169
5
Bacteria and Marine Biogeochemistry
BO BARKER JØRGENSEN
Geochemical cycles on Earth follow the basic laws
of thermodynamics and proceed towards a state of
maximal entropy and the most stable mineral
phases. Redox reactions between oxidants such as
atmospheric oxygen or manganese oxide and
reductants such as ammonium or sulfide may
proceed by chemical reaction, but they are most
often accelerated by many orders of magnitude
through enzymatic catalysis in living organisms.
Throughout Earth’s history, prokaryotic physiology has evolved towards a versatile use of chemical energy available from this multitude of
potential reactions. Biology, thereby, to a large
extent regulates the rate at which the elements are
cycled in the environment and affects where and
in which chemical form the elements accumulate.
By coupling very specifically certain reactions
through their energy metabolism, the organisms
also direct the pathways of transformation and the
ways in which the element cycles are coupled.
Microorganisms possess an enormous diversity
of catalytic capabilities which is still only
incompletely explored and which appears to
continuously expand as new organisms are
discovered. A basic understanding of the
microbial world and of bacterial energy metabolism is therefore a prerequisite for a proper
interpretation of marine geochemistry - a
motivation for this chapter on biogeochemistry.
The role of microorganisms in modern biogeochemical cycles is the result of a long evolutionary history. The earliest fossil evidence of
prokaryotic organisms dates back three and a half
billion years (Schopf and Klein 1992; Brasier et al.
2002). Only some 1.5 billion years later did the
evolution of oxygenic photosynthesis lead to a
build-up of oxygen on the surface of our planet
and it may have taken another 1.5 billion years
before the oxygen level in the atmosphere and
ocean rose to the present-day level, thus triggering the rapid evolutionary radiation of
metazoans at the end of the Proterozoic era.
Through the two billion years that Earth was
inhabited exclusively by microorganisms, the main
element cycles and biogeochemical processes
known today evolved. The microscopic prokaryotes developed the complex enzymatic machinery
required for these processes and are even today
much more versatile with respect to basic types of
metabolism than plants and animals which
developed over the last 600 million years. In spite
of their uniformly small size and mostly inconspicuous morphology, the prokaryotes are thus
physiologically much more diverse than the
metazoans. In the great phylogenetic tree of all
living organisms, humans are more closely related
to slime molds than the sulfate reducing bacteria
are to the methanogenic archaea. The latter two
belong to separate domains of prokaryotic
organisms, the Bacteria and the Archaea, respectively (the term ‘prokaryote’ is used rather than
‘bacteria’ when also the archaea are included).
Animals and plants, including all the eukaryotic
microorganisms, belong to the third domain,
Eukarya.
5.1
Role of Microorganisms
5.1.1
From Geochemistry to
Microbiology – and back
Due to the close coupling between geochemistry
and microbiology, progress in one of the fields has
often led to progress in the other. Thus, analyses
of chemical gradients in the pore water of marine
sediments indicate where certain chemical species
are formed and where they react with each other.
The question is then, is the reaction biologically
catalyzed and which microorganisms may be
involved?
5
Bacteria and Marine Biogeochemistry
BO BARKER JØRGENSEN
Geochemical cycles on Earth follow the basic laws
of thermodynamics and proceed towards a state of
maximal entropy and the most stable mineral
phases. Redox reactions between oxidants such as
atmospheric oxygen or manganese oxide and
reductants such as ammonium or sulfide may
proceed by chemical reaction, but they are most
often accelerated by many orders of magnitude
through enzymatic catalysis in living organisms.
Throughout Earth’s history, prokaryotic physiology has evolved towards a versatile use of chemical energy available from this multitude of
potential reactions. Biology, thereby, to a large
extent regulates the rate at which the elements are
cycled in the environment and affects where and
in which chemical form the elements accumulate.
By coupling very specifically certain reactions
through their energy metabolism, the organisms
also direct the pathways of transformation and the
ways in which the element cycles are coupled.
Microorganisms possess an enormous diversity
of catalytic capabilities which is still only
incompletely explored and which appears to
continuously expand as new organisms are
discovered. A basic understanding of the
microbial world and of bacterial energy metabolism is therefore a prerequisite for a proper
interpretation of marine geochemistry - a
motivation for this chapter on biogeochemistry.
The role of microorganisms in modern biogeochemical cycles is the result of a long evolutionary history. The earliest fossil evidence of
prokaryotic organisms dates back three and a half
billion years (Schopf and Klein 1992; Brasier et al.
2002). Only some 1.5 billion years later did the
evolution of oxygenic photosynthesis lead to a
build-up of oxygen on the surface of our planet
and it may have taken another 1.5 billion years
before the oxygen level in the atmosphere and
ocean rose to the present-day level, thus triggering the rapid evolutionary radiation of
metazoans at the end of the Proterozoic era.
Through the two billion years that Earth was
inhabited exclusively by microorganisms, the main
element cycles and biogeochemical processes
known today evolved. The microscopic prokaryotes developed the complex enzymatic machinery
required for these processes and are even today
much more versatile with respect to basic types of
metabolism than plants and animals which
developed over the last 600 million years. In spite
of their uniformly small size and mostly inconspicuous morphology, the prokaryotes are thus
physiologically much more diverse than the
metazoans. In the great phylogenetic tree of all
living organisms, humans are more closely related
to slime molds than the sulfate reducing bacteria
are to the methanogenic archaea. The latter two
belong to separate domains of prokaryotic
organisms, the Bacteria and the Archaea, respectively (the term ‘prokaryote’ is used rather than
‘bacteria’ when also the archaea are included).
Animals and plants, including all the eukaryotic
microorganisms, belong to the third domain,
Eukarya.
5.1
Role of Microorganisms
5.1.1
From Geochemistry to
Microbiology – and back
Due to the close coupling between geochemistry
and microbiology, progress in one of the fields has
often led to progress in the other. Thus, analyses
of chemical gradients in the pore water of marine
sediments indicate where certain chemical species
are formed and where they react with each other.
The question is then, is the reaction biologically
catalyzed and which microorganisms may be
involved?