Skip to main content

Aerobic Hydrocarbon-Degrading Alphaproteobacteria: Sphingomonadales

  • Living reference work entry
  • First Online:
Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes

Abstract

The bacterial order Sphingomonadales includes many Sphingomonadaceae and Erythrobacteraceae isolates that have the ability to degrade a wide range of hydrocarbons. Hydrocarbon-degrading members of the Sphingomonadaceae (mainly belonging to the genera Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis) are common Gram-negative aerobic organisms that have been isolated from a wide variety of environments, including temperate and polar soils, marine sediments, and plant surfaces and tissues. They degrade a broad range of mono- and polycyclic aromatic compounds, and the genetics and enzymology of these processes have been elucidated in some detail. Recently, the genome sequences of several hydrocarbon-degrading strains have been determined. In sphingomonads, the biodegradation gene loci are often widely distributed in the genome and are not colocalized as in other hydrocarbon-degrading genera, which has hindered genetic manipulation. The relevant degradative genes are very often located on specific large plasmids (“megaplasmids”). Sphingomonad strains are easy to cultivate and are strong candidates for bioremediation applications, but the recent results suggest that their role in the degradation of recalcitrant aromatics in contaminated soils in situ may be less than previously thought.

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

Access this chapter

Institutional subscriptions

References

  • Adam IKU, Rein A, Miltner A, Fulgêncio ACD, Trapp S, Kästner M (2014) Environmental results and integrated modelling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene). Env Sci Technol 48:8717–8726

    Article  CAS  Google Scholar 

  • Aislabie JM, Balks MR, Foght JM, Waterhouse EJ (2004) Hydrocarbon spills on Antarctic soils: effects and management. Env Sci Technol 38:1265–1274

    Article  CAS  Google Scholar 

  • Aislabie J, Saul DJ, Foght JM (2006) Bioremediation of hydrocarbon-contaminated polar soils. Extremophiles 10:171–179

    Article  CAS  PubMed  Google Scholar 

  • Angel R, Conrad R, Dvorsky M, Kopecky M, Kotilinek M, Hiiesalu I, Schweingruber F, Doležal J (2016) The root-associated microbial community of the world’s highest growing vascular plants. Microb Ecol 72:394–406

    Article  PubMed  PubMed Central  Google Scholar 

  • Armengaud J, Happe B, Timmis KN (1998) Genetic analysis of dioxin dioxygenase of Sphingomonas sp. strain RW1: catabolic genes dispersed on the genome. J Bacteriol 180:3954–3966

    CAS  PubMed  PubMed Central  Google Scholar 

  • Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA, Goodwin LA, Woyke T, Currie CR, Suen G, Poulsen M (2013) Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol 79:3724–3733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Basta T, Keck A, Klein J, Stolz A (2004) Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J Bacteriol 186:3862–3872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Basta T, Buerger S, Stolz A (2005) Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds. Microbiology 151:2025–2037

    Article  CAS  PubMed  Google Scholar 

  • Bastiaens L, Springael D, Dejonghe W, Wattiau P, Verachtert H, Diels L (2001) A transcriptional luxAB reporter fusion responding to fluorene in Sphingomonas sp. LB126 and its initial characterisation for whole-cell bioreporter purposes. Res Microbiol 152:849–859

    Article  CAS  PubMed  Google Scholar 

  • Begonja Kolar A, Hršak D, Fingler S, Ćetković H, Petrić I, Udiković Kolić N (2007) PCB-degrading potential of aerobic bacteria enriched from marine sediments. Int Biodeter Biodegr 60:16–24

    Article  CAS  Google Scholar 

  • Boersma FGH, Warmink JA, Andreote FA, van Elsas JD (2009) Selection of Sphingomonadaceae at the base of Laccaria proxima and Russula exalbicans fruiting bodies. Appl Environ Microbiol 75:1979–1989

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bünz PV, Cook AM (1993) Dibenzofuran 4,4a-dioxygenase from Sphingomonas sp. strain RW1: angular dioxygenation by a three-component enzyme system. J Bacteriol 175:6467–6475

