1887

Abstract

Two Gram-stain-negative, short rod-shaped and non-flagellated strains, designated 17-4A and L52-1-41, were isolated from the surface seawater of the Indian Ocean and South China Sea, respectively. The 16S rRNA genes of the two strains shared sequence similarity of 99.45 %. Strain 17-4A shared the highest 16S rRNA gene similarity of 98.02 % with EBR-8-1, followed by BN9 (97.47 %), MJ07 (96.93 %), Ch07 (96.68 %), DCY25 (96.65 %), PB3-7B (96.63 %), 24 (96.34 %), 54Pin (96.28 %) and B201 (96.05 %). L52-1-41 shared the highest 16S rRNA gene similarity of 97.74 % with EBR-8-1, followed by BN9 (97.47 %), MJ07 (96.65 %), Ch07 (96.41 %), DCY25 (96.37 %), PB3-7B (96.35 %), B201 (96.28 %), and 24 (96.06 %). The results of phylogenetic analyses indicated that 17-4A and L52-1-41 formed a stable, distinct and highly supported lineage affiliated to the genus . The results of the digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses indicated that they represented a single species. They featured similar genomic DNA G+C contents of 53.2–53.4 mol%. Activities of catalase and oxidase were negative for both strains. The fatty acids patterns of 17-4A and L52-1-41 were most similar, mostly comprised of C, Ccyclo, C, Cω9 and summed feature 8 (Cω7 and/or C ω6). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The respiratory quinone of the two strains was Q-8. Hence, on the basis of the phenotypic, chemotaxonomic and genotypic data presented in this study, we proposed the classification of both strains as representatives of a novel species named sp. nov., with the type strain 17-4A (=MCCC 1A12670=KCTC 62121=NBRC 113794), and another strain L52-1-41 (=MCCC 1A05046=KCTC 52313).

Funding
This study was supported by the:
  • National Infrastructure of Microbial Resources of China (Award NIMR-2019-9)
    • Principle Award Recipient: Zongze Shao
  • NSFC Hydrosphere Project (Award 91851203)
    • Principle Award Recipient: Zongze Shao
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004202
2020-05-05
2024-10-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/5/3483.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004202&mimeType=html&fmt=ahah

References

  1. Stolz A, Bürger S, Kuhm A, Kämpfer P, Busse H-J. Pusillimonas noertemannii gen. nov., sp. nov., a new member of the family Alcaligenaceae that degrades substituted salicylates. Int J Syst Evol Microbiol 2005; 55:1077–1081 [View Article][PubMed][PubMed]
    [Google Scholar]
  2. Srinivasan S, Kim MK, Sathiyaraj G, Kim Y-J, Yang D-C. Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:1783–1787 [View Article][PubMed][PubMed]
    [Google Scholar]
  3. Lee M, Woo S-G, Chae M, Ten LN. Pusillimonas soli sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 2010; 60:2326–2330 [View Article][PubMed][PubMed]
    [Google Scholar]
  4. Park MS, Park Y-J, Jung JY, Lee SH, Park W et al. Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas . Int J Syst Evol Microbiol 2011; 61:2901–2906 [View Article][PubMed][PubMed]
    [Google Scholar]
  5. Jin L, Ko S-R, Cui Y, Lee CS, Oh H-M et al. Pusillimonas caeni sp. nov., isolated from a sludge sample of a biofilm reactor. Antonie van Leeuwenhoek 2017; 110:125–132 [View Article][PubMed][PubMed]
    [Google Scholar]
  6. Koh H-W, Song M-S, Do K-T, Kim H, Park S-J. Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge. Int J Syst Evol Microbiol 2019; 69:1041–1046 [View Article][PubMed][PubMed]
    [Google Scholar]
  7. Hilyard EJ, Jones-Meehan JM, Spargo BJ, Hill RT. Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth river sediments. Appl Environ Microbiol 2008; 74:1176–1182 [View Article][PubMed][PubMed]
    [Google Scholar]
  8. Karvelis L, Gasparavičiūtė R, Klimavičius A, Jančienė R, Stankevičiūtė J et al. Pusillimonas sp. 5HP degrading 5-hydroxypicolinic acid. Biodegradation 2014; 25:11–19 [View Article][PubMed][PubMed]
    [Google Scholar]
  9. Stabler RA, Negus D, Pain A, Taylor PW. Draft genome sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, soil bacteria that cooperate to degrade the poly-γ-d-glutamic acid anthrax capsule. Genome Announc 2013; 1:e00057–12 [View Article][PubMed][PubMed]
    [Google Scholar]
  10. Huang X-F, Guan W, Liu J, Lu L-J, Xu J-C et al. Characterization and phylogenetic analysis of biodemulsifier-producing bacteria. Bioresour Technol 2010; 101:317–323 [View Article][PubMed][PubMed]
    [Google Scholar]
  11. Shapiro OH, Kushmaro A, Brenner A. Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater. Isme J 2010; 4:327–336 [View Article][PubMed][PubMed]
    [Google Scholar]
  12. Li J, Huang Z, Lai Q, Liu X, Wang G et al. Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:4930–4935 [View Article][PubMed][PubMed]
    [Google Scholar]
  13. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed][PubMed]
    [Google Scholar]
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed][PubMed]
    [Google Scholar]
  15. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed][PubMed]
    [Google Scholar]
  16. Lagesen K, Hallin P, Rødland E, Stærfeldt HH, Rognes T et al. RT: RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 2007; 35:3100–3108
    [Google Scholar]
  17. 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][PubMed]
    [Google Scholar]
  18. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed][PubMed]
    [Google Scholar]
  19. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article][PubMed][PubMed]
    [Google Scholar]
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed][PubMed]
    [Google Scholar]
  21. 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][PubMed]
    [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed][PubMed]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed][PubMed]
    [Google Scholar]
  25. Yoon S-H, Ha S-M, 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][PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed][PubMed]
    [Google Scholar]
  27. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article][PubMed][PubMed]
    [Google Scholar]
  28. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  30. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  31. Ross HNM, Collins MD, Tindall BJ, Grant WD. A rapid procedure for the detection of archaebacterial lipids in halophilic bacteria. Microbiology 1981; 123:75–80 [View Article]
    [Google Scholar]
  32. Collins M. Isoprenoid quinone analyses in bacterial classification and identification. Society for Applied Bacteriology Technical Series 1985; 20:267–287
    [Google Scholar]
  33. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [View Article]
    [Google Scholar]
  34. Busse H-J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . System 1988; 11:1–8
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004202
Loading
/content/journal/ijsem/10.1099/ijsem.0.004202
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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