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Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer Shu-Kuan Wong,a Susumu Yoshizawa,a Yu Nakajima,a Yoshitoshi Ogura,b Tetsuya Hayashi,b Koji Hamasakia Division of Marine Life Science, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japana; Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japanb
We report here the draft genome of Lewinella sp. strain 4G2, isolated from the sea surface microlayer (SML) of a coastal marine inlet. The genome sequence of strain 4G2 should contribute to understanding the lifestyles of bacteria living in the SML. Received 6 June 2016 Accepted 10 June 2016 Published 28 July 2016 Citation Wong S-K, Yoshizawa S, Nakajima Y, Ogura Y, Hayashi T, Hamasaki K. 2016. Draft genome sequence of Lewinella sp. strain 4G2 isolated from the coastal sea surface microlayer. Genome Announc 4(4):e00754-16. doi:10.1128/genomeA.00754-16. Copyright © 2016 Wong et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Shu-Kuan Wong, [email protected].
T
he sea surface microlayer (SML), defined as the topmost 1,000 m of the sea surface, has been found to possess different physicochemical and biological properties from the underlying water directly below it (1). To date, the microbiology of the SML still remains poorly understood, with only one representative SML isolate having been characterized so far (2). Here, we present the draft genome sequence of a novel strain, designated 4G2, isolated from the SML of a coastal marine inlet. Strain 4G2 was isolated from the SML of Aburatsubo Inlet, Misaki, Japan. Water samples from the SML (42-m depth) were collected using the glass plate method (3) and isolated using methods described previously (4). Genomic DNA was extracted using phenol-chloroform and ethanol precipitation (5). An 800-bp paired-end library and an 8-kb mate-pair library were prepared using the Nextera XT DNA library preparation kit (Illumina) and Nextera mate-pair sample preparation kit (Illumina), respectively; 300 bp of each end of the libraries were sequenced on the MiSeq instrument with the MiSeq Reagent kit version 3 (Illumina). A total of 870,144 mate-paired and 1,793,514 paired-end reads were assembled using Platanus version 1.2.4 (6). The sequences were annotated automatically using the NCBI PGAAP (7) and reviewed with RAST version 2.0 (http://rast.nmpdr.org). The 16S rRNA gene sequence taxonomic identification using EzTaxon (8) revealed that strain 4G2 belongs to the genus Lewinella and is most similar to Lewinella antarctica IMCC3223T (95.72%) from the family Saprospiraceae in the class Sphingobacteriia. The Lewinella sp. strain 4G2 genome sequence consisted of 21 scaffolds (5,219,850 bp in total, N50 ⫽ 4,178,312 bp) with a median read coverage of 53.0⫻. The estimated genome size (5.22 Mb) of strain 4G2 was smaller than two other draft genome sequences of Lewinella strains available in GenBank (L. persica DSM 23188, 6.67 Mb, G⫹C 53.0%; L. cohaerens DSM 23179, 7.30 Mb, G⫹C 45.0%) (9) but with a higher G⫹C content (55.3%). PGAAP identified 3,830 genes, including 3,776 protein-coding sequences (CDSs), 42 tRNAs, three noncoding RNA genes, and 28 pseudogenes. The RAST annotation also identified 3,768 CDSs. Strain 4G2 possessed 61 gene homologs responsible for DNA re-
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pair and 81 stress-response gene homologs, which are mostly involved in regulating heat shock and osmotic and oxidative stress and possibly play roles in helping the organism to cope with high radiation and temperature stresses in the SML. Interestingly, gene homologs involved in nitrate and nitrite ammonification as well as organic sulfur assimilation were present in the genome of strain 4G2 but not in the genomes of L. cohaerens and L. persica. The draft genome sequence of Lewinella sp. strain 4G2 will provide further insight into the role of the organism in the SML, as well as the physiology and mechanism that the organism employs to cope with the living conditions in the SML. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number LVWJ00000000. The version described in this paper is the second version, LVWJ02000000. FUNDING INFORMATION This work, including the efforts of Koji Hamasaki, was funded by Japan Society for the Promotion of Science (JSPS) (16H02562). This work, including the efforts of Susumu Yoshizawa, was funded by Japan Society for the Promotion of Science (JSPS) (15H02800). This work, including the efforts of Koji Hamasaki, was funded by University of Tokyo (Utokyo) (Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute).
