Complete Genome Sequence of the Arcobacter ellisii Type Strain LMG 26155

Arcobacter spp. are highly prevalent in contaminated environmental waters and have been recovered from both freshwater and seawater, with several species isolated from shellfish.

ABSTRACT

Arcobacter spp. are highly prevalent in contaminated environmental waters and have been recovered from both freshwater and seawater, with several species isolated from shellfish. Arcobacter ellisii was recovered from mussels collected in Catalonia, Spain. This study describes the whole-genome sequence of the A. ellisii type strain LMG 26155 (=F79-6^T =CECT 7837^T).

ANNOUNCEMENT

Arcobacter species are a common contaminant of freshwater and seawater (1–3) and molluscs (4–8). Arcobacter ellisii was isolated during a survey in Catalonia, Spain, to detect Arcobacter spp. in shellfish (9). Although isolated originally from mussels, A. ellisii has also been detected at a spinach processing plant (10) and at a wastewater treatment plant (11), suggesting that this species might be a general water contaminant that concentrates in mussels through filter feeding. In this study, we report the first closed genome sequence of the A. ellisii type strain LMG 26155 (=F79-6^T =CECT 7837^T), isolated from mussels of the Ebro Delta.

Arcobacter ellisii strain LMG 26155^T was grown aerobically at 30°C for 48 h on anaerobe basal agar (Oxoid) amended with 5% horse blood. A loop (∼5 µl) of cells was harvested, and genomic DNA was isolated using the Promega Wizard kit, as described previously (12). Shotgun and paired-end Roche 454 reads were generated on a GS-FLX+ instrument, with the Titanium chemistry and standard protocols; these were assembled into 77 contigs and a single chromosomal scaffold containing 27 unique contigs using Newbler (version 2.6; Roche), with default settings. Contigs of low quality that were composed of <100 reads were deleted. The Perl script contig_extender3 (12) was used to place within the chromosomal scaffold the 25 remaining contigs that mostly represent repeat regions. Library preparation and sequencing on the PacBio RS II platform (Pacific Biosciences, Menlo Park, CA) were performed as described previously (12), using standard methodology. RS_HGAP_Assembly v3 (Pacific Biosciences) with default settings was used to assemble the reads. A single chromosomal contig was obtained which was subjected to one round of polishing using RS_resequencing.1 and quality trimmed and circularized within Geneious (version 8.0; Biomatters Ltd., Auckland, New Zealand). The PacBio contig was assembled along with the 454 contigs using SeqMan Pro (version 8.0.2; DNAStar, Madison, WI), with the unique 454 contigs assembled onto the PacBio contig automatically and the repeat 454 contigs added in manually. Base calls within the composite 454/PacBio assembly were verified using Illumina HiSeq reads (SeqWright, Houston, TX), as described previously (13). The final coverage across the genome was 925×. Chromosomal assembly was also validated using an optical restriction map (restriction enzyme XbaI; OpGen, Gaithersburg, MD).

The LMG 26155^T genome features are summarized in Table 1. A. ellisii strain LMG 26155^T has a circular genome of 2,799,949 bp, with an average GC content of 26.9%. Protein-, rRNA-, and tRNA-encoding genes were identified and annotated as described previously (14, 15). The genome is predicted to contain 2,743 putative protein-coding genes, 32 pseudogenes, five rRNA operons, and 60 tRNA-encoding genes. A type III-B CRISPR/Cas system and at least eight genomic islands, ranging in size from 5.8 kb to 37.5 kb, were identified in the LMG 26155^T genome. Fourteen insertion sequences (IS) from the following families are present in the A. ellisii chromosome: IS3 (n = 6), IS4 (n = 2), IS21 (n = 4), IS1249 (n = 1), and IS1634 (n = 1). Similar to Arcobacter mytili (16), a large type 1 secretion system (T1SS) repeat domain-containing protein-encoding gene with a tandem-repeat internal motif (29 × 414 bp) was identified.

TABLE 1.

Sequencing metrics and genomic data for A. ellisii strain LMG 26155^T

Featurea	Value(s)b
Sequencing metrics
454 (shotgun) platform
No. of reads	141,497
No. of bases	87,366,368
Avg length (bases)	617.4
Coverage (×)	31.2
454 (paired-end) platform
No. of reads	78,872
No. of bases	24,957,376
Avg length (bases)	316.4
Coverage (×)	8.9
Illumina HiSeq 2000 platform
No. of reads	15,212,786
No. of bases	1,529,278,600
Avg length (bases)	101
Coverage (×)	546.2
PacBio platform
No. of reads	328,963
No. of bases	947,635,645
Avg length (bases)	2,880.7c
Coverage (×)	338.4
Genomic data
Chromosome
Size (bp)	2,799,949
G+C content (%)	26.92
No. (%) of CDSd	2,743
Assigned function	973 (35.5)
General function annotation	1,049 (38.2)
Domain/family annotation only	178 (6.5)
Hypothetical	543 (19.8)
Pseudogenes	32
Genomic islands/CRISPR
No. of genetic islands	8
No. of CDS in genetic islands	157, [2]
CRISPR/Cas loci	III-B
Gene content/pathways
IS elements, mobile elements, or transposases	6, [1] (IS3); 2 (IS4); 4 (IS21); 1 (IS1249); 1 (IS1634); 1 (other)
Signal transduction
Che proteins	cheABCDRVW(Y)2
No. of methyl-accepting chemotaxis proteins	26
No. of response regulators	51, [1]
No. of histidine kinases	60, [2]
No. of response regulator/histidine kinase fusions	7
No. of diguanylate cyclases	24
No. of diguanylate phosphodiesterases (HD-GYP, EAL)	8, 4
No. of diguanylate cyclase/phosphodiesterases	14
No. of other proteins	13
Motility
Flagellin gene	fla
Restriction/modification (no.)
Type I systems (hsd)	3
Type II systems	0
Type III systems	0
Transcription/translation
No. of transcriptional regulatory proteins	60, [1]
Non-ECF σ factors	σ54, σ70
No. of ECF σ factors	0
No. of tRNAs	60
No. of ribosomal loci	5
CO dehydrogenase (coxSLF)	Yes
Ethanolamine utilization (eutBCH)	No
Nitrogen fixation (nif)	Yes
Osmoprotection	BCCT, betA, ectABCD
Pyruvate → acetyl-CoA
Pyruvate dehydrogenase (E1/E2/E3)	No
Pyruvate:ferredoxin oxidoreductase	porABDG
Urease	ureAB, ucaA
Vitamin B12 biosynthesis	No

^aCDS, coding sequences; ECF, extracytoplasmic function; CoA, coenzyme A.

^bNumbers in square brackets indicate pseudogenes or fragments. BCCT, betaine-carnitine-choline transporter.

^cMaximum length, 25,296 bases.

^dNumbers do not include pseudogenes.

Data availability.

The complete genome sequence of A. ellisii strain LMG 26155^T has been deposited in GenBank under the accession number CP032097. The 454, HiSeq, and PacBio sequencing reads have been deposited in the NCBI Sequence Read Archive (SRA; accession number SRP155046).