1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

sp. nov., a novel hydrocarbon-degrading bacterium isolated from deep chlorophyll maximum layer seawater of the West Pacific Ocean and emended description of the genus No Access

Abstract

A Gram-stain-negative, motile, non-spore-forming, strictly aerobic and rod-shaped bacterial strain, Adcm-6A, was isolated from a seawater sample collected from the deep chlorophyll maximum layer in the West Pacific Ocean. Strain Adcm-6A grew at 20–37 °C (optimum, 28–32 °C), at pH 6–11 (pH 7) and in the presence of 0–6 % (1–2 %) NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it belonged to the genus and had 97.7 and 96.9 % sequence similarity to DSM 1231 and JCM 32263, respectively. Digital DNA–DNA hybridization and average nucleotide identity values between strain Adcm-6A and the two type strains were 22.2–22.9 % and 79.7–80.4 %, respectively. The principal fatty acids were C cyclo 8, summed feature 8 (C 6 and/or C 7) and C. The predominant respiratory quinone was Q-10. The polar lipids were diphosphatidylglycerol, two phosphatidylethanolamines, two phosphatidyglycerols and an unidentified lipid. The genomic DNA G+C content of strain Adcm-6A was 67.7 %. Based on phylogenetic analysis and genomic-based relatedness indices, as well as phenotypic and genotypic characteristics, strain Adcm-6A represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is Adcm-6A (=MCCC M24951=KCTC 82849).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): deep chlorophyll maximum layer , hydrocarbon degradation , polyphasic taxonomy , West Pacific Ocean and Zavarzinia marina sp. nov.
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005527
2022-10-17
2024-05-18
Loading full text...

Full text loading...

References

  1. Meyer O, Stackebrandt E, Auling G. Reclassification of ubiquinone Q-10 containing carboxidotrophic bacteria: transfer of “[Pseudomonas] carboxydovorans” OM5T to Oligotropha, gen. nov., as Oligotropha carboxidovorans, comb. nov., transfer of “[Alcaligenes] carboxydus” DSM 1086T to Carbophilus, gen. nov., as Carbophilus carboxidus, comb. nov., transfer of “[Pseudomonas] compransoris” DSM 1231T to Zavarzinia, gen. nov., as Zavarzinia compransoris, comb. nov., and amended descriptions of the new genera. Syst Appl Microbiol 1993; 16:390–395
     [Google Scholar]
  2. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article]
     [Google Scholar]
  3. Boone D, Castenholz R, Garrity G. Taxonomic outline of the archaea and bacteria. In Whitman WB. eds Bergey’s Manual of Systematic Bacteriology: The Archaea and the Deeply Branching and Phototrophic Bacteria New York, NY: Springer; 2001 pp 155–166
     [Google Scholar]
  4. Nozhevnikova AN, Zavarzin GA. Taxonomy of CO-oxidizing Gram negative bacteria. Izv Akad Nauk SSSR Biol 1974436–440
     [Google Scholar]
  5. Cypionka H, Meyer O, Schlegel HG. Physiological characteristics of various species of strains of carboxydobacteria. Arch Microbiol 1980; 127:301–307 [View Article]
     [Google Scholar]
  6. Lee Y, Park HY, Jeon CO. Zavarzinia aquatilis sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2019; 69:727–731 [View Article]
     [Google Scholar]
  7. Cullen JJ. Subsurface chlorophyll maximum layers: enduring enigma or mystery solved?. Ann Rev Mar Sci 2015; 7:207–239 [View Article] [PubMed]
     [Google Scholar]
  8. Biller SJ, Berube PM, Lindell D, Chisholm SW. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol 2015; 13:13–27 [View Article]
     [Google Scholar]
  9. Lea-Smith DJ, Biller SJ, Davey MP, Cotton CAR, Perez Sepulveda BM et al. Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle. Proc Natl Acad Sci USA 2015; 112:13591–13596 [View Article]
     [Google Scholar]
  10. McGenity TJ, McKew BA, Lea-Smith DJ. Cryptic microbial hydrocarbon cycling. Nat Microbiol 2021; 6:419–420 [View Article] [PubMed]
     [Google Scholar]
  11. Love CR, Arrington EC, Gosselin KM, Reddy CM, Van Mooy BAS et al. Microbial production and consumption of hydrocarbons in the global ocean. Nat Microbiol 2021; 6:489–498 [View Article]
     [Google Scholar]
  12. Lane DJ. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley & Sons; 1991 pp 115–175
     [Google Scholar]
  13. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  14. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing latforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  20. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 2020; 70:e102 [View Article]
     [Google Scholar]
  21. 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]
  22. Chen M, Ma Y, Wu S, Zheng X, Kang H et al. Genome warehouse: a public repository housing genome-scale data. Genomics Proteomics Bioinformatics 2021; 19:584–589 [View Article]
     [Google Scholar]
  23. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  24. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article]
     [Google Scholar]
  25. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  26. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article]
     [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
     [Google Scholar]
  29. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  30. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  31. 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]
     [Google Scholar]
  32. Dyksterhouse SE, Gray JP, Herwig RP, Lara JC, Staley JT. Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 1995116–123 [View Article]
     [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 North Newark, Del, USA: MIDI Inc; 1990
     [Google Scholar]
  34. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
  35. Kates M. Techniques of lipidology:Isolation, Analysis, and Identification of Lipids, 2nd rev. edn. Amsterdam: Elsevier; 1986
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005527
Loading
Zavarzinia marina sp. nov., a novel hydrocarbon-degrading bacterium isolated from deep chlorophyll maximum layer seawater of the West Pacific Ocean and emended description of the genus Zavarzinia
Int J Syst Evol Microbiol 72, 005527 (2022); https://doi.org/10.1099/ijsem.0.005527
/content/journal/ijsem/10.1099/ijsem.0.005527
/content/journal/ijsem/10.1099/ijsem.0.005527
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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