Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20

  • Jung-Yun Lee (Groundwater Environment Research Center, Korea Institute of Geoscience and Mineral Resources) ;
  • Dong-Hun Kim (Groundwater Environment Research Center, Korea Institute of Geoscience and Mineral Resources)
  • Received : 2022.08.09
  • Accepted : 2022.10.05
  • Published : 2022.11.28
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Abstract

Two novel, halotolerant strains of Martelella soudanensis, NC18T and NC20, were isolated from deep subsurface sediment, deeply sequenced, and comparatively analyzed with related strains. Based on a phylogenetic analysis using 16S rRNA gene sequences, the two strains grouped with members of the genus Martelella. Here, we sequenced the complete genomes of NC18T and NC20 to understand the mechanisms of their halotolerance. The genome sizes and G+C content of the strains were 6.1 Mb and 61.8 mol%, respectively. Moreover, NC18T and NC20 were predicted to contain 5,849 and 5,830 genes, and 5,502 and 5,585 protein-coding genes, respectively. Both strains contain the identically predicted 6 rRNAs and 48 tRNAs. The harboring of halotolerant-associated genes revealed that strains NC18T and NC20 might tolerate high salinity through the accumulation of potassium ions in a "salt-in" strategy induced by K+ uptake protein (kup) and the K+ transport system (trkAH and kdpFABC). These two strains also use the ectoine transport system (dctPQM), the glycine betaine transport system (proVWX), and glycine betaine uptake protein (opu) to accumulate "compatible solutes," such as ectoine and glycine betaine, to protect cells from salt stress. This study reveals the halotolerance mechanism of strains NC18T and NC20 in high salt environments and suggests potential applications for these halotolerant and halophilic strains in environmental biotechnology.

Keywords

Acknowledgement

This work was supported by the Basic Research Project (GP2020-012 and GP2020-024) of the Korea Institute of Geoscience and Mineral Resources (KIGAM) funded by the Ministry of Science and ICT (MSIT). We are grateful to Professor Michael J. Sadowsky at BioTechnology Institute, University of Minnesota, MN, USA.

