Marine Microbes: Kim B. Ritchie’s Research on Coral Reefs and Beneficial Bacteria

Richard Jacobs: Hello, this is Richard Jacobs with the Finding Genius podcast. I have Kim Ritchie. She is an associate professor of genetics and prokaryotic cell biology at the University of South Carolina at Buford. We are going to talk about microbes associated with corals and coral reefs and go into that. So, Kim, thanks for coming. 

Kim B. Ritchie: Thank you for having me.    

Richard Jacobs: Yeah, what got you into coral reefs and studying them and prokaryotes? It seems that everyone is into eukaryotes and prokaryotes are forbidden. 

Kim B. Ritchie: Yeah, that’s the challenge. I actually got started as an undergraduate in the University of South Carolina, Akon, working on; actually, my project was looking at bacteria on corals and at the time, very little was known about that so very little work was done on this and it’s also a time when coral diseases started exploding. I don’t know how familiar listeners are with coral bleaching and then coral diseases. Corals are animals but they have this obligate symbiosis with the intercellular single-celled algae, it’s a single-celled dinoflagellate really that photosynthesizes. 

Richard Jacobs: a quick question here. Is this an endosymbiosis? Is the photosynthetic organism inside the cells that make up the coral or just next to them?  

Kim B. Ritchie: it’s inside the gastrodermal tissue in the coral. So, yes and I get that was actually known about that symbiosis. At the time, very little was known about other types of microbial symbiosis with corals and that’s what I studied, particularly bacteria that I could culture from corals and we began looking into some of the diseases that corals have because they are so super-sensitive to temperature changes and this was right about the time the 70s, 80s, and early 90s when coral bleaching and coral diseases started getting a lot of attention. 

Richard Jacobs: So, what causes coral bleaching and corals to die off? What is that process and why does it happen?   

Kim B. Ritchie: So, as I mentioned, this is an obligate symbiosis with those single-celled algae that live inside the coral tissue. Corals actually lay down a calcium carbonate with the help of that endosymbiont and that’s just part of the reef structure that we are so used to seeing that’s so important in the oceans for nurturing habitats and shoreline protection and other types of ecosystems. But they are super-sensitive. So, this symbiosis, this mutualism is actually very sensitive to even a little bit of temperature change and other things now but temperature change was the big thing that got noticed early on and when the corals get stressed out sometimes they will expel those single-celled algae and it’s called coral bleaching because corals are very thin tissue layers to the tissue layers.

So, that essentially pretty much the colors that you see in the corals come from the endosymbiotic algae, and when it’s expelled all that you see is that white calcium carbonate skeleton underneath those, kind of referred to as bleaching but the tissue is actually still there. 

Richard Jacobs: Quick question, what’s to prevent the photosynthetic algae from repopulating the coral?  

Kim B. Ritchie: Well, that’s a good question because they often do. So, the idea, my understanding is that there are low levels of these cells still present and they may repopulate and then the alternate hypothesis is that they acquire these free-living versions of single-celled algae from the environment and repopulate. So, some corals are better repopulating after their bleach than others. Some are a little more sensitive and almost always die. The tissue will fluff off or they will start to get disease in the footprint of where the bleaching was. So, it depends on the coral but it generally is trouble or the coral. 

Richard Jacobs: So, what is it? The temperature of the ambient water, probably pH, maybe nutrient availability, things like that?  

Kim B. Ritchie:  Exactly. 

Richard Jacobs: So you think perhaps it’s some; so, do you think it’s the coral expelling the photosynthetic bacteria or do you think the bacteria are saying, hey, the environment here is not working out and we are getting out of here? 

Kim B. Ritchie: So, the photosynthetic algae, that actually is a eukaryote but not a bacteria and in the past, some people have done experiments very carefully showing that both can happen. So, it’s kind of either the algae decides to hit the road or the corals expel them. So, I think a general idea is that both can happen. 

Richard Jacobs: Yeah, because I’ve learned about viruses that seem to be like commensal with their host, sometimes when conditions get bad, this guy Forest Rohwer says they are like rats leaving the ship. They say we are out of here. So, they will turn into a more adversarial form and then blow their way out. I guess it’s them evaluating their conditions the same inside instead of one skeleton. So, okay, you have been studying corals for quite a long time. How long? 

