Complete Genome Sequence of Sulfurospirillum Strain ACSTCE, a Tetrachloroethene-Respiring Anaerobe Isolated from Contaminated Soil

Abstract

Here, we report the complete genome sequence of the tetrachloroethene-to-trichloroethene dechlorinator Sulfurospirillum sp. strain ACSTCE The genome consists of a 38.05-kb circular plasmid and a 2.69-Mb circular chromosome, which encodes 3 identical reductive dehalogenases with 91.47% amino acid identity to the PceA of Sulfurospirillum multivorans strain DSM 12446.

Full text

Complete Genome Sequence of Sulfurospirillum Strain ACS
TCE
,
a Tetrachloroethene-Respiring Anaerobe Isolated from
Contaminated Soil
Leitao Huo,
a,b
Yi Yang,
a
Yan Lv,
a,b
Xiuying Li,
a
Frank E. Löffler,
c,d,e,f,g,h
Jun Yan
a
a
Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
b
University of Chinese Academy of Sciences, Beijing, China
c
Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
d
Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
e
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
f
Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
g
Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
h
Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
ABSTRACT Here, we report the complete genome sequence of the tetrachloroethene-
to-trichloroethene dechlorinator Sulfurospirillum sp. strain ACS
TCE
. The genome con-
sists of a 38.05-kb circular plasmid and a 2.69-Mb circular chromosome, which en-
codes 3 identical reductive dehalogenases with 91.47% amino acid identity to the
PceA of Sulfurospirillum multivorans strain DSM 12446.
Some members of the genus Sulfurospirillum have versatile energy metabolisms,
including organohalide respiration, a vital process for the turnover of chlorinated
compounds in environmental systems (1–4). Sulfurospirillum sp. strain ACS
TCE
, which
reductively dechlorinates tetrachloroethene (PCE) to trichloroethene, was isolated
from a PCE-dechlorinating consortium derived from contaminated soil collected at
the Axton Cross Superfund site near Holliston, MA (5). Sanger sequencing revealed
that strain ACS
TCE
shares 98.6% 16S rRNA gene sequence identity with the PCE-to-
cis-1,2-dichloroethene dechlorinator Sulfurospirillum multivorans strain DSM 12446
(4, 5).
Strain ACS
TCE
was grown in anoxic, bicarbonate-buffered mineral salt medium under
PCE-dechlorinating conditions (5). Cells were harvested by centrifugation at 21,000 ⫻g
for 30 min, and genomic DNA was extracted using the cetyltrimethylammonium bro-
mide method (6). The genome was sequenced using a dual-platform approach. For
Illumina sequencing, DNA was sonicated to generate ⬍500-bp fragments, followed by
T-A ligation to add adaptors and library preparation using the VAHTS universal DNA
library prep kit (Vazyme Biotech Co., Nanjing, China) following the manufacturer’s
instructions. Paired-end sequencing (2 ⫻150 bp) of the DNA library with an average
insert size of 350 bp was performed on a HiSeq 2000 instrument (Illumina, San Diego,
CA, USA). For PacBio sequencing, DNA was sheared using g-TUBEs (Covaris, Inc.,
Woburn, WA, USA) to generate 10-kb fragments, which were subsequently end repaired
and ligated with universal hairpin adapters using the SMRTbell template prep kit 1.0
(Pacific Biosciences, Menlo Park, CA, USA) following the manufacturer’s instructions. The
library was sequenced in a single single-molecule real-time (SMRT) cell using a PacBio
RS II/Sequel SMRT instrument (7). The PacBio raw read N
50
value is 2,794 bp. The
genome sequence was assembled with 840,203 PacBio raw long reads (coverage,
712⫻) using WGS-Assembler version 8.2 and polished with 12,672,060 Illumina short
reads (coverage, 701⫻) using Pilon version 1.22 (8, 9). Circlator version 1.5.1 was used
Citation Huo L, Yang Y, Lv Y, Li X, Löffler FE,
Yan J. 2020. Complete genome sequence of
Sulfurospirillum strain ACS
TCE
,a
tetrachloroethene-respiring anaerobe isolated
from contaminated soil. Microbiol Resour
Announc 9:e00941-20. https://doi.org/10.1128/
MRA.00941-20.
Editor J. Cameron Thrash, University of
Southern California
Copyright © 2020 Huo et al. This is an open-
access article distributed under the terms of
the Creative Commons Attribution 4.0
International license.
Address correspondence to Jun Yan,
junyan@iae.ac.cn.
Received 9 August 2020
Accepted 14 September 2020
Published 1 October 2020
GENOME SEQUENCES
crossm
Volume 9 Issue 40 e00941-20 mra.asm.org 1

to evaluate genome completeness, remove overlapping ends, and circulate the ge-
nome (10). Default parameters were used for all software unless otherwise specified.
Functional annotation was performed using the NCBI Prokaryotic Genome Annotation
Pipeline (PGAP) (11).
The final assembly resulted in a 2,685,870-bp circular chromosome and a 38,046-bp
circular plasmid (Table 1). Using the genome of S. multivorans strain DSM 12446
(GenBank accession number CP007201.1) as a reference, the replication origin in the
chromosome of strain ACS
TCE
was rotated to the 159-bp position (noncoding region)
upstream of the dnaA gene, which encodes the replication initiator protein DnaA. The
strain ACS
TCE
chromosome harbors two rRNA operons organized in the order 16S-23S-
5S. Four reductive dehalogenase (RDase) A genes, of which three are identical and
adjacent to a downstream RDase B gene encoding a membrane-bound anchor protein,
are present on the chromosome. The protein encoded by the three identical RDase A
genes shares 91.47% amino acid identity with the PceA RDase (GenBank accession
number AHJ12791)ofS. multivorans strain DSM 12446 (12, 13). The chromosome also
harbors complete nap and nrf clusters and a fumarate reductase gene (frdA), suggesting
other electron acceptors support growth. On the strain ACS
TCE
plasmid, genes encod-
ing the plasmid replication initiator protein RepB (FA592_13925) and subunits
(FA592_13805 and FA592_13810) of a type II toxin-antitoxin system were functionally
annotated by PGAP. The majority of plasmid-associated genes encode proteins with
unknown function. The genome and novel RDase genes reported in this study can be
used to better understand the physiology and evolution in organohalide-respiring
Sulfurospirillum members.
Data availability. The genome sequences and assembly projects reported in this
article have been deposited in DDBJ/ENA/GenBank under the accession numbers listed
in Table 1. Raw reads have been deposited in the Sequence Read Archive (SRA) under
accession numbers SRR12303098 (Illumina) and SRR12303097 (PacBio).
ACKNOWLEDGMENTS
This work was funded by the National Natural Science Foundation of China (grant
numbers 41673126, 41977295, and 41907287), Key Research Program of Frontier
Science of Chinese Academy of Sciences (ZDBS-LY-DQC038), and Liaoning Revitaliza-
tion Talents Program (XLYC1807139). F.E.L. acknowledges support from the Strategic
and Environmental Research and Development Program (SERDP).
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TABLE 1 Genome features of strain ACS
TCE
Feature
Data for:
Chromosome Plasmid
Assembly length (bp) 2,685,870 38,046
G⫹C content (%) 38.84 35.71
No. of assembled contigs 1 1
No. of coding sequences 2,704 62
No. of tRNAs 45 0
No. of rRNAs (5S, 16S, 23S) 6 (2, 2, 2) 0
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