3 Biotech

, 9:35 | Cite as

Diesel degrading bacterial endophytes with plant growth promoting potential isolated from a petroleum storage facility

  • Aneela Iqbal
  • Muhammad ArshadEmail author
  • Raghupathy Karthikeyan
  • Terry J. Gentry
  • Jamshaid Rashid
  • Iftikhar Ahmed
  • Arthur Paul Schwab
Original Article


Thirteen (13) endophytic bacterial strains were isolated from Echinochloa crus-galli (Cockspur grass) and Cynodon dactylon (Bermuda grass) growing in an oil-contaminated site at a petroleum storage and transportation facility. Of the 13 strains assessed for their potential to degrade monoaromatic compounds (phenol, toluene, and xylene) and diesel and for their plant growth promoting (PGP) ability (phosphate solubilization, siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production), isolate J10 (identified as Pseudomonas sp. by 16S rRNA gene sequencing) was found to the best diesel biodegrader with the best PGP traits. The Monod model used for Pseudomonas sp. J10 growth kinetics on diesel fuel as the sole carbon source showed that the maximum specific bacterial growth rate was 0.0644 h− 1 and the half velocity constant (Ks) was estimated as 4570 mg L− 1. The overall growth yield coefficient and apparent growth yield were determined to be 0.271 g h− 1 and 0.127 g cells/g substrate, respectively. Pseudomonas sp. J10 removed 69% diesel in four days as determined by gas chromatographic (GC) analysis. These findings could assist in developing an endophyte assisted efficient diesel biodegradation system using Pseudomonas sp. J10 isolated from Echinochloa crus-galli.


Endophytic bacteria Diesel Phenol Toluene Xylene Phytoremediation 



The authors would like to acknowledge the Higher Education Commission of Pakistan for financing this research through International Research Support Initiative Program. We thank Dr. Sergio Capareda and Dr. Amado Maglinao Jr. for Gas Chromatographic analysis.

Author contributions

AI: performed lab and field work, analyzed the data and wrote the manuscript. MA: supervised, advised lab work and data analyses. RK: advised biodegradation experiments, GC analysis and data analyses. TJG: advised lab work, experimental design and data analysis, JR: helped in GC and kinetic analysis, IA: helped in phylogenetic analysis of the strain, APS: supervised field work and data analyses.

Compliance with ethical standards

Conflict of interest

Authors declare that there are no competing financial as well as individual interests.