Kim B. Ritchie: Since 1992. 

Richard Jacobs: Oh wow. Okay. So what has changed in your study over time? What do you know now that wasn’t known at first and what are the implications? 

Kim B. Ritchie: At first I was studying microbial shifts, so I was looking at what types of bacteria that are associated with the coral and the single-celled algae are present under normal conditions. So, they were non-stressful conditions and how that shifts when the temperature is increased. So that was one of the early; the early thing we discovered that was a little surprising is you get a shift from a normal bacterial composition to more of a pathogenic realm. The pathogen, because it’s a type of takeover because of vibrio type organisms which are known to be marine pathogens kind of shift into a higher abundance on these corals. 

Richard Jacobs: Do they take up residence on the coral just like the photosynthetic bacteria did? What do they do? How do they change that ambient environment, the pathogens, once they are there?  

Kim B. Ritchie: That’s a good point and it’s hard to know if that’s correlated but temperature, they also grow better in warmer temperatures but they seem to dominate the reefs and there are a lot of people that have been working on this since then and show that you can actually add some of these pathogenic bacteria, these vibrions back and it can actually cause bleaching or disease in corals. So, that was some of the earlier work but I actually wasn’t all that interested in pathogenic work, looking at the bad bacteria. So, all oceans, all organisms actually have microbes associated with them. Very few of them are pathogenic. The vast majority of microbes associated with hosts are beneficial. So, I became interested in what these bacteria associated with corals may be doing for the host. So that was the next leg of research on beneficial microbes in corals. 

Richard Jacobs: well, the bacteria probably is, it’s like a coral’s microbiome. They are probably relying on the metabolites from the photosynthetic bacteria and perhaps from the coral itself and they are ingesting them and then spitting out their own metabolites which benefit the corals. 

Kim B. Ritchie: Exactly. So many different roles, so many different potentially beneficial roles, and nutrients. 

Richard Jacobs: Have you tried to culture, I don’t know if you call it culturing but have you tried to culture coral in a tank to make sure that there are no bacteria or actively kill them off to see if they will still function as a coral with the photosynthetic organisms? 

Kim B. Ritchie: Some people have tried that; it doesn’t work out well. That’s another problem with studying corals is that they are so intricately intertwined with their endosymbiotic algae and they also seem to need their beneficial bacteria as well. So, if you add antibiotics back to corals in tanks, you get a microbial shift but it’s generally not beneficial for the coral. 

Richard Jacobs: So, it sounds like they are similar to us. We have our gut bacteria and everything and without them, we don’t function as well. 

Kim B. Ritchie: That’s exactly the same kind of example.  

Richard Jacobs: So, what are you trying to figure out right now? What’s your current research?

Kim B. Ritchie: So, I tend to do a culture-based approach, meaning when I say culture-based, I’m not talking about the coral at this point but the bacteria. So, I like to grow the bacteria from the coral and then ask what they do. An awful lot of people are doing metagenomics type approaches but I like to be able to grow them in labs so that I can do experiments with them. The problem with this is that less than 1% of the bacteria can be cultured. That’s an estimate. I’m not sure how accurate that is but still, it’s kind of a good little single-celled model system to be able to grow some of the bacteria that are on corals and ask what they do, and one of the things that I look for is antibiotic production. So, antibiotics are produced naturally from microbes and they produce them as chemical weapons to help secure a niche for themselves. 

So, it makes perfect sense that bacteria who have been evolving in the oceans for billions of years would kind of co-evolve this beneficial association with other ancient organisms like corals and might provide kind of the first line of defense like an innate immune system for the coral. So, some of the types of experiments that I would do would be to actually remove the surface slime off the coral and see if it has antibiotic activities and you can show that it does and then culture some of the bacteria from the surface slime and ask if they produce antibiotics and roughly 30% of them do. 

Richard Jacobs: I don’t know if you could study them alone because it sounds like the bacteria, without the coral and without the photosynthetic organisms, they may not produce anything that they produce in that context and you probably can’t even culture them. So, it sounds like the only way to study them is in their full context, in their full environment. You may have other trade-offs, figuring out what’s going on. 

