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OPEN

Received: 10 October 2016
Accepted: 11 April 2017
Published: xx xx xxxx

Isolation and genomic
characterization of a
Dehalococcoides strain suggests
genomic rearrangement during
cultureMasafumi Yohda1, Kentaro Ikegami1, Yuto Aita1, Mizuki Kitajima1, Ayane Takechi1, Megumi
Iwamoto2, Tomomi Fukuda2, Noriyoshi Tamura2, Junji Shibasaki3, Seiji Koike3, Daisuke
Komatsu4, Sakari Miyagi4, Minoru Nishimura4, Yoshihito Uchino5, Akino Shiroma6, Makiko
Shimoji6, Hinako Tamotsu6, Noriko Ashimine6, Misuzu Shinzato6, Shun Ohki6, Kazuma
Nakano6, Kuniko Teruya6, Kazuhito Satou6, Takashi Hirano6 & Osami Yagi7
We have developed and characterized a bacterial consortium that reductively dechlorinates
trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase
genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl
chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase
gene, tceA. The metagenome analysis of the consortium by the next generation sequencer SOLiD 3
Plus suggests that a Dehalococcoides sp. that is highly homologous to D. mccartyi 195 and equippedwith vcrA and tceA exists in the consortium. We isolated this Dehalococcoides sp. and designated it as D.
mccartyi UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated conditions, weconstructed a consortium by mixing D. mccartyi UCH-ATV1 with several other bacteria and performed
metagenomic sequencing using the single molecule DNA sequencer PacBio RS II. We successfully
determined the complete genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrAand tceA, but lacks bvcA. Comparison with tag sequences of SOLiD 3 Plus from the original consortium
shows a few differences between the sequences. This suggests that a genome rearrangement of
Dehalococcoides sp. occurred during culture.
Volatile chlorinated hydrocarbons, such as tetrachloroethene (PCE) and trichloroethene (TCE), are among themost abundant soil and groundwater contaminants in the world. Some microbes perform dehalorespiration,
which uses chlorinated organic compounds as electron acceptors1. PCE and TCE are reductively dechlorinated
via less-chlorinated intermediates, dichloroethene (DCE) and vinyl chloride (VC), to harmless ethene. Such insitu bioremediation via activation of dehalorespiration by exogenous electron donors is thought to be the mostpromising means of remediating soil or groundwater contaminated with chloroethenes2. Reductive dechlorination of PCE and TCE are performed by several bacteria species, including Dehalococcoides spp., but only a few
Dehalococcoides spp. members can dechlorinate DCE and VC to ethene3. Supply of electron donors, such as
Hydrogen Releasing Compound (HRC ), to soil contaminated with PCE or TCE often results in incomplete
dechlorination to ethene and accumulation of DCE or VC. To avoid such problems, the administration of cultured®

1

Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo,
184-8588, Japan. 2PaGE Science, Koganei, Tokyo, 184-8588, Japan. 3ADEKA Co., Ltd., Arakawa, Tokyo, 116-8554,
Japan. 4In Situ Solutions, Co., Ltd., Chiyoda, Tokyo, 101-0044, Japan. 5Biological Resource Center, National Instituteof Technology and Evaluation, Shibuya, Tokyo, 151-0066, Japan. 6Okinawa Institute of Advanced Sciences, Uruma,
904-2234, Okinawa, Japan. 7Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon
University, Narashino, Chiba, 275-8575, Japan. Correspondence and requests for materials should be addressed to
M.Y. (email: yohda@cc.tuat.ac.jp)
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Figure 1. Construction of a bacterial consortium that dechlorinates cis-DCE to ethane. (A) Reductive
dechlorination of cis-DCE to ethene by the 4th-generation consortium. DCE (open circle), VC (closed
circle), and ethene (open square). (B) Increase in Dehalococcoides spp. in the culture-by-culture generation.
Relative amounts of the Dehalococcoides 16S rRNA, vcrA and bvcA genes were monitored by real time qPCR.
Dehalococcoides 16S rRNA (open circle), bvcA (closed circle), and vcrA (open square) genes.

