materials represent what is likely the least understood area
of chemistry in reef aquaria. This fact is not especially
surprising as they also represent a very poorly understood
aspect of chemical oceanography. A recent article in the journal
"Seawater dissolved organic matter
(DOM) is the largest reservoir of exchangeable organic carbon
in the ocean, comparable in quantity to atmospheric carbon
dioxide. The composition, turnover times and fate of all but
a few planktonic constituents of this material are, however,
largely unknown." 1
This article will provide a basic review
of what organic materials are, what is known and unknown about
them in the oceans, how these organics may be different in
reef aquaria, and a summary of some of the effects, both positive
and negative, that organics may have in such aquaria.
What are Organic Compounds?
are defined by chemists as those that contain carbon and hydrogen
atoms. They can contain other atoms as well, but must contain
both carbon and hydrogen. A few exceptions to this
naming convention are worth pointing out. Carbonic acid (the
combination of carbon dioxide (CO2)
and water (H2O), H2CO3)
and bicarbonate ion (HCO3-)
are the two primary exceptions that aquarists encounter.
The name "organic" stems from
the belief derived centuries ago that such compounds could
be made only by living organisms. The name has stuck, despite
this belief being disproved as early as 1828, when a chemist
synthesized urea (a primary component of urine: NH2CONH2)
out of two inorganic compounds: potassium cyanate (KOCN) and
ammonium chloride (NH4Cl).
It should also be made perfectly clear that the chemical
definition of "organic" has absolutely nothing to
do with the marketing and regulatory way that the term organic
is used in many countries to apply to certain methods of farming
or food processing.
All living organisms are composed of organic materials to
a great extent. Other organic materials include sugars, starches,
proteins, DNA, fats, gasoline, natural gas, alcohol, automobile
tires, Corian countertops©,2
super glue, computer keyboards, and acrylic aquaria.
Dissolved and Particulate Organics
classify organic materials as being either dissolved organic
matter (DOM) or particulate organic matter (POM). The definition
is operational, with DOM being defined as all organic materials
that can pass through 0.2 - 1.0 mm
filters, and POM being all materials that are retained by
such filters. While this definition is useful and easy to
interpret, it can be somewhat misleading. A chemist asked
about a 0.2 mm
droplet of oil in water would not claim that it was "dissolved"
in the water, yet it would fall into the definition of DOM.
In a reef aquarium, the things described as POM would include
living organisms, such as some bacteria and phytoplankton
(and all of the "dissolved" organic materials inside
of their bodies). It would also include what aquarists frequently
refer to as detritus: the accumulated particulate organic
material that arises from parts of dead organisms and the
clumping of dissolved organic materials.
Organics in the Ocean
The nature of the
organic matter in the ocean is poorly understood. Part of
the reason for this lack of understanding stems from the tremendous
variety of organic material that exists. There is essentially
no limit to the number of different organic compounds that
are theoretically possible, and the fact is that many millions
of organic compounds have been synthesized or identified.
Identifying and quantifying every possible organic material
in seawater is just not possible, at least with present day
technology. Consequently, identifying the form organic materials
take in the ocean most often involves grouping them into classes
by a functional test, such as whether they can be extracted
from the water with a hydrophobic solvent, whether they contain
nitrogen or phosphorus, etc.
A small number of organic compounds have been individually
identified and quantified in seawater, but they represent
only a small percentage of the total mass of organic material.
Those examined in detail include simple sugars and amino acids,
and the very simplest organic molecules, such as derivatives
of methane (CH4) or ethane (CH3CH3),
including acetate (CH3CO2-).3
One interesting aspect of organic compounds in the ocean
is that some have been there for thousands of years.1,3
Many organic compounds, especially in surface waters, are
rapidly cycling between living organisms that consume and
modify them, and the dissolved forms that are just floating
about. Acetate, for example, can have a turnover rate as high
as once per day on average in the water column, and once per
hour or two in pore water inside sediments.3
With each turn of this cycle, some of these organic materials
become more and more refractory. That is, they become less
and less palatable to organisms, and are turned over more
and more slowly. Eventually, some remain that are largely
resistant to further biodegradation and processing, and these
can then stay as DOM for many thousands of years. Essentially,
they are the waste that is left after every organism has had
its shot at using them.
