Getting to the Bottom of Refugium Substrates by Kenneth WingerterThese days, it seems as though a pretty solid majority of reef aquarium systems include a refugium. The growing popularity of refugia has been more a glorious resurgence than a successively rising trend. Indeed, they were quite commonly used in the hobby in the early 1990s. Unlike the refugia we’ve been seeing today, however, the set-ups of yesteryear much more often featured a deep, soft substrate as well as a lush bed of macroalgae (typically Caulerpa spp.). It seems that refugia went away, substrate and all, with the plummeting popularity of Caulerpa later in that decade (no other macroalgae were widely available to aquarists at that time). Improved lighting technology and increased availability of non-caulerpoid macroalgae (e.g. Chaetomorpha) have, at least in part, spurred the presently renewed interest in planted refugia. Given the significant improvements to refugium design and methodology, they appear poised to stay. As we look ahead to possibilities for future innovations, we should perhaps also look back and ask ourselves, “What about refugium substrate?” Another big change since the early 90s is the prominence of SPS corals. Among other things, this has led to a reliance on much higher water flow rates. The use of stronger water movement has caused a lot of frustration with aquarists who find that the brisk currents tend to blow sand all over tank (including over corals, clams, etc.). Interestingly, these issues have helped to restore the popularity of another oldschool reefkeeping MO: bare bottoms. Bare bottoms actually make a lot of sense for reef tanks, especially those dominated by SPS species. Natural coral reefs get pounded and ripped by powerful waves and currents, yet they hold firm because they are, well, reefs–big, solid, rocky structures. Our reef tanks should reflect this. Yet, in the wild, soft-bottom habitats are never far from reefs. Not only are they physically close, but they also are tightly interconnected ecologically. So, how can we incorporate that element into aquarium systems that feature bare-bottomed display tanks? With refugia that feature deep sand or mud beds! Sorting out refugium substrates Stronger water currents transport larger particles. Therefore, median grain diameter of your refugium substrate increases where there is higher current velocity, as erosion transports finer sediments to other, calmer areas. In highly turbulent waters, all that may be left behind is solid reef base or rubble. This separation of sediments according to size class is referred to as sorting. Sediments may be thoroughly sorted where current strength is steady. These same processes tend to deposit particulate organic matter in areas of lesser water movement. As these deposits accumulate, they form the silty, mucky bottoms that are typical in estuaries, lagoons and sheltered bays. These sinks of organic material often support huge, rich communities of deposit-feeding bacteria, protists and animals. Most of these are infaunal (i.e. spend most of the time with most of their bodies beneath the substrate surface). If you dig into a natural soft-bottom environment, you’ll see that colors and even odors change with depth. There are typically several layers (referred to as microzones) present. At the top is a more-or-less “clean” surface layer. In addition to receiving ever fresh deposits, the surface grains are constantly disturbed by waves and/or animal activity. Thus, it is well-oxygenated. Diverse animals, protists and aerobic microbes (especially cyanobacteria, nitrifying bacteria and various aerobic heterotrophic bacteria) live here. Oxygen could diffuse deeper into the refugium substrate but nevertheless doesn’t make it very far. That is because it is rapidly consumed (i.e. respired) by aerobic organisms that dwell in the surface layer. The boundary between the upper, oxygenated zone and the lower, anoxic zone is known as the redox potential discontinuity (RPD). The RPD might be greyish in color. Below this, the substrate takes on a black color. This (and an unmistakable rotten egg smell) is due to an abundance of hydrogen sulfide. Particularly in well-established, minimally disturbed deposits, the space beneath the RPD may be divided several distinct microzones. Photoheterotrophs such as purple non-sulfur bacteria (PNSB) may reside in or just below the grey region; these tolerate microaerobic conditions. They get first grabs at fresh organic material that seeps below the RPD from above and additionally benefit from the wee bit of light that peeks through the surface. Just below them are purple and/or green sulfur bacteria (PSB/GSB). While not at all tolerant of oxygen, these are even more efficient than PNSB at harvesting light. They also are more tolerant of the