Skip to main content
SpringerLink
Log in

Abundance and diversity of Sphingomonas in Shenfu petroleum-wastewater irrigation zone, China

  • Research Article
  • Published:
Environmental Science and Pollution Research Aims and scope Submit manuscript

Abstract

Introduction

Members of the genus Sphingomonas have raised increasing attention due to their ability for polycyclic aromatic hydrocarbon (PAH) degradation and their ubiquity in the environment. However, few studies have revealed the ecological information on the abundance and diversity of Sphingomonas in the environment.

Materials and methods

A primer set targeting the Sphingomonas 16S rRNA gene was designed. The specificity was tested with four petroleum-contaminated soils by construction of clone libraries and further restriction fragment length polymorphism analysis. Subsequently, real time PCR and denaturing gradient gel electrophoresis (DGGE) assays were used to evaluate the abundance and diversity of Sphingomonas in the Shenfu irrigation zone, China.

Results

A genus-specific primer set SA/429f-933r was developed, and 90% of the sequences retrieved from soil clone libraries were related to Sphingomonas. Members of the genus Sphingomonas were detected in all soils, and significant correlation (p < 0.05) was observed between the Sphingomonas abundance and the ratios of PAHs to total petroleum hydrocarbon (TPH). DGGE profiles revealed Sphingomonas population structures differed greatly in different sites. The Sphingomonas diversity was not statistically (p > 0.05) correlated with the contamination level. Some of the soil-derived sequences were not grouped phylogenetically with sequences of known Sphingomonas, indicating new members of the Sphingomonas genus might be present in the Shenfu irrigation zone.

Conclusion

The newly designed Sphingomonas-selective primers were specific and practicable for analyzing Sphingomonas abundance and diversity in petroleum-contaminated soils. The significant correlation between the abundance and the ratios of PAHs to TPH suggested an important role of Sphingomonas in PAH bioremediation.

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
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Google Scholar 

  • Bastiaens L, Springael D, Wattiau P, Harms H, DeWachter R, Verachtert H et al (2000) Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl Environ Microbiol 66:1834–1843

    Article  CAS  Google Scholar 

  • Brito E, Guyoneaud R, Go i-Urriza M, Ranchou-Peyruse A, Verbaere A, Crapez M et al (2006) Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 157:752–762

    Article  CAS  Google Scholar 

  • Bron S, Venema G (1972) Ultraviolet inactivation and excision-repair in Bacillus subtilis II. Differential inactivation and differential repair of transforming markers. Mutat Res Fund Mol Mech Mutagen 15:11–22

    Article  CAS  Google Scholar 

  • Cole J, Chai B, Marsh T, Farris R, Wang Q, Kulam S et al (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443

    Article  CAS  Google Scholar 

  • Eguchi M, Ostrowski M, Fegatella F, Bowman J, Nichols D, Nishino T et al (2001) Sphingomonas alaskensis strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific. Appl Environ Microbiol 67:4945–4954

    Article  CAS  Google Scholar 

  • Fegatella F, Lim J, Kjelleberg S, Cavicchioli R (1998) Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl Environ Microbiol 64:4433–4438

    CAS  Google Scholar 

  • Filion M, St-Arnaud M, Jabaji-Hare SH (2003) Direct quantification of fungal DNA from soil substrate using real-time PCR. J Microbiol Methods 53:67–76

    Article  CAS  Google Scholar 

  • Guo C, Zhou H, Wong Y, Tam N (2005) Isolation of PAH-degrading bacteria from mangrove sediments and their biodegradation potential. Mar Pollut Bull 51:1054–1061

    Article  CAS  Google Scholar 

  • Ho Y, Jackson M, Yang Y, Mueller J, Pritchard P (2000) Characterization of fluoranthene-and pyrene-degrading bacteria isolated from PAH-contaminated soils and sediments. J Ind Microbiol Biotechnol 24:100–112

    Article  CAS  Google Scholar 

  • Jansson J, Leser T, Kowalchuk G, Bruijn F, Head I, Akkermans A et al (2004) Quantitative PCR of environmental samples. Molecular Microbial Ecology Manual 1, 2:445–463

    Google Scholar 

  • Khan IUH, Yadav JS (2004) Real-time PCR assays for genus-specific detection and quantification of culturable and non-culturable mycobacteria and pseudomonads in metalworking fluids. Mol Cell Probe 18:67–73

    Article  CAS  Google Scholar 

  • Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the Ribosomal RNA Operon Copy Number database. Nucleic Acids Res 29:181–184

    Article  CAS  Google Scholar 

  • Laurel DC, Craig SC (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34:2–9

    Google Scholar 

  • Leung K, Chang Y, Gan Y, Peacock A, Macnaughton S, Stephen J et al (1999) Detection of Sphingomonas spp in soil by PCR and sphingolipid biomarker analysis. J Ind Microbiol Biotechnol 23:252–260

    Article  CAS  Google Scholar 

  • Leys N, Ryngaert A, Bastiaens L, Verstraete W, Top E, Springael D (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70:1944–1955

    Article  CAS  Google Scholar 

  • Leys N, Ryngaert A, Bastiaens L, Top E, Verstraete W, Springael D (2005) Culture independent detection of Sphingomonas sp. EPA 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Microb Ecol 49:443–450

    Article  CAS  Google Scholar 

  • Li H, Zhang Y, Zhang C, Chen G (2005) Effect of petroleum-containing wastewater irrigation on bacterial diversities and enzymatic activities in a paddy soil irrigation area. J Environ Qual 34:1073–1080

