Tag Archives: science

The Dirty Work

Tanya Rogers FSU Coastal & Marine Lab

IGOR chip- biogeographic 150IGOR chip- habitat 150IGOR chip- employment 150(Editor’s Note.  Although David refers to Randall’s participation on this study, her role was not elaborated upon in this video.  That will be a part of the next video, on David’s collaborators, as Randall is David’s Co-PI- or Primary Investigator)


Tanya measures a fish caught in a gill net.

It’s been said that research techs are those who do the dirty work in science. Although true in many ways, I love being where the action is, collecting the data, turning ideas into reality. That said, here is some of my perspective on what went into our October trip and what days in the field were like.

A busy field trip like our October sampling push typically takes at least as many days to prepare for as the length of the trip itself. Although the daily blog posts covered our time in action, David and I spent most of the previous couple weeks just planning for this trip so that it could run as smoothly as it did. I feel it worth mentioning the many hours I spent pouring over tide charts and editing and re-editing our complicated schedule so that we could accomplish everything as efficiently as possible, factoring in all manner of time and tidal constraints, travel time, land and sea transportation, overnight stays, and numerous other variables, plus designing it with enough flexibility that we could adjust our plans in the field at a moments notice (and indeed we did). In addition to scheduling I also had to make sure we had all the materials we needed to for our trip, that those materials were all in working order, and that they are all packaged up accordingly and conveniently in our two vehicles. The last thing you want is to be out in the field and realize you’re missing some critical piece of equipment.

striped burrfish

As they conduct these initial sampling trips every few months, they keep finding new and interesting species living in and around the reefs. Here, Tanya is taking measurement of one of her favorite finds of this last trip, a striped burrfish.

Out in the field, going to retrieve our traps and nets is always the most exciting for me, since you never know what we’re going to catch, and I was interested to see how the October fish community compared with that of July. We caught a few new fish species in our traps this round, including a beautiful spotfin butterflyfish (Chaetodon ocellatus), juvenile snapper (Lutjanus sp.), and a couple tiny pufferfish (technically striped burrfish, Chilomycterus schoepfi – they were very adorable). Equally exciting was getting to use the new motor on our skiff for the first time at our sites. Although noisy and bizarre-looking, it performed admirably in shallow water, as it was designed to. At least in terms of temperature and humidity, conditions on the reefs were considerably more pleasant for us than during the summer. It was wonderful not to be wiping sweat from your face every 10 minutes. The dramatic increase in the no-see-um population at dawn and dusk was not so pleasant however, as David has duly noted. The dawn low tide at Jacksonville brought the worst swarms we’d ever encountered in the field. Incredibly irritating both physically and mentally, they made work nearly impossible, and forced me to spend the subsequent week covered in uncountable numbers of ravenously itchy welts.


Despite its exotic look, the spotfin butterfly fish is a native of both the Gulf and Atlantic coasts of Florida.

When not out on the reefs, there was rarely a moment when something didn’t need to be done – whether filtering water samples, rinsing gear, or (most frequently) extracting spat. Our only breaks seemed to be for the necessities of eating, showering, sleeping, and making coffee. (For David, coffee appears to rank just below data and samples in terms of his most valued possessions in the field.) Our biggest and most time-consuming challenge was whether we could get all of the spat extracted and tiles made for our predator-exclusion experiment in the time allotted between netting and trapping. The process of isolating spat was incredibly tedious to say the least, and particularly frustrating when, after you’ve been working on a spat for several minutes, your tool slips and the spat gets crushed, or it flies across the patio, never to be seen again. You couldn’t help but feel the spat always picked the most inconvenient places to settle. It was also quite a messy process, with water and oyster bits flying everywhere and various crabs skittering across the counter. The oysters also love to slice your fingers open during the few moments when you neglect to wear gloves. Yet in spite of the tedium, we couldn’t help noticing new and interesting critters living amongst the oysters as we broke them apart. For instance, we noticed considerably more porcelain crabs (Petrolisthes sp.) and Boonea impressa (a small, white snail that parasitizes oysters) than we’d seen in previously collected oyster samples. We also found an oyster pea crab (Pinnotheres ostreum), which lives on and steals food from the gills of oysters, and a number of dark brown cylindrical mussels (Lithophaga bisulcata) that bore into the calcareous shells of oysters. It always amazes me how many different animals can be found living within the structurally complex habitat created by species like oysters.


