-: Hello and welcome
to the annual Seaside Chat Speaker Series.
We're glad to have you here
for the last presentation of the 2023 season.
This speaker series focuses on topics associated
with Flower Garden Banks National Marine Sanctuary,
and the Gulf of Mexico, and we're also part
of the National Marine Sanctuary Webinar Series
and the NOAA Science Seminar Series.
During the presentation, all attendees will be
in listen only mode.
You are welcome to type questions for the presenter
into the questions box at the bottom of the control panel
on the right hand side of your screen.
You may also let us know about any technical difficulties
you are experiencing,
and we will monitor both incoming questions
and technical questions.
Respond to them as soon as we can.
In addition, we encourage you to close
all other programs you may have open
during this webinar or close
any non webinar tabs on your computer.
This will allow for the webinar to flow
in more easily for you at your end.
We are recording this session
and we'll post the recording
to the National Marine Sanctuary
and Flower Garden banks National Marine Sanctuary Websites
within a few weeks after the presentation.
We'll notify registered participants
via email when these recordings are available.
And for those of you who are interested, we have a document
of links to additional resources on today's topic.
You'll find this in the handout pane of the control panel.
Simply click on the item to download it.
Hello everyone.
My name is Kelly Drinnen
and I'm the Education Outreach Coordinator
for Flower Garden Bank National Marine Sanctuary.
I'll be facilitating today's webinar from Dickinson, Texas.
Also with me today is Kelly O'Connell, one
of our research specialists who will be helping me
with backend administration of the webinar.
In 1972, the United States ushered
in a new era of conservation
by creating the National Marine Sanctuary system.
Since then, we've grown into a nationwide network
of 15 National Marine Sanctuaries
and two Marine National Monuments conserving an area
of more than 620,000 square miles, about the size of Alaska.
These marine protected areas are kind
of like national parks, but underwater.
The National Marine Sanctuaries Act gives NOAA the authority
to designate special areas of the marine environment
as National Marine Sanctuaries.
It also mandates
that the Office of National Marine Sanctuaries
conduct research, monitoring, resource protection,
education, outreach and management of America's
underwater treasures to preserve them
for future generations.
In addition to being places for recreation
and research, National Marine Sanctuaries are
also living classrooms where people can see, touch,
and learn about the nation's great lakes
and ocean treasures.
This webinar series is just one part of
that national education and outreach effort.
The Seaside Chat series is hosted
by Flower Garden Banks National Marine Sanctuary,
the only National Marine Sanctuary in the Gulf of Mexico.
This sanctuary consists of 17 banks,
or small underwater mountains, that are home to some
of the healthiest coral reefs in the world,
amazing algal and sponge habitats,
and deep reef habitats featuring an abundance
of black coral and gorgonians.
We invite you to learn, learn more about us
by visiting the sanctuary website at flowergarden.noaa.gov.
Today's presentation focuses on exploration
in the deepest parts of the sanctuary.
Like all marine animals, corals leave
behind genetic traces in their environment.
Scientists refer to these genetic traces
as environmental DNA or eDNA.
Similar to forensics, Marine biologists can sequence
this eDNA to determine what animals have passed
through an area or even nearby and not easily seen.
Today we'll learn how Luke McCartin sequences eDNA
to better understand the corals that live
in the deepest waters
of Flower Garden Banks National Marine Sanctuary,
even the ones we can't see.
Luke is originally from Massachusetts and in one way
or another, he has been studying the ocean
for his entire life.
He's an avid recreational angler and some
of his fondest childhood memories are of chasing schools
of bluefish with his dad in his grandfather's Boston Whaler.
He received his undergraduate degree
from the University of Vermont and then returned
to Massachusetts to work in oceanography at Woods Hole.
Now as a PhD student at Lehigh University in Pennsylvania.
Luke been studying the corals
in the deepest parts of the sanctuary.
He has spent months at sea and has been fortunate
to participate in research expeditions
to explore the abundant corals that thrive in the deep Gulf.
Welcome, Luke.
-: Hi, Kelly. Thanks so much.
-: Hi, good to have you.
All right, here comes the control over to you.
-: Great.
-: Looks good.
-: All right.
All right, so thank you again Kelly for having me.
I'm really happy to be here.
I also wanna thank you all for joining in.
I know I have some friends and family here,
so thank you all for showing up.
Kelly: You're not on your starting slide.
-: Oh.
Kelly: There we go.
-: Am I back on the starting slide?
Kelly: Yes.
-: Okay. I see what's going on.
Okay, so again, thanks Kelly so much.
My name is Luke McCartin, I'm a PhD student.
I'm currently at Lehigh University in Pennsylvania,
and I'm a member of Dr. Santiago Herrera's Lab.
And in the Herrera Lab we study deep sea corals
and specifically I work on environmental DNA sequencing
like Kelly mentioned.
And so today I'm gonna talk with you about that
and the title of my talk is
Coral Forensics in the Deep Flower Garden Banks.
All right,
so I just wanna give you a little bit more information
about myself and tell you kind of how I got here.
So as Kelly mentioned, I'm originally
from coastal Massachusetts, so I grew up on Cape Cod
and lived there year round, kind of surrounded
by the water in all directions.
And like Kelly said, some
of my favorite childhood memories were going out
and actually exploring the coastal ecosystems around me.
And so this photo here is a photo
of my father, my younger sister
and I on my grandfather's Boston Whaler.
And while I didn't necessarily know going
through kind of my career path that I was going
to be a marine biologist, I have always been surrounded
by the ocean and in one way
or another, I think it's the perfect fitting for me.
So like Kelly mentioned, I worked in Woods Hole
in Massachusetts and studied deep sea biology.
And this was right after I finished my undergraduate degree
at the University of Vermont.
And I guess now I've been, I've working
as a deep sea biologist for quite a while.
So it's been about five years.
And in that time I've gotten
to explore some really awesome places.
I've been around the world and I've also gotten
to explore the Gulf Coast,
which has been a really great experience.
Spent some time of course in the Gulf of Mexico at sea,
but also in some other destinations
like Gulfport, even spent a few days
in Ocean Springs, Mississippi.
And I've really gotten to enjoy that part of my research.