References

  1. Rivas R, Sanchez-Marquez S, Mateos PF, Martinez-Molina E, Velazquez E. 2005. Martelella mediterranea gen. nov., sp. nov., a novel α-proteobacterium isolated from a subterranean saline lake. Int. J. Syst. Evol. Microbiol. 55: 955-959. https://doi.org/10.1099/ijs.0.63438-0
  2. Bibi F, Chung EJ, Khan A, Jeon CO, Chung YR. 2013. Martelella endophytica sp. nov., an antifungal bacterium associated with a halophyte. Int. J. Syst. Evol. Microbiol. 63: 2914-2919. https://doi.org/10.1099/ijs.0.048785-0
  3. Zhang D and Margesin R. 2014. Martelella radicis sp. nov. and Martelella mangrovi sp. nov., isolated from mangrove sediment. Int. J. Syst. Evol. Microbiol. 64: 3104-3108. https://doi.org/10.1099/ijs.0.066373-0
  4. Chung EJ, Hwang JM, Kim KH, Jeon CO, Chung YR. 2016. Martelella suaedae sp. nov. and Martelella limonii sp. nov., isolated from the root of halophytes. Int. J. Syst. Evol. Microbiol. 66: 3917-3922. https://doi.org/10.1099/ijsem.0.001288
  5. Lee SD. 2019. Martelella caricis sp. nov., isolated from a rhizosphere mudflat. Int. J. Syst. Evol. Microbiol. 69: 266-270. https://doi.org/10.1099/ijsem.0.003149
  6. Kim Y and Lee SD. 2019. Martelella lutilitoris sp. nov., isolated from a tidal mudflat. J. Microbiol. 57: 976-981. https://doi.org/10.1007/s12275-019-9259-4
  7. Li M, Gao C, Feng Y, Liu K, Cao P, Liu Y, et al. 2021. Martelella alba sp. nov., isolated from mangrove rhizosphere soil within the Beibu Gulf. Arch. Microbiol. 203: 1779-1786. https://doi.org/10.1007/s00203-020-02178-2
  8. Cui C, Li Z, Qian J, Shi J, Huang L, Tang H, et al. 2016. Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium. J. Biotechnol. 225: 29-30. https://doi.org/10.1016/j.jbiotec.2016.03.014
  9. Remonsellez F, Castro-Severyn J, Pardo-Este C, Aguilar P, Fortt J, Salinas C, et al. 2018. Characterization and salt response in recurrent halotolerant Exiguobacterium sp. SH31 isolated from sediments of Salar de Huasco, Chilean Altiplano. Front. Microbiol. 9: 2228.
  10. Oren A. 2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 4: 2.
  11. Weinisch L, Kuhner S, Roth R, Grimm M, Roth T, Netz DJ, et al. 2018. Identification of osmoadaptive strategies in the halophile, heterotrophic ciliate Schmidingerothrix salinarum. PLoS. Biol. 16: e2003892.
  12. Christian J and Waltho JA. 1962. Solute concentrations within cells of halophilic and non-halophilic bacteria. Biochim. Biophys. Acta. 65: 3-17.
  13. Zou YJ, Yang LF, Wang L, Yang SS. 2008. Cloning and characterization of a Na /H antiporter gene of the moderately halophilic bacterium Halobacillus aidingensis AD-6T. J. Microbiol. 46: 415-421. https://doi.org/10.1007/s12275-008-0009-2
  14. Kempf B and Bremer E. 1998. Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch. Microbiol. 170: 319-330. https://doi.org/10.1007/s002030050649
  15. Wood JM, Bremer E, Csonka LN, Kraemer R, Poolman B, Van der Heide, et al. 2001. Osmosensing and osmoregulatory compatible solute accumulation by bacteria. Comp. Biochem. Physiol. A. 130: 437-460. https://doi.org/10.1016/S1095-6433(01)00442-1
  16. Lee J, Lee D, Kim D. 2021. Characterization of Martelella soudanensis sp. nov., isolated from a mine sediment. Microorganisms 9: 1736.
  17. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  18. Bushnell B. 2014. BBMap: a fast, accurate, splice-aware aligner. Available from https://www.osti.gov/biblio/1241166. Accessed Mar. 10, 2022.
  19. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16: 294.
  20. Lee I, Chalita M, Ha S, Na S, Yoon S, Chun J. 2017. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol. 67: 2053-2057. https://doi.org/10.1099/ijsem.0.001872
  21. Hyatt D, Chen G, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
  22. Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33: W686-W689. https://doi.org/10.1093/nar/gki366
  23. Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, et al. 2015. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43: D130-D137. https://doi.org/10.1093/nar/gku1063
  24. Edgar RC. 2007. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8: 18.
  25. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, et al. 2007. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 8: 209.
  26. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42: D199-D205. https://doi.org/10.1093/nar/gkt1076
  27. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. 2014. eggNOG v4. 0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42: D231-D239. https://doi.org/10.1093/nar/gkt1253
  28. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H, Cohoon M, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33: 5691-5702. https://doi.org/10.1093/nar/gki866
  29. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Gennomics 9: 75.
  30. Yoon S, Ha S, Kwon S, Lim J, Kim Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613.
  31. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  32. Hall T, Biosciences I and Carlsbad C. 2011. BioEdit: an important software for molecular biology. GERF Bull Biosci. 2: 60-61.
  33. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729. https://doi.org/10.1093/molbev/mst197
  34. Meier-Kolthoff JP, Auch AF, Klenk H, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
  35. Yoon S, Ha S, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek. 110: 1281-1286. https://doi.org/10.1007/s10482-017-0844-4