toxic hydrogen sulfide (in fact they utilize it metabolically) that seeps upward from the sulfate reducing bacteria in your refugium below them. Many obligately anaerobic “fermenters” such as denitrifying bacteria also inhabit this zone. Any organic materials that make their way down past the sulfate reducers are consumed by methanogenic bacteria; methanogens produce methane as a waste product, which is evidenced by an unmistakably poopy odor. You would think that animals cannot live below the RPD–but they do. Some are surprisingly adapted to “holding their breath” and even withstanding exposure to sulfides; many construct well-irrigated burrows that exchange waters from far above. Together as one Traditionally, deep aquarium substrates have been aimed at supporting large populations of denitrifying bacteria–controlling nitrate concentrations. But they can do way, way more than that! Consider them complete recycling centers for particulate organic waste; the refugium itself is a sediment settling basin, the substrate is a biomedium and the critters therein are agents of degradation/mineralization. A scheme such as this allows the keeper to scrap mechanical filter media, which correspondingly decreases zooplankton (e.g. pod) mortality. The increase of zooplankton abundance intensifies detritivory, leading to better nutrient cycling and a cleaner tank! Pretty much all of the commonly used refugium macroalgae can be cultivated over a soft bottom. Drifting forms such as Chaetomorpha and Ulva (including the former Enteromorpha) are most appropriate here. Deeper substrates additionally permit plantings of some really cool ornamental types such as shaving brush and mermaid’s fan. The tiniest infaunal organisms live interstitially, moving on or between grains of sand. Larger organisms must displace sediment grains in bulk (i.e. burrow). Some such animals (e.g. bristle worms) are mobile, constantly moving around below the surface in search of food; others are sedentary (tube anemones), usually poking out from the substrate surface to catch food particles as they drift by. And that’s just the beginning of a long list of possible inhabitants. A large refugium with a sufficiently deep refugium substrate can house everything from sludge-eating nematodes to larger animals such as tube worms, burrowing shrimp, deposit-feeding sea cucumbers, etc. With or without the stunning coloration of your SPSs, your soft-bottom refugium might be just as fun and interesting to keep as your “main” tank!
Joe Camejo says October 12, 2020 at 2:06 pm I’ve had really good luck in different systems I’ve set up through the years. Really good luck with both a DSB and Mud. Reply
randles.17 says October 12, 2020 at 6:08 pm I belive that if you have the right setup a DSB, is the perfect things for a fuge. Reply
Regina Heitschmidt says October 19, 2020 at 1:42 pm Same here! My cheato is growing like crazy! Reply
Alan George says October 14, 2020 at 5:40 am For a refugium I’ve always used live rock rubble. In my opinion it makes the fuge easier to clean out. I’ve seen refugium mud or “miracle mud” used a few times. But I’ve never thought to use life sand. I think you would need a pretty big area for you fuge to have as much surface area as you would with live rock. Reply
chahine29 says October 12, 2020 at 2:51 pm I’ve been using marinepure blocks since day one. They have worked great Reply
Matt Traylor says October 12, 2020 at 4:12 pm Not only do they look good, but they are functional! Reply
Tommy says October 12, 2020 at 7:22 pm My substrate will be sand and my refugium will be bioplates..having chaeto and pods will help feed and get rid of nitrites and phos. Reply
jose.caraveo1 says October 12, 2020 at 7:40 pm I need to do some improvements to my refugium, I currently only have bioballs Reply
Jesse says October 12, 2020 at 7:46 pm DSB’s for me. Gonna give mud in the fuge a try this next go around though. Reply
Mike says October 12, 2020 at 7:48 pm I have ran with a deep and without and for me was really up to what was going to be housed there. I didnt see any differences other than maintenance . Reply
Eric caraveo says October 12, 2020 at 8:39 pm No sand in my fuge. Looming for new ideas on my.165 gallon build thats in the works Reply
Andrew says October 12, 2020 at 10:45 pm Sand I find super essential to any reef tank aquarium but it’s nice to see how the hobby has changed over the years with bare bottom and maintaining integrity of a reef tank. Reply
nicole morrison says October 13, 2020 at 4:12 am I need more cheato 🙁 always selling out so fast Reply
Greg McCarty says October 13, 2020 at 5:05 am I usually go with a deep sand bed and have gotten great results. I have not tried the mud though. I currently am just running a chaeto reactor Reply
