Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment

Abstract

Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413T, was 98.5%. However, the DNA–DNA hybridization values (8–58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0  to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020T (= DSM 19416T = KCTC 32390T).

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2

Change history

  • 28 December 2017

    In the original publication of the article, it was noted that Fig. 1 present an image of Cupriavidus malaysiensis strain USMAHM13 and not of strain USMAA1020, as indicated in the figure legend. The image in the original version is thus noted to serve as a record of strain USMAHM13 and the corrected version of Fig. 1 is reprinted below.

References

  1. Akaraonye E, Keshavarz T, Roy I (2010) Production of polyhydroxyalkanoates: the future green materials of choice. J Chem Technol Biotechnol 85:732–743

    CAS  Article  Google Scholar 

  2. Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrere S, Cruveiller S, Dossat C, Lajus A, Marchetti M, Poinsot V, Rouy Z, Servin B, Saad M, Schenowitz C, Barbe V, Batut J, Medigue C, Masson-Boivin C (2008) Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res 18:1472–1483

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. Amirul AA, Yahya ARM, Sudesh K, Azizan MNM, Majid MIA (2008) Biosynthesis of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer by Cupriavidus sp. USMAA1020 isolated from Lake Kulim, Malaysia. Bioresour Technol 99:4903–4909

    CAS  Article  PubMed  Google Scholar 

  4. Anderson AJ, Dawes EA (1990) Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev 54:450–472

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. Bmc Genom 9:75

    Article  Google Scholar 

  6. Bruce JL (1996) Automated system rapidly identifies and characterizes microorganisms in food. Food Technol 50:77–81

    Google Scholar 

  7. Chen W-M, Laevens S, Lee T-M, Coenye T, de Vos P, Mergeay M, Vandamme P (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51:1729–1735

    CAS  Article  PubMed  Google Scholar 

  8. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569

    CAS  Article  PubMed  Google Scholar 

  9. Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JRW, Kersters K, Vandamme P (1999) Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 49:405–413

    Article  PubMed  Google Scholar 

  10. Coenye T, Vandamme P, LiPuma JJ (2003) Ralstonia respiraculi sp. nov., isolated from the respiratory tract of cystic fibrosis patients. Int J Syst Evol Microbiol 53:1339–1342

    CAS  Article  PubMed  Google Scholar 

  11. Cuadrado V, Gomila M, Merini L, Giulietti AM, Moore ERB (2010) Cupriavidus pampae sp. nov., a novel herbicide degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 60:2606–2612

    CAS  Article  PubMed  Google Scholar 

  12. Estrada-de los Santos P, Martínez-Aguilar L, López-Lara IM, Caballero-Mellado J (2012) Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils. Syst Appl Microbiol 35:310–314

    CAS  Article  PubMed  Google Scholar 

  13. Estrada-de los Santos P, Solano-Rodríguez R, Matsumura-Paz LT, Vásquez-Murrieta MS, Martínez-Aguilar L (2014) Cupriavidus plantarum sp. nov., a plant-associated species. Arch Microbiol 196:811–817

    CAS  Article  PubMed  Google Scholar 

  14. Fang L-C, Chen Y-F, Zhou Y-L, Wang D-S, Sun L-N, Tang X-Y, Hua R-M (2016) Complete genome sequence of a novel chlorpyrifos degrading bacterium, Cupriavidus nantongensis X1. J Biotechnol 227:1–2

    CAS  Article  PubMed  Google Scholar 

  15. Felsenstein J (1985) Confidence limits on the phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  16. Fitch W (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416

    Article  Google Scholar 

  17. Goris J, De Vos P, Coenye T, Hoste B, Janssens D, Brim H, Diels L, Mergeay M, Kersters K, Vandamme P (2001) Classification of metal-resistant bacteria from industrial biotopes as Ralstonia campinensis sp. nov., Ralstonia metallidurans sp. nov. and Ralstonia basilensis Steinle et al. 1998 emend. Int J Syst Evol Microbiol 51:1773–1782

    CAS  Article  PubMed  Google Scholar 

  18. Huss VAR, Festl H, Schleifer KH (1984) Nucleic acid hybridization studies and deoxyribonucleic acid base compositions of anaerobic, Gram-positive cocci. Int J Syst Bacteriol 34:95–101

