Skip to main content
SpringerLink
Log in
Book cover

Microbial Action on Hydrocarbons pp 387–414Cite as

Plant-Microbe Association for Bioremediation of Hydrocarbon Substrates

  • Chapter
  • First Online:

  • 1273 Accesses

Abstract

Advancement in the standards of life quality along with awareness for environmental issues and the remediation of contaminated sites has attracted attention from society. Due to high cost of mechanical and chemical techniques for hydrocarbon remediation, the utilization of biological processes is gaining considerable attention. Plant-microbe association has been widely studied during the second half of the last century yet focusing on pathogenicity and plant-saprophytic associations like nitrogen fixation, improving soil nutrient cycles and plant growth, etc. However during the last decade, the emphasis has been shifted upon microbial communication with plants for remediation of hydrocarbon-contaminated sites. The efficacy of the remediation process mainly depends on the availability and performance of microbes having degradation genes responsible for enzymatic breakdown of organic contaminants as well as chemotaxis for hydrocarbons, biofilm production, cell surface hydrophobicity, and ability to produce biosurfactants. The rhizosphere and apoplast of the plants have been testified as the potential dwellings for microbes having degradation genes, but comparatively petite information is available about the degradation activities and metabolic pathways of endophytes. Diversity of biological systems warrants deep understanding of the mechanisms involved for utilizing plant-microbe association for bioremediation of hydrocarbons. This chapter focuses on an insight of the existing biological approaches for bioremediation of hydrocarbon-contaminated sites with emphasis upon required advancements in bioremediation and phytoremediation strategies to improve efficiency.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Abbasnezhad H, Gray M, Foght JM (2011) Influence of adhesion on aerobic biodegradation and bioremediation of liquid hydrocarbons. Appl Microbiol Biotechnol 92:653–675

    Article  CAS  PubMed  Google Scholar 

  • Afzal M, Yousaf S, Reichenauer TG, Kuffner M, Sessitsch A (2011) Soil type affects plant colonization, activity and catabolic gene expression of inoculated bacterial strains during phytoremediation of diesel. J Hazard Mater 186:1568–1575

    Article  CAS  PubMed  Google Scholar 

  • Afzal M, Yousaf S, Reichenauer TG, Sessitsch A (2012) The inoculation method affects colonization and performance of bacterial inoculant strains in the phytoremediation of soil contaminated with diesel oil. Int J Phytoremediation 14:35–47

    Article  PubMed  Google Scholar 

  • Akbari A, Ghoshal S (2014) Pilot-scale bioremediation of a petroleum hydrocarbon contaminated clayey soil from a sub-arctic site. J Hazard Mater 280:595–602

    Article  CAS  PubMed  Google Scholar 

  • Almeida R, Mucha AP, Teixeira C, Bordalo AA, Almeida CMR (2013) Biodegradation of petroleum hydrocarbons in estuarine sediments: metal influence. Biodegradation 24:111–123

    Article  CAS  PubMed  Google Scholar 

  • Álvarez LM, Balbo AL, Mac Cormack W, Ruberto L (2015) Bioremediation of a petroleum hydrocarbon-contaminated Antarctic soil: optimization of a biostimulation strategy using response-surface methodology (RSM). Cold Reg Sci Technol 119:61–67

    Article  Google Scholar 

  • Andria V, Reichenauer TG, Sessitsch A (2009) Expression of alkane monooxygenase (alkB) genes by plant-associated bacteria in the rhizosphere and endosphere of Italian ryegrass (Lolium multiflorum L.) grown in diesel contaminated soil. Environ Pollut 157:3347–3350

    Article  CAS  PubMed  Google Scholar 

  • Anokhina TO, Kochetkov VV, Zelenkova NF, Balakshina VV, Boronin AM (2004) Biodegradation of phenanthrene by Pseudomonas bacteria bearing rhizospheric plasmids in model plant–microbial associations. Appl Biochem Microbiol 40:568–572

    Article  CAS  Google Scholar 

  • Ayed HB, Jemil N, Maalej H, Bayoudh A, Hmidet N, Nasri M (2015) Enhancement of solubilization and biodegradation of diesel oil by biosurfactant from Bacillus amyloliquefaciens An6. Int Biodeterior Biodegrad 99:8–14

    Article  CAS  Google Scholar 

  • Azubuik CC, Chikere CB, Okpokwasili GC (2016) Bioremediation techniques–classification based on site of application: principles, advantages, limitations and prospects. World J Microbiol Biotechnol 32:1–18

    Article  CAS  Google Scholar 

  • Balcom IN, Crowley DE (2010) Isolation and characterization of pyrene metabolizing microbial consortia from the plant rhizoplane. Int J Phytoremediation 12:599–615

    Article  CAS  PubMed  Google Scholar 

  • Banat IM, Satpute SK, Cameotra SS, Patil R, Nyayanit NV (2014) Cost effective technologies and renewable substrates for biosurfactants’ production. Front Microbiol 5:697