The pathways for degradation of such refractory molecules
are not well known, but likely reflect some rare biological
events (rare bacteria encounter them, they encounter a rare
enzyme, or they are acted upon by an enzyme that does not
normally process them, etc.). The long term degradation likely
also includes physical and chemical processes, such as oxidation
by oxygen, ozone, or other oxidizing agents, and being hit
by appropriate radiation (UV, x-rays, gamma rays, etc.).
Concentration of DOM in Seawater
organic material in the oceans is often measured in terms
of its carbon content, and is referred to as dissolved organic
carbon (DOC) and particulate organic carbon (POC). Surface
ocean water typically has about 60-90 mM
DOC. That range corresponds to 0.7-1.1 ppm. Table 1 shows
the breakdown of this DOC into a variety of chemical classes.
1. Components of dissolved organic material.
of Total DOC:
(especially glycine, alanine, aspartic acid, serine,
and glutamic acid)
Only about 4-11% of the DOC in seawater
has been quantified as discrete, identifiable molecules. Much
of the nature of the remaining DOC remains unknown.
Organics also are often measured in terms
of their nitrogen content, such as dissolved organic nitrogen
(DON) and particulate organic nitrogen (PON). The same is
true for phosphorus, using the terms dissolved organic phosphorus
(DOP) and particulate organic phosphorus (POP). Table 2 shows
the relative concentrations of C, N, and P in dissolved organic
material. In dissolved organic material, nitrogen is about
ten-fold less prevalent than carbon, and phosphorus is several
hundred-fold lower in concentration than carbon.
2. Elemental composition of dissolved organic material.
Concentration of POM in Seawater
organic material (POM) is more complicated to quantify than
DOM, because by definition POM includes all organic materials
larger than 1 mm.
That definition includes everything from bacteria to whales.
Identifying it as discrete chemicals is also a fruitless exercise.
Nevertheless, suspended POC is frequently less plentiful than
DOC, often by an order of magnitude (unless, of course, a
whale passes through the sampling zone!).
Regardless of these complications, particulate
organic material can have important implications for a reef
aquarium. Its export by skimming or mechanical filtration,
for example, can greatly reduce the amount of nitrogen and
phosphorus eventually released to the water column, supplying
nutrients for algae. It also comprises an important trophic
resource for filter-feeding and sediment deposit-feeding organisms.
I have not, however, seen any measurements of POM in reef
DOM in Reef Aquaria
have not seen reliable studies on the levels of DOM in reef
aquaria. Such studies would be valuable, for example, in comparing
different methods of organic export such as activated carbon
and skimming. Even more useful would be tracking specific
individual organics that have been thought to be of concern,
either because of a desire tomaintain them (such as certain
amino acids, for example), or because of a concern about toxicity
(such as caulerpicin and caulerpin, for example, which are
In addition to the DOM that arises from
natural sources in reef aquaria, we must also keep in mind
that many medications, vitamins, food supplements and additives,
the acetic acid in vinegar, methanol, the ethanol in vodka,
and a host of other things that aquarists are inclined to
add are included in DOM. It is obviously beyond the scope
of this article to discuss the effects of all of these materials,
although some I will mention in passing and will discuss them
in greater detail in future articles.
Nevertheless, one point that aquarists must keep in mind
concerning these organic additives is that the methods used
to export naturally occurring organics (carbon, skimming,
etc.) may also export the organics in the additives faster
than might be preferred.