  36. Darling AE, Treangen TJ, Messeguer X, Perna NT. 2007. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol. Biol. 396: 135-152 https://doi.org/10.1007/978-1-59745-515-2_10
  37. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68: 461-466. https://doi.org/10.1099/ijsem.0.002516
  38. Richter M and Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Nat. Acad. Sci. USA 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106
  39. Wu H and Moore E. 2010. Association analysis of the general environmental conditions and prokaryotes' gene distributions in various functional groups. Genomics 96: 27-38. https://doi.org/10.1016/j.ygeno.2010.03.007
  40. Maurel C, Reizer J, Schroeder JI, Chrispeels MJ. 1993. The vacuolar membrane protein gamma-TIP creates water specific channels in Xenopus oocytes. EMBO J. 12: 2241-2247. https://doi.org/10.1002/j.1460-2075.1993.tb05877.x
  41. Bontemps-Gallo S, Lacroix J, Sebbane F. 2021. What do we know about osmoadaptation of Yersinia pestis? Arch. Microbiol. 204: 11.
  42. Wood JM. 2007. Bacterial osmosensing transporters. Methods Enzymol. 428: 77-107. https://doi.org/10.1016/S0076-6879(07)28005-X
  43. Sleator RD and Hill C. 2002. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol. Rev. 26: 49-71. https://doi.org/10.1111/j.1574-6976.2002.tb00598.x
  44. Altendorf K, Booth IR, Gralla J, Greie J, Rosenthal AZ, Wood JM. 2009. Osmotic stress. EcoSal Plus. 3: 2.
  45. Grammann K, Volke A, Kunte HJ. 2002. New type of osmoregulated solute transporter identified in halophilic members of the bacteria domain: TRAP transporter TeaABC mediates uptake of ectoine and hydroxyectoine in Halomonas elongata DSM 2581T. J. Bacteriol. 184: 3078-3085. https://doi.org/10.1128/JB.184.11.3078-3085.2002
  46. Wood JM, Bremer E, Csonka LN, Kraemer R, Poolman B, Van der Heide T, et al. 2001. Osmosensing and osmoregulatory compatible solute accumulation by bacteria. Comp. Biochem. Physiol. A-Mol. Integr. Physiol. 130: 437-460. https://doi.org/10.1016/S1095-6433(01)00442-1
  47. Bucur FI, Grigore-Gurgu L, Crauwels P, Riedel CU, Nicolau AI. 2018. Resistance of Listeria monocytogenes to stress conditions encountered in food and food processing environments. Front. Microbiol. 9: 2700.
  48. Plantinga TH, Van Der Does C, Badia J, Aguilar J, Konings WN, Driessen AJ. 2004. Functional characterization of the Escherichia coli K-12 yiaMNO transport protein genes. Mol. Membr. Biol. 21: 51-57. https://doi.org/10.1080/09687680310001607369
  49. Liu D, Huang Y, Liang M. 2022. Analysis of the probiotic characteristics and adaptability of Lactiplantibacillus plantarum DMDL 9010 to gastrointestinal environment by complete genome sequencing and corresponding phenotypes. LWT 158: 113129.
  50. Marti-Arbona R, Maity TS, Dunbar JM, Unkefer CJ, Unkefer PJ. 2013. Discovery of a choline-responsive transcriptional regulator in Burkholderia xenovorans. J. Mol. Biol. Res. 3: 91.
  51. Zhang H, Murzello C, Sun Y, Kim M, Xie X, Jeter RM, et al. 2010. Choline and osmotic-stress tolerance induced in Arabidopsis by the soil microbe Bacillus subtilis (GB03). Mol. Plant-Microbe Interact. 23: 1097-1104. https://doi.org/10.1094/MPMI-23-8-1097
  52. Widderich N, Kobus S, Hoppner A, Riclea R, Seubert A, Dickschat JS, et al. 2016. Biochemistry and crystal structure of ectoine synthase: a metal-containing member of the cupin superfamily. PLoS One 11: e0151285.
  53. Hung C and Lai M. 2013. The phylogenetic analysis and putative function of lysine 2, 3-aminomutase from methanoarchaea infers the potential biocatalysts for the synthesis of β-lysine. J. Microbiol. Immunol. Infect. 46: 1-10. https://doi.org/10.1016/j.jmii.2011.12.031
  54. Godard T, Zuhlke D, Richter G, Wall M, Rohde M, Riedel K, et al. 2020. Metabolic rearrangements causing elevated proline and polyhydroxybutyrate accumulation during the osmotic adaptation response of Bacillus megaterium. Front. Bioeng. Biotechnol. 8: 47.
  55. Tanudjaja E, Hoshi N, Su Y, Hamamoto S, Uozumi N. 2017. Kup-mediated Cs+ uptake and Kdp-driven K+ uptake coordinate to promote cell growth during excess Cs+ conditions in Escherichia coli. Sci. Rep. 7: 2122.
  56. Alvarez-Ordonez A, Begley M, Prieto M, Messens W, Lopez M, Bernardo A, et al. 2011. Salmonella spp. survival strategies within the host gastrointestinal tract. Microbiology 157: 3268-3281. https://doi.org/10.1099/mic.0.050351-0
  57. Mainka T, Weirathmuller D, Herwig C, Pflugl S. 2021. Potential applications of halophilic microorganisms for biological treatment of industrial process brines contaminated with aromatics. J. Ind. Microbiol. Biotechnol. 48: kuab015.
  58. Oren A. 2010. Industrial and environmental applications of halophilic microorganisms. Environ. Technol. 31: 825-834. https://doi.org/10.1080/09593330903370026
  59. Dumorne K, Cordova DC, Astorga-Elo M, Renganathan P. 2017. Extremozymes: a potential source for industrial applications. J. Microbiol. Biotechnol. 27: 649-659. https://doi.org/10.4014/jmb.1611.11006
  60. Amoozegar MA, Safarpour A, Noghabi KA, Bakhtiary T, Ventosa A. 2019. Halophiles and their vast potential in biofuel production. Front. Microbiol. 10: 1895.
  61. Corral P, Amoozegar MA, Ventosa A. 2020. Halophiles and their biomolecules: recent advances and future applications in biomedicine. Mar. Drugs 18: 33.