    Article  PubMed  PubMed Central  Google Scholar 

  • Bünz PV, Buck M, Hebenbrock S, Fortnagel P (1999) Stability of mutations in a Sphingomonas strain. Can J Microbiol 45:404–407

    Article  PubMed  Google Scholar 

  • Cavicchioli R, Fegatella F, Ostrowski M, Eguchi M, Gottschal J (1999) Sphingomonads from marine environments. J Ind Microbiol Biotechnol 23:268–272

    Article  CAS  PubMed  Google Scholar 

  • Cavicchioli R, Ostrowski M, Fegatella F, Goodchild A, Guixa-Boixereu N (2003) Life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis). Microb Ecol 45:203–217

    Article  CAS  PubMed  Google Scholar 

  • Chadhain SMN, Moritz EM, Kim E, Zylstra GJ (2007) Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1. J Ind Microbiol Biotechnol 34:605–613

    Article  CAS  PubMed  Google Scholar 

  • Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra G, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM (2016) Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay. PLoS One 11(6):e157008

    Article  CAS  Google Scholar 

  • Cho OY, Choi KY, Zylstra GJ, Kim YS, Kim SK, Lee JH, Sohn HY, Kwon GS, Kim YM, Kim E (2005) Catabolic role of a three-component salicylate oxygenase from Sphingomonas yanoikuyae B1 in polycyclic aromatic hydrocarbon degradation. Biochem Biophys Res Commun 327:656–662

    Article  CAS  PubMed  Google Scholar 

  • Choi DH, Kwon YM, Kwon KK, Kim S-J (2015) Complete genome sequence of Novosphingobium pentaromaticivorans US6-1T. Stand Genomic Sci 10:107

    Article  PubMed  PubMed Central  Google Scholar 

  • Colores GM, Schmidt SK (1999) Colonization of contaminated soil by an introduced bacterium: effects of initial pentachlorophenol levels on the survival of Sphingomonas chlorophenolica strain RA2. J Ind Microbiol Biotechnol 23:326–331

    Article  CAS  PubMed  Google Scholar 

  • Colores GM, Radehaus PM, Schmidt SK (1995) Use of a pentachlorophenol degrading bacterium to bioremediate highly contaminated soil. Appl Biochem Biotech 54:271–275

    Article  CAS  Google Scholar 

  • Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M (2012) The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol 4:184–198

    Article  PubMed  Google Scholar 

  • Coronado E, Roggo C, Johnson DR, van der Meer JR (2012) Genome-wide analysis of salicylate and dibenzofuran metabolism in Sphingomonas wittichii RW1. Front Microbiol 3:300

    Article  PubMed  PubMed Central  Google Scholar 

  • Cunliffe M, Kertesz MA (2006) Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly PAH-contaminated soils. Environ Pollut 144:228–237

    Article  CAS  PubMed  Google Scholar 

  • Cunliffe M, Kawasaki A, Fellows E, Kertesz MA (2006) Effect of inoculum pretreatment on survival, activity and catabolic gene expression of Sphingobium yanoikuyae B1 in an aged polycyclic aromatic hydrocarbon-contaminated soil. FEMS Microbiol Ecol 58:364–372

    Article  CAS  PubMed  Google Scholar 

  • DÁrgenio V, Notomista E, Petrillo M, Cantiello P, Cafaro V, Izzo V, Naso B, Cozzuto L, Durante L, Troncone L, Paolella G, Salvatore F, Di Donato A (2014) Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern. BMC Genomics 15:384

    Article  CAS  Google Scholar 

  • Dimitriou-Christidis P, Autenrieth RL, McDonald TJ, Desai AM (2007) Measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions. Biotechnol Bioeng 97:922–932

    Article  CAS  PubMed  Google Scholar 

  • Ederer MM, Crawford RL, Herwig RP, Orser CS (1997) PCP degradation is mediated by closely related strains of the genus Sphingomonas. Mol Ecol 6:39–49