    Article  PubMed  PubMed Central  Google Scholar 

  • Barac T, Taghavi S, Borremans B, Provoost A, Oeyen L, Colpaert JV, Vangronsveld J, van der Lelie D (2004) Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotechnol 22:583–588

    Article  CAS  PubMed  Google Scholar 

  • Barac T, Weyens N, Oeyen L, Taghavi S, van der Lelie D, Dubin D, Spliet M, Vangronsveld J (2009) Fields note: hydraulic containment of a BTEX plum using poplar trees. Int J Phytoremediation 11:416–424

    Article  CAS  PubMed  Google Scholar 

  • Bastida F, Jehmlich N, Lima K, Morris B, Richnow H, Hernández T, von Bergen M, García C (2016) The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost. J Proteome 1(135):162–169

    Article  CAS  Google Scholar 

  • Basumatary B, Bordoloi S, Sarma HP (2012) Crude oil-contaminated soil phytoremediation by using Cyperus brevifolius (Rottb.) Hassk. Water Air Soil Pollut 223:3373–3383

    Article  CAS  Google Scholar 

  • Becerra-Castro C, Kidd P, Prieto-Fernández Á, Weyens N, Acea M-J, Vangronsveld J (2011) Endophytic and rhizoplane bacteria associated with Cytisus striatus growing on hexachlorocyclohexane-contaminated soil: isolation and characterization. Plant Soil 340:413–433

    Article  CAS  Google Scholar 

  • Bell TH, Joly S, Pitre FE, Yergeau E (2014) Increasing phytoremediation efficiency and reliability using novel omics approaches. Trends Biotechnol 32:271–280

    Article  CAS  PubMed  Google Scholar 

  • Beškoski VP, Gojgić-Cvijović G, Milić J, Ilić M, Miletić S, Šolević T, Vrvić MM (2011) Ex situ bioremediation of a soil contaminated by mazut (heavy residual fuel oil)–a field experiment. Chemosphere 83:34–40

    Article  CAS  PubMed  Google Scholar 

  • Bezza FA, Chirwa EMN (2015) Biosurfactant from Paenibacillus dendritiformis and its application in assisting polycyclic aromatic hydrocarbon (PAH) and motor oil sludge removal from contaminated soil and sand media. Process Saf Environ Prot 98:354–364

    Article  CAS  Google Scholar 

  • Bordoloi NK, Konwar BK (2009) Bacterial biosurfactant in enhancing solubility and metabolism of petroleum hydrocarbons. J Hazard Mater 170:495–505

    CAS  PubMed  Google Scholar 

  • Canosa I, Sanchez-Romero JM, Yuste L, Rojo F (2000) A positive feedback mechanism controls expression of AlkS, the transcriptional regulator of the Pseudomonas oleovorans alkane degradation pathway. Mol Microbiol 35:791–799

    Article  CAS  PubMed  Google Scholar 

  • Cao B, Nagarajan K, Loh KC (2009) Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 85(2):207–228

    Article  CAS  PubMed  Google Scholar 

  • Child R, Anderson A, Miller C, Liang Y, Sims R (2007a) Pyrene mineralization by sp. strain KMS in a barley rhizosphere. J Environ Qual 36:1260–1265

    Article  CAS  PubMed  Google Scholar 

  • Child R, Miller C, Liang Y, Narasimham G, Chatterton J, Harrison P, Sims R, Britt D, Anderson A (2007b) Polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates: their association with plant roots. Appl Microbiol Biotechnol 75:655–663

    Article  CAS  PubMed  Google Scholar 

  • Chouychai W, Thongkukiatkul A, Upatham S, Lee H, Pokethitiyook P, Kruatrachue M (2009) Plant-enhanced phenanthrene and pyrene biodegradation in acidic soil. J Environ Biol 30:139–144

    CAS  PubMed  Google Scholar 

  • Chouychai W, Thongkukiatkul A, Upatham S, Pokethitiyook P, Kruatrachue M, Lee H (2012) Effect of corn plant on survival and phenanthrene degradation capacity of Pseudomonas sp. UG14Lr in two soils. Int J Phytorem 14:585–595

    Article  CAS  Google Scholar 

  • Compan S, Duffy B, Nowak J, Clément C, Barka EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71(9):4951–4959

    Article  CAS  Google Scholar 

  • Das N, Chandran P (2010) Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int 2011:941810

    PubMed  PubMed Central  Google Scholar 

  • Das P, Mukherjee S, Sen R (2008) Improved bioavailability and biodegradation of a model polyaromatic hydrocarbon by a biosurfactant producing bacterium of marine origin. Chemosphere 72:1229–1234

    Article  CAS  PubMed  Google Scholar 

  • de Garcia Salamone I, Hynes R, Nelson L (2006) Role of cytokinins in plant growth promotion by rhizosphere bacteria. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 173–195

    Google Scholar 

  • Demain AL, Sanchez S (2009) Microbial drug discovery: 80 years of progress. J Antibiot 62:5–16

    Article  CAS  Google Scholar 

  • Dobler L, Vilela LF, Almeida RV, Neves BC (2016) Rhamnolipids in perspective: gene regulatory pathways, metabolic engineering, production and technological forecasting. New Biotechnol 33:123–135

