by O 2 , nitrate, or ferric iron (Amend and Shock, 2001).
Oxidation and reduction of S compounds are widely used
energy sources for archaea in hydrothermal and marine
ecosystems.
Several processes of nitrogen-based energy metabolism
are known in archaea inhabiting extreme and moderate
environments, including aerobic ammonia oxidation,
dissimilatory reduction of nitrate to nitrite and of nitrite
to ammonium, and all steps of denitrification. Archaea
may also use nitrate assimilation or N 2 fixation to meet
their cellular N demand (Zumft, 1997; Amend and Shock,
2001; Philippot, 2002; Cabello et al., 2004; Francis et al.,
2005). One handful of cultured and numerous uncultured
members of Thaumarchaeota share the metabolic capacity
of aerobic ammonia oxidation. Given their ubiquity
and abundance in diverse habitats, archaeal ammonia
oxidizers may play a major role in the global N cycle
(Francis et al., 2005; Prosser and Nicol, 2008; Stahl and
de la Torre, 2012).
Methanogenesis is catalyzed exclusively by Archaea and
may proceed via three different pathways: reduction of CO
or CO 2 , reduction of methyl groups in small organic compounds, or cleavage of acetate. The strictly anaerobic
methanogenic archaea occur abundantly in natural and agricultural wetlands, hydrothermal environments, and the
digestive tracts of ruminants and termites (Liu and Whitman, 2008; Conrad, 2009). The oxidation of methane with
O 2 is known only in Bacteria, whereas its anaerobic oxidation with sulfate, iron, or manganese is catalyzed by diverse
and mostly uncultured Archaea, with or without the help of
bacterial symbionts (Beal et al., 2009; Knittel and Boetius,
2009; Milucka et al., 2012).
Ecology
Archaea occur in virtually any habitat that supports life.
They are adapted to salt concentrations of up to 5.2 M,
to temperatures above 120
C, and to life in permafrost
environments. Archaeal species inhabit mine drainage of
pH <0 and soda lakes of pH >11 and thrive at hydrostatic
pressures of up to 120 MPa in the deep sea and below
the sea floor (Valentine, 2007; Lipp et al., 2008; Bowers
and Wiegel, 2011; Takai and Nakamura, 2011). Although
best known for their endurance of one or more extreme
conditions, Archaea are also ubiquitous and vital parts of
communities in moderate environments. Their metabolic
activities contribute to the major element (C, N, S, Fe)
cycles on local to global scales.
Representatives of Cren-, Eury-, Nano-, and
Thaumarchaeota engage in mutualistic and parasitic symbioses with ruminants, insects, corals, sponges, molluscs,
ciliates, sulfate-reducing and sulfide-oxidizing bacteria,
and among archaea (Moissl-Eichinger and Huber, 2011;
Wrede et al., 2012). Archaea are also hosts of diverse
viruses (Pina et al., 2011) and subject to predation by zooplankton and zoobenthos. To date, neither predatory nor
pathogenic Archaea are known.
Current knowledge on Archaea in moderate marine,
estuarine, and freshwater environments is largely confined
to methanogenic Euryarchaeota and ammonia-oxidizing
Thaumarchaeota. Methanogens grow in the strict absence
of O 2 and rely on H 2 or acetate produced by fermenting
organisms. Their effective competition for these substrates
decreases with increasing availability of electron acceptors other than CO 2 . Between the three metabolic types
of methanogenic archaea, relative abundance and activity
appear to depend on redox potential, pH, temperature,
salinity, and the concentrations of phosphate, sulfate, and
organic C compounds (Liu and Whitman, 2008; TorresAlvarado et al., 2013).
The ubiquity, abundance, and diversity of ammoniaoxidizing archaea in aquatic environments have largely
been inferred from abundance and diversity of archaeal
amoA, a gene encoding the key enzyme of aerobic ammonia oxidation. Although the postulated activity was
confirmed in all four cultured species, the biochemistry
of this enzyme allows for the turnover of several other
substrates, including methane. The archaeal enzyme
shows much higher substrate affinity than its bacterial
counterpart, making archaea strong competitors at low
concentrations of ammonium or O 2 . Distribution patterns
of archaeal and bacterial amoA suggest greater tolerance
to sulfide, acidity, and high temperatures in archaeal compared to bacterial ammonia oxidizers (Francis et al., 2005;
Erguder et al., 2009; Martens-Habbena et al., 2009;
Pester et al., 2011; Hatzenpichler, 2012; Stahl and de la
Torre, 2012). In estuaries, steep gradients of multiple
environmental factors coincide to confound evidence for
possible effects of salt or sulfide (Bernhard and
Bollmann, 2010).
Summary
Archaea constitute one of the three domains of life, as
distinct from the domains Bacteria and Eukarya both
phylogenetically and by cell structure. Still limited
sequence information suggests six phyla within the
archaeal domain.
Archaea show diverse forms of chemotrophic metabolism, including both the formation and the anaerobic
oxidation of methane, oxidation and reduction of CO, aerobic oxidation of H 2 , many oxidative and reductive
processes in the N and S cycle, and redox reactions of various metals and metalloids. Bacteriorhodopsin facilitates
a simple mechanism of phototrophic energy conversion
without assimilation of CO 2 .
While Archaea are most famous for enduring extreme
temperature, salinity, pH, or pressure, they are also
widespread in a broad range of moderate habitats. Their
metabolism makes a relevant contribution to global biogeochemical cycles. Archaea interact with members of
all domains in mutualistic or parasitic symbioses, host
viruses, and fall prey to bacterivores, but are not known
in the roles of predator or pathogen.