    Article  CAS  PubMed  Google Scholar 

  • Endo R, Ohtsubo Y, Tsuda M, Nagata Y (2007) Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of gamma-hexachlorocyclohexane in Sphingobium japonicum UT26. J Bacteriol 189:3712–3720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fialho AM, Moreira LM, Granja AT, Popescu AO, Hoffmann K, Sa-Correia I (2008) Occurrence, production, and applications of gellan: current state and perspectives. Appl Microbiol Biotechnol 79:889–900

    Article  CAS  PubMed  Google Scholar 

  • Fida TT, Moreno-Forero SK, Breugelmans P, Heipieper HJ, Röling WFM, Springael D (2017) Physiological and transcriptome response of polycyclic aromatic hydrocarbon degrading Novosphingobium sp. LH128 after inoculation in soil. Env Sci Technol 51:1570–1579

    Article  CAS  Google Scholar 

  • Fredrickson JK, Brockman FJ, Workman DJ, Li SW, Stevens TO (1991) Isolation and characterization of a subsurface bacterium capable of growth on toluene, naphthalene, and other aromatic-compounds. Appl Environ Microbiol 57:796–803

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB, White DC (1995) Aromatic-degrading Sphingomonas Isolates from the deep subsurface. Appl Environ Microbiol 61:1917–1922

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fredrickson JK, Balkwill DL, Romine MF, Shi T (1999) Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp. J Ind Microbiol Biotechnol 23:273–283

    Article  CAS  PubMed  Google Scholar 

  • Gan HM, Hudson AO, Rahman AYA, Chan KG, Savka MA (2013) Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation. BMC Genomics 14:431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gan HM, Gan HY, Ahmand NH, Aziz NA, Hudson AO, Savka MA (2015) Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family. Front Cell Infect Microbiol 4:188

    Article  PubMed  PubMed Central  Google Scholar 

  • Gauthier E, Deziel E, Villemur R, Juteau P, Lepine F, Beaudet R (2003) Initial characterization of new bacteria degrading high-molecular weight polycyclic aromatic hydrocarbons isolated from a 2-year enrichment in a two-liquid-phase culture system. J Appl Microbiol 94:301–311

    Article  CAS  PubMed  Google Scholar 

  • Gibson DT (1999) Beijerinckia sp strain B1: a strain by any other name. J Ind Microbiol Biotechnol 23:284–293

    Article  CAS  PubMed  Google Scholar 

  • Gibson DT, Roberts RL, Wells MC, Kobal VM (1973) Oxidation of biphenyl by a Beijerinckia species. Biochem Biophys Res Commun 50:211–219

    Article  CAS  PubMed  Google Scholar 

  • Gilewicz M, Ni’matuzahroh N, Nadalig T, Budzinski H, Doumenq P, Michotey V, Bertrand JC (1997) Isolation and characterization of a marine bacterium capable of utilizing 2-methylphenanthrene. Appl Microbiol Biotechnol 48:528–533

    Article  CAS  PubMed  Google Scholar 

  • Glaeser SP, Kämpfer P (2014) The family Sphingomonadaceae. In: Rosenberg E, EF DL, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin, pp 642–707

    Google Scholar 

  • Godoy F, Vancanneyt M, Martinez M, Steinbuchel A, Swings J, Rehm BHA (2003) Sphingopyxis chilensis sp nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int J Syst Evol Microbiol 53:473–477

    Article  CAS  PubMed  Google Scholar 

  • Gutman J, Herzberg M, Walker SL (2014) Biofouling of reverse osmosis membranes: positively contributing factors of Sphingomonas. Env Sci Technol 48:13941–13950

    Article  CAS  Google Scholar 

  • Habe H, Ashikawa Y, Saiki Y, Yoshida T, Nojiri H, Omori T (2002) Sphingomonas sp. strain KA1, carrying a carbazole dioxygenase gene homologue, degrades chlorinated dibenzo-p-dioxins in soil. FEMS Microbiol Lett 211:43–49