Positive Effects of DOM: Energy and Nutrients
matter can exert a host of positive, or potentially positive,
effects in a reef aquarium. Some of these are outlined in
the following sections. Some are obvious, but others are more
subtle. Most obviously, DOM can provide energy and nutrients
(C, N, P, iron, etc) to many organisms, from bacteria to corals.
Additionally, since bacteria can thrive on DOM, and themselves
act as a food source for many organisms, the DOM is part of
the base of a food chain that rises to the top with the predators
in reef aquaria.
Positive Effects of DOM: Specific Organics
Some organisms may
benefit from specific organic materials in the water column
that they cannot make for themselves, or do not get enough
of in their particulate diet, and that are not used simply
as an energy source. These may include, for example, toxins
that they absorb from the water column and that thereby can
provide some benefit by making the organishm toxic to predators.11
Another example is aspartic acid (a natural amino acid).
It is readily taken up by certain corals, which rapidly incorporate
it into proteins that may play an important role in calcification.12
The relationship between certain amino acids and calcification
in corals was briefly mentioned in a previous
article on the mechanism of calcification and will be
discussed in detail in a future article. A brief explanation
of how and why aspartic acid and certain other amino acids
and organic materials may be involved in calcification is
Organic molecules are known to play a substantial role in
the formation of calcium carbonate in many organisms, including
abalone shells13 and other
mollusk shells.14 These
materials can be proteins, glycoproteins, mucopolysaccharides,
and phospholipids (and likely others that have not yet been
identified). They help to induce the nucleation and growth
of aragonite and are often referred to as the "organic
matrix" because much of the corals' skeleton is composed
of these organic materials.
In the case of corals, relatively little information is available
about what, exactly, these organic materials are doing. The
structures of some of these proteins contain an unusually
large amount of aspartic acid residue. These amino acids are
capable of binding to calcium, but whether that is a critical
function or not has not been established. Here is some speculation
about what these organics might be doing with respect to calcification:
They may help control the concentration of free calcium
in the coral, and thereby help control the rate of precipitation
of calcium carbonate.
They may control the location of crystal growth by binding
free calcium and ferrying it to the location where the
coral wants precipitation to take place.
They may bind to the aragonite crystal face and thereby
control the rate of precipitation.
They may bind to the aragonite crystal face and thereby
prevent precipitation in places where the coral does not
want the skeleton to grow.
They may bind to the aragonite crystal face and thereby
inhibit binding of magnesium, phosphate, or other ions
that are known to inhibit the growth of calcium carbonate
Regardless of the mechanisms involved, the need for these
organics in calcification is easily verified. Allemand, et
al15 have studied the
role of such materials in Stylophora pistillata. Interestingly,
they find that inhibitors of protein synthesis reduce the
rate of calcification considerably. For example, reducing
protein synthesis by 60-85% reduced calcification by 50%.
Inhibiting glycoprotein synthesis yielded a similar result.
These results did not arise from reduced metabolism, but rather
were the effects of specifically reducing only protein and
glycoprotein synthesis. The most important conclusion in their
paper may be that the rate of skeletogenesis may be limited
more by the rate of biosynthesis and exocytosis of organic
matrix proteins than by calcium deposition.
Interestingly, the apparently large need for a particular
amino acid (aspartic acid) to synthesize these proteins is
satisfied by external sources, rather than by either the coral
itself or its zooxanthellae. For this reason, some aquarists
add aspartic acid, or commercial preparations containing it,
to their aquaria. Whether there is a clear benefit to that
addition remains to be established.
Positive Effects of DOM: Bioavailability of Metals
organic material may bind to and modulate the solubility,
bioavailability, and toxicity of many metals, such as iron
and copper. Whether this is good or bad depends entirely on
the metal, its concentration, the particular organism involved,
and the nature and concentration of the organic matter.
