Chapter 5
A sea of microbes: archaea, bacteria, protists, and
viruses in the marine pelagial
New organic matter generated by phytoplankton in the sea is partly added to the
structural and storage components of the producing cells, but a substantial fraction is
released directly into the adjacent water. Some of this secretion, particularly that of
diatoms, is transparent exopolymer (TEP), which exists as amorphous flakes and
strings among the phytoplankton cells. Some is small organic molecules. In addition,
both protist and mesozooplankton grazers release organic matter when undigested
remains are emptied from food vacuoles, when spine- or tooth-punctured food is
squeezed into throats, and when fecal pellets leach soluble matter. The portion of this
material that passes through a filter is termed “dissolved organic matter”, and the
acronym “DOM” is standard terminology (as are “DOC” and “DON” for the carbon
and nitrogen contents of the dissolved organic matter, respectively).
(^) DOM is a resource for heterotrophic, pelagic bacteria. Bacteria are fed upon by
protists, mostly nanoflagellates, and infected by viruses. Nanoflagellates are preyed
upon by larger protozoans (heterotrophic protists) and to some extent by either young
mesozooplankton (e.g. crustacean nauplii) or mucoid filter-feeders (e.g.
appendicularians). Herbivorous protists feed upon phytoplankton, release some DOM
in the process, and serve as a food source for mesozooplankton. These food-chain
links “return” the DOM to the progression from unicells toward whales, fish, and
fishermen. Thus, the sequence from DOM to bacteria to protists to mesozooplankton
is another pathway in the marine food web parallel to the direct consumption of
phytoplankton by mesozooplankton. The microbial loop (Azam et al. 1983) refers
specifically to the loss of DOC from all organisms and its recovery in the food web by
heterotrophic bacteria (Fig. 5.1). Viral infection causes bacterial lysis, which releases
cell contents back into the DOM pool, in a process termed the “viral shunt”, which
lowers the overall efficiency of the microbial food web. Viral infection of
phytoplankton also releases organic material to the DOM pool.
Fig. 5.1 All components of the microbial loop are shown in gray. “Phytoplankton”
includes cyanobacteria, which are major components of the phytoplankton community
in most ocean regions. Protists are single-celled eukaryotes. The “loop” refers to
losses of dissolved organic carbon (DOC) from all organisms, and its recovery into