ABSTRACT
The draft genome sequences of 5 type strains of species of the halophilic genus Salinivibrio and 29 new isolates from different hypersaline habitats belonging to the genus Salinivibrio have been determined. The genomes have 3,123,148 to 3,641,359 bp, a G+C content of 49.2 to 50.9%, and 2,898 to 3,404 open reading frames (ORFs).
GENOME ANNOUNCEMENT
The genus Salinivibrio, within the class Gammaproteobacteria, family Vibrionaceae, currently includes four species, one of them with three subspecies. Members of this genus are moderately halophilic bacteria, growing in the presence of 0 to 25% NaCl, and inhabit salted meats, brines, and hypersaline environments (saline lakes and salterns) (1–6). The members of the genus Salinivibrio grow optimally at ca. 7.5% NaCl, 37°C (range, 17 to 55°C), and pH 7.5 (range, pH 5 to 11). Therefore, they have developed cellular mechanisms to thrive under extreme conditions, such as high salt concentrations, alkaline pH values, UV radiation, or the presence of arsenic and other metals (3, 7, 8). Salinivibrio costicola subsp. costicola is considered a representative model for studies on moderately halophilic bacteria, and it has been used for osmoregulation and other physiological studies (9, 10). The genome of this bacterium, as well as those of Salinivibrio spp. S10B, S34, and S35, have already been published (8, 11); here, we report the draft genome sequences of the other species or subspecies of this genus, as well as of 29 new strains isolated from pond water of different salterns located in Spain and Puerto Rico (Table 1).
TABLE 1 .
Features of the 34 draft genomes of Salinivibrio strains sequenced
| Strain | Place of isolation | Genome size (bp) | N50 (bp) | No. of contigs | Sequencing depth (×) | % G+C | No. of ORFs | Sequencing technology | DDBJ/ENA/GenBank accession no. |
|---|---|---|---|---|---|---|---|---|---|
| S. costicola subsp. alcaliphilus DSM 19052 | Campania, Italy | 3,326,316 | 74,560 | 104 | 74 | 49.3 | 3,114 | Illumina HiSeq | MUFR00000000 |
| S. costicola subsp. vallismortis DSM 8285 | Death Valley, USA | 3,478,614 | 196,230 | 44 | 83 | 49.7 | 3,218 | Illumina HiSeq | MUFQ00000000 |
| S. proteolyticus DSM 19052 | Bakhtegan Lake, Iran | 3,603,496 | 143,067 | 51 | 11 | 49.8 | 3,338 | Illumina MiSeq | MUFP00000000 |
| S. sharmensis DSM 18182 | Ras Mohammed Park, Egypt | 3,326,895 | 229,272 | 40 | 35 | 50.4 | 3,028 | Illumina MiSeq | MUFC00000000 |
| S. siamensis JCM 14472 | Nakornnayok, Thailand | 3,442,185 | 114,651 | 61 | 17 | 50.3 | 3,126 | Illumina MiSeq | MUFB00000000 |
| Salinivibrio sp. AL184 | Santa Pola, Alicante, Spain | 3,398,626 | 198,024 | 42 | 100 | 50.3 | 3,132 | Illumina HiSeq | MUEK00000000 |
| Salinivibrio sp. AR640 | Aragonesas, Huelva, Spain | 3,256,021 | 87,861 | 60 | 31 | 49.3 | 2,962 | Illumina MiSeq | MUFD00000000 |
| Salinivibrio sp. AR647 | Aragonesas, Huelva, Spain | 3,281,043 | 311,807 | 22 | 22 | 49.3 | 3,002 | Illumina MiSeq | MUFE00000000 |