Young oyster spat, beginning their new careers in science.

I remember on one of the last days of our trip, I kayaked out to our St. Augustine reefs for a final service and check while David finished up the dremeling. I remember looking upon reef #5, seeing our newly deployed, spat-covered tiles and cages, our cleaned tidal data logger housing, and our newly replaced spat stick, arranged so neatly on our marked reef, and feeling delighted at our accomplishment, knowing how much effort has gone into this setup. I remembered that in my position it’s easy to get sucked into the details, but it’s equally important to remember the big picture, and how this research will contribute to our greater understanding of oyster reef ecology.

After our field trip, as we recover from battle wounds and wait for the mud to work its way out from under our fingernails, work on the oyster project continues at the lab. For me this has meant entering lots of data and starting to process our many samples. Before you know it though, it’s time to start to preparing for our next journey onto the reefs and the adventures that await.

The Kimbro, Hughes, et al. biogeographic oyster study is funded by the National Science Foundation.
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Day 7: October Oyster Push- Last Day

Rob Diaz de Villegas WFSU-TV

Thursday, October 28- Finish up, head back home


(Farthest to nearest) Hanna, Tanya, and Cristina perform some of the more glamorous work of this trip- cracking oysters apart and finding spat (oyster babies). David needed everyone on his team to perform, or this week would be wasted.

IGOR chip- biogeographic 150A while back, I was talking to Randall or David, I forget which one, and they were telling me about building a research crew.  Obviously you need people who have the knowledge and skills to do what needs to be done- from identifying fish to driving a boat, or setting a gill net.  But just as important, they said, was that you had people you could get along with, since you practically live with them sometimes.

Weeks like this one are where building the team pays off.  When you’re getting bitten up by gnats on an oyster reef at 6:45 in the morning, you don’t want a crew member sniping at another about losing a fish out of the gill net.  David remarked to me that the morale of this team had stayed strong, despite the schedule always changing and everyone having to shoulder more of the load while David got the tiles ready.  They did a lot of work on their own, and made it possible to get everything done even as plans shifted.

On a day like today, it was good that David has the crew he has.


A swarm of gnats hovers over the oyster reef water.

6:45 AM– Retrieved fish from nets, deployed traps.

After a night of battling cockroaches in their “haunted” house, they might have been happier to be out on oyster reefs at this early hour.  They might have, had it not been for the no see-ums.  They were getting eaten alive, which made it hard to work.  And it got worse from there, as if the universe decided to pile it on in this last day.

As early as it was, the birds had gotten to their fish before they did and there were no stomachs to examine.  And then there were the injuries.  David cut his finger on a catfish spine, and then, within about ten minutes, a stone crab got a hold of Hanna’s finger and inflicted some pain.  They’re both okay.  Their truck, however, is a little worse off.

Truck accident in Jacksonville

Banged up over the course of the week, the crew- and their truck- are ready to come home.

When they got back, they glued spat onto tiles one more time to deploy this afternoon.

3:00 PM– Tanya, Hanna, and Cristina retrieved the traps and set the tiles.

7:00 PM– The girls headed back to the FSU Coastal & Marine Lab.  When they got there, they cleaned all of their gear, even though it was late.  They figured that it was better to wash the salt off sooner than later.

