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Olson and Kellogg
2010
) with known limitations in adequately describing the
composition of natural microbial communities. This chapter focuses on studies
analyzing the composition of bacterial communities using molecular biology
approaches by sequence information, thereby allowing to identify individual com-
munity members based on phylogenetic and functional traits.
10.2 Microbial Communities Associated with Macroalgae
The past two decades have seen tremendous efforts to unravel the diversity of
microorganisms in the marine environment (Pernthaler and Amann
2005
; Rappe
and Giovannoni
2003
). Among sessile eukaryotes with microbial colonization,
sponges and corals have received the greatest interest, whereas comparatively
few studies have analyzed the microbial diversity associated with the surface of
macroalgae (Egan et al.
2008
), and specifically macroalgae thriving at mesophotic
depths are understudied (Olson and Kellogg
2010
). Apart from microorganisms of
the domain bacteria (see below), protists as well as fungi occur on macroalgae,
including a number of pathogenic fungal species (Armstrong et al.
2000
; Correa
1997
; Raghukumar et al.
1992
), but nothing is known about Archaea (Olson and
Kellogg
2010
).
Traditionally, classification of microorganisms has relied on cultivation, which
requires pure cultures for testing physiological, biochemical, and cell biological
properties, and suitable media for their growth. Only a small fraction of
microorganisms grow on standard media, in some environments this has been
estimated to be as low as 0.001-
1%, e.g., in seawater (Amann et al.
1995
; Eilers
et al.
2000
; Fuhrman and Campbell
1998
); thus, cultivation of microorganisms may
not reflect numerically abundant microbial populations in the habitat they were
retrieved from. Until recently, cultivation-based approaches have nevertheless
contributed most of our knowledge regarding microorganisms associated with the
surface of macroalgae (Goecke et al.
2010
). Microscopy and cultivation-based
techniques have revealed densities of 10
4
-10
7
cells g
1
(wet weight) of algal
biomass for healthy individuals (Largo et al.
1997
; Lewis et al.
1985
; Weinberger
et al.
1994
). Most common isolates retrieved from algal surfaces comprise the
genera
Flavobacterium
,
Bacillus
,
Vibrio
,
Pseudomonas
, and
Moraxella
(Bolinches
et al.
1988
; Chan and Mcmanus
1969
; Egan et al.
2008
; Lewis et al.
1985
). A large
number of novel bacteria have been isolated from diverse macroalgal species over
the last decade and a number of novel genera especially in the family Flavobac-
teriaceae have been described (Goecke et al.
2010
).
Given the inherent limitations of cultivation-based approaches, cultivation-
independent molecular biology approaches are nowadays used to assess the struc-
ture of a microbial community (i.e., its diversity and abundance of microbial
populations) (Liesack et al
.
1997
). Cultivation-independent molecular approaches
for community study rely on the concept to clone and sequence genes (e.g., the 16S
rRNA gene is predominantly used) directly from biomass rather from cultures
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