So I moved to Pennsylvania to actually pursue my PhD,
and as soon as I moved to Pennsylvania, I started working
in the Flower Garden Banks National Marine Sanctuary.
So I think just a month after I started my PhD, I was asked
by my advisor to go on a research cruise.
And here we spent four
or five days actually collecting samples
to sequence environmental DNA.
And then about a year and a half ago now, I went out
for a second cruise in the Gulf of Mexico
and we spent almost 20 days going around
and looking at the deep water habitats that exist
in the Flower Garden Banks National Marine Sanctuary,
taking really fantastic pictures of corals
and collecting more eDNA samples.
And most, most, if not all of the pictures
that I'm gonna show you today were all taken
during this cruise and are
from the National Marine Sanctuary.
So today I hope to answer a few questions for you
and teach you not only about my research,
but also about deep coral habitats in general.
So the first question I hope
to answer is, what do deep coral habitats look like?
So you might have some familiarity
with coral reefs, you might have learned about coral reefs
in the news or been to a coral reef yourself
and gone snorkeling.
But I imagine that few of you
actually know about deep sea corals
and what they might look like in the habitats
that they create.
The next thing I'd like to talk about
is how we actually study these deep corals.
So deep corals, for the purposes
of this talk, are those corals
that exist below the depths of recreational scuba diving.
So there are some techniques that can be used
to actually get to the deep ocean
to study corals as a diver.
So there are techniques called technical diving
that involve using different mixed gases.
But today I'm gonna focus on what I do
and what our lab does, which is
to actually use both submersibles as well
as robotic vehicles to study these deep corals.
And then lastly, I'm gonna talk about my research.
And my research involves actually trying
to identify corals, not just by looking at them in video,
but also by sequencing the genetic traces
that they might leave behind in their environment.
And so let's get started.
So let's talk about what deep sea coral habitats
actually look like.
So this photo here is a photo
that I actually took myself off the coast of Hawaii.
So this is in a place called
Kaneohe Bay, which is really fantastic.
I admittedly don't have
that much experience actually snorkeling.
This was kind of only my second
or third opportunity actually snorkeling on a coral reef.
Growing up in Massachusetts, it's pretty cold for most
of the year and I don't have many friends
that were actually into snorkeling,
so it's just something I didn't necessarily do,
although I was always on the water, mostly fishing.
And so what you can see here is
that off the coast of Hawaii there are these really awesome
coral reef habitats like there are
in the Flower Garden Banks National Marine Sanctuary.
And what really struck me as I went through
and snorkeled here and took a look
around is how the coral grows.
So this was just during a swim I took with a mask
and a snorkel off of one of the public beaches,
and all of a sudden I ran into these fields of corals.
And now this coral is called rice coral
and it's a stony coral.
And as you can see, it creates this reef habitat.
You might be able to make it out,
but there's a butterfly fish in the middle here.
And so this reef habitat kind of expands upon the bottom
and creates habitat for different fish as well
as invertebrate species.
So things like crabs and shrimps and other animals.
And the reason why corals
in the shallow water would grow this way is
because they're trying to soak up
as much sunlight as possible.
So shallow coral reefs, for the most part rely on sunlight.
The coral here, as you can see, is this brown gold color
and it's that color
because these corals have photosynthetic algae
that actually live within their tissues.
And so these algae can actually take in the sunlight
from the surface and convert that to energy
that the coral uses.
And so that's why you see these habitats that grow like this
and spread out in this expansive way.
Now I'm gonna show you some images from the Gulf of Mexico.
And so both of these images were taken
at a place called Green Canyon, which is south of the Texas
and Louisiana coasts, and at a depth of
around 1700 feet deep.
So this is a pretty deep place.
And the first thing you'll notice is
that here it's perpetually dark.
So in the deep ocean at these depths, there's no light
that would penetrate down to these corals.
The only light that you're seeing in this image
is actually light we are actually introducing
into the environment using the submersible.
And so what I want you to notice is
that these corals look very different
than the stony reef corals that I showed you
in the previous slide.
So these corals actually grow in this fan shape here,
and you can see some more in the background.
These are called soft corals.
And then another type of coral that grows in this fan shape
in the deep sea are called black corals
and they're called black corals
because of the color of their skeleton mainly.
And both of these types of corals are growing
in a way that resembles a tree.
And there's a really nice word for that that we use
and that's called arborescent.
So they look like trees. And they're doing this
because they don't have sunlight in the photosynthetic algae
to rely on to actually create energy here.
What they're doing is they're trying
to prop themselves up into the current so
that that current brings them food.
And they might be feeding on things
like plankton that are swept by them.
They might also be catching small prey
like small shrimp and other crustaceans.
And so these habitats look quite different,
but they're just as fantastic, I think.
One thing I want you to remember though is
that in the deep ocean, stony corals also build reefs.
So this is something that's pretty, pretty fantastic
is that these habitats can in a way look
like shallow water habitats in some places.
This is also a picture taken at Green Canyon,
and what you're seeing here is you're seeing
a stony coral reef that's been formed by the growth
of a coral called Lophelia.
And this coral in the deep ocean forms
these really large reefs that grow up on themselves
and create habitat.
And here we have some interesting deep sea organisms
that have called this habitat home.
So you have things like squat lobsters, you can kind
of think of these as somewhere between a crab and a lobster.
Other animals like this really cool shrimp here
that has this interesting white and red color pattern.
And then lots of anemones.
And when I was actually looking through the video
at this site, I only saw these anemones living
on this stony hard coral structure.
You also see this big fish here.
And what I want you to take away from this is
that just like in the shallow water,
in some places, these stony corals actually create habitat
for other animals.
And now the last type of coral ecosystem that I'd like
to introduce you to is called a mesophotic coral ecosystem.
And this is the type of ecosystem that comprises most
of the Flower Garden Banks National Marine Sanctuary.
I think this picture is just fantastic.
I'm so glad that we were able to capture this
because we actually turned the lights
off when we took this picture.
One thing we tend to do when we are exploring the deep ocean
is we want to be able to see around so we don't get lost
or bump into things, but every once
in a while when we're sitting still, it's fine
to turn off the lights and you can really take
in what the animals that live there are actually seeing.
And so what you're seeing
in this image is a huge black coral fan.
This is called Plumapathes.
