metabolized by bacteria and fungi. This form of mineralization, while resulting in inorganic products, does not
imply the development of “minerals” in the sense of geology (see Bates and Jackson, 1987). Biologists, as anatomists, view mineralization as the formation of crystalline
or amorphous minerals or mineral/organic materials such
as exoskeletons and endoskeletons in plants and animals,
i.e., biomineralization – the formation of calcitic mollusc
shells is an example. Biologists, geochemists, and geologists view mineralization as the formation of crystalline
or amorphous substances as precipitates in sediment or
other substrates facilitated by organisms, i.e., biomediated
mineralization – pyrite framboids in anoxic sediments are
an example. Geologists also view mineralization as the
precipitation of minerals (inorganic elements and/or compounds) into a preexisting medium or directly onto
a substrate, i.e., geological mineralization – precipitation
of gypsum from water is an example. In the case of estuarine environments, geological mineralization is the formation of inorganic crystalline minerals or amorphous
minerals by direct precipitation from estuarine water onto
and into substrates. Geologists also view synsedimentary
diagenesis or early diagenesis as a variant of mineralization, where there is chemical or crystallographic alteration
of preexisting minerals into new mineral species or
crystallographically altered species – the oxidation of
pyrite in formerly anoxic sulfidic sediments is an example.
Conversion of organic molecules to inorganic
molecules (biological mineralization)
Biological mineralization (or biotransformation) is the
conversion of organic molecules to inorganic molecules
and ions and can be complex and multidimensional. In
fact, there are many pathways and processes subsumed
under the term “mineralization” in which organic matter
is mineralized by fermenting, denitrifying, sulfatereducing, and methane-producing bacteria (Jørgensen,
1982), some under anaerobic conditions and some under
aerobic conditions. One major pathway, for instance,
involves the breakdown of organic molecules and their
oxidation by sulfate-reducing bacteria, which utilize the
sulfate exogenically in the environment as the energy
source for the decomposition.
Many organic molecules may have attachments, or substituents, of NH 4 , NO 3 , SO 4 , and PO 4 , which are important for plant growth, but the N, S, and P in their
organically bonded forms are not available for plant
uptake. Biochemical decay, or microbial decay driven by
bacteria and fungi, result in breakdown of such molecules
and the production in solution of inorganic free radicals
such as NH 4
+ , NH 3 , NO 3
À , SO 4
2À , PO 4
3À (i.e., mineralization) that are available for plant uptake. Mineralization
also involves the transformation of organic compounds
to free C-bearing ions or C-bearing molecules such as
carbon dioxide (CO 2 ) and methane (CH 4 ). In these cases,
mineralization is the transformation of organic
compounds, often with attached N, P, S, and C, into
plant-accessible inorganic forms. Once incorporated into
plants, it is then available to be digested and incorporated
into animals.
Some of the best studied mineralization pathways in the
transformation of organic compounds to inorganic ions
and compounds is the conversion of nitrogen, bonded as
an element or part of a radicle, in proteins, amines, and
nucleic acids, among others, to ammonium ions, ammonia, and nitrates (i.e., NH 4
+ , NH 3 , NO 3
À
). The details of
mineralization of organic compounds with nitrogen and
the re-incorporation of nitrogen into organisms is complex
and variable depending on the primary material, the
environmental conditions, and the microorganisms.
The processes have been assembled from studies of the
nitrogen cycle (Canfield et al., 2010; Fowler et al., 2013;
Galloway et al., 2013) wherein nitrogen, as atmospheric
gas, is incorporated into organic compounds in plants
and animals initially via nitrogen-fixing bacteria or
compounded as inorganic nitrogen compounds via lightning and then cycled through various biological processes
to ultimately return to the atmosphere. At intermediate
stages, upon the death of a plant or animal, or when an animal expels waste, nitrogen is present in a variety of
organic molecules. Bacteria, or fungi, by use of enzymes,
convert the organic compound bearing the nitrogen into
ammonia, becoming ammonium ions (NH 4
+ ) when
dissolved in water. This particular process of mineralization is termed “ammonification.”
The conversion of ammonia/ammonium to nitrite and
nitrate is performed primarily by bacteria and other nitrifying bacteria (Kaplan, 1983; Henriksen and Kemp, 1988).
In the primary stage of nitrification, the oxidation of
ammonia is performed by bacteria such as Nitrosomonas,
which converts ammonia to nitrites (NO 2
À ). Other
bacteria, such as Nitrobacter, are responsible for the
oxidation of the nitrites into nitrates (NO 3
À ) since it is
important for the ammonia to be converted to nitrates
because accumulated nitrites are toxic to plant life. Denitrification, the next step in the nitrogen cycle, is the reduction of nitrates back to nitrogen gas (N 2 ), which then
completes the nitrogen cycle. This process is performed
facultatively by bacteria such as Pseudomonas and Clostridium in anaerobic conditions, using the nitrate as an
electron acceptor in the place of oxygen during
respiration.
Other well-studied mineralization pathways include
the conversion of organic compounds with P, such as
in phytin, proteins, DNA, RNA, nucleic acids, and phospholipids, to inorganic PO 4
3À . The process of deriving
inorganic phosphorous from phosphorous-bearing minerals (e.g., apatite) or from decaying organisms, released
as PO 4
3À in solution, and its incorporation into organic
compounds and return after death and decay of the
organisms to the environment as inorganic ions or
precipitated as apatite are part of the phosphorus cycle
(Filippelli, 2008).
