Biology Reference
In-Depth Information
Geo-
chemistry
Biogeo-
chemistry
Molecular
ecology
Microbial
physiology
Proteo-
genomics
Biologically
driven
process
Process
relevant
phylotypes
Process
relevant
physiology
Process
relevant
biocatalysts
Fig. 1. Modern marine microbiology pursues identifi cation of key redox biocatalysts
underlying biogeochemical processes. In the 1970s-1980s, many geochemical processes
were discovered to be biologically driven, coining the term biogeochemistry. In the 1990s,
cultivation-independent (16S rRNA-based) diversity analysis allowed correlating in situ
presence and abundance of microorganisms (phylotypes) with in situ biogeochemical
processes, thereby detecting potential key players in the environment. Enrichment and
isolation of such key players or representative model organisms form the basis for explain-
ing biogeochemical processes with physiological capacities. Finally, since about 2000,
genomics and proteomics are increasingly applied to identify key biocatalysts in process-
relevant model organisms and to determine their regulation in response to changing
environmental conditions.
is rapidly degraded by heterotrophic bacteria in the near-surface
waters. A minor part of the remaining organic carbon is further
transformed to refractory dissolved organic matter (DOM) persisting
in deeper ocean waters, while the rest sinks as particulate organic
matter (POM) to the seafl oor (
14, 15
). In the upper sediment
layers, organic matter (OM) is largely oxidized by sulfate-reducing
bacteria (
16
). However, over geological time scales, the remaining
small fraction of OM has accumulated in the deep sediments to the
largest global reservoir of organic carbon or has thermally trans-
formed into oil and gas. Hydrocarbons can enter the highly active
upper sediment layers following tectonic activities, by recent for-
mation in hydrothermal systems or due to anthropogenic impact
(Fig.
2
).
1.2. Anaerobic
Degradation of
Aromatic Compounds
The aromatic ring belongs, next to the glycosyl ring, to the most
abundant organic chemical structures in the biosphere. Aromatic
compounds are major constituents of proteins, lignin, fl avonoids,
tannins, and crude oil and are widely used as solvents or starting
compounds in industrial chemical synthesis. Thus, aromatic com-
pounds represent microbial substrates that are abundant in nature
and structurally diverse. The aromatic system conveys high chemi-
cal stability, posing biochemical hurdles to the biodegradability of
these compounds. Aerobic microorganisms employ O
2
-derived
highly reactive oxygen species in oxygenase-catalyzed reactions for
activation and cleavage of the aromatic ring (
17, 18
). Due to rapid
oxygen consumption by aerobic heterotrophs, anoxic conditions
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