Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group
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Peer reviewed; Journal articlePeer reviewed
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Date
2012-06-20
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Ammonia-oxidizing archaea (AOA) have recently been recognized as a significant compo-
nent of many microbial communities and represent one of the most abundant prokaryotic
groups in the biosphere. H
owever,
only few AOA have been successfully cultivated so
far and information on the physiology and genomic content remains scarce. We have per-
formed a metagenomic analysis to extend the knowledge of the AOA affiliated with group
I.1b that is widespread in terrestrial habitats and of which no genome sequences has
been described yet. A fosmid library was generated from samples of a radioactive ther-
mal cave (46 ̊C) in the Austrian Central Alps in which AOA had been found as a major
part of the microbial community. Out of 16 fosmids that possessed either an
amo
Aor
16S rRNA gene affiliating with AOA, 5 were fully sequenced, 4 of which grouped with
the soil/I.1b (
Nitrososphaera
-) lineage, and 1 with marine/I.1a (
Nitrosopumilus
-) lineage.
Phylogenetic analyses of
amo
BC and an associated conserved gene were congruent with
earlier analyses based on
amo
A and 16S rRNA genes and supported the separation of
the soil and marine group. Several putative genes that did not have homologs in currently
available marine Thaumarchaeota genomes indicated that AOA of the soil group contain
specific genes that are distinct from their marine relatives. Potential
cis
-regulatory elements
around conserved promoter motifs found upstream of the
amo
genes in sequenced (meta-)
genomes differed in marine and soil group AOA. On one fosmid, a group of genes including
amo
A and
amo
B were flanked by identical transposable insertion sequences, indicating
that
amo
AB could potentially be co-mobilized in the form of a composite transposon. This
might be one of the mechanisms that caused the greater variation in gene order compared
to genomes in the marine counterparts. Our findings highlight the genetic diversity within
the two major and widespread lineages of Thaumarchaeota.
Citation
Frontiers in Microbiology 3:208Publisher
FrontiersCollections
Copyright: 2012 Bartossek, Spang, Weidler, Lanzen and Schleper. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.