Biological Oceanography

(^) Many culturable pelagic bacteria are gamma-proteobacteria, a group that also
includes E. coli and Vibrio, and with which SAR86 associates in the phylogeny.
However, SAR86 is distinct from the culturable forms in DNA sequence, and it has
not yet been cultured. Its SSU rRNA sequence resembles that of some bacterial
methanotrophs, and there are hints that SAR86 subgroups are related to hydrothermal
vent chemolithotrophs (Giovannoni & Rappé 2000). Some progress is now being
made on identifying aspects of function in near-surface variants of SAR86. Béjà et al.
(2000) sequenced SAR86 DNA contiguous with the SSU rRNA gene and found a
gene similar to those for archaeal rhodopsins, which they called proteorhodopsin.
Rhodopsins are photopigments; in archaea they are membrane-associated parts of a
mechanism generating ATP from the action of sunlight. The cells do not fix CO 2 and
thus are not autotrophic, but the availability of “free” ATP for energetic purposes
supplements their primarily heterotrophic metabolism. They generate NADPH for
other redox-reactions by organic carbon oxidation. Apparently SAR86 has similar
physiology. A study of membrane-bound proteins in open-ocean bacterioplankton
(Morris et al. 2010) indicates association of transporter molecules with rhodopsin
proton pumps. Thus, these photoheterotrophs may use light energy to facilitate
transport of substrates for growth.
(^) Kolber et al. (2000) found evidence of another type of photoheterotroph. They
report that fluorescence responses to strobe flashes resembling those of phototrophic
alpha-proteobacteria (Rhodobacter and Rhodospirillum, examples of “purple
photosynthetic” bacteria, again actually phototrophs, not autotrophs) are a consistent
part of the bacterioplankton in the eastern tropical Pacific. Their fluorescence output
was >5% that of associated phytoplankton in very oligotrophic waters. These bacteria
are now known to be aerobic anoxygenic phototrophic (AAP) bacteria: they require
oxygen (they are aerobic), but they do not evolve oxygen (anoxygenic) by their
simple, one photosystem reaction center. It remains to be seen how important these
two photoheterotrophic bacteria are in the sea. The gene for proteorhodopsin is found
in about half of all bacteria in the ocean, while AAP bacteria typically make up 1–7%
of the bacterial community in oligotrophic areas and up to 30% of total prokaryotes in
more productive environments (Koblizek 2011). So, photoheterotrophic bacteria are
likely to be important in the ocean, but their exact roles remain to be determined.
(^) Not surprisingly, fully photosynthetic cyanobacteria, such as Synechococcus, show
up in the SSU rRNA clone libraries, but they are not as dominant as groups that
remain uncultured. Some gram-positive forms, the marine Actinobacteria, are present
(∼7% of clones). Their relatives in richer environments grow on such a wide variety
of substrates that few clues are provided about their activity in the marine pelagial.
Tracking down the ecological roles of these many uncultured, but abundant, bacteria
remains an active line of research in marine microbiology.