REFERENCES 1. Cunliffe M, Engel A, Frka S, Gašparovic´ B, Guitart C, Murrell JC, Salter M, Stolle C, Upstill-Goddard R, Wurl O. 2013. Sea surface microlayers: a unified physicochemical and biological perspective of the air– ocean interface. Prog Oceanogr 109:104 –116. http://dx.doi.org/10.1016/ j.pocean.2012.08.004. 2. Glöckner FO, Babenzien HD, Amann R. 1998. Phylogeny and identification in situ of Nevskia ramosa. Appl Environ Microbiol 64:1895–1901. 3. Harvey GW, Burzell LA. 1972. A simple microlayer method for small samples. Limnol Oceanogr 17:156 –157. http://dx.doi.org/10.4319/ lo.1972.17.1.0156. 4. Wong S-K, Park S, Lee J-S, Lee KC, Chiura HX, Kogure K, Hamasaki K. 2015. Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water. Int J Syst Evol Microbiol 65:3276 –3280. http:// dx.doi.org/10.1099/ijsem.0.000405. 5. Marmur J. 1961. A procedure for the isolation of deoxyribonucleic acid
Genome Announcements
genomea.asm.org 1
Wong et al.
from micro-organisms. J Mol Biol 3:208 –218. http://dx.doi.org/10.1016/ S0022-2836(61)80047-8. 6. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T. 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24: 1384 –1395. http://dx.doi.org/10.1101/gr.170720.113. 7. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013. Prokaryotic genome annotation pipeline. The NCBI handbook, 2nd ed. NCBI, Bethesda, MD.
2 genomea.asm.org
8. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J. 2012. Introducing EzTaxon: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716 –721. http://dx.doi.org/10.1099/ ijs.0.038075-0. 9. Khan ST, Fukunaga Y, Nakagawa Y, Harayama S. 2007. Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov. Int J Syst Evol Microbiol 57:2946 –2951. http:// dx.doi.org/10.1099/ijs.0.65308-0.
Genome Announcements
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Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer Shu-Kuan Wong,a Susumu Yoshizawa,a Yu Nakajima,a Yoshitoshi Ogura,b Tetsuya Hayashi,b Koji Hamasakia Division of Marine Life Science, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japana; Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japanb
We report here the draft genome of Lewinella sp. strain 4G2, isolated from the sea surface microlayer (SML) of a coastal marine inlet. The genome sequence of strain 4G2 should contribute to understanding the lifestyles of bacteria living in the SML. Received 6 June 2016 Accepted 10 June 2016 Published 28 July 2016 Citation Wong S-K, Yoshizawa S, Nakajima Y, Ogura Y, Hayashi T, Hamasaki K. 2016. Draft genome sequence of Lewinella sp. strain 4G2 isolated from the coastal sea surface microlayer. Genome Announc 4(4):e00754-16. doi:10.1128/genomeA.00754-16. Copyright © 2016 Wong et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Shu-Kuan Wong, [email protected].