    Article  CAS  PubMed  Google Scholar 

  • Halden RU, Halden BG, Dwyer DF (1999) Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin from soils inoculated with Sphingomonas sp. strain RW1. Appl Environ Microbiol 65:2246–2249

    CAS  PubMed  PubMed Central  Google Scholar 

  • Happe B, Eltis LD, Poth H, Hedderich R, Timmis KN (1993) Characterization of 2,2′,3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran-p-dioxin-degrading and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1. J Bacteriol 175:7313–7320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hartmann EM, Armengaud J (2014) Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1. Environ Microbiol 16:162–176

    Article  CAS  PubMed  Google Scholar 

  • Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K (2007) Characterization of diverse hydrocarbon-degrading bacteria isolated from Indonesian seawater. Microbes Environ 22:412–415

    Article  Google Scholar 

  • Hashidoko Y, Kitagawa E, Iwahashi H, Purnomo E, Hasegawa T, Tahara S (2007) Design of sphingomonad-detecting probes for a DNA array, and its application to investigate the behavior, distribution, and source of rhizospherous Sphingomonas and other sphingomonads inhabiting an-acid sulfate soil paddock in Kalimantan, Indonesia. Biosci Biotechnol Biochem 71:343–351

    Article  CAS  PubMed  Google Scholar 

  • Horemans B, Breugelmans P, Saeys W, Springael D (2016) Soil-bacterium compatibility model as a decision-making tool for soil bioremediation. Env Sci Technol 51:1605–1615

    Article  CAS  Google Scholar 

  • Horvath M, Ditzelmüller G, Loidl M, Streichsbier F (1990) Isolation and characterization of a 2-(2,4-dichlorophenoxy) propionic acid-degrading soil bacterium. Appl Microbiol Biotechnol 33:213–216

    Article  CAS  PubMed  Google Scholar 

  • Huang Y, Zeng Y, Feng H, Wu Y, Xu X (2015) Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus. Int J Syst Evol Microbiol 65:1531–1536

    Article  CAS  PubMed  Google Scholar 

  • Huang Y, Feng H, Lu H, Zeng Y (2017) Novel 16 S rDNA primers revealed the diversity and habitat-related community structure of sphingomonads in 10 different niches. Antonie Van Leeuwenhoek 110:877–889

    Article  CAS  PubMed  Google Scholar 

  • Iffis B, St-Arnaud M, Hijri M (2014) Bacteria associated with arbuscular mycorrhizal fungi within roots of plants growing in a soil highly contaminated with aliphatic and aromatic petroleum hydrocarbons. FEMS Microbiol Lett 358:44–54

    Article  CAS  PubMed  Google Scholar 

  • Imai R, Nagata Y, Fukuda M, Takagi M, Yano K (1991) Molecular-cloning of a Pseudomonas paucimobilis gene encoding a 17-kilodalton polypeptide that eliminates HCL molecules from gamma-hexachlorocyclohexane. J Bacteriol 173:6811–6819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jogler M, Siemens H, Chen H, Bunk B, Sikorski J, Overmann J (2011) Identification and targeted cultivation of abundant freshwater sphingomonads and analysis of their population substructure. Appl Environ Microbiol 77:7355–7364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jogler M, Chen H, Simon J, Rohde M, Busse HJ, Klenk HP, Tindall BJ, Overmann J (2013) Description of Sphingorhabdus planktonica gen.nov., sp.nov. and relassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen.nov. Int J Syst Evol Microbiol 63:1342–1349

    Article  PubMed  Google Scholar 

  • Johnsen AR, Winding A, Karlson U, Roslev P (2002) Linking of microorganisms to phenanthrene metabolism in soil by analysis of C-13-labeled cell lipids. Appl Environ Microbiol 68:6106–6113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson JE, Hill RT (2003) Sediment microbes of deep-sea bioherms on the Northwest Shelf of Australia. Microb Ecol 46:55–61

