Towards Predicting the Fate of Reef Corals (2020-US-45MP-615)

[#1]

Level: Intermediate

Anderson Mayfield, Dr. (assistant scientist), University of Miami

Coral reefs around the globe are threatened by the changing climate, particularly the ever-rising temperature of the oceans. As marine biologists, we normally document death, carrying out surveys on degraded reefs and quantifying the percentage of corals that have succumbed to "bleaching" (the breakdown of the anthozoan-dinoflagellate endosymbiosis upon which reefs are based) or disease. Although these data are critical for managing coral reefs, they come too late to benefit the resident corals. Ideally, we should instead seek to assess the health of corals before they display more visible, late-stage manifestations of severe health decline. Through a series of laboratory and field studies carried out over the past 20 years, we have now developed a better understanding of the cellular cascades involved in the coral stress response; this has resulted in a series of putative molecular biomarkers that could be used to assess reef corals health on a proactive, pre-death timescale. In this presentation, I will review progress in reef coral diagnostics and show how I have used JMP Pro to develop models with the predictive capacity to forecast which corals are most susceptible to environmental change. A similar approach for instead identifying resilient corals will also be presented.

Auto-generated transcript...

Speaker	Transcript
Anderson Mayfield	Alright everybody, thanks for tuning in. My name is Anderson Mayfield and I'm an assistant scientist at NOAA as well as the University of Miami.
	And today I'm going to be talking to you about some of the research I've been doing over the past 20 or so years on towards predicting the fate of reef corals.
	And because I'm going to try to cover a lot of material in the next 35-40 minutes, I want to go ahead and acknowledge my funding agencies right here from the get go, particularly NSF, NOAA,
	Living Oceans Foundation. A lot of the work I've been fortunate enough to be able to do over my career has taken place in remote
	locations using some pretty new technologies that tend to be expensive, so I've been really fortunate to partner with these excellent agencies that have supported this work.
	So I'm actually interested in all facets of coral biology from the basic cell biology. How do the cells function on a day in, day out basis. Cells are really crowded as I'm going to show you.
	I did a pretty long stint where I was basically doing the aquarium studies where I challenged corals with different stressors like temperatures and ocean acidification,
	PCO2 levels. and we were doing this in microcosms and mesocosms. We call this environmental physiology and...I'm actually going to show you some data on this today.
	What I've really gotten into the last few years, which is kind of the heart of this presentation is predictions.
	Here I'm referring to it is molecular diagnostics. How do we know if a coral is sick? We usually wait until it's almost dead to diagnose it. What I want to do is kind of try to push...
	push it from this retroactive diagnostic approach to a more proactive one. Can we detect subtle decreases in coral health before they start to get sick?
	Can we make predictions about which ones will fare best in the coming decades and which ones will not?
	So this is kind of the heart of what I do on my day in and day out basis, as well as one I'm going to talk about today.
	So I apologize to those of you have heard some of my JMP talks before; you're going to see a lot of repetition,
	but I basically want to get everybody on the same page with some of their coral reef biology that will be critical to understanding
	why I did things the way I did them. I'm going to talk about some problems facing coral reefs. Unfortunately, most of us now working in the coral reef field,
	not only just studying coral reefs because they're beautiful and fascinating, but also because they're dying at such rapid rates.
	Then I'm going to talk about two completely different, but potentially complimentary approaches for predicting coral fate. One of them's looking at basically global temperature trends from satellite data. This is what most people rely on
	as we speak right now. Then I'll talk to you about some new data and I'm going to use JMP to show you how quickly you can go from getting some some molecular analyte data right off the machine
	and go directly into making predictions using a cell-based approach. So instead of looking at global temperature patterns to make predictions about coral health, we're actually looking inside of the coral cells to see if we can diagnose anything that might be going awry.
	Because I'm going to try to cover so much in a relatively compressed amount of time, I'm inherently going to gloss over things. So if you have any questions, I'm uploading
	all the data I'm going to show you today. There's hidden slides. So there's some things that you may see me make in JMP and you don't understand what happened.