Dehalococcoides spp. that can dechlorinate DCE and VC in contaminated ground, has been proposed. However, it
is very difficult to isolate and culture Dehalococcoides spp. Among Dehalococcoides spp., D. mccartyi 195 was firstreported to dechlorinate PCE to ethene4. Although D. mccartyi 195 has reductive dehalogenase (RDase) genes for
PCE and TCE (pceA and tceA)5, it lacks VC RDase genes. Thus, VC is slowly degraded by co-metabolic pathways,
and VC may accumulate. In 2003, a VC-dechlorinating enrichment culture was established, and D. mccartyi
BAV1 was isolated as a VC-reducing bacterium6. In D. mccartyi BAV1, bvcA is involved in VC-reductive dechlorination7. D. mccartyi VS and FL2 have subsequently been reported to dechlorinate DCE and VC to ethene8, 9.
These strains are equipped with another RDase gene (vcrA)10. VcrA can dechlorinate all of the isomers of DCE
as well as VC11. To date, most Dehalococcoides spp. that can perform complete dechlorination to ethene have thevcrA gene, for example, D. mccartyi GT has vcrA and can dechlorinate TCE to ethene12. However, it is unknown
how TCE is dechlorinated, as this species lacks the TCEase gene tceA5. Recently, D. mccartyi UCH007 and BTF08
have been identified to possess pceA, tceA and vcrA and can dechlorinate of PCE or TCE to ethene13, 14.
Dehalococcoides spp. share extremely high DNA sequence homology. Dehalococcoides spp. are separated
into three subgroups—the Cornell, Victoria, and Pinellas sub-branches—according to slight differences in their
16S rRNA gene sequences15. Recent developments in DNA sequencing technology and isolation methods enabled us to determine the genome sequences of Dehalococcoides spp. The genome sequences of more than ten
Dehalococcoides spp. have been reported to date. Genome sequence similarities correlate with their classification
using 16S rRNA sequences. D. mccartyi CG5 (CP006950) and 195 (CP000027) belong to the Cornell group; D.
sp. UCH007 (CP006951), D. mccartyi GY50 (CP006730), VS (CP001827) and CG1 (CP006949) belong to theVictoria group; and D. mccartyi BTF08 (CP004080), BAV1 (CP000688), CBDB1 (AJ965256), GT (CP001924),
DCMB5 (CP004079), CG5 (CP006951) and IBARAKI (AP014563) belong to the Pinellas group.
The isolation and application of Dehalococcoides spp. is hampered by their very slow growth rates.
As Dehalococcoides is commonly found in microbial communities that contain other anaerobes, such as
Desulfovibrio, Eubacterium, Acetobacterium, Citrobacter, Spirochetes and Clostridium16–19, and it is suggested thatsymbiotic interactions are indispensable for the growth of Dehalococcoides spp. The growth of D. mccartyi 195 issustained by Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense20.
In this study, we constructed a bacteria consortium that dechlorinates TCE to ethene and succeeded in isolating and characterizing novel Dehalococcoides mccartyi UCH-ATV1, which belongs to the Cornell group andpossesses tceA and vcrA. Careful analysis suggests that a genome rearrangement occurred during culture.

Results

Construction of a bacterial consortium that can dechlorinate cis- DCE to ethene.

Groundwater
was obtained from a site contaminated with TCE and used as a source of bacteria. Dechlorination of cis-DCE wasobserved from primary culture, and bacteria responsible for cis-DCE dechlorination were enriched and maintained by consecutive 4% (v/v) transfers. Figure 1A shows changes in the concentration of cis-DCE and VC inthe 4th generation culture. As cis-DCE decreased, VC appeared, and cis-DCE was almost completely converted toethene after three weeks. Similar dechlorination activity was observed in subsequent generations. Genes for the
16S rRNA of Dehalococcoides spp. and RDases, vcrA10 and bvcA7 were quantified by qPCR (Fig. 1B). The quantities of Dehalococcoides 16S rRNA and vcrA genes have increased with generation number and reached plateau.
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Different from them, bvcA increased in the beginning and then decreased gradually. The result suggests existenceof two different Dehalococcoides spp., one with bvcA and the other without bvcA.

Metagenome analysis of the consortium by the next generation DNA sequencer SOLiD 3
Plus. As Dehalococcoides spp. appeared to dominate the 4th generation of the bacterial consortium, themetagenome of this consortium was analyzed by the next generation DNA sequencer SOLiD 3 Plus (Thermo
Fisher Scientific), and 332,003,834 reads of 50-base were obtained. Among them, 4,961,715 reads with unreliablesequences were excluded and 327,042,119 reads were used for analysis. The obtained data were compared withgenome sequences of the Dehalococcoides strains D. mccartyi 195 (CP000027)21, D. mccartyi BAV1 (CP000688),
D. mccartyi CBDB1 (AJ965256)22, D. mccartyi VS (CP001827), and D. mccartyi GT (CP001924). The numbers oftag sequences matched by comparison to reference genome sequences, with an allowance of two mismatches in
50 nt, coverage depths, are shown. The results clearly show that a Dehalococcoides sp. in the consortium are highly
homologous to D. mccartyi 195 (Fig. 2).
To investigate the presence of RDase genes, the average coverage depths for the RDase genes were analyzed(Supplementary Table S3). Among the 17 RDase genes in D. mccartyi 195, the presence of four genes, including
TCE RDase, tceA, was suggested. However, the PCE RDase gene pceA was not detected in the metagenome of theconsortium. The VC RDase genes bvcA of D. mccartyi BAV1 and vcrA of D. mccartyi VS were present with significantly high average coverages, consistent with the results of qPCR for these genes. However, the presence of other
RDase genes from D. mccartyi BAV1 and D. mccartyi VS was not observed. Figure 3 shows the coverage depthof the genes for Dehalococcoides 16S rRNA, tceA, bvcA and vcrA. Reflecting the high homology of 16S rRNAs in
Dehalococcoides spp., Dehalococcoides 16S rRNA exhibited a consistently high coverage depth throughout theentire gene. The coverage depth of 16S rRNA reflects the population of Dehalococcoides spp. In the consortium.
Compared with 16S rRNA genes, the three RDase genes, bvcA, tceA and vcrA, showed some sequence variation.
However, all exhibited significantly high identity across entire sequences. Sequence variation in vcrA is small
compared with bvcA or tceA. Considering highly conserved sequences, the maximal coverage value should correlate with the abundance of the gene. The maximal coverage values for Dehalococcoides 16S rRNA, bvcA, tceAand vcrA are 4318, 3694, 4140 and 4878. The value for vcrA is significantly higher than those for Dehalococcoides
16S rRNA and tceA. It is reasonable that the difference is caused by variations in PCR amplification or sequence
preference. Thus, we concluded that a single species Dehalococcoides sp. equipped with bvcA, tceA and vcrA dominantly existed in the consortium, and the other one without bvcA gradually increased. However, we don’t havesolid evidence for the existence of Dehalococcoides sp. equipped with bvcA, tceA and vcrA.
The presence of tceA suggested that the consortium can dechlorinate TCE to ethene. The consortium was cultured in media containing 100 µM TCE to confirm this hypothesis, and this TCE was completely dechlorinatedby the consortium (Supplementary Fig.S1). Therefore, we conclude that a Dehalococcoides sp. in the consortium
can dechlorinate TCE to ethene.
We attempted to examine the bacteria comprising the consortia. Comparison against 16S rRNA genesequences in the public database was performed as described previously 19. We compared the obtained tag
sequences with the reference sequences constructed from 357,656 bacterial 16S rRNA gene sequences. The genes
were sorted according to coverage values. Homologous genes were grouped together, and the sequences thatshowed the highest coverage depths were selected as the representative sequences. Based on the average coverage
depth, the relative populations of them were estimated assuming that each species has only one 16S rRNA gene
(Table 1). Dehalococcoides spp. were the most abundant and were estimated to cover 47.1% of all microbes in the
consortium.