    Article  CAS  PubMed  Google Scholar 

  • Kaczmarczyk A, Vorholt JA, Francez-Charlot A (2012) Markerless gene deletion system for sphingomonads. Appl Environ Microbiol 78:3774–3777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kästner M, Breuer-Jammali M, Mahro B (1998) Impact of inoculation protocols, salinity, and pH on the degradation of polycyclic aromatic hydrocarbons (PAHs) and survival of PAH-degrading bacteria introduced into soil. Appl Environ Microbiol 64:359–362

    PubMed  PubMed Central  Google Scholar 

  • Katayama Y, Nishikawa S, Murayama A, Yamasaki M, Morohoshi N, Haraguchi T (1988) The metabolism of biphenyl structures in lignin by the soil bacterium Pseudomonas paucimobilis Syk-6. FEBS Lett 233:129–133

    Article  CAS  Google Scholar 

  • Keck A, Conradt D, Mahler A, Stolz A, Mattes R, Klein J (2006) Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152:1929–1940

    Article  CAS  PubMed  Google Scholar 

  • Khan AA, Wang RF, Cao WW, Franklin W, Cerniglia CE (1996) Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp strain B1, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing. Int J Syst Bacteriol 46:466–469

    Article  CAS  PubMed  Google Scholar 

  • Kim E, Zylstra GJ (1999) Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 23:294–302

    Article  PubMed  CAS  Google Scholar 

  • Kim E, Aversano PJ, Romine MF, Schneider RP, Zylstra GJ (1996) Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface Sphingomonas strains. Appl Environ Microbiol 62:1467–1470

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kolvenbach BA, Corvini PF (2012) The degradation of alkylphenols by Sphingomonas sp. strain TTNP3- a review of seven years of research. Nat Biotechnol 30:88–95

    CAS  Google Scholar 

  • Kosako Y, Yabuuchi E, Naka T, Fujiwara N, Kobayashi K (2000) Proposal of Sphingomonadaceae fam, nov., consisting of Sphingomonas Yabuuchi et al, 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al, 1994, Porphyrobacter Fuerst et al, 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al, 1997, with the type genus Sphingomonas Yabuuchi et al, 1990. Microbiol Immunol 44:563–575

    Article  CAS  PubMed  Google Scholar 

  • Kumar R, Verma H, Haider S, Bajaj A, Sood U, Ponnusamy K, Nagar S, Shakarad MN, Negi RK, Singh Y, Khurana JP, Gilbert JA, Lal R (2017) Comparative genomic analysis reveals habitat-specific genes and regulatory hubs within the genus Novosphingobium. MSystems 2:e00020–e00017

    Article  PubMed  PubMed Central  Google Scholar 

  • Lamberts RF, Christensen JH, Mayer P, Andersen O, Johnsen AR (2008) Isomer-specific biodegradation of methylphenanthrenes by soil bacteria. Environ Sci Technol 42:4790–4796

    Article  CAS  PubMed  Google Scholar 

  • Lee K-B, Liu C-T, Anzai Y, Kim H, Aono T, Oyaizu H (2005) The hierarchical system of the “Alphaproteobacteria”: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 55:1907–1919

    Article  CAS  PubMed  Google Scholar 

  • Leung KT, Cassidy MB, Shaw KW, Lee H, Trevors JT, LohmeierVogel EM, Vogel HJ (1997) Pentachlorophenol biodegradation by Pseudomonas spp. UG25 and UG30. World J Microbiol Biotechnol 13:305–313

    Article  CAS  Google Scholar 

  • Leys N, Ryngaert A, Bastiaens L, Verstraete W, Top EM, 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  PubMed  PubMed Central  Google Scholar 

  • Leys NM, Ryngaert A, Bastiaens L, Top EM, 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  PubMed  Google Scholar 

  • Li J, Luo C, Song M, Dai Q, Jiang L, Zhang D, Zhang G (2017) Biodegradation of phenanthrene in polycyclic aromatic hydrocarbon-contaminated wastewater revealed by coupling cultivation-dependent and -independent approaches. Env Sci Technol 51:3391–3401

