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Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Xanthomonadales

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Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes

Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

The Xanthomonadales comprises a morphologically and physiologically diverse order of bacteria, though its classification has been contentious pertaining to its division into families. Currently, the order is divided into the two families, Xanthomonadaceae and Rhodanobacteraceae, that collectively contain members from approximately 29 genera. Hydrocarbon degraders of the family Xanthomonadaceae include members of the genera Arenimonas, Luteimonas, Pseudoxanthomonas, Stenotrophomonas, Xanthomonas, and Xylella, whereas those of the family Rhodanobacteraceae include Dokdonella, Dyella, Frateuria, Luteibacter, Oleiagrimonas, Rhodanobacter, and Rudaea. These organisms are categorized as generalist hydrocarbon-degraders based on their ability to also utilize various other carbon substrates as a sole source of carbon and energy. To-date, of the nine recognized genera of obligate hydrocarbonoclastic bacteria that are able to degrade hydrocarbons almost exclusively as a preferred carbon and energy source, only Algiphilus and Polycyclovorans are represented within the order Xanthomonadales, principally within the family Xanthomonadaceae. The type species of these two genera are Algiphilus aromaticivorans and Polycyclovorans algicola, which respectively were originally isolated from the phycosphere of a marine dinoflagellate and diatom. Members of these two genera have also been identified living associated with various other species of marine eukaryotic phytoplankton, and sequencing surveys have identified their presence in a wide variety of environments that include oil-contaminated and noncontaminated marine and terrestrial environments as well as human skin.

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References

  • Bacosa HP, Inoue C (2015) Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan. J Hazard Mater 283:689–697

    Article  CAS  PubMed  Google Scholar 

  • Braaz R, Armbruster W, Jendrossek D (2005) Heme-dependent rubber oxygenase RoxA of Xanthomonas sp. cleaves the carbon backbone of poly(cis-1,4-isoprene) by a dioxygenase mechanism. Appl Environ Microbiol 71:2473–2478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cébron A, Louvel B, Faure P, France-Lanord C, Chen Y, Murrell JC, Leyval C (2011) Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates. Environ Microbiol 13:722–736

    Article  PubMed  Google Scholar 

  • Chang H-K, Zylstra GJ (2010) Xanthomonads. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg, pp 1805–1811. https://doi.org/10.1007/978-3-540-77587-4_131

    Chapter  Google Scholar 

  • Chen S, Yin H, Ye J, Peng H, Zhang N, He B (2013) Effect of copper(II) on biodegradation of benzo[a]pyrene by Stenotrophomonas maltophilia. Chemosphere 90:1811–1820

    Article  CAS  PubMed  Google Scholar 

  • Chen S, Yin H, Ye J, Peng H, Liu Z, Dang Z, Chang J (2014) Influence of co-existed benzo[a]pyrene and copper on the cellular characteristics of Stenotrophomonas maltophilia during biodegradation and transformation. Bioresour Technol 158:181–187

    Article  CAS  PubMed  Google Scholar 

  • Cheng T-W, Chang Y-H, Tang S-L, Tseng C-H, Chiang P-W, Chang K-T, Sun C-H, Chen Y-G, Kuo H-C, Wang C-H, Chu P-H, Song S-R, Wang P-L, Lin L-H (2012) Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano. ISME J 6:2280–2290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choi EJ, Jin HM, Lee SH, Math RK, Madsen EL, Jeon CO (2013) Comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) degradation pathways of Pseudoxanthomonas spadix BD-a59. Appl Environ Microbiol 79:663–671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fang T, Wang H, Huang Y, Zhou H, Dong P (2015) Oleiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield. Int J Syst Evol Microbiol 65:1666–1671

    Article  CAS  PubMed  Google Scholar 

  • Friedrich MM, Lipski A (2008) Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter. Int J Syst Evol Microbiol 58:2324–2329

    Article  CAS  PubMed  Google Scholar 

  • Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA (2009) Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gutierrez T (2017) Cultivating aerobic hydrocarbon-degrading bacteria from micro-algae. In: McGenity TJ et al (eds) Hydrocarbon and lipid microbiology protocols, Springer protocols handbooks. Springer, Berlin/Heidelberg. https://doi.org/10.1007/8623_2014_1

    Google Scholar 

  • Gutierrez T, Green DH, Nichols PD, Whitman WB, Semple KT, Aitken MD (2012) Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov. Int J Syst Evol Microbiol 62:2743–2749

    Article  CAS  PubMed  Google Scholar 

  • Gutierrez T, Green DH, Whitman WB, Nichols PD, Semple KT, Aitken MD (2013) Polycyclovorans algicola gen. nov., sp. nov., an aromatic hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton. Appl Environ Microbiol 79:205–214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamann C, Hegemann J, Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173:255–263

    Article  CAS  PubMed  Google Scholar 

  • Head IM, Jones DM, Röling WF (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4:173–182

