Complete Genome Sequence of  Alteromonas  sp. Strain I4, Isolated from the Japan Sea

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Abstract

A novel strain of Alteromonas, I4, was isolated from a shallow beach of the Japan Sea. Here, we report the complete genome sequence of I4; this strain contains a single circular chromosome (5,133,645 bp; G+C content, 48.4%) and a single circular putative plasmid (123,836 bp; G+C content, 45.1%).

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DFAST and DAGA: web-based integrated genome annotation tools and resources

Yasuhiro Tanizawa, Takatomo Fujisawa, Eli Kaminuma … (2016)

Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus, obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii, whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.

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Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations.

Paul P. G. Gauthier, R Christen, Gregory M. Gauthier (1995)

Small-subunit ribosomal DNA sequences were determined for 17 strains belonging to the genera Alteromonas, Shewanella, Vibrio, and Pseudomonas, and these sequences were analyzed by phylogenetic methods. The resulting data confirmed the existence of the genera Shewanella and Moritella, but suggested that the genus Alteromonas should be split into two genera. We propose that a new genus, the genus Pseudoalteromonas, should be created to accommodate 11 species that were previously Alteromonas species, including Pseudoalteromonas atlantica comb. nov., Pseudoalteromonas aurantia comb. nov., Pseudoalteromonas carrageenovoa comb. nov., Pseudoalteromonas citrea comb. nov., Pseudoalteromonas denitrificans comb. nov., Pseudoalteromonas espejiana comb. nov., Pseudoalteromonas haloplanktis comb. nov. (with two subspecies, Pseudoalteromonas haloplanktis subsp. haloplanktis comb. nov. and Pseudoalteromonas haloplanktis subsp. tetraodonis comb. nov.), Pseudoalteromonas luteoviolacea comb. nov., Pseudoalteromonas nigrifaciens comb. nov., Pseudoalteromonas rubra comb. nov., and Pseudoalteromonas undina comb, nov., and one species that previously was placed in the genus Pseudomonas, Pseudoalteromonas piscicida comb. nov. We propose that P. haloplanktis (type strain, ATCC 14393) should be the type species of the genus Pseudoalteromonas. At this time the emended genus Alteromonas is restricted to a single species, Alteromonas macleodii.

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Taxonomy of aerobic marine eubacteria.

Ellen M. Mandel, P. Baumann, Adrian Allen … (1972)

Two hundred and eighteen strains of nonfermentative marine bacteria were submitted to an extensive morphological, physiological, and nutritional characterization. All the strains were gram-negative, straight or curved rods which were motile by means of polar or peritrichous flagella. A wide variety of organic substrates served as sole sources of carbon and energy. The strains differed extensively in their nutritional versatility, being able to utilize from 11 to 85 carbon compounds. Some strains had an extracellular amylase, gelatinase, lipase, or chitinase and were able to utilize n-hexadecane and to denitrify. None of the strains had a yellow, cell-associated pigment or a constitutive arginine dihydrolase system, nor were they able to hydrolyze cellulose or agar. The results of the physiological and nutritional characterization were submitted to a numerical analysis which clustered the strains into 22 groups on the basis of phenotypic similarities. The majority of these groups were separable by a large number of unrelated phenotypic traits. Analysis of the moles per cent guanine plus cytosine (GC) content in the deoxyribonucleic acid of representative strains indicated that the peritrichously flagellated groups had a GC content of 53.7 to 67.8 moles%; polarly flagellated strains had a GC content of 30.5 to 64.7 moles%. The peritrichously flagellated groups were assigned to the genus Alcaligenes. The polarly flagellated groups, which had a GC content of 43.2 to 48.0 moles%, were placed into a newly created genus, Alteromonas; groups which had a GC content of 57.8 to 64.7 moles% were placed into the genus Pseudomonas; and the remaining groups were left unassigned. Twelve groups were given the following designations: Alteromonas communis, A. vaga, A. macleodii, A. marinopraesens, Pseudomonas doudoroffi, P. marina, P. nautica, Alcaligenes pacificus, A. cupidus, A. venustus, and A. aestus. The problems of assigning species of aerobic marine bacteria to genera are discussed.

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Contributors

J. Cameron Thrash: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (hwp): ga

Journal ID (pmc): mra

Journal ID (publisher-id): MRA

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic): 21 November 2019

Publication date Collection: November 2019

Volume: 8

Issue: 47

Electronic Location Identifier: e01277-19

Affiliations

[a ]Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan

[b ]Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

[c ]Faculty of Life Sciences, Toyo University, Itakura, Gunma, Japan

University of Southern California

Author notes

Address correspondence to Kentaro Miyazaki, miyazaki-kentaro@ 123456aist.go.jp .

Citation Miyazaki K, Izumi K. 2019. Complete genome sequence of Alteromonas sp. strain I4, isolated from the Japan Sea. Microbiol Resour Announc 8:e01277-19. https://doi.org/10.1128/MRA.01277-19.

Author information

Kentaro Miyazaki https://orcid.org/0000-0002-4349-566X

Article

Publisher ID: MRA01277-19

DOI: 10.1128/MRA.01277-19

PMC ID: 6872891

PubMed ID: 31753949

SO-VID: d2dc3ef3-841c-4d9e-b19d-9555476a145e

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 10 October 2019

Date accepted : 1 November 2019

Page count

Figures: 0, Tables: 0, Equations: 0, References: 11, Pages: 2, Words: 1257

Funding

Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), https://doi.org/10.13039/501100001691;

Award ID: 19H00936

Award Recipient : Kentaro Miyazaki

Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), https://doi.org/10.13039/501100001691;

Award ID: 19H05538

Award Recipient : Kentaro Miyazaki

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cover-date November 2019

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Complete Genome Sequence of Alteromonas sp. Strain I4, Isolated from the Japan Sea

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DFAST and DAGA: web-based integrated genome annotation tools and resources

Phylogenetic analysis of the genera Alteromonas, Shewanella, and Moritella using genes coding for small-subunit rRNA sequences and division of the genus Alteromonas into two genera, Alteromonas (emended) and Pseudoalteromonas gen. nov., and proposal of twelve new species combinations.

Taxonomy of aerobic marine eubacteria.

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