Vertebrate fauna also specialize in the development of magnetite in tissue (Fe 3 O 4 ; Kirschvink and Gould, 1981; Diebel
et al., 2000) and otoliths (CaCO 3 in fish; Gauldie, 1993;
Campana, 1999). Bone is a composite material composed
of organic components (primarily collagen) and inorganic
components (bio-apatite, Ca 10 (PO 4 ) 3 (OH) 2 ), as well as
lipids and water. As a crystalline solid, bone has a special
form of the mineral apatite that dominates its composite
structure, being composed of extremely small-sized crystallites (Wopenka and Pasteris, 2005).
The long-term products of biomineralization of biota in
estuaries is biogenic sediment through the accumulation
and formation of foraminiferal sand, molluscan shell grit
and gravel, diatomaceous mud, and carbonate mud.
Formation of minerals via biomediation
(biomediated mineralization)
The bacterial reduction of sulfate to sulfide at the sediment
bed is a key process in the coastal sulfur cycle and is
responsible for the oxidation of organic matter which
becomes buried below the oxic and suboxic zones of the
sediment bed (Lovley and Phillips, 1986; Machel, 2001).
The sulfate ion is common in seawater, sediment, or in
waters rich with decaying organic material (with SO 4
2À
deriving from organic matter). Sulfate-reducing bacteria
are common in anaerobic environments wherein they utilize the sulfate ion as an electron donor and thus aid in
the degradation of organic materials. Sulfate reduction is
the dominant terminal step in the mineralization processes
of sulfate-rich sediments where the sulfate reducers inhibit
the methanogens by competing for common substrates.
Sulfate reduction thus is quantitatively important in the
overall oxidation of organic matter in sediments (Barton
and Fauque, 2009).
Various minerals can be precipitated by biomediation,
with the best known being pyrite. If Fe, Mn, Cu, and Zn
are present in the environment, they can be involved in
the formation of sulfides, however, since Fe is generally
the most common transition metal cation in natural
environments, sulfides of Fe (as pyrite) will be the most
common mineral. Precipitates of pyrite, mediated by
sulfate-reducing bacteria, are commonly framboidal
(Sawlowlicz, 1993). Framboids (after the French word
framboise for “raspberry”) are small clusters of pyrite
crystals resembling a raspberry that can be < 1 mm in size
but range in size from 0.5 mm to 40 mm in diameter, with
the average aggregate size about 5 mm (Wilkin et al.,
1996). That FeS 2 , as framboids, is associated with microbial activity has been known for some time and has been
implicated in the development of sedimentary pyrite in
the rock record (Schieber, 2002). While organic-matterrich sediments inherently tend to be black or dark gray,
the fine-grained precipitated iron sulfide disseminated
throughout the sediment as a result of bacterial degradation of organic material typically also renders sediments
to various shades of gray to black depending on the
concentration of the pyrite in the sediment.
Iron sulfides as pyrite (FeS 2 ) and iron monosulfide
(FeS) can play a central role in the sulfur and iron cycles
of estuarine, coastal, and marine sediments. They may be
buried in the sediment (remaining gray to dark gray) or
oxidized by O 2 when brought to the near surface or surface
by wave action or by bioturbation. FeS 2 and FeS may also
be oxidized within the anoxic sediment in which NO 3
À , Fe
(III) oxides, or MnO 2 are available as potential electron
acceptors (Schippers and Jørgensen, 2002).
As a result of the shell-forming processes, organic matter
may be embedded in molluscan calcitic/aragonitic
shells and crustacean chitinous/carbonate exoskeletons
where, if decayed by bacteria, becomes a micro-site
for biomediated precipitation of fine-grained pyrite
framboids. The scattered occurrence of fine-grained pyrite
may impart a speckled appearance to shells and, in
the extreme, may turn them gray. Also, when embedded
in sulfidic sediment, shells often become blackened with
pyrite through sulfide diffusion. As such, calcitic/aragonitic
shells and chitinous/carbonate shells become sparsely to
moderately impregnated with pyrite. Blackened shells and
foraminifera have been reported by Ginsburg (1957),
Pilkey et al. (1969), and Davies (1970). In each case, iron
sulfide was implicated as the blackening agent.
