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diversity of the microbial food web. Rapid i nger-
printing methods such as denaturing gradient gel
electrophoresis (DGGE; Muyzer
et al.
1993 ), termi-
nal fragment length polymorphism (TRFLP; Moyer
et al.
1994), and automated ribosomal intergenic
spacer analysis (ARISA; Fisher and Triplett 1999), as
well as single-cell techniques such as l uorescence
in situ
hybridization (FISH; Amann
et al.
1990 ) are
available to assess the community structure of
Bacteria, Archaea, and Eukarya. Large-scale
sequencing techniques, such as pyrosequencing
based on 16S rRNA genes, now enable the study of
'true' species diversity. It is noteworthy that these
techniques do not allow for a full species identii ca-
tion, for which an isolation is obligatory. However,
they allow for the distinction of phylogenetic types
(phylotypes), which are sometimes also called
operational taxonomic units (OTUs). For example, a
large number of highly diverse, low-abundance
OTUs was found in bacterioplankton using large-
scale sequencing. This constitutes a 'rare biosphere'
that is largely unexplored (Sogin
et al.
2006 ). Some
of its members might serve as keystone species
within complex consortia; others might simply be
the products of historical ecological change with the
potential to become dominant in response to shifts
in environmental conditions (e.g. when local or glo-
bal change favours their growth). The use of such
techniques has provided new answers for old ques-
tions (what is the diversity of microorganisms in a
system?) and provoked new questions (what is the
role of a rare biosphere?).
Large-scale sequencing techniques and progress
in bioinformatics now allow us to study the genomics
(organization of genes), transcriptomics (set of all
RNA molecules, i.e. expressed genes), and proteom-
ics (structure and function of proteins) of microbial
communities. Such metagenomics and metatran-
scriptomics approaches have been successfully used
to detect new metabolic pathways and assess envi-
ronment-specii c activities of microorganisms (Shi
et al.
2009). New pathways have been found such as
aerobic anoxygenic phototrophs (AAnP) mediated
by bacteriorhodopsin (Béjà
et al.
2000 ). Such studies
now allow for assessing the functional diversity of
microorganisms. Characterization of the metapro-
teome is expected to provide a link to genetic and
functional diversity of microbial communities.
Studies on the metaproteome together with those on
the metagenome and the metatranscriptome will
contribute to progress in our knowledge of micro-
bial communities and their role in ecosystem func-
tioning. More specii cally, the analysis of the
metaproteome in contrasting environmental situa-
tions should allow tracking new functional genes
and metabolic pathways (Maron
et al.
2007 )
.
These
advancements have started to revolutionize our
understanding of the role of microbes in the ocean
and their response to environmental change.
5.2.2
Microbial food webs
In the late 1970s and early 1980s, it became obvious
that microorganisms play a crucial role in microbial
food webs and biogeochemical cycles (Pomeroy
1974 ; Azam
et al.
1983). The classical grazing food
chain composed of phytoplankton and herbivorous
and carnivorous zooplankton (see Fig. 5.1) was
extended by several concepts on microorganisms.
Phytoplankton, even when healthy, release or
'exude' dissolved organic matter (DOM). Another
form of release of DOM is the sloppy feeding of
zooplankton. Prokaryotes are the main users of this
DOM, and are themselves grazed upon by l agellates
and ciliates, which are eaten in turn by meso- and
macrozooplankton. Thus, prokaryotic assimilation
and subsequent grazing on prokaryotes return car-
bon that would otherwise be lost, back to the food
web. These pathways are collectively referred to as
the microbial loop (see Fig. 5.1). Related to this con-
cept is the i nding that the grazing activity is an
important factor for the remineralization of nutri-
ents and that prokaryotes are competing with phy-
toplankton for nutrients. It was subsequently shown
that viral lysis is another important cause of
prokaryotic (and phytoplankton) mortality (Proctor
and Fuhrman 1990). Viral lysis not only kills cells
and releases new viral particles, but it also sets free
the cell content and converts cell walls into small
debris. This material is taken up by prokaryotes
generating a viral loop or viral shunt (Wilhelm and
Suttle 1999 ; Fig. 5.1 ), which stimulates bacterial pro-
duction and respiration (Fuhrman 1999). Thus, viral
lysis catalyses nutrient generation and lubricates
the microbial food web (Suttle 2007). Coagulation of
DOM can result in the formation of transparent
