Abstract
The rhizosphere is a soil hot spot where, due to a tight plant-bacteria interaction, plants recruit a beneficial microbiome, enhancing its density and activity. Rhizosphere microbial communities have the potential to provide several services, and their management and “engineering” can be exploited to set up agro-environmental biotechnologies. In this chapter, after a brief overview of the array of services that we can obtain from rhizosphere beneficial microbiome, two case studies are presented: (i) the exploitation of plant growth-promoting bacteria to increase plant tolerance to drought, potentially able to improve crop yield in arid and semiarid lands, and (ii) the exploitation of plant biostimulation effects over degrading microbial populations in the rhizosphere, sustaining phyto-rhizoremediation approaches in PCB-contaminated soils. In each case study, experimental settings, in vitro and in vivo tests, and the result evaluation and modeling are reported together with a discussion of the critical issues.
Valentina Riva and Elisa Terzaghi are contributed equally to the work.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Ahmad F, Ahmad I, Khan MS (2008) Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181
Ancona V, Barra Caracciolo A, Grenni P, Di Lenola M, Campanale C, Calabrese A, Uricchio VF, Mascolo G, Massacci A (2017) Plant-assisted bioremediation of a historically PCB and heavy metal-contaminated area in Southern Italy. New Biotechnol 38:65–73
Belimov AA, Hontzeas N, Safronova VI, Demchinskaya SV, Piluzza G, Bullitta S, Glick BR (2005) Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.). Soil Biol Biochem 37:241–250
Berendsen RL, Pieterse C, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486
Bric JM, Bostock RM, Silverstone SE (1991) Rapid in situ assay for indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane. Appl Environ Microbiol 57:535–538
Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P (2013) structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838
Canales-Pastrana RR, Paredes M (2013) Phytoremediation dynamic model as an assessment tool in the environmental management. Open J Appl Sci 03:208–217
Cappuccino JC, Sherman N (1992) Negative staining. In: Cappuccino JC, Sherman N (eds) Microbiology: a laboratory manual, 3rd edn. Benjamin/Cummings, Redwood City, pp 125–179
Chan Y, Van Nostrand JD, Zhou J, Pointing SB, Farrell RL (2013) Functional ecology of an Antarctic dry valley. Proc Natl Acad Sci 110:8990–8995
Chekol T, Vough LR, Chaney RL (2004) Phytoremediation of polychlorinated biphenyl-contaminated soils: the rhizosphere effect. Environ Int 30:799–804
Chen C, Yu C, Shen C, Tang X, Qin Z, Yang K, Hashmi MZ, Huang R, Shi H (2014) Paddy field – a natural sequential anaerobic–aerobic bioreactor for polychlorinated biphenyls transformation. Environ Pollut 190:43–50
Chen C, Xin K, Liu H, Cheng J, Shen X, Wang Y, Zhang L (2017) Pantoea alhagi, a novel endophytic bacterium with ability to improve growth and drought tolerance in wheat. Sci Rep 7:41564
Cho SM, Kang BR, Kim YC (2013) Transcriptome analysis of induced systemic drought tolerance elicited by Pseudomonas chlororaphis O6 in Arabidopsis thaliana. Plant Pathol J 29:209
Chowdhary A, Meis JF (2018) Emergence of azole resistant Aspergillus fumigatus and one health: time to implement environmental stewardship. Environ Microbiol. In press
Chu WK, Wong MH, Zhang J (2006) Accumulation, distribution and transformation of DDT and PCBs by Phragmites australis and Oryza sativa L.: I. Whole plant study. Environ Geochem Health 28:159–168
