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Volume 72, Issue 4

sp. nov., a novel species of the family isolated from plastic waste Open Access

Abstract

Strain NGK35 is a motile, Gram-stain-negative, rod-shaped (1.0–2.1 µm long and 0.6–0.8 µm wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 °C (optimum, 28 °C), in 0–10 % NaCl (optimum, 1 %) and at pH 6.0–9.5 (optimum, pH 7.5–8.5). It was positive for cytochrome c oxidase, catalase as well as HS production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C cis9 and C, followed by C cyclo and C cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35 belongs to the genus (family ), appearing most closely related to CCUG 53761A (96.90 %) and ABC02-12 (96.94 %). The genomic DNA G+C content of strain NGK35 was 52.1 mol %. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus . Based on phenotypic and molecular characterization, strain NGK35 can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name sp. nov. is proposed. The type strain is NGK35 (=DSM 113270=NCCB 100854).

  • Received:
  • Accepted:
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Keyword(s): bacteria , Paenalcaligenes niemegkensis , plastic pollution and terrestrial plastisphere
Funding
This study was supported by the:
  • Helmholtz Recruiting Initiative (Award I-044-16-01)
    • Principle Award Recipient: VladimirRoddatis
  • Bundesministerium für Bildung und Forschung (Award 02WPL1449D)
    • Principle Award Recipient: DirkWagner
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-04-25
2024-12-14
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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. Kämpfer P, Falsen E, Langer S, Lodders N, Busse H-J. Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae. Int J Syst Evol Microbiol 2010; 60:1537–1542 [View Article]
     [Google Scholar]
  5. Lee YY, Lee JK, Park KH, Kim S-Y, Roh SW et al. Paenalcaligenes hermetiae sp. nov., isolated from the larval gut of Hermetia illucens (Diptera: Stratiomyidae), and emended description of the genus Paenalcaligenes. Int J Syst Evol Microbiol 2013; 63:4224–4229 [View Article] [PubMed]
     [Google Scholar]
  6. Moon J-Y, Lim J-M, Ahn J-H, Weon H-Y, Kwon S-W et al. Paenalcaligenes suwonensis sp. nov., isolated from spent mushroom compost. Int J Syst Evol Microbiol 2014; 64:882–886 [View Article] [PubMed]
     [Google Scholar]
  7. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Tech Bact Syst 1991115–175
     [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. Felsenstein J. PHYLIP (Phylogeny Inference Package), version 3.6a3 Seattle, WA: University of Washington; 2002
     [Google Scholar]
  14. 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 USA 2016; 113:E8396–E8405 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. Süßmuth R, Eberspächer J, Haag R, Springer W. Biochemisch-mikrobiologisches Praktikum, 1. Auflage. Stuttgart/New York: Thieme Verlag; 1987
     [Google Scholar]
  22. 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]
  23. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
     [Google Scholar]
  24. Dela Cruz TEE, Torres JMO. Gelatin hydrolysis test protocol. Am Soc Microbiol 2016; 1–10:
     [Google Scholar]
  25. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Tech Note 19901–6
     [Google Scholar]
  26. 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]
  27. 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]
  28. 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. Organic Geochemistry 2017; 108:30–42 [View Article]
     [Google Scholar]
  29. 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]
  30. 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]
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Paenalcaligenes niemegkensis sp. nov., a novel species of the family Alcaligenaceae isolated from plastic waste
Int J Syst Evol Microbiol 72, 005333 (2022); https://doi.org/10.1099/ijsem.0.005333
/content/journal/ijsem/10.1099/ijsem.0.005333
/content/journal/ijsem/10.1099/ijsem.0.005333
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