The Microbial Community in a Professional Coral Aquaculture System

EM: Ever since I started trying to grow corals, I’ve been awed by some reef-keepers’ abilities to duplicate a coral reef ecosystem in their living rooms. You know the reef tanks I’m talking about, the ones filled with bushy colonies of Acropora growing so fast the tips are almost sticking out of the water. After years of reading and comparing notes with other hobbyists I couldn’t escape the conclusion there was something different about the water their tanks… something not measured in all our water quality testing. So I embarked on a new project to study the microbial communities that support aquarium ecosystems.

We’ve already learned a lot by comparing hobbyist’s tanks. But I still wondered what the microbiome of a dedicated coral aquaculture facility would look like. Are the professionals doing something different? So when I had the opportunity to test the microbiome in the main system at BattleCorals I jumped at it. We’ve all drooled over pictures of the corals grown in this tank… see for example the random selection of recently posted images from BattleCorals that I compiled for Figure 1.



Here’s a chance to learn something new about the system where those corals grew.

In this article, I’ll discuss these results with Adam Derickson of BattleCorals, who has been kind enough to share these findings with the community and answer some of our questions. Adam, thanks for your time and willingness to share these data with the community!


AD: My pleasure. I am truly impressed with this whole concept and humbled to be a part of your research.


EM: DNA sequencing is easy compared with growing corals that look like that!

But in hopes of learning a little about how you do it, lets talk about your test results. I’ve summarized some key findings in Figure 2 so the reader can easily find the numbers we’ll be discussing.

Let’s start with diversity. The diversity in this tank is similar to the average diversity in other tanks I’ve sampled. Between your biofilm and water samples we found just over 200 different types in your sample (212). This is right in the middle of the pack: half the tanks I’ve surveyed had higher diversity, and half had lower.

Experiments have shown that diverse communities like this don’t just happen on their own. Can you share any details about how you established the microbial community in this tank?



AD: Great question. The system tested is not that old. I set it up in the spring of 2017, after construction of my new facility was completed. While I actually didn't use any of the rock from my older system, I did use a lot of the water. I transferred a few hundred gallons from the old, to the new when I initially set it up. Some of the rock in my older system had been in saltwater tanks dating back 20+ years, most of the rock over 15 at least. So it's been long established, built from many different sources, and through a great deal of ups and downs over the years.


EM: Really interesting that you used old water but not old rock. I sometimes encounter the view that “most of the microbes are in the rock, what’s in the water doesn’t matter”. Of course, direct counts show tens of thousands of bacteria per ml of aquarium water, and DNA evidence shows these include many of the ones hobbyists care about.

Your experience shows that this water can also be used to establish a healthy microbiome in a new aquarium. At least if you add enough of it!

Next lets talk about the levels of microbes in your results. The balance of different bacterial families in your tank was very different from the average aquarium I’ve sampled. In other words, the families that are typically present at high levels (Flavobacteriaceae and Pelagibacteraceae) were low in your sample. In their place, a few families typically present at low levels were much higher in your sample (Vibrionaceae, Verrucomicrobiaceae, and Fusobacteriaceae).

Researchers studying microbial “blooms” in the ocean (when one group of microbes rises to high levels) have found these are driven by environmental conditions, especially the kinds and amounts of nutrients available. So when I see an unusual balance of microbial families, I start by looking for possible explanations in the water chemistry.

I notice that you’re running at a higher salinity than many reefers which may play a role here since many microbes are really sensitive to salt levels. I’m guessing this is to maximize growth rates, right? I’d be curious to hear about your experience when you increased salinity.


AD: Its was a fluke actually that it happened in the first place. Here's the story (excerpt from write up). One day many years ago, and it really was one of those "well one day" type instances, I couldn't help but notice that my SPS were looking good, and I mean really good, like that thick powdery looking flesh that I had never quite been able to achieve, in all my years. I saw deep coloration and bursting new growth at every node. It was remarkable! Overall things were just doing much better than I was generally used too. After simple rundown of some basic params, the only real blaring change from my norm of many years, was that rather than seeing 1.025 on my refracto it was closer to 1.027.

So what happened was that over time, my rogue water replacement methods had crept my salinity up. And seeing the apparent effects on my own tank inhabitants, I have been keeping it high ever since. Really, it's just that simple. I stumbled upon something that seemed to be a good thing, and I have been riding high ever since.




EM: I’ll add that while your salinity isn’t that much higher than a natural reef, many of the tanks I’ve sampled run at substantially lower levels (33 ppt or below). This makes me wonder whether differences in salinity within this range affect the microbial community… I think an experiment may be needed!

Dissolved nutrients are also likely to affect these levels. Based on the phosphate levels logged for your sample I would guess this system gets fed pretty generously. Can you share any details about what you feed this tank, and how frequently?


AD: Yeah, I have never been one to shy away from nutrients in the system. I like to see some measurable amount of phosphate and nitrate in my systems. I have a lot of fish and feed them well. Some of the only times I've really seen a definite noticeable reduction in polyp extension was when my phosphate levels bottomed out.


EM: Your description of a lot of well fed fish is interesting. Your tank has more Fusobacteriaceae than most, and in your case they’re almost all in the genus Cetobacterium, which is a well-known member of the fish gut microbiome. In other words, your tank’s microbiome shows evidence of a lot of fish poop!

