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Fig. 10. Tentative affiliation of clone sequences to phyla from the tufa biofilm (BF) and in the 6 layers of the tufa core
(CL1 - CL6). The phylogenetic affiliation of isolates from the biofilm is included for comparison. Rare phyla:
Gemmatimonadetes, Lentisphaerae, Dictyoglomi, Chrysiogenetes, Chlamydiae, Spirochaetes, Thermodesulfobacteria,
Aquificae and Thermomicrobia and Candidate phyla OP10, OD1, WS3, SR1, BRC1, TM7.
1008 isolates were recovered from the tufa core
layers beneath the biofilm and their phylogenetic
affiliation determined (unpublished). Flavobacteria
were present in CL 1 (15%) but rarely in the deeper
core layers. A second most obvious difference is
the presence of Actinobacteria (mainly Arthrobacter
spp.) in all core samples. While members of Alpha-
proteobacteria and Betaproteobacteria are con-
sistently found in small numbers throughout the
core layers, members of Gammaproteobacteria are
mainly present in the biofilm and the following 4
core layers; in the deepest 3 layers they constitute
only a minor part of the population. Members of
Firmicutes dominate all layers, especially the
deepest 3 layers where they constitute more than
75% of the bacterial communities (Table 4).
from the microbial community, subsequent ampli-
fication and cloning of the 16S rRNA genes
provides a significantly broader assessment of
phylotypes, as this approach will also include
those organisms that failed to grow on artificial
growth media provided. A preliminary phylogenetic
analysis revealed membership of clone sequences
to more than 25 phyla and candidate phyla, among
which the most dominant (more than 100 clone
sequences) were members of Cyanobacteria
(mainly biofilm and core layer 1; see above), and
Proteobacteria. Other phyla, like Acidobacteria,
Actinobacteria, Nitrospira, Chloroflexi, and Firmi-
cutes, encompassed between 20 and 100 clones
each. Yet other phyla included less than 20 clones
and were affiliated to candidate phyla, such as
BRC1, TM7, SR1, WS3, OD1 and OP10. About
45 clones from layers 2 through 6 stood isolated
in
Molecular approach. In contrast to the rather
narrow view of diversity obtained by isolating cul-
tures
the tree
and
might
represent
putative novel
on
R2A
medium
the
isolation
of
DNA
candidate phyla.
Table 4. Examples of affiliation of isolates to non-phototrophic prokaryote phyla (in percentage) from rivulet
water, biofilm and different tufa core layers from the Westerh¨ fer Bach lower section (site WB5). One tufa
layer represents one annual laminae couplet
Sample
flavobacteria
alpha-
proteobacteria
beta-
proteobacteria
gamma-
proteobacteria
bacilli
actinobacteria
Rivulet water
56
-
4
40
-
-
Biofilm
22
3
4
17
40
14
Tufa core layer 1
15
6
3
38
24
14
Tufa core layer 2
-
5
1
33
48
13
Tufa core layer 3
1
4
5
38
41
11
Tufa core layer 4
1
13
4
43
25
14
Tufa core layer 5
-
2
-
2
75
21
Tufa core layer 6/7
1
6
2
0
71
20
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