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In-Depth Information
the coral holobiont (coral plus microorganisms) that
is best suited to the prevailing environmental con-
ditions. A generalization of the coral probiotic
hypothesis has led to the proposition of the holog-
enome theory of evolution (Rosenberg
et al.
2007 ).
Much of this theory applies to sponges. Despite this
progress, little is known about the interactions
between microorganisms, i.e. on the microbial food
web within invertebrates.
Heterotrophic microorganisms are among the
main drivers of the carbon and nutrient cycles in
the ocean (Azam and Malfatti 2007). For example,
some metabolic pathways, such as ammonium oxi-
dation or denitrii cation, are only performed by
heterotrophic organisms. Most of the organic car-
bon generated by primary production in the upper
ocean is remineralized to CO
2
which accumulates in
deep waters until it is eventually ventilated again at
the sea surface. However, a small fraction of the
i xed carbon is not mineralized but stored for mil-
lennia as recalcitrant DOM. The processes and
mechanisms involved in the generation of this large
carbon reservoir are poorly understood. Recently,
the microbial carbon pump has been proposed as a
conceptual framework to address this important,
multifaceted biogeochemical problem ( Jiao
et al.
2010 ).
Prokaryotes are major remineralizers of nutrients
such as nitrogen, phosphorus, iron, and sulphur in
the water column and sediments by degrading
organic matter. However, they also use nutrients
and compete with phytoplankton for nutrients such
as nitrate or phosphate. Another important group
of remineralizers are the protists, which egest
organic matter as well as inorganic nutrients. Viral
lysis is also considered as a catalyst of nutrient
regeneration (see above and Fig. 5.1). The link
between microbial food webs and microbe-medi-
ated ecosystem functions and biogeochemical cycles
(and the potential consequences of ocean acidii ca-
tion) in the pelagic realm is shown in Figure 5.2.
Tropical coral reefs exhibit important ecological
and biogeochemical functions (Gattuso
et al.
1998 ).
Corals and coralline algae are ecosystem engineers
which provide the physical structure of coral reefs
and thus provide a plethora of ecological niches
explaining the high biodiversity found in reefs. The
build-up of coral skeletons is possible due to sym-
biosis between the animal and symbiotic dinol ag-
ellates. The loss of the symbionts ('bleaching') can
jeopardize the ecosystem function of reef corals.
Bleaching can be caused by bacteria such as
Vibrio
coralliilyticus
which can become pathogenic at ele-
vated temperatures (Rosenberg
et al.
2007 ). It has
been argued that changes in the microbial commu-
nity associated with corals can prevent new
Vibrio
infections (Ainsworth
et al.
2009 ), thus sustaining
5.2.3 Microbe-mediated ecosystem functions
and biogeochemical cycles
The carbon pool in DOM is approximately as large
as the carbon pool in atmospheric CO
2
( Hedges
2002). Thus, the fate of dissolved organic carbon
(DOC) and particulate organic carbon (POC),
which is strongly mediated by microorganisms, is
an important factor inl uencing climate. Organic
matter in pelagic systems is separated operation-
ally into DOM and particulate organic matter
(POM). Non-living organic matter occurs in a size
continuum from dissolved molecules to marine
snow (Nagata and Kirchman 1997) and several
types of non-living organic particles have been
described in marine environments (Nagata 2008).
Seawater is considered as a diluted medium with
gels or gel-like structures of different size, that can
be formed in minutes to hours from DOM or poly-
mer chains released by phyto- or bacterioplankton,
hence bridging the DOM-POM continuum
(Verdugo
et al.
2004 ).
At the microscale level, the microbial community
is operationally structured into free and particle-
attached microorganisms. Attached microorgan-
isms are embedded in a nutrient-rich organic matrix,
thus particles can be considered as a physical refuge
for microorganisms (Alldredge and Cohen 1987).
Particles can be characterized by strong chemical
microgradients. This patchiness of chemical proper-
ties within the particles at the microscale level can
modify the processes which rely upon the concen-
tration of organic carbon and nutrients, such as
bacterial activity (Simon
et al.
2002 ). Marine snow
and the plume of sinking (or rising) particles are
considered to be hot spots of biogeochemical trans-
formations mediated by microorganisms (Azam
and Long 2001 ; Kiørboe and Jackson 2001 ).