  1. Ahmad SA, Ku Ahamad KNE, Wan Johari WL, Halmi MIE, Shukor MY, Yusof MT (2014) Kinetics of diesel degradation by an acrylamide-degrading bacterium. Rend Fis Acc Lincei 25:505–512CrossRefGoogle Scholar
  2. Ahmed I, Sin Y, Paek J, Ehsan M, Hayat R, Iqbal M, Chang YH (2014) Description of Lysinibacillus pakistanensis. Int J Agric Biol 16:447–450Google Scholar
  3. Baek KH, Kim HS, Oh HM, Yoon BD, Kim J, Lee IS (2004) Effects of crude oil, oil components, and bioremediation on plant growth. J Environ Sci Heal A 39:2465–2472CrossRefGoogle Scholar
  4. Baoune H, Hadj-Khelil AO, Pucci G, Sineli P, Loucif L, Polti MA (2018) Petroleum degradation by endophytic Streptomyces spp. isolated from plants grown in contaminated soil of southern Algeria. Ecotoxicol Environ Saf 147:602–609CrossRefGoogle Scholar
  5. Barns SM, Takala SL, Kuske CR (1999) Wide distribution and diversity of members of the bacterial kingdom acidobacterium in the environment. Appl Environ Microbiol 65:1731–1737PubMedPubMedCentralGoogle Scholar
  6. Basak SP, Sarkar P, Pal P (2014) Isolation and characterization of phenol utilizing bacteria from industrial effluent-contaminated soil and kinetic evaluation of their biodegradation potential. J Environ Sci Heal A 49:67–77CrossRefGoogle Scholar
  7. Blain NP, Helgason BL, Germida JJ (2017) Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial historic site. Can J Microbiol 63:502–515CrossRefGoogle Scholar
  8. Cavalva L, Di Gennaro P, Colombo M, Anderoni V, Bernasconi S, Ronco I, Bestelti G (2000) Distribution of catabolic pathways in some hydrocarbon degrading bacteria from a subsurface polluted soil. Res Microbiol 151:877–887CrossRefGoogle Scholar
  9. Chaîneau CH, Morel JL, Oudot J (1997) Phytotoxicity and plant uptake of fuel oil hydrocarbons. J Environ Qual 26:1478–1483CrossRefGoogle Scholar
  10. Chen J, Zhang L, Jin Q, Su C, Zhao L, Liu X, Kou S, Wang Y, Xiao M (2017) Bioremediation of phenol in soil through using a mobile plant-endophyte system. Chemosphere 182:194–202CrossRefGoogle Scholar
  11. Crueger W, Crueger A (1990) Biotechnology: a textbook of Industrial Microbiology, 2nd edn. English edition edited by Brock TD, Sinauer Associates, Sunderland, USA, pp 1–368Google Scholar
  12. Cruz JM, Tamada IS, Lopes PRM, Montagnolli RN, Bidoia ED (2014) Biodegradation and phytotoxicity of biodiesel, diesel, and petroleum in soil. Water Air Soil Pollut 225:1962–1965CrossRefGoogle Scholar
  13. Diaz-Ramos MC, Suarez A, Rubies A, Companyo R, Korte-McIllrick E (2012) Determination of 24 PAHs in drinking water. Agilent technologies application note #5990-7686EN: in sample prepration for chromatography book. Accessed 10 Feb 2017
  14. Dworkin M, Foster J (1958) Experiments with some microorganisms which utilize ethane and hydrogen. J Bacteriol 75:592–601PubMedPubMedCentralGoogle Scholar
  15. Gaskin SE, Bentham RH (2010) Rhizoremediation of hydrocarbon contaminated soil using Australian native grasses. Sci Total Environ 408:3683–3688CrossRefGoogle Scholar
  16. Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60(4):579–598CrossRefGoogle Scholar
  17. Ho YN, Mathew DC, Hsiao SC, Shih CH, Chien MF, Chiang HM, Huang CC (2012) Selection and application of endophytic bacterium Achromobacter xylosoxidans strain F3B for improving phytoremediation of phenolic pollutants. J Hazard Mater 219–220:43–49CrossRefGoogle Scholar
  18. Iqbal A, Arshad M, Hashmi I, Karthikeyan R, Gentry TJ, Schwab AP (2018) Biodegradation of phenol and benzene by endophytic bacteria from refinery wastewater fed Cannabis sativa. Environ Technol 39(13):1705–1714CrossRefGoogle Scholar
  19. Jasim B, Joseph AA, John CJ, Mathew J, Radhakrishnan EK (2014) Isolation and characterization of plant growth promoting endophytic bacteria from the rhizome of Zingiber officinale. 3 Biotech 4:197–204CrossRefGoogle Scholar
  20. Kukla M, Płociniczak T, Piotrowska-Seget Z (2014) Diversity of endophytic bacteria in Lolium perenne and their potential to degrade petroleum hydrocarbons and promote plant growth. Chemosphere 117:40–46CrossRefGoogle Scholar
  21. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  22. Lane D (1991) 16S\23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–147Google Scholar
  23. Ledezma-Villanueva A, Adame-Rodríguez JM, O’Connor-Sánchez IA, Villarreal-Chiu JF, Aréchiga-Carvajal ET (2016) Biodegradation kinetic rates of diesel-contaminated sandy soil samples by two different microbial consortia. Ann Microbiol 66:197–206CrossRefGoogle Scholar
  24. Liu R, Jadeja RN, Zhou Q, Liu Z (2012) Treatment and remediation of petroleum-contaminated soils using selective ornamental plants. Environ Eng Sci 29:494–501CrossRefGoogle Scholar
