These 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
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.
randles.17 says
I belive that if you have the right setup a DSB, is the perfect things for a fuge.
rayhaley says
My dsb is only about 2 inches but does well.
gerardobarbaro says
I have a live rock, cheato and a great light.
Regina Heitschmidt says
Same here! My cheato is growing like crazy!
nurkkaj says
I also have the same set up.
Alan George says
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.
lapisyogajulianne says
Great info
chahine29 says
I’ve been using marinepure blocks since day one. They have worked great
Mark Clark says
I use live rock and various types of mico algea.
Christopher skates says
Mud is what I want to use
John Hoang Phan says
Just feels messy to me.
henleyshannon08 says
Very informative.
Matt Traylor says
Not only do they look good, but they are functional!
Tommy says
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.
Joshua Wheat says
I have a deep sand bed in mine.
jeffery486 says
Debating on the deep sand vs mud route
Mark Clark says
I just use live rock and different types of algea.
jose.caraveo1 says
I need to do some improvements to my refugium, I currently only have bioballs
Jesse says
DSB’s for me. Gonna give mud in the fuge a try this next go around though.
Mike says
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 .
Linda Montgomery says
Great information
Eric caraveo says
No sand in my fuge. Looming for new ideas on my.165 gallon build thats in the works
pumas0511 says
Great information. Thanks.
Andrew says
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.
Bob Trimper says
Only bio balls now – thinking about sand or mud
Bob Trimper says
Only bio balls now – thinking about sand or mud
nicole morrison says
I need more cheato 🙁 always selling out so fast
Greg McCarty says
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
Jennifer Lye says
I have a HOB refugium. Not sure a deep bed is appropriate due to weight?
jenniferlye74 says
I have a HOB refugium. Not sure a deep bed is appropriate due to weight?
rpg56185 says
Sand is a must I think. Helps to keep a more balanced tank.
Ron Oppor says
I have had no issues with having a clear bottom refugium.
Mr Papu says
Great info! Great read.
trevorpem10 says
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.
chrisj7705-8921 says
I love using sand as substrate
Ben says
Great info, I always do a medium grade sand
ambermk22 says
We have deep sand beds in both of our setups
Andrew Welsh Welsh says
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!
Victoria Brewer says
I have sand in my tank would none in the sump.
Victoria Joy Brewer says
Good read might try adding substrate to my fuge
Victoria Joy Brewer says
Might have to try adding a substrate to my fuge
Usman Qamar says
I have rocks and chaeto in mind. would sand be better?
SAMANTHA MARTIN says
Might start mine soon!!
zadok jollie says
Great information. I never thought about sand in refugium.
bb00th638 says
Great read. Thanks.
Tammy J Stebbins says
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.
mlashawnbenton says
I’m thinking about doing sand in the region now.
Matthew Smoyer says
I add enough to have wrasses.
lefflerrm38 says
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
jayfl77 says
Great info
Rose Reeder says
I am not familiar with this.
jbean_911 says
I tried mud, but had to many problems. I do DSB now.
jenniferlye74 says
I have a HOB refugium so my sandbed in is not very deep
B says
Seems we need to start showing off the sump, just as much as the display tank.
Fabian Noggle says
im just using a block of marine pure in my fuge area instead of normal substrate
devon maynard says
This gave some great things to think about when i get a tank big enough to have a refugium.
C Reab says
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.
angelyrojas23 says
Knowledge is key ? wish I had it a sump
BLAKE ROBERTS says
I just use rock rubble myself. Thanks for the info!
sam0919906 says
Have about 2” sand bed. Works really well and looks good.
Ron Daige says
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
cyberkiller6 says
Good read
Bryant Carrasquillo says
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.
tony_garcia18 says
I want a system like this someday! I’m working hard for things like this!
Kyle collins says
Sand is a great part of the natural bi filtration.
Joshua Kerstetter says
Substrates are great! I’m running a deep argonite and sand bed in my refugium.
TJ Saffioti says
I like using mud or dirt as my bottom layer, fluval is my favorite!!
Dallas T. says
I love sand!
shanemsalhus-7885 says
i have stuck with caribsea live sand for past five years on all my builds
andrew babcock says
Interesting
Reilly Kelsen says
I just use a crap ton of live rock lol
blue2bulldog says
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!
Brandon Rush says
I hope I win this pack!
jeffery486 says
No sand or mud yet. Thinking about doing mud and mangrove seeds
Kyle says
Would love to do a mangrove fuge.
Kyle says
No sand looks odd to me
Kristin Randles says
Love all the information
Leighla Wolfe says
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!
printwithdrew says
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.
Andrew Haslem says
Another great article! Thanks!
ANDREW DEAN HASLEM says
Thank you for these articles
Robert Parsons says
Have had great results with the mud
Robin Michelle Guffey says
Black sand bed all the way
Drew C says
I’m upgrading my sump this weekend adding a refugium. I will be using sand and live rock
Chitterman says
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
Tim Tran says
great info
B.J. Bernal says
I use sand in mine!
david w sheffield says
I use rock rubble as myt fuge substrate
David Sheffield says
I use rock rubble as my fuge substrate
Carl Lusk says
I have fuge with rubble and chaeto.
ZACHARY Deptawa says
I use a standard 2-ish inch sand bed.
Don says
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.
purelakerfan says
My refugium (when I had it) was bare bottom.
Megan Herbert says
My refugum is bare but we have pods along with live rock and lights.
Kurt Kidder says
Nice
scottmenath says
Thanks for all the great content.
gabrielw94106 says
I need to grav vac my sand bed better in the future I am noticing some build up in spots.
michael_barrioz says
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
Justin Walz says
This is good information, agree with discussion topics especially speaking of fauna flora
lee1 says
Would love to try substrate with my mangroves.
lapisyogajulianne says
Great information … thank you so much
lapisyogajulianne says
love this all… great deals…
scotty8284 says
Doing my first ‘fuge, and this info really helps in ‘doing it right’!
dubster says
I continue to try out different methods
dubster says
I continue to try out different methods
Ricky says
Really informative
Jelani Register says
Best substrate is aragonite in my opinion
Will says
Mine just has marine cubes
William Benavides says
I just have marine cubes
sbgriffin27 says
Dsb for me
Brian says
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.
Bert Blank says
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.
Alfie Henshaw says
Another great article
James Wohler says
Good to see DSB getting some love.
James Wohler says
Good to see DSB getting some love. Usually bare bottoms are more popular.
James Wohler says
Sorry for the duplicate.
James Wohler says
My fuge is now just rock … best it was had miracle mud rubble and cheato.
jhernandez16172 says
Love to see it
oodydog says
Might just try
weshamand says
Mud for the win
luke.helleksen says
I like to use crushed coral.
jeffery486 says
I’m interested in trying out Mud with mangroves.
meganpratt27 says
Very informative
meganpratt27 says
DSB in the fuge has worked great for my reef!
mark says
maybe there is a third alternative to sand or bare bottom in a reef tank. perhaps a live rock substrate. hmmmm
Shawn Innes says
Wish I had room for a fuge
David says
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?
David says
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??
rpkneumann says
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.
Chris Montesione says
Good info
Scott says
Marine pure blocks have worked the best for me since the beginning.
Scott says
Very informative! I would be curious to try the mud and mangrove refugium.
Jeremy Pryes says
I love the added color and brightness from the pink substrate.
Leo says
I’ve had good luck with mud in the past.
Mark says
Never used mud but I have read on it.
jason.kkemp101 says
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.
Josh Stevens says
I think it’s great for beneficial bacteria in saltwater tank.