    Article  CAS  PubMed  Google Scholar 

  • Jiang X, Jiao N (2016) Vertical distribution of bacterial communities in the Indian Ocean as revealed by analyses of 16S rRNA and nasA genes. Indian J Microbiol 56:309–317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Juhasz AL, Stanley GA, Britz ML (2000) Microbial degradation and detoxification of high molecular weight polycyclic aromatic hydrocarbons by Stenotrophomonas maltophilia strain VUN 10,003. Lett Appl Microbiol 30:396–401

    Article  CAS  PubMed  Google Scholar 

  • Juteau P, Larocque R, Rho D, LeDuy A (1999) Analysis of the relative abundance of different types of bacteria capable of toluene degradation in a compost biofilter. Appl Microbiol Biotechnol 52:863–868

    Article  CAS  PubMed  Google Scholar 

  • Kanaly RA, Harayama S, Watanabe K (2002) Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing bacterial consortium. Appl Environ Microbiol 68:5826–5833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim JS, Crowley DE (2007) Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits. Appl Environ Microbiol 73:4579–4591

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, NISC Comparative Sequence Program, Murray PR, Turner ML, Segre JA (2012) Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22:850–859

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larsen H (1986) Halophilic and halotolerant microorganisms – an overview and historical perspective. FEMS Microbiol Rev 39:3–7

    Article  CAS  Google Scholar 

  • Lee EY, Jun YS, Cho K-S, Ryu HW (2002) Degradation characteristics of toluene, benzene, ethylbenzene, and xylene by Stenotrophomonas maltophilia T3-c. J Air Waste Manage Assoc 52:400–406

    Article  CAS  Google Scholar 

  • Li A, Qu YY, Zhou JT, Gou M (2009) Isolation and characteristics of a novel biphenyl degrading bacterial strain, Dyella ginsengisoli LA-4. J Environ Sci 21:211–217

    Article  CAS  Google Scholar 

  • Liu R, Zhang Y, Ding R, Li D, Gao Y, Yang M (2009) Comparison of archaeal and bacterial community structures in heavily oil-contaminated and pristine soils. J Biosci Bioeng 108:400–407

    Article  CAS  PubMed  Google Scholar 

  • Luo YR, Tian Y, Huang X, Yan CL, Hong HS, Lin GH, Zheng TL (2009) Analysis of community structure of a microbial consortium capable of degrading benzo[a]pyrene by DGGE. Mar Pollut Bull 58:1159–1163

    Article  CAS  PubMed  Google Scholar 

  • Mahjoubi M, Jaouani A, Guesmi A, Amor SB, Jouini A, Cherif H, Najjari A, Boudabous A, Koubaa N, Cherif A (2013) Hydrocarbonoclastic bacteria isolated from petroleum contaminated sites in Tunisia: isolation, identification and characterization of the biotechnological potential. New Biotechnol 30:723–733

    Article  CAS  Google Scholar 

  • Mangwani N, Shukla SK, Kumari S, Rao TS, Das S (2014) Characterization of Stenotrophomonas acidaminiphila NCW-702 biofilm for implication in the degradation of polycyclic aromatic hydrocarbons. J Appl Microbiol 117:1012–1024

    Article  CAS  PubMed  Google Scholar 

  • Manickam N, Misra R, Mayilraj S (2007) A novel pathway for the biodegradation of γ-hexachlorocyclohexane by a Xanthomonas sp. strain ICH12. J Appl Microbiol 102:1468–1478

    Article  CAS  PubMed  Google Scholar 

  • Muangchinda C, Pansri R, Wongwongsee W, Pinyakong O (2013) Assessment of polycyclic aromatic hydrocarbon biodegradation potential in mangrove sediment from Don Hoi Lot, Samut Songkram Province, Thailand. J Appl Microbiol 114:1311–1324

    Article  CAS  PubMed  Google Scholar 

  • Mukherjee P, Roy P (2013) Copper enhanced monooxygenase activity and FT-IR spectroscopic characterization of biotransformation products in trichloroethylene degrading bacterium: Stenotrophomonas maltophilia PM102. Biomed Res Int 2013. https://doi.org/10.1155/2013/723680

  • Nalin R, Simonet P, Vogel TM, Normand P (1999) Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 49:19–23

    Article  PubMed  Google Scholar 

  • Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS (2015) A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie Van Leeuwenhoek 107(2):467–485

    Article  PubMed  Google Scholar 

  • Nopcharoenkul W, Netsakulnee P, Pinyakong O (2013) Diesel oil removal by immobilized Pseudoxanthomonas sp. RN402. Biodegradation 24:387–397

    Article  CAS  PubMed  Google Scholar 

  • Palleroni NJ, Port AM, Chang H-K, Zylstra GJ (2004) Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the γ-Proteobacteria active in alkane and aromatic hydrocarbon degradation. Int J Syst Evol Microbiol 54:1203–1207

    Article  CAS  PubMed  Google Scholar 

  • Papizadeh M, Ardakani MR, Motamedi H, Rasouli I, Zarei M (2011) C–S targeted biodegradation of dibenzothiophene by Stenotrophomonas sp. NISOC-04. Appl Biochem Biotechnol 165:938–948

