Draft Genome Sequence of
Levilinea saccharolytica
KIBI-1, a Member
of the
Chloroflexi
Class
Anaerolineae
James Hemp,
a
Lewis M. Ward,
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 the draft genome sequence of
Levilinea saccharolytica
KIBI-1
,
a facultative anaerobic member of the
Chloroflexi
class
Anaerolineae
. While
L. saccharolytica
was characterized as an obligate anaerobe, genome analysis provides evidence for the pres-
ence of both aerobic respiration and partial denitrification pathways.
Received
29 September 2015
Accepted
5 October 2015
Published
19 November 2015
Citation
Hemp J, Ward LM, Pace LA, Fischer WW. 2015. Draft genome sequence of
Levilinea saccharolytica
KIBI-1, a member of the
Chloroflexi
class
Anaerolineae
. Genome
Announc 3(6):e01357-15. doi:10.1128/genomeA.01357-15.
Copyright
© 2015 Hemp 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.
L
evilinea saccharolytica
KIBI-1 was isolated from sludge gran-
ules of a mesophilic wastewater reactor (
1
). A closely related
strain was detected in a trichlorobenzene-transforming micro-
bial consortium (
2
).
L. saccharolytica
was characterized as an
obligately anaerobic, nonmotile, filamentous microbe capable
of growth on a range of carbohydrates when supplemented with
yeast extract (
1
). It grows optimally at 37°C and pH 7.0.
The genome of
Levilinea saccharolytica
KIBI-1 (DSM 16555)
was sequenced as part of a project to expand the phylogenetic
breadth of
Chloroflexi
genomes. Genome sequencing was per-
formed at Seqmatic using the Illumina MiSeq sequencing plat-
form. SPAdes version 3.1.1 (
3
) was used to assemble the genome.
The genome was screened for contaminants based on sequence
coverage, GC composition, and BLAST hits of conserved single-
copy genes. Genome annotation was performed using the NCBI
Prokaryotic Genome Annotation Pipeline. The draft genome is
4.30 Mb in size, assembled into 65 contigs. It encodes 3,672 genes,
3,173 coding sequences, 1 16S RNA, and 46 tRNAs. It is estimated
to be ~99% complete based on conserved single-copy genes (110/
111).
The
Anaerolineae
described to date have all been classified as
strict anaerobes; however,
L. saccharolytica
encodes for a branched
aerobic respiration pathway. It has a Complex I (NADH dehydro-
genase), Complex II (succinate dehydrogenase), an Alternative
Complex III (ACIII) (
4
), and both an A-family heme-copper ox-
ygen reductase and a
bd
oxidase. It also encodes for two nitrite
reduction pathways: a NirS nitrite reductase that reduces nitrite
into nitric oxide, and an NrfA protein that reduces it into ammo-
nia. The presence of aerobic respiration genes in
L. saccharolytica
and other recently sequenced
Anaerolineae
suggests that this
Chlo-
roflexi
class is substantially more physiologically diverse than pre-
viously recognized (
5
).
Nucleotide sequence accession number.
This whole-genome
shotgun project has been deposited in DDBJ/EMBL/GenBank un-
der the accession number
LGCM00000000
.
ACKNOWLEDGMENTS
Genomic DNA was obtained from the Leibniz-Institut DSMZ-Deutsche
Sammlung von Mikroorganismen und Zellkulturen GmbH. Sequencing
was performed at Seqmatic, Fremont, CA, USA.
This work was funded in part by the Center for Environmental Micro-
bial Interactions (CEMI) at Caltech, the Packard Foundation (W.W.F.),
the Agouron Institute (J.H. and W.W.F.), and NSF GRFP (L.M.W.).
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