I'm gonna use some scientific names today, not
because you necessarily need to remember them, but only
because they're quite nice.
And so this Plumapathes coral is called Plumapathes
because it grows like a plume or like a feather.
And this coral is fantastic, it's really large.
There's also some creole fish over here as well
as grouper that are swimming by.
And this coral lives
in an environment where there is some light
but not that much.
And so this picture was actually taken
at Bright Bank, which is part
of the Flower Garden Banks National Marine Sanctuary
at a depth of around 200 feet.
And so here there's some light that penetrates
towards these coral ecosystems,
but it's still mostly dimly lit or dark.
And so what's really interesting about the mesophotic ocean,
and so that is the area
of a coral reef where there is some light,
but it's dimly lit, it means middle light in a sense, is
that you can see a really fantastic number
of different coral types in these habitats.
There are some corals that are adapted to shallower depths
and other corals that are adapted to deeper depths.
And in my experience, we see them all converge
in the mesophotic.
And you really see these fantastic coral fans
that all live together.
And so the takeaway from my first point here is
that deep coral habitats can in a way look like those
in shallow water so they can form reefs,
but they can also look quite different
and be composed of coral fans.
And the mesophotic ocean has a lot of coral species.
And now going ahead, what I want to talk about is
how we can actually study these deep corals.
So if you were unaware,
the Flower Garden Banks National Marine Sanctuary
was very recently expanded.
So the Flower Garden Banks National Marine Sanctuary
started as just three banks, west Flower Garden,
Stetson Bank, and East Flower Garden.
And then in 2021 it was expanded to include a number
of other banks that are all shown on this map here
in our highlighted in white.
Bright Bank, where the coral is
from that I just showed you, is right here in the middle.
And so with the expansion of
the Flower Garden banks National Marine Sanctuary,
now we have all of these important coral habitats
that are protected from bottom damaging activities,
as we call them.
And so that means here only recreational hook
and line fishing is allowed.
And what I wanna point out from this figure is
that while we know quite a bit about some
of these coral reef banks, we don't know all
that much about some of them.
So, this figure here shows the number of different corals
that are found in these different places based on data
from NOAA's Deep Sea Coral data portal.
And the search that I did includes those corals
that live at mesophotic or deeper depths.
And so as you can see, some of these banks
or habitats, we know a lot of coral species from them
and others, we know very little.
And the total number of observations
in this database is given at the top of each of these bars.
I've colored the bars based on whether
or not they were part of the original
Flower Garden banks National Marine Sanctuary or whether
or not they were just recently incorporated
into the sanctuary.
And those that are in blue have been a part
of the sanctuary since its beginning.
And as you can see, well we know quite a bit about some
of the banks that were just recently protected,
such as Geyer Bank here, where we know there's
at least over 20 different coral types
and we have some observations from there.
Some of these other banks, at least
in this deep sea coral database, are relatively unknown.
So the place I've been showing you, Bright Bank,
in this database, at least, all we know is
that there are a few different types of corals
and there's only a few observations too.
And so what we try and do as deep sea explorers, I guess,
and what I try and do in my research is to try
and characterize the diversity of different corals
that live in this place and the habitats that they support.
And so next I'm gonna talk about how we actually do that.
And so I mentioned earlier that you can dive
to these depths if you have the right training,
but the ways that we do it in the lab largely rely
on different technologies including submersibles as well
as remotely operated vehicles, which I'll touch on.
So here I'm just gonna talk
to you about one deep sea submersible
that's really close to my heart because I actually got
to dive in it just a month ago.
And this is the deep sea submersible Alvin. If you happened
to tune in for Tom Bright's talk last week, Tom talked about
his experiences diving in a deep ocean submersible
to actually explore the Flower Garden Banks.
And so in these deep sea submersibles, like Alvin
or like the one that Tom dove in,
essentially what happens is you have a couple
of scientists, and maybe another person who's
actually piloting the sub, who go down and look around
and collect samples for the entire scientific group
that's conducting the expedition.
And so I was really fortunate to be able to go
on a cruise where we used Alvin just a month ago
and I got a chance to actually dive down
and see corals for the first time.
It was a little nerve wracking at the start,
I'm not gonna lie, we were going pretty deep down
to about a mile and a half.
But as I got comfortable, it was just fantastic.
And so I was really fortunate to be a part
of the dive where I actually got to see a deep sea coral.
And so this is what is called a bamboo coral.
And I saw this coral at 2,500 meters,
which is about a mile and a half deep.
This is probably the worst picture, quality-wise,
that I'll actually show you for the duration of the talk,
but I took it myself out of the window of the sub,
so I really wanna share it
with everyone who cares to listen.
And so after I saw this coral
and we conducted all the other things that we needed
to do when we were
on the sea floor, I did make it up safely.
So here I am getting out of the sub.
And so I just want to kind of talk about my own experience
and talk about how this is something
that happens in deep sea exploration.
But I think it's pretty rare.
Not too many cruises or research expeditions actually go out
and use submersibles.
And I'm just fortunate to have gotten the chance
to see these things firsthand.
What we normally do is we don't see things firsthand.
We actually put a robotic vehicle over the side of the ship
and take a look around
and then watch the video feed back at the surface.
And we do this using a vehicle called
a remotely operated vehicle.
And the one you're seeing here is called
the Global Explorer.
The pictures I showed you previously from deeper depths
as well as the Flower Garden Banks Marine Sanctuary were
all taken using the Global Explorer a couple of years ago.
And how these work is they're actually connected
to the ship and you can see this here.
So what we have here is called a tether,
and that tether connects to the ship
and actually transmits the information down to the ship.
So electricity, power and all the sorts of things
that the ROV or the remotely operated vehicle needs to move
around, take pictures and collect samples.
So all the while, while it's connected
to the ship, we are actually controlling it
from the surface.
And so this is what it looks like during a an ROV dive.
And so in the ROV control room, there's always a lot
of screens to see what's going on.
And while we are mostly concerned with some
of these screens here to actually look
at the animals, a lot of the other screens are there
because it helps the pilots, who are actually flying
the ROV around, navigate.
And so what's really neat,
and I thought quite serendipitous, is
that I had actually snapped a picture on my cell phone,
inside the ROV control room, when we saw
that really fantastic coral
that I've been showing you, the Plumapathes coral.