| Salinivibrio sp. IB282 | Isla Bacuta, Huelva, Spain | 3,226,186 | 40,759 | 157 | 11 | 50.7 | 3,021 | Illumina MiSeq | MUET00000000 |
| Salinivibrio sp. IB560 | Isla Bacuta, Huelva, Spain | 3,492,326 | 111,814 | 65 | 28 | 50.5 | 3,194 | Illumina MiSeq | MUEM00000000 |
| Salinivibrio sp. IB563 | Isla Bacuta, Huelva, Spain | 3,483,818 | 42,363 | 173 | 16 | 50.5 | 3,276 | Illumina MiSeq | MUEN00000000 |
| Salinivibrio sp. IB574 | Isla Bacuta, Huelva, Spain | 3,612,537 | 106,472 | 69 | 9 | 49.8 | 3,385 | Illumina MiSeq | MUFN00000000 |
| Salinivibrio sp. IB643 | Isla Bacuta, Huelva, Spain | 3,123,148 | 79,381 | 91 | 20 | 49.4 | 2,898 | Illumina MiSeq | MUFF00000000 |
| Salinivibrio sp. IB868 | Isla Bacuta, Huelva, Spain | 3,440,756 | 206,501 | 30 | 29 | 50.5 | 3,112 | Illumina MiSeq | MUEW00000000 |
| Salinivibrio sp. IB870 | Isla Bacuta, Huelva, Spain | 3,437,860 | 138,190 | 42 | 26 | 50.5 | 3,104 | Illumina MiSeq | MUEX00000000 |
| Salinivibrio sp. IB872 | Isla Bacuta, Huelva, Spain | 3,641,359 | 82,702 | 102 | 11 | 49.8 | 3,398 | Illumina MiSeq | MUFO00000000 |
| Salinivibrio sp. IC202 | Isla Cristina, Huelva, Spain | 3,608,911 | 72,723 | 111 | 25 | 50.5 | 3,404 | Illumina MiSeq | MUEO00000000 |
| Salinivibrio sp. IC317 | Isla Cristina, Huelva, Spain | 3,278,261 | 21,208 | 236 | 8 | 50.9 | 3,116 | Illumina MiSeq | MUEP00000000 |
| Salinivibrio sp. MA351 | La Malahá, Granada, Spain | 3,308,854 | 95,545 | 59 | 25 | 49.3 | 3,000 | Illumina MiSeq | MUFG00000000 |
| Salinivibrio sp. MA421 | La Malahá, Granada, Spain | 3,535,899 | 94,274 | 70 | 26 | 50.4 | 3,251 | Illumina MiSeq | MUER00000000 |
| Salinivibrio sp. MA427 | La Malahá, Granada, Spain | 3,263,514 | 9,975 | 513 | 7 | 49.3 | 3,296 | Illumina MiSeq | MUFH00000000 |
| Salinivibrio sp. MA440 | La Malahá, Granada, Spain | 3,421,552 | 59,971 | 102 | 35 | 49.5 | 3,107 | Illumina MiSeq | MUFI00000000 |
| Salinivibrio sp. MA607 | La Malahá, Granada, Spain | 3,352,168 | 87,592 | 68 | 26 | 49.2 | 3,043 | Illumina MiSeq | MUFJ00000000 |
| Salinivibrio sp. ML198 | Es Trenc, Mallorca, Spain | 3,433,707 | 163,752 | 44 | 24 | 50.4 | 3,134 | Illumina HiSeq | MUEZ00000000 |
| Salinivibrio sp. ML277 | Es Trenc, Mallorca, Spain | 3,446,273 | 117,752 | 73 | 31 | 50.4 | 3,146 | Illumina MiSeq | MUEL00000000 |
| Salinivibrio sp. ML290 | Es Trenc, Mallorca, Spain | 3,523,661 | 168,056 | 36 | 15 | 50.2 | 3,224 | Illumina MiSeq | MUEY00000000 |
| Salinivibrio sp. ML318 | Es Trenc, Mallorca, Spain | 3,361,480 | 65,785 | 96 | 14 | 50.7 | 3,080 | Illumina MiSeq | MUEQ00000000 |
| Salinivibrio sp. ML323 | Es Trenc, Mallorca, Spain | 3,233,876 | 132,870 | 63 | 16 | 50.8 | 2,960 | Illumina MiSeq | MUES00000000 |
| Salinivibrio sp. ML328A | Es Trenc, Mallorca, Spain | 3,392,891 | 172,729 | 38 | 55 | 50.5 | 3,124 | Illumina HiSeq | MUEU00000000 |
| Salinivibrio sp. ML331 | Es Trenc, Mallorca, Spain | 3,545,121 | 128,351 | 60 | 86 | 50.4 | 3,262 | Illumina HiSeq | MUEV00000000 |
| Salinivibrio sp. PR5 | Cabo Rojo, Puerto Rico | 3,456,024 | 68,288 | 105 | 23 | 49.9 | 3,141 | Illumina MiSeq | MUFK00000000 |
