Vibrio natriegens

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1. Classification

a. Higher order taxa

Higher order taxa: Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae

Species: Vibrio natriegens

2. Description and significance

Vibrio is a genus of bacillus shaped, Gram-negative, facultatively aerobic, halophilic bacteria (1). Vibrio natriegens, specifically requires 1.5% NaCl concentration for growth (1), and is both oxidase-positive and catalase-positive (2). Like other members of the Vibrio genus, V. natriegens is cold-sensitive owing to impaired ability to detoxify reactive oxygen species at temperatures around 4 ℃ (3). Owing to this phenomena, for refrigerated storage, catalase must be supplemented into V. natriegens cultures to prevent the bacteria from being harmed by hydrogen peroxide present in agar medium (3). Vibrio species inhabit aquatic environments, primarily salt-water; however Vibrio species are also detected in tissues and organs of various marine algae and animals (4). Some Vibrio species have been found to have synergistic effects with organisms with which they interact such as how some Vibrio biofilms promote the survival of marine microorganisms like zooplankton, especially during starvation and in coping with global climate changes (4). However, other Vibrio species are the causative agents of diseases. One well-known Vibrio species, Vibrio cholerae, causes cholera, which continues to cause death in countries that have poor sanitation of food and water (5). V. natriegens has gained widespread attention due to it having the fastest growth rate of any known organism with a reported doubling time of less than 10 minutes (6). This rapid doubling has led to some scientists advocating that V. natriegens replace E. coli as the standard model bacteria used in experiments in molecular biology and genetics as it would increase the speed with which experiments could be carried out (3). Additionally, the fast growth rate of V. natriegens interests scientists as a means of understanding the rapid growth rates of other Vibrio species, which scientists theorize contributes to the virulence of pathogenic Vibrio species (7). Although scientists have begun to uncover some genetic characteristics that likely contribute to the rapid growth of V. natriegens such as increased rRNA promoter activity (7), much remains unknown about what makes this bacterium capable of such short doubling times. Particularly, the fact that the V. natriegens genome is 0.5 Mb larger than the genome of E. coli yet is still capable of its rapid rate of division has yet to be fully explained (8).

3. Genome structure

The genome size of V. natriegens is 5,131,685 bp in length and contains a total of 4,587 open reading frames (9). Like many other species in the Vibrio genus, the genome of V. natriegens consists of two chromosomes (10).The larger chromosome, referred to as chromosome I, is 3,202,568 bp in length, has a G/C content of 43.7%, and is comprised of 86.1% coding sequences including around 103 tRNAs and 11 rRNA operons (9). The smaller chromosome, referred to as chromosome II, is only 1,929,117 bp in length, has a G/C content of 42.1%, is comprised of 85.2% coding sequences, and has only 1 rRNA operon and approximately 21 tRNAs (9). The richness of rRNA operons and tRNAs in the V. natriegens genome relative to other bacteria is important to note, as it is widely thought that these factors contribute to the fast generation time of V. natriegens (7). In total, the genome contains seven insertion sites but entirely lacks retrons (9). The asymmetry in terms of size and distribution of key genes for metabolism (including the rRNA operons and tRNAs) between the two chromosomes and the mere fact that the smaller chromosome has been integrated into the larger chromosome has caused researchers to theorize that the smaller chromosome in Vibrio species may have arose as mega plasmid that has a highly specialized role that, through selective pressures, prevented its recombination into the larger chromosome (10). Some researchers suggest the two chromosome structure allows for faster DNA replication, which facilitates the rapid doubling time observed in V. natriegens and other members of the Vibrio genus (11). Another theory is that aberrant segregation of these two chromosomes will lead to one cell that is unable to divide but would still be metabolically active (10). These nonculturable Vibrio bacteria have been observed in biofilms of the related species Vibrio cholerae, and are thought to serve a role in promoting the survival of the bacteria in the biofilm by secreting molecules such as degradative enzymes without competing for nutrients (12).

4. Cell structure

V. natriegens is a Gram-negative bacteria, meaning the bacterium has an outer membrane with outward facing lipopolysaccharides and inward-facing lipoproteins, a periplasm containing a thin peptidoglycan layer, and an inner membrane composed of phospholipids (13). The bacterium is classified as a bacillus (rod-shaped) and has been observed to often have one or occasionally two polar flagella that are enclosed in a sheath that is continuous with the outer membrane (13). V. natriegens have also been reported to produce poly-𝛽-hydroxybutyrate (PHB) granules (14), which are complex organelles at which the biopolymer poly-𝛽-hydroxybutyrate is simultaneously synthesized and degraded (15). The poly-𝛽-hydroxybutyrate contained within PHB granules are thought to serve as a source of carbon to be used when a suitable carbon source is unavailable (15).