Isolation of D. mccartyi UCH-ATV1. Following repeated transfers to cis-DCE amended media in the presence of ampicillin or 2-bromoethanesulfonate, a series of dilution-to-extinction culturing and several agar shakeprocesses were performed, and the strain D. mccartyi UCH-ATV1 was obtained in pure culture (Supplementary
Fig. S2). The presence of the RDase genes tceA and vcrA was confirmed by PCR (Supplementary Fig. S3).
However, PCR amplification of bvcA was in vain (data not shown).
Obtaining bacteria that support the growth of Dehalococcoides sp. Similar to otherDehalococcoides spp., the growth and dechlorination of the isolated D. mccartyi UCH-ATV1 was very slow compared with that of the consortium as a whole (Supplementary Fig. S4). Thus, we tried to obtain bacteria that
support the growth of D. mccartyi UCH-ATV1. As the constructed consortium contained various species, we isolated Dehalococcoides-supporting bacteria from the consortium obtained in our previous study19. DGGE analysis
showed that only three bacterial species including D. mccartyi IBARAKI dominantly existed in the Ibaraki consortium. The sequences of 16S rRNA identified the other members of the IBARAKI consortium as Desulfovibrio
desulficans and Eubacterium acidaminophilus. At first, we grew the Ibaraki consortium in the absence of chloroethenes to remove D. mccartyi IBARAKI, and then mixed with isolated D. mccartyi UCH-ATV1. The preparedculture was able to convert TCE to ethene (Supplementary Fig. S5). As D. mccartyi IBARAKI cannot dechlorinate TCE, other bacteria in the IBARAKI consortium thus support the growth of D. mccartyi UCH-ATV1.
Assuming that Desulfovibrio supports the growth of D. mccartyi IBARAKI, we performed single colony isolationfrom a shake agar culture in the media for Desulfobivrio species. We obtained single colonies after several rounds.
However, 16S rRNA sequence analysis of the clone indicated a mixture of Desulfovibrio and Petrimonas spp.
Although Petrimonas species were not detected by DGGE analysis in the enriched culture, they were observed in
the Ibaraki consortium at an earlier stage. Thus, it is reasonable to conclude that Petrimonas spp. remained in the
consortium and its populations increased during the single colony selection procedures. We were not able to isolate the Desulfovibrio species despite repeated attempts. Thus, we used a mixture of Desulfovibrio and Petrimonas
spp. in culture with D. mccartyi UCH-ATV1. As expected, the mixed consortium exhibited significantly highScientific Reports | 7: 2230 | DOI:10.1038/s41598-017-02381-0

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Figure 2. Comparison of consortium metagenome sequence data with the that of the Dehalococcoides sp.
genome. Tag sequences for the metagenome of the consortium by SOLiD 3 Plus were matched to the genome
sequences of five Dehalococcoides spp. (D. mccartyi 195, D. mccartyi BAV1, D. mccartyi CBDB1, D. mccartyi GT,
and D. mccartyi VS).

dechlorination activity for TCE (Fig. 4A). Unexpectedly, when we analyzed the consortium by DGGE, six bands
were observed (Supplementary Fig. S6). Among them, three major bands were identified as Petrimonas sp.,
Dehalococcoides ap. And Desulfovibrio sp. We could not clearly identify the other three bands due to poor resolution. However, only the sequences for Dehalococcoides, Desulfovibrio and Petrimonas species were observed in
the sequences from their amplicons.
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Figure 3. Coverage of SOLiD 3 Plus tag sequences for Dehalococcoides 16S rRNA and RDase genes. Tagsequences of the metagenome of the consortium by SOLiD 3 Plus were matched to sequences of Dehalococcoides
16S rRNA, bvcA, vcrA and tceA genes.

