For those who aren't familiar with it, cryptic, twilight, or benthic zones are areas in a reef where little or no light penetrates due to shadowing from corals and rock and shear depth as tiny particles in the water refract light. These areas are also low flow for more or less the same reasons.
The invertebrates that grow in cryptic zones have adapted to be opportunistic feeders, dining on excess nutrients such as nitrogen & phosphate, heavy metals, bacteria, free-floating algae and other junk from the illuminated reef above. Corals growing on the sunny side of the reef have adapted to utilize algae within their tissue to derive energy from carbohydrates (sugars) that their symbiotic algae partners (zooxanthellae) produce through photosynthesis. Cryptic inverts have adapted in a non-photosynthetic environment. To make up for the lack of free energy from the sun and algae, cryptic inverts have taken advantage of what they have a lot of, and that's a steady rain of garbage (detritus & nutrients) from the reef above.
Cryptic zones in aquariums don't need to be highly engineered as they occur naturally as a matter of course. Anywhere there is a dark area where algae won't grow, miraculously small cryptic inverts will appear like the guys selling $5.00 water at music festivals. These inverts include sponges, sea squirts (tunicates), fan/feather duster worms, serpulid/fire worms (look like sea earthworms and often sting like a cactus), bivalves (clams, scallops etc.), barnacles, and plankton. The areas you will find them in your tank are overflow boxes, sumps, in the substrate, and on the undersides of rock and coral in the display tank.
There is a saying that "nature doesn't like empty spaces". Wherever there is an excess of food, or available home, an opportunistic organism will find it and set up shop. When you feed your tank a good portion of that food goes right over the overflow box unless you have a system to shut down the pumps or a feeding station of some sort. Aiptasia and majano anemones are photosynthetic, but they are also active filter feeders and collect passing food with their handy tentacles so overflow boxes are a perfect environment for them. Filter feeders draw in water through their tissue and polish it by removing the nutrients, heavy metals, and organic carbon (TOC). The removal of these food items not only helps with he chemical composition of the water, it also improves water clarity which helps light penetrate as the yellow pigmented organics are removed.
We can replicate the natural balance of organisms that nature uses by providing more homes for cryptic inverts. In nature, the cryptic zone is exponentially larger than the illuminated reef. By spacing our live rock and adding structures to overflow boxes and sumps, we can make up for the chief growth limiting factor (real estate).
The key to cryptic filtration is location... location... location. I build eggcrate structures and place them in sumps below the refugium as a "Duplex System" for better use of space. The duplex term refers to the upper illuminated refugium and lower basement apartment for our cryptic friends. The network of eggcrate panels allow water to passively move through while providing a 360 degree surface for cryptic inverts to attach. I call these natural/biological filters "benthic zones" due to the replication of a substrate, rather than an underside of a reef rock like the cryptic zones that Steve Tyree has created. Tyree's systems are comprised of unique rock formations that allows for more shadowed areas. You can read more on his systems here.
http://www.dynamicecomorphology.com/ and here
http://archive.reefcentral.com/forums/showthread.php?t=1020248 and you can read more about similar benthic systems here.
http://www.reefcentral.com/forums/showthread.php?t=969713
Cryptic inverts get into your tank as hitchhikers on the dark side of live rock and corals. Some sponges and sea squirts (looks like a sponge but with two vents/mouths) are very colourful and can be bought as specific pieces. While the actual effectiveness of cryptic zones on water quality is hard to measure and separate from other filtration efforts, at the very least they offer a fascinating look at a different level of the natural reef ecosystem.
In theory and in specific scientific studies, sponges and other water polishing inverts have proven to be beneficial to water quality management, but feedback on how much impact they actually make on a reef tank are slow to come. Part of this issue is due to a lack of hype typically surrounding commercial products catering to the niche market. In the case of protein skimmers, they have been proven to only remove 80% of available proteins and 20% of available TOC (total available carbon). It has also been proven that there is little difference between the results from high end skimmers and cheaper models of the same size rating. Despite this knowledge, protein skimmers are highly credited and revered for success. The same is true of LED lighting. Aquarium shows are wall to wall LED manufacturers now but the truth of that matter is mass produced LED light fixtures pale in comparison to MHL, no pun intended. There is a strong positive feedback for these systems with very few unsatisfied users, so that is encouraging.
I think we are getting honest, unbiased feedback on cryptic and benthic zone filtration and it's something we aren't entirely used to. We are accustomed to measuring the merits of a technology or methodology by reviewing numerous articles and threads expounding their virtues. You just have to filter out the hype and commercial biased. The only criticism I have heard is in regard to detritus build-up if the area is unaccessible but in my opinion this is due to poor design/access for cleaning and skipping important details such as pre-filtration (mechanical filtration) and omitting larger voracious critters like starfish, urchins, and crabs to keep the zone clean. We need to reflect on nature to focus on ways to replicate its success. In nature there are micro (small) as well as macro (larger) invertebrate janitors in the cryptic/benthic zone. A benthic zone sump is a perfect area to throw unwanted reef bandits like parasitic coral picker crabs, fish or coral eating starfish, and coraline algae eating urchins etc. Sea cucumbers are another good addition, as well as non-photosynthetic bivalves such as flame scallops that polish the water by removing diatoms, cyanobacteria spores, phytoplankton, ammonia, phosphate and nitrogen.
A rich biodiversity in your system is the key to striking a natural balance. We can tip the scale a bit to our favour by providing more real estate for cryptic invertebrates, thus eliminating the growth limiting factor. Cryptic zones are not only a method of removing excess nutrients, but a way of providing nourishment for fish and corals in the display tank as it is a perfect plankton farm/nursery (plankton like slow flow and darkness).
Some critics claim that cryptic zones are contributing to the bioload and are nutrient producers not consumers. The food these inverts are consuming is not being added (imported) for them, and they are consumers not producers like algae. They are just cleaning up (assimilating and dissimilating) a nutrient and organic load that already exists as a surplus. The members of the cryptic community are diverse enough to assimilate organics without leaving residual nitrate. The chief denizens of the cryptic zone are detrivorous (detritus/debris eaters) worms and sponges & sea squirts that directly consume nitrogen (ammonia, nitrite & nitrate), as well as bacteria, free floating algae, and iron.
Whether you want it or not, you have cryptic zones and subsequent filtration. The question is how to make the most of it.