	They're actually within the PowerPoint. So if you go to download it, you can see the nitty gritty, step by step, analytical details.
	You can either do that. You can, you can, I'm making all the data open access, the PowerPoint, so email me. You can check out my personal website that I've listed here.
	I'm definitely happy to answer any questions. And I think these data are important. So, you know, they're not published yet. But, you know, feel free to take a look at them at you at your leisure.
	So I think most people have a general idea of what a coral reef is. I'm I just want to throw out the definition right from the get go, it's a calcium carbonate based structure.
	It's been built by an animal-plant symbiosis. They like warmer water. But as you'll see soon, not too warm.
	They tend to be near the equator and the tropics, tend to have very high biodiversity, of fish, invertebrates. As you can see from this picture,
	there's tons of hiding places for small organisms. This means they're important nurseries for commercially important fisheries and literally buffer coastline
	from...coastlines from storm and wave damage that provide a number of ecosystem services to humans. Frankly, that's not why I studied coral reefs. I study them because I think
	they're beautiful. I love to scuba dive. And I think the underlying framework-building organisms are really fascinating in and of themselves and thus, the reef coral.
	A reef coral, actually, it's not just an animal. It has plant cells specifically dinoflagellate algae within about half of its tissues.
	These dinoflagellates, which I've shown you here, this tongue twisting family name is Symbiodiniaceae, these dinoflagellates are photosynthetically active. They fix carbon from some sunlight, just like a plant would and they translocate the carbon they fix into their host
	Yes. Corals can feed; they've got specialized stinging cells called nematocysts that all cnidarians have,
	but frankly they rely on their endosymbiots for most of their nutritional needs. The endosymbiots are also getting
	something, they're getting the waste products from the coral for their metabolism. They're getting shelter. It's a really intricate
	mutualistic association that's been the focus of study for over 50 years, but there's still many key facets that we don't understand.
	Fact of the matter is, what you need to know for this talk is coral is about a two-third animal, one-third plant from a physiological
	physiologist perspective. So it's basically the physiological oxymoron, in the sense that it's an animal that can photosynthesize via this mutualistic symbiosis with the dinoflagellate algae.
	You want to understand the health of a coral, you're going to need to focus not just on the coral itself, but on its dinoflagellate endosymbiots. And it's actually goes beyond that.
	Corals host an entire mini ecosystem that we call the microbiome. There's a plethora of bacteria, viruses, fungi that live on, within, or even inside of the coral skeleton.
	I'm only really going to talk about the dinoflagellates and the coral host today, but suffice to say if you really want to have a holistic understanding you need to consider the, the whole what we call a quote unquote holobiont, which is an amalgamation of host and symbiot.
	So I think this is probably something that's already known to most to you. There's numerous global threats to coral reefs. There's things like coastal development, leading to seawater pollution. There's overfishing.
	In Florida, we are particularly concerned with disease. Right now there's one called stony coral tissue loss diseases ravaging Florida's reefs.
	But on a global scale, what I would, what I would hazard to say most coral biologists would put as the major threat to coral reefs is climate change. The reason
	these corals are basically already living near the upper threshold of their thermo tolerance. If you push that temperature a little bit higher
	than what they can take, they're going to bleach. So you're going to see what you see in this picture here. And what that means is they either lost their dinoflagellates.
	They've either expelled them, they've digested them. The dinoflagellants might still be in the coral, but they've lost their
	these corals can no longer photosynthesize, which means they can no longer nourish themselves.
	If they're not able to rapidly reacquire symbionts, or perhaps get a flush of ...a food rich seawater that goes past them, they're going to starve to death and die.
	So usually what you see is when you go about one degree Celsius above the trailing mean high temperature of the year, that's when you see bleaching.
	And this has been known for decades. So what NOAA did about 20 years ago, they started this program called Coral Reef Watch. It's really nice website. I recommend you to check it out. And it's based on a really simple idea. You expose corals to water that's hotter than normal for them
	for long periods of time, that's universally bad. The idea is known as the degree heating week, so I'll try to explain it.