Kim B. Ritchie: Yes, exactly. It’s very hard to say for sure that they are going to be producing antibiotics on the coral surface but it’s also impossible to study them in that setting. So, one of the ways that I try to get around that is by using the coral mucus as a selection scheme. So, the antibiotic activity in the coral mucus, I use to see if I can enrich the number of antibiotic-producing bacteria. So, the idea is that if bacteria really are producing antibiotics on the coral surface, they would be immune to or resistant to the antibiotic that is present on the surface of the coral. So, when I did this, I could actually enrich for antibiotic-producing bacteria. So, we get a higher percentage of bacteria that I culture who produce antibiotics against a range of different pathogens. 

Richard Jacobs: What do you mean they are producing antibiotics? Against who or what? 

Kim B. Ritchie: Well, when I test for antibiotic production, I will test them against a range of different gram-positive and gram-negative pathogens. Some of these are marine pathogens, some of them are coral pathogens, some of them are human pathogens as well. 

Richard Jacobs: So, the antibiotic that they produce, is that to keep other bacteria away or what would be the purpose of that? 

Kim B. Ritchie:  The idea is that they keep other pathogenic bacteria away. One thing that I notice when I sample coral, seasonally is that during warmup months and during bleaching months they lose that antibiotic activity in the surface mucus of the coral and they also lose the bacteria that may be producing antibiotics for them. What they gain is there are pathogenic bacteria. So there are vibrio type bacteria that swamp out the other types of bacteria and you no longer can culture bacteria that produce antibiotics and you can no longer measure antibiotic activity on the surface of the coral.  

Richard Jacobs: So, is it just antibiotics, you think the predominant thing it is making or is there again, helpful metabolites that will help the photosynthetic organisms and the coral itself continue?

Kim B. Ritchie: Well, there could be a number of things. So, it’s also possible that the symbiont or the single-celled algae that’s inside the coral are producing compounds. So, when they bleach or when the temperature goes lower, they go away so you no longer have antibiotic activity. So, it could be a number of things. That’s part of the problem with corals and it’s very hard to find a good model organism for corals. 

Richard Jacobs: Is it difficult to study everything in situ? I mean, again, why not culture a coral with photosynthetic bacteria, everything all in one place in a tank and then sample and then sequence? Why not do it in situ and see?

Kim B. Ritchie: Because you still never would be able to tease apart whether it was the coral animal, the endosymbiotic algae or the bacteria that were really producing this activity. Unless you mean to be able to do exactly or orderly you try to get rid of the bacteria and see if that made a difference but that’s hard to do. 

Richard Jacobs: But at least if you could see the presence of certain compounds, I mean that would tell you something about their existence or the lack of them. You may not know who produced them but at least you’d see the existence of them and that might be a start. Like, if you know what’s there, you just don’t know who is producing it or   

Kim B. Ritchie: Yeah, we know what’s there. We know that there is an antibiotic activity associated with corals. We don’t know what the compound is exactly. We know that there is an antibiotic activity associated with bacteria that you can culture from them but being able to say definitively what organism is producing it is a little tricky. 

Richard Jacobs: So, what is the majority of things that are produced? Is it just antibiotics to stave off other hostile bacteria or again, have you classified even a class of compounds and metabolites that are helpful so the whole aqua system can continue like. In addition, above and beyond antibiotics, there must be other things there? 

Kim B. Ritchie: yeah, there seems to be a wide range of different things, and a lot of the chemistry hasn’t been done. One thing that I do know just based on bio essays is that a lot of these compounds are anti-microbial peptides or roughly half of them are anti-microbial peptides and others are other types of compounds. But the interesting thing is maybe not what they are but that the corals have this protection on them, regardless of where it comes from, and when the temperature is increased that protection goes away. So they tend to be more susceptible to diseases and this is one potential mechanism for why they are more susceptible to diseases when the temperatures increase. 

Richard Jacobs: So, have you looked at many different types of coral to see the expression of the anti-microbial peptides or just one? 

Kim B. Ritchie: I mostly did my work with one of the threatened corals, the Crawford corals called elkhorn corals, it’s a common name in the Florida Keys and I’ve looked at other aquaporins and yeah, other types of coral species in the Caribbean. Since that time, a lot of different people worldwide have looked at these types of activities of corals in their oceans. So, yeah, it’s been more carefully done 

Richard Jacobs: So, what important questions are you trying to answer right now? Are you trying to see who is producing these antimicrobial peptides or what the roles are or what specific microbes they would counter?