Classification

Representative
Sequence

Average
Coverage

Ratio[%]

Dehalococcoides

DQ8551293140.946.2

Enterobacter

AM937487

1555.922.9

Azospira (Dechlorosoma)

AY604956

1025.6

15.1

Spirochaetes

EF581152

569.1

8.4

Bacteroidetes/Chlorobi

AY280650

500.1

7.4

Table 1. Population of representative bacteria constituting the original consortium.
The metagenome of the consortium was subjected to sequencing by PacBio RS II. At first, PCR-amplified
bacterial 16S rRNA genes were sequenced. From 14742 CCS (Circular Consensus Sequencing) reads, 2760
non-redundant sequences were obtained. Among them, 11 were chimera of two 16S rRNA sequences, and 146
were not 16S rRNA genes. Then, we compared 2525 sequences with the SILVA 123 SSURef sequences23. Amongthem 2495 sequences showed more than 99% identities with 16S rRNA sequences of Dehalococcoides sp. (144),
Clostridium sp. (237), Desulfovibrio sp. (658) and Petrimonas sp. (1456) (Fig. 4B). Although remaining 130
sequence showed less than 99% identities with 16S rRNA genes in the data base. However, the most homologous 16S rRNA genes of them are 16S rRNA genes of Dehalococcoides sp., Clostridium sp., Desulfovibrio sp. andPetrimonas sp. It seems that the relatively low identity (90–98%) should be due to the mutations by PCR amplification or the sequence errors. Thus, we concluded that the consortium was composed of four species.
The unidentified weak bands in PCR-DGGE should correspond to the 16S rRNA genes from Clostridium
sp. Generally, Clostridium spp. have multiple 16S rRNA genes, and we found slight sequence variations among
Clostridium 16S rRNA genes.

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Figure 4. Characterization of the constructed consortium containing D. mccartyi UCH-ATV1. (A) Reductive
dechlorination of TCE to ethene by the consortium. TCE (closed diamond), DCE (open circle), VC (closed
circle), ethene (open square). (B) Classification and quantification of the 16S rRNA genes of the consortium.

Determination of the Complete Genome Sequence of D. mccartyi UCH-ATV1.

The metagenomeof the constructed consortium was submitted to sequencing by the PacBio RS II platform with a 20-kb insert
library and P6-C4 chemistry. We used 30 SMRT cells to record 240-min movies. In the first sequencing run using
16 cells, 1.4 M reads with an average length of 4.2 kb were obtained. In the second sequencing run using 14 cells,
533 K reads with an average length of 3.9 kb were obtained. We applied HGAP version 2 and version 3 to each of
the sequencing data with a 6-kb Minimum Seed Read Length and a 1.4-Mb Genome Size. A total of 485 contigs
was assembled, and of those, 61 contigs had similarity with Dehalococcoides species. We attempted to overlap
and join those contigs using Minimus2, and a circular sequence was constructed. During the final circularization
process with Minimus2, we achieved a complete genome sequence of a Dehalococcoides-like strain of 1387782 nt(Supplementary Fig. S7). The genome sequence was deposited in DDBJ with the accession number, AP017649.
The number of CDS was 1498, which includes three rRNA genes (5S rRNA, 16S rRNA, 23S rRNA) and 47 tRNA
genes.
To confirm that the genome actually corresponded to that of D. mccartyi UCH-ATV1, we matched the
SOLiD 3 Plus tag sequences of the original consortium to the genome sequence (Fig. 5A). Very similar constant high-coverage values were observed throughout the genome sequence. However, several gap regions wereobserved where the coverage values were significantly reduced. However, PacBio RS II data matched the genome
sequence in an almost uniform fashion throughout the genome (Fig. 5B).
Genome annotation also indicates that the regions do not arise from Dehalococcoides spp. Large gap regions
are surrounded by phage recombinase-like protein-coding regions or phage-related genes (Fig. 5C and D). The
red and blue lines in Fig. 5C correspond to DEHALATV1_0058 (57900 nt – 58898 nt), a site-specific recombinase
phage integrase family, and DEHALATV1_0098 (84056 nt – 84679 nt), a phage-repressor-like transcriptional
regulator, respectively. In Fig. 5D, the regions for DEHALATV1_0629 Restriction endonuclease S subunit-likeprotein, DEHALATV1_0630 SAM-dependent methyltransferase, DEHALATV1_0631 hypothetical protein, andDEHALATV1_0632 5-methylcytosine-specific restriction enzyme subunit McrC are shown as the red line, andthe DEHALATV1_0669 site-specific recombinase phage integrase family is shown as a blue line.
Thus, it is reasonable to conclude that these regions originate through recombination. To confirm that they are
not artifacts resulting from the contig assembly, we performed PCR amplification of the junction region between
the high-coverage and low-coverage regions. We obtained a PCR product spanning the high coverage region(604436nt (coverage = 3108)) and low coverage region (609373nt (coverage = 134)) (Supplementary Fig. S8).
In addition to the genome for D. mccartyi UCH-ATV1, contigs for Desulfovibrio, Petrimonas and Clostridium
species were also present, corresponding to our 16S rRNA gene analysis.

Comparison with other Dehalococcoides genomes.

The genome sequence was compared to the
genome sequences of various Dehalococcoides spp. using GenomeMatcher24 (Supplementary Fig. S9). The results
clearly show that D. mccartyi UCH-ATV1 has high homology with D. mccartyi 195.
The results of the gene annotation are summarized in Table 2. Compared with other Dehalococcoides spp.,
there is a relatively modest number of RDase genes in the genome of D. mccartyi UCH-ATV1 (Table 3). EightRDase genes were full-length, and all of these, including tceA and vcrA, were found in the SOLiD 3 Plus data, but
bvcA was lost from the genome. Most genes were accompanied by an anchor protein gene. DEHALATV1_1300
and DEHALATV1_1301 seemed to share one anchor protein gene (DEHALATV1_1302). In addition, several
nonfunctional truncated RDase genes were found. Most were also accompanied by an anchor protein gene.

