1887

Abstract

Strain NGK65, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65 hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0–1% NaCl and at pH 7.5–8.0. Glycerol, -glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C followed by iso-C and C 9. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with -diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65 belongs to the genus (phylum ), appearing most closely related to MJ31 (98.6%) and KSL-104 (98.3%). The genomic DNA G+C content of strain NGK65 was 68.2%. Strain NGK65 and the type strains of species involved in the analysis had average nucleotide identity values of 78.3–71.9% as well as digital DNA–DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus . Based on phenotypic and molecular characterization, strain NGK65 can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name sp. nov. is proposed. The type strain is NGK65 (=DSM 113112=NCCB 100846).

Funding
This study was supported by the:
  • German Helmholtz Recruiting Initiative (Award I-044-16-01)
    • Principle Award Recipient: VladimirRoddatis
  • Bundesministerium für Bildung und Forschung (Award 02WPL1449D)
    • Principle Award Recipient: DirkWagner
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005319
2022-04-28
2022-07-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/72/4/ijsem005319.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005319&mimeType=html&fmt=ahah

References

  1. MacLean J, Mayanna S, Benning LG, Horn F, Bartholomäus A et al. The terrestrial plastisphere: diversity and polymer-colonizing potential of plastic-associated microbial communities in soil. Microorganisms 2021; 9:1–19 [View Article]
    [Google Scholar]
  2. Burd D. Plastic not fantastic. Proj Reports Canada Wide Sci Fair 20081–5
    [Google Scholar]
  3. Gyung Yoon M, Jeong Jeon H, Nam Kim M. Biodegradation of polyethylene by a soil bacterium and AlkB cloned recombinant cell. J Bioremed Biodegrad 2012; 03:1–8 [View Article]
    [Google Scholar]
  4. Prauser H. Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 1976; 26:58–65 [View Article]
    [Google Scholar]
  5. Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. Nocardioides. Bergey’s Man Syst Archaea Bact 2015 pp 1–81
    [Google Scholar]
  6. Barton H, Taylor N, Kreate M, Springer A, Oehrle S et al. The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. IJS 2007; 36:93–104 [View Article] [PubMed]
    [Google Scholar]
  7. Boivin-Jahns V, Bianchi A, Ruimy R, Garcin J, Daumas S et al. Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl Environ Microbiol 1995; 61:3400–3406 [View Article] [PubMed]
    [Google Scholar]
  8. Gontang EA, Fenical W, Jensen PR. Phylogenetic diversity of Gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 2007; 73:3272–3282 [View Article] [PubMed]
    [Google Scholar]
  9. Saiz-Jimenez IC. Actinomycetes in hypogean environments. Geomicrobiol J 1999; 16:1–8 [View Article]
    [Google Scholar]
  10. Katayama T, Fukuda M, Moriizumi J, Nakamura T, Brouchkov A et al. A late quaternary ice wedge from the fox permafrost tunnel in central alaska is A time capsule for gas and bacteria; 2006
  11. Rintala H, Pitkäranta M, Toivola M, Paulin L, Nevalainen A. Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 2008; 8:1–13 [View Article] [PubMed]
    [Google Scholar]
  12. Vishnivetskaya TA, Petrova MA, Urbance J, Ponder M, Moyer CL et al. Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology 2006; 6:400–414 [View Article] [PubMed]
    [Google Scholar]
  13. Ward AC, Bora N. Diversity and biogeography of marine actinobacteria. Curr Opin Microbiol 2006; 9:279–286 [View Article] [PubMed]
    [Google Scholar]
  14. Zhang JY, Liu XY, Liu SJ. Nocardioides terrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2009; 59:2444–2448 [View Article] [PubMed]
    [Google Scholar]
  15. Evtushenko LI, Ariskina EV. Nocardioidaceae. Bergey’s Man Syst Archaea Bact 20151–18