Kim B. Ritchie: Yeah, I am mostly interested in what they are doing and if they are doing that for the coral species. I am also interested in other types of interactions. So, kind of in an attempt to get at what organisms might be producing this, you could actually culture this single-celled algae that live within the coral tissue. The corals don’t live without them but if you give them the right nutrients, you can culture them and I got some of these cultures from different laboratories and to see if they produced antimicrobial compounds. But one thing I discovered before I got too far was that they also have bacteria associated with them that you can’t get rid of. If you try to treat them with antibiotics, they don’t grow very well. 

They just need their bacteria to grow in these cultures in the laboratory so I started looking to see what bacteria were associated with them to find a least common denominator and I found about 3 main groups of bacteria that were in common, no matter what culture I used and some of these produce antibiotics as well. So I’m going to attempt to try to tease these things apart. So I am also interested in that multipartite symbiosis aspect because some of these bacteria seem to help the symbiogenium grow better, they produce antibiotics. They are always associated with them. So, it’s kind of a worlds within worlds scenario where you’ve got the coral and you’ve got the single-celled algae and then you’ve got the bacteria that help the algae grow and then we even did a study with some collaborators at the University of South Florida that found a potentially beneficial virus associated with the bacteria that seems to help the symbiogenium of the bacteria, the single-celled algae grow that helps the coral grow. 

Richard Jacobs: I was going to say, right. There are phages, I’m sure associated with them and they may be parasites. I mean, why not assume that they are like just any other organism, like us, like dogs, like any halobiont? It seems like there is a resistance to think that something like a coral could be complicated in its own way as we are, but it sounds like it is. 

Kim B. Ritchie: It’s less of resistance, I think and just a really unknown and we studied symbiotic associations between hosts and microbes for the past 30 years. So, very little is known unless it’s an obvious symbiosis like the bacteria that glow in the dark inside of the Hawaiian bobtail squid. It’s kind of an obvious one to notice. But these subtle ones fascinate me and I am really more interested in multi-partite symbiosis and what they are doing for the host.  

Richard Jacobs: Do you think; are you willing to look at a different system to get at. I mean, my thought here is that since it seems like a lot of different halobionts have this same scheme, bacteria, the cells of the creature or phages, their own viruses, etc. this whole complicated system. Is there a system that you could postulate or think of that would be easier to study, that still has all these dynamics, that may answer the question at least in that system, and then it will probably translate into this system pretty closely? 

Kim B. Ritchie: yeah, that is the question and people are trying to come up with a good model system for corals and some researchers have made a lot of progress a little sea anemone called Aiptasia palladia is a model system for corals. It doesn’t lay down calcium carbonate so it has a lot of resistors to people who think that it should not be a model system for corals but it’s really easy to handle in a lab and we’ve actually done experiments using that particular sea anemone and looking at some of these potentially beneficial bacteria to see if they can fight off coral disease pathogens and we show that it’s a great model system for showing that you can actually use some of these beneficial. I think it’s hard to prove bacteria that produce antibiotics and pre-treat these anemones or co-infect them with coral pathogens and it prevents pathogen infection and death. 

Richard Jacobs: Then you have the creatures that grow on the coral and creatures that, even fish swim in and out of corals and they brush against it and eventually their skin is altered by that constant contact and certainly anemones or other things that grow on the coral as a base, I mean they are definitely going to be benefiting from something in the coral. The bacteria, I mean the whole thing is just one ecosystem. 

Kim B. Ritchie: The corals are all connected, yes and that’s the challenge with studying things on coral reefs. That’s why the model system approach that you mentioned, bringing it into a laboratory is at least you can control some things. You can’t get rid of all of their beneficial microbes or you kill it but you can at least control some of those types of variables. 

Richard Jacobs: Maybe it’s useful to study what is thought of as dead corals because they probably are not. there is probably some pathogenic regime, there is probably something there. Maybe it’s more similar and stripped down. 

Kim B. Ritchie: Well, the entire microbiome changes when something is dead or overgrown.  

Richard Jacobs: Alright, but it still may have some kind of all these levels of complexity. Maybe it’s easier to study for some reason. Maybe it’s in a regime where we think it’s dead but it’s still study-able and still these relationships, even though they’re just not is healthy, is there more to this?