    Article  CAS  Google Scholar 

  • Luo YR, Kang SG, Kim S-J, Li N, Lee J-H, Kwon KK (2012) Complete genome sequence of benzo[a]pyrene-degrading bacterium Novosphingobium pentaromaticivorans US6-1. J Bacteriol 194:907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lyu Y, Zheng W, Zheng T, Tian Y (2014) Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromaticivorans US6-1. PLoS One 9:e101438

    Article  PubMed  PubMed Central  Google Scholar 

  • Masai E, Katayama Y, Fukuda M (2007) Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem 71:1–15

    Article  CAS  PubMed  Google Scholar 

  • Megharaj M, Wittich RM, Blasco R, Pieper DH, Timmis KN (1997) Superior survival and degradation of dibenzo-p-dioxin and dibenzofuran in soil by soil-adapted Sphingomonas sp strain RW1. Appl Microbiol Biotechnol 48:109–114

    Article  CAS  Google Scholar 

  • Miller TR, Deicher AL, Salzberg SL, Saunders E, Detter JC, Halden RU (2010) Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol 192:6101–6102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moore FP, Barac T, Borrernans B, Oeyen L, Vangronsveld J, van der Lelie D, Campbell CD, Moore ERB (2006) Endophytic bacterial diversity in poplar trees growing on a BTEX-contaminated site: the characterisation of isolates with potential to enhance phytoremediation. Syst Appl Microbiol 29:539–556

    Article  CAS  PubMed  Google Scholar 

  • Mueller JG, Chapman PJ, Blattmann BO, Pritchard PH (1990) Isolation and characterization of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl Environ Microbiol 56:1079–1086

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nagata Y, Miyauchi K, Takagi M (1999) Complete analysis of genes and enzymes for gamma- hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. J Ind Microbiol Biotechnol 23:380–390

    Article  CAS  PubMed  Google Scholar 

  • Nagata Y, Endo R, Ito M, Ohtsubo Y, Tsuda M (2007) Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. Appl Microbiol Biotechnol 76:741–752

    Article  CAS  PubMed  Google Scholar 

  • Nagata Y, Natsui S, Endo R, Ohtsubo Y, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N, Tsuda M (2011) Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium. Enzym Microb Technol 49:499–508

    Article  CAS  Google Scholar 

  • Nam IH, Kim YM, Schmidt S, Chang YS (2006) Biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by Sphingomonas wittichii strain RW1. Appl Environ Microbiol 72:112–116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nielsen TK, Xu Z, Gözdereliler E, Aamand J, Hansen LH, Sørensen SR (2013) Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid degrading Sphingomonas. PLoS One 8:e83346

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nörtemann B, Knackmuss HJ, Rast HG (1986) Bacterial communities degrading aminonaphthalene-2-sulfonates and hydroxynaphthalene-2-sulfonates. Appl Environ Microbiol 52:1195–1202

    PubMed  PubMed Central  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  PubMed  Google Scholar 

  • Prakash O, Lal R (2006) Description of Sphingobium fuliginis sp nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov. Int J Sys Evol Microbiol 56:2147–2152

    Article  CAS  Google Scholar 

  • Radehaus PM, Schmidt SK (1992) Characterization of a novel Pseudomonas sp. that mineralizes high-concentrations of pentachlorophenol. Appl Environ Microbiol 58:2879–2885

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roh H, Chu KH (2010) A 17beta-estradiol-utilizing bacterium, Sphingomonas strain KC8: part1- characterization and abundance in wastewater treatment plants. Environ Sci Technol 44:4943–4950

    Article  CAS  PubMed  Google Scholar 

  • Romine MF, Fredrickson JK, Li SMW (1999a) Induction of aromatic catabolic activity in Sphingomonas aromaticivorans strain F199. J Ind Microbiol Biotechnol 23:303–313

    Article  CAS  PubMed  Google Scholar 

  • Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD (1999b) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181:1585–1602

    CAS  PubMed  PubMed Central  Google Scholar 

  • Saber DL, Crawford RL (1985) Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol. Appl Environ Microbiol 50:1512–1518

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Segura A, Hernández-Sánchez V, Marquės S, Molina L (2017) Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1 and utilization of this regulatory system as a tool for the detection of PAHs. Sci Total Environ 590–591:381–393