Di Guardo A, Terzaghi E, Raspa G, Borin S, Mapelli F, Chouaia B, Zanardini E, Morosini C, Colombo A, Fattore E, Davoli E, Armiraglio S, Sale VM, Anelli S, Nastasio P (2017) Differentiating current and past PCB and PCDD/F sources : The role of a large contaminated soil site in an industrialized city area. Environ Pollut 223:367–375
Dudášová H, Lukáčová L, Murínová S, Puškárová A, Pangallo D, Dercová K (2014) Bacterial strains isolated from PCB-contaminated sediments and their use for bioaugmentation strategy in microcosms: Bacterial strains from PCB-contaminated sediments. J Basic Microbiol 54:253–260
Dzantor EK, Chekol T, Vough LR (2000) Feasibility of using forage grasses and legumes for phytoremediation of organic pollutants. J Environ Sci Health A 35:1645–1661
East R (2013) Soil science comes to life. Nature 501:S18
EPA (2011) U.S. Environmental Protection Agency soil sampling operating procedure. SESDPROC-300-R2
Erickson MD (1997) Analytical chemistry of PCBs, 2nd edn. CRC/Lewis Publishing, Boca Raton. 667p
Falkenmark M (2013) Growing water scarcity in agriculture: future challenge to global water security. Phil Trans R Soc A 371:20120410
Fantke P, Juraske R, Antón A, Friedrich R, Jolliet O (2011) Dynamic multicrop model to characterize impacts of pesticides in food. Environ Sci Technol 45:8842–8849
Ficko SA, Rutter A, Zeeb BA (2010) Potential for phytoextraction of PCBs from contaminated soils using weeds. Sci Total Environ 408:3469–3476
Ficko SA, Rutter A, Zeeb BA (2011a) Phytoextraction and uptake patterns of weathered polychlorinated biphenyl–contaminated soils using three perennial weed species. J Environ Qual 40:1870–1877
Ficko SA, Rutter A, Zeeb BA (2011b) Effect of pumpkin root exudates on ex situ polychlorinated biphenyl (PCB) phytoextraction by pumpkin and weed species. Environ Sci Pollut R 18:1536–1543
Gagné-Bourque F, Bertrand A, Claessens A, Aliferis KA, Jabaji S (2016) Alleviation of drought stress and metabolic changes in timothy (Phleum pratense L.) colonized with Bacillus subtilis B26. Front Plant Sci 7:584
Gerhardt KE, Huang X-D, Glick BR, Greenberg BM (2009) Phytoremediation and rhizoremediation of organic soil contaminants: potential and challenges. Plant Sci 176:20–30
Gomes HI, Dias-Ferreira C, Ribeiro AB (2013) Overview of in situ and ex situ remediation technologies for PCB-contaminated soils and sediments and obstacles for full-scale application. Sci Total Environ 445–446:237–260
Hardoim PR, Van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320
Hu et al (2016) Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. MBio 7:e01790–e01716
Hülster A, Müller JF, Marschner H (1994) Soil-plant transfer of polychlorinated dibenzo-p-dioxins and dibenzofurans to vegetables of the cucumber family (Cucurbitaceae). Environ Sci Technol 28:1110–1115
IARC (2015) International Agency for Research on Cancer monographs on the evaluation of carcinogenic risk to humans. Polychlorinated biphenyls and polybrominated biphenyls, vol. 107, Lyon-France
ITRC (2012) Incremental Sampling Methodology. (No. ISM-1). Interstate Technology & Regulatory Council, Incremental Sampling Methodology Team, Washington, D.C. www.itrcweb.org
Javorská H, Tlustoš P, Kaliszová R (2009) Degradation of polychlorinated biphenyls in the rhizosphere of rape, Brassica napus L. Bull Environ Contam Toxicol 82:727–731
Kacálková L, Tlustoš P (2011) The uptake of persistent organic pollutants by plants. Cen Eur J Biol 6:223–235
Kavamura VN, Taketani RG, Lançoni MD, Andreote FD, Mendes R, de Melo IS (2013) Water regime influences bulk soil and rhizosphere of Cereus Jamacaru bacterial communities in the Brazilian Caatinga biome. PLoS One 8:e73606