    Article  CAS  Google Scholar 

  • Li H, Zhang Y, Kravchenko I, Xu H, Zhang C (2007) Dynamic changes in microbial activity and community structure during biodegradation of petroleum compounds: a laboratory experiment. J Environ Sci (China) 19:1003–1013

    Article  Google Scholar 

  • Li H, Zhang Y, Li D, Xu H, Chen G, Zhang C (2009) Comparisons of different hypervariable regions of rrs genes for fingerprinting of microbial communities in paddy soils. Soil Biol Biochem 41:954–968

    Article  CAS  Google Scholar 

  • Murakami Y, Otsuka S, Senoo K (2010) Abundance and community structure of Sphingomonads in leaf residues and nearby bulk soil. Microbes Environ 25:183–189

    Article  Google Scholar 

  • Mushinsky HR (1985) Fire and the Florida sandhill herpetofaunal community: with special attention to responses of Cnemidophorus sexlineatus. Herpetologica 41:333–342

    Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  Google Scholar 

  • Nakatsu C (2007) Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Sci Soc Am J 71:562–571

    Article  CAS  Google Scholar 

  • Padidam M, Beachy R, Fauquet C (1995) Classification and identification of geminiviruses using sequence comparisons. J Gen Virol 76:249–263

    Article  CAS  Google Scholar 

  • Pielou EC (1969) An introduction to mathematical ecology. Wiley, New York

    Google Scholar 

  • Pinyakong O, Habe H, Omori T (2003) The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 49:1–19

    Article  CAS  Google Scholar 

  • Salazar O, Gonzalez I, Genilloud O (2002) New genus-specific primers for the PCR identification of novel isolates of the genera Nocardiopsis and Saccharothrix. Int J Syst Evol Microbiol 52:1411–1421

    Article  CAS  Google Scholar 

  • Saul D, Aislabie J, Brown C, Harris L, Foght J (2005) Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol Ecol 53:141–155

    Article  CAS  Google Scholar 

  • Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana

    Google Scholar 

  • Shi T, Fredrickson J, Balkwill D (2001) Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface. J Ind Microbiol Biotechnol 26:283–289

    Article  CAS  Google Scholar 

  • Shokrollahzadeh S, Azizmohseni F, Golmohammad F, Shokouhi H, Khademhaghighat F (2008) Biodegradation potential and bacterial diversity of a petrochemical wastewater treatment plant in Iran. Bioresource Technol 99:6127–6133

    Article  CAS  Google Scholar 

  • Skovhus TL, Ramsing NB, Holmstrom C, Kjelleberg S, Dahllof I (2004) Real-time quantitative PCR for assessment of abundance of Pseudoalteromonas species in marine samples. Appl Environ Microbiol 70:2373–2382

    Article  CAS  Google Scholar 

  • Ter Braak CJF, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows user's guide: Software for canonical community ordination (version 4.5). Microcomputer Power, Ithaca, NY, USA

  • Tiirola MA, Männistö MK, Puhakka JA, Kulomaa MS (2002) Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in groundwater bioremediation system. Appl Environ Microbiol 68:173–180

    Article  CAS  Google Scholar 

  • Vanbroekhoven K, Ryngaert A, Bastiaens L, Wattiau P, Vancanneyt M, Swings J et al (2004) Streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples. Environ Microbiol 6:1123–1136

    Article  CAS  Google Scholar 

  • Vitzthum F, Geiger G, Bisswanger H, Brunner H, Bernhagen J (1999) A quantitative fluorescence-based microplate assay for the determination of double-stranded DNA using SYBR Green I and a standard ultraviolet transilluminator gel imaging system. Anal Biochem 276:59–64

    Article  CAS  Google Scholar 

  • White DC, Sutton SD, Ringelberg DB (1996) The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol 7:301–306

    Article  CAS  Google Scholar 

  • Widmer F, Seidler R, Gillevet P, Watrud L, Di Giovanni G (1998) A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl Environ Microbiol 64:2545–2553

    CAS  Google Scholar 

  • Wilsey B, Stirling G (2007) Species richness and evenness respond in a different manner to propagule density in developing prairie microcosm communities. Plant Ecol 190:259–273

    Article  Google Scholar 

  • Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H (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

    CAS  Google Scholar 

  • Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I, Ogura H, Kobayashi K (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 conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 52:1485–1496

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Nature Sciences Foundation of China No. 30800157 and the Knowledge Innovation Program of the Chinese Academy of Sciences, No. KSCX2-YW-G-071.

Author information

Authors and Affiliations

  1. Key Laboratory of Terrestrial Ecological Process, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China

    Lisha Zhou, Hui Li, Ying Zhang, Yafei Wang, Siqin Han & Hui Xu

  2. Graduate University of Chinese Academy of Sciences, Beijing, 100049, China

    Lisha Zhou & Yafei Wang

Authors
  1. Lisha Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hui Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ying Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yafei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Siqin Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hui Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hui Li.

Additional information

Responsible editor: Elena Maestri

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhou, L., Li, H., Zhang, Y. et al. Abundance and diversity of Sphingomonas in Shenfu petroleum-wastewater irrigation zone, China. Environ Sci Pollut Res 19, 282–294 (2012). https://doi.org/10.1007/s11356-011-0552-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11356-011-0552-y

Keywords

Search

Navigation