And so this kind of gets you an idea of what it looks like.
It's really dark in there, but we have all these views
of the corals we can move around and take pictures
of everything.
On the far left is my advisor Santiago Herrera,
and he's there kind of leading the dive as I take notes
and then flying the ROV is Jim and Jim is flying it
around, making sure we don't bump into anything
and actually helping us do our science,
and see corals that we might not be seeing ourselves.
And so what's really interesting about using ROVs,
and I think really fantastic, which is a little different
than using a submarine, is
that everyone is kind of involved.
So while we were conducting these dives,
we were not only looking at it ourselves in the control room
and moving around, we were also live streaming the feed
down to the rest of the ship.
So you could be potentially eating your lunch
and watching deep sea exploration going
on, which is really fun and makes everyone feel
a part of the expedition.
Okay, now I'm gonna get into the last part of my talk
and the most of my talk, which is gonna be talking
about how we can actually identify corals
from their genetic traces.
So this image here is another image taken
in the Flower Garden Banks National Marine Sanctuary.
And what I want you to take away from this picture is
that there are a lot of corals here.
This is a zoomed in photo.
So most of these corals are quite small
and there's multiple different types of corals here.
And what I'm gonna do for your entertainment is kind
of quiz myself on how well I can identify these species just
from the picture alone.
Let's see how I do. So the first coral I would go
for when I was actually looking
at this picture would be this one in the middle.
And this is called Antipathes atlantica,
and this is a coral that is a black coral.
So it's closely related
to the Plumapathes I showed you earlier,
and it's pretty distinct.
So when I see this one, although it might be pretty small,
there's a good chance that I'll be able
to identify it pretty readily.
It comes in a couple of different shades.
So you can see there's kind of a lighter gray color here,
and then a darker one, but overall it's not too bad.
The next one I would go for if I was trying
to identify these corals is this one on the right,
and this is called Ellisella.
This is more closely related actually
to the soft coral fan I showed you earlier,
or the gorgonian corals that Kelly mentioned,
but it grows in a single stick-like
fashion with some curve to it.
And the little coral polyps kind of extend off
of the sides as you can see in the picture.
That one I'm pretty good at.
There's a few different species that look similar,
but at least I know what type it is in a pretty good way.
And so I can be confident telling you that that's Ellisella.
The next one I'm going to look
at is this one over here on the left.
Now this is another type of black coral,
and I think it might be Tanacetipathes, except
that Tanacetipathes, in my experience tends
to branch differently and not form as many plumes
like the Plumapathes.
Now, I don't think this is Plumapathes,
although it's possible it might be a very small Plumapathes.
And I don't think it's another species called Elatopathes
because Elatopathes, I'm used
to seeing quite a bit more deep than this.
So what I would do with this picture, is I would take it
and I would send it to our collaborators.
So these might be folks who their expertise is really
in identifying corals
and they can identify corals sometimes just
from pictures alone based off of all
of the corals they've actually held in their hands in places
like museums around the world.
The next coral I'm gonna look at is this one here.
This one you might not have seen, it's quite small,
but there are many of them if you look very closely.
And this coral is a small red branch branching coral
that I think is Scleracis.
Now, Scleracis though, can be pretty tough
to tell from some other small red corals.
Sometimes color isn't the best way
to tell coral species apart.
And I wouldn't really know unless I actually took a sample
of this coral and we brought it up on the deck
and took a look.
And then the last one here is some
unidentified soft coral fan.
So just in my experience alone, I'm not super familiar
with this coral, so I would definitely be taking
this screenshot here and sending it to someone else
who has the expertise to tell me what I might be looking at.
Now the problem with that is it's not always possible
to identify corals just from pictures alone.
So these corals have been described by scientists
in museums, for decades and millennia,
who have actually had them in their hand
and taken a look at them.
And so sometimes what you need to do is you need
to take an actual sample of the coral
and either give it to a museum or sequence its genetics.
And so now what I'm gonna talk to you about is how,
in addition to actually looking at pictures
and video, I am trying to identify corals not
by taking a sample, but actually by taking a sample
of the water that they live in or the coral forensics
that I alluded to earlier.
And so this process is called collecting environmental DNA
or sequencing environmental DNA to identify species.
So this illustration here was done
by another lab member, my friend Nicole.
And Nicole is kind of drawn two corals for us.
So the first one is this red, fluffy coral.
Sometimes we call it a mushroom coral.
And this other one, not necessarily drawn
to scale though, is a much larger bamboo fan.
I kind of sized these just so you could make
out the differences between the two.
In reality, this one's pretty small
and this one's actually rather large.
Now these corals are living in the deep sea
and they're very happy.
They might be feeding on passing plankton
like I talked about earlier.
They might be just kind of making a living,
maybe even reproducing,
so releasing gametes, like eggs, into the environment.
And as they do this and live
in the ocean, they're gonna be releasing traces
of genetic material into the environment.
And so what this looks like is that if you have this pink
or red coral here, it might be releasing
its unique genetic DNA into the environment.
And then this white coral fan is
also releasing its unique DNA into the environment too.
And in these habitats, which in the open ocean are
really dynamic and constantly changing,
the ocean currents are coming in
and they're sweeping up this DNA
that the corals might be releasing.
Some of that DNA might be transported some distance,
and some of that DNA might also be recirculated
into the water above these corals.
And so what I can do, as a geneticist, is I can go in
and try and take a sample of this water
and actually sequence the DNA
that might be in the environment
around these corals, to identify them.
And when we do this, what we'd find out is
that the DNA from these different coral species
likely looks very different.
So if you're not familiar with DNA,
or it's been a little while since you took a biology class
where you talked about it,
DNA can be kind of summarized into a four letter code.
And that four letter code consists of A, C, G, and T.
And those are different molecules that make up the DNA.
And so each animal on earth,
or each plant, has its own unique sequence of ACGs
and Ts that can help identify that animal.
And so on the top here is this pink bushy coral.
And as you can see, the sequence that I've assigned
to this coral, just for the sake of the talk, is AAC
and then a space which I'll explain in a second,
and then TTTGA.
Now this other coral, the white coral fan, we might be able
to sequence its DNA too.
