4
Organic Matter: The Driving Force for Early Diagenesis
138
is the anaerobic methane oxidation by consortia of
archaea and sulfate-reducing bacteria, formally the
reverse of methanogenesis (AOM; see Chap. 8).
4.3.2
Chemical Composition of Biomass
Apart from considering the fate of bulk organic matter
(or organic carbon) during diagenesis, organic geochemistry has developed a more sophisticated understanding of diagenetic organic matter transformation
down to the molecular level. Fundamental to this
understanding is a comparison of the organic constituents of geological samples with the inventory of
extant organisms. This was, and still partly is, hampered
by the limited knowledge of the natural product
chemistry particularly of unicellular marine algae,
protozoans and bacteria.
The simplest way of describing the chemical nature
of biomass is by its elemental composition. For marine
phytoplankton as primary producers a relationship was
found to the nutrients available in seawater which led
to the definition of the Redfield ratio as C:N:P = 106:16:1
(Redfield et al. 1963). Derived from this is an average
molecular formula of phytoplankton organic matter
related to the general process of phytosynthesis (of
which the reverse signifies remineralization):
106 CO 2 + 106 H 2 O + 16 NH 3 + H 3 PO 4 →
→ →
→ →
(CH 2 O) 106 (NH 3 ) 16 H 3 PO 4 + 106 O 2
(4.8)
The formula of the organic matter product is often
reduced to the summary version of C 106 H 263 N 16 O 110 P. It
has no real chemical meaning in terms of molecular
structure because it contains more hydrogen than the
bonds of all the other atoms can account for. The
reason is that the generalized average formula (i.e. the
product in Eq. 4.8) is just the sum of separate neutral
molecules which are involved in biosynthesis of
organic matter. The formation of a molecular structure
requires the formal loss of a number of molecules of
water for condensation. Whereas the formula does not
represent the correct elemental organic matter composition of marine phytoplankton, at least not for
hydrogen and oxygen, it has to be kept in mind that it
is a crude generalisation in itself. It would certainly
vary with nutrient conditions and planktonic species
as has been observed, e.g., by Takahasi et al. (1985) in
a study of plankton biomass from the Atlantic and
Indian Oceans which resulted in a modified Redfield
ratio of 122(±18) : 16 : 1. There are quite a number of
more recent studies that confirm this kind of deviation
from the Redfield ratio or extend the ratio by inclusion
of trace metals (e.g. Leonardos and Geider 2004; Ho et
al. 2003; cf. also Chap. 6).
Food chain and early diagenetic processes change
the initial elemental composition drastically. Organic
matter in sediments relative to the primary producers is
enriched particularly in carbon and hydrogen, whereas
it is depleted in oxygen (but the degree depends on the
extent of oxidation of sedimentary organic matter),
nitrogen and phosphorus. Depletion in phosphorus is
due to the facile hydrolytic cleavage of bound
phosphate groups. Loss of nitrogen occurs by preferential degradation of organic nitrogen compounds as
discussed later (see Sect. 4.4 for a discussion of C/N
ratios). Sulfur, not originally included in the general
formula, would be equal to or less in content than
phosphorus. The enrichment of sulfur in fossil organic
matter is, however, not due to a relative enrichment in
the course of preferential loss of other elements (as is
the case for C and H). Sulfur enrichment rather is a
consequence of diagenetic incorporation of reduced
inorganic sulfur species (like HS
-
or corresponding
polysulfides) which are formed from seawater sulfate
by sulfate-reducing microorganisms in shallow
sediments under anoxic conditions (see Chap. 8).
On the next higher level, the chemical composition
of living organisms in the biosphere, despite their
diversity, can be confined to a limited number of
principal compound classes. Their proportions vary in
the different groups of organisms as is evident from
the estimates of Romankevitch (1984) for a few types
of marine organisms (Table 4.3). Also, within the groups
the compound class composition is highly variable
(Table 4.4). It may even depend on the growth stage
for a single species. The compound classes in turn
comprise a very large number of single compounds
with different individual chemical structures, although
enzymatic systems limit the potential chemical diversity
(that is why there are chemical biomarkers of taxonomic
significance). Many of the compound classes are also
represented in fossil organic matter, although not in
the same proportions as they occur in the biosphere
because of their different stabilities toward degradation
and modification of original structures during
sedimentation and diagenesis.
Nucleic Acids and Proteins
Nucleic acids, as ribonucleic acids (RNA) or desoxyribonucleic acids (DNA), are biological macromolecules
carrying genetic information. They consist of a regular
sequence of phosphate, sugar (pentose) and a small
variety of base units, i.e. nitrogen-bearing heterocyclic
Organic Matter: The Driving Force for Early Diagenesis
138
is the anaerobic methane oxidation by consortia of
archaea and sulfate-reducing bacteria, formally the
reverse of methanogenesis (AOM; see Chap. 8).
