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Abstract:
Except for environmental 16S rRNA gene sequences,
no information is available for members of the candidate
division OP3. These bacteria appear to thrive in
anoxic environments, such as marine sediments,
hypersaline deep sea, freshwater lakes, aquifers,
flooded paddy soils and methanogenic bioreactors.
The 16S rRNA phylogeny suggests that OP3
belongs to the Planctomycetes/Verrucomicrobia/
Chlamydiae (PVC) superphylum. Metagenomic
fosmid libraries were constructed from flooded paddy
soil and screened for 16S rRNA gene-containing fragments
affiliated with the PVC superphylum. The
screening of 63 000 clones resulted in 23 assaypositive
fosmids, of which three clones were affiliated
with OP3. The 16S rRNA gene sequence divergence
between the fragments OP3/1, OP3/2 and OP3/3
ranges from 18% to 25%, indicating that they belong
to different OP3 subdivisions. The 23S rRNA phylogeny
confirmed the membership of OP3 in the PVC
superphylum. Sequencing the OP3 fragments
resulted in a total of 105 kb of genomic information
and 90 ORFs, of which 47 could be assigned a putative
function and 11 were conserved hypothetical.
Using BLASTP searches, a high proportion of ORFs
had best matches to homologues from Deltaproteobacteria,
rather than to those of members of the PVC superphylum. On the fragment OP3/3, a cluster of
nine ORFs was predicted to encode the bacterial
NADH dehydrogenase I. Given the high proportion of
homologues present in deltaproteobacteria and
anoxic conditions in the natural environment of OP3
bacteria, the detection of NADH dehydrogenase I may
suggest an anaerobic respiration mode. Oligonucleotide
frequencies calculated for OP3/1, OP3/2 and
OP/3 show high intraphylum correlations. This novel
sequence information could therefore be used to
identify OP3-related fragments in large metagenomic
data sets using marker gene-independent procedures
in the future. In addition to the OP3 fragments, a
single metagenomic fragment affiliated with the candidate
division BRC1 was obtained and analysed.