    Article  PubMed  CAS  Google Scholar 

  • Shah AK, Ashtaputre AA (1999) Evaluation of rheological properties of the exopolysaccharide of Sphingomonas paucimobilis GS-1 for application in oil exploration. J Ind Microbiol Biotechnol 23:442–445

    Article  CAS  PubMed  Google Scholar 

  • Sohn JH, Kwon KK, Kang JH, Jung HB, Kim SJ (2004) Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54:1483–1487

    Article  CAS  PubMed  Google Scholar 

  • Stolz A (2009) Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 81:793–811

    Article  CAS  PubMed  Google Scholar 

  • Stolz A (2014) Degradative plasmids from sphingomonads. FEMS Microbiol Lett 350:9–19

    Article  CAS  PubMed  Google Scholar 

  • Story SP, Parker SH, Kline JD, Tzeng TRJ, Mueller JG, Kline EL (2000) Identification of four structural genes and two putative promoters necessary for utilization of naphthalene, phenanthrene and fluoranthene by Sphingomonas paucimobilis var. EPA505. Gene 260:155–169

    Article  CAS  PubMed  Google Scholar 

  • Story SP, Kline EL, Hughes TA, Riley MB, Hayasaka SS (2004) Degradation of aromatic hydrocarbons by Sphingomonas paucimobilis strain EPA505. Arch Environ Contam Toxicol 47:168–176

    Article  CAS  PubMed  Google Scholar 

  • Suzuki S, Hiraishi A (2007) Novosphingobium naphthalenivorans sp nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J Gen Appl Microbiol 53:221–228

    Article  CAS  PubMed  Google Scholar 

  • Tabata M, Ohhata S, Nikawadori Y, Kishida K, Sato T, Kawasumi T, Kato H, Ohtsubo Y, Tsuda M, Nagata Y (2016) Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide. DNA Res 23:581–599

    Article  CAS  PubMed  PubMed Central  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 

  • Tanghe T, Dhooge W, Verstraete W (1999) Isolation of a bacterial strain able to degrade branched nonylphenol. Appl Environ Microbiol 65:746–751

    CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson IP, van der Gast CJ, Ciric L, Singer AC (2005) Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol 7:909–915

    Article  CAS  PubMed  Google Scholar 

  • Tonon LAC, Moreira APB, Thompson F (2014) The family Erythrobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin, pp 213–235

    Chapter  Google Scholar 

  • Toyama T, Momotani N, Ogata Y, Miyamori Y, Inoue D, Sci K, Mori K, Kikuchi S, Ike M (2010) Isolation and characterization of 4-tert-butylphenol-utilizing Sphingobium fuliginis strains from Phragmitis australis rhizosphere sediment. Appl Environ Microbiol 76:6733–6740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uchida H, Hamana K, Miyazaki M, Yoshida T, Nogi Y (2012) Parasphingopyxis lamellibrachiae gen.nov., sp.nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 62:2224–2228

    Article  PubMed  Google Scholar 

  • van Herwijnen R, Joffe B, Ryngaert A, Hausner M, Springael D, Govers HAJ, Wuertz S, Parsons JR (2006) Effect of bioaugmentation and supplementary carbon sources on degradation of polycyclic aromatic hydrocarbons by a soil-derived culture. FEMS Microbiol Ecol 55:122–135

    Article  PubMed  CAS  Google Scholar 

  • Vanbroekhoven K, Ryngaert A, Bastiaens L, Wattiau P, Vancanneyt M, Swings J, De Mot R, Springael D (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  PubMed  Google Scholar 

  • Varman AM, He L, Follenfant R, Wu W, Wemmer S, Wrobel SA, Tang YJ, Singh S (2016) Decoding how a soil bacterium extracts building blocks and metabolic energy from lignolysis provides road map for lignin valorization. Proc Natl Acad Sci U S A 113:5802–5811

