5
Bacteria and Marine Biogeochemistry
190
to inorganic sediment grains. Freshly arrived
material often forms a thin detritus layer at the
sediment-water interface, in particular after the
sedimentation of a phytoplankton bloom. This
detritus is a site of high microbial activity and
rapid organic matter degradation, even in the deep
sea where the bacterial metabolism is otherwise
strongly limited by the low organic influx (Lochte
and Turley 1988). Due to the feeding by benthic
invertebrates and to the mixing of sediment by
their burrowing activity (bioturbation) the deposited organic particles are gradually buried into the
sediment and become an integral part of the
sedimentary organic matter.
5.5.1
Depolymerization of
Macromolecules
The organic detritus is a composite of macromolecular compounds such as structural carbohydrates, proteins, nucleic acids and lipid complexes.
Prokaryotic organisms are unable to take up
particles or even larger organic molecules and are
restricted to a molecular size less than ca 600
daltons (Weiss et al. 1991). A simple organic
molecule such as sucrose has a molecular size of
342 daltons. Thus, although some bacteria are
able to degrade and metabolize fibers of cellulose,
lignin, chitin or other structural polymers, they
must first degrade the polymers before they can
assimilate the monomeric products (Fig. 5.11).
This depolymerization is caused by exoenzymes
produced by the bacteria and either released
freely into their environment or associated with
the outer membrane or cell wall. The latter requires
a direct contact between the bacterial cells and the
particulate substrate and many sediment bacteria
are indeed associated with solid surfaces in the
sediment. The excretion of enzymes is a loss of
carbon and nitrogen and thus an energy investment of the individual bacterial cells, but these
have strategies of optimizing the return of monomeric products (Vetter et al. 1998) and may
regulate the enzyme production according to the
presence of the polymeric target compound in
their environment (‘substrate induction’). Thus,
there is a positive correlation between the
availability of specific polymeric substances in the
sediment and the concentration of free enzymes
which may degrade them (Boetius and Damm
1998; Boetius and Lochte 1996).
The depolymerization of sedimentary organic
matter is generally the rate-limiting step in the
sequence of mineralization processes (Arnosti
2004). This may be concluded from the observation that the monomeric compounds and the
products of further bacterial degradation do not
accumulate in the sediment but are rapidly
assimilated and metabolized. Thus, the concentrations of individual free sugars, amino acids or
lipids in the pore water are generally low. Dissolved organic matter (DOM) is a product of partial
degradation and may be released from the
sediment to the overlying water. It mainly consists
of complex dissolved polymers and oligomers
rather than of monomers. Dissolved organic
molecules may not only be taken up by bacteria
but may also be removed from the pore water by
adsorption onto sediment particles or by
condensation reactions, such as monosaccharides
and amino acids forming melanoidins (Sansone et
al. 1987; Hedges 1978). Organic matter that is not
mineralized may be adsorbed to mineral surfaces
and transformed to ‘geomacromolecules’ which
are highly resistant to enzymatic hydrolysis and
bacterial degradation and which become more
permanently buried with the sediment (Henrichs
1992; Keil et al. 1994). This buried fraction also
contains some of the original organic matter which
was deposited as refractory biomolecules such as
lignins, tannins, algaenan, cutan and suberan
(Tegelaar et al. 1989). The burial of organic matter
deep in the sediment shows a positive correlation
with the rate of deposition and constitutes in the
order of 5-20% of the initially deposited organic
matter in shelf sediments and 0.5-3% in deep-sea
sediments (Henrichs and Reeburgh 1987)
5.5.2
Aerobic and Anaerobic
Mineralization
The particulate detritus consumed by metazoans,
and the small organic molecules taken up by
microorganisms in the oxic zone, may be
mineralized completely to CO 2 through aerobic
respiration within the individual organisms. The
aerobic food chain consists of organisms of very
diverse feeding biology and size, but of a
uniform type of energy metabolism, namely the
aerobic respiration. The oxic zone is, however,
generally only mm-to-cm thick in finegrained
shelf sediments as shown by measurements with
O 2 microsensors (Chap. 3). In slope and deep-sea
sediments the oxic zone expands to reach depths
of many cm or dm (Reimers 1987; Wenzhöfer and
Glud 2002).
