Coral reefs seethe with life. Awash in the barren tides of the booming deeps, the life forms of these oases spin in a perpetual dance of biochemistry. Exchanging nutrients with one another, and always, always sweeping the water clean of every iota of sustenance, they ensure the poverty of their environment even as they struggle with it. Beneath the reef lie vast sand beds, the ground skeletons of a hundred thousand generations of coral organisms. This, too, is awash in life - millions of meiofauna, churning the sand in search of debris fallen from above, and the numberless, tireless bacteria of the nitrogen cycle, turning the poisonous fallout of terrestrial biology into harmless nitrogen gas. And all you need to see it all happen in the comfort of your own home is a saltwater aquarium!
Saltwater aquaria come in two varieties: the "sterile" kind, that rely on trickle filters, UV sterilizers, and ozone generators to keep things clean, and the "natural" kind, which tries to recreate an ecosystem that keeps itself clean. If you're going for the latter approach (and you really should be) then it's to your advantage to add a deep sand bed. The reef relies on it, and so can you (TM).
What are the advantages of a deep sand bed in a reef aquarium?
Filtration, and filtration. First of all, the deeper regions of the sandbed provide a great anaerobic environment for denitrifying bacteria. Live rock may not provide enough living area for sufficient bacteria to keep all the nitrates out of your water, but a sand bed will. Second, sandbeds are home to numerous meiofauna which will enthusiastically devour any uneaten food or waste material that falls from above. Every bit they consume is a little less material to be converted directly into ammonia.
Biodiversity. The key to a natural reef's success is the wide range of organisms that keep the system in balance. The diverse life in a sandbed ensures that all of the necessary roles are filled, and can compensate if another population crashes for some reason.
Food supply. A sand bed provides a fertile breeding ground for all manner of critters, many of which will prove more tasty and nutritious to your fish and invertebrates than anything you can buy in a store and chuck into the aquarium. If nothing else, it's a lot cheaper to let your food grow itself.
They're pretty. Caribbean beaches are mainly just reef sand beds washed up onto the shore, and you like those, don't you?
What do I need?
Sand. Seriously, that's it. More specifically, you want sand with grain sizes that range from .05 to 1mm, with a mean size of .1 to .25mm, which is commonly referred to as oolitic or "sugar" sand. There's some debate as to whether the sand bed infauna care about the chemical composition of the sand, but a natural reef sand bed is made of aragonite. The traditional belief is that this helps maintain good water chemistry, it's the tried-and-true standard, so unless you're an expert and would like to experiment, aragonite is probably the safest way to go.
A "deep" sand bed should be at least 4 inches in depth. 4 to 6 inches in your main tank is the norm - it's deep enough, but not too deep to be aesthetically pleasing. A deeper bed provides an even larger environment, which can have beneficial effects on denitrification. Adding a sandbed to your sump (if you have one) is a great idea, too - it's an area free of predation, and can be deeper without having a negative impact on your setup's appearance. At any rate, a square foot of sand 1" thick weights about 11 lbs.
There are numerous vendors who sell oolitic aragonite sand specifically for aquariums (Caribsea in particular.) Southdown-Cemex (an industrial supply company) sells a product called "Tropical Play Sand" that is essentially the same thing, but packaged for kiddie sand boxes and thus far less expensive. It's sold at Home Depot but is hard to get in parts of the country; still, the price difference makes it worth looking into. Do not use regular sand box sand, or just scoop some off your local beach - this is silicate sand, and will make your aquarium a playground for choking masses of diatoms.
How do I set it up?
First, rinse the sand. Put 10 or 20 pounds at a time into a bucket, and run water into it. Stir it thoroughly, until the water is milky and gross. Pour off the water, and repeat two or three times. This will get any contaminants and unwanted detritus out before the sand goes into your tank, and will reduce the amount of fine silt that will want to stay perpetually suspended in the water. You'll never be able to rinse out all of the silt (nor do you want to - small and differing grain sizes, remember?) so don't try. Just give it a few good repetitions and move on.