Discussion

In this study, we developed a bacterial consortium that reductively dechlorinates cis-DCE and vinyl chloride VC
to ethene from groundwater contaminated with trichloroethene TCE. To characterize the Dehalococcoides spp.
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Figure 5. Comparison of the genome sequence of D. mccartyi UCH-ATV1 with the metagenome analysis
data. The genome sequence of D. mccartyi UCH-ATV1 was compared with metagenomic data of the original
consortium obtained by SOLiD 3 Plus (A) or the constructed consortium obtained by PacBio RS II (B). (C,D)
Two large gap regions in comparison to the metagenome data of the original consortium (A) are shown. Red
and blue lines represent phage- or recombinase-related genes, respectively.

D. mccartyi UCH-ATV1
Size (bp)1387782

G + C content (%)

49

Stable RNAs
rRNAs

3

tRNAs

47

Protein-coding sequences

1448

Table 2. Genome overview of D. mccartyi UCH-ATV1.

and other bacterial members, genome sequencing was used to deduce the metagenome of the consortium using
the next generation sequencer SOLiD 3 Plus. The genome sequence of the Dehalococcoides spp. was highly homologous to that of D. mccartyi 195 across the total genome. Interestingly, two known RDase genes for VC, bvcA andvcrA, were found in addition to the TCE RDase gene, tceA. Results of quantitative PCR for the RDase genes suggested existence of two difference of Dehalococcoides spp., one with bvcA and the other without bvcA at the fourth
generation. The quantification of genes for Dehalococcoides 16S rRNA and RDases from the metagenomic data by
SOLiD 3 Plus has suggested existence of a Dehalococcoides sp. equipped with three RDase genes, tceA, vcrA andbvcA. Although there is no solid evidence for the existence of such Dehalococcoides sp., the idea is supported byfact that the genome sequence of D. mccartyi UCH-ATV1 retains the trace of genome rearrangement.
We next isolated a Dehalococcoides sp. We designated it D. mccartyi UCH-ATV1. Counter to our expectation, it contained tceA and vcrA, but lacked bvcA. Further study of D. mccartyi UCH-ATV1 was hampered byits slow growth rate. We tried to enhance the growth of D. mccartyi UCH-ATV1 by mixing it with several bacteria spp. As Desulfovibrio sp. is thought to support the growth of Dehalococcoides spp.20, we tried to isolate a
Desulfovibrio sp. from the consortium that was obtained in our previous studies. In the shake agar culture, we
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Functional/
partial
DEHALATV1_0101

