Biology Reference
In-Depth Information
Primary production:
C
ARBOHYDRATES,
P
ROTEINS
etc.
O
2
Heterotrophs
Rhodopirellula baltica
Phaeobacter gallaeciensis
CO
2
+
H
2
O
Sedimentation
OXIC
WATER COLUMN
ANOXIC
SEDIMENT
Fermenting bacteria
Denitrifiers
Aromatoleum aromaticum
Ar. alkani
NO
3
-/SO
4
2-
, etc.
Sulfate reducers
Db. toluolica
Dc. oleovorans, etc.
F
ATTY
A
CIDS
,
A
LCOHOLS
CO
2
+
N
2
/H
2
S
Sulfate reducers
Db. autotrophicum
Dt. psychrophila
Dv. vulgaris, etc.
H
YDROCARBONS
Biological
formation
2-
Diagenesis
Catagenesis
CO
2
+
H
2
S
4
Anthropogenic input
Recent formation
Oil reservoirs
Fig. 2. Microbial mineralization of organic carbon in the marine/aquatic systems. Indicated organisms are studied in our
group (
bold
, analyzed to date by 2D DIGE).
are established and prevail in many environments, such as marine
and freshwater sediments, ground water aquifers, soils, deep bio-
sphere, and oil reservoirs. Due to the absence of molecular oxygen
under anoxic conditions, a variety of alternative, oxygenase-
independent reactions are employed by diverse anaerobic bacteria
that have both (reactions and bacteria) been discovered only dur-
ing the last 10-20 years (
19-22
). Considering that aromatic com-
pounds were present in the biosphere long before the evolution of
an oxic atmosphere, their anaerobic biodegradation is probably an
evolutionary rather old metabolic trait of bacteria.
1.3. Importance
of Pure Culture-Based
Proteogenomics
The sheer size of emerging (meta)genomic data is impressive,
providing unprecedented insights into the genetic blueprints of
microbes, as well as their diversity, biogeography, and in situ gene
pools. However, the “true biology” unfolds at the proteome level,
as the functional output of a (meta)genome in response to prevailing
and/or changing environmental conditions. To gain causal under-
standing of an organism's functions and dynamics in ecosystems,
pure culture studies mimicking nutritional or other environmental
conditions are essential. Model organisms should be selected
according to their ecosystem relevance: cultivated member of a highly
abundant group (
23
), process relevant (
24
), and/or intriguing
metabolism (
25
).
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