Draft Genome Sequence of Aliivibrio fischeri Strain 5LC, a Bacterium Retrieved from Gilthead Sea Bream (Sparus aurata) Larvae Reared in Aquaculture

Abstract

To shed light on the putative host-mediated lifestyle of the quintessential marine symbiont Aliivibrio fischeri, and on the symbiosis versus potentially pathogenic features of bacteria associated with farmed fish, we report the draft genome sequence of A. fischeri strain 5LC, a bacterium retrieved from gilthead sea bream (Sparus aurata) larvae.

GENOME ANNOUNCEMENT

The bacterium Aliivibrio fischeri, formerly Vibrio fischeri (1), is widely known for its unique symbiotic relationship with the bobtail squid Euprymna scolopes, whereby the luminescent symbiont is thought to provide the host with sophisticated antipredatory skills through a highly specialized bipartite interaction (2). Recently, strains of A. fischeri have been associated with disease outbreaks in farmed fish (3), raising concerns about the pathogenic potential of A. fischeri in fish-rearing systems. To improve the understanding of the adaptive strategies of this species, we announce the draft genome sequence of Aliivibrio fischeri 5LC, a strain isolated from larvae of Sparus aurata (gilthead seabream), the most cultured fish of the family Sparidae and a model taxon in aquaculture research (3).

A. fischeri 5LC was retrieved from gilthead sea bream larvae, 34 days after hatching, on thiosulfate-citrate-bile salts-sucrose agar (TCBS, Oxoid, USA) after 7 days of incubation at 22°C (4). Genomic DNA was extracted from a pure culture grown in marine broth for 2 days at 19°C using the Wizard Genomic DNA purification kit (Promega Corporation, USA). Paired-end sequence reads (125 cycles) were generated using an Illumina HiSeq2500 platform at BaseClear (Leiden, The Netherlands). Sequencing output was 393 Mb, consisting of 2 × 128-bp quality-filtered paired-end reads, leading to genome coverage of ~92×. Sequence reads were assembled into 54 contigs with the “de novo assembly” option within the CLC Genomics Workbench (version 7.0.4), and annotation was performed with the RAST (Rapid Annotation using Subsystem Technology) server, version 2.0 (5). A. fischeri 5LC shares 99.8% 16S rRNA gene homology with the type strain of the species, A. fischeri ATCC 744 (1), and 99.3% and 100% homology with the canonical strains ES114, isolated from E. scolopes (6), and MJ11, isolated from the pinecone fish Monocentris japonica (7), respectively. The A. fischeri 5LC draft genome has 4,250,496 bp and a GC content of 39.0%. Altogether, 3,846 coding sequences (CDSs), 79 tRNAs, and one complete rRNA operon were identified. As usual among the Vibrionaceae, the occurrence of the full bacterial luciferase gene cassette luxCDABE, along with the autoinducer and transcriptional activator genes luxI and luxR, is suggestive of a cell density-dependent regulation of bioluminescence in A. fischeri 5LC. Conspicuously, all 18 genes of the Syp exopolysaccharide biosynthetic operon, which underpins biofilm formation in A. fischeri (8), is present in the 5LC genome. However, in line with observations made for strains MJ11 (7) and SR5—isolated from the squid Sepiola robusta (9)—we did not find the regulatory gene rscS needed for successful squid colonization by strain ES114 (7). Several other traits encrypted in the 5LC genome serve as hallmarks of a true host-associated lifestyle. These include a vast gene repertoire underlying chemotaxis and flagellar motility, type I, II, III, IV, and VIII protein secretion systems, and bacteriocin biosynthesis potential. Future in-depth mining of the A. fischeri 5LC data will contribute to a better understanding of the extent of functional conservation versus plasticity of the species through comparative genomics.

Nucleotide sequence accession numbers.

The genome sequence of Aliivibrio fischeri strain 5LC has been deposited in the DDBJ/ENA-EBI/NCBI databases under the accession number CVOI00000000. The version described in this study is the first version, CVOI01000000, and consists of contig sequences CVOI01000001 to CVOI01000054.