And using some computer algorithms and programs,
we can kind of line the two sequences up
between the two species.
And what you'll notice is that
at this position, the sequence for this coral is different.
So instead of the sequence being a AAC space
and then TTTGA, the white coral fan sequence is AGCATTTGA.
And so what I can do is if I can actually grab a sample
of the water here and sequence the DNA within
that sample, that will help me identify these species.
And that will be particularly helpful
for identifying species
that we can't distinguish easily just from pictures alone.
So now the question becomes, well,
how do we actually capture that environmental DNA?
And while the laboratory work that I won't get too
into can be quite complicated, it's rather routine
if you're a molecular biologist
and collecting water is essentially collecting water.
But we get to use some pretty fancy tools to do it.
So the first way we can collect water
in the deep ocean is we can use what's called a CTD rosette.
And this rosette is called a CTD, usually,
because it usually also has a sensor
that measures conductivity, temperature, and depth.
And all of these bottles here we call Niskin bottles,
but they're essentially just water bottles
that can capture water wherever the CTD is.
And so how this actually works in practice is
that it's connected to the ship in a winch
on the ship via a cable.
We lower the CTD over the side of the ship and we bring it
down to the depth that we want to sample at.
We get a live stream of the condition,
so we'll know the conductivity and the temperature
and the depth live when we have the CTD over the side,
and we can tell maybe bottles 1, 2, and 3
to close at any particular depth.
And what they're doing is they're actually capturing
the water that is found there because they go down open
and they snap shut with both of these caps on the bottom
and the top enclosing the water that's there.
And so what I can do then is I can pull this CTD rosette
back up onto the ship. I can go ahead and take the water
outta the bottom here, and I can actually go ahead back
to the lab after the expedition is over and sequence the DNA
that might have been captured in that water sample.
The next way I've used these bottles is actually using
an ROV or the remotely operated vehicle.
And so this is a picture of the Global Explorer,
the ROV I showed you earlier, and there are a number
of different water sampling bottles up
and down the sides here. So we have six here.
And what we can do when we attach these bottles
to an ROV is we can actually fly around
and take video of the ecosystems
and decide when exactly we want
to capture water samples for eDNA.
So maybe I'm in a place like the image I just showed you
and there's a lot of coral species around
and I wanna know more about them.
I wanna be able to more confidently identify them.
And one of the ways in which I can do that is
to collect their DNA from the water.
So what I can do is I can tell the ROV pilot,
"Hey, could you please close bottles 1, 2, and 3,"
and those bottles can be closed by the ROV.
And then when the ROV comes up at the end
of the dive, I can actually go ahead and take samples
and sequence environmental DNA.
And then later on in the dive, maybe we're
in a different place and I see five
or six other coral species
that I haven't been observing yet.
I can say, "This is a great place to get some more DNA.
So let's close some bottles," and we'll close
bottles 4, 5, and 6.
And again, once the ROV comes up,
then I have six nice samples taken at depth.
I also have a picture of the corals that were there.
And so in this way I can get more information about
the corals that are living there based off the
genetic material they've shed into the water.
And now I'm gonna talk to you about how this actually works
and some data that I've collected
as I develop these methods.
And to do that, I'm gonna take you to two places
in the Flower Garden Banks National Marine Sanctuary.
The first is Stetson Bank.
So Stetson Bank is in the top northwest here of this map.
And this is a bank that is on the continental shelf.
So the continental shelf is this part of the ocean
that's colored a little lighter here,
and that's a little bit shallower.
And then you can see there's a really steep slope
as it gets deeper.
In some parts
of the world, this continental shelf only extends
for a short distance and then it drops off really deeply.
In the Gulf of Mexico, there's a pretty
extensive continental shelf
and then some really interesting habitat
along this large continental slope.
But Stetson is right at the top here,
and we're gonna go take a look at what it looks like
at a deep coral habitat near Stetson Bank.
And so this is what it looks like.
And this picture is a little blurry by design
because that's actually what it looks like
at Stetson Bank at a depth of around 60 meters.
And so here you're seeing a few different corals,
but the turbidity is really high.
And so that means there are just more particles
in the water, which might be a function
of being at this depth near Stetson
and also being a little bit deeper,
or excuse me, also being a little bit further up
on the continental shelf.
And so in this picture,
there are a few different coral species.
And I'm gonna point out a few that I've counted
by actually looking at video taken at Stetson Bank.
One of them is called Stichopathes,
and this is the most abundant coral.
That one is in the top right over here.
If you can see my laser pointer,
it's this big curled wire coral, we call it.
The next one is Thesea nivea.
So this is this purple soft coral fan that's in the middle.
This one can be really common as well.
And in the back if you can make it out, it's called Muricea.
And Muricea can be a really large coral
that exists in very large numbers at some places.
And then this other one here is one
that we're not quite sure exactly what it is.
So we've taken a sample of it and we've sequenced its DNA,
but we're not entirely sure what it is.
And for now we call it the spongey coral.
'Cause in a way it kind of resembles a sponge.
And now I wanna show you what happened when I took some
water samples here and then tried to sequence the DNA
of these corals in the sample.
So first what I found is
that I got a sequence from Muricea pendula,
and how I know this is that I've also taken some sequences
that are publicly available that have been collected
by museums or other researchers, and I matched it
to the sequence that I found in the water sample.
And so I can with high confidence, say
that I'm detecting this coral not only by seeing it,
but also by capturing the water around it.
The next one is Thesea nivea. I also got a sequence from.
And so this sequence at the location I've decided
to show you here, which is only five different nucleotide
letters, is different than Muricea pendula.
So that tells me not only that these species are different
from each other, but having that database of all corals
that have been sequenced
to date helps me identify it pretty confident.
The same can be said for Stichopathes.
And so this makes sense.
These are the three most abundant corals
that are found at this habitat, and I can find their DNA
in the water, now the last one is a little problematic.
And so this spongey coral here,
I actually did not detect any DNA
that I can confidently assign belongs to that coral.
And so what this points out is that the kind of utility,
if you will, of using something
like eDNA sequencing might depend on the abundance
of the corals.
So things that might be at really low abundance might not be
as easily detectable when you just take a water sample
and sequence eDNA.