    Article  CAS  Google Scholar 

  • Doty SL (2008) Enhancing phytoremediation through the use of transgenics and endophytes. New Phytol 179:318–333

    Article  CAS  PubMed  Google Scholar 

  • Doughty DM, Sayavedra-Soto LA, Arp DJ, Bottomley PJ (2006) Product repression of alkane monooxygenase expression in Pseudomonas butanovora. J Bacteriol 188:2586–2592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doughty DM, Halsey KH, Vieville CJ, Sayavedra-Soto LA, Arp DJ, Bottomley PJ (2007) Propionate inactivation of butane monooxygenase activity in ‘Pseudomonas butanovora’: biochemical and physiological implications. Microbiology 153:3722–3729

    Article  CAS  PubMed  Google Scholar 

  • Fajardo A, Martinez JL (2008) Antibiotics as signals that trigger specific bacterial responses. Curr Opin Microbiol 11:161–167

    Article  CAS  PubMed  Google Scholar 

  • Ferradji FZ, Mnif S, Badis A, Rebbani S, Fodil D, Eddouaouda K, Sayadi S (2014) Naphthalene and crude oil degradation by biosurfactant producing Streptomyces spp. isolated from Mitidja plain soil (north of Algeria). Int Biodeterior Biodegrad 86:300–308

    Article  CAS  Google Scholar 

  • Foght J (2010) Nitrogen fixation and hydrocarbon-oxidizing bacteria. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 1661–1668

    Chapter  Google Scholar 

  • Franco MG, Corrêa SM, Marques M, Perez DV (2014) Emission of volatile organic compounds and greenhouse gases from the anaerobic bioremediation of soils contaminated with diesel. Water Air Soil Pollut 225:1–9

    Article  CAS  Google Scholar 

  • Funhoff EG, Bauer U, Garcia-Rubio I, Witholt B, vanBeilen JB (2006) CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation. J Bacteriol 188:5220–5227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao Y-c, Guo S-H, Wang J-N, Li D, Wang H, Zeng D-H (2014) Effects of different remediation treatments on crude oil contaminated saline soil. Chemosphere 117:486–493

    Article  CAS  PubMed  Google Scholar 

  • Geng X, Boufadel MC, Personna YR, Lee K, Tsao D, Demicco ED (2014) BioB: a mathematical model for the biodegradation of low solubility hydrocarbons. Mar Pollut Bull 83:138–147

    Article  CAS  PubMed  Google Scholar 

  • Germaine KJ, Liu X, Cabellos GG, Hogan JP, Ryan D, Dowling DN (2006) Bacterial endophyte-enhanced phytoremediation of the organochlorine herbicide 2,4-dichlorophenoxyacetic acid. FEMS Microbiol Ecol 57(2):302–310

    Article  CAS  PubMed  Google Scholar 

  • Germaine KJ, Keogh E, Ryan D, Dowling DN (2009) Bacterial endophyte mediated naphthalene phytoprotection and phytoremediation. FEMS Microbiol Lett 296:226–234

    Article  CAS  PubMed  Google Scholar 

  • Glick BR (2010) Using soil bacteria to facilitate phytoremediation. Biotechnol Adv 28:367–374

    Article  CAS  PubMed  Google Scholar 

  • Golubev SN, Muratova AY, Wittenmayer L, Bondarenkova AD, Hirche F, Matora LY, Merbach W, Turkovskaya OV (2011) Rhizosphere indole-3-acetic acid as a mediator in the Sorghum bicolor–phenanthrene–Sinorhizobium meliloti interactions. Plant Physiol Biochem 49:600–608

    Article  CAS  PubMed  Google Scholar 

  • Gomez F, Sartaj M (2013) Field scale ex-situ bioremediation of petroleum contaminated soil under cold climate conditions. Int Biodeterior Biodegrad 85:375–382

    Article  CAS  Google Scholar 

  • Gomez F, Sartaj M (2014) Optimization of field scale biopiles for bioremediation of petroleum hydrocarbon contaminated soil at low temperature conditions by response surface methodology (RSM). Int Biodeterior Biodegrad 89:103–109

    Article  CAS  Google Scholar 

  • Guo M, Gong Z, Miao R, Rookes J, Cahill D, Zhuang J (2017) Microbial mechanisms controlling the rhizosphere effect of ryegrass on degradation of polycyclic aromatic hydrocarbons in an aged-contaminated agricultural soil. Soil Biol Biochem 113:130–142

    Article  CAS  Google Scholar 

  • Hamdi H, Benzarti S, Manusadzianas L, Aoyama I, Jedidi N (2007) Bioaugmentation and biostimulation effects on PAH dissipation and soil ecotoxicity under controlled conditions. Soil Biol Biochem 39:1926–1935

    Article  CAS  Google Scholar 

  • Harayama S (1997) Polycyclic aromatic hydrocarbon bioremediation design. Curr Opin Biotechnol 8:268–273