Köberl M, Müller H, Ramadan EM, Berg G (2011) Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 6:e24452
Kučerová P, Macková M, Chromá L, Burkhard J, Tríska J, Demnerová K, Macek T (2000) Metabolism of polychlorinated biphenyls by Solanum Nigrum hairy root clone SNC-9O and analysis of transformation products. Plant Soil 225:109–115
Kumar A, Verma JP (2018) Does plant—microbe interaction confer stress tolerance in plants? A review. Microbiol Res 207:41–52
Kurzawova V, Stursa P, Uhlik O, Norkova K, Strohalm M, Lipov J, Kochankova L, Mackova M (2012) Plant–microorganism interactions in bioremediation of polychlorinated biphenyl-contaminated soil. New Biotechnol 30:15–22
Lebre PH, De Maayer P, Cowan DA (2017) Xerotolerant bacteria: surviving through a dry spell. Nat Rev Microbiol 15:285
Legind CN, Kennedy CM, Rein A, Snyder N, Trapp S (2011) Dynamic plant uptake model applied for drip irrigation of an insecticide to pepper fruit plants. Pest Manag Sci 67:521–527
Leigh MB, Prouzova P, Mackova M, Macek T, Nagle DP, Fletcher JS (2006) Polychlorinated Biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site. Appl Environ Microbiol 72:2331–2342
Leitão AL, Enguita FJ (2016) Gibberellins in Penicillium strains: challenges for endophyte-plant host interactions under salinity stress. Microbiol Res 183:8–18
Li H, Liu L, Lin C, Wang S (2011) Plant uptake and in-soil degradation of PCB-5 under varying cropping conditions. Chemosphere 84:943–949
Li Y, Liang F, Zhu Y, Wang F (2013) Phytoremediation of a PCB-contaminated soil by alfalfa and tall fescue single and mixed plants cultivation. J Soils Sed 13:925–931
Liang Y, Meggo R, Hu D, Schnoor JL, Mattes TE (2014) Enhanced polychlorinated biphenyl removal in a switchgrass rhizosphere by bioaugmentation with Burkholderia xenovorans LB400. Ecol Eng 71:215–222
Liang Y, Meggo R, Hu D, Schnoor JL, Mattes TE (2015) Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination. Appl Environ Microbiol 99:6515–6526
Low JE, Whitfield Åslund ML, Rutter A, Zeeb BA (2010) Effect of plant age on PCB accumulation by ssp. J Environ Qual 39:245–250
Lu Y-F, Lu M, Peng F, Wan Y, Liao M-H (2014) Remediation of polychlorinated biphenyl-contaminated soil by using a combination of ryegrass, arbuscular mycorrhizal fungi and earthworms. Chemosphere 106:44–50
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–94
Mackova M, Prouzova P, Stursa P, Ryslava E, Uhlik O, Beranova K, Rezek J, Kurzawova V, Demnerova K, Macek T (2009) Phyto/rhizoremediation studies using long-term PCB-contaminated soil. Environ Sci Pollut Res 16:817–829
Manzoni S, Molini A, Porporato A (2011) Stochastic modelling of phytoremediation. Proc R Soc A 467:3188–3205
Mapelli F, Marasco R, Rolli E, Barbato M, Cherif H, Guesmi A et al (2013) Potential for plant growth promotion of rhizobacteria associated with Salicornia growing in Tunisian hypersaline soils. Biomed Res Int
Marasco R, Rolli E, Ettoumi B, Vigani G, Mapelli F, Borin S, Zocchi G (2012) A drought resistance-promoting microbiome is selected by root system under desert farming. PLoS One 7:e48479
Marasco R, Rolli E, Vigani G, Borin S, Sorlini C, Ouzari H, Daffonchio D (2013) Are drought-resistance promoting bacteria cross-compatible with different plant models? Plant Signal Behav 8:e26741
Meggo RE, Schnoor JL (2013) Rhizosphere redox cycling and implications for rhizosphere biotransformation of selected polychlorinated biphenyl (PCB) congeners. Ecol Eng 57:285–292
Mehmannavaz R, Prasher SO, Ahmad D (2002) Rhizospheric effects of alfalfa on biotransformation of polychlorinