Advertisement

Rheinheimera pleomorphica sp. nov., a Novel Alkali-Tolerant Bacteria Isolated from Chilika Lake, India

  • Ananta N. Panda
  • Lopamudra Ray
  • Samir Ranjan Mishra
  • Vishakha RainaEmail author
Article
  • 3 Downloads

Abstract

A novel Gram-negative gamma-proteobacterium, non-sporulating motile, rod or coccus-shaped bacterium designated as strain PKS7T was isolated from a sediment sample collected from Chilika Lake, Odisha, India and characterized taxonomically using a polyphasic approach. The major quinone was Q8 and major cellular fatty acids were C16:0, C17:0, C15:1w8c, C17:1w8c, C12:03-OH. The chemotaxonomic features confirmed the isolate to be a member of genus Rheinheimera. 16SrRNA gene sequence of strain PKS7T was closest in similarity to R. aquimaris SW-353T (99.36% identity), R. muenzenbergensis E49T (98.63%), R. nanhaiensis E407-8T (98.35%), R. japonica KMM 9513T (98.35%) and R. baltica DSM-14885T (98.08%). The 16S rRNA gene sequence-based phylogenetic analysis and sequence similarity between the isolated strain and type strains also revealed its affiliation to genus Rheinheimera. DNA–DNA relatedness with closest type strain R. aquimaris SW-353T was 25.0% (±3.40) and in silico DDH showed values in the range of 17.7–37.1% with the type strains of the genus Rheinheimera for which whole genome sequence are available. Strain PKS7T was also distinguished by a multi-locus sequence analysis (MLST) by alingning gyrB gene sequences of the closest type strains of Rheinheimera. The draft genome of strain PKS7T contained 32 contigs of total size 3,963,569 bp comprising of 3763 predicted coding sequences with a G + C content of 50.7 mol%. Comparision of phenotypic and genotypic data with its closest neighbours and closely related species confirm the strain PKS7T to be recognised as a novel species within the genus Rheinheimera, for which the name Rheinheimera pleomorphica sp. nov. is proposed. The type strain is PKS7T (= KCTC 42365 = JCM 30460).

Abbreviations

KCTC

Korean Collection for type culture

DSMZ

Deutsche Sammlung von Mikroorganismen und Zellkulturen

JCM

Japan Collection of Microorganisms

FAME

Fatty acid methyl ester

ZMB/ZMA

Zobell’s marine broth/agar

L

Lipid

PL

Phospholipid

GL

Glycolipid

AL

Aminolipid

PE

Phosphatidylethanolamine

PG

Phosphatidylglycerol

PN

Phosphoaminolipid

RAST

Rapid annotation using subsystem technology

CDSs

Coding sequences

Notes

Acknowledgements

The authors are grateful to the staffs of Chilika Development Authority (CDA) for their help in collection of samples. We are grateful to Dr. Cathrin Spӧrer and Dr. Susanne Verbarg, DSMZ for their assistance with DNA–DNA hybridization and chemotaxonomic analysis.

Funding

The authors received no specific grant from any funding agency.

Compliance with Ethical Standards

Conflict of interest

The authors declare that there are no conflicts of interest.

Ethical Approval

No animal or human were used for experimental purpose in the current work.

Supplementary material

284_2019_1802_MOESM1_ESM.docx (897 kb)
Supplementary file1 (DOCX 897 kb)

