Fig. 5.4 A more detailed phylogenetic tree, also based on SSU rRNA, for the domains
Archaea and Bacteria, showing only the major marine groups. Groups with a single
asterisk are mostly found in the mesopelagic zone and in polar surface waters during
winter; those with two asterisks live mostly in the euphotic zone; those with a + are
mostly coastal. Others seem ubiquitous in seawater.
(^) (After Giovannoni & Stingl 2005.)
The SSU rRNA classification gives a phylogenetic picture of the prokaryotes (and
every other organism, too). The value for pelagic marine bacteria, which are very
difficult to culture, is to give them identity, to place them in the phylogenetic scheme,
and to examine their metabolic and ecological functions. A cultivation-independent
approach based on earlier work on bacteria from ponds (Olsen et al. 1986) was
adapted to PCR techniques and applied by Giovannoni and coworkers (Britschgi &
Giovannoni 1991; Mullins et al. 1995) to marine bacteria. Rather than grow bacteria
in quantities sufficient for identification, the approach (detailed in Box 2.4) is to
sample the DNA of the entire bacterial assemblage, and then randomly amplify
dozens to thousands of SSU rRNA genes to see where their original owners fit in the
phylogeny, a “shotgun” approach to the collective microbial gene pool in the habitat.
If a few gene types predominate, then those are presumably the most abundant types
in the bacterioplankton.
(^) A gene clone survey of this sort was first done in the Sargasso Sea near Bermuda,
and it has been repeated in all of the world’s oceans. Similar dominant groups are
found in all places. Groups are designated by their initial Sargasso Sea clone numbers,
as for example SAR11 or SAR324. In the upper water column, the dominant group is
alphaproteobacteria (Fig. 5.5). The most abundant of these, SAR11, is about 25% of
pelagic bacteria. For about a decade, the SAR11-clade defied attempts at being
cultured, but this was eventually achieved (Rappé et al. 2002). Seawater samples with