So that was the week.  They’ll go back to each of the sites about every six weeks, though it won’t always be this intensive.  David, Jeb (SC/ GA), and Jon (NC) will start to see seasonal patterns in the fish that they find- when do certain fish tend to show up on what reef?  They’ll check in on their tiles and take photos, and over the months the photos should play like a flip book in showing the growth of the oysters on each site.  They’ll gain understanding, and they’ll run into more road blocks.  They have about two-and-a-half years left on this study, so while Thursday was the last day of the push, they’re nowhere near the end of the road.


Assuming no one tampers with them, we should be able to watch these oysters grow up over the next year.

Check back in a couple of weeks for wrap-up posts from David and Tanya.

Tide Times and height (ft.) for Jacksonville, October 28, 2010
Low- 6:44 AM (0.3)

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

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Day 6: October Oyster Push- Home Stretch

Rob Diaz de Villegas WFSU-TV

Wednesday, October 27- Finish tiles, go to Jacksonville


When not losing sleep over whether the tile experiment will work, David dreams of making the tiles. They'll be back in six weeks to check on the progress of the baby oysters they set upon the reefs.

IGOR chip- biogeographic 150Walking down the hall of our dorm at 7 AM, I heard the familiar sound of the dremel from across the street in the lab area.  This time the whole crew was there- Tanya, Hanna, and Cristina cleaning and separating oysters and David Kimbro slicing shells into similarly sized pieces.  The Jacksonville oysters they’re processing have an entirely different kind of predator than the Marineland oysters have in crown conchs.  The Jax shells were speckled with little greenish spots- these are boring sponges.  They bore holes through the shell and take up residence within it.  The specks were making it harder to spot spat.

I was thinking about predators when I was driving today, in particular the crown conchs here.  A1A runs alongside the intercoastal waterway where the oyster reefs are.  Driving north towards the Matanzas Inlet, which is the northern boundary of the crown conch problem, there is a bridge under construction.  While getting some footage of oyster reefs earlier, I noticed how close many of the reefs are to the road and its runoff.  Overall, the area is more heavily settled than the Forgotten Coast sites where David and Randall do their studies.  This drive I took today put a slightly different light on the work they do.  When I’m shooting on the reefs, or in the salt marshes, it sometimes seem like a different world.  But it isn’t, really.  Not that this sudden and very focused problem may not have an entirely natural cause.  But there are a lot of potential factors in play outside of trophic cascades and water salinity.


Those innocuous looking spots are trying to kill the oyster and take over its shell.

2:00 PM– Hanna, and Cristina drove to Jacksonville to deploy nets at low tide.  Cristina found a deep spot in the mud and sank in waist deep, which is a concern at this site.  The new boat was purchased specifically for this site, as it’s a long kayak trip in somewhat treacherous waters.


So far, so good for the Saint Augustine spat tiles.

4:30 PM– David and Tanya finish making the Jacksonville tiles and spend about two hours cleaning up the lab space.  Tanya kayaked out to check on the St. Augustine tiles they deployed yesterday before heading to Jax.  David said he had lost sleep last night over whether the tiles would still be there, or if the glue would even hold the spat onto the tile.  Jon Grabowski (NC team leader) has a site with easy public access.  This morning he showed up to find his sites being harvested, the tiles already removed.  So you can see where David would worry.  But, at least over the first night, the SA tiles were fine.

David and Tanya joined the rest of the team in Jacksonville for another awesome Tanya-cooked meal.  I feel I did her a disservice yesterday by not mentioning the zucchini bread and double chocolate biscotti she made, so I’ll do so now.  Yum!  Perhaps On the Reef needs a cooking segment.  Everyone is now settled into a house they all think is haunted.  Hanna put together a makeshift tub on their screened-in porch to keep the spat alive to deploy tomorrow.  One more day to go…


On Thursday, the October oyster push concludes and the FL, GA/ SC, and NC teams will start looking at the data and continue establishing patterns.

