al. (2004) first detected archaeal ammonium oxidizing genes in the Sargasso Sea, and
Francis et al. (2005) used PCR techniques to demonstrate the widespread presence of
these archaeal genes in the water column and sediments of the ocean.
(^) Wuchter et al. (2003) confirmed that crenarchaea are autotrophic organisms capable
of light-independent bicarbonate uptake by measuring ^13 C incorporation into the
unique ether-bonded membrane lipids of natural populations in the North Sea. A
cultured species of crenarchaea was found to be autotrophic and could also oxidize
ammonium to nitrite. Positive correlations of the abundance of crenarchaea with
nitrite and the detection of putative archaeal genes for an enzyme required for
ammonia oxidation in seawater hint that crenarchaea may also play a role in the
marine nitrogen cycle as nitrifiers. Until this study by Wuchter et al., marine
nitrification had been attributed to two groups of bacteria belonging to the beta- and
gamma-proteobacteria. Wuchter et al. (2006) conducted a time-series experiment in
the North Sea and showed that the abundance of archaeal genes for ammonium
oxidation is correlated with a decline in ammonium and an increase in the abundance
of crenarchaea. Bacterial genes for ammonium oxidation were one to three orders of
magnitude less abundant than the archaeal gene. Their results and genomic studies
(Walker et al. 2010) suggest a major role for archaea in oceanic nitrification.
(^) Ingalls et al. (2006) compared the natural radiocarbon levels in DIC and in
crenarchaeal ether-bonded membrane lipids in surface and mesopelagic waters to
identify the source of carbon used in each part of the water column. Values of Δ^14 C in
DIC (+71‰, relative to an oxalic acid standard, see Box 9.1) and archaeal lipids
(+82‰) in surface water were close, indicating that archaeal lipids were produced
from DIC or freshly produced DOC. Values of Δ^14 C in DIC and archaeal lipids in
mesopelagic waters were (−151‰ and −77‰, respectively) indicating a much older
(deeper) source of DIC for the mesopelagic archaea. Ingalls et al. (2006) calculated
that 83% of archaeal metabolism is autotrophic rather than heterotrophic. This
suggests that the archaeal community either includes heterotrophs and autotrophs or is
a single population of mixotrophs. The abundances of archaeal genes for the enzyme
required for ammonia oxidation and for the dark fixation of carbon decrease
dramatically with depth below the mesopelagic zone (Agogue et al. 2008). Although
archaea are present in both zones, they appear to play different metabolic and
ecological roles. In the mesopelagic zone, archaea are predominantly autotrophic,
with bicarbonate as the carbon source and ammonia as the energy source. This
chemoautotrophic fixation of carbon in the mesopelagic zone is about 1% of annual
primary production in the euphotic zone (Ingalls et al. 2006), and it makes a
significant contribution to the carbon budget of deeper waters. Moreover, if archaeal
autotrophy is fueled by the oxidation of ammonia, these organisms generate >1.2 Gt
yr−1 of N as NO 2 −. This estimate is enough to account for all of the first step of
nitrification below the photic zone.