    Article  CAS  PubMed  Google Scholar 

  • Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471

    Article  CAS  PubMed  Google Scholar 

  • Harmsen J (2007) Measuring bioavailability: from a scientific approach to standard methods. J Environ Q 36:1420–1428

    Article  CAS  Google Scholar 

  • Hasinger M, Scherr KE, Lundaa T, Bräuer L, Zach C, Loibner AP (2012) Changes in iso- and n-alkane distribution during biodegradation of crude oil under nitrate and sulphate reducing conditions. J Biotechnol 157:490–498

    Article  CAS  PubMed  Google Scholar 

  • Hazelbauer GL, Lai W-C (2010) Bacterial chemoreceptors: providing enhanced features to two-component signaling. Curr Opin Microbiol 13:124–132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 219–220:43–49

    Article  CAS  PubMed  Google Scholar 

  • Hong SH, Ryu HW, Kim J, Cho KS (2011) Rhizoremediation of diesel contaminated soil using the plant growth-promoting rhizobacterium Gordonia sp. S2RP-17. Biodegradation 22:593–601

    Article  CAS  PubMed  Google Scholar 

  • Horel A, Mortazavi B, Sobecky PA (2015) Input of organic matter enhances degradation of weathered diesel fuel in sub-tropical sediments. Sci Total Environ 533:82–90

    Article  CAS  PubMed  Google Scholar 

  • Hosoda YK, Hamamura N, Takahata Y, Watanabe K (2005) Development of a PCR method for the detection and quantification of benzoyl-CoA reductase genes and its application to monitored natural attenuation. Biodegradation 16(6):591–601

    Article  CAS  PubMed  Google Scholar 

  • Huang X-D, El-Alawi Y, Penrose DM, Glick BR, Greenberg BM (2004) A multi-process phytoremediation system for removal of polycyclic aromatic hydrocarbons from contaminated soils. Environ Pollut 130(3):465–476

    Google Scholar 

  • Huesemann MH, Hausmann TS, Fortman TJ (2004) Does bioavailability limit biodegradation? A comparison of hydrocarbon biodegradation and desorption rates in aged soils. Biodegradation 15:261–274

    Article  CAS  PubMed  Google Scholar 

  • Jidere CM, Akamigbo FOR, Ugwuanyi JO (2012) Phytoremediation potentials of cowpea (Vigina unguiculata) and maize (Zea mays) for hydrocarbon degradation in organic and inorganic manure-amended tropical typic paleustults. Int J Phytoremediation 14:362–373

    Article  CAS  PubMed  Google Scholar 

  • Johnson DL, Maguire KL, Anderson DR, McGrath SP (2004) Enhanced dissipation of chrysene in planted soil: the impact of a rhizobial inoculum. Soil Biol Biochem 36:33–38

    Article  CAS  Google Scholar 

  • Juhanson J, Truu J, Heinaru E, Heinaru A (2009) Survival and catabolic performance of introduced Pseudomonas strains during phytoremediation and bioaugmentation field experiment. FEMS Microbiol Ecol 70:446–455

    Article  CAS  PubMed  Google Scholar 

  • Kamath R, Rentz JA, Schnoor JL, Alvarez PJJ (2004) Phytoremediation of hydrocarbon-contaminated soils: principles and applications. Pet Biotechnol Dev Perspect 151:447–478

    CAS  Google Scholar 

  • Kathi S, Khan AB (2011) Phytoremediation approaches to PAH contaminated soil. Indian J Sci Technol 4:56–63

    CAS  Google Scholar 

  • Katiyar V, Goel R (2004) Siderophore mediated plant growth promotion at low temperature by mutant of fluorescent pseudomonad. Plant Growth Regul 42:239–244

    Article  CAS  Google Scholar 

  • Kaul S, Sharma T, Dhar MK (2016) “Omics” tools for better understanding the plant-endophyte interactions. Front Plant Sci 7:955. https://doi.org/10.3389/fpls.2016.00955

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim S, Krajmalnik-Brown R, Kim J-O, Chung J (2014) Remediation of petroleum hydrocarbon-contaminated sites by DNA diagnosis-based bioslurping technology. Sci Total Environ 497:250–259

    Article  CAS  PubMed  Google Scholar 

  • Krell T, Lacal J, Munoz-Martinez F, AntonioReyes-Darias J, HilalCadirci B, Garcia-Fontana C (2011) Diversity at its best: bacterial taxis. Environ Microbiol 13:1115–1124

    Article  CAS  PubMed  Google Scholar 

  • Kuiper I, Bloemberg GV, Lugtenberg BJJ (2001) Selection of a plant–bacterium pair as a novel tool for rhizostimulation of polycyclic aromatic hydrocarbon degrading bacteria. Mol Plant-Microbe Interact 14:1197–1205

    Article  CAS  PubMed  Google Scholar 

  • Kurth EG, Doughty DM, Bottomley PJ, Arpi DJ, Sayavedra-Sotol LA (2008) Involvement of BmoR and BmoGinn-alkane metabolism in ‘Pseudomonas butanovora. Microbiology 154:139–147