I also notice you dose Iodide. While this is not uncommon in the hobby, few of the tanks I’ve sampled dose Iodide regularly, and this is known to affect the composition of marine microbial communities. I’d be curious to hear about your Iodide dosing practices and your experience with its effects.


AD: Another great question. This is something that came out of ICP testing. I have never paid much attention to iodine. When Triton first hit the scene I had my tank tested and at one point early on I had extremely low, undetectable iodine. And at the same time was seeing some abnormalities in a lot of my sps colonies. Mainly thinned tissue and minor tissue recession around bases. I went ahead and boosted my iodine levels and things did seem to perk up. Many of the symptoms I was seeing did subside after the iodine was brought up, so I've been supplementing lightly ever since.


EM: One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample.

This may not come as a surprise, since we expect to find these in a tank with a functional biofilter. But in fact, many established tanks have very low levels of these microbes. In some cases, nitrite-oxidizing bacteria aren’t even detected (although they’re likely still present at low levels).

As I review these surveys from different tanks, lately I’ve been thinking about competition between microbes and other organisms for ammonia. I’m considering the hypothesis that some tanks process most of the ammonia through nitrification, some through assimilation by invertebrates or heterotrophic bacteria, and some through assimilation by algae. In this framework, your tank appears to process most of its ammonia through nitrification, the classic pathway we all learn about when cycling a new tank.

To evaluate this interpretation of your system as “nitrification-dominated” I’d like to ask, do you deliberately grow any macroalgae in this system (e.g. in a reactor?) Similarly, would you say your tank has a large biomass of sponges or very little?




AD: I dont run algae or any means to keep macro in my systems any more but I do have a lot of different sponges in “cryptic” zones.


EM: So it sounds like no major algal populations to compete for ammonia, but perhaps some competition by sponges. Since I believe you don’t carbon dose, heterotrophic bacterial uptake is also likely pretty low in this system. This seems consistent with a system processing most of its ammonia through nitrification rather than heterotrophic or photoautotrophic assimilation.

Another factor that’s likely to influence these communities is the total amount of ammonia processed through the system. In principle an aquarium can maintain stable levels by matching high nutrient export to high nutrient import, or by matching low export to low import. But the former would be expected to support higher populations of ammonia-oxidizing microbes.

Based on your tank’s bioload and nutrient export, would you say your tank falls closer to the high-export, high-import end of the range, or the low-import, low-export end?


AD: I think I'm on the higher end for sure.


EM: So lots of ammonia moving through the system, and high levels of nitrifying microbes but very little competition by algae. Sounds like a very different situation from my display tanks, all of which process a lot of nitrogen through macroalgae, and have very low levels of nitrifying microbes. Interesting…

Another piece of good news in your results was the absence of known bacterial pathogens of fish or corals. I screened for almost 50 different pathogens and found none in your sample. Meanwhile, 1 out of 10 tanks I’ve tested has a coral pathogen, and 1 out of 8 has a fish pathogen.

I’m especially interested in wild imported corals, since a recent study shows that about 1 out of 3 corals sampled in nature has a parasitic bacterium that can behave as a pathogen under some conditions. I’ve found this bug (Aquarickettsia rohweri) in other tanks, but not your system!

As a profession coral grower I imagine you add new corals to the tank regularly. The absence of any detectable pathogens in your tank suggests you’ve come up with some successful practices for avoiding introducing pathogens or pests into your system. Are there any secrets you can share about how you treat and introduce new corals to keep your system?


AD: Hmm well this is a topic that may deserve its own discussion actually. But in short, over the years I've developed definitely a pretty good routine to prevent unwanted organisms from getting into my systems. Patience, a keen eye, and a “no exceptions” policy are at the heart of this routine.


EM: I would definitely be interested in reading more about this! I’ve encountered lots of variation in how different reefers treat new corals before adding them to the tank. Since you’re doing it on a larger scale without introducing pathogens or parasites it would be great to hear more about what you’re looking for as you decide whether a coral is ready to be added to the main system.

It’s been really interesting for me check out the microbial community in your tank - it turns out that there is something different in your water. It’s providing a lot of food for thought about how to adjust the microbial communities in my own aquariums.

The science of aquarium microbiomes has not yet reached a stage where anyone can offer guaranteed prescriptions. This is the era of study and experiments. I believe that studying the microbiomes of successful tanks, and identifying the practices that led to the development of these communities will help the hobbyist community to develop evidence-based practices for establishing a healthy microbiome. So thank you again, Adam, for your contribution toward this effort! I hope this discussion was interesting for readers of Reef2Reef and inspires further experiments to understand the complex ecosystems in our aquariums.


AD: It has been my pleasure completely! I am in awe of what you are doing here and am honored to be included in your studies. I think this is a really exciting time for reef aquarists and it’s amazing to see testing of this sort made available to hobbyists. I see it as a new frontier of exploration and understanding of our reefs and the data you collect will greatly benefit the entire community in years to come. Thanks again for the consideration. I really look forward to what’s in store.

[edit - sorry for issues with images in the first version of this post. I think I have them fixed now!]