	This is...I apologize for the low resolution figure, but it's it's their instructional one they include on their website. So let's walk through this figure, because this is important.
	So on the left y axis, you have SST that stands for sea surface temperature, that's satellite inferred temperature data.
	On the right we have a degree heating week, which is basically an integral of the degrees in Celsius above normal multiplied by the time. So in this case, that the hatched blue line at about 29 degrees is the trailing mean of the hottest month of the year, which in this case looks to be perhaps
	I guess in the summer.
	So you start accruing stress at one degree above this trailing monthly mean. So that would be 29 plus one is 30.
	So the time these corals spend above 30 degrees, and this example is from Palmyra Atoll,
	is when you're accruing these degree heating weeks. So if you have one degrees Celsius above the mean monthly high for four weeks, that would be four degree heating weeks.
	You had two degrees Celsius above the mean monthly high, so in this case 31, for two weeks, that would also be four degree heating weeks. So, this...
	their kind of underlying hypothesis is, you know, two degrees C above the mean monthly high for two weeks is going to result in kind of the same bleaching endpoint
	as the one degree for four weeks. From a physiologist physiologist perspective there might be some issues with this, but I think overall, this is a pretty good
	metric. And what their kind of underlying benchmark is, once you get above about four degree heating weeks, once you get into that four to eight window, you're probably going to start to see bleaching.
	So,
	they've got some really nice gifs on the website that are showing you past data. So this is looking at the trailing, I think, three or four months.
	So this is looking at the Caribbean and there, basically where you're seeing red, this is when you're having the degree heating weeks of four to eight. This is where they're predicting bleaching is actually going to happen.
	They don't do...NOAA itself doesn't do really any ground truthing so
	they rely on individuals to, you know, email and phone in saying, "Hey you know your prediction in this particular reef that I like is wrong.
	Or this was right." I think, you know, and these days for a lot of us are sitting at home. We can't dive.
	This kind of in silico science is, you know, maybe it's going to be the best we can do. And this summer is just, is watch how the temperatures progress and then hope the corals can weather the storm.
	And there's a totally different predictive, I would say, approach for looking at coral health
	and this is actually not looking at...so the Coral Reef Watch is looking kind of within a year, showing you the progression of bleaching
	over the hottest part of the year. And they actually extend four months into the future. So their algorithms will try to project
	as you would with weather, what's going to happen on those reefs in the coming four months. In this model, which is kind of a
	combination of the NOAA's Coral Watch with some some UN models based on IBCC climate change production...projections,
	it's looking at something a little bit different. So here, instead of seeing temperatures in the cells, you're actually seeing year of onset of annual severe bleaching.
	What does that mean? This is the year they predict, based on temperature records and protect...projected degree heating weeks, you're going to start seeing bleaching
	every year. And that's scary because if corals bleach for one year,
	in one hot summer, for instance, you might see some death but corals are going to recover. Some are going to acclimatize. You might even see adaptation
	When you start having repeat years of bleaching, where there's basically no respite, this is when corals will, coral reefs really start to degrade. And you can see this is scary, because if you look at the scale,
	2015, that's obviously already past. We've got reefs (this is a map of South Florida here) we've got reefs that are already predicted to be bleaching in the entirety of these pixels which are about 25 by 25 kilometers, to already be bleaching every year.
	So what I'm interested in, I'm a a physiologist. I want...I don't want to try to contradict these models, what I want to try to do
	is delve into each of these 25 by 25 kilometers squares, because we know these are global scale models. They're not telling you
	that every single coral and in these pixels is going to bleach. We know there's going to be heterogeneity. We know there's going to be some stronger species. Even within species, there's going to be stronger genotypes.
	This is what people like me are interested in. Can we improve the spatial resolution of these models and maybe even the temporal resolution by factoring in
	data from the coral themselves? This is just looking at temperature. How could we merge this with the health of the actual corals? So prior to my coming to NOAA,
	a year and a half ago, there's actually been a great body of work done in the upper Florida Keys, which is excellent for me. We've already got
	coral reefs, we know everything about their oceanography, their ecology for the past 20 or 30 years. For somebody like me who wants to go
	take samples, do some analyses, make predictions, this is a really great setup to have. So I'm going to be talking about four sites in particular, really. I'm just going to be talking about Cheeca Rocks, but I just want to show you right here is we've got this
	The Rocks and Cheeca Rocks is our kind of our preferred inshore reef sites. Little Conch and Crocker Reef are offshore, there's actually many more than this.