    Article  CAS  PubMed  Google Scholar 

  • Lawniczak L, Marecik R, Chrzanowski L (2013) Contributions of biosurfactants to natural or induced bioremediation. Appl Microbiol Biotechnol 97:2327–2339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li JH, Gao Y, Wu SC, Cheung KC, Wang XR, Wong MH (2008) Physiological and biochemical responses of rice (Oryza sativa L.) to phenanthrene and pyrene. Int J Phytoremediation 10:106–118

    Article  CAS  Google Scholar 

  • Li J, Zhao GZ, Huang HY, Qin S, Zhu WY, Zhao LX, Xu LH, Zhang S, Li WJ, Strobel G (2012) Isolation and characterization of culturable endophytic actinobacteria associated with Artemisia annua L. Anton Leeuwenhoek 101:515–527

    Article  Google Scholar 

  • Liang J-L, JiangYang J-H, Nie Y, Wu X-L (2016) Regulation of the alkane hydroxylase CYP153 gene in a gram-positive alkane-degrading bacterium, Dietzia sp Strain DQ12-45-1b. Appl Environ Microbiol 82:608–619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Locksley RM (2010) Asthma and allergic inflammation. Cell 140:777–783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lodewyckx C, Taghavi S, Mergeay M, Vangronsveld J, Clijsters H, van der Lelie D (2001) The effect of recombinant heavy metal-resistant endophytic bacteria on heavy metal uptake by their host plant. Int J Phytoremediation 3:173–187

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Madigan MT, Martinko JM, Dunlap PV, Clark DP (2010) Brock biology of microorganisms, 12th edn. Benjamin Cummings, San Francisco, pp 1–1050

    Google Scholar 

  • Malfanova VN (2013) Endophytic bacteria with plant growth promoting and biocontrol abilities. http://hdl.handle.net/1887/20732

  • Marin MM, Yuste L, Rojo F (2003) Differential expression of the components of the two alkane hydroxylases from Pseudomonas aeruginosa. J Bacteriol 185:3232–3237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meyer DD, Beker SA, Bücker F, Peralba MDCR, Guedes Frazzon AP, Osti JF, Andreazza R, Anastácio de Oliveira Camargo F, Bento FM (2014) Bioremediation strategies for diesel and biodiesel in oxisol from southern Brazil. Int Biodeterior Biodegrad 95:356–363

    Article  CAS  Google Scholar 

  • Montagnolli RN, Lopes PRM, Bidoia ED (2015) Assessing Bacillus subtilis biosurfactant effects on the biodegradation of petroleum products. Environ Monit Assess 187:1–17

    Article  CAS  Google Scholar 

  • Moore FP, Barac T, Borremans 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 characterization of isolates with potential to enhance phytoremediation. Syst Appl Microbiol 29:539–556

    Article  CAS  PubMed  Google Scholar 

  • Muratova AY, Turkovskaya OV, Antonyuk LP, Makarov OE, Pozdnyakova LI, Ignatov VV (2005) Oil-oxidizing potential of associative rhizobacteria of the genus Azospirillum. Microbiology 74:210–215

    Article  CAS  Google Scholar 

  • Muratova AY, Dmitrieva T, Panchenko L, Turkovskaya O (2008) Phytoremediation of oil-sludge-contaminated soil. Int J Phytoremediation 10:486–502

    Article  CAS  PubMed  Google Scholar 

  • Muratova AY, Golubev S, Wittenmayer L, Dmitrieva T, Bondarenkova A, Hirche F, Merbach W, Turkovskaya O (2009) Effect of the polycyclic aromatic hydrocarbon phenanthrene on root exudation of Sorghum bicolor (L.) Moench. Environ Exp Bot 66:514–521

    Article  CAS  Google Scholar 

  • Muratova AY, Bondarenkova A, Panchenko L, Turkovskaya O (2010) Use of integrated phytoremediation for cleaning-up of oil-sludge-contaminated soil. Appl Biochem Microbiol 46:789–794

    Article  CAS  Google Scholar 

  • Newman LA, Reynolds CM (2004) Phytodegradation of organic compounds. Curr Opin Biotechnol 15:225–230

    Article  CAS  PubMed  Google Scholar 

  • Nguyen TT, Sabatini DA (2011) Characterization and emulsification properties of rhamnolipid and sophorolipid biosurfactants and their applications. Int J Mol Sci 12:1232–1244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nisenbaum M, HernanSendra G, CerdaGilbert GA, Scagliola M, Froilan Gonzalez J, ElenaMurialdo S (2013) Hydrocarbon biodegradation and dynamic laser speckle for detecting chemotactic responses at low bacterial concentration. J Environ Sci (China) 25:613–625

    Article  CAS  Google Scholar 

  • Pacwa-Plociniczak M, Plaza GA, Piotrowska-Seget Z, Cameotra SS (2011) Environmental applications of biosurfactants: recent advances. Int J Mol Sci 12:633–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petrikov K, Delegan Y, Surin A, Ponamoreva O, Puntus I, Filonov A, Boronin A (2013) Glycolipids of Pseudomonas and Rhodococcus oil-degrading bacteria used in bioremediation preparations: formation and structure. Process Biochem 48:931–935