Metals take a variety of different forms
in seawater, and these different forms have very different
properties. Copper, for example, exists in a multitude of
forms.16 In natural seawater
it has recently become clear that copper is almost completely
bound by organic materials.17
Many of these organics are called chelators. A chelating agent
is one that can grab onto the copper from two or more directions
In natural seawater these organics take many forms. Humic
and fulvic acids, for example, are two of the most important
types of materials that bind copper and other metals in seawater.17-19
They are also known to greatly reduce the toxicity of metals,
because in many cases it is the free copper that is the most
toxic.17 These classes of
organic materials comprise what remains when proteins, carbohydrates,
and many other naturally occurring organic materials are biodegraded
to a state where further degradation is very slow. Humic and
fulvic acids (the distinction between the two being only that
humic acids are more hydrophobic than fulvic acids) have a
wide range of structures and physical properties. They typically
are high molecular weight organic acids, with sizes ranging
from 500 to 10,000 daltons (grams/mole). They can also be
parts of larger assemblies of organic materials that would
be called colloidal (very small particulates) rather than
truly "dissolved." They can, of course, be part
of particulate organic matter as well if they accumulate into
a particle of sufficient size. The humic and fulvic acids
are comprised of amino acids, sugars, amino sugars, fatty
acids, and other organic functional groups. Different localities
and depths in the ocean contain different amounts and specific
types of these organic materials. As mentioned above, typical
values for the total dissolved organic carbon are on the order
of 1 ppm carbon for tropical surface seawater.19
Humic substances typically account for about 10-20 % of that
total, and fulvic substances can account for more than 50%
in some cases.19
Since trace metals are present in seawater
at far below 1 ppm, there may be plenty of organic material
to bind most or all of these metals in aquaria. Within these
organic materials will be sites where several carboxylic acid,
phenolate, thiolate, amino, or other metal-binding groups
come together. These sites are where a metal ion will be most
strongly bound. Structurally, it is hard to show a "typical"
humic acid binding to copper, but the structure in Figure
1 shows one possibility.
Figure 1. A schematic of a copper ion (Cu++;
shown in red) being chelated by
a naturally occurring humic acid (shown in green).
In this figure, the central positively-charged
copper ion (Cu++) is chelated
by the larger humic acid shown in green. It is bound ionically
by two negatively charged carboxylic acid groups and complexed
by one neutral amino group. Together these three groups may
hold the copper ion many orders of magnitude more strongly
than could any individual binding group.
The very extensive book, "Biogeochemistry
of Marine Dissolved Organic Matter,"19
"The collective findings establish
that a significant component of bioactive, or nutrient, metals
(Mn, Fe, Co, Ni, Cu, Zn, Cd) occur in the colloidal phase
along with numerous other trace metals."
What does this mean for aquarists? Simply
that we do not know much of anything about whether the trace
elements in our aquaria are adequately or excessively bioavailable,
regardless of concentration. In fact, reef aquaria might even
have situations where there is enough of some metal (say,
copper) to kill one organism that can readily absorb the organics
that it is bound to, and actually have copper depletion in
another organism that is unable to take advantage of that
Positive Effects of DOM: Inhibition of Abiotic
Precipitation of CaCO3
oganic material may bind to the surface of calcium carbonate
in reef aquaria, slowing the precipitation of calcium carbonate,
helping to raise the levels of calcium,
alkalinity, and pH with less precipitation of calcium
carbonate onto objects such as heaters and pumps, than would
otherwise take place. Magnesium
also play this role in seawater. Whenever calcium carbonate
begins to precipitate, these ions, and possibly organics as
well, bind onto the growing surface of the calcium carbonate
crystal. In effect they clog up the surface so that it no
longer looks like calcium carbonate, making it unable to attract
more calcium and carbonate, and precipitation stops. If not
for these ions, the abiotic (nonbiological) precipitation
of calcium carbonate would likely increase to the point where
aquarists could no longer maintain natural levels of calcium
The importance of organic matter for this
effect in a reef aquarium is unclear. As long as the process
happens exclusively for abiotic precipitation of calcium carbonate,
and not where corals deposit their skeletons, it is likely
a positive effect. When it inhibits calcification by corals
or coralline algae, however, such an effect is likely to be
viewed as detrimental.