Another well-known biological form of mineralization
is the oxidation of organic molecules, including those
MINERALIZATION
439
imply the development of “minerals” in the sense of geology (see Bates and Jackson, 1987). Biologists, as anatomists, view mineralization as the formation of crystalline
or amorphous minerals or mineral/organic materials such
as exoskeletons and endoskeletons in plants and animals,
i.e., biomineralization – the formation of calcitic mollusc
shells is an example. Biologists, geochemists, and geologists view mineralization as the formation of crystalline
or amorphous substances as precipitates in sediment or
other substrates facilitated by organisms, i.e., biomediated
mineralization – pyrite framboids in anoxic sediments are
an example. Geologists also view mineralization as the
precipitation of minerals (inorganic elements and/or compounds) into a preexisting medium or directly onto
a substrate, i.e., geological mineralization – precipitation
of gypsum from water is an example. In the case of estuarine environments, geological mineralization is the formation of inorganic crystalline minerals or amorphous
minerals by direct precipitation from estuarine water onto
and into substrates. Geologists also view synsedimentary
diagenesis or early diagenesis as a variant of mineralization, where there is chemical or crystallographic alteration
of preexisting minerals into new mineral species or
crystallographically altered species – the oxidation of
pyrite in formerly anoxic sulfidic sediments is an example.
Conversion of organic molecules to inorganic
molecules (biological mineralization)
Biological mineralization (or biotransformation) is the
conversion of organic molecules to inorganic molecules
and ions and can be complex and multidimensional. In
fact, there are many pathways and processes subsumed
under the term “mineralization” in which organic matter
is mineralized by fermenting, denitrifying, sulfatereducing, and methane-producing bacteria (Jørgensen,
1982), some under anaerobic conditions and some under
aerobic conditions. One major pathway, for instance,
involves the breakdown of organic molecules and their
oxidation by sulfate-reducing bacteria, which utilize the
sulfate exogenically in the environment as the energy
source for the decomposition.
Many organic molecules may have attachments, or substituents, of NH 4 , NO 3 , SO 4 , and PO 4 , which are important for plant growth, but the N, S, and P in their
organically bonded forms are not available for plant
uptake. Biochemical decay, or microbial decay driven by
bacteria and fungi, result in breakdown of such molecules
and the production in solution of inorganic free radicals
such as NH 4
+ , NH 3 , NO 3
À , SO 4
2À , PO 4
3À (i.e., mineralization) that are available for plant uptake. Mineralization
also involves the transformation of organic compounds
to free C-bearing ions or C-bearing molecules such as
carbon dioxide (CO 2 ) and methane (CH 4 ). In these cases,
mineralization is the transformation of organic
compounds, often with attached N, P, S, and C, into
plant-accessible inorganic forms. Once incorporated into
plants, it is then available to be digested and incorporated
into animals.
Some of the best studied mineralization pathways in the
transformation of organic compounds to inorganic ions
and compounds is the conversion of nitrogen, bonded as
an element or part of a radicle, in proteins, amines, and
nucleic acids, among others, to ammonium ions, ammonia, and nitrates (i.e., NH 4
+ , NH 3 , NO 3
À
). The details of
mineralization of organic compounds with nitrogen and
the re-incorporation of nitrogen into organisms is complex
and variable depending on the primary material, the
environmental conditions, and the microorganisms.
The processes have been assembled from studies of the
nitrogen cycle (Canfield et al., 2010; Fowler et al., 2013;
Galloway et al., 2013) wherein nitrogen, as atmospheric
gas, is incorporated into organic compounds in plants
and animals initially via nitrogen-fixing bacteria or
compounded as inorganic nitrogen compounds via lightning and then cycled through various biological processes
to ultimately return to the atmosphere. At intermediate
stages, upon the death of a plant or animal, or when an animal expels waste, nitrogen is present in a variety of
organic molecules. Bacteria, or fungi, by use of enzymes,
convert the organic compound bearing the nitrogen into
ammonia, becoming ammonium ions (NH 4
+ ) when
dissolved in water. This particular process of mineralization is termed “ammonification.”
The conversion of ammonia/ammonium to nitrite and
nitrate is performed primarily by bacteria and other nitrifying bacteria (Kaplan, 1983; Henriksen and Kemp, 1988).
In the primary stage of nitrification, the oxidation of
ammonia is performed by bacteria such as Nitrosomonas,
which converts ammonia to nitrites (NO 2
À ). Other
bacteria, such as Nitrobacter, are responsible for the
oxidation of the nitrites into nitrates (NO 3
À ) since it is
important for the ammonia to be converted to nitrates
because accumulated nitrites are toxic to plant life. Denitrification, the next step in the nitrogen cycle, is the reduction of nitrates back to nitrogen gas (N 2 ), which then
completes the nitrogen cycle. This process is performed
facultatively by bacteria such as Pseudomonas and Clostridium in anaerobic conditions, using the nitrate as an
electron acceptor in the place of oxygen during
respiration.
Other well-studied mineralization pathways include
the conversion of organic compounds with P, such as
in phytin, proteins, DNA, RNA, nucleic acids, and phospholipids, to inorganic PO 4
3À . The process of deriving
inorganic phosphorous from phosphorous-bearing minerals (e.g., apatite) or from decaying organisms, released
as PO 4
3À in solution, and its incorporation into organic
compounds and return after death and decay of the
organisms to the environment as inorganic ions or
precipitated as apatite are part of the phosphorus cycle
(Filippelli, 2008).
Another well-known biological form of mineralization
is the oxidation of organic molecules, including those
MINERALIZATION
439