Jennifer Lye says October 13, 2020 at 7:06 am I have a HOB refugium. Not sure a deep bed is appropriate due to weight? Reply
jenniferlye74 says October 13, 2020 at 7:09 am I have a HOB refugium. Not sure a deep bed is appropriate due to weight? Reply
rpg56185 says October 13, 2020 at 7:10 am Sand is a must I think. Helps to keep a more balanced tank. Reply
Ron Oppor says October 13, 2020 at 7:16 am I have had no issues with having a clear bottom refugium. Reply
trevorpem10 says October 13, 2020 at 8:20 am I keep my sandbed no more then 1 1/2 inches deep, plenty for pods and not too much to be afraid to stir it around if need be. Reply
Andrew Welsh Welsh says October 13, 2020 at 12:58 pm Could be interesting to use a deeper bed in the fuge on my big tank. Might be able to create a more efficient filter. Great info! Reply
Victoria Brewer says October 13, 2020 at 1:31 pm I have sand in my tank would none in the sump. Reply
Victoria Joy Brewer says October 13, 2020 at 1:35 pm Good read might try adding substrate to my fuge Reply
Victoria Joy Brewer says October 13, 2020 at 1:42 pm Might have to try adding a substrate to my fuge Reply
Usman Qamar says October 13, 2020 at 4:30 pm I have rocks and chaeto in mind. would sand be better? Reply
zadok jollie says October 13, 2020 at 7:19 pm Great information. I never thought about sand in refugium. Reply
Tammy J Stebbins says October 14, 2020 at 1:25 am I’ve always love Aquariums. Ive seen some of the stuff your showing, put to use on the show tank. I’ve never had a salt water tank, but I would love to have one. I can see you are using top quality pumps and filters. I know to have a healthy tank, you need to use the best. Reply
mlashawnbenton says October 14, 2020 at 3:33 am I’m thinking about doing sand in the region now. Reply
lefflerrm38 says October 14, 2020 at 6:07 am I had sand in my first tank , tried second tank without sand an I must say I did like the sand just not the cleaning lol Reply
jbean_911 says October 15, 2020 at 7:11 am I tried mud, but had to many problems. I do DSB now. Reply
jenniferlye74 says October 15, 2020 at 8:36 am I have a HOB refugium so my sandbed in is not very deep Reply
B says October 15, 2020 at 9:45 am Seems we need to start showing off the sump, just as much as the display tank. Reply
Fabian Noggle says October 15, 2020 at 10:15 am im just using a block of marine pure in my fuge area instead of normal substrate Reply
devon maynard says October 15, 2020 at 8:23 pm This gave some great things to think about when i get a tank big enough to have a refugium. Reply
C Reab says October 16, 2020 at 4:23 am I have done dsb in the past but I don’t think they are all that useful as we have progressed with the hobby. The cons far outweigh the pros in my opinion, however for the instant bacterial breeding ground, stability, and overall cosmetics that a sand bed provides, I will continue to use them. Reply
BLAKE ROBERTS says October 17, 2020 at 12:06 pm I just use rock rubble myself. Thanks for the info! Reply
sam0919906 says October 16, 2020 at 6:57 am Have about 2” sand bed. Works really well and looks good. Reply
Ron Daige says October 16, 2020 at 4:44 pm I have tried sand, miracle mud, bio cubes ect. Personally every substrate I have used in a refugium has worked out well. The media balls I think were my favorite simply because I could pull some to quick start qt tanks when needed Reply
Bryant Carrasquillo says October 17, 2020 at 6:32 pm No room for mud or a fuge in my nano unfortunately – I am running a chaeto reactor. I would love a good DSB, but room is an issue. Reply
tony_garcia18 says October 18, 2020 at 1:45 pm I want a system like this someday! I’m working hard for things like this! Reply
Kyle collins says October 19, 2020 at 5:30 am Sand is a great part of the natural bi filtration. Reply
Joshua Kerstetter says October 19, 2020 at 7:33 am Substrates are great! I’m running a deep argonite and sand bed in my refugium. Reply
TJ Saffioti says October 19, 2020 at 11:47 am I like using mud or dirt as my bottom layer, fluval is my favorite!! Reply
shanemsalhus-7885 says October 19, 2020 at 2:02 pm i have stuck with caribsea live sand for past five years on all my builds Reply
blue2bulldog says October 19, 2020 at 2:25 pm For my refugium, I have constant water flowing through the 2nd of 3 chambers. Because my tank is a AIO, I find the marine blocks are awesome because they don’t create a serious amount of detritus (I also keep sponges for filtration that maybe once a month rinse in the tank water from a water change) build up AND house copepods as well as my Chaeto! It’s a great way to help keep a clean system in the back of the tank and create surface area for beneficial bacteria too! Reply
jeffery486 says October 19, 2020 at 2:41 pm No sand or mud yet. Thinking about doing mud and mangrove seeds Reply
