennis Tinsley, our Facilities Manager. Both Mary and Dennis show a great deal of good humor in receiving my seemingly hair-brained requests (e.g., a deck that can hold 16 plastic kiddie pools full of sand and water!), and they work with me to find (or devise) a suitable space to get the job done. Our incredible carpenter, Dan Overlin, then has the task of modifying or creating that space.


The newer "large" deck, obscuring the view of the small deck closer to the water's edge


Another view of the small deck, with the large seawater tanks in the background. (Photo credit: Nancy Smith)

b. Seawater. Since we work with marine critters, access to seawater is critical. FSUCML pumps seawater from the bay in front of the lab into large holding tanks that feed the entire facility.

Mark Daniels and Bobby Henderson then create the plumbing system that gets that water where it needs to go. They know everything there is to know about PVC pipes, water filters, pumps – you name it! As I mentioned in my response to John, it was Bobby who came up with the incredible pump apparatus (and several subsequent revisions) that has enabled us to conduct several experiments examining the effects of predator cues on prey behavior.


Robyn and Emily working to set up a recent experiment on the large deck. Although the plants love all the light, we decided to erect a tent as a refuge from the sun/heat.

c. Light. When working with plants, light is key. I’m fortunate to have access to a greenhouse, as well as abundant outdoor space at the lab to set up experiments. Or perhaps I should say once-abundant outdoor space, since David and my decks now cover a good chunk of it! Dennis is a pro at thinking of suitable and available spaces to squeeze in a few tanks.

Robyn and Emily releasing grasshoppers into one of our cages. (Photo credit: Nancy Smith)

3. The supplies. Once the infrastructure is in place, it’s time to buy the supplies needed to make each experimental unit. The job then falls to Kathy Houck and Maranda Marxsen to explain to the accountants at FSU why I purchased several large bolts of tulle fabric (grasshopper cages), or 24 pair of knee-high panty hose (they make great filters when filled with gravel), or lots and lots of nail polish (for marking snails). For field experiments, Sharon Thoman is helpful in arranging vehicles and boat reservations, sometimes at the very last minute!


Robyn and Liz cheerfully using nail polish to mark snails



A thundercloud looms in the distance. Once this summer we were stranded in a storm and Dan came to retrieve us.

4. Set-up. Once things start to come together, there are inevitable surprises the crop up. In our recent predator-prey experiments, we had issues with flow from the pump being greater than that from the regular seawater lines, which required some brain-storming from Bobby, David, Kelly, Meagan, and myself. Or, a plumbing line will clog, and I’ll run to find Mark.  Or, we’ll get stranded in a thunderstorm while collecting mud crabs and Dan will come pick us up.   At least we often provide fodder for funny stories!

5. The experiment. And at last, the actual experiment can begin. When I come up with particularly high-maintenance experiments, it’s useful to utilize the lab dorms for the night. Linda Messer is always understanding of last minute housing requests and changes, making sure the lights (and, more importantly, the A/C) are on! Sometimes, the experiment itself is much shorter than the time required to set it up – duration never seems to equate with complexity. But one of the benefits of consulting with the staff is to ensure that the same space can be used for multiple purposes. And the second experiment is always easier to set up than the first!

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

Scared hungry?

Dr. Randall Hughes FSU Coastal & Marine Lab

A hardhead catfish, one of a mud crab's primary predators on North Florida oyster reefs.

IGOR chip_ predators_NCE 150As David has mentioned previously, predators can affect their prey by eating them (a very large effect to the prey individual concerned!) or by changing their behavior. And exactly how the prey change their behavior can have large consequences for the things that they eat. For instance, if you’re out camping and hear a bear lumbering around, do you quickly pack up all your food and put it out of reach of the bear and yourself? Or do you quickly eat as much as you can?

This summer we worked with Kelly, an undergraduate from Bridgewater College, to document how mud crabs deal with this dilemma of getting enough to eat but not getting eaten themselves.


Kelly with the broken down truck on an ill-fated return trip from St. Augustine.

Specifically, we wanted to know how they respond to the presence or absence of catfish, and how this response affects the survival of juvenile oysters. Sounds straightforward, right? Well, yes, in concept, but as Kelly quickly discovered, putting that “on paper” concept into reality at the lab took a lot of time and effort!


First, she had to get the “mesocosms” (aka large tubs) ready to serve as adequate habitat for the crabs, with plenty of sand and dead oyster shell for them to hide in.


Next, Kelly took individual juvenile oysters, or “spat”, and used a marine adhesive to attach them to small tiles that we could distribute among all of the mesocosms.


Juvenile oysters attached with Zspar (a marine adhesive) to a tile so we could assess mud crab predation.