36
ARCHAEA
Oxidation and reduction of S compounds are widely used
energy sources for archaea in hydrothermal and marine
ecosystems.
Several processes of nitrogen-based energy metabolism
are known in archaea inhabiting extreme and moderate
environments, including aerobic ammonia oxidation,
dissimilatory reduction of nitrate to nitrite and of nitrite
to ammonium, and all steps of denitrification. Archaea
may also use nitrate assimilation or N 2 fixation to meet
their cellular N demand (Zumft, 1997; Amend and Shock,
2001; Philippot, 2002; Cabello et al., 2004; Francis et al.,
2005). One handful of cultured and numerous uncultured
members of Thaumarchaeota share the metabolic capacity
of aerobic ammonia oxidation. Given their ubiquity
and abundance in diverse habitats, archaeal ammonia
oxidizers may play a major role in the global N cycle
(Francis et al., 2005; Prosser and Nicol, 2008; Stahl and
de la Torre, 2012).
Methanogenesis is catalyzed exclusively by Archaea and
may proceed via three different pathways: reduction of CO
or CO 2 , reduction of methyl groups in small organic compounds, or cleavage of acetate. The strictly anaerobic
methanogenic archaea occur abundantly in natural and agricultural wetlands, hydrothermal environments, and the
digestive tracts of ruminants and termites (Liu and Whitman, 2008; Conrad, 2009). The oxidation of methane with
O 2 is known only in Bacteria, whereas its anaerobic oxidation with sulfate, iron, or manganese is catalyzed by diverse
and mostly uncultured Archaea, with or without the help of
bacterial symbionts (Beal et al., 2009; Knittel and Boetius,
2009; Milucka et al., 2012).
Ecology
Archaea occur in virtually any habitat that supports life.
They are adapted to salt concentrations of up to 5.2 M,
to temperatures above 120
C, and to life in permafrost
environments. Archaeal species inhabit mine drainage of
pH <0 and soda lakes of pH >11 and thrive at hydrostatic
pressures of up to 120 MPa in the deep sea and below
the sea floor (Valentine, 2007; Lipp et al., 2008; Bowers
and Wiegel, 2011; Takai and Nakamura, 2011). Although
best known for their endurance of one or more extreme
conditions, Archaea are also ubiquitous and vital parts of
communities in moderate environments. Their metabolic
activities contribute to the major element (C, N, S, Fe)
cycles on local to global scales.
Representatives of Cren-, Eury-, Nano-, and
Thaumarchaeota engage in mutualistic and parasitic symbioses with ruminants, insects, corals, sponges, molluscs,
ciliates, sulfate-reducing and sulfide-oxidizing bacteria,
and among archaea (Moissl-Eichinger and Huber, 2011;
Wrede et al., 2012). Archaea are also hosts of diverse
viruses (Pina et al., 2011) and subject to predation by zooplankton and zoobenthos. To date, neither predatory nor
pathogenic Archaea are known.
Current knowledge on Archaea in moderate marine,
estuarine, and freshwater environments is largely confined
to methanogenic Euryarchaeota and ammonia-oxidizing
Thaumarchaeota. Methanogens grow in the strict absence
of O 2 and rely on H 2 or acetate produced by fermenting
organisms. Their effective competition for these substrates
decreases with increasing availability of electron acceptors other than CO 2 . Between the three metabolic types
of methanogenic archaea, relative abundance and activity
appear to depend on redox potential, pH, temperature,
salinity, and the concentrations of phosphate, sulfate, and
organic C compounds (Liu and Whitman, 2008; TorresAlvarado et al., 2013).
The ubiquity, abundance, and diversity of ammoniaoxidizing archaea in aquatic environments have largely
been inferred from abundance and diversity of archaeal
amoA, a gene encoding the key enzyme of aerobic ammonia oxidation. Although the postulated activity was
confirmed in all four cultured species, the biochemistry
of this enzyme allows for the turnover of several other
substrates, including methane. The archaeal enzyme
shows much higher substrate affinity than its bacterial
counterpart, making archaea strong competitors at low
concentrations of ammonium or O 2 . Distribution patterns
of archaeal and bacterial amoA suggest greater tolerance
to sulfide, acidity, and high temperatures in archaeal compared to bacterial ammonia oxidizers (Francis et al., 2005;
Erguder et al., 2009; Martens-Habbena et al., 2009;
Pester et al., 2011; Hatzenpichler, 2012; Stahl and de la
Torre, 2012). In estuaries, steep gradients of multiple
environmental factors coincide to confound evidence for
possible effects of salt or sulfide (Bernhard and
Bollmann, 2010).
Summary
Archaea constitute one of the three domains of life, as
distinct from the domains Bacteria and Eukarya both
phylogenetically and by cell structure. Still limited
sequence information suggests six phyla within the
archaeal domain.
Archaea show diverse forms of chemotrophic metabolism, including both the formation and the anaerobic
oxidation of methane, oxidation and reduction of CO, aerobic oxidation of H 2 , many oxidative and reductive
processes in the N and S cycle, and redox reactions of various metals and metalloids. Bacteriorhodopsin facilitates
a simple mechanism of phototrophic energy conversion
without assimilation of CO 2 .
While Archaea are most famous for enduring extreme
temperature, salinity, pH, or pressure, they are also
widespread in a broad range of moderate habitats. Their
metabolism makes a relevant contribution to global biogeochemical cycles. Archaea interact with members of
all domains in mutualistic or parasitic symbioses, host
viruses, and fall prey to bacterivores, but are not known
in the roles of predator or pathogen.
36
ARCHAEA