However, what I hope you see
at the next place I'm gonna take you is that
that can change depending on where you are.
And so now we're gonna go to Bright Bank.
And so Bright Bank is a place that's kind of near
and dear to my heart at this point
because I've done a lot of research there
and I feel like I've gotten to know it pretty well.
And Bright Bank is further out on the continental shelf,
so it's right out here.
And the habitats that we study at Bright Bank are
for the most part a little bit deeper
than those at Stetson Bank.
So here we go to Bright.
And what I want you to see about this graph here is
that there are a number of different coral species
at Bright, more so than I see in the video at Stetson Bank.
That doesn't necessarily mean that there are
overall more species at Bright than Stetson.
We can't say that for certainty,
but at least in the video that I've analyzed
from the ROV dives that I've been a part of,
I do tend to see more species here.
And so now I'm gonna give you an idea of which
of those species I can detect with environmental DNA.
So the first one that I detect is this Ellisella coral.
So this is a cool coral.
It's pretty similar to the one I showed you
in a previous slide, if you remember, except
that this one branches a little differently.
It's a little more curvy
in some odd ways, which is pretty neat.
The next one I also detected is indeed Stichopathes.
So I did detect this one, I'm just not showing it to you
because that would be a lot of pictures on the screen,
but Stichopathes is also very abundant
and I detect it in the DNA.
The next one I'm gonna show you is Nicella.
So this is a neat little coral.
So this is actually closely related
to this Ellisella, believe it or not, except
that it branches very differently.
So while it's a similar color, it branches
in a very different way and forms these short fans.
And as you can see, I not only obtained a sequence
for Ellisella and Stichopathes, but also for Nicella.
And then the last one I'm gonna point out
to you in the imagery is this Antipathes atlantica.
And I've chosen to show you a sequence that has a lot
of spaces missing because I wanna point out
that this is a black coral, and as a result, its sequence
at this position is very different
than Ellisella or Nicella.
What you're seeing here is that the algorithm I've used
has taken a much longer sequence of DNA,
of which these six letters are a part of,
and mapped them together so
that you can compare across species.
And what the algorithm found is that
for Antipathes atlantica, while there might be some regions
of that longer sequence I'm not showing you,
that match up perfectly with Ellisella.
There's a big space missing here.
And so these differences in the DNA code reflect
how evolutionarily different these coral species are,
where Antipathes atlantica is a much different type
of coral, a black coral, then these two closely related
species which are soft corals.
And now what I wanna point out is
that it's not always the case that we see more species
or corals in video than we detect in their DNA.
And Bright Bank is a good example of that.
So there's one species here that I'm gonna point out,
among a few, that I didn't see in the video,
but I detect its DNA,
and this is Muricea pendula, the coral I showed you
on the last slide, that in certain places
can form really high density coral gardens,
as we call them.
And so, what I found is
that while I can detect Muricea pendula, I'm not seeing it
in the video.
And so this begs the question, where did
that DNA sequence come from?
So what can we do to go out
and actually find Muricea pendula to confirm
that it is present at Bright Bank?
Well, the first answer is pretty straightforward.
It's that when you're doing an ROV dive,
like if you were going for a scuba dive
or a snorkel, you're not able
to see everything around you, right?
There's a certain limit to what you can see,
and you're probably moving in maybe a systematic way to try
and accurately quantify the different types of animals
that live in a certain place.
And so perhaps it's as simple as we didn't turn a corner
and take a look and find a ton of Muricea pendula.
The other answer, or possible answer, to this question is
that DNA could be coming from somewhere far away.
So based on my experience annotating a lot of video
and counting the corals that exist at Bright Bank, I know
that while there's not really a lot
of Muricea here exactly where this video is collected,
I have other videos that are deeper off of the side
of Bright Bank where there is tons of Muricea.
And so part of my PhD research, that I'm not gonna go
into depth about today, is actually understanding how large
amounts of DNA from distant places might be transported.
And so that might make this environmental DNA data
a little trickier to interpret,
but it also makes the technique more powerful
because in a way we can now detect corals
that we might not be able to see.
And while we might not know exactly where they could be,
this could, you know, point us towards places
that require further exploration
to actually characterize exactly how many corals are there.
And so with that, I'm just gonna summarize
what I've talked with you about today.
And my takeaway message is that coral habitats
in the deep ocean are just really awesome.
They've kind of fascinated me and written my life story
for the past five years.
So I'm really excited
to share some things about them with you.
And as far as my research goes, what I'm finding is
that yeah, we can use coral forensics
or actually sequencing the genetic traces of corals
in water to detect corals.
And in some cases it might tell us
a little bit more about the environment
than one single ROV video might might be able to.
And so the takeaway is we need
to do more deep sea exploration.
The Flower Garden Banks National Marine Sanctuary is
a spectacular place to do that
because there are so many species,
and I'm just really excited to be able to do this
for a living and to continue
to do this as I finish up my PhD.
And so with that, I'm just gonna acknowledge some people.
First of all, I'd like
to acknowledge the sanctuary specifically Kelly,
for having me.
I'd also like to acknowledge my lab.
So Dr. Santiago Herrera's Lab, these other folks,
Sam Vohsen, Nicole Pittoors,
and Penny Demetriades were a big part
of our lab's efforts
on the cruise where I showed you all these pictures.
In addition, I'd like to thank the captain
and the crews of the Research Vessel MANTA, as well
as the Research Vessel POINT SUR,
that are both operated out of the Gulf,
and I've been a part, I've been fortunate to sail on
and actually do some of this research.
And then I'd also like
to thank the Global Explorer ROV team.
So if they put us down there
with an ROV, we wouldn't be producing
too much useful information.
These folks actually make things work, they fly the robot
around and take these really fantastic pictures for us.
And then lastly, I'd like to thank our funding sources
that have funded the research that's a part of my PhD.
So first the NOAA Office of Exploration, as well
as some other offices at NOAA.
And I'd just like to thank you all for tuning in today
and hearing my talk, and I'm really excited to chat
with you more about my research
and whatever you might've found interesting
about what I said today.
Kelly: Thank you, Luke. That was fantastic.
Great explanations about
how all this complicated stuff works.
You really simplified it very nicely.
So folks, if you do have questions for Luke, now is the time
to put them into the question box over there
in the control panel, and we will ask him for you.