You may have noticed that I mentioned catfish, and that these mesocosms are not particularly large relative to the size of a catfish. Never fear – because we wanted to separate the effects of catfish cues from the effects of catfish actually eating mudcrabs, the catfish were kept in a much larger tank, and then water from this tank was pumped into the mesocosms receiving catfish cues. (Setting up the pump and tubing to 60+ tanks was a several-day effort in itself!)


The catfish tank, with tubing carrying catfish "cues" to individual mesocosms.

Once everything was in place, it was time to collect the mud crabs. We couldn’t collect the crabs gradually, because they like to eat each other when confined in small spaces in the lab, so we garnered as much help as we could and held our own little mud crab rodeo. (And got caught in quite a thunderstorm in Alligator Harbor, but that’s another story).

Finally, it was time to start the experiment! We measured the size of each of the mud crabs, added them to the mesocosms, and let them eat (or not). Each day, Kelly would count the number of live oysters remaining, and she would remove a few mud crabs from some of the mesocosms to simulate catfish predation. There were a lot of moving parts to this experiment, and Kelly did a great job managing it!

And what did we find? Turns out that individual mud crabs actually eat more juvenile oysters when they are exposed to catfish cues and the removal / disappearance of some of their neighboring mud crabs, compared to just the removal of neighboring mud crabs or the absence of catfish cues. But overall, the the removal of mud crabs have a positive effect on oyster survival. (Even though individual crabs may eat more, there are not as many crabs around, so it’s a net positive for oysters.)


Mud crabs ate more oysters per individual in buckets with exposure to catfish cues and high rates of manual removal of mud crabs (to simulate predation).

Kelly has returned to classes, so we’ve now recruited a new assistant, Meagan, to help us with an experiment to address the additional questions that inevitably arise as you learn more about a system – for example, do mud crabs behave differently if catfish are around all the time versus only some of the time? We’ll keep you posted…

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

Are two friends better than one?

Dr. Randall Hughes FSU Coastal & Marine Lab

IGOR chip- biodiversity 150

Sand fiddler crab.

This summer we’ve been conducting an experiment on our new deck to look at the effects of fiddler crabs and ribbed mussels on Spartina alterniflora (smooth cordgrass).

Past studies by Dr. Mark Bertness have shown that crabs and mussels by themselves can have positive effects on plant growth – most likely because crabs can reduce the stress of low oxygen in the sediments by building their burrows, and mussels can add nutrients to the sediments.

Fig. 3 from Bertness 1984, Ecology 65: 1794-1807

Figure 3 from Mark Bertness's 1984 Ecology study illustrating the positive effects of mussel presence (white bars) on Spartina

Table 3 from Bertness 1985, Ecology 66: 1042-1055

Table 3 from Mark Bertness's 1985 Ecology study. Fiddler removal has a negative effect on Spartina in the marsh flat, but not the marsh edge.

Although both fiddlers and mussels occur together in the field, no studies have looked at how the combination affects the plants. Are the positive effects of each species by itself doubled? Or are they redundant with each other? Do crabs somehow reduce the positive effect of mussels, or vice-versa? How many crabs or mussels do you need to get a positive effect on Spartina? These are some of the questions that we hope to answer with our experiment.


Our new deck at FSUCML.

But first, we had to get everything set up. There were several long and hot days of shoveling sand into our “mesocosms” (10 gallon buckets) – many thanks to Robyn, Chris, Althea, and all the others who took care of that task! Then there was another day spent transplanting the Spartina.


Chris, Randall, and Robyn work to transplant Spartina from the greenhouse to the mesocosms.

Finally, it was time to add the fiddlers and mussels, and everything began!


Mussels nestled among the Spartina stems in one of our experimental mesocosms

Althea and Chris have been leading the charge on this experiment, and they’ve spent a lot of time getting to know (and identify) the fiddler crabs. All in all, a pretty fun study organism!


Althea working to identify fiddler crab species.

We’ll continue the experiment another month and then measure the height and density of the plants in each treatment to see if there are any differences. Once this experiment is complete, we’ll set up a separate one asking somewhat of the converse question – are two enemies (periwinkle snails and grasshoppers) worse than one? We’ll keep you posted.

Randall’s research is funded by the National Science Foundation.
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The End of an Era

Dr. Randall Hughes FSU Coastal & Marine Lab

Randall examines an experiment cage as Robyn looks on.

IGOR chip- biodiversity 150Calling a one year experiment an “era” is probably a bit of an over-statement, but the end of our snail field experiment definitely feels significant. Especially for Robyn, who has traveled to St. Joe Bay at least once a week for the past year to count snails and take other data. And also for the Webbs, who were kind enough to let us put cages up in the marsh right in front of their house and then proceed to show up to check on them at odd hours for the last year!  And finally for this blog, because the beginning of the snail experiment was the first thing we documented last summer when we started this project with WFSU.  It’s nice to come full circle.

