Abstract
Four Psychrobacter strains, JCM 18900, JCM 18901, JCM 18902, and JCM 18903, related to either Psychrobacter nivimaris or Psychrobacter cibarius, were isolated from frozen marine animals. The genome information of these four strains will be useful for studies of their physiology and adaptation properties to frozen conditions.
GENOME ANNOUNCEMENT
The genus Psychrobacter comprises Gram-negative, psychrotolerant, aerobic, and nonmotile bacteria (1). They are able to grow at 5°C. They are halotolerant and grow in the presence of ≥6.5% NaCl. Psychrobacter species have been isolated from various cold habitats (1).
We found that Psychrobacter strains related to Psychrobacter nivimaris (2) and Psychrobacter cibarius (3) were preferentially isolated from various frozen marine animals, such as the finless porpoise Neophocaena phocaenoides, the scavenging gastropod Nassarius (Alectrion) glans, the silver jewfish Pennahia argentata, and the skipjack tuna Katsuwonus pelamis. Psychrobacter strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903 (originally described as strains B120, B216, B295, and B296, respectively) were isolated from intestinal samples of the frozen finless porpoise N. phocaenoides and stored for approximately 1 year at −20°C.
The genomes of Psychrobacter strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903 were sequenced using an Ion Torrent PGM system. The sequence reads of 769,319 for JCM 18900, 537,775 for JCM 18901, 610,006 for JCM 18902, and 643,259 for JCM 18903 were assembled using Newbler version 2.8 (Roche) into 35, 58, 33, and 56 contigs with N50 lengths of 249,741, 117,508, 264,897, and 162,339 bp, respectively. These assemblies resulted in draft genome sequences of 3,272,645 bp for JCM 18900, 3,145,827 bp for JCM 18901, 3,274,327 bp for JCM 18902, and 3,427,960 bp for JCM 18903, with 51×, 38×, 36×, and 36× redundancies and G+C contents of 42.7, 42.7, 42.9, and 42.7%, respectively. A total of 2,893, 2,875, 2,798, and 3,004 protein-coding genes and 40, 44, 45, and 45 RNA-coding sequences for JCM 18900, JCM 18901, JCM 18902, and JCM 18903, respectively, were identified using the RAST server (4).
Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains JCM 18900 and JCM 18901 are closely related to the type strain of P. nivimaris (sequence identity, 99%), while strains JCM 18902 and JCM 18903 are closely related to the type strain of P. cibarius (sequence identity, 100%). These four strains possess genes for a wax ester synthase, production of capsular type extracellular polymeric substances, and three cold shock proteins, which are important factors for adaptation to the cold (5). The genome information of these four strains will be useful for studies of their physiology and adaptation properties to frozen conditions.
Nucleotide sequence accession numbers.
The genome sequences of Psychrobacter strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903 have been deposited at DDBJ/EMBL/GenBank under accession no. BAWG01000001 to BAWG01000035, BAWH01000001 to BAWH01000058, BAWI01000001 to BAWI01000033, and BAWJ01000001 to BAWJ01000056, respectively.
ACKNOWLEDGMENTS
This work was supported by the Genome Information Upgrading Program of the National BioResource Project from the Ministry of Education, Culture, Sports, Science and Technology of Japan to M.O. and M.H., and in part by a Grant-in-Aid for Scientific Research (C) from the Japan Society for the Promotion of Science (21580098) to T.K.
We thank Hiromi Kuroyanagi (the University of Tokyo) for technical support.
Footnotes
Citation Kudo T, Kidera A, Kida M, Kawauchi A, Shimizu R, Nakahara T, Zhang X, Yamada A, Amano M, Hamada Y, Taniyama S, Arakawa O, Yoshida A, Oshima K, Suda W, Kuwahara H, Nogi Y, Kitamura K, Yuki M, Iida T, Moriya S, Inoue T, Hongoh Y, Hattori M, Ohkuma M. 2014. Draft genome sequences of Psychrobacter strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903, isolated preferentially from frozen aquatic organisms. Genome Announc. 2(2):e00280-14. doi:10.1128/genomeA.00280-14.
REFERENCES
- 1. Juni E. 2005. Genus III. Psychrobacter, p 437–441 In Brenner DJ, Krieg NR, Staley JR. (ed), Bergey’s manual of systematic bacteriology, vol 2, 2nd ed. Springer Verlag, New York, NY. [Google Scholar]
- 2. Heuchert A, Glöckner FO, Amann R, Fischer U. 2004. Psychrobacter nivimaris sp. nov., a heterotrophic bacterium attached to organic particles isolated from the South Atlantic (Antarctica). Syst. Appl. Microbiol. 27:399–406. 10.1078/0723202041438455 [DOI] [PubMed] [Google Scholar]
- 3. Jung SY, Lee MH, Oh TK, Park YH, Yoon JH. 2005. Psychrobacter cibarius sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 55:577–582. 10.1099/ijs.0.63398-0 [DOI] [PubMed] [Google Scholar]
- 4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Ayala-del-Río HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, Murray A, Thomashow M, Tiedje JM. 2010. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl. Environ. Microbiol. 76:2304–2312. 10.1128/AEM.02101-09 [DOI] [PMC free article] [PubMed] [Google Scholar]