Effects of DOM: Odor
any smell that is encountered in the context of a reef aquarium
is an organic molecule. The one big exception to that being
hydrogen sulfide (a rotten egg odor that is sometimes generated
in anaerobic environments). These odors include the "ocean"
smell that many people find pleasing, as well as the foul
odors from dead corals and clams, or that some find in skimmate
(mine always smells fine).
Negative Effects of DOM: Energy and Nutrients
same effect of providing energy and nutrients to organisms
that may be considered a benefit when the organism is something
that aquarists prefer to thrive, might well be considered
a detriment when the organisms in question are cyanobacteria
or microalgae. Aquarist preferences aside, however, organic
materials can provide such "benefits" to organisms
whether they are preferred or not.
Not only can DOM be taken up directly to
provide carbon, nitrogen, and phosphorus, but it can be broken
down by organisms and released as inorganic nutrients, such
as orthophosphate, ammonia, nitrite, and nitrate: 16
+ 138 O2
106 CO2 + 122 H2O
+ 19 H+ + PO4---
+ 16 NO3-
+ oxygen à
carbon dioxide + water + hydrogen ion + phosphate +
These inorganic nutrients can then drive the growth of undesirable
aquarium algae aquaria, and can cause other problems (such
as phosphate inhibiting
calcification by corals). Consequently, DOM (and also
POM) can act both directly as a nutrient source, and also
as a source of inorganic nutrients.
Some aquaria have large growths of cyanobacteria or microalgae,
and in these cases exporting some of the DOM and POM from
the water column may be beneficial in reducing the problem.
The addition of vinegar to limewater has been correlated with
the growth of what appear to be bacterial mats in some aquaria.
Presumably, the bacteria thrive on the acetate provided by
Negative Effects of DOM: Oxygen Levels
drawback to organics that are taken up by bacteria and other
organisms is that in order to metabolize them, such organisms
use oxygen (if they are aerobic organisms). Equation 1 (above)
shows the net effect of what happens when organics are metabolized.
For each carbon atom in a typical organic molecule in seawater,
1.3 oxygen molecules are consumed. At levels of DOM in natural
seawater, on the order of 1 ppm, this result implies that
oxygen would drop by 3.5 ppm if it were all fully oxidized.
Obviously, not all of the carbon will be rapidly and completely
oxidized, but if organic levels are appreciably higher in
some aquaria than in the ocean, then the oxygen depletion
potential may be very important relative to normal saturation
levels on the order of 7 ppm oxygen.
The consequence of this oxygen consumption
is that oxygen levels may be lower in aquaria with high organic
levels, especially at night when photosynthesis is not producing
excess oxygen. Moreover, during a power failure when both
aeration and photosynthesis are greatly reduced, the metabolism
of organics proceeds merrily along, reducing the oxygen content
of the water faster than it would in the absence of DOM.
Negative Effects of DOM: ORP
aquarists attribute low ORP readings to elevated DOM (and
POM) levels in aquaria. That is likely true in many cases.
However, the drawbacks of lower ORP that many aquarists fear
may well be caused directly by the organics themselves, rather
than by the ORP. So it may, in effect, be double counting
to claim that high DOM is undesirable purely because it causes
lower ORP. In a previous
article I argued that ORP itself, especially when being
perturbed with an oxidizer such as ozone, is not a good indicator
of water quality generally, or organics in the water specifically.
Nevertheless, there is a strong connection between organics
in the water and ORP that aquarists should be aware of. Exactly
how they are related in reef aquaria is complicated and not
all aspects are well known, but what is known is described
in the article linked above in both easy to understand and
also in more rigorously scientific discussions.