    Article  CAS  Google Scholar 

  • Verma H, Kumar R, Oldach O, Sangwan N, Khurana JP, Gilbert JA, Lal R (2014) Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics 15:1014

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vinas M, Sabate J, Espuny MJ, Solanas AM (2005) Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71:7008–7018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Waigi MG, Kang F, Goikavi C, Ling W, Gao Y (2015) Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments; a review. Int Biodeterior Biodegrad 104:333–349

    Article  CAS  Google Scholar 

  • Wang L, Li F, Zhan Y, Zhu L (2016) Shifts in microbial community structure during in situ surfactant-enhanced bioremediation of polycyclic aromatic hydrocarbon-contaminated soil. Environ Sci Pollut Res 23:14451–14461

    Article  CAS  Google Scholar 

  • Wattiau P, Bastiaens L, van Herwijnen R, Daal L, Parsons JR, Renard ME, Springael D, Cornelis GR (2001) Fluorene degradation by Sphingomonas sp. LB126 proceeds through protocatechuic acid: a genetic analysis. Res Microbiol 152:861–872

    Article  CAS  PubMed  Google Scholar 

  • Williams TJ, Erlan H, Ting L, Cavicchioli R (2009) Carbon and nitrogen substrate utilization in the marine bacterium Sphingopyxis alaskensis strain RB2256. ISME J 3:1036–1052

    Article  CAS  PubMed  Google Scholar 

  • Willison JC (2004) Isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source. FEMS Microbiol Lett 241:143–150

    Article  CAS  PubMed  Google Scholar 

  • Wittich RM, Wilkes H, Sinnwell V, Francke W, Fortnagel P (1992) Metabolism of dibenzo-para-dioxin by Sphingomonas sp. strain RW1. Appl Environ Microbiol 58:1005–1010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wittich RM, Busse HJ, Kampfer P, Macedo AJ, Tiirola M, Wieser M, Abraham WR (2007a) Sphingomonas fennica sp nov and Sphingomonas haloaromaticamans sp nov., outliers of the genus Sphingomonas. Int J Syst Evol Microbiol 57:1740–1746

    Article  CAS  PubMed  Google Scholar 

  • Wittich RM, Busse HJ, Kampfer P, Tiirola M, Wieser M, Macedo AJ, Abraham WR (2007b) Sphingobium aromaticiconvertens sp nov., a xenobiotic-compound-degrading bacterium from polluted river sediment. Int J Syst Evol Microbiol 57:306–310

    Article  CAS  PubMed  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 2 genospecies of the genus Sphingomonas. Microbiol Immunol 34:99–119

    Article  CAS  PubMed  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 Blastomas ursincola. Int J Syst Evol Microbiol 52:1485–1496

    CAS  PubMed  Google Scholar 

  • Ye DY, Siddiqi MA, Maccubbin AE, Kumar S, Sikka HC (1996) Degradation of polynuclear aromatic hydrocarbons by Sphingomonas paucimobilis. Environ Sci Technol 30:136–142

    Article  CAS  Google Scholar 

  • Yrjala K, Paulin L, Romantschuk M (1997) Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid. FEMS Microbiol Lett 154:403–408

    Article  CAS  PubMed  Google Scholar 

  • Zhao Q, Hu H, Wang W, Peng H, Zhang X (2015) Genome sequence of Sphingobium yanoikuyae B1, a polycyclic hydrocarbon-degrading strain. Genome Announc 3:e01522–e01514

    PubMed  PubMed Central  Google Scholar 

  • Zhuang L, Liu Y, Wang L, Wang W, Shao Z (2015) Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 65:3714–3719

    Article  CAS  PubMed  Google Scholar 

  • Zylstra GJ, Kim E (1997) Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 19:408–414

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Andreas Stolz .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this entry

Cite this entry

Kertesz, M.A., Kawasaki, A., Stolz, A. (2018). Aerobic Hydrocarbon-Degrading Alphaproteobacteria: Sphingomonadales. In: McGenity, T. (eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-60053-6_9-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-60053-6_9-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-60053-6

  • Online ISBN: 978-3-319-60053-6

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics