Distribution and Molecular Systematics of
Planktonic Archaea
(^) In addition to planktonic bacteria, there are planktonic archaea, and archaeal SSU
rRNA clones appear in shotgun DNA libraries derived from prokaryotic plankton.
However, better quantitative evaluation of their relative importance has come from
studies (e.g. DeLong et al. 1999) with molecular probes specific to archaea. Water
samples are suitably preserved, and fluorescent polyribonucleotide probes are added
that leach through prokaryote cell walls. Cells filtered on to black backgrounds only
appear in epifluorescence microscopy when the probe binds to the highly specific
target RNA sequence, a technique called fluorescent in situ hybridization (FISH, of
course). See Plate 5.1. Karner et al. (2001) found that archaea are only a few percent
of prokaryotes above 100 m depth, but they increase below that to maximal densities
of ∼ 105 ml−1 and ∼20% of prokaryotes below the euphotic zone.
(^) Knowledge of the distributions and activity of archaea in coastal and open oceans
has advanced rapidly. The use of probes and biomarkers has now documented the
distributions of archaea in all of the oceans and peripheral seas. The main findings of
these studies are that: (i) some of the microbes previously counted as bacteria were
actually archaea; (ii) crenarchaea are generally 10–20% of prokaryotic biomass in the
water column and are much more abundant than euryarchaea; and (iii) relative
contributions to prokaryotic biomass of crenarchaea increase with depth. Euryarchaea
include many methanogenic forms, and they appear to be more abundant in sediments
than in the pelagial.
(^) Clearly archaea are widely distributed in the ocean. What are their metabolic
capabilities, and how do those compare with bacterial metabolism? Ouverney &
Fuhrman (1999) showed that, like some bacteria, crenarchaea can assimilate free
amino acids, suggesting a heterotrophic role. Evidence for a quite different role has
been found by geochemists. Pearson et al. (2001) looked at the compound-specific
distributions of stable isotopes and bomb ^14 C from nuclear tests during the fall of
1961 and 1962 to distinguish the sources of carbon to the sediments. Different lipid
biomarkers allowed identification of the relative contributions of phytoplanktonic,
zooplanktonic, bacterial, archaeal, and terrestrial sources of carbon reaching the
sediments in the Santa Barbara and Santa Monica Basins. Most of the lipid
biomarkers were derived from marine euphotic zone primary production or
heterotrophic consumption of that biomass. In contrast, the abundance of ^14 C in
isoprenoids (ether-linked lipids found only in archaea) showed no change over time
(i.e. between pre- and post-bomb levels) indicating that the carbon source for these
organisms remained isolated from the atmosphere. This finding suggests that archaea
are acting as chemoautotrophs in the dark waters below the euphotic zone. Venter et