Bacteria and Marine Biogeochemistry
190
to inorganic sediment grains. Freshly arrived
material often forms a thin detritus layer at the
sediment-water interface, in particular after the
sedimentation of a phytoplankton bloom. This
detritus is a site of high microbial activity and
rapid organic matter degradation, even in the deep
sea where the bacterial metabolism is otherwise
strongly limited by the low organic influx (Lochte
and Turley 1988). Due to the feeding by benthic
invertebrates and to the mixing of sediment by
their burrowing activity (bioturbation) the deposited organic particles are gradually buried into the
sediment and become an integral part of the
sedimentary organic matter.
5.5.1
Depolymerization of
Macromolecules
The organic detritus is a composite of macromolecular compounds such as structural carbohydrates, proteins, nucleic acids and lipid complexes.
Prokaryotic organisms are unable to take up
particles or even larger organic molecules and are
restricted to a molecular size less than ca 600
daltons (Weiss et al. 1991). A simple organic
molecule such as sucrose has a molecular size of
342 daltons. Thus, although some bacteria are
able to degrade and metabolize fibers of cellulose,
lignin, chitin or other structural polymers, they
must first degrade the polymers before they can
assimilate the monomeric products (Fig. 5.11).
This depolymerization is caused by exoenzymes
produced by the bacteria and either released
freely into their environment or associated with
the outer membrane or cell wall. The latter requires
a direct contact between the bacterial cells and the
particulate substrate and many sediment bacteria
are indeed associated with solid surfaces in the
sediment. The excretion of enzymes is a loss of
carbon and nitrogen and thus an energy investment of the individual bacterial cells, but these
have strategies of optimizing the return of monomeric products (Vetter et al. 1998) and may
regulate the enzyme production according to the
presence of the polymeric target compound in
their environment (‘substrate induction’). Thus,
there is a positive correlation between the
availability of specific polymeric substances in the
sediment and the concentration of free enzymes
which may degrade them (Boetius and Damm
1998; Boetius and Lochte 1996).
The depolymerization of sedimentary organic
matter is generally the rate-limiting step in the
sequence of mineralization processes (Arnosti
2004). This may be concluded from the observation that the monomeric compounds and the
products of further bacterial degradation do not
accumulate in the sediment but are rapidly
assimilated and metabolized. Thus, the concentrations of individual free sugars, amino acids or
lipids in the pore water are generally low. Dissolved organic matter (DOM) is a product of partial
degradation and may be released from the
sediment to the overlying water. It mainly consists
of complex dissolved polymers and oligomers
rather than of monomers. Dissolved organic
molecules may not only be taken up by bacteria
but may also be removed from the pore water by
adsorption onto sediment particles or by
condensation reactions, such as monosaccharides
and amino acids forming melanoidins (Sansone et
al. 1987; Hedges 1978). Organic matter that is not
mineralized may be adsorbed to mineral surfaces
and transformed to ‘geomacromolecules’ which
are highly resistant to enzymatic hydrolysis and
bacterial degradation and which become more
permanently buried with the sediment (Henrichs
1992; Keil et al. 1994). This buried fraction also
contains some of the original organic matter which
was deposited as refractory biomolecules such as
lignins, tannins, algaenan, cutan and suberan
(Tegelaar et al. 1989). The burial of organic matter
deep in the sediment shows a positive correlation
with the rate of deposition and constitutes in the
order of 5-20% of the initially deposited organic
matter in shelf sediments and 0.5-3% in deep-sea
sediments (Henrichs and Reeburgh 1987)
5.5.2
Aerobic and Anaerobic
Mineralization
The particulate detritus consumed by metazoans,
and the small organic molecules taken up by
microorganisms in the oxic zone, may be
mineralized completely to CO 2 through aerobic
respiration within the individual organisms. The
aerobic food chain consists of organisms of very
diverse feeding biology and size, but of a
uniform type of energy metabolism, namely the
aerobic respiration. The oxic zone is, however,
generally only mm-to-cm thick in finegrained
shelf sediments as shown by measurements with
O 2 microsensors (Chap. 3). In slope and deep-sea
sediments the oxic zone expands to reach depths
of many cm or dm (Reimers 1987; Wenzhöfer and
Glud 2002).