Many have proclaimed that genomics will revolutionize geomicrobiology. This
revolution seems to have arrived now. At the turn of the millennium, approximately
20 microbial genomes had been sequenced. Most were from thermophilic archaea
and bacteria with small genomes (1.5 to 2 megabase pairs) or from pathogens,
parasites and other model organisms. In the last four years, researchers fully
sequenced and at least partially annotated more than 100 additional genomes,
several key players in geomicrobiology among them.
To understand better how microbes drive geologic processes, we are beginning
to study the blueprints of cellular function: genes and the proteins they encode.
Genomic data, when interpreted in the context of geochemistry and microbial
ecology, will on the one hand help elucidate the co-evolution of Earth and its
biota through geologic time, and on the other, help identify the capabilities
of modern organisms to alter their geochemical environments and serve as agents
for bioremediation. Since November 2002, researchers published genome sequences
for several of the most important microorganisms found in natural and contaminated
geologic environments.
John Heidelberg and colleagues description of the genome of Shewanella oneidensis
(Nature Biotechnology, v. 20, p. 1118) confirms and further reveals this
bacterium's ability to function both aerobically and anaerobically; its full
suite of respiratory metabolisms is staggering. The researchers identified dozens
of new genes, including 32 novel cytochromes, that relate to Shewanella's
electron transport system. Deciphering such data will cement the link between
microbial metabolic activities and redox processes in Earth's geochemical cycles.
In addition, a phage identified in the genome may permit molecular engineering
to improve Shewanella's role in the bioremediation of pollutant organic
compounds and radioactive or otherwise toxic metals. And genome analysis can
clarify how Shewanella attaches to and then exploits solid phases, in particular
metal (oxy)hydroxides.
The metabolic diversity of Geobacter is also explained by its genome (Methé
et al., Science, v. 302, p. 1967). This proteobacterium — which is
abundant in diverse soils, the deep continental subsurface and marine sediments
— is capable of oxidizing organic matter with various metal oxides, making
it another prime target for use in bioremediation. Genetic evidence also points
to unsuspected aerobic metabolism, diverse carbon metabolisms, motility and
chemotactic behavior. In addition, Daniel Bond and Derek Lovley explored the
biotechnological potential of Geobacter — specifically its ability
during organic waste oxidation to produce electricity, which can be captured
by platinum electrodes (Applied and Environmental Microbiology, v. 69, p.
1548). Furthermore, Kazem Kashefi and colleagues (Applied and Environmental
Microbiology, v. 69, p. 2985) expanded the impressive list of physiologic
characteristics by showing that a close relative of Geobacter, called Geothermobacter,
thrives at temperatures as high as 65 degrees Celsius in deep-sea hydrothermal
vent environments.
Phytoplankton floating in the ocean may not catalyze much mineral precipitation
or dissolution, but they nevertheless play vital roles in biogeochemical processes
and account for half of the global oxygen production annually. The genomes of
two Prochlorococcus strains reveal what may be the minimum genetic requirements
for an oxygenic photoautotroph (Rocap et al., Nature, v. 424, p. 1042
and Dufresne et al., Proceedings of the National Academy of Sciences,
v. 100, p. 10,020). Combined with genome analyses of Synechococcus (Palenik
et al., Nature, v. 424, p. 1037) and another Prochlorococcus strain,
evolutionary events, including gene transfer, in oxygen producing photosynthetic
microbes are beginning to emerge. In addition, we are starting to understand
how the open ocean cycles and conserves nutrients, such as nitrogen and iron,
and how planktonic organisms respond to changing light intensity and other environmental
variables.
The genomes of Shewanella, Geobacter and the cyanobacteria will help
to unravel the evolution of microbial metal cycling on Earth and nutrient cycling
in the upper oceans. Other geologic targets are waiting. This year, highlights
will include the sequencing of Marinobacter, a key organism in iron-cycling
in the oceans, and whole genome shotgun sequencing of microbial populations,
not merely individual species; Craig Venter and colleagues (Science, in
press) used this approach on North Atlantic surface seawater to identify 1.2
million new genes from at least 1,800 species.
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