Skip to main content
SpringerLink
Log in

Sphingomonas caeni sp. nov., a phenolic acid-degrading bacterium isolated from activated sludge

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A Gram-stain-negative, rod-shaped, polar flagellated or stalked and non-spore-forming bacterium, designated LB-2T, was isolated from activated sludge. Growth was observed at 20–30 °C (optimum 28 °C), pH 6.0–8.0 (optimum pH 7.0) and salinity of 0–0.5% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene indicated that strain LB-2T belongs to the genus Sphingomonas and showed the highest sequence similarity (96.7%) and less than 96.7% similarities to other type strains. The genome size of strain LB-2T was 4.10 Mb, with 66.8 mol% G + C content. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strains LB-2T and S. canadensis FWC47T were 77.8% and 21%, respectively. The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18 : 1ω6c) and C16:0. The major polar lipids were aminolipid, glycolipid, sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, four unidentified lipids, glycophospholipid, phosphatidylethanolamine and diphosphatidylglycerol. The predominant respiratory quinone was Q-10 and the major polyamine was sym-homospermidine. On the basis of phenotypic, genotypic and phylogenetic evidences, strain LB-2T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas caeni sp. nov. is proposed. The type strain is LB-2T (GDMCC 1.3630T = NBRC 115,102T).

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Data availability

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain LB-2T is OP610062. The whole-genome shotgun sequence of strains LB-2T and S. canadensis FWC47T have been deposited in GenBank/EMBL/DDBJ under the accession numbers JAPDOK000000000 and JAPDRA000000000, respectively.

References

  • Aziz RK, Bartels D, Best AA, et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  Google Scholar 

  • Bernardet J-F, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    CAS  PubMed  Google Scholar 

  • Beveridge TJ, Lawrence JR, Murray RGE (2007) Sampling and staining for light microscopy. Methods for general and molecular microbiology, 3rd edn. American Society of Microbiology, pp 19–33

  • Busse J, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    Article  CAS  Google Scholar 

  • Busse HJ, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 47:698–708

    Article  CAS  Google Scholar 

  • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    Article  CAS  PubMed  Google Scholar 

  • Cha I, Kang H, Kim H, Joh K (2019) Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of ginkgo biloba. Int J Syst Evol Microbiol 69:3224–3229

    Article  CAS  PubMed  Google Scholar 

  • Chaudhari NM, Gupta VK, Dutta C (2016) BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 6:24373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Chen Q, Wang GX, et al (2015) Sphingomonas chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge. Antonie van Leeuwenhoek 108:703–710

    Article  CAS  PubMed  Google Scholar 

  • Chun J, Oren A, Ventosa A, et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  PubMed  Google Scholar 

  • Chung EJ, Jo EJ, Yoon HS, et al (2011) Sphingomonas oryziterrae sp. nov. and sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (oryza sativa l.). Int J Syst Evol Microbiol 61:2389–2394

    Article  PubMed  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiology 100:221–230

    Article  CAS  Google Scholar 

  • Dong XZ, Cai MY (2001) General Bacterial Identification System Handbook. Beijing, China: Scientific Press, pp. 377–385.

    Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Fraser SL, Jorgensen JH (1997) Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 41:2738–2741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gai Z, Yu B, Li L, et al (2007) Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol 73:2832–2838.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang HD, Wang W, Ma T, et al (2009) Sphingomonas sanxanigenens sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:719–723

    Article  CAS  PubMed  Google Scholar 

  • Jackman SD, Vandervalk BP, Mohamadi H, et al (2017) ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res 27:768–777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kates M (1986) Techniques of lipidology, 2nd edn. Elsevier, Amsterdam

    Google Scholar 

  • Kim SJ, Moon JY, Lim JM, et al (2014) Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 64:926–932

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee I, Ouk Kim Y, Park S-C, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    Article  CAS  PubMed  Google Scholar 

  • Lee JH, Kim DI, Choe HN, et al (2017) Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 67:2834–2841

    Article  CAS  PubMed  Google Scholar 

  • Minnikin DE, O’donnell AG, Goodfellow M, et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274.

    Article  CAS  PubMed  Google Scholar 

  • Niharika N, Jindal S, Kaur J, Lal R (2012) Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil. Int J Syst Evol Microbiol 62: 2997–3002

    Article  CAS  PubMed  Google Scholar 

  • Overbeek R, Olson R, Pusch GD, et al (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42: D206–D214

    Article  CAS  PubMed  Google Scholar 

  • Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution 9:945

    CAS  Google Scholar 

  • 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 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: a laboratory manual, 2nd edn, vol. 3. Cold Springs Harbor Laboratory Press, Cold Springs Harbor, NY

    Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI, Inc

    Google Scholar 

  • Takeuchi M, Hamana K, Hiraishi A (2001) Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51:1405–1417

    Article  CAS  PubMed  Google Scholar 

  • Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    Article  CAS  Google Scholar 

  • Xue H, Piao CG, Wang XZ, et al (2018) Sphingomonas aeria sp. nov., isolated from air. Int J Syst Evol Microbiol 68:2866–2871

    Article  CAS  PubMed  Google Scholar 

  • Yabuuchi E, Yano I, Oyaizu H et al (1990) Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 34:99–119

    Article  CAS  PubMed  Google Scholar 

  • Yabuuchi E, Kosako Y, Fujiwara N et al (2002) Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjuction with Blastomonas ursincola. Int J Syst Evol Microbiol 52:1485–1496

    CAS  PubMed  Google Scholar 

  • Zhang J, Chen S-A, Zheng J-W, et al (2012) Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium. Int J Syst Evol Microbiol 62:495–499

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Yu T, Li X, et al (2019) The fate and enhanced removal of polycyclic aromatic hydrocarbons in wastewater and sludge treatment system: a review. Crit Rev Environ Sci Technol 49:1425–1475

    Article  CAS  Google Scholar 

Download references

Funding

This work was supported by the Natural Science Foundation of Jiangxi Province (20224BAB215005, 20202BAB213024), the Special fund for science and technology program of Jiangsu province (BM2022019) and the Youth Technology Fund Project of Gansu Province (20JR5RA124).

Author information

Authors and Affiliations

  1. College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China

    Bin Liu, Yingying Wan, Mingzhu Huang, Xuelan Chen & Haiyan Ni

  2. Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Bin Liu & Jian He

  3. The Environmental Monitoring Center of Gansu Province, Lanzhou, 730020, China

    E. Chen

Authors
  1. Bin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yingying Wan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. E. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mingzhu Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xuelan Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Haiyan Ni
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jian He
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization, funding acquisition, and supervision: HN; Laboratory work, data analysis and writing-original draft: BL; Writing-review and editing: YW, EC, MH, XC, JH. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Haiyan Ni.

Ethics declarations

Conflict of interest

The research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. All the authors declare that they have no conflict of interest.

Ethical approval

The authors have declared that no ethical issues exist.

Consent to participate

All authors agree to have participated in the research proposed to be published and agree to be published in the journal.

Consent for publication

All authors agree to have participated in the research proposed to be published and agree to be published in the journal.

Human and animal participants

This article does not contain any studies with human participants or animals performed.

by any of the author.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, B., Wan, Y., Chen, E. et al. Sphingomonas caeni sp. nov., a phenolic acid-degrading bacterium isolated from activated sludge. Antonie van Leeuwenhoek 116, 687–695 (2023). https://doi.org/10.1007/s10482-023-01837-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-023-01837-w

Keywords

Search

Navigation