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Fig. 9. (a) Navicula cf. tripunctata in a squash preparation of the biofilm (scale 20 mm). (b) Scanning electron
micrograph of a Nitzschia cf. palea frustule from a culture (scale 4 mm).
WB5 site. One of the WB5 species, Navicula cryp-
totenella Lange-Bertalot (corresponding to 'Navi-
cula sp. 5' of Brinkmann et al. 2007b) was found
at all tufa sampling sites of both karstwater streams.
concentrate exclusively on DNA-based assess-
ments, we attempted to obtain a broader overview
by targeting molecular diversity and the diversity
of aerobic and heterotrophic bacteria along the
rivulet in which the tufa is deposited. Only then it
is possible to meaningfully explain the occurrence
of the same and other types of bacteria in the
biofilm and underlying annual stromatolite lami-
nae couplets, here investigated using a tufa core
sample (Fig. 10). The majority of the 960 rivulet
organisms belong to the genus Flavobacterium
(56%), 40% were affiliated to the Gammaproteo-
bacteria (e.g. pseudomonads, aeromonads) and 4%
to the Betaproteobacteria (Brambilla et al. 2007;
Cousin 2009; Cousin et al. 2008). Several novel
species and genera have been found to thrive
in the river environment (Cousin et al. 2007;
Muurholm et al. 2007; Stackebrandt et al. 2007;
Ali et al. 2009).
Conclusions and perspective. For the cyanobacteria,
the morphological approach may underestimate the
actual diversity of cyanobacteria associated with
tufa. Six cyanobacteria morphotypes detected in
biofilms of both karstwater streams together were
opposed to nine different lineages of the 16S
rDNA phylogeny which were retrieved just from a
single representative site. Interestingly, the cyano-
bacteria exhibited a certain spatial distribution
with several taxa likely to live endo- or chasmo-
lithically in the tufa layers below the biofilm. The
detected diatom diversity is considerable; it is
even higher than that of the cyanobacteria. This
may indicate that diatoms are involved in the calci-
fication processes as well. Molecular signatures
provided through environmental rDNA libraries
allow to unambiguously distinguish and detect
cyanobacteria and diatoms present in rock tufa
biofilms. While 18S rDNA sequence compari-
sons allowed to identify most diatoms even at the
the species level, the majority of cyanobacteria
were left without genus and species names
because the cyanobacterial diversity of tufa bio-
films is still poorly represented by the currently
available 16S rDNA sequences. Cultures of the
tufa cyanobacteria will be required to allocate
species names commonly used for the morphotypes
in the literature to certain lineages in the 16S
rDNA phylogenies.
Cultivation approach. 133 aerobic and hetero-
trophic strains were isolated from the biofilm
located on top of the tufa core sample (Fig. 10).
The difference in composition between water and
biofilm was significant. Of total bacteria isolated
the percentage of flavobacteria in the biofilm
decreased from 56% in the water to only 22%.
Only in a few cases the flavobacteria sequences of
the biofilm matched those of the rivulet waters.
The majority of isolates (40%) belong to the
phylum Firmicutes (mainly Bacillus and Paeniba-
cillus), while the water contained only 1% of these
organisms. The percentage of Proteobacteria
present in the water and in the biofilm was 40%
and 24%, respectively. Actinobacteria, encountered
rarely in water samples, were present at 14%.
Without going into details of the phylogenetic
affiliation of isolates at the level of genera and
species, the taxon distribution demonstrates quali-
tative and quantitative differences between water
and biofilm samples, indicating that certain meta-
bolic types were enriched in the biofilm.
Non-phototrophic prokaryotes
It is well documented (Amann et al. 1995; Pace
1997) that neither cultured organisms nor the mol-
ecular assessment of diversity, either alone or in
combination, is able to describe the full diversity
of a
natural
habitat. While most
studies today
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