So you're not gonna be able to unmute yourself
and ask the questions out loud, but type them
into the question box and then we will start sharing them
with Luke and see how many we can get answered
before we run out of time.
So Luke, one of the questions,
We've been answering some of them
behind the scenes a little bit where we had the knowledge,
but one of them that I would like to clarify
for everyone is, what is the size space you're looking
at when you see one of those pictures?
Is it a matter of feet or inches you're looking at?
-: Yeah, no, that's a great question.
And that's something
that's actually not very apparent even when you've done this
for a long time because you're looking at things
in two dimensions, it's really hard
to give yourself a sense of scale.
You might have noticed it in the picture,
I think there might have been some lasers on.
But what we do is we take green lasers
and actually shine them 10 centimeters apart
at the sea floor to kind of give us a sense of scale.
But what you're looking at and least in some
of the pictures is definitely feet.
So out to maybe 20 feet.
The picture with the big Plumapathes coral,
that's certainly a radius of, you know, 20 feet or so.
You can see pretty far.
But in that zoomed in picture where I showed you five
or six different corals, that's really small.
So that's probably, yeah, a couple of feet across.
Honestly, that's a pretty zoomed in picture.
So there are a lot of corals
that you really need to zoom in to see.
Kelly: Great, we also use those lasers a lot,
but if there's no coral for them
to hit, then you have the lasers just shoot off
into space and you don't measure anything.
I've done that. (laughs) -: Got it.
Kelly: Alright, so question, getting into the weeds here.
First off the bat, do you have access to all the PCR primers
for species you are interested in?
And are new unanticipated species primers becoming available
over time?
-: Yeah, that's an awesome question.
I'm actually the person to ask, (chuckles)
so that's fantastic.
Kelly: Could you explain the terminology please,
because it's talking to me. (laughs)
-: Good point.
Yeah, I almost jumped right
into the weeds without (chuckles) explaining it there.
So PCR first of all is it's a type of reaction
that we can do in the lab that will take a sample of DNA
and amplify or enrich that sample
for a certain number of species in that sample.
So for instance, if I have a sample
of water, I'm capturing DNA from every organism
that might be swimming in that environment.
So that doesn't only include corals that might include fish,
of course, it might include other marine invertebrates.
And so what I wanna do is I wanna actually take the DNA
from corals and basically copy it many, many,
many, many times.
And what a PCR does is exactly
that, it'll just copy it exponentially until you end up
with a sample that is full of coral DNA.
And that's what I'll actually send out
to the sequencing facility to sequence for me.
Now to actually amplify the species you're interested in.
What you need are PCR primers
and these primers are just sequences
that match only to the species you are interested in.
Now, some primers have been developed to amplify
or enrich for sequences from different organisms.
Like there are some that do a really good job
for all marine animals, for instance, there are some
that are really well established for fish.
And so as this technology becomes more
and more accessible, mainly because it's becoming cheaper,
and more and more labs get involved, more
and more PCR primers are being developed.
And so actually a big part of my PhD research
and what you don't see that's behind the scenes,
at least in this talk, is
that I have developed PCR primers specifically
for black corals and soft coral fans.
And I'm actually using those to get the data
that I shared with you today.
And so I guess what I would say to anyone who's interested
in doing this is that more
and more PCR primers will definitely come online.
It's a tricky business to actually get it to work perfectly,
but what I've found is that it's definitely doable
and hopefully we'll have more and more resources
for doing this sort of work in the future.
Kelly: Thank you for explaining that.
So the primer is something you add, an additive
to the water sample, is that what I'm understanding?
-: In a way, so what happens is you take the water sample
and then what I didn't show you is you're actually
going filter that water sample.
What you do is you save the filter
and you'll have captured any particles in the water
that might contain DNA, and then you do one reaction
before the PCR, and that's what we call a DNA purification.
And in that step, you take all the DNA out of the sample
and then the PCR comes next and the PCR actually amplifies
or copies the DNA you're interested in.
Kelly: Got it.
-: So yeah, generally yes, it's taking DNA
from a water sample that you're interested in
and making it much more available to you
and then allowing you to actually sequence it.
Kelly: Thank you.
-: Yep. Sure.
Kelly: Next question, why can't the DNA codes released
from corals at the Flower Garden Banks be matched
with DNA released from reefs off Mexico
and the Caribbean to determine which
reefs originally seeded the Flower Garden Banks?
-: That's a fantastic question.
So to give you an idea
of what I'm doing when I'm talking about sequencing DNA,
at least from environmental DNA, is I'm usually dealing
with pretty short sequences.
And the reason for that is that the sequencing technologies
that we're using are for the moment to
at least do exactly what I want, kind of limited
in that regard.
So I showed you only short sequences of like five letters.
In actuality it's longer than that, it's around 350
to 400 letters, at least the sequences I'm dealing with.
But with that much information,
what you can do pretty confidently
is you can identify corals to the species level.
Now, what you could do with that information
if you collect samples from the Gulf of Mexico
and from the Caribbean,
is you can see how those two habitats might share species.
So in a way, you might be able
to say this coral habitat, let's say Bright Bank
for example, has X, Y, and Z coral species.
And we know that this part of the Caribbean
also has the same three coral species.
And if we know something about the physical oceanography
or how currents move, we might be able
to generate some hypotheses or guesses about how corals
in the Flower Garden Banks
in the Caribbean might be similar,
and how they might actually be exchanging coral colonies
through reproduction.
However, that's as far as you can get
with eDNA to this point.
But some studies have tried to do it a little bit more,
and what you need to do is you need
to sequence a longer part, or you need to target a part
of the genome that's super variable for a given species
to look at how like, let's say a population of one type
of coral is different or more related to a population
of another type of coral in the Caribbean
than it might be into the Atlantic.
And so when you're looking within coral types
to actually see how genetically similar, the same type
of coral is to each other, we're still kind of
in the, I guess we're on the forefront of doing
that from environmental DNA, but
for the time being, it's not something that's widely done.
And that's a big area of ongoing research.
So I hope that helped answer your question.
Kelly: Yes, thank you. And I'm glad somebody asked that.
I've always wondered that.
-: Yeah.