4.3.2
Chemical Composition of Biomass
Apart from considering the fate of bulk organic matter
(or organic carbon) during diagenesis, organic geochemistry has developed a more sophisticated understanding of diagenetic organic matter transformation
down to the molecular level. Fundamental to this
understanding is a comparison of the organic constituents of geological samples with the inventory of
extant organisms. This was, and still partly is, hampered
by the limited knowledge of the natural product
chemistry particularly of unicellular marine algae,
protozoans and bacteria.
The simplest way of describing the chemical nature
of biomass is by its elemental composition. For marine
phytoplankton as primary producers a relationship was
found to the nutrients available in seawater which led
to the definition of the Redfield ratio as C:N:P = 106:16:1
(Redfield et al. 1963). Derived from this is an average
molecular formula of phytoplankton organic matter
related to the general process of phytosynthesis (of
which the reverse signifies remineralization):
106 CO 2 + 106 H 2 O + 16 NH 3 + H 3 PO 4 →
→ →
→ →
(CH 2 O) 106 (NH 3 ) 16 H 3 PO 4 + 106 O 2
(4.8)
The formula of the organic matter product is often
reduced to the summary version of C 106 H 263 N 16 O 110 P. It
has no real chemical meaning in terms of molecular
structure because it contains more hydrogen than the
bonds of all the other atoms can account for. The
reason is that the generalized average formula (i.e. the
product in Eq. 4.8) is just the sum of separate neutral
molecules which are involved in biosynthesis of
organic matter. The formation of a molecular structure
requires the formal loss of a number of molecules of
water for condensation. Whereas the formula does not
represent the correct elemental organic matter composition of marine phytoplankton, at least not for
hydrogen and oxygen, it has to be kept in mind that it
is a crude generalisation in itself. It would certainly
vary with nutrient conditions and planktonic species
as has been observed, e.g., by Takahasi et al. (1985) in
a study of plankton biomass from the Atlantic and
Indian Oceans which resulted in a modified Redfield
ratio of 122(±18) : 16 : 1. There are quite a number of
more recent studies that confirm this kind of deviation
from the Redfield ratio or extend the ratio by inclusion
of trace metals (e.g. Leonardos and Geider 2004; Ho et
al. 2003; cf. also Chap. 6).
Food chain and early diagenetic processes change
the initial elemental composition drastically. Organic
matter in sediments relative to the primary producers is
enriched particularly in carbon and hydrogen, whereas
it is depleted in oxygen (but the degree depends on the
extent of oxidation of sedimentary organic matter),
nitrogen and phosphorus. Depletion in phosphorus is
due to the facile hydrolytic cleavage of bound
phosphate groups. Loss of nitrogen occurs by preferential degradation of organic nitrogen compounds as
discussed later (see Sect. 4.4 for a discussion of C/N
ratios). Sulfur, not originally included in the general
formula, would be equal to or less in content than
phosphorus. The enrichment of sulfur in fossil organic
matter is, however, not due to a relative enrichment in
the course of preferential loss of other elements (as is
the case for C and H). Sulfur enrichment rather is a
consequence of diagenetic incorporation of reduced
inorganic sulfur species (like HS
-
or corresponding
polysulfides) which are formed from seawater sulfate
by sulfate-reducing microorganisms in shallow
sediments under anoxic conditions (see Chap. 8).
On the next higher level, the chemical composition
of living organisms in the biosphere, despite their
diversity, can be confined to a limited number of
principal compound classes. Their proportions vary in
the different groups of organisms as is evident from
the estimates of Romankevitch (1984) for a few types
of marine organisms (Table 4.3). Also, within the groups
the compound class composition is highly variable
(Table 4.4). It may even depend on the growth stage
for a single species. The compound classes in turn
comprise a very large number of single compounds
with different individual chemical structures, although
enzymatic systems limit the potential chemical diversity
(that is why there are chemical biomarkers of taxonomic
significance). Many of the compound classes are also
represented in fossil organic matter, although not in
the same proportions as they occur in the biosphere
because of their different stabilities toward degradation
and modification of original structures during
sedimentation and diagenesis.
Nucleic Acids and Proteins
Nucleic acids, as ribonucleic acids (RNA) or desoxyribonucleic acids (DNA), are biological macromolecules
carrying genetic information. They consist of a regular
sequence of phosphate, sugar (pentose) and a small
variety of base units, i.e. nitrogen-bearing heterocyclic