Homologous RDases

DET0180/100%

WP_010935983/100%

Anchoring protein

partial

DEHALATV1_0166
DEHALATV1_0203

Homology with
195 RDases

partial

DEHALATV1_0167
DEHALATV1_0205

DEHALATV1_0204

partial

DEHALATV1_0909

tceA

DET0079/97%

WP_015407437/100%

DEHALATV1_0908

DEHALATV1_0205

DEHALATV1_1275

vcrA

—

WP_061977500/100%

DEHALATV1_1274

DEHALATV1_1288

partial

DEHALATV1_1300—

WP_058292018/100%

DEHALATV1_1302

DEHALATV1_1301—

WP_058292017/100%

DEHALATV1_1302

DET1522/84%

WP_058291931/100%

DEHALATV1_1341

DET1528/100%

WP_010937203/100%

DEHALATV1_1335

partial

DEHALATV1_1342
DEHALATV1_1346
DEHALATV1_1351

DEHALATV1_1339

partial

DEHALATV1_1367

DEHALATV1_1345
DEHALATV1_1350

DET1545/99%

WP_010937220/100%

DEHALATV1_1366

Table 3. Reductive dehalogenase genes in the genome of D. mccartyi UCH-ATV1.
isolated black colonies, reflecting the production of sulfides by Desulfovibrio sp. Although we repeated the isolation process several times, only a Petrimonas sp. was obtained. As expected, the mixed consortium exhibited highdechlorination activity on TCE. DGGE and metagenome analysis indicated that the consortium is composed of
Desulfovibrio sp., Petrimonas sp., and Clostridium sp. in addition to D. mccartyi UCH-ATV1. We have assembled
the draft genome sequence of Clostridium sp. in the constructed consortium. The genome sequence matchedwell with the metagenome data of Ibaraki consortium almost throughout the genome (Supplementary Fig. S10).
On the contrary, it does not match with the metagenome data of the original consortium containing D. mccartyi
UCH-ATV1 (Supplementary Fig. S10). We observed almost same results for Petrimonas sp. and Desulfovibrio sp.
Consequently, only the genome sequence of D. mccartyi UCH-ATV1 retains the traces of the original metagenome data. Therefore, we can conclude that D. mccartyi UCH-ATV1 was isolated before mixing with the bacteria
from Ibaraki consortium.
Finally, we determined the complete genome sequence of D. mccartyi UCH-ATV1. Reflecting previous
results, there was significantly high sequence identity with D. mccartyi 195 throughout the genome, which was
equipped with tceA and vcrA. Eight full-length RDase genes and seven nonfunctional truncated RDase genes
were detected. The presence of nonfunctional truncated RDase genes has also been reported in the genomes ofother Dehalococcoides spp.25. Thirty-eight orthologous RDase genes were identified in D. mccartyi MB, of whichfour (DehaMB_1_0001, DehaMB_1_0161, DehaMB_1_0162, and DehaMB_8_0246) were partial sequences.
Eleven RDase genes were identified in D. mccartyi 11a, of which Deha11a_2_0134 (281 bp) and Deha11a_6_0020(542 bp) were truncated sequences. Surprisingly, the genome sequence differs from the metagenome analysis
data of the initial consortium. As D. mccartyi UCH-ATV1 originated from the consortium, the genome mustcompletely match the tag sequences of the metagenome obtained by SOLiD 3 Plus. We suspect that the differenceis caused by chimera formation during the contig assembly process. However, this was ruled out by both theuniform coverage values throughout the genome and by PCR amplification of the suspicious region. In addition,
the GC content values of the gap regions clearly different from those of the high coverage regions (Supplementary
Fig. S11). Since the low-coverage regions are surrounded by phage-related genes or recombinase genes, we conclude that the difference is due to genome rearrangement by recombination during isolation. We hypothesizethat the disappearance of the bvcA gene might be due to such recombination. Although further study is needed
to confirm this hypothesis, it is plausible, as genome rearrangement frequently occurs in Dehalococcoides spp.
Genome-wide studies of Dehalococcoides spp. will be required to confirm this hypothesis.

Methods

Chemicals and materials.

TCE, cis-DCE and VC were purchased from Wako Pure Chemical Ind. Ltd.
(Osaka, Japan). Ethene and H2 were obtained from GL Sciences Inc. (Tokyo, Japan). Sediment mud used for
culture was obtained from a lotus field and sterilized by autoclave before use. All other chemicals used were reagent-grade or higher unless otherwise specified.

Analytical methods.

The concentrations of chloroethenes and ethene were determined using a Shimadzu
GC 1024 gas chromatograph (Shimadzu Co., Kyoto, Japan) equipped with a DB-624 column (60 m length, 0.32
mm diameter, 1.80 μm film thickness, Agilent Technology, Santa Clara, CA, USA) and a flame ionization detector
by injecting 100 μl of reactor headspace using a gas-tight syringe.

Culture medium. The composition of the culture medium was as follows: 10 (ml/L) salt stock solution, 1(ml/L) trace element A solution, 1 (ml/L) trace element B solution, 10 (ml/L) vitamin solution, 0.68 (g/L) sodium
acetate, 2.52 (g/L) sodium bicarbonate, 1 (mg/L) resazurin-Na, 10 (ml/L) reducing agent solution and appropriate quantities of TCE or cis-DCE. Ingredients except for vitamin, reducing agents and chlorinated ethylenes
were mixed, and the medium was dispensed into suitable culture vessels under a stream of H2/CO2 (80/20),
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sealed with Teflon-coated butyl rubber stoppers, and autoclaved at 121 °C for 20 min. After autoclaving, vitamin,
reducing agents and chlorinated ethylenes were aseptically and anaerobically added to the respective vessels. The
contents of the salt stock solution, trace element A, trace element B and reducing agent solution are described in
Supplementary Table S1.

Enrichment and cultivation. Groundwater was obtained from a site contaminated with TCE and used
as a source of bacteria. The first-stage enrichment culture was carried out as follows: 4.5 g of sediment mud and86.4 ml of the medium were added to 100-ml glass vials. The vials were sealed with Teflon-coated butyl rubber
caps and crimped with aluminum rings. Vials were purged by injecting nitrogen gas for 3 min and were autoclaved at 121 °C for 15 min. After cooling, 3.6 ml of ground water was added, 5 ml of headspace gas was withdrawn
from each bottle using a syringe, and 5 ml of hydrogen was then injected. Finally, cis-DCE was added to an initialconcentration of 100 µM, and the cultures were incubated at 21 °C without shaking in the dark. After nearly all
cis-DCE was dechlorinated, 3.6 ml of the culture was used for a successive culture in the same manner. The culture
was maintained in media supplemented with TCE.
DNA extraction. DNA was extracted from 0.5 ml of enrichment culture using the ISOIL for Beads Beating
Kit (Nippon Gene Co. Ltd., Tokyo, Japan) according to the manufacturer’s instructions. The extracted DNA wassuspended in 100 μl of TE buffer (pH 8.0). DNA extracts were stored at −20 °C for further analysis.
Quantitative PCR (qPCR) for Dehalococcoides 16S rRNA gene and dehalogenase genes (tceA,
bvcA, vcrA). The Dehalococcoides 16S rRNA gene and dehalogenase genes (tceA, bvcA, vcrA) were quantified™

by qPCR using a StepOne real time PCR system (Thermo Fisher Scientific, Waltham, MA). The quantities of
the Dehalococcoides 16S rRNA, tceA and bvcA genes were analyzed using a TaqMan method with TaqMan
Universal PCR Master Mix (Thermo Fisher Scientific) following the supplier’s instruction. VcrA was quantified using a SYBR Green Dye method and Fast SYBR Green Master Mix (Thermo Fisher Scientific). The
sequences of primers and probes are shown in Supplementary Table S2.