    Article  CAS  Google Scholar 

  • Pham VH, Kim J, Jeong S-W (2014) Enhanced isolation and culture of highly efficient psychrophilic oil-degrading bacteria from oil-contaminated soils in South Korea. J Environ Biol 35:1145–1149

    PubMed  Google Scholar 

  • Qin S, Xing K, Jiang J-H, Xu L-H, Li W-J (2011) Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 89:457–473

    Article  CAS  PubMed  Google Scholar 

  • Raaijmakers JM, Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic Bacteria. Annu Rev Phytopathol 50(1):403–424

    Google Scholar 

  • Reinhold-Hurek B, Hurek T (2011) Living inside plants: bacterial endophytes. Curr Opin Plant Biol 14:435–443

    Article  PubMed  Google Scholar 

  • Rojo F (2009) Degradation of alkanes by bacteria. Environ Microbiol 11(10):2477–2490

    Google Scholar 

  • Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Golyshin PN (2006) Proteomic insights into metabolic adaptations in Alcanivoraxbor kumensis induced by alkane utilization. J Bacteriol 188:3763–3773. https://doi.org/10.1128/JB.00072-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santos DKF, Rufino RD, Luna JM, Santos VA Sarubbo LA (2016) Biosurfactants: multifunctional biomolecules of the 21st century. Int J Mol Sci 17:401. https://doi.org/10.3390/ijms17030401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schneiker S, dos Santos VM, Bartels D, Bekel T, Brecht M, Buhrmester J (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivoraxbor kumensis. Nat Biotechnol 24:997–1004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schulz S, Giebler J, Chatzinotas A, Wick LY, Fetzer I, Welzl G, Harms H, Schloter M (2012) Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments. ISME J 6:1763–1774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scoma A, Yakimov MM, Boon N (2016) Challenging oil bioremediation at deep-sea hydrostatic pressure. Front Microbiol 7:1203. https://doi.org/10.3389/fmicb.2016.01203

    Article  PubMed  PubMed Central  Google Scholar 

  • Shemesh M, Kolter R, Losick R (2010) The biocide chlorine dioxide stimulates biofilm formation in Bacillus subtilis by activation of the histidine kinase KinC. J Bacteriol 192:6352–6356

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sheng XF, Gong JX (2006) Increased degradation of phenanthrene in soil by Pseudomonas sp. GF3 in the presence of wheat. Soil Biol Biochem 38:2587–2592

    Article  CAS  Google Scholar 

  • Sheng X, Chen X, He L (2008) Characteristics of an endophytic pyrene-degrading bacterium of Enterobacter sp. 12J1 from Allium macrostemon Bunge. Int Biodeterior Biodegrad 62:88–95

    Article  CAS  Google Scholar 

  • Siciliano SD, Fortin N, Mihoc A, Wisse G, Labelle S, Beaumier D, Ouellette D, Roy R, Whyte LG, Banks MK, Schwab AP, Lee K, Greer CW (2001) Selection of specific endophytic bacterial genotypes by plants in response to soil contamination. Appl Environ Microbiol 67:2469–2475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Siddique T, Penner T, Semple K, Foght JM (2011) Anaerobic biodegradation of longer chain n-alkanes coupled to methane production in oil sands tailings. Environ Sci Technol 45:5892–5899

    Article  CAS  PubMed  Google Scholar 

  • Sierra-Garcia IN, Alvarez JC, de Vasconcellos SP, de Souza AP, dos Santos EV, de Oliveira VM (2014) New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PLoS One 9:e90087. https://doi.org/10.1371/journal.pone.0090087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh R, Paul D, Jain RK (2006) Biofilms: implications in bioremediation. Trends Microbiol 14:389–397

    Article  CAS  PubMed  Google Scholar 

  • Smith RJ, Jeffries TC, Adetutu EM, Fairweather PG, Mitchell JG (2013) Determining the metabolic footprints of hydrocarbon degradation using multivariate analysis. PLoS One 8:e81910. https://doi.org/10.1371/journal.pone.0081910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soleimani M, Afyuni M, Hajabbasi MA, Nourbakhsh F, Sabzalian MR, Christensen JH (2010) Phytoremediation of an aged petroleum contaminated soil using endophyte infected and non-infected grasses. Chemosphere 81:1084–1090

    Article  CAS  PubMed  Google Scholar 

  • Song XY, Li XX, Wang Y, Hu XJ (2012) Long-term phytoremediation process of diesel oil-contaminated soil. Adv Mater Res 414:280–283

    Article  CAS  Google Scholar 

  • Strobel KL, McGowan S, Bauer RD, Griebler C, Liu J, Ford RM (2011) Chemotaxis increases vertical migration and apparent transverse dispersion of bacteria in a bench-scale microcosm. Biotechnol Bioeng 108:2070–2077

    Article  CAS  PubMed  Google Scholar 

  • Sturz AV, Christie BR, Nowak J (2000) Bacterial endophytes: potential role in developing sustainable systems of crop production. Crit Rev Plant Sci 19:1–30

