Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments
Mami Tanaka
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
Search for more papers by this authorDaiki Kumakura
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
Search for more papers by this authorSayaka Mino
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
Search for more papers by this authorHidetaka Doi
R&D Strategic Group, R&D Planning Department, Ajinomoto Co., Inc., Tokyo, Japan
Search for more papers by this authorYoshitoshi Ogura
Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
Search for more papers by this authorTetsuya Hayashi
Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
Search for more papers by this authorIsao Yumoto
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
Search for more papers by this authorMan Cai
China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
Search for more papers by this authorYu-Guang Zhou
China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
Search for more papers by this authorBruno Gomez-Gil
CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, Sinaloa, AP 711 Mexico
Search for more papers by this authorToshiyoshi Araki
Iga Community-based Research Institute, Mie University, Iga, Japan
Search for more papers by this authorCorresponding Author
Tomoo Sawabe
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
For correspondence. E-mail [email protected]; Tel. +81-138-40-5569; Fax +81-138-40-5569.Search for more papers by this authorMami Tanaka
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
Search for more papers by this authorDaiki Kumakura
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
Search for more papers by this authorSayaka Mino
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
Search for more papers by this authorHidetaka Doi
R&D Strategic Group, R&D Planning Department, Ajinomoto Co., Inc., Tokyo, Japan
Search for more papers by this authorYoshitoshi Ogura
Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
Search for more papers by this authorTetsuya Hayashi
Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
Search for more papers by this authorIsao Yumoto
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
Search for more papers by this authorMan Cai
China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
Search for more papers by this authorYu-Guang Zhou
China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
Search for more papers by this authorBruno Gomez-Gil
CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, Sinaloa, AP 711 Mexico
Search for more papers by this authorToshiyoshi Araki
Iga Community-based Research Institute, Mie University, Iga, Japan
Search for more papers by this authorCorresponding Author
Tomoo Sawabe
Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Hakodate, Japan
For correspondence. E-mail [email protected]; Tel. +81-138-40-5569; Fax +81-138-40-5569.Search for more papers by this authorSummary
Members of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non-marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non-marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species-specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.
Supporting Information
| Filename | Description |
|---|---|
| emi15062-sup-0001-supinfo.fastaPDF document, 7.3 MB | Appendix S1: Supporting information |
| emi15062-sup-0001-Tables.xlsxExcel 2007 spreadsheet , 35.3 KB | Table S1 List of insertion sequences identified in the genome of the Rumoiensis clade species Table S2 List of integrons identified in the genome of the Rumoiensis clade species Table S3 List of genomes used in this study Table S4 List of genes related to compatible solute metabolism in Vibrio aphrogenes Table S5 Differentially expressed genes in salt-shifting with/without nitrogen depletion in Vibrio aphrogenes |
| emi15062-sup-0001-Figures.pdfPDF document, 1,002.1 KB | Fig. S1 Genome size and G+C content comparison of the family Vibrionaceae. Each circle represents genome size and G+C content from a genome from each species. Genomes included are listed in Table S1. Paraphotobacterium marinum (Huang et al., 2017) possessed the smallest genome among the cultured members of the family, and Vibrio aphrogenes possessed the smallest genome among the members of the genus Vibrio. Fig. S2 The genomic region containing genes related to algal carbohydrate utilization in Vibrio algivorus. (a) The genomic region containing genes related to algal carbohydrate utilization in V. algivorus. Percentage in the parentheses represents the amino acid identity against the corresponding gene of Pseudoalteromonas atlanticaT6c (Lee et al., 2014; Lee et al., 2016). (b) The genomic region containing genes related to alginate degradation in Vibrio algivorus, V. aphrogenes, and V. litoralis. Fig. S3 The genomic region containing hydrogenase genes in Vibrio aphrogenes. (a) Comparison of formate hydrogen lyase (FHL) gene clusters from Vibrio aphrogenes, Escherichia coli K-12, and four hydrogen producing Vibrio species. Double slash in V. aerogenes represents that the two regions are not continuous. (b) Comparison of the Group 1b [NiFe] hydrogenase gene clusters in three Vibrio species with representative organisms possessing the same type of hydrogenase. Fig. S4 Comparison of genomic loci containing iRon Uptake/SiderophoreTransport Island (RUSTI) (Bonham et al., 2017) in Vibrio casei DSM 22364T and the reference strain JB196. Fig. S5 Comparison of flagellar gene cluster of Vibrio casei and lateral flagellar gene cluster of V. parahaemolyticus RIMD 2210633. Fig. S6 Putative plasmid of Vibrio rumoiensis containing high-activity catalase gene (Ichise et al., 1999). Inner to outer ring represents (1) genes on forward strand (2) genes on reverse strand (3) G+C content (4) GC skew. Genes are coloured based on the COG category assignment, with colours in correspondence with Fig. 5. Fig. S7 The genomic organization of the genes related to glucosylglycerate metabolism in the Rumoiensis clade species and glucosylglycerate accumulating organisms. gpgS, glucosyl 3-phosphoglycerate synthase; gpgP, glucosyl 3-phosphoglycerate phosphatase; ggaP, glucosylglycerate phosphorylase; ggs, glucosylglycerate synthase; gK, putative glycerate kinase/dehydrogenase. Fig. S8 Transcriptome analysis of osmoregulation-related genes in V. aphrogenes. Details of the genes are listed in Table S4. The parenthesis after the gene names represents gene ID. N+, control (1.0 g NH4Cl/L); N-, nitrogen limited condition (0.2 g NH4Cl/L). (a) CPM (counts per million) values of the three genes related to glucosylglycerate metabolism. (b) Overview of the gene expression for genes related to compatible solute metabolism based on the CPM values. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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