Abstract
Recalcitrant organic toxic chemicals have been accumulating for decades as a consequence of industrial activity. Concerns about environmental contamination have been rising in the last three decades and therefore the need for soil remediation has become a priority. Although physicochemical techniques are currently the most efficient methods being used to remove contaminants, they are very expensive and therefore impractical in many locations. The use of plants in the bioremediation of soils has been proposed as an attractive strategy; however, plants lack the extraordinary biodegradative capabilities of microorganisms. Consequently rhizoremediation, a technology which combines microorganisms that eliminate contaminants in the plant roots which provide nutrients for these microorganisms, has emerged. To design a successful rhizoremediation strategy, microorganisms need to proliferate in the root system, and the bacterial catabolic pathways have to be operative. Recent advances in these aspects, together with some techniques to improve biodegradation in the rhizosphere will be presented in this chapter.
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References
Afzal M, Khan QM, Sessitsch A (2014) Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants. Chemosphere 117:232–342. https://doi.org/10.1016/j.chemosphere.2014.06.078
Attila C, Ueda A, Cirillo SLG, Chen W, Wood TK (2008) Pseudomonas aeruginosa PAO1 virulence factors and poplar tree response in the rhizosphere. Microb Biotechnol 1:17–29
Böltner D, Godoy P, Muñoz-Rojas J, Duque E, Moreno-Morillas S, Sánchez L, Ramos JL (2008) Rhizoremediation of lindane by root-colonizing Sphingomonas. Microbial Biotech 1:87–93
Buddrus-Schiemann K, Schmid M, Schreiner K, Welzl G, Hartmann A (2010) Root colonization by Pseudomonas sp. DSMZ 13134 and impact on the indigenous rhizosphere bacterial community of barley. Microb Ecol 60:381–393. https://doi.org/10.1007/s00248-010-9720-8
Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95. https://doi.org/10.1038/nature11336
Burges A, Alkorta I, Epelde L, Garbisu C (2017) From phytoremediation of soil contaminants to phytomanagement of ecosystem services in metal contaminated sites. Int J Phytoremediation. https://doi.org/10.1080/15226514.2017.1365340
Burken JG (2004) Uptake and metabolism of organic compounds: green-liver model. In: McCutcheon SD, Schnoor JL (eds) On phytoremediation. Wiley, New York, pp 59–84
Casavant NC, Thompson D, Beattie GA, Phillips GJ, Halverson LJ (2003) Use of a site-specific recombination-based biosensor for detecting bioavailable toluene and related compounds on roots. Environ Microbiol 5:238–249
Cennerazzo J, de Junet A, Audinot J-N, Leyval C (2017) Dynamics of PAHs and derived organic compounds in a soil-plant mesocosm spiked with 13C-phenanthrene. Chemosphere 168:1619–1627
Choudhary KS, Hudaiberdiev S, Gelencser Z, Goncalves Coutinho B, Venturi V, Pongor S (2013) The organization of the quorum sensing luxI/R family genes in Burkholderia. Int J Mol Sci 14:13727–13747. https://doi.org/10.3390/ijms140713727
Colleran E (1997) Uses of bacteria in bioremediation. In: Sheehan D (ed) Methods in biotechnology, vol 2: bioremediation protocols. Humana Press Inc., Totowa
Diplock EE, Alhadrami HA, Paton GI (2010) Application of microbial bioreporters in environmental microbiology and bioremediation. Adv Biochem Eng Biotechnol 118:189–209
Dos Santos JJ, Maranho LT (2018) Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: a review. J Environ Manage 210:104–113. https://doi.org/10.1016/j.jenvman.2018.01.015
Duetz WA, Marqués S, Wind B, Ramos JL, van Andel JG (1996) Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture. Appl Environ Microbiol 62:601–606
Dupuy J, Leglize P, Vincent Q, Zelko I, Mustin C, Ouvrard S, Sterckeman T (2016) Effect and localization of phenanthrene in maize roots. Chemosphere 149:130–136
Fuqua C (2006) The QscR quorum-sensing regulon of Pseudomonas aeruginosa: an orphan claims its identity. J Bacteriol 188:3169–3171. https://doi.org/10.1128/JB.188.9.3169-3171.2006
Fuqua C, Greenberg EP (2002) Listening in on bacteria: acyl-homoserine lactone signalling. Nat Rev Mol Cell Biol 3:685–695. https://doi.org/10.1038/nrm907
Gómez-Sagasti MT, Epelde L, Alkorta I, Garbisu C (2016) Reflections on soil contamination research from a biologist’s point of view. Appl Soil Ecol 105:207–210. https://doi.org/10.1016/j.apsoil.2016.04.004
