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Microbial Ecology
a global metabolic map for Earth (Fig. 2). The genes
REVIEW encoding the machinery responsible for the redox
chemistry of half-cells form the basis of the major
The Microbial Engines That Drive energy-transducing metabolic pathways. The con-
temporary pathways invariably require multimeric
Atmosphere
Anoxygenic Oxygenic
photosynthesis photosynthesis
NH4+
HS–/S0 CO2 + H2O
CO2
CO2 N2 fixation
SO42–
SO42–/S0 Fe3+
Mn2+
SO42–/S0 Fe2+ NO3–/NO 2–
2+
respiration CO2 Fe N4 Mn4+
CO2
H2O + respiration
Mn SO42–
SO42–/S+ O2 respiration
[CH2O]
H2 + CO2 H2
CH4 Fe3+ respiration [CH2O] NO3–/NO2– [CH2O]
H2 respiration H2
Fermentation HS–/S0 CH4
Methanogenesis [CH2O] Fe2+ HS–/S0
[CH2O] [CH2O]
H2 H2 Fe2+
HS–/S0 HS–/S0 Mn2+
H2 + CO2
NH4+ NH4+
–0.5 0 0.5 1
E0 (V)
CH4 [CH2O] Metals
Metals H2, CH4 CO2 PO43–
FeS2 CO32–
HS-, SO3 CO2 NH4+
PO43– Ca3 (PO4)2 SiO3 SO42–
O2-mediated
Mn-mediated
Fe-mediated
S-mediated
N-mediated
H2- or C-mediated
O2
Respiration
N2 N2 fixation
Fe3+
SO2–
4
CO2
H2O
+CO2
Photosynthesis
Fig. 2. A schematic diagram depicting a global, interconnected network of the biologically mediated cycles for hydrogen, carbon, nitrogen, oxygen,
sulfur, and iron. A large portion of these microbially mediated processes are associated only with anaerobic habitats.
photosynthesis, and the electrons and protons gen- less, one of the last metabolic pathways to emerge tainty. These events took place before any geogical
erated in the process are used to reduce inorganic was oxygenic photosynthesis. evidence of life, and while phylogenetic trees and
carbon to organic matter with the formation of higher- Oxygenic photosynthesis is the most complex structural analyses provide clues regarding key
energy bonds. The resulting oxidized metabolites energy transduction process in nature: More than motifs, so far they have not provided a blueprint for
may in turn serve as electron acceptors in aerobic or 100 genes are involved in making several macro- how life began. Stable-isotope fractionation has
anaerobic respiration for the photosynthetic orga- molecular complexes (22). Nevertheless, indirect provided evidence for sulfate reduction and meth-
nisms themselves or by other, nonphototrophic orga- evidence shows that this series of reactions had anogenesis in 3.5-billion-year-old deposits (28), but
nisms that use these “waste products” as oxidants (21). evolved by ~3 billion years ago (23), although the these metabolic processes are presumably older.
The outcome of the coupled metabolic path- atmosphere and the upper ocean maintained a very
ways is that on geological time scales, the biosphere low concentration of O2 for the next ~0.5 billion Modes of Evolution
can rapidly approach relatively self-sustaining ele- years (24, 25). The production and respiration of ni- Molecular evidence, based on gene order and the
ment cycling on time scales of centuries to millen- trate must have evolved after the advent of oxygenic distribution of metabolic processes, strongly sug-
nia. On longer time scales, perpetuation of life photosynthesis, as there can be no nitrate without gests that early cellular evolution was probably
remains contingent on geological processes and the oxygen (16). Although the succession of probable communal, with promiscuous horizontal gene flow
constant flux of solar energy. Essential elements or events that led to the global production of O2 is probably representing the principal mode of evo-
compounds, such as phosphate, carbon (either as becoming increasingly clear (26, 27), the evolu- lution (29). The distribution of genes responsible
carbonate or organic matter), and metals, are con- tionary details delimiting important events for other for the major extant catabolic and anabolic pro-
tinuously buried in sediments and are returned to redox cycles and elements are more ambiguous. cesses may have been distributed across a common
the biosphere only through mountain building and Attempts to reconstruct the evolution of major global gene pool, before cellular differentiation and
subsequent erosion or geothermal activity (Fig. 1). dissimilatory metabolic pathways are mainly vertical genetic transmission evolved as we know it
There is little understanding of how long it based on geological evidence for the availability today. In the microbial world, not only individual
took for reaction cycles to develop from local of potential electron donors and oxidants during genes but also entire metabolic pathways central to
events to global alteration of prevailing geolog- the early Precambrian (23). Although we can gain specific biogeochemical cycles appear to be fre-
ically produced redox set points. The last com- some idea of the relative quantitative importance quently horizontally transferred; a contemporary
mon ancestor of extant life presumably possessed of different types of energy metabolism, we do not analog is the rapid acquisition of antibiotic re-
genes for the adenosine triphosphatase complex know the order in which they evolved. Indeed, the sistance in pathogenic bacteria (30). The dissimi-
required to maintain ion gradients generated by origin of life and the first reactions in energy me- latory sulfite reductases found in contemporary
photochemical or respiratory processes. Regard- tabolism probably never will be known with cer- sulfate-reducing d-proteobacteria, Gram-positive
Microbial Biogeography:
respond to environmental change. Although plants
have been the focal group in this emerging
research area, recent advances in environmental
From Taxonomy to Traits molecular biology such as genomics, proteomics,
transcriptomics, and metabolomics place microbi-
al ecology in a unique position to move trait-based
Jessica L. Green,1* Brendan J. M. Bohannan,1 Rachel J. Whitaker2 biogeography forward.