At this point, you may also wish to let the sand stew in some water from an existing tank for a few days, if you can. Add some flake food to the mix, and stir it frequently. This will allow a bacterial film to develop on the sand, which will cut down the silt problems inherent to the next step. It will also prevent bacteria from "gluing" the sand together, which has been reported in some cases. This isn't strictly necessary, but is recommended by some.
Now you're ready to add the sand to your tank. If you are setting up a new tank, the process is simple. Fill the tank with water (but not all the way - leave room for the sand!) and add your salt mix of choice, and be sure to let it dissolve thoroughly. You don't want the salinity of the water in the depths of the bed to be wrong! Once the water's ready, dump the sand in. Fwoosh. You'll get a horrid cloud of silt that will take days to subside.
Don't panic! As time passes, bacteria will colonize the tank and help settle the particles, and many of them will settle out on their own. If you want, you can add a trickle filter with some filter floss or, if you have a sump, just stuff the floss into the water pathway somewhere so that the flow goes through it. Rinse it out with tap water occasionally, and replace it when it gets too matted down. To speed the settling process, try adding some water and substrate from an established tank to seed yours with bacteria, or even add a piece of cruddy filter material or small piece of live rock. Then wait, and occasionally wipe the silty film from the inside of the tank (you don't want the bacteria to cement it into place!) The silt is a test of faith from the reefkeeping gods, and it will settle eventually.
On the other hand, if your tank is already established you'll have to be a bit more careful, as you don't want everything buried under a layer of fine sand. One good method for getting the sand to the bottom of the tank without it going everywhere is to put it into a large ziploc bag and lower it to the bottom before dumping the sand out. You can also try pouring the sand down a large-diameter piece of PVC pipe (although I found that difficult, as my sand was still wet from rinsing.) Bacteria from your existing rock should quickly colonize the sand bed.
Next, you want to increase the biodiversity of your new sand bed. These are the life forms that will be eating junk from the rest of your animals, stirring the sand to keep poisonous hydrogen sulfide from forming in anoxic zones, and entertaining you with their antics. You'll need to be creative: creatures from live rock will move into the sand, but many sand bed life forms are unique and will not be found in rock, and most commercial "live sand" is good for bacteria but not much else. Get a bit of substrate from every reef tank you can find and add it to your own. Go to your local fish store and get some of their sand, as well. There are also several companies - IPSF and Inland Aquatics are among the better known - that sell sand bed infauna kits. The more the better! If possible, this should be done before other livestock is added to the tank - you want the sand bed life really rocking before other critters start snacking on it. Then you'll be ready to enjoy all the benefits of a deep sand bed (including spacing out for hours on end, watching all the crawlies!)
How do I maintain it?
The main rule of thumb is: leave it alone. Natural sand beds don't have some crazy person stirring them up all the time, and neither should yours. In fact, stirring the sand bed can be very harmful to the creatures you've worked so hard to cultivate; for this reason, you should steer clear of animals that are major substrate-stirrers as well. These were considered important before, when tank substrate was just gravel or a thin layer of sand, but with a full-fledged sand bed the meiofauna keep things mixed up quite well. You also shouldn't need to siphon sediment off of the bottom, as you would with gravel or a bare bottom. Your new sand friends will take care of it for you (which was one of the goals all along!)
One thing you will need to do is to make sure that the critters have something to eat. In most cases, the leftovers from what you feed the rest of your livestock will be sufficient, but you might need to increase the quantity or frequency of your feedings just a bit. Also, if you're just getting set up and don't have anything else in the tank yet, don't forget to feed the sand! It'd be a shame to starve all of your new friends to death.
So, there you have it
A deep sand bed can be very helpful to the biological milieu of a reef aquarium, and both aesthetically pleasing and intellectually fascinating. What more can one ask for?
I learned most of what I know about this from Charles DeVito's sand bed FAQ at reefkeepers.org, and from a lot of very knowledgeable folks (notably, Ron Shimek and Mike Kirda) on the reefkeepers mailing list. As always, please /msg me if you have any thoughts, questions, or corrections!