	But we know from our large data set from the past 20 or 30 years, that these inshore reefs are more resilient.
	Corals are stronger, coral covers higher, they resist disease and high temperatures better. And this is because they've been stress hardened
	These environments are abysmal. So it's kind of a paradox, they are living in dirty
	turbid water that corals..high-nutrient water the corals normally wouldn't thrive in but they've adapted or perhaps acclimatized to living there. So now when there's future stressors that come at them, they're better able to resist them. So
	while the offshore reefs might be the ones you want to spend your vacation at, the water has that beautiful Caribbean look,
	but the corals look like you see on the right. They're just little patches of coral. Most of it has been killed by bleaching and disease. Inshore reefs, you can still see these large
	massive coral colonies. This species you see here is Orbicella faveolata, and that's going to be the one I feature in this talk.
	You actually can get some really nice images from Cheeca Rocks, in particular. Some National Marine Sanctuary on some NOAA websites, particularly this one, you can do a virtual dive.
	So let's look at the temperature data from Cheeco Rocks and kind of consider it in the context of what I was telling you earlier about those degree heating weeks and
	NOAA's coral watch predictions. So actually I made this in Graph Builder, I should mention that when I go to JMP later I'm actually using
	a beta version of 16. But as I'm not going to feature any tools that aren't already available to JMP 15 users.
	It's going to be very basic things. So there's nothing inherently JMP 16 specific that I'm going to show you in this talk.
	So here I use Graph Builder, what I've done, I've tried to kind of emulate NOAA's coral watch graph, but just focusing on Cheeca Rocks. So we've got the sea surface temperature on the left y axis,
	the degree heating weeks on the right. So the trailing mean temperature at Cheeca Rocks, so the highest temperature of the year is in July and August. And it's 31 degrees, which is already really hot for a coral reef.
	If you use the kind of UN NOAA recommendation of the mean monthly maximum plus one, that would be 32 degrees. So you would expect corals to start accruing stress
	above 32 degrees. You would calculate your degree heating weeks based on the time the temperature was above 32. However, we know that that's actually too hot. If you
	did your degree heating weeks based on 32, you would never reach that four degree heating week threshold, which you can see is the bottom-most hatched red line here.
	Instead, what I've done in this plot is I reset the degree heating week calculation in JMP to 31.3. That's
	kind of our bleaching threshold. We know since we go to these sites so often, 32 is too high. Once these corals are above 31.3
	for four to eight weeks, that's when they start to bleach. So you know it's not to say that the NOAA coral watch models are bad, it's just in particular locations, they might need some tweaking with your own field observations.
	So this is actually looking at the years we've been studying Cheeca Rocks in detail. And you can see, we first started seeing bleaching in 2014 and 15 and the degree heating weeks in those years, based on our 31.3
	threshold, which is the solid red line, was over 10, which is a lot.
	So we would definitely expect to see bleaching in those years. The anomaly is 2016. 2016 is kind of obscured in the graph, but you can see the top of that, the top-most red
	column is pretty much in that nine to 10 degree heating week ballpark. The reefs should have bleached that year, but they didn't.
	So that could be, you know, acclimatization or just recovery in general, but that's the anomalous year. 2017 was a cooler year even though we saw degree heating weeks of eight, the reefs didn't bleach, but then 2018 bleaching, 2019 bleaching.
	And then I just this morning updated this to zoom in to 2020 and sadly, when I first made this presentation a few weeks ago,
	you know, we didn't have any bleaching threats, but now you can see the red bars creeping above four as the temperature's been above 31.3 these past few weeks, so unfortunately we're probably going to have another bleaching year.