Gonzalez JF, Venturi V (2013) A novel widespread interkingdom signaling circuit. Trends Plant Sci 18:167–174. https://doi.org/10.1016/j.tplants.2012.09.007
Hernández-Sánchez V, Molina L, Ramos JL, Segura A (2016) New family of biosensors for monitoring BTX in aquatic and edaphic environments. Microb Biotechnol 9:858–867. https://doi.org/10.1111/1751-7915.12394
Kappell AD, Wei Y, Newton RJ, Van Nostrand JD, Zhou J, McLellan SL, Hristova KR (2014) The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill. Front Microbiol 5:205. https://doi.org/10.3389/fmicb.2014.00205
Kohlmeier S, Mancuso M, Deepthike U, Tecon R, van der Meer JR, Harms H, Wells M (2008) Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax. Environ Pollut 156:803–808. https://doi.org/10.1016/j.envpol.2008.06.001
Kuiper I, Lagendijk EL, Bloemberg GV, Lugtenberg BJJ (2004a) Rhizoremediation: a beneficial plant–microbe interaction. Mol Plant Microbe Interact 17:6–15
Kuiper I, Lagendijk EL, Pickford R, Derrick JP, Lamers GEM, Thomas-Oates JE, Lugtenberg BJJ, Bloember GV (2004b) Characterization of two Pseudomonas putida lipopeptide biosurfactants, putisolvin I and II, which inhibit biofilm formation and breakdown existing biofilms. Mol Microbiol 51:97–113
Liduino VS, Servulo EFC, Oliveira FJS (2018) Biosurfactant-assisted phytoremediation of multi-contaminated industrial soil using sunflower (Helianthus annuus L.). J Environ Sci Health A Tox Hazard Subst Environ Eng 1:1–8. https://doi.org/10.1080/10934529.2018.1429726
Limmer M, Burken J (2016) Phytovolatilization of organic contaminants. Environ Sci Technol 50:6632–6643. https://doi.org/10.1021/acs.est.5b04113
Liu J, Xiang Y, Zhang Z, Ling W, Gao Y (2017) Inoculation of a phenanthrene-degrading endophytic bacterium reduces the phenanthrene level and alters the bacterial community structure in wheat. Appl Microbiol Biotechnol 101:5199–5212. https://doi.org/10.1007/s00253-017-8247-z
Lu XY, Zhang T, Fang HH (2011) Bacteria-mediated PAH degradation in soil and sediment. Appl Microbiol Biotechnol 89:1357–1371. https://doi.org/10.1007/s00253-010-3072-7
Lu H, Sun J, Zhu L (2017) The role of artificial root exudate components in facilitating the degradation of pyrene in soil. Sci Rep 7:7130. https://doi.org/10.1038/s41598-017-07413-3
Lugtenberg BJ, Dekkers L, Bloemberg GV (2001) Molecular determinants of rhizosphere colonization by Pseudomonas. Annu Rev Phytopathol 39:461–490
Macek T, Mackova M, Kas J (2000) Exploitation of plants for the removal of organics in environmental remediation. Biotechnol Adv 18:23–34
Marchant R, Banat IM (2012) Biosurfactants: a sustainable replacement for chemical surfactants? Biotechnol Lett 34:1597–1605. https://doi.org/10.1007/s10529-012-0956-x
Mastretta C, Barac T, Vangronsveld J, Newman L, Taghavi S, Van der Lelie D (2006) Endophytic bacteria and their potential application to improve the phytoremediation of contaminated environments. Biotechnol Genet Eng Rev 23:175–207
Matilla MA, Espinosa-Urgel M, Rodríguez-Hervá JJ, Ramos JL, Ramos-González MI (2007) Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol 8:R179
Olson PE, Castro A, Joern M, DuTeau NM, Pilon SEAH, Reardon KF (2007) Comparison of plant families in a greenhouse phytoremediation study on an aged polycyclic aromatic hydrocarbon contaminated soil. J Environ Qual 36:1461–1469
Ortega-Calvo JJ, Tejeda-Agredano MC, Jimenez-Sanchez C, Congiu E, Sungthong R, Niqui-Arroyo JL, Cantos M (2013) Is it possible to increase bioavailability but not environmental risk of PAHs in bioremediation? J Hazard Mater 261:733–745. https://doi.org/10.1016/j.jhazmat.2013.03.042
Radwan S, Sorkhoh N, El-Nemr I (1995) Oil biodegradation around roots. Nature 376:302
Rainey PB, Preston GM (2000) In vivo expression technology strategies: valuable tools for biotechnology. Curr Opin Biotechnol 11:440–444
Ramos C, Molina L, Mølbak L, Ramos JL, Molin S (2000) A bioluminescent derivative of Pseudomonas putida KT2440 for deliberate release into the environment. FEMS Microbiol Ecol 34:91–102
Ramos-González MI, Campos MJ, Ramos JL (2005) Analysis of Pseudomonas putida KT2440 gene expression in the maize rhizosphere: in vivo expression technology capture and identification of root activated promoters. J Bacteriol 187:4033–4041