Tide Times and height (ft.) for Jacksonville, October 27, 2010
Low- 5:56 AM (0.2)
High- 12:25 PM (5.7)
Low- 6:42 PM (0.5)

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

We’d love to hear from you! Leave your comments and questions below:

Day 5: October Oyster Push- A Change of Plans

Rob Diaz de Villegas WFSU-TV

Tuesday, October 26- Tile Team heads to Jacksonville


The whirring sound, the smell of calcium carbonate dust, the warmth of his face behind the mask and goggles- this is the stuff of David Kimbro's dreams.

IGOR chip- biogeographic 150The WFSU crew stayed the night in St. Augustine to accompany both the Net/ Fish and Tile teams when they headed out at sunrise.  After breakfast, I went out to the lab space (we’re all staying at a research facility very near the reefs they study), and David Kimbro was there, before the sun had made its way out, separating shards of shell with spat on them.  He’d missed all of the field work here up to that point so that this experiment could work.  Until this afternoon, it was all I had seen him do here.  If he was able to focus in on this one aspect of this large an undertaking, it is because Hanna and Tanya have been able to operate independently and pick up the slack.  By the time he actually made it into the field, David followed Tanya’s lead.

Also working hard on this trip are my poor sneakers.  I have an old pair that I designated for my work on this project, shoes I knew I would never wear for anything else.  The reefs in Cedar Key and St. Augustine have torn them up.  I keep stepping in soft mud that hides oysters, or stray clumps cloaked by muddy water.  It might be time to invest in boots.


There's nothing like the smell of dead fish in the morning.

7:30 AM– Hanna, Tanya, and Cristina went out to retrieve the catch from the gill nets, take sediment samples, retrieve the data loggers, and take some fish stomachs (how else would you know what the predators were eating?).  They also replaced the spat sticks, which were still only attracting barnacles.  Tanya noticed, however, that spat would settle on the rebar below the stick.

A couple of Environmental Scientists from the St. Johns River Water Management System agency kayaked up at some point to watch the proceedings.  They are working with David’s lab to determine why these once commercially viable reefs were overrun and depleted by crown conchs.  The problem seems to be very localized, occurring between Ponce Inlet in New Smyrna Beach and Matanzas Inlet.  David is hoping for more “spinoff projects” like this one, in which he and his lab can use applied science to help specific reef systems.

And while we’re on the topic of predatory snails, Here’s that pic of the Atlantic Oyster Drill:


Crown conch, tulip snails, and oyster drills heavily populate these Marineland, FL reefs.

2:30 PM– Hanna and Cristina headed to Jacksonville to begin removing clumps of reef with Jacksonville spat on them. But first they were to inspect the house they were renting to see if there was a suitable area to make their Jacksonville spat tiles. That process involves keeping oysters in large tubs of water, prying shells off of the clump, and using a dremel to make the pieces somewhat uniform in size. If I was renting someone a house, I wouldn’t want them doing that in my bathroom. Hanna determined that the house did not have a workable area, causing a shift in their plans. Hanna and Cristina now had to bring the reef segments back to St. Augustine to process. Instead of deploying nets in Jacksonville Wednesday morning, they’ll have to do this in the afternoon after processing the spat all day. And instead of finishing with Jacksonville on Thursday morning, they’ll be there all day (causing David to make his three hour drive home at night).

5:00 PM– David and Tanya retrieve the small fish traps.  A couple of the fish they catch are pretty colorful, I suspect they’re something that once lived in a saltwater aquarium.  They also deployed the tiles into which so much effort had been expended.  It’s a major part of this study, and David is happy to get started on it just five months after that first day in Alligator Harbor.  And it’s still early enough in this three year study that they can tweak the experiment and try it again next year (experiments of this nature don’t always work the first time).

After all the work was done, Tanya made a tasty four-bean vegetarian chili, and everyone enjoyed a relaxed dinner before convening again at 7:30 AM to process more spat.


David finally makes it out into the field.