Kim B. Ritchie: Yeah, that’s a good point when you are thinking about bleached corals where that animal is still alive but they don’t have the single-celled algae within, and that sort of is variable control. One thing we see when corals die though is that they immediately get overgrown back in. so, it’s not normally in healthy corals because they get swamped out in a hurry. It seems like that. 

Richard Jacobs: So things are kept at bay. When I think of a, for instance, if I take kombucha. If I make one, it’s bacteria there that come in and set up shop and acidify the environment and keep out other bacteria. So, if something like that happens and I’m sure it happens in every environment with every creature, there are microbes that associate with that creature and they want to keep out other ones. So, as I said, they produce antimicrobial peptides, they set up shop and keep everyone else out 

Kim B. Ritchie: Yes. 

Richard Jacobs: Well, very good. So what are some of the, just recently, what are the breakthroughs or insights you had or what do you think you are approaching?   

Kim B. Ritchie: Another thing that’s been interesting about this is that looking at other ancient herds in the ocean as well. So, one of the other things that I have started working on is we recently are working on bacterial associations with sharks and rays. So, this kind of came about based on my co-workers at Milton Marine Laboratory which is where I worked for many years.

We have a big shark research group there and Carl Lure and Cathy Walsh were looking at wound healing in sharks and rays so they are interested in sort of anecdotal information based on observations showing that sharks and rays heal their wounds very quickly and these are ancient organisms that also have an ancient immune system that’s not based on bone marrow like our immune system. They are cartilaginous fishes. 

So we ended up doing some work where their portion of the research, it was looking at wound healing and what types of compounds are produced and my portion was looking to see if any bacteria associated with that epidermal surfaces produced antibiotics as well. So, I mentioned my main area of research is microbial ecology. So, I’m really interested in what the microbes are doing for the host. But another way to get people interested in the conservation of some of these animals, especially if they are more human-centric versus planet centric is by pointing out that there are so many novel compounds associated with these ancient organisms that could be used for new antibiotics. So, one of the problems that humans have is the antibiotic-resistant bacteria that are in hospitals now in various different health care organizations. 

We are running out of antibiotics that actually treat them because there are so many resistant organisms. So, one of the pathogens that I screen these marine bacteria against is MRSA, Methicillin-resistant Staphylococcus aureus, also vancomycin-resistant staphylococcus, and some other human pathogens. So, another avenue is potential drug discovery for human use or so, I feel like that can kind of help towards the conservation question as well. If we can get people interested in the fact that these organisms whether they are sharks or coral reefs are declining worldwide very quickly. Maybe if they were more human-centric, they would understand the importance of conservation of these organisms. 

Richard Jacobs: Yeah, that makes a lot of sense. Are there any interesting or unique or novel classes of compounds that you are finding that are produced by the bacteria in or around a coral?   

Kim B. Ritchie: Well, right now, I’m in the screening stages. So, I’m just sampling as many different types of sharks and rays. There are some publications that are out on that and then screening them for antibiotic activity and then I will do some bioassays seeing if they are small peptides or other compounds and I do some other assays showing whether or not they are hemolytic, so would they actually be good drugs. If they are hemolytic then they wouldn’t be a very good drug for humans but yeah, this is just starting. So, we are still looking for partners for scaling up for the chemistry aspect of it. so, are they novel compounds and could they be good drugs for humans?  

Richard Jacobs: Well, has anyone sequenced sharks and rays, and has anyone looked at their microbiome as an accelerant to what you are doing? 

Kim B. Ritchie: Yeah there are a couple of groups that are doing that and I am actually collaborating with one group on this work as well and yeah, so the collaboration is a great aspect because I am culturing them. Obviously, I am not culturing many of them because most bacteria can’t be cultured. So, looking at these along with the metagenomic type work will be how we try to understand what compounds they are producing and it could be producing a function for the shark and if they could be producing a novel compound even.  

Richard Jacobs: Well, very good. What’s the best way for people to find out more about your work and get in touch?   

Kim B. Ritchie: I suppose it would be to look at my website and look at the publications which need to be updated on that website at the University of South Carolina Buford.  

Richard Jacobs: Okay, well very good. Thanks for coming on the podcast. It’s been really interesting.   

Kim B. Ritchie: Thanks for having me.