T
he sea surface microlayer (SML), defined as the topmost 1,000 m of the sea surface, has been found to possess different physicochemical and biological properties from the underlying water directly below it (1). To date, the microbiology of the SML still remains poorly understood, with only one representative SML isolate having been characterized so far (2). Here, we present the draft genome sequence of a novel strain, designated 4G2, isolated from the SML of a coastal marine inlet. Strain 4G2 was isolated from the SML of Aburatsubo Inlet, Misaki, Japan. Water samples from the SML (42-m depth) were collected using the glass plate method (3) and isolated using methods described previously (4). Genomic DNA was extracted using phenol-chloroform and ethanol precipitation (5). An 800-bp paired-end library and an 8-kb mate-pair library were prepared using the Nextera XT DNA library preparation kit (Illumina) and Nextera mate-pair sample preparation kit (Illumina), respectively; 300 bp of each end of the libraries were sequenced on the MiSeq instrument with the MiSeq Reagent kit version 3 (Illumina). A total of 870,144 mate-paired and 1,793,514 paired-end reads were assembled using Platanus version 1.2.4 (6). The sequences were annotated automatically using the NCBI PGAAP (7) and reviewed with RAST version 2.0 (http://rast.nmpdr.org). The 16S rRNA gene sequence taxonomic identification using EzTaxon (8) revealed that strain 4G2 belongs to the genus Lewinella and is most similar to Lewinella antarctica IMCC3223T (95.72%) from the family Saprospiraceae in the class Sphingobacteriia. The Lewinella sp. strain 4G2 genome sequence consisted of 21 scaffolds (5,219,850 bp in total, N50 ⫽ 4,178,312 bp) with a median read coverage of 53.0⫻. The estimated genome size (5.22 Mb) of strain 4G2 was smaller than two other draft genome sequences of Lewinella strains available in GenBank (L. persica DSM 23188, 6.67 Mb, G⫹C 53.0%; L. cohaerens DSM 23179, 7.30 Mb, G⫹C 45.0%) (9) but with a higher G⫹C content (55.3%). PGAAP identified 3,830 genes, including 3,776 protein-coding sequences (CDSs), 42 tRNAs, three noncoding RNA genes, and 28 pseudogenes. The RAST annotation also identified 3,768 CDSs. Strain 4G2 possessed 61 gene homologs responsible for DNA re-
July/August 2016 Volume 4 Issue 4 e00754-16
pair and 81 stress-response gene homologs, which are mostly involved in regulating heat shock and osmotic and oxidative stress and possibly play roles in helping the organism to cope with high radiation and temperature stresses in the SML. Interestingly, gene homologs involved in nitrate and nitrite ammonification as well as organic sulfur assimilation were present in the genome of strain 4G2 but not in the genomes of L. cohaerens and L. persica. The draft genome sequence of Lewinella sp. strain 4G2 will provide further insight into the role of the organism in the SML, as well as the physiology and mechanism that the organism employs to cope with the living conditions in the SML. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number LVWJ00000000. The version described in this paper is the second version, LVWJ02000000. FUNDING INFORMATION This work, including the efforts of Koji Hamasaki, was funded by Japan Society for the Promotion of Science (JSPS) (16H02562). This work, including the efforts of Susumu Yoshizawa, was funded by Japan Society for the Promotion of Science (JSPS) (15H02800). This work, including the efforts of Koji Hamasaki, was funded by University of Tokyo (Utokyo) (Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute).
REFERENCES 1. Cunliffe M, Engel A, Frka S, Gašparovic´ B, Guitart C, Murrell JC, Salter M, Stolle C, Upstill-Goddard R, Wurl O. 2013. Sea surface microlayers: a unified physicochemical and biological perspective of the air– ocean interface. Prog Oceanogr 109:104 –116. http://dx.doi.org/10.1016/ j.pocean.2012.08.004. 2. Glöckner FO, Babenzien HD, Amann R. 1998. Phylogeny and identification in situ of Nevskia ramosa. Appl Environ Microbiol 64:1895–1901. 3. Harvey GW, Burzell LA. 1972. A simple microlayer method for small samples. Limnol Oceanogr 17:156 –157. http://dx.doi.org/10.4319/ lo.1972.17.1.0156. 4. Wong S-K, Park S, Lee J-S, Lee KC, Chiura HX, Kogure K, Hamasaki K. 2015. Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water. Int J Syst Evol Microbiol 65:3276 –3280. http:// dx.doi.org/10.1099/ijsem.0.000405. 5. Marmur J. 1961. A procedure for the isolation of deoxyribonucleic acid
Genome Announcements
genomea.asm.org 1
Wong et al.
from micro-organisms. J Mol Biol 3:208 –218. http://dx.doi.org/10.1016/ S0022-2836(61)80047-8. 6. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T. 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24: 1384 –1395. http://dx.doi.org/10.1101/gr.170720.113. 7. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013. Prokaryotic genome annotation pipeline. The NCBI handbook, 2nd ed. NCBI, Bethesda, MD.
2 genomea.asm.org
8. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J. 2012. Introducing EzTaxon: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716 –721. http://dx.doi.org/10.1099/ ijs.0.038075-0. 9. Khan ST, Fukunaga Y, Nakagawa Y, Harayama S. 2007. Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov. Int J Syst Evol Microbiol 57:2946 –2951. http:// dx.doi.org/10.1099/ijs.0.65308-0.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00754-16