Tide Times and height (ft.) for Saint Augustine, October 26, 2010
Low- 8:oo AM (0.3)
High- 2:17 PM (5.2)
Low- 8:41 PM (0.7)
Tide Times and height (ft.) for Jacksonville, October 25, 2010
High- 5:56 PM (0.5)
We’d love to hear from you! Leave your comments and questions below:

Day 3: October Oyster Push “No Nap Time”

Rob Diaz de Villegas WFSU-TV
David Kimbro’s crew has been split into two teams, the Net/Trap team (N/T) and the Tile team (TI). For a closer look at how David’s team nets and traps larger fish and crabs, click here. To learn more about what the Tile team will be doing, click here. And if you click On the Reef under categories in the sidebar, you can track David’s progress over the course of this study.

Sunday, October 24- Net / Trap team in Cedar Key

Randall places traps on a Cedar Key reef

Randall places traps on a Cedar Key reef.

IGOR chip- biogeographic 150After months of walking around In the Grass, Dr. Randall Hughes stepped out On the Reef Sunday, pitching in for some fieldwork with David’s tech, Hanna Garland. They were the Net / Trap team working Cedar Key, while Tanya Rogers is heading up the Tile team in Saint Augustine. Randall, in addition to heading the salt marsh biodiversity study we also follow on this blog, is the co-PI (Primary Investigator) on this biogeographic oyster study. With her other study taking so much of her time and David having things well in hand with this one, she hadn’t made it out into the field until Sunday.  We tagged along with her today.

This was our first time documenting this study outside of Alligator Harbor (which is located a short hour from WFSU-TV) and, actually, it was my first time on any oyster reef other than those. I noticed that the water was a little clearer- I could actually see some of the oyster clumps for a foot or so under water as opposed to not at all. Few of the oyster reefs were as large as in AH, tending more often than not to stay a collection of clumps than an expansive reef. There were also stretches where reefs had been, and all that remained were broken shells. Randall told me that these had either been harvested or that the reefs had just plain failed (Tanya recounted finding two of the Cedar Key reefs obliterated in her last post).


Scientific equipment being used in an entirely lawful way. This machine filters the sediment floating in the water- including the phytoplankton that oysters eat.

If you take a look at the schedule below, you can see that the events are spread out based on the tide schedule; and there are a couple of days during this push where they start around sunrise and work well into the night. So there are breaks from fieldwork built into the day. I had assumed that this would be “nap time.” To my surprise, this is actually “lab time.” The water samples they had taken on our boat ride had to be filtered, and the filters frozen as fast as possible to prevent bacteria from contaminating them. They set up their “lab” in the kitchen of a condo they were renting. The apparatus they use is a collection of PVC pipes, tubing, and a motor into which they pour the liquid from clear test tubes. Randall had seen a news story this last week where some college kids were arrested for turning their dorm room into a crystal meth lab. She wondered aloud whether someone looking in their window might suspect the same of her and Hanna.

8:00 AM– Travel to Cedar Key


Boating from reef to reef, we would see places like this where a reef had been decimated. Two of the original Cedar Key sites for this study were destroyed. These are the kinds of things that happen outside of the controlled environment of a laboratory.

12:23 PM– Deploy traps, collect spat sticks, water samples. They once again made use of the new boat, though the public boat ramp is on the other side of the island from where their sites are located. They were going to look for a boat ramp closer to their sites to save a little more time.

The spat sticks so far have only collected barnacles at all of their sites, meaning that they may have started using them past the season in which oysters spawn.

6:00 PM– Retrieve traps, High tide activities: reference water level, replace spat sticks (if possible).

9:00 PM– Deploy nets. Randall and Hanna will retrieve these in the morning before Hanna heads to Saint Augustine to meet up with David Kimbro and the rest of the crew.

Tide Times and height (ft.) for Cedar Key, October 24, 2010
Low- 9:23 AM (-0.3)
High- 3:48 PM (3.3)
Low- 9:13 PM (1.4)

Sunday, October 24- Tile team in Saint Augustine

1:00 PM– Tanya Rogers and new crew member Cristina drive to Saint Augustine.