    CAS  Article  Google Scholar 

  19. Janssen P, Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Medigue C, Taghavi S, McCorkle S, Dunn J, Lelie DVD, Mergeay M (2010) Complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS ONE 5:e10433

    Article  PubMed  PubMed Central  Google Scholar 

  20. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  PubMed  PubMed Central  Google Scholar 

  21. Khambata SR, Bhat JV (1953) Studies on a new oxalate-decomposing bacterium, Pseudomonas oxalaticus. J Bacteriol 66:505–507

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Koller M, Gasser I, Schmid F, Berg G (2011) Linking ecology with economy: insights into polyhydroxyalkanoate-producing microorganisms. Eng Life Sci 11:222–237

    CAS  Article  Google Scholar 

  23. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38:358–361

    CAS  Article  Google Scholar 

  24. Lester RL, Crane FL (1959) The natural occurrence of coenzyme Q and related compounds. J Biol Chem 234:2169–2175

    CAS  PubMed  Google Scholar 

  25. Loo CY, Lee WH, Tsuge T, Doi Y, Sudesh K (2005) Biosynthesis and characterization of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from palm oil products in a Wautersia eutropha mutant. Biotechnol Lett 27:1405–1410

    CAS  Article  PubMed  Google Scholar 

  26. Maidak BL, Cole JR, Parker CT, Garrity JGM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27:171–173

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. Makkar NS, Casida LE (1987) C. necator gen. nov., sp. nov.: a nonobligate bacterial predator of bacteria in soil. Int J Syst Bacteriol 37:323–326

    Article  Google Scholar 

  28. Martínez-Aguilar L, Caballero-Mellado J, Estrada-de los Santos P (2013) Transfer of Wautersia numazuensis to Cupriavidus genus as Cupriavidus numazuensis comb. nov. Int J Syst Evol Microbiol 63:208–211

    Article  PubMed  Google Scholar 

  29. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia FF, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214

    CAS  Article  PubMed  Google Scholar 

  30. Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Potter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbuchel A, Friedrich B, Bowien B (2006) Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16. Nat Biotechnol 24:1257–1262

    Article  PubMed  Google Scholar 

  31. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E (1996) The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct Actinomycete lineage: proposal of Nocardiomaceae fam. nov. Int J Syst Bacteriol 142:2087–2095

    CAS  Google Scholar 

  32. Ramachandran H, Iqbal MA, Amirul AA (2014) Identification and characterization of the yellow pigment synthesized by Cupriavidus sp. USMAHM13. Appl Biochem Biotechnol 174:461–470

    CAS  Article  PubMed  Google Scholar 

  33. Ray J, Waters RJ, Sherker JM, Kuehl JV, Price MN, Huang J, Chakraborty R, Arkin AP, Deutschbauer A (2015) Complete genome sequence of Cupriavidus basilensis 4G11, isolated from the oak ridge field research center site. Genome Announc 3:e00322-15

    Article  PubMed  PubMed Central  Google Scholar 

  34. Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118

    Google Scholar 

  35. Rodriguez-R LM, Konstantinidis KT (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomics. Peer J Preprints

  36. Rojas-Rojas FU, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Shapiro N, Ibarra JA, Estrada-des los Santos P (2016) Draft genome sequence of heavy metal-resistant Cupriavidus alkaliphilus ASC-732T, isolated from agave rhizosphere in the Northeast of Mexico. Genome Announc 4:e01013-16

    Article  PubMed  PubMed Central  Google Scholar 

  37. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  38. Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD, Concepcion RN, Ohta H (2006) Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. Int J Syst Evol Microbiol 56:973–978

    CAS  Article  PubMed  Google Scholar 

  39. Shafie NAH, Lau N-S, Ramachandran H, Amirul A-AA (2017) Complete genome sequences of three Cupriavidus strains isolated from various Malaysian environments. Genome Announc 5:e01498-16

    Article  PubMed  PubMed Central  Google Scholar 

  40. Singh P, Kim Y-J, Nguyen N-L, Hoang V-A, Sukweenadhi J, Farh ME-A, Yang D-C (2015) Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng. Antonie van Leeuwenhoek 107:749–758