So why, you may wonder, are we ending things now? Is it simply because one year is a nice round number? Not really, though there is some satisfaction in that. The actual reasons include:

(1) The experiment has now run long enough that if snails were going to have an effect on cordgrass, we should have seen it by now. (At least based on prior studies with these same species in GA.)
(2) In fact, we have seen an effect of periwinkle snails, and in some cages there are very few plants left alive for us to count! (And lots of zeros are generally not good when it comes to data analysis.)
(3) Perhaps the most important reason to end things now:  it’s become increasingly difficult in some cages to differentiate the cordgrass that we transplanted from the cordgrass that is growing there naturally. Being able to tell them apart is critical in order for our data to be accurate.
(4) The results of the experiment have been consistent over the last several months, which increases my confidence that they are “real” and not simply some fluke of timing or season.

And what are the results? As I mentioned above, snails can have a really dramatic effect on cordgrass, most noticeably when our experimental transplant is the only game in town (i.e., all the neighboring plants have been removed). And not surprisingly, cordgrass does just fine in the absence of snails and neighbors – they’re not competing with anyone or being eaten!


Snails also have a pretty strong effect on the experimental cordgrass transplant (compared to when no snails are present) when all of its neighbors are cordgrass.


Most interestingly, snails do not have a big effect on the experimental cordgrass transplant when some of the neighboring plants are needlerush.


This result is consistent with some of the patterns we’ve observed in natural marshes, where cordgrass growing with needlerush neighbors is taller and looks “healthier” than nearby cordgrass growing without needlerush.

Having decimated the plants in the cage, the snails move towards the tallest structure they can reach- a PVC pipe.

But why? Those snails are pretty smart. They generally prefer to climb on the tallest plant around, because it gives them a better refuge at high tide when their predators move into the marsh. (We’ve shown this refuge effect in the lab – fewer snails get eaten by blue crabs  in tanks with some tall plants  than in tanks with all short plants.) Needlerush is almost always taller than cordgrass in the marshes around here, so this preference for tall plants means that snails spend less time on cordgrass when needlerush is around. And finally, less time on cordgrass means less time grazing on cordgrass, so the cordgrass growing with needlerush experiences less grazing pressure.

These results – consumer (snail) effects on cordgrass are lower when cordgrass grows mixed with needlerush – are consistent with theory on the effect of diversity, even though in this case we’re only talking about a “diversity” of 2 plant species.  And they could be important in the recovery or restoration of marsh areas where snails are causing a large reduction in cordgrass biomass.

The one thing we still don’t know with certainty – how do the snails determine which plant is taller??

I guess that’s the beauty of this job, in that there are always more questions to answer.

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

The new documentary, In the Grass, On the Reef: Testing the Ecology of Fear had a segment on the snail experiment.  Watch the full program here.  You can also read Randall’s post from the beginning of the experiment, and watch a video, here.

We want to hear from you! Add your question or comment.
We spent one day learning about invasive Hydrilla and alligators at Wakulla Springs, and then of course had to cool off!

In the (wire)grass

Dr. Randall Hughes FSU Coastal & Marine Lab

We spent one day learning about invasive Hydrilla and alligators at Wakulla Springs, and then of course had to cool off!

For most of the month of May, I was busy teaching an undergraduate course at FSUCML. The course – Marine Biodiversity and Conservation in Florida – was a new offering, and it was lots of fun to put together. And, at least from my perspective, it went pretty well! (I guess you’d have to poll my students to get the true picture of how it went down.)

One of the best aspects of the course, for me, was to learn so much about the special part of Florida that we call home. We spent one day trying our hand at tonging oysters in Apalachicola, Continue reading

How much is a salt marsh worth?

Dr. Randall Hughes FSU Coastal & Marine Lab


IGOR chip- habitat 150IGOR chip- filtration 150IGOR chip- gastronomy 150The answer to this seemingly rhetorical question was the subject of a recent review by Edward Barbier and colleagues in the journal Ecological Monographs. They focused not only on salt marshes, but also coral reefs, seagrass beds, mangroves, and sand beaches / dunes. The impetus for the analysis was the recognition that many coastal habitats are in decline – for instance, 50% of salt marshes are lost or degraded around the world – and the belief that we need a better understanding of the true costs of these losses. Continue reading

Come see us!

IGOR chip- employment 150Writing grants, collecting field data, looking at samples in the lab- activities such as these occupy the majority of a researcher’s time.  But sharing why the subject of the research is cool and interesting with the public is an important part of the job as well.

Dr. Randall Hughes FSU Coastal & Marine Lab

Open House at the FSU Coastal and Marine Laboratory
Saturday, April 16
10:00am – 3:00pm

Picture 056

David and an undergraduate research assistant at FSUCML Open House 2009

If you’ve been holding back your comments and questions as you read the blog, then this weekend is your chance to ask them in person! David and I, along with our graduate students and technicians, will be participating in the FSU Coastal and Marine Lab Open House on Saturday from 10:00am to 3:00pm.

Continue reading