| Salinivibrio sp. PR6 | Cabo Rojo, Puerto Rico | 3,443,918 | 165,099 | 49 | 28 | 50.4 | 3,140 | Illumina MiSeq | MUFA00000000 |
| Salinivibrio sp. PR919 | Cabo Rojo, Puerto Rico | 3,489,646 | 33,984 | 176 | 14 | 49.9 | 3,269 | Illumina MiSeq | MUFL00000000 |
| Salinivibrio sp. PR932 | Cabo Rojo, Puerto Rico | 3,497,261 | 90,599 | 74 | 31 | 49.9 | 3,171 | Illumina MiSeq | MUFM00000000 |
The draft genome sequences of the 34 strains were determined using a whole-genome shotgun strategy (12) with two Illumina sequencing systems, Illumina MiSeq (2 × 300-bp paired-end reads) (Swansea University, United Kingdom) and Illumina HiSeq (2 × 100-bp paired-end reads) (Macrogen, South Korea). The sequencing depth ranged between 7- and 100-fold coverage of the entire genome, and the resulting genome assemblies possessed N50 values between 9,975 and 311,807 bp. All reads were assembled in a range of 22 to 513 contigs (≥1,000 bp) using A5-MiSeq (13) and were used to identify open reading frames (ORFs) and provide a functional annotation of predicted proteins, rRNAs, and tRNA genes. Genome annotation was performed using RAST (14).
The draft genomes were estimated to contain between 3,123,148 and 3,641,359 bp, with a G+C content between 49.2 and 50.9% and a range of 2,898 to 3,404 putative ORFs (Table 1).
Genes involved in osmoregulation mechanisms included ectoine and hydroxyectoine synthesis genes, transporters for betaine, and other compatible solutes, like proline and choline. A complete set of genes encoding RecBCD helicase/nuclease and UvrABC endonuclease holoenzymes were found; these genes are involved in the recombinational repair of DNA double-strand breaks. Enzyme-encoding genes involved in anaerobic respiration were found, such as arsenate reductase (asrR) and flavodoxin reductase (FIR). These halophilic bacteria are widely isolated from aquatic hypersaline environments and salted food products. Thus, the availability of their genome sequences, combined with other physiological and biochemical data, will advance our understanding of haloadaptation and other stress defense mechanisms of halophilic bacteria to extreme conditions.
Accession number(s).
The draft genome sequences of the 34 strains of Salinivibrio have been deposited in DDBJ/ENA/GenBank with accession numbers listed in Table 1.
ACKNOWLEDGMENTS
This work was funded by the Spanish Ministry of Science and Innovation (grant CGL2013-46941-P), with FEDER funds (to A. Ventosa) and wgs-aqua.net project funded by BBSRC/NERC as part of the sustainable aquaculture call (BB/Mo26388/1) (to E. Feil). C. López-Hermoso was the recipient of a postgraduate fellowship from the Spanish Ministry of Education, Culture and Sports.
Footnotes
Citation López-Hermoso C, de la Haba RR, Sánchez-Porro C, Bayliss SC, Feil EJ, Ventosa A. 2017. Draft genome sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 new isolates belonging to the genus Salinivibrio. Genome Announc 5:e00244-17. https://doi.org/10.1128/genomeA.00244-17.
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