    Article  Google Scholar 

  • Szulc A, Ambrożewicz D, Sydow M, Ławniczak Ł, Piotrowska-Cyplik A, Marecik R, Chrzanowski Ł (2014) The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: feasibility during field studies. J Environ Manag 132:121–128

    Article  CAS  Google Scholar 

  • Taghavi S, Barac T, Greenberg B, Borremans B, Vangronsveld J, van der Lelie D (2005) Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl Environ Microbiol 71:8500–8505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tani A, Ishige T, Sakai Y, Kato N (2001) Gene structures and regulation of the alkane hydroxylase complex in Acinetobacter sp. strain M-1. J Bacteriol 183:1819–1823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teng Y, Shen Y, Luo Y, Sun X, Sun M, Fu D, Li Z, Christie P (2011) Influence of Rhizobium meliloti on phytoremediation of polycyclic aromatic hydrocarbons by alfalfa in an aged contaminated soil. J Hazard Mater 186:1271–1276

    Article  CAS  PubMed  Google Scholar 

  • Thomas F, Cébron A (2016) Short-term rhizosphere effect on available carbon sources, Phenanthrene degradation, and active microbiome in an aged-contaminated industrial soil. Front Microbiol 7:92. https://doi.org/10.3389/fmicb.2016.00092

    Article  PubMed  PubMed Central  Google Scholar 

  • Toyama T, Furukawa T, Maeda N Inoue D, Sei K, Mori K (2011) Accelerated biodegradation of pyrene and benzo-a-pyrene in the Phragmites australis rhizosphere by bacteria-root exudates interactions. Water Res 45:1629–1638. https://doi.org/10.1016/j.watres.2010.11.044

    Article  CAS  PubMed  Google Scholar 

  • Tyagi M, da Fonseca MMR, deCarvalho C (2011) Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 22:231–241

    Article  CAS  PubMed  Google Scholar 

  • Tzintzun-Camacho O, Loera O, Ramirez-Saad HC, Gutierrez-Rojas M (2012) Comparison of mechanisms of hexadecane uptake among pure and mixed cultures derived from a bacterial consortium. Int Biodeterior Biodegrad 70:1–7

    Article  CAS  Google Scholar 

  • Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB (2013) Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 31:154–165

    Article  CAS  PubMed  Google Scholar 

  • Uzoigwe C, Burgess JG, Ennis CJ, Rahman PKSM (2015) Bioemulsifiers are not biosurfactants and require different screening approaches. Front Microbiol 6:245. https://doi.org/10.3389/fmicb.2015.00245

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Aken B, Peres CM, Doty SL, Yoon JM, Schnoor JL (2004) Methylobacterium populi sp. nov, a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoidesxnigra DN34). Int J Syst Evol Microbiol 54:1191–1196

    Article  CAS  PubMed  Google Scholar 

  • van Beilen JB, Funhoff EG (2007) Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 74(1):13–21

    Article  CAS  PubMed  Google Scholar 

  • van Beilen JB, Wubbolts MG, Witholt B (1994) Genetics of alkane oxidation by Pseudomonas oleovorans. Biodegradation 5(3–4):161–174

    Article  PubMed  Google Scholar 

  • van Beilen JB, Panke S, Lucchini S, Franchini AG, Rothlisberger M, Witholt B (2001) Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147(6):1621–1630

    Article  PubMed  Google Scholar 

  • van Beilen JB, Marin MM, Smits THM, Rothlisberger M, Franchini AG, Witholt B (2004) Characterization of two alkane hydroxylase genes from the marine hydrocarbon oclastic bacterium Alcanivoraxbor kumensis. Environ Microbiol 6:264–273

    Article  CAS  PubMed  Google Scholar 

  • van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Mol Biol Rev 67(4):503–549

    Article  CAS  Google Scholar 

  • Venosa AD, Campo P, Suidan MT (2010) Biodegradability of lingering crude oil 19 years after the Exxon Valdez oil spill. Environ Sci Technol 44:7613–7621

    Article  CAS  PubMed  Google Scholar 

  • Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586

    Article  CAS  Google Scholar 

  • Wang W, Shao Z (2013) Enzymes and genes involved in aerobic alkane degradation. Front Microbiol 4:116. https://doi.org/10.3389/fmicb.2013.00116

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Li H, Zhao W, He X, Chen J, Geng X, Xiao M (2010) Induction of toluene degradation and growth promotion in corn and wheat by horizontal gene transfer within endophytic bacteria. Soil Biol Biochem 42:1051–1057

    Article  CAS  Google Scholar 

  • Wang MC, Chen YT, Chen SH, Chang CSW, Sunkara SV (2012) Phytoremediation of pyrene contaminated soils amended with compost and planted with ryegrass and alfalfa. Chemosphere 87:217–225

    Article  CAS  PubMed  Google Scholar 

  • Wang SY, Kuo YC, Hong A, Chang YM, Kao CM (2016) Bioremediation of diesel and lubricant oil-contaminated soils using enhanced land farming system. Chemosphere 164:558–567