5. Metabolic processes

V. natriegens is a facultative anaerobe and thus is able to produce ATP via aerobic respiration in the process and is likewise able to perform fermentation and anaerobic respiration in the absence of oxygen (13). Under anaerobic conditions, V. natriegens has also been shown to be capable of nitrogen fixation (16). This bacterium is an extremely versatile chemorganoheteroph as it has been shown that V. natriegens can use a wide range of common organic molecules as its sole source of carbon and energy (13). A few but not all of these carbon sources include cellobiose, ethanol, sodium acetate, sodium butyrate, and sodium citrate (13). Additionally, V. natriegens is a halophilic (salt-loving) bacterium that requires approximately the presence of 1.5% NaCl for optimal growth (1). A recent study performing 13C metabolic flux analysis has indicated that the core metabolic processes of V. natriegens includes glycolysis, the pentose phosphate pathway, the Entner-Doudoroff pathway, the TCA cycle, glyoxylate shunt, and various anaplerotic and cataplerotic reactions (17). Also, it has been shown that V. natriegens follows the same amino acid biosynthesis pathways as organism E. coli (17). The high metabolic similarity shared between E.coli and V. natriegens has been encouraging to scientists that have been calling for V. natriegens to replace the comparably slow growing E. coli as the main organism to be used in biotechnology and molecular biology research (17).

6. Ecology

V. natriegens is found primarily in coastal seawater and sediments such as the salty marsh mud from which it was originally discovered (16). While relatively little has been studied about the ecological role of V. natriegens, it has been shown that V. natriegens is capable of nitrogen fixation and will readily produce a large amount of nitrogen when placed in a nitrogen depleted environment in the absence of oxygen (16). This capacity for nitrogen fixation, suggests that V. natriegens may play a role in replenishing nitrogen levels to the marine and estuary environments in which it resides. Additionally, many vibrio species including V. natriegens have been found to contain genes encoding for indole-3-acetic acid, which is a phytohormone that induce a variety of developmental processes in plants, suggesting that V. natriegens and other closely related Vibrio species may have close relationship with the marine and estuary plants (18).

7. Pathology

Unlike many well-characterized members of the Vibrio genus, such as Vibrio cholerae, V. natriegens is non-pathogenic to humans (3). However, studies indicate that V. natriegens is pathogenic to a handful of marine animals including species of shrimp (20), scallops (21), clams (22), and swimming crabs (19). Although the fact that V. natriegens can act as a pathogen to marine organisms is known, the extent of V. Natriegens’ role as a marine pathogen has not been fully characterized.

8. Current Research

V. natriegens’ rapid doubling time of as little as 9.8 minutes (6) is a source of much fascination and scientific research. In particular, there is substantial interest in elucidating the mechanisms and machinery that enable V. natriegens to multiply this fast. Additionally, there is considerable focus within ongoing research on optimizing molecular biology techniques for V. natriegens and exploring potential applications of this bacteria in molecular biology research in the biotechnology industry (17). For example, a study conducted in 2016 aimed to develop genetic tools and evaluate the performance of V. natriegens in common biotechnological applications (3). Weinstock, et. al determined that plasmid DNA can be introduced into V. natriegens through electroporation or conjugation (3). These researchers also discovered four functional inducible promoters and a toxin (ccdB) that can be employed for negative selection. In addition, they assessed the performance of V. natriegens as a cloning host and suitability for storage in various media types (3). In another recent study, Long, et. al conducted a comprehensive study comparing the metabolisms of V. natriegens and E. coli in order to both fill critical gaps in the understanding of V. natriegens metabolism and to uncover any metabolic attributes that might contribute to its rapid growth. This study demonstrated that the central carbon metabolism and amino acid biosynthesis pathways of V. natriegens are very similar to that of E. coli, which is an unexpected result given their difference in growth rates (17). Furthermore, this study found that RNA content was higher for V. natriegens (29%) compared to E. coli (21%). Previous studies have shown that RNA content is often higher for fast growing strains, which may reflect the need for more ribosomes to support the higher growth rates (17). On a related note, another less recent study found that there is a larger number of rRNA genes contained in the V. natriegens genome compared to E. coli and its higher promoter activity results in greater ribosome synthesis (7).

9. References

1. Delpech, R. 2001. Using Vibrio Natriegens for Studying Bacterial Population Growth, Artificial Selection, and the Effects of UV Radiation and Photo-reactivation. Journal Of Biological Education 35: 93-97.

2. Garrity, G., Brenner, D. J., Krieg, N. R., and Staley, J. R. 2007. Bergey’s Manual of Systematic Bacteriology: Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria. Springer US.