7:00 PM– Retrieve tiles/oysters.

Tide Times and height (ft.) for Saint Augustine, October 24, 2010
Low- 7:21 PM (0.5)
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Autumn in the marsh

Dr. Randall Hughes FSU Coastal & Marine Lab

Marsh periwinkles climbing on a cordgrass reproductive stem

A cordgrass reproductive stem stands above the surrounding plants.

IGOR chip- biodiversity 150 One doesn’t need to look at a calendar to realize that fall is upon us – recent cool mornings are a welcome sign. The marsh is also showing signs of change, with cordgrass flowering shoots springing up everywhere.

These stems are quite noticeable – they are taller than non-reproductive plants, and they have a “feathery” appearance due to the reproductive structures at the tops of the stems.

As I’ve mentioned before, cordgrass is one of those plants (like strawberries) that can spread by underground rhizomes, putting up new stems along the way. Alternatively, it can reproduce the “traditional” way, with reproductive stems that broadcast and receive pollen via the wind, ultimately producing seeds that fall to the sediment, get buried, and then germinate to produce new seedlings. Though conventional wisdom is that most new cordgrass stems are produced vegetatively by spreading rhizomes, it’s clear at our sites that these plants are investing a lot of energy in the other form of reproduction! Continue reading

Searching for alternative explanations

Dr. David Kimbro FSU Coastal & Marine Lab

IGOR chip- biogeographic 150In many of our previous posts, we focused on how predator patterns may dictate why oyster reefs look different from NC to Florida. While a cursory look at results thus far supports this hypothesis, we’ve yet to consider alternate explanations. And failing to consider alternatives would not be very objective or scientific. After all, our job is to collect a lot of data and perform a lot of experiments that could possibly refute our predator hypothesis. Only by surviving all of these data and tests can our hypothesis gain strength, and of course it can never be proved. Continue reading

A walk “in the grass”

Rob Diaz de Villegas WFSU-TV


Last week we had a post on what it was like on an oyster reef, the idea being that many people have never really seen one.  Continuing with that theme, I thought it might be interesting to take a closer look into a salt marsh.  This is a trickier proposition because, well, what is a typical salt marsh?  Some of them grow in muddy waters next to oyster reefs, or they can be found along beaches, in wide expanses or in small islands just off the coast.  I’ll keep today’s imaginary journey confined to marshes in St. Joseph Bay, where Randall Hughes conducts her biodiversity study- that is what I am most familiar with.

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This is what an oyster reef looks like…

Rob Diaz de Villegas WFSU-TV


The photo above is my work computer’s desktop picture. Most of the time, when people see it, I find that they had no idea what an oyster reef looked like.  One coworker thought it was a muddy cabbage patch.  To be honest, until I first stepped on one for this project, I wouldn’t have known a reef from a pile of rocks.  And, like a lot of people, I love eating the things- right out of the shell with a little grit and juice.  That’s the disconnect we sometimes have between the food we eat and from where it comes.  So it occurred to me that, while we’ve been talking these last few months about the complex relationships between predators and prey on the reef, it might be helpful to get back to oyster basics.  Over the following weeks, we’ll cover various topics (like why subtidal oysters are harvested more often than intertidal ones like those up there).  We’ll start with what it’s actually like out on a reef, and what you’d see there.

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The Prairie of the Sea

Dr. Randall Hughes FSU Coastal & Marine Lab


A local crustacean (hiding in a snail shell) makes a snack of epiphytic algae.

IGOR chip- biodiversity 150Most of my blog posts have revolved around my research in salt marsh habitats, with mention of seagrasses only in the context of their role as wrack in the salt marsh. However, I’m also interested specifically in seagrasses and the community of animals that they support, and particularly in understanding why seagrasses are experiencing declines in so many regions of the world. First, a little background on the plants themselves:

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