  25. Louden BC, Haarmann D, Lynne AM (2011) Use of blue agar CAS assay for siderophore detection. J Microbiol Biol Educ 12:51–53CrossRefGoogle Scholar
  26. Lumactud R, Shen SY, Lau M, Fulthorpe R (2016) Bacterial endophytes isolated from plants in natural oil seep soils with chronic hydrocarbon contamination. Front Microbiol 7:755. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Marin MM, Yuste L, Rojo F (2003) Differential expression of the components of the two alkane hydroxylases from Pseudomonas aeruginosa. J Bacteriol 185:3232–3237CrossRefGoogle Scholar
  28. Mohanty G, Mukherji S (2007) Effect of an emulsifying surfactant ondiesel degradation by cultures exhibiting inducible cell surface hydrophobicity. J Chem Technol Biotechnol 82:1004–1011CrossRefGoogle Scholar
  29. Moliterni E, Jimenez-Tusset RG, Villar Rayo M, Rodriguez L, Fernandez FJ, Villasenor J (2012) Kinetics of biodegradation of diesel fuel by enriched microbial consortia from polluted soils. Int J Environ Sci Technol 9:749–758CrossRefGoogle Scholar
  30. Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394CrossRefGoogle Scholar
  31. Paslawski JC, Headley JV, Hill GA, Nemati M (2009) Biodegradation kinetics of trans-4-methyl-1-cyclohexane carboxylic acid. Biodegradation 20:125–133CrossRefGoogle Scholar
  32. Pawlik M, Cania B, Thijs S, Vangronsveld J, Piotrowska-Seget Z (2017) Hydrocarbon degradation potential and plant growth-promoting activity of culturable endophytic bacteria of Lotus corniculatus and Oenothera biennis from a long-term polluted site. Environ Sci Pollut Res 24:19640–19652CrossRefGoogle Scholar
  33. Peng C, Lee JW, Sichani HT, Ng JC (2015) Toxic effects of individual and combined effects of BTEX on Euglena gracilis. J Hazard Mater 284:10–18CrossRefGoogle Scholar
  34. Qi Y-B, Chen-Yu W, Cheng-Yuan L, Zeng-Min L, Cheng-Gang Z (2017) Removal capacities of polycyclic aromatic hydrocarbons (PAHs) by a newly isolated strain from oilfield produced water. Int J Env Res Public Health 14:E215CrossRefGoogle Scholar
  35. Sauvêtre A, May R, Harpaintnera R, Poschenriederc C, Schröder P (2018) Metabolism of carbamazepine in plant roots and endophytic rhizobacteria isolated from Phragmites australis. J Hazard Mater 342:85–95CrossRefGoogle Scholar
  36. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56CrossRefGoogle Scholar
  37. Sharma B, Dangi AK, Shukla P (2018) Contemporary enzyme based technologies for bioremediation: A review. J Environ Manage 210:10–22CrossRefGoogle Scholar
  38. USEPA (1996) Preliminary data summary for the petroleum refining category. EPA 821-R-96-015. U.S. EPA Office of Water, Wash. D.C. Accessed 16 Feb 2017
  39. USEPA (2014) Priority Pollutant List. (Accessed on 10th November, 2017)
  40. Van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503–549CrossRefGoogle Scholar
  41. Wang L, Lina H, Donga Y, He Y, Liua C (2018) Isolation of vanadium-resistance endophytic bacterium PRE01 from Pteris vittata in stone coal smelting district and characterization for potential use in phytoremediation. J Hazard Mater 341:1–9CrossRefGoogle Scholar
  42. Yates GT, Smotzer T (2007) On the lag phase and initial decline of microbial growth curves. J Theor Biol 244:511–517CrossRefGoogle Scholar
  43. Zahid MSB, Iqbal A, Arshad M (2016) Benzene degradation with bacterial strains isolated from rhizosphere of Cannabis sativa being irrigated with petroleum refinery wastewater. Desalin Water Treat 57:17579–17584CrossRefGoogle Scholar
  44. Zhang X, Xu D, Zhu C, Lundaa T, Scherr KE (2012) Isolation and identification of biosurfactant producing and crude oil degrading Pseudomonas aeruginosa strains. Chem Eng J 209:138–146CrossRefGoogle Scholar
  45. Zhang X, Liu X, Wang Q, Chen X, Li H, Wei J, Xu G (2014) Diesel degradation potential of endophytic bacteria isolated from Scirpus triqueter. Int Biodeter Biodegrad 87:99–105CrossRefGoogle Scholar
  46. Zhang J, Xue Q, Gao H, Lai H, Wang P (2016) Bacterial degradation of crude oil using solid formulations of Bacillus strains isolated from oil contaminated soil towards microbial enhanced oil recovery application. RSC Adv 6:5566–5574CrossRefGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.Institute of Environmental Sciences and Engineering, School of Civil and Environmental EngineeringNational University of Sciences and TechnologyIslamabadPakistan
  2. 2.Biological and Agricultural EngineeringTexas A&M UniversityCollege StationUSA
  3. 3.Soil and Crop SciencesTexas A&M UniversityCollege StationUSA
  4. 4.Department of Environmental Science, Faculty of Biological SciencesQuaid-i-Azam UniversityIslamabadPakistan
  5. 5.Bio-resource Conservation Institute (BCI)National Culture Collection of Pakistan (NCCP), National Agricultural Research Centre (NARC)IslamabadPakistan

Personalised recommendations