Negative Effects of DOM: Toxins
organisms can produce a multitude of organic toxins. It is
beyond the scope of this article to go into the many toxins
that might concern aquarists, but some discussion is certainly
merited. These toxins may be intentionally released by organisms
to kill neighbors or competitors, or they may be kept internally
to ward off predators (being released only during predatory
encounters which may or may not end in death). Some are fairly
simple biochemicals. Domoic acid, for example (Figure 2),
is a fairly simple biochemical that is produced by many species
Ciguatoxin, on the other hand (Figure 3), is a complicated
molecule made by a dinoflagellate. As it works its way up
through the food chain to people, it has been implicated in
many fatalities and is reported to sicken 20,000 people per
Figure 2. Domoic acid, a toxin produced by diatoms.
Figure 3. Ciguatoxin, a toxin produced by dinoflagellates.
Caulerpin (Figure 4) and caulerpicin are
sometimes referred to as toxins, although they appear to be
primarily growth regulators present in various species of
macroalgae, especially Caulerpa. They are not particularly
toxic to animals or bacteria in most studies.4-10
Many aquarists decline to keep Caulerpa sp. in their
aquaria, sometimes citing the possibility of elevated levels
of such toxins as a reason. Whether these particular "toxins"
are of primary concern or not, looking at the structures of
these sorts of toxins can help suggest ways to remove them
(carbon, for example, since they are very hydrophobic), but
I have never seen measurements of the levels of any toxins
in aquaria, or comparisons of how well different export mechanisms
might reduce those levels. I would consider such measurements
to be of significant value to aquarists.
Figure 4. Caulerpin, a compound produced by macroalgae,
including Caulerpa species.
Negative Effects of DOM: Light Absorption
concern with DOM is that it can absorb light. That absorption
serves to decrease the intensity of light reaching photosynthetic
organisms, and can also yellow the aquarium's water. The use
of activated carbon to remove the yellow coloration in aquaria
by binding organic materials has been addressed in a
previous article. Other organic export and degradation
methods can also serve to reduce light absorption and coloration,
including skimming, ozone and other oxidizers, and the use
of organic resins such as the Poly-filter.
Effects of POM
of the effects of DOM also extend to particulate organic matter
(POM). This may happen both directly, or by POM producing
DOM as it is broken down in the aquarium or incorporating
DOM within the particulate matrix. Some effects, however,
are different. Particulate organic material, for example,
does not have the same sorts of highly toxic organic molecules
in it that DOM can have (e.g., ciguatoxin). It also is used
as a food source by a different subset of reef aquarium inhabitants
than is DOM. It is, however, a very important contributor
to many processes involving organic matter in reef aquaria.
DOM and POM Export Methods
are a variety of ways to export organics from reef aquaria.
These include the use of activated carbon,
polymer resins, and mechanical filtration, and may also include
and sulfur denitrators. These export methods may all have
different efficacies for different constituents of the total
organic matter. Consequently, combinations of different methods
may be more useful than a single method alone. This export
of organic matter is, however, too lengthy a subject to go
into detail about here, and will be covered in more detail
in future articles.
my opinion, organic materials are one of the biggest chemical
mysteries in reef aquarium husbandry. This lack of understanding
stems from two primary issues: huge numbers of different organic
chemicals are present in aquaria, and they are all difficult
to quantify (relative to testing for inorganic ions, for example).
This lack of understanding may be leading aquarists to fear
things that are not a problem, and to miss things that are.
Hopefully, reef aquarists of the future will have a better
handle on what is happening with organics in their aquaria.
I talked to a number of professional chemists at the recent
MACNA conference in Boston, and several indicated a willingness
and capability to begin addressing these issues. To get such
folks started, we need to figure out what the most pressing
issues are that are solvable with currently available technologies.
Once that has been determined, it is largely a matter of time
and money before useful results might be obtained.
In the meantime, Happy Reefing!