Algae boring into shells often are micro-sites for the
precipitation of aragonite, Mg calcite, or calcite in the
algal thread tubules. They also are sites for pyrite precipitation. The calcitic/aragonitic shells become riddled with
ultrafine carbonate-filled borings, and in the extreme, the
carbonate-filled borings coalesce and form a thin carbonate envelope around the shell (Bathurst, 1975). In the case
of pyrite, the fine-scale algal tubules are lined with or partially filled with pyrite, which imparts a gray external tinge
to the shells.
Organisms, especially bacteria, are instrumental in facilitating the precipitation of microcrystals and nanocrystals
of the calcium carbonates (calcite, Mg calcite, aragonite),
dolomite (Castanier et al., 2000; Sánchez-Román et al.,
2007, 2008), and phosphates (Sánchez-Román et al.,
2007). Though not volumetrically important, this process
results in contribution to the mineral record in estuaries.
Minerals directly crystallized from estuarine water
(geological primary mineralization)
Minerals can also directly crystallize from estuarine water,
either from the water column or from pore waters, if the
hydrochemistry, salinity, or concentration of the open
estuarine water or tidal flat pore water is appropriate.
These are primary precipitates. The minerals usually
involved are calcite, aragonite, siderite, gypsum, silica,
iron oxide, iron sulfide, apatite, and, if the cationic chemistry and pore water chemistry are appropriate, minerals in
complexes such as siderite, calcite, Fe monosulfide, and
Zn sulfide/sulfate (Postma, 1982; Pirrie et al., 2000),
occurring as cements, cemented layers, intra-skeletal
crystal crusts, and nodules. The controls on precipitation
of minerals can be complex involving salinity, the
MINERALIZATION
441
et al., 2000) and otoliths (CaCO 3 in fish; Gauldie, 1993;
Campana, 1999). Bone is a composite material composed
of organic components (primarily collagen) and inorganic
components (bio-apatite, Ca 10 (PO 4 ) 3 (OH) 2 ), as well as
lipids and water. As a crystalline solid, bone has a special
form of the mineral apatite that dominates its composite
structure, being composed of extremely small-sized crystallites (Wopenka and Pasteris, 2005).
The long-term products of biomineralization of biota in
estuaries is biogenic sediment through the accumulation
and formation of foraminiferal sand, molluscan shell grit
and gravel, diatomaceous mud, and carbonate mud.
Formation of minerals via biomediation
(biomediated mineralization)
The bacterial reduction of sulfate to sulfide at the sediment
bed is a key process in the coastal sulfur cycle and is
responsible for the oxidation of organic matter which
becomes buried below the oxic and suboxic zones of the
sediment bed (Lovley and Phillips, 1986; Machel, 2001).
The sulfate ion is common in seawater, sediment, or in
waters rich with decaying organic material (with SO 4
2À
deriving from organic matter). Sulfate-reducing bacteria
are common in anaerobic environments wherein they utilize the sulfate ion as an electron donor and thus aid in
the degradation of organic materials. Sulfate reduction is
the dominant terminal step in the mineralization processes
of sulfate-rich sediments where the sulfate reducers inhibit
the methanogens by competing for common substrates.
Sulfate reduction thus is quantitatively important in the
overall oxidation of organic matter in sediments (Barton
and Fauque, 2009).
