Effects of ocean acidification on the diversity and activity of heterotrophic marine microorganisms - Ocean Acidification - page 85

Phytoplankton Fish

Zooplankton

Nutrients

Protists

DOM Prokaryotes

Virus

TEP

Figure 5.1 Simplii ed scheme of the pelagic food web. Four major conceptual pathways are shown, the classical food chain (green), the microbial loop
(yellow), the viral shunt (red) and the abiotic loop (blue). Nutrient pathways are shown in black. See the main text for details.

exopolymeric particles (TEP) in seawater (Alldredge
et al. 1993), which can be used or ingested by
prokaryotes, protists, and zooplankton; this is
sometimes called the abiotic loop (Fig. 5.1). In the
dark ocean, i.e. below ~200 m, the food web has a
reduced complexity and consists of sinking parti-
cles, prokaryotes, protists, and (in the upper layers)
zooplankton. The dark ocean is the largest habitat
in the biosphere and harbours 75% of the prokaryo-
tic biomass and 50% of the prokaryotic production
of the global ocean (Arístegui et al. 2009).
The concept of the microbial loop has been
developed for planktonic systems; however, a
microbial food web also exists in sediments. The
functioning of sedimentary systems mainly relies
on carbon supplied by particles that sink from the
surface or are transported horizontally, except in
shallow waters where microphytes that include
cyanobacteria and algae provide autochthonous
carbon. Other carbon sources can be locally impor-
tant for sediments (and systems close to sediments)
in the dark ocean. Methane can be used (Boetius et
al. 2000) and chemoautotrophic microorganisms are
the base of the food web in environments such as
hot vents (Nakagawa and Takai 2008). The abundance

of heterotrophic microorganisms is high in marine
sediments; they populate the porewater and are key
components of bioi lms. Meiofauna, such as nema-
todes, are the trophic equivalent to zooplankton in
the sediment. The digging and burrowing activity
of macrofauna such as enteropneusts or crustaceans
can change the strong chemical gradients typically
found in sediments and also inl uence microbial
activity (see Chapter 9 ).
Benthic and pelagic animals can host viral and
microbial pathogens as well as symbionts. They can
also be associated with non-pathogenic and non-
symbiotic microbial communities, for example in
sponges (Taylor et al. 2007 ). Many sponges harbour
a dense and diverse community of Bacteria and
Archaea that are involved in element cycles within
the animals or at their surface, i.e. in their mucus.
Recently, major progress has been made for corals of
tropical or cold-water communities (Ainsworth et al.
2009). It has been suggested that microorganisms
associated with corals function as an equivalent to
an immune system (the coral probiotic hypothesis;
Reshef et al. 2006). The coral probiotic hypothesis
proposes that there is a dynamic relationship
between microorganisms and corals that selects for