Leighla Wolfe says October 19, 2020 at 3:14 pm I did a mixture of sand and marine block. Ultimately I went to just the marine blocks from this site because the sand would blow into my aio back pump chamber and clog the pump. I also had to pay more care with detritus buildup. I use foam sponge to increase beneficial bacteria and put it under and to the sides of my marine block so detritus is easier to clean in the back chamber and acts as a pod hotel! Reply
printwithdrew says October 19, 2020 at 5:15 pm 46 gallon bow front with 10 gallon sump. 10”x9” refugium with marine pure blocks and Chaeto and I even grabbed one of those small trees. Lol so far so good but I was wondering if adding some mud to fill the cracks between the blocks would be beneficial? Anyway I’m going to continue working this refugium idea. Reply
Drew C says October 19, 2020 at 7:24 pm I’m upgrading my sump this weekend adding a refugium. I will be using sand and live rock Reply
Chitterman says October 19, 2020 at 7:49 pm I do not use su strate anymore. I found it to be biggest problem with keeping regular levels. I do however have a 6 inch crushed coral sand bed in my 300 gallon top refugium tank or settling tank. That then drains into my 250 gallon macro refugium that then drains into my 300 gallon rock tank. That then drains into 240 gallon filter tank. That then drains into my 110 galon return tank this tank also houses my skimmer. Hope this helps someone Reply
Don says October 20, 2020 at 7:50 am I use MarinePure Block Plate 8x8x4 and Chaeto Algae along with a variety of Pods. When I need to trim the Chaeto I add it to the tank for an hour, then shake it off to get any pods on it in the tank for my mandarin goby to enjoy. Reply
Megan Herbert says October 20, 2020 at 12:59 pm My refugum is bare but we have pods along with live rock and lights. Reply
gabrielw94106 says October 21, 2020 at 10:55 am I need to grav vac my sand bed better in the future I am noticing some build up in spots. Reply
michael_barrioz says October 21, 2020 at 12:29 pm I like using rubble rock with no other substrate. I also make sure the rubble rock has lots of surface area and plenty of hiding spots for pods Reply
Justin Walz says October 21, 2020 at 10:58 pm This is good information, agree with discussion topics especially speaking of fauna flora Reply
scotty8284 says October 22, 2020 at 7:58 pm Doing my first ‘fuge, and this info really helps in ‘doing it right’! Reply
Brian says October 23, 2020 at 5:39 pm I had a bag of substrate left over from my tank setup so I just dumped it in the fuge. I figured it can’t hurt and if I ever need to seed a new tank I have something to use. Reply
Bert Blank says October 24, 2020 at 9:34 am Great information here. I currently have a smaller hang on fuge and I keep it simple without our sand or rock. Just makes it easier to clean and perform maintenance. If it were larger, I might try mud or sand but, rock pebble would likely be my go to. Reply
James Wohler says October 24, 2020 at 5:46 pm Good to see DSB getting some love. Usually bare bottoms are more popular. Reply
James Wohler says October 24, 2020 at 5:58 pm My fuge is now just rock … best it was had miracle mud rubble and cheato. Reply
mark says October 26, 2020 at 10:35 pm maybe there is a third alternative to sand or bare bottom in a reef tank. perhaps a live rock substrate. hmmmm Reply
David says October 27, 2020 at 4:55 pm I have lava rock in the bottom of mine, seems to be doing great so far. I have been told it can leech metals into my tank though. Maybe that is why I can’t keep sps alive? Reply
David says October 27, 2020 at 4:55 pm I have lava rock in the bottom of mine, seems to be doing great so far. I have been told it can leech metals into my tank though. Maybe that is why I can’t keep sps alive?? Reply
rpkneumann says October 28, 2020 at 8:35 am Using a 3 to 4 inch substrate. Happy nassarius and it seems to help my water quality. By the way. Add you aquascape first and then the substrate. I have and overactive pistol shrimp redesigning the landscape and tunneling under every rock every day. Reply
Scott says October 29, 2020 at 8:57 am Marine pure blocks have worked the best for me since the beginning. Reply
Scott says October 29, 2020 at 9:05 am Very informative! I would be curious to try the mud and mangrove refugium. Reply
Jeremy Pryes says October 29, 2020 at 10:08 am I love the added color and brightness from the pink substrate. Reply
jason.kkemp101 says October 31, 2020 at 6:35 am One of my tanks is no bed and the other is deep bed, but I don’t see much of a difference. No bed is easier to keep clean, but beep bed allows for many different fish. Reply
Josh Stevens says October 31, 2020 at 10:28 pm I think it’s great for beneficial bacteria in saltwater tank. Reply
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