Draft Genome Sequence of
Herpetosiphon geysericola
GC-42
,
a
Nonphototrophic Member of the
Chloroflexi
Class
Chloroflexia
Lewis M. Ward,
a
James Hemp,
a
Laura A. Pace,
b
Woodward W. Fischer
a
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
a
; Department of Medicine, University of California San Diego,
La Jolla, California, USA
b
We report here the draft genome sequence of
Herpetosiphon geysericola
GC-42
,
a predatory nonphototrophic member of the
class
Chloroflexia
in the phylum
Chloroflexi
. This genome provides insight into the evolution of phototrophy and aerobic respi-
ration within the
Chloroflexi
.
Received
29 September 2015
Accepted
5 October 2015
Published
19 November 2015
Citation
Ward LM, Hemp J, Pace LA, Fischer WW. 2015. Draft genome sequence of
Herpetosiphon geysericola
GC-42
,
a nonphototrophic member of the
Chloroflexi
class
Chloroflexia
. Genome Announc 3(6):e01352-15 doi:10.1128/genomeA.01352-15.
Copyright
© 2015 Ward et al. This is an open-access article distributed under the terms of the
Creative Commons Attribution 3.0 Unported license
.
Address correspondence to James Hemp, jimhemp@caltech.edu.
T
he majority of cultured members of the bacterial phylum
Chloroflexi
belong to the class
Chloroflexia
, which are promi-
nently anoxygenic phototrophs (
1
). However, the most basal
Chloroflexia
, members of the orders
Herpetosiphonales
and
Kallot-
enuales
, are nonphototrophic (
2
). This makes these clades of cen-
tral importance to understanding the evolution of phototrophy
within the
Chloroflexi
. The
Herpetosiphonales
order currently
contains only two species,
Herpetosiphon geysericola
and
Herpeto-
siphon aurantiacus
, which are pigmented filamentous organohet-
erotrophs that exhibit gliding motility (
3
). In culture,
Herpetosi-
phon
strains are obligate aerobes that prefer microaerobic
conditions (
3
). The physiology and ecology of these organisms are
not well understood, but it has been suggested that members of the
Herpetosiphon
genus might be capable of predation via a “wolf
pack” strategy (
4
).
H. geysericola
was isolated from a biofilm at a
hot spring in Baja California, Mexico (
5
).
The genome of
H. geysericola
GC-42 (DSM 7119) was se-
quenced as part of a project to expand the phylogenetic breadth of
Chloroflexi
genomes. Genome sequencing was performed at Seq-
Matic using the Illumina MiSeq sequencing platform. SPAdes
3.1.1 (
6
) was used to assemble the genome. The genome was
screened for contaminants based on sequence coverage, G
C
composition, and BLAST hits of conserved single-copy genes. Ge-
nome annotation was performed using the NCBI Prokaryotic Ge-
nome Annotation Pipeline. The draft genome is 6.24 Mb in size,
assembled into 46 contigs. It contains 5,335 genes, 4,688 coding
sequences (CDSs), 2 16S RNAs, 47 tRNAs, and 6 clustered regu-
larly interspaced short palindromic repeat (CRISPR) arrays. It is
estimated to be ~99% (111/111) complete based on conserved
single-copy genes.
Analysis of the
H. geysericola
genome revealed genes for a
branched aerobic respiratory chain, including two different com-
plex Is (NADH dehydrogenase), complex II (succinate dehydro-
genase), complex III (cytochrome
bc
complex), an A-family
heme-copper oxygen reductase, and a quinol
bd
oxidase. No genes
for phototrophy were found. In addition, no genes associated with
the 3-hydroxypropionate cycle, a CO
2
fixation pathway present in
photosynthetic members of
Chloroflexi
(
7
), were found in
H. gey-
sericola
; this is consistent with its predicted heterotrophic physi-
ology.
The sequencing of
H. geysericola
, along with
Herpetosiphon au-
rantiacus
(
4
), completes the genomic knowledge of the cultured
members of the genus
Herpetosiphon
. These data provide impor-
tant constraints that help ordinate the acquisition of phototrophy,
aerobic respiration, and carbon fixation within the
Chloroflexi
.
Nucleotide sequence accession number.
This whole-genome
shotgun project has been deposited in DDBJ/EMBL/GenBank un-
der the accession no.
LGKP00000000
.
ACKNOWLEDGMENTS
Genomic DNA was obtained from the Leibniz-Institut DSMZ-Deutsche
Sammlung von Mikroorganismen und Zellkulturen GmbH. Sequencing
was performed at SeqMatic, Fremont, CA.
This work was funded in part by the Center for Environmental Micro-
bial Interactions (CEMI) at Caltech, the Packard Foundation (to
W.W.F.), the Agouron Institute (to J.H. and W.W.F.), and NSF GRFP (to
L.M.W.).
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