    [Google Scholar]
  16. Coleman NV, Mattes TE, Gossett JM, Spain JC. Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites. Appl Environ Microbiol 2002; 68:6162–6171 [View Article] [PubMed]
    [Google Scholar]
  17. Golovleva LA, Pertsova RN, Evtushenko LI, Baskunov BP. Degradation of 2,4,5-trichlorophenoxyacetic acid by a Nocardioides simplex culture. Biodegradation 1990; 1:263–271 [View Article] [PubMed]
    [Google Scholar]
  18. Futamata H, Uchida T, Yoshida N, Yonemitsu Y, Hiraishi A. Distribution of dibenzofuran-degrading bacteria in soils polluted with different levels of polychlorinated dioxins. Microb Environ 2004; 19:172–177 [View Article]
    [Google Scholar]
  19. Fredrickson JK, Zachara JM, Balkwill DL, Kennedy D, Li SW et al. Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington State. Appl Environ Microbiol 2004; 70:4230–4241 [View Article] [PubMed]
    [Google Scholar]
  20. Kubota M, Kawahara K, Sekiya K, Uchida T, Hattori Y et al. Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst Appl Microbiol 2005; 28:165–174 [View Article] [PubMed]
    [Google Scholar]
  21. Jung CM, Broberg C, Giuliani J, Kirk LL, Hanne LF. Characterization of JP-7 jet fuel degradation by the bacterium Nocardioides luteus strain BAFB. J Basic Microbiol 2002; 42:127–131 [View Article] [PubMed]
    [Google Scholar]
  22. Hamamura N, Arp DJ. Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8. FEMS Microbiol Lett 2000; 186:21–26 [View Article] [PubMed]
    [Google Scholar]
  23. Fida TT, Palamuru S, Pandey G, Spain JC. Aerobic biodegradation of 2,4-Dinitroanisole by Nocardioides sp. strain JS1661. Appl Environ Microbiol 2014; 80:7725–7731 [View Article] [PubMed]
    [Google Scholar]
  24. Yoon JH, Cho YG, Lee ST, Suzuki K, Nakase T et al. Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 1999; 49:675–680 [View Article] [PubMed]
    [Google Scholar]
  25. Satsuma K. Mineralization of s-triazine herbicides by a newly isolated Nocardioides species strain DN36. Appl Microbiol Biotechnol 2010; 86:1585–1592 [View Article] [PubMed]
    [Google Scholar]
  26. Topp E, Mulbry WM, Zhu H, Nour SM, Cuppels D. Characterization of S-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils. Appl Environ Microbiol 2000; 66:3134–3141 [View Article] [PubMed]
    [Google Scholar]
  27. Piutti S, Semon E, Landry D, Hartmann A, Dousset S et al. Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil. FEMS Microbiol Lett 2003; 221:111–117 [View Article] [PubMed]
    [Google Scholar]
  28. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Tech Bact Syst 1991115–175
    [Google Scholar]
  29. Muyzer G, Teske A, Wirsen CO, Jannasch HW. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 1995; 164:165–172 [View Article] [PubMed]
    [Google Scholar]
  30. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article] [PubMed]
    [Google Scholar]
  31. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
    [Google Scholar]
  32. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article] [PubMed]
    [Google Scholar]
  33. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article] [PubMed]
    [Google Scholar]
  34. Felsenstein J. PHYLIP (Phylogeny Inference Package), version 3.6a3 Seattle, WA: University of Washington; 2002
    [Google Scholar]
  35. Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M et al. Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci U S A 2016; 113:E8396–E8405 [View Article] [PubMed]
    [Google Scholar]
  36. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  37. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  38. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
    [Google Scholar]
  39. Mohanan N, Montazer Z, Sharma PK, Levin DB. Microbial and enzymatic degradation of synthetic plastics. Front Microbiol 2020; 11:2837 [View Article] [PubMed]
