of 2
Draft Genome Sequence of
Hydrogenibacillus schlegelii
MA48, a
Deep-Branching Member of the
Bacilli
Class of
Firmicutes
Allison Maker,
a
James Hemp,
a
Laura A. Pace,
b
Lewis M. Ward,
a
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
ABSTRACT
We report here the draft genome sequence of
Hydrogenibacillus schlegelii
MA48, a thermophilic facultative anaerobe that can oxidize hydrogen aerobically.
H. schlegelii
MA48 belongs to a deep-branching clade of the
Bacilli
class and provides
important insight
into the acquisition of aerobic respiration within the
Firmicutes
phylum.
H
ydrogenibacillus schlegelii
MA48 was isolated from a eutrophic lake in Neufchatel,
Switzerland (
1
). Closely related strains have also been found in volcanic soils in
Antarctica
(
2
) and various small pools and volcanic ash in Switzerland (
3
).
H.
schlegelii
-
related spores are widely distributed in cold environments; however, they appear to
grow only in hot geothermal regions (
3
).
H.
schlegelii
MA48 is thermophile (70°C [
1
,
2
])
that
grows under mildly acidic conditions (4.2 to 7.5 pH [
4
]). It is a facultative chemo-
lithoautotroph
that can couple hydrogen oxidation to aerobic respiration (
5
). It can also
grow
chemoorganoheterotrophically on numerous amino and organic acids. One study
found
H. schlegelii
MA48 to be Gram positive (
2
), but others found it to be Gram variable
(
1
,
4
).
The
genome of
Hydrogenibacillus schlegelii
MA48 (DSM 2000) was sequenced as part
of a project to elucidate the evolutionary history of aerobic respiration within the
Firmicutes
phylum. Genome sequencing was performed at SeqMatic 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 composi-
tion, and BLAST hits of conserved single-copy genes. Genome annotation was per-
formed using the NCBI Prokaryotic Genome Annotation Pipeline. The draft genome is
2.61 Mb in size, assembled into 67 contigs. It contains 3,846 genes, 3,347 coding
sequences (CDSs), two 16 small RNAs (sRNAs), 50 tRNAs, and three clustered regularly
interspaced short palindromic repeat (CRISPR) arrays. It is estimated to be ~97%
complete based on conserved single-copy genes (108/111).
Analysis of the genome identified numerous genes for aerobic respiration: complex
I (NADH dehydrogenase), complex II (succinate dehydrogenase), complex III (cyto-
chrome
bc
complex), an A-family heme-copper oxygen reductase, two B-family heme-
copper oxygen reductases (
7
), a quinol
bd
oxidase,
and a novel
bd
oxidase-related
protein that receives electrons from cytochrome
c
instead of quinol (
8
,
9
). Since
H.
schlegelii
MA48 has a basal phylogenetic position within the
Bacilli
(
4
), these data
help
to constrain the relative timing of the acquisition of aerobic respiration within the
Firmicutes
. Genes for a Gram-positive type flagellum were also observed, suggesting the
presence of only one membrane under certain physiological conditions.
Accession number(s).
This whole-genome shotgun project has been deposited in
DDBJ/EMBL/GenBank under the accession number
JXBB00000000
.
Received
23 March 2016
Accepted
22
November 2016
Published
19 January 2017
Citation
Maker A, Hemp J, Pace LA, Ward LM,
Fischer WW. 2017. Draft genome sequence of
Hydrogenibacillus schlegelii
MA48, a deep-
branching member of the
Bacilli
class of
Firmicutes
. Genome Announc 5:e00380-16.
https://doi.org/10.1128/genomeA.00380-16
.
Copyright
©
2017 Maker et al. This is an open-
access article distributed under the terms of
the
Creative Commons Attribution 4.0
International
license
.
Address
correspondence to James Hemp,
jimhemp@caltech.edu.
PROKARYOTES
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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 Microbial Interactions
(CEMI) at Caltech, the Packard Foundation (to W.W.F.), and the Agouron Institute (to J.H.
and W.W.F.), and NSF GRFP (to L.M.W.).
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