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Substrate in the Marine Aquarium
Substrate in the aquarium serves two main purposes.  First, it is aesthetically pleasing.  That
is to say that hobbyists will add different types of substrate to their display tanks to make
them more attractive to the eye.  Second, it provides a place for beneficial bacteria to
colonize.  This will be discussed in detail later.  Substrates used in the marine aquarium are
almost always calcium based.  This serves several purposes, including water chemistry
control (buffer and pH among other factors).

Broken down into the simplest categories, there are four options for substrate.
The first option is to use none at all.  This
has the benefit of being very easy to keep
clean.  When detritus accumulates on the
bottom of the aquarium, it is simply
vacuumed up during a water change or
other tank maintenance.  There are,
however, several drawbacks to going “bare
bottom”.  The surface area available for
beneficial bacteria is greatly reduced.  One
could speculate that this may reduce the
bioload that a system could safely maintain.  
Less bacteria to eat up fish wastes = less
fish in the system.  Additionally, you would
lose the ocean look of the aquarium.  After
all, there is no place in the ocean with a bare
glass bottom.  Then the light shines through
the bottom and into any sump type filtration that is below.  This can cause a myriad of
problems including dirtying the filter and clogging it with algae growth that would otherwise
not be present.  Some hobbyists have attempted to grow soft coral such as star polyps
across the bottom glass as if it were grass in a lawn.  I have seen very limited success with
long term maintenance of this strategy.  
This photo shows my 90 gallon in a "bare bottom" setup.
The second option is to use a very fine
grain size substrate.  This is often referred
to as “sugar sand” because it is very
similar in consistency to sugar.  This type
has the benefit of being very attractive.  It
closely simulates the true ocean bottom in
many parts of the world.  This type of
substrate is similar to the white sandy
beaches found in some locales.  There are
several drawbacks to using the sugar
sand though.  One being that it is generally
considered more difficult to keep clean.  
Due to the size of the grain it cannot be
vacuumed and collects debris quickly.  To
make matters worse, any attempt to clean
the sand stirs it up and such fine grains
Very fine sand can be difficult to keep clean.
are easily suspended in the water column.  This poses two problems in a closed system.  The
tank will be impossible to view until the sand settles out and in the mean time most
inhabitants will be extremely irritated.  Sand suspended in the water causes filter problems as
well.   Prefilters will quickly clog with fine sand causing the need for frequent (and expensive)
replacements.  Additionally, pumps are not designed to operate in sandy conditions and
impellers will soon wear out bringing costly repairs.  Even if maintenance doesn’t stir the
sand, the fish often will.  Any specimen larger than a few inches will stir the substrate enough
to cause problems.  Any hope of keeping this substrate naturally clean will require an army of
sand sifting starfish and snails.  
The third option is to use a medium grain
size substrate.  This is the most common
type of substrate found in reef aquariums.  
It combines the benefits of being relatively
easy to keep clean with the natural look.  It
tends to stay anchored to the bottom and
only on occasion when it is greatly
disturbed with particles be suspended in
the water.  Usually even then it is only a
fine powder that is a combination of
substrate that is being chemically broken
down and debris.  This powder causes
minimal problems and usually dissipates
quickly.  Medium grain substrate is
generally easy on filters as well.  Since it
tends to stay on the bottom, it rarely ends up on prefilter pads.  Keeping a few sand sifting
starfish and/or snails is generally a good idea as they help to naturally turn the sand and
keep it clean.  Burrowing fish such as gobies and jawfish generally do best in medium grain
substrate.  It provides material that is easy to move when making a burrow, but large enough
to give support to the walls of the structure.
Medium substrate tends to be the best choice for the reef aquarium.
The last option is to use a coarse grain substrate.  This
is often referred to as a “crushed coral” substrate.  It is
called this because it literally looks like hard coral
skeletons that have been crushed and mixed with
small and broken shells.  This type is generally
considered to be the best for FO (fish only) or FOWLR
(fish only with liverock) aquariums.  This is because it
is very easy to keep clean and in most cases can
actually be vacuumed.  Since FO tanks generally
house large or aggressive specimens that have large
appetites and produce large amounts of waste, it is
important to have something that is easy to clean on
the bottom.  In addition, the grains are large enough
that it is very difficult for the tanks inhabitants to
disturb them to the point that they end up in the filter.  
One drawback is that many hobbyists don’t feel that
the crushed coral is as pleasing to the eye as medium
or fine grain substrates.  
This photo (taken from petstore.com) shows an example
of a crushed coral substrate.
Maintaining substrate is just as important at choosing it.  Click here for
some tips on substrate maintenance.