    CAS  Article  PubMed  Google Scholar 

  41. Spiekermann P, Rehm BHA, Kalscheuer R, Baumeister D, Steinbüchel A (1999) A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 171:73–80

    CAS  Article  PubMed  Google Scholar 

  42. Sudesh K, Abe H, Doi Y (2000) Synthesis, structure and properties of polyhydroxyalkanoates: biological polyesters. Prog Polym Sci 25:1503–1555

    CAS  Article  Google Scholar 

  43. Sun LN, Wang DS, Yang ED, Fang LC, Chen YF, Tang XY, Hua RM (2016) Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge. Int J Syst Evol Microbiol 66:2335–2341

    CAS  Article  PubMed  Google Scholar 

  44. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526

    CAS  PubMed  Google Scholar 

  45. 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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  46. Thompson J, Higgins D, Gibson T (1994) ClustalW: improving the sensitivity of progressive multiple sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  47. Tindall BJ (1990a) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130

    CAS  Article  Google Scholar 

  48. Tindall BJ (1990b) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    CAS  Article  Google Scholar 

  49. Vandamme P, Coenye T (2004) Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol 54:2285–2289

    Article  PubMed  Google Scholar 

  50. Vandamme P, Goris J, Coenye T, Hoste B, Janssens D, Kersters K, de Vos P, Falsen E (1999) Assignment of centers for disease control group IVc-2 to the genus Ralstonia as Ralstonia paucula sp. nov. Int J Syst Bacteriol 49:663–669

    Article  PubMed  Google Scholar 

  51. Wang X, Chen M, Xiao J, Hao L, Crowley DE, Zhang Z, Yu J, Huang N, Huo M, Wu J (2015) Genome sequence analysis of the naphthenic acid degrading and metal resistant bacterium Cupriavidus gilardii CR3. PLoS ONE 10:e0132881

    Article  PubMed  PubMed Central  Google Scholar 

  52. Watanabe T, Yamazoe A, Hosoyama A, Fujihara H, Suenaga H, Hirose J, Futagami T, Goto M, Kimura N, Furukawa K (2015) Draft genome sequence of C. pauculus strain KF709, a biphenyl-utilizing bacterium isolated from biphenyl contaminated soil. Genome Announc 3:e00222-15

    Article  PubMed  PubMed Central  Google Scholar 

  53. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  54. Weinitschke S, Hollemeyer K, Kusian B, Bowien B, Smits THM, Cook AM (2010) Sulfoacetate is degraded via a novel pathway involving sulfoacetyl-CoA and sulfoacetaldehyde in C. necator H16. J Biol Chem 285:35249–35254

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. Williams SF, Martin DP (2002) Applications of PHAs in medicine and pharmacy. In: Doi Y, Steinbüchel A (eds) Biopolymers: polyesters. Wiley, Weinhem, pp 91–128

    Google Scholar 

Download references

Acknowledgements

The authors acknowledge the technical expertise of the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures for providing bacterial systematic analysis based on a polyphasic approach. This work was supported by the MOSTI, Malaysia and Universiti Sains Malaysia, Penang, Malaysia.

Funding

This study was funded by the Ministry of Science, Technology and Innovation, Malaysia, (09-05-IFN-BPH-002, 02-05-23-SF0003 and 02-05-23-SF0023), Universiti Sains Malaysia (1001/PBIOLOGI/811304, 1001/PCCB/870009) and also USM Science Fellowship (RU: 1001/441/29301/CIPS/AUPE001) awarded to Hema Ramachandran.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Al-Ashraf Abdullah Amirul.

Ethics declarations

Conflict of interest

The author(s) declare that they have no competing interests.

Additional information

A correction to this article is available online at https://doi.org/10.1007/s10482-017-0998-0.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 212 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ramachandran, H., Shafie, N.A.H., Sudesh, K. et al. Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment. Antonie van Leeuwenhoek 111, 361–372 (2018). https://doi.org/10.1007/s10482-017-0958-8

Download citation

Keywords

  • Cupriavidus malaysiensis
  • Polyphasic taxonomy
  • P(3HB-co-4HB) copolymer
  • Proteobacteria