Various minerals can be precipitated by biomediation,
with the best known being pyrite. If Fe, Mn, Cu, and Zn
are present in the environment, they can be involved in
the formation of sulfides, however, since Fe is generally
the most common transition metal cation in natural
environments, sulfides of Fe (as pyrite) will be the most
common mineral. Precipitates of pyrite, mediated by
sulfate-reducing bacteria, are commonly framboidal
(Sawlowlicz, 1993). Framboids (after the French word
framboise for “raspberry”) are small clusters of pyrite
crystals resembling a raspberry that can be < 1 mm in size
but range in size from 0.5 mm to 40 mm in diameter, with
the average aggregate size about 5 mm (Wilkin et al.,
1996). That FeS 2 , as framboids, is associated with microbial activity has been known for some time and has been
implicated in the development of sedimentary pyrite in
the rock record (Schieber, 2002). While organic-matterrich sediments inherently tend to be black or dark gray,
the fine-grained precipitated iron sulfide disseminated
throughout the sediment as a result of bacterial degradation of organic material typically also renders sediments
to various shades of gray to black depending on the
concentration of the pyrite in the sediment.
Iron sulfides as pyrite (FeS 2 ) and iron monosulfide
(FeS) can play a central role in the sulfur and iron cycles
of estuarine, coastal, and marine sediments. They may be
buried in the sediment (remaining gray to dark gray) or
oxidized by O 2 when brought to the near surface or surface
by wave action or by bioturbation. FeS 2 and FeS may also
be oxidized within the anoxic sediment in which NO 3
À , Fe
(III) oxides, or MnO 2 are available as potential electron
acceptors (Schippers and Jørgensen, 2002).
As a result of the shell-forming processes, organic matter
may be embedded in molluscan calcitic/aragonitic
shells and crustacean chitinous/carbonate exoskeletons
where, if decayed by bacteria, becomes a micro-site
for biomediated precipitation of fine-grained pyrite
framboids. The scattered occurrence of fine-grained pyrite
may impart a speckled appearance to shells and, in
the extreme, may turn them gray. Also, when embedded
in sulfidic sediment, shells often become blackened with
pyrite through sulfide diffusion. As such, calcitic/aragonitic
shells and chitinous/carbonate shells become sparsely to
moderately impregnated with pyrite. Blackened shells and
foraminifera have been reported by Ginsburg (1957),
Pilkey et al. (1969), and Davies (1970). In each case, iron
sulfide was implicated as the blackening agent.
Algae boring into shells often are micro-sites for the
precipitation of aragonite, Mg calcite, or calcite in the
algal thread tubules. They also are sites for pyrite precipitation. The calcitic/aragonitic shells become riddled with
ultrafine carbonate-filled borings, and in the extreme, the
carbonate-filled borings coalesce and form a thin carbonate envelope around the shell (Bathurst, 1975). In the case
of pyrite, the fine-scale algal tubules are lined with or partially filled with pyrite, which imparts a gray external tinge
to the shells.
Organisms, especially bacteria, are instrumental in facilitating the precipitation of microcrystals and nanocrystals
of the calcium carbonates (calcite, Mg calcite, aragonite),
dolomite (Castanier et al., 2000; Sánchez-Román et al.,
2007, 2008), and phosphates (Sánchez-Román et al.,
2007). Though not volumetrically important, this process
results in contribution to the mineral record in estuaries.
Minerals directly crystallized from estuarine water
(geological primary mineralization)
Minerals can also directly crystallize from estuarine water,
either from the water column or from pore waters, if the
hydrochemistry, salinity, or concentration of the open
estuarine water or tidal flat pore water is appropriate.
These are primary precipitates. The minerals usually
involved are calcite, aragonite, siderite, gypsum, silica,
iron oxide, iron sulfide, apatite, and, if the cationic chemistry and pore water chemistry are appropriate, minerals in
complexes such as siderite, calcite, Fe monosulfide, and
Zn sulfide/sulfate (Postma, 1982; Pirrie et al., 2000),
occurring as cements, cemented layers, intra-skeletal
crystal crusts, and nodules. The controls on precipitation
of minerals can be complex involving salinity, the
MINERALIZATION
441