™

™

™

™

Denaturing Gradient Gel Electrophoresis (DGGE). PCR amplification was conducted using the prim-ers 341fGC (5′- CGC CCG CCG CGC GCG GCG GGC GGG GCG GGG GCA CGG GGG GCC TAC GGG
AGG CAG CAG -3′) and 534r (5′-ATT ACC GCG GCT GCT GC-3′) to amplify fragments of 16S rRNA genes.
The PCR cycling conditions were as follows: initial denaturation at 95 °C for 10 min; eight cycles (95 °C for 1 min,annealing at 64 °C for 1 min, and extension at 72 °C for 2 min); 30 cycles (95 °C for 1 min, annealing at 55 °C for
1 min, and extension at 72 °C for 2 min); and a final extension at 72 °C for 10 min. PCR amplification reactions
were carried out as described previously. DGGE was performed according to a modification of the describedmethods. We used 10% polyacrylamide gels with a urea-formamide denaturant gradient of 40–60%, and gels wererun on a DCode Universal Mutation Detection system (Bio-Rad) for 5 h at 60 °C and 130 V. After electrophoresis,
the gels were stained with SYBR Green (TAKARA BIO Ink, Shiga, Japan). Prominent bands were excised and dissolved in 200 μl of TE buffer. Each target fragment of DNA was recovered by ethanol precipitation and amplified
using the primer sets 341fGC and 534r. The PCR cycling conditions were as described above. The PCR products
were purified and sequenced as described previously19. The PCR products were purified using the Wizard SV Gel
and PCR Clean-Up System (Promega). Each DNA fragment was subcloned into a plasmid by TA cloning andsubmitted for DNA sequencing. Sequencing reactions were run according to manufacturer’s instructions for the
ABI Big Dye Terminator KIT version 3.1 (Thermo Fisher Scientific). Sequence analysis was performed using a
3130xl Genetic Analyzer (Thermo Fisher Scientific). The similarities between the obtained DNA sequences wereanalyzed using BLAST.

Metagenomic Sequencing by SOLiD 3 Plus. Fragment libraries were constructed according to manufacturer’s instructions using the SOLiD Fragment Library Construction Kit and sequenced on a single plate ofan ABI SOLiD 3 Plus sequencer (Thermo Fisher Scientific) to generate 50-nt reads. The short reads were mapped
to the genome sequences of various Dehalococcoides spp. and reference DNA constructed from 16S rRNA genesequences in color space using Corona-Lite or Bowtie26. The coverage values were calculated from Bowtie reads
obtained using mpileup in SAMTools. The average coverage was calculated by averaging the coverage values forthe gene or whole genome.

™

Metagenomic Assembly by PacBio RS II.

SMRTbell libraries were constructed according to manufacturer’s instructions using the Greater Than 10 kb Template Preparation Using AMPure PB Beads and Sequencing(MagBead Station) protocols (Pacific Biosciences, Menlo Park, CA, USA). The extracted DNA was purified usinga PowerClean DNA Clean-Up Kit (MoBio laboratories, Carlsbad, CA, USA). Small fragments of DNA were
removed using AMPure PB Beads (Pacific Biosciences) of 0.45x. SMRTbell 20-kb libraries were prepared using
a SMRTbell Template Prep Kit 1.0 (Pacific Biosciences). Libraries were subsequently sequenced on PacBio RS
II (Pacific Biosciences) using DNA/Polymerase Binding Kit P6 v2 (Pacific Biosciences) and a DNA Sequencing
Reagent Kit 4.0 (Pacific Biosciences). The titration density was 0.025 nM. The template was loaded into SMRT Cell
v3 (Pacific Biosciences) using a Mag Bead Kit (Pacific Biosciences). Sequencing was performed using 30 cells in
total. A 240-min movie was recorded for each cell. Metagenomic assembly was performed using a Hierarchical
Genome Assembly Process (HGAP)27. Minimus2 was used to attempt to overlap and join the resulting contigs28.
Final assemblies were achieved by polishing the draft assemblies using Quiver27.