Kelly: Next question, does eDNA degrade
at different rates in the ocean?
Is that something you're able to quantify in your research?
-: Yeah, that's a fantastic question.
And it's something that I actually have quantified.
So I conducted some lab experiments, I guess
over the past couple of years.
That was a project that I started as soon
as I joined the graduate program
and joined Dr. Herrera's Lab.
And what I did is I took coral tissue
and I actually introduced it into experimental tanks
at different temperatures.
And what I did was I just left it there.
I left, I controlled the temperature,
the oxygen concentration and the pH in those tanks.
And then I sampled those tanks every single day
to see how much eDNA was left after a certain time point.
And so what I found, and what a lot
of other studies have found from marine animals, is
that the environmental DNA will degrade faster
at higher temperatures.
And so this makes sense in a lot of ways.
First of all, it may be just
because temperature increases the rate
of chemical reactions.
And so DNA, like any molecule will break down.
And so that might happen faster at higher temperatures.
The other reason could be that things like microbes
that might actually be, in a way, degrading the DNA
by using it for the compounds that it they need for
to make a living themselves, they might also contribute
to breaking down DNA molecules and they might do that faster
at higher temperatures because they can grow faster.
And so that's a great question and what I think I would end
with in regards to that question is
that what you should be aware
of when you're studying a place that's as vast
as the deep sea is what the temperature
is when you're taking an environmental DNA sample.
If you're extremely deep
in the ocean, the temperature is gonna be really low.
And so potentially that means the DNA that is there,
if it hasn't sunk to the bottom and settled
in the sediments, it might be transported
by currents a long distance.
And that's also an area of ongoing research.
And a lot of experiments have looked into that.
And as more and more field data is collected from
around the world from deep sea habitats
with eDNA, we'll certainly be able
to know a lot more confidently about how long exactly
that can last and what your data can look like
from different places.
Kelly: Fantastic, I think we have time
for two more questions.
This one is, are you finding DNA
from unknown species of corals?
-: Yes. Yeah, I am.
That's one
of the coolest parts I think about studying the deep ocean
or the mesophotic ocean, is that, I don't know.
I can't tell you that I'm finding new species,
but what I can tell you is that a lot
of the species I'm finding,
we haven't sequenced their genomes yet.
And so what that means is that this method is only
as powerful as the reference database
that I mentioned earlier.
And so that's built off of research
from around the world, you know, different museums,
different people conducting this sort of research.
And what we really need to do is try
and sequence the genome of every coral that exists
in the ocean and then we could help
to identify all of the species.
But yeah, when I take a look at my data, while I'm able
to confidently identify, you know, a fair amount
of the sequences that I find, there are a lot of sequences
that I can't identify just because
we haven't even sequenced the genome of that coral.
So it's still an area that, you know, there's a lot
of exploration left to do, which is I think why I've been
so kind of intrigued with studying the deep ocean
for so long now.
Kelly: Always plenty to learn.
-: Yep.
Kelly: All right. I think this will be our last question.
What was something that you found most surprising
in your submersible experience?
Any aha or wow moments?
-: Yeah, so this sounds, this sounds silly,
but honestly when we talked about understanding the size
of things, for the longest time I had always been
so confused when a coral would come up onto the deck
of the ship if we had collected it and I take a look at it
and go, oh my gosh, this thing is puny
or this thing is huge.
Because when you see it in two dimensions,
you really just have no idea what it looks like.
And so when you see things
in three dimensions, when you're actually
in the sub, you see how the bottom changes.
There's where I was is very volcanic, so there are big lobes
of lava and so it's a really complex environment.
And then I saw this fish that
for the longest time I had thought was huge.
It's called the tripod fish
and you should definitely Google image search
that deep sea tripod fish like the camera tripod.
And I thought it was huge and then I actually saw one
and it was very small, it was like this big
and it kind of just took, took my breath away.
So, yep. Very cool.
Kelly: Thank you so much, Luke.
So folks, that's all the questions we can take for now,
but Luke, we do have quite a passel of them left.
So I'll be touching base with you
after the program to see what we can do about those.
-: All right, sounds great. Thanks, Kelly.
Thank you all for joining.
Kelly: All right, we're not done yet.
Got a few things to wrap up here folks,
so let me get back to my part of my presentation.
Here we go.
So folks, we hope you enjoyed this final webinar
of our 2023 Seaside Chat series.
Be sure to check back with us next January
and see what we have in store
for the 2024 schedule. You never know.
And depending on the number of questions we have left,
as I mentioned, there are quite a few, we will get with Luke
and see what we can get answered after the webinar ends.
And then we will email out the responses.
For those of you who have participated in the previous three
we've been sending 'em out about a week after the fact.
It'll depend how quickly we can get these answers back
from Luke and some of them we can answer ourselves,
but we will do our best
to get them out to you fairly promptly.
If you'd like to learn more
on your own, we have provided a document full
of resource links in the handouts pane of the control panel,
and if you haven't yet downloaded it,
now would be a very good time.
As always, we welcome your feedback and questions
and you can submit input by replying
to the follow-up email you receive after the webinar,
or by emailing us at flowergarden@noaa.gov.
Today's presentation has also been part
of the National Marine Sanctuary Webinar Series.
While Seaside Chat lasts just one month.
Our National Webinar Series continues throughout the year
to provide you with educational
and scientific expertise, resources,
and training to support ocean and climate literacy.
Be sure to check the website for recordings of past webinars
and the schedule of what's to come.
As a reminder, we will share the recording
of this webinar via the National Marine Sanctuaries
and Flower Garden Banks National Marine Sanctuary website.
Following this webinar, attendees will receive a PDF copy
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If you are an educator
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Please complete this survey immediately
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It should only take you about three minutes,
and we greatly appreciate any feedback you are
willing to share.
Thanks again to Luke McCartin
for a great presentation about coral forensics
in the Mesophotic Zone
at the Flower Garden Banks National Marine Sanctuary.
Luke, it was a pleasure to have you
as our presenter this evening.
Luke: Thank you so much for having me, Kelly.
It was a really great time and super fun to talk
with you all about my research.
Kelly: We enjoyed it. I enjoyed it for sure. (chuckles)
And thanks to all of you for taking the time to join us.
This concludes today's webinar.