    [Google Scholar]
  40. Rojo F. Degradation of alkanes by bacteria. Environ Microbiol 2009; 11:2477–2490 [View Article] [PubMed]
    [Google Scholar]
  41. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: A web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  42. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  43. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article] [PubMed]
    [Google Scholar]
  44. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  45. Yoon JH, Lee CH, Oh TK. Nocardioides dubius sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 2005; 55:2209–2212 [View Article] [PubMed]
    [Google Scholar]
  46. Süßmuth R, Eberspächer J, Haag R, Springer W. Biochemisch-mikrobiologisches Praktikum, 1. Auflage. Stuttgart/New York: Thieme Verlag; 1987
    [Google Scholar]
  47. Bajerski F, Ganzert L, Mangelsdorf K, Lipski A, Busse H-J et al. Herbaspirillum psychrotolerans sp. nov., a member of the family Oxalobacteraceae from a glacier forefield. Int J Syst Evol Microbiol 2013; 63:3197–3203 [View Article] [PubMed]
    [Google Scholar]
  48. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
    [Google Scholar]
  49. Dela Cruz TEE, Torres JMO. Gelatin hydrolysis test protocol. Am Soc Microbiol 2016; 1–10:
    [Google Scholar]
  50. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Tech Note 1990 pp 1–6
    [Google Scholar]
  51. Derichs J, Kämpfer P, Lipski A. Pedobacter nutrimenti sp. nov., isolated from chilled food. Int J Syst Evol Microbiol 2014; 64:1310–1316 [View Article] [PubMed]
    [Google Scholar]
  52. Lipski A, Altendorf K. Identification of heterotrophic bacteria isolated from ammonia-supplied experimental biofilters. Syst Appl Microbiol 1997; 20:448–457 [View Article]
    [Google Scholar]
  53. Nichols PD, Guckert JB, White DC. Determination of monosaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulphide adducts. J Microbiol Methods 1986; 5:49–55 [View Article]
    [Google Scholar]
  54. Genderjahn S, Alawi M, Kallmeyer J, Belz L, Wagner D et al. Present and past microbial life in continental pan sediments and its response to climate variability in the southern Kalahari. Org Geochem 2017; 108:30–42 [View Article]
    [Google Scholar]
  55. Müller K-D, Husmann H, Nalik HP. A new and rapid method for the assay of bacterial fatty acids using high resolution capillary gas chromatography and trimethylsulfonium hydroxide. Zentralblatt für Bakteriologie 1990; 274:174–182 [View Article]
    [Google Scholar]
  56. Evtushenko LI, Krausova VI, Yoon J. Nocardioides. Bergey’s Man Syst Archaea Bact 20151–81
    [Google Scholar]
  57. Wiertz R, Schulz SC, Müller U, Kämpfer P, Lipski A. Corynebacterium frankenforstense sp. nov. and Corynebacterium lactis sp. nov., isolated from raw cow milk. Int J Syst Evol Microbiol 2013; 63:4495–4501 [View Article] [PubMed]
    [Google Scholar]
  58. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
  59. Behrend C, Heesche-Wagner K. Formation of hydride-meisenheimer complexes of picric acid (2,4,6-Trinitrophenol) and 2,4-dinitrophenol during mineralization of picric acid by Nocardioides sp. strain CB 22-2. Appl Environ Microbiol 1999; 65:1372–1377 [View Article]
    [Google Scholar]
  60. Zhang D-C, Schumann P, Redzic M, Zhou Y-G, Liu H-C et al. Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:445–450 [View Article] [PubMed]
    [Google Scholar]
  61. Ahn JH, Lim JM, Kim SJ, Song J, Kwon SW et al. Nocardioides paucivorans sp. nov isolated from soil. J Microbiol 2014; 52:990–994
    [Google Scholar]
  62. Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK et al. Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewagedisposal plant. Int J Syst Evol Microbiol 2012; 62:1199–1203 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005319
Loading
/content/journal/ijsem/10.1099/ijsem.0.005319
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error