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References

1. El Fantroussi, S., Naveau, H. & Agathos, S. N. Anaerobic dechlorinating bacteria. Biotechnol Prog 14, 167–188, doi:10.1021/
bp980011k (1998).
2. Semprini, L. In situ bioremediation of chlorinated solvents. Environ Health Perspect 103(Suppl 5), 101–105, doi:10.1289/
ehp.95103s4101 (1995).
3. Loffler, F. E. et al. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant tohalogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord.
nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 63, 625–635, doi:10.1099/
ijs.0.034926-0 (2013).
4. Maymo-Gatell, X., Anguish, T. & Zinder, S. H. Reductive dechlorination of chlorinated ethenes and 1, 2-dichloroethane by“Dehalococcoides ethenogenes” 195. Appl Environ Microbiol 65, 3108–3113 (1999).
5. Magnuson, J. K., Romine, M. F., Burris, D. R. & Kingsley, M. T. Trichloroethene reductive dehalogenase from Dehalococcoides
ethenogenes: sequence of tceA and substrate range characterization. Appl Environ Microbiol 66, 5141–5147, doi:10.1128/
AEM.66.12.5141-5147.2000 (2000).
6. He, J., Ritalahti, K. M., Yang, K. L., Koenigsberg, S. S. & Loffler, F. E. Detoxification of vinyl chloride to ethene coupled to growth ofan anaerobic bacterium. Nature 424, 62–65, doi:10.1038/nature01717 (2003).
7. Krajmalnik-Brown, R. et al. Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl
Environ Microbiol 70, 6347–6351, doi:10.1128/AEM.70.10.6347-6351.2004 (2004).
8. Cupples, A. M., Spormann, A. M. & McCarty, P. L. Growth of a Dehalococcoides-Like Microorganism on Vinyl Chloride and cisDichloroethene as Electron Acceptors as Determined by Competitive PCR. Applied and Environmental Microbiology 69, 953–959,
doi:10.1128/aem.69.2.953-959.2003 (2003).
9. He, J., Sung, Y., Krajmalnik-Brown, R., Ritalahti, K. M. & Loffler, F. E. Isolation and characterization of Dehalococcoides sp. strain
FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe. Environ Microbiol 7, 1442–1450,
doi:10.1111/j.1462-2920.2005.00830.x (2005).
10. Muller, J. A. et al. Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its
environmental distribution. Appl Environ Microbiol 70, 4880–4888, doi:10.1128/AEM.70.8.4880-4888.2004 (2004).
11. Parthasarathy, A. et al. Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive
dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 137, 3525–3532, doi:10.1021/ja511653d (2015).
12. Sung, Y., Ritalahti, K. M., Apkarian, R. P. & Loffler, F. E. Quantitative PCR confirms purity of strain GT, a novel trichloroethene-toethene-respiring Dehalococcoides isolate. Appl Environ Microbiol 72, 1980–1987, doi:10.1128/AEM.72.3.1980-1987.2006 (2006).
13. Uchino, Y. et al. Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.
Stand Genomic Sci 10, 102, doi:10.1186/s40793-015-0095-9 (2015).
14. Poritz, M. et al. Genome sequences of two dehalogenation specialists - Dehalococcoides mccartyi strains BTF08 and DCMB5
enriched from the highly polluted Bitterfeld region. FEMS Microbiol Lett 343, 101–104, doi:10.1111/1574-6968.12160 (2013).
15. Hendrickson, E. R. et al. Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites
throughout North America and Europe. Appl Environ Microbiol 68, 485–495, doi:10.1128/aem.68.2.485-495.2002 (2002).
16. Richardson, R. E., Bhupathiraju, V. K., Song, D. L., Goulet, T. A. & Alvarez-Cohen, L. Phylogenetic characterization of microbialcommunities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ Sci Technol 36,
2652–2662, doi:10.1021/es0157797 (2002).
17. Ritalahti, K. M. & Loffler, F. E. Populations implicated in anaerobic reductive dechlorination of 1,2-dichloropropane in highly
enriched bacterial communities. Appl Environ Microbiol 70, 4088–4095, doi:10.1128/AEM.70.7.4088-4095.2004 (2004).
18. Duhamel, M. & Edwards, E. A. Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides.
FEMS Microbiol Ecol 58, 538–549, doi:10.1111/j.1574-6941.2006.00191.x (2006).
19. Yohda, M. et al. Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on
cis-1,2-dichloroethene. J Biosci Bioeng 120, 69–77, doi:10.1016/j.jbiosc.2014.12.001 (2015).
20. Men, Y. et al. Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenboroughand Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME J 6, 410–421, doi:10.1038/ismej.2011.111(2012).
21. Seshadri, R. et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307, 105–108,
doi:10.1126/science.1102226 (2005).
22. Kube, M. et al. Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat
Biotechnol 23, 1269–1273, doi:10.1038/nbt1131 (2005).
23. Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible
with ARB. Nucleic Acids Res 35, 7188–7196, doi:10.1093/nar/gkm864 (2007).
24. Ohtsubo, Y., Ikeda-Ohtsubo, W., Nagata, Y. & Tsuda, M. GenomeMatcher: a graphical user interface for DNA sequence comparison.
BMC bioinformatics 9, 376, doi:10.1186/1471-2105-9-376 (2008).
25. Low, A. et al. A comparative genomics and reductive dehalogenase gene transcription study of two chloroethene-respiring bacteria,
Dehalococcoides mccartyi strains MB and 11a. Sci Rep 5, 15204, doi:10.1038/srep15204 (2015).
26. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to thehuman genome. Genome biology 10, R25, doi:10.1186/gb-2009-10-3-r25 (2009).
27. Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10,563–569, doi:10.1038/nmeth.2474 (2013).
28. Myers, E. W. et al. A whole-genome assembly of Drosophila. Science 287, 2196–2204, doi:10.1126/science.287.5461.2196 (2000).

Acknowledgements

This research was partially supported by the Okinawa Life Science Network Program, Okinawa Intellectual
Cluster Program and Okinawa Cutting-edge Genome Project.

Author Contributions

M.Y. designed the experiments, analyzed the data, wrote the paper and prepared the figures. M.K., A.T., M.I.,
T.F., N.T., J.S., S.K., S.M. and M.N. obtained and maintained the initial consortium. Y.U. isolated Dehalococcoides
mccartyi UCH-ATV1. Y.A., D.K. and O.Y. reconstructed the consortium by mixing Dehalococcoides mccartyi
UCH-ATV1 and other bacteria. K.I., Y.A., A.S., M.S., H.T., N.A., M.S., S.O., K.N., K.T., K.S. and T.H. conducted
genome sequence and analyzed the consortium.

Additional Information

Supplementary information accompanies this paper at doi:10.1038/s41598-017-02381-0

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