Rentz JA, Alvarez PJJ, Schnoor JL (2004) Repression of Pseudomonas putida phenanthrene-degrading activity by plant root extracts and exudates. Environ Microbiol 6:574–583
Rodriguez-Conde S, Molina L, González P, García-Puente A, Segura A (2016) Degradation of phenanthrene by Novosphingobium sp. HS2a improved plant growth in PAHs-contaminated environments. Appl Microbiol Biotechnol 100:10627–10636
Salt DE, Smith RD, Raskin I (1998) Phytoremediation. Annu Rev Plant Physiol Plant Mol Biol 49:643–668
Scharf BE, Hynes MF, Alexandre GM (2016) Chemotaxis signaling systems in model beneficial plant-bacteria associations. Plant Mol Biol 90:549–559. https://doi.org/10.1007/s11103-016-0432-4
Segura A, Ramos JL (2013) Plant–bacteria interactions in the removal of pollutants. Curr Opin Biotechnol 24:467–473. https://doi.org/10.1016/j.copbio.2012.09.011
Segura A, Hernández-Sánchez V, Marqués S, Molina L (2017) Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs. Sci Total Environ 590–591:381–393. https://doi.org/10.1016/j.scitotenv.2017.02.180
Sevilla E, Yuste L, Rojo F (2015) Marine hydrocarbonoclastic bacteria as whole-cell biosensors for n-alkanes. Microb Biotechnol 8:693–706. https://doi.org/10.1111/1751-7915.12286
Shaw LJ, Burns RG (2003) Biodegradation of organic pollutants in the rhizosphere. Adv Appl Microbiol 53:1–60
Siciliano SD, Fortin N, Mihoc A, Wisse G, Labelle X, Beaumier D, Ouellette D, Roy R, Whyte LG, Banks MK, Schwab P, Lee K, Greer CW (2002) Selection of specific endophytic bacterial genotypes by plants in response to soil contamination. Appl Environ Microbiol 67:2469–2475
Siciliano SD, Germida JJ, Banks K, Greer CW (2003) Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial. Appl Environ Microbiol 69:483–489
Singer AC, Crowley DE, Thompson IP (2003) Secondary plant metabolites in phytoremediation and biotransformation. Trends Biotechnol 21:123–130
Stevens AM, Greenberg EP (1997) Quorum sensing in Vibrio fischeri: essential elements for activation of the luminescence genes. J Bacteriol 179:557–562
Subramoni S, Venturi V (2009) LuxR-family ‘solos’: bachelor sensors/regulators of signaling molecules. Microbiology 155:1377–1385. https://doi.org/10.1099/mic.0.026849-0
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
Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, Barac T, Vangronsveld J, van der Lelie D (2009) Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl Environ Microbiol 75:748–757. https://doi.org/10.1128/AEM.02239-08
Tecon R, Van der Meer JR (2008) Bacterial biosensors for measuring availability of environmental pollutants. Sensors 8:4062–4080
Thijs S, Sillen W, Rineau F, Weyens N, Vangronsveld J (2016) Towards an enhanced understanding of plant–microbiome interactions to improve phytoremediation: engineering the metaorganism. Front Microbiol 7:341. https://doi.org/10.3389/fmicb.2016.00341
Uhlik O, Wald J, Strejcek M, Musilova L, Ridl J, Hroudova M, Vlcek 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
Van Dillewijn P, Caballero A, Paz JA, González-Pérez MM, Oliva JM, Ramos JL (2007) Bioremediation of 2,4,6-trinitrotoluene under field conditions. Environ Sci Technol 41:1378–1383
Venturi V, Keel C (2016) Signaling in the rhizosphere. Trends Plant Sci 21:187–198. https://doi.org/10.1016/j.tplants.2016.01.005
Vergani L, Mapelli F, Zanardini E, Terzaghi E, Di Guardo A, Morosini C, Raspa G, Borin S (2017) Phyto-rhizoremediation of polychlorinated biphenyl contaminated soils: an outlook on plant-microbe beneficial interactions. Sci Total Environ 575:1395–1406. https://doi.org/10.1016/j.scitotenv.2016.09.218
Zafra G, Absalón ÁE, Anducho-Reyes MÁ, Fernandez FJ, Cortés-Espinosa DV (2017) Construction of PAH-degrading mixed microbial consortia by induced selection in soil. Chemosphere 172:120–126. https://doi.org/10.1016/j.chemosphere.2016.12.038
Acknowledgments
The work by authors was supported by research grants from the Spanish Ministry of Science and Innovation and the Andalusian Regional Government, (Junta de Andalucía). We thank Angela Tate for improving the use of English in the manuscript.
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Molina, L. et al. (2019). Removal of Hydrocarbons and Other Related Chemicals via the Rhizosphere of Plants. In: Steffan, R. (eds) Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-50433-9_10
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