References

  1. 1.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedPubMedCentralGoogle Scholar
  2. 2.
    Auch AF, Klenk HP, Göker M (2010) Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genom Sci 2:142–148CrossRefGoogle Scholar
  3. 3.
    Aygan A, Arikan B (2007) An overview on bacterial motility detection. Int J Agric Biol 9:193–196Google Scholar
  4. 4.
    Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, Edwards RA et al (2008) The rast server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
  5. 5.
    Baek K, Jeon CO (2016) Rheinheimera gaetbuli sp. nov., a marine bacterium isolated from a tidal flat. Curr Microbiol 72:344–350PubMedGoogle Scholar
  6. 6.
    Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917CrossRefGoogle Scholar
  7. 7.
    Brettar I, Christen R, Höfle MG (2002) Rheinheimera baltica gen. nov., sp. nov., a blue-coloured bacterium isolated from the central Baltic Sea. Int J Syst Evol Microbiol 52:1851–1857PubMedGoogle Scholar
  8. 8.
    Cashion P, Holder-Franklin MA, McCully J, Franklin M (1977) A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466CrossRefGoogle Scholar
  9. 9.
    Chen WM, Chang YL, Chiu CY, Shih YS (2010) Rheinheimera aquatica sp. nov., antimicrobial activity-producing bacterium isolated from freshwater culture pond. J Microbiol Biotechnol 20:1386–1392CrossRefGoogle Scholar
  10. 10.
    Collee JG, Miles RS, Watt B (1996) Tests for identification of bacteria. Mackie and McCartney practical medical microbiology 14:131–149Google Scholar
  11. 11.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  12. 12.
    Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416CrossRefGoogle Scholar
  13. 13.
    Hayashi K, Busse HJ, Golke J, Anderson J et al (2018) Rheinheimera salexigens sp. nov., isolated from a fishing hook, and emended description of the genus Rheinheimera. Int J Syst Evol Microbiol 68:35–41CrossRefGoogle Scholar
  14. 14.
    Hopwood DA, Bibb MJ, Chater KF, Kieser T et al (1985) Preparation of chromosomal, plasmid and phase DNA. In: Genetic manipulation of Streptomyces: a laboratory manual. John Innes Foundation, Norwich, pp 79–80Google Scholar
  15. 15.
    Huss VA, Festl H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192CrossRefGoogle Scholar
  16. 16.
    Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  17. 17.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  18. 18.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefGoogle Scholar
  19. 19.
    Leifson E (1951) Staining, shape, and arrangement of bacterial flagella. J Bacteriol 62:377PubMedPubMedCentralGoogle Scholar
  20. 20.
    Ley JD, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefGoogle Scholar
  21. 21.
    Li HJ, Zhang XY, Zhang YJ, Zhou MY, Gao ZM, Chen XL, Dang HY, Zhang YZ (2011) Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007. Int J Syst Evol Microbiol 61:1016–1022CrossRefGoogle Scholar
  22. 22.
    Liu Y, Jiang JT, Xu CJ, Liu YH, Song XF, Li H, Liu ZP (2012) Rheinheimera longhuensis sp. nov., isolated from a slightly alkaline lake, and emended description of genus Rheinheimera Brettar et al. 2002. Int J Syst Evol Microbiol 62:2927–2933CrossRefGoogle Scholar
  23. 23.
    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  24. 24.
    Merchant MM, Welsh AK, McLean RJ (2007) Rheinheimera texasensis sp. nov., a halointolerant freshwater oligotroph. Int J Syst Evol Microbiol 572:376–2380Google Scholar
  25. 25.
    Park S, Park JM, Won SM, Jung YT, Yoon JH (2014) Rheinheimera arenilitoris sp. nov., isolated from seashore sand. Int J Syst Evol Microbiol 64:3749–3754CrossRefGoogle Scholar
  26. 26.
    Richter M, Rosselló MR, Oliver Glöckner F, Peplies J (2015) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931CrossRefGoogle Scholar
  27. 27.
    Richter M, Rossello MR (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefGoogle Scholar
  28. 28.
    Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI, Mikhailov VV (2015) Rheinheimera japonica sp. nov., a novel bacterium with antimicrobial activity from seashore sediments of the Sea of Japan. Arch Microbiol 197:613–620CrossRefGoogle Scholar
  29. 29.
    Rzhetsky A, Mei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9:945–967Google Scholar
  30. 30.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  31. 31.
    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc., Newark, DEGoogle Scholar
  32. 32.
    Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069CrossRefGoogle Scholar
  33. 33.
    Sheu SY, Chen WT, Young CC, Chen WM (2018) Rheinheimera coerulea sp. nov., isolated from a freshwater creek, and emended description of genus Rheinheimera Brettar et al. 2002. Int J Syst Evol Microbiol 68:2340–2347CrossRefGoogle Scholar
  34. 34.
    Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P (ed) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
  35. 35.
    Stackebrandt E (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155Google Scholar
  36. 36.
    Suarez C, Ratering S, Geissler-Plaum R, Schnell S (2014) Rheinheimera hassiensis sp. nov. and Rheinheimera muenzenbergensis sp. nov., two species from the rhizosphere of Hordeum secalinum. Int J Syst Evol Microbiol 64:1202–1209CrossRefGoogle Scholar
  37. 37.
    Tindall BJ (1990) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130CrossRefGoogle Scholar
  38. 38.
    Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol 66:199–202CrossRefGoogle Scholar
  39. 39.
    Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Methods for general and molecular microbiology, 3rd edn. American Society of Microbiology, Washington, DC, pp 330–393Google Scholar
  40. 40.
    Wang LT, Lee FL, Tai CJ, Kasai H (2007) Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group. Int J Syst Evol Microbiol 57:846–1850Google Scholar
  41. 41.
    Wayne LG, Brenner DJ, Colwell RR, Grimont PA et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464CrossRefGoogle Scholar
  42. 42.
    Yoon JH, Park SE, Kang SJ, Oh TK (2007) Rheinheimera aquimaris sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 57:1386–1390CrossRefGoogle Scholar
  43. 43.
    Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefGoogle Scholar
  44. 44.
    Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:9–821CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Ananta N. Panda
    • 1
  • Lopamudra Ray
    • 1
    • 2
  • Samir Ranjan Mishra
    • 1
  • Vishakha Raina
    • 1
    Email author
  1. 1.School of BiotechnologyKIIT UniversityBhubaneswarIndia
  2. 2.School of LawKIIT UniversityBhubaneswarIndia

Personalised recommendations