    Article  CAS  PubMed  Google Scholar 

  • Weyens N, Taghavi S, Barac T, van der Lelie D, Boulet J, Artois T (2009) Bacteria associated with oak and ash on a TCE-contaminated site: characterization of isolates with potential to avoid evapotranspiration of TCE. Environ Sci Pollut Res 16:830–843

    Article  CAS  Google Scholar 

  • Weyens N, Croes S, Dupae J, Newman L, van der Lelie D, Carleer R, Vangronsveld J (2010) Endophytic bacteria improve phytoremediation of Ni and TCE co-contamination. Environ Pollut 158:2422–2427

    Article  CAS  PubMed  Google Scholar 

  • Weyens N, Boulet J, Adriaensen K, Timmermans J-P, Prinsen E, Van Oevelen S, D’Haen J, Smeets K, Van Der Lelie D, Taghavi S, Vangronsveld J (2012) Contrasting colonization and plant growth promoting capacity between wild type and a gfp-derivative of the endophyte Pseudomonas putida W619 in hybrid poplar. Plant Soil 356(1):217–230

    Article  CAS  Google Scholar 

  • Xia W, Du Z, Cui Q, Dong H, Wang F, He P, Tang Y (2014) Biosurfactant produced by novel Pseudomonas sp.WJ6 with biodegradation of n-alkanes and polycyclic aromatic hydrocarbons. J Hazard Mater 276:489–498

    Article  CAS  PubMed  Google Scholar 

  • Xue JL, Yu Y, Bai Y, Wang LP, Wu YN (2015) Marine oil-degrading microorganisms and biodegradation process of petroleum hydrocarbon in marine environments: a review. Curr Microbiol 71:220–228

    Article  CAS  PubMed  Google Scholar 

  • Yadav A, Yadav K (2017) Exploring the potential of endophytes in agriculture: a minireview. Adv Plants Agric Res 6(4):102–106

    Google Scholar 

  • Yousaf S, Andria V, Reichenauer TG, Smalla K, Sessitsch A (2010a) Phylogenetic and functional diversity of alkane degrading bacteria associated with Italian ryegrass (Lolium multiflorum) and birdsfoot trefoil (Lotus corniculatus) in a petroleum oil-contaminated environment. J Hazard Mater 184:523–532

    Article  CAS  PubMed  Google Scholar 

  • Yousaf S, Ripka K, Reichenauer T, Andria V, Afzal M, Sessitsch A (2010b) Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birdsfoot trefoil. J Appl Microbiol 109:1389–1401

    Article  CAS  PubMed  Google Scholar 

  • Yousaf S, Afzal M, Reichenauer TG, Brady CL, Sessitsch A (2011) Hydrocarbon degradation, plant colonization and gene expression of alkane degradation genes by endophytic Enterobacter ludwigii strains. Environ Pollut 159:2675–2683

    Article  CAS  PubMed  Google Scholar 

  • Yu XZ, Wu SC, Wu FY, Wong MH (2011) Enhanced dissipation of PAHs from soil using mycorrhizal ryegrass and PAH-degrading bacteria. J Hazard Mater 186:1206–1217

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Rengel Z, Chang H, Meney K, Pantelic L, Tomanovic R (2012a) Phytoremediation potential of Juncus subsecundus in soils contaminated with cadmium and polynuclear aromatic hydrocarbons (PAHs). Geoderma 175:176:1–176:8

    Google Scholar 

  • Zhang XS, Xu DJ, Zhu CY, Lundaam T, Scherr KE (2012b) Isolation and identification of biosurfactant producing and crude oil degrading Pseudomonas aeruginosa strains. Chem Eng J 209:138–146

    Article  CAS  Google Scholar 

  • Zhong Y, Wang J, Song Y, Liang Y, Li G (2012) Microbial community and functional genes in the rhizosphere of alfalfa in crude oil-contaminated soil. Front Environ Sci Eng 6(6):797–805

    Article  CAS  Google Scholar 

  • Zin NM, Sarmin NI, Ghadin N, Basri DF, Sidik NM, Hess WM, Strobel GA (2007) Bioactive endophytic streptomycetes from the Malay Peninsula. FEMS Microbiol Lett 274:83–88

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan

    Aneela Iqbal & Muhammad Arshad

  2. Microbial Genetic Resources Program (MGRP), Bioresource Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, Pakistan

    Iftikhar Ahmed

Authors
  1. Aneela Iqbal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Muhammad Arshad
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Iftikhar Ahmed
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, Uttarakhand, India

    Vivek Kumar

  2. Centre for Life Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India

    Manoj Kumar

  3. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Ram Prasad

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Iqbal, A., Arshad, M., Ahmed, I. (2018). Plant-Microbe Association for Bioremediation of Hydrocarbon Substrates. In: Kumar, V., Kumar, M., Prasad, R. (eds) Microbial Action on Hydrocarbons. Springer, Singapore. https://doi.org/10.1007/978-981-13-1840-5_16

Download citation

Publish with us

Policies and ethics

Search

Navigation