3. Weinstock, M. T., Hesek, E. D., Wilson, C. M., and Gibson, D. G. 2016. Vibrio natriegens as a fast-growing host for molecular biology. Nature Methods, 13, 849–851.

4. Thompson, F. L., Iida, T., and Swings, J. 2004. Biodiversity of vibrios. Microbiology and Molecular Biology Reviews. 68: 403-431.

5. Silva, A. J., and Benitez, J. A. 2016. Vibrio cholerae Biofilms and Cholera Pathogenesis. PLoS Neglected Tropical Diseases, 10: e0004330.

6. Eagon, R. G. 1961. Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. Journal of Bacteriology. 83: 736-737.

7. Aiyar, S. E., Gaal, T., and Gourse, R. L. 2002. rRNA Promoter Activity in the Fast-Growing Bacterium Vibrio natriegens rRNA Promoter Activity in the Fast-Growing Bacterium Vibrio natriegens. Journal of Bacteriology, 184: 1349–1358.

8. Lee, H. H., Ostrov, N., Wong, B. G., Gold, M. A., Khalil, A., and Church, G. M. 2016. Vibrio natriegens, a new genomic powerhouse. bioRxiv. Retrieved from

9. Wang, Z., Lin, B., Hervey, W. J., IV, and Vora, G. J. 2013. Draft genome sequence of the fast-growing marine bacterium Vibrio natriegens strain ATCC 14048.Genome Announcements. 1(4):e00589-13. doi:10.1128/genomeA.00589-13

10. Okada, K., Iida, T., Kita-Tsukamoto, K., and Honda, T. 2005. Vibrios commonly possess two chromosomes. Journal of Bacteriology. 187: 752-757.

11. Yamaichi, Y., Iida, T., Park, K.-S., Yamamoto, K. and Honda, T. 1999. Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species. Molecular Microbiology. 31: 1513–1521.

12. Heidelberg, J.F., Eisen, J.A, Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E. K., Peterson, J., D., Umayam, L. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 406: 477-483.

13. Austin, B., Zachary, A., and Colwell, R. R. 1978. Recognition of Beneckea natriegens (Payne et al.) Baumann et al. as a member of the genus Vibrio, as previously proposed by Webb and Payne. International Journal of Systematic Bacteriology. 28: 315–317.

14. Chien, C.-C., Chen, C.-C., Choi, M.-H., Kung, S.-S., an Wei, Y.-H. 2007. Production of poly-β-hydroxybutyrate (PHB) by Vibrio spp. isolated from marine environment. Journal of Biotechnology. 132: 259–263.

15. Uchino, K., Saito, T., Gebauer, B., and Jendrossek, D. 2007. Isolated poly(3-hydroxybutyrate) (PHB) granules are complex bacterial organelles catalyzing formation of PHB from acetyl coenzyme A (CoA) and degradation of PHB to acetyl-CoA. Journal of Bacteriology. 189: 8250–8256.

16. Coyer, J. A., Cabello-Pasini, A., Swift, H., and Alberte, R. S. 1996. N2 fixation in marine heterotrophic bacteria: dynamics of environmental and molecular regulation. Proceedings of the National Academy of Sciences of the United States of America. 93: 3575–3580.

17. Long, C. P., Gonzalez, J. E., Cipolla, R. M., and Antoniewicz, M. R. 2017. Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis. Metabolic Engineering. 44:191–197.

18. West, G. C. K.. 2012 Symbiotic associations and pathogenic potential of vibrios in the north inlet estuary. Ph.D. Dissertation. University of South Carolina.

19. Bi, Keran, Zhang, Xiaojun, Yan, Binlun, Gao, Huan, Gao, Xiaojian, and Sun, Jingjing. 2016. Isolation and Molecular Identification of Vibrio Natriegens from Diseased Portunus Trituberculatus in China. Journal of the World Aquaculture Society 47: 854-61.

20. Wang, B., H. Li, and Y. F. He. 1993. Study on two new pathogens of “Red Leg Disease” found in Penaeus chinensis. Journal of Dalian Fisheries University 8:43–48.

21. Deng, H., Q. Chen, H. Shu, D. S. Zhang, and Z. Q. Ma. 2004. The epizootic vibriosis in the larval bay scallop Argopecten irradians. Journal of Dalian Fisheries University 19:258–263.

22. Li, G., M. C. Yan, J. Sun, Z. H. Lin, A. M. Ma, and W. S. Chang. 2009. Identification and biological characteristics of pathogen Vibrio natriegens from clam Meretrix meretrix. Progress in Fishery Sciences 30:103–109.