    Article  CAS  PubMed  Google Scholar 

  • Patel V, Cheturvedula S, Madamwar D (2012) Phenanthrene degradation by Pseudoxanthomonas sp. DMVP2 isolated from hydrocarbon contaminated sediment of Amlakhadi canal, Gujarat, India. J Hazard Mater 201–202:43–51

    Article  PubMed  Google Scholar 

  • Patel V, Munot H, Shouche Y, Madamwar D (2014) Response of bacterial community structure to seasonal fluctuation and anthropogenic pollution on coastal water of Alang-Sosiya ship breaking yard, Bhavnagar, India. Bioresour Technol 161:362–370

    Article  CAS  PubMed  Google Scholar 

  • Saddler GS, Bradbury JF (2005) Family I. Xanthomonadaceae fam. nov. The Proteobacteria, part B. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, p 63

    Chapter  Google Scholar 

  • Singh SK, Kotakonda A, Kapardar RK, Kankipati HK, Rao PS, Sankaranarayanan PM, Vetaikorumagan SR, Gundlapally SR, Nagappa R, Shivaji S (2015) Response of bacterioplankton to iron fertilization of the Southern Ocean. Antarctica Front Microbiol 6:863. https://doi.org/10.3389/fmicb.2015.00863

    PubMed  Google Scholar 

  • Sivakumar T, Sivasankara Narayani S, Shankar T, Vijayabaskar P (2012) Optimization of cultural conditions for exopolysaccharides production by Frateuria aurentia. Int J Appl Biol Pharm Technol 3:133–143

    CAS  Google Scholar 

  • Sheu S-Y, Cho N-T, Arun AB, Chen W-M (2011) Proposal of Solimonas aquatic sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli. Int J Syst Evol Microbiol 61:2284–2291

    Google Scholar 

  • Somaraja PK, Gayathri D, Ramaiah N (2013) Molecular characterization of 2-chlorobiphenyl degrading Stenotrophomonas maltiphilia GS-103. Bull Environ Contam Toxicol 91:148–153

    Article  CAS  PubMed  Google Scholar 

  • Susilaningsih D, Okazaki F, Yopi, Widyastuti Y, Harayama S (2013) Isolation and screening of surfactant-producing bacteria from Indonesian marine environments and its application on bioremediation. Ann Bogorienses 17:43–53

    Google Scholar 

  • Uhlik O, Wald J, Strejcek M, Musilova L, Ridl J, Hroudova M, Vicek C, Cardenas E, Mackova M, Macek T (2012) Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. PLoS One 7(7):e40653. https://doi.org/10.1371/journal.pone.0040653

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xin Y, Cao X, Wu P, Xue S (2014) Luteimonas dalianensis sp. nov., an obligate marine bacterium isolated from seawater. J Microbiol 52:729–733

    Article  CAS  PubMed  Google Scholar 

  • Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 18:257–266

    Article  CAS  PubMed  Google Scholar 

  • Yi J-L, Wang J, Li Q, Liu Z-X, Zhang L, Liu A-X, Yu J-F (2015) Draft genome sequence of the bacterium Lysobacter capsici X2-3, with a broad spectrum of antimicrobial activity against multiple plant-pathogenic microbes. Genome Announc 3(3):e00589-15

    Article  PubMed  PubMed Central  Google Scholar 

  • Young C-C, Kämpfer P, Ho M-J, Busse H-J, Huber BE, Arun AB, Shen F-T, Lai W-A, Rekha PD (2007) Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site. Int J Syst Evol Microbiol 57:2790–2793

    Article  CAS  PubMed  Google Scholar 

  • Yuste L, Corbella ME, Turiegano MJ, Karlson U, Puyet A, Rojo F (2000) Characterization of bacterial strains able to grow on high molecular mass residues from crude oil processing. FEMS Microbiol Ecol 32:69–75

    Article  CAS  PubMed  Google Scholar 

  • Zeng J, Deng L-J, Lou K, Zhang T, Yang H-M, Shi Y-W, Lin Q (2014) Molecular characterization of the planktonic microorganisms in water of two mountain brackish lakes. J Basic Microbiol 54:509–520

    Article  CAS  PubMed  Google Scholar 

  • Zhang D-C, Liu H-C, Xin Y-H, Zhou Y-G, Schinner F, Margesin R (2010) Luteimonas terricola sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 60:1581–1584

    Article  CAS  PubMed  Google Scholar 

  • Zhou Y, Zhang Y-Q, Zhi X-Y, Wang X, Dong J, Chen Y, Lai R, Li W-J (2008) Description of Sinobacter flavus gen. nov., sp. nov., and proposal of Sinobacteraceae fam. nov. Int J Syst Evol Microbiol 58:184–189

    Article  CAS  PubMed  Google Scholar 

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Gutierrez, T. (2017). Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Xanthomonadales . 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_4-1

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