	So we have...the good thing about working with corals is they're sessile, so they don't move, except for when their larvae. So within these sites,
	not only can we go look at, you know, bleaching
	on a year in, year out basis, we've got tagged colonies. We can sample them at different times, we can see how their physiology changes in concert with these temperature changes.
	And then we could actually, we actually have the luxury, since we know what ended up happening each year with respect to bleaching, you know, we can hindcast. We know, hey, I took the sample in March;
	that coral bleached in August. Maybe we could look into those biopsies that we took earlier and see if we can detect any stress.
	What I really want to do is not so much look at the timeline of bleaching process, because I think Coral Watch is doing that well enough,
	more bleaching in the summer. We're not going to be able to improve upon that. Maybe you can get the timing a little bit better. What I really want to know is,
	why in this particular instance, do you see partially bleached (that's the PB), bleached (that's the BL), or the NB (not bleached), why do you see
	this heterogeneity? It's not as obvious except for maybe if you look in the bottom right, you see paling colonies. You see colonies that aren't paling.
	Why are some corals stronger than others? Can we use information from these colonies to basically make a test that would create a signature, a proteomic or a molecular signature of a stressed colony
	versus a resilient one. This is what I think would actually be more useful. Might not be able to to
	...to know ahead of time which corals are going to bleach first or bleach second. But we might be able to know, hey, based on my
	biopsy, based on my molecular analysis and based on my resulting predictive model, this coral, I'm predicting, is going to be able to better resist bleaching from this one over here.
	So that's kind of my goal. And I've been trying to tackle this over the past, since I was a PhD student in Hawaii.
	It's mainly doing gene expression stuff, looking to see if we can find any gene ??? that shoot up an expression in corals that are more stress-susceptible.
	And maybe they are not used at all in resilient corals or maybe it's vice versa. Maybe there's genes that are only used by the hardy corals. These are things we can measure.
	I later found out that there's really no correlation between gene expression and protein concentrations
	in corals. So yes, you could still use the gene data for biomarker analysis. Gene expression data might still be really useful in making predictions about coral health,
	but if you want to know what's going on in the cells simultaneously, if you want to know about the cellular behavior, you actually need to look at the proteins. You can't infer
	the protein levels from the gene expression levels, because the R squared for corals is essentially, and for their symbiots, is essentially zero. So I made a kind of a dramatic shift in my research into proteomics about two or three years ago.
	So what I wanted to show you today originally, when I first wrote this abstract was
	field data from our tagged colonies to show how their protein signatures move over time
	for the stress-susceptible and the resilient corals. And that's going to be my number one thing I'm going to do when when our labs reopen. Unfortunately,
	we're not allowed to do lab work right now because of COVID. We're not actually allowed to do field work. So instead what I'm going to show you some experimental data that I think still might be useful
	at getting to some of these questions. So basically we have our favorite coral, Orbicella faveolata, here.
	This is a paling one from the upper Florida Keys. We took them from those four fields sites I showed you earlier,
	and we did a simple experiment. We did a five-day study at a controlled temperature of 30 versus a very high temperature of 33. These are going to be coded red
	in the figures, or maybe with a V which is for very high. And then we did some kind of a more realistic study with a 31-day exposure of the same control temperature, but to a more environmentally relevant high temperature of 32.
	You remember 32 is getting into that area where most corals can't resist exposure to 32 over prolonged period.
	So what I did...well, what I wanted to do was look into the cells of these corals and see if there any proteins that are only found in corals that proceed to bleach.
	Are there any that are only found in the resilient ones that are able to acclimate?
	So I took a shotgun proteomics approaches. It's a fancy way of just saying I just sequenced all the proteins that were in that sample with mass spectrometry.
	It's actually not simple at all if you get into the nitty gritty of the molecular analyses and the mass spectrometer. Not going to go into that today, just want to mention that we use this
	Thermo Fisher mass spectrometer called the Q Exactive. It's one of the best analytical instruments ever developed. It's amazing what it can do and its sensitivity.
	But I do want to reemphasize that when you do these types of analyses with coral, we're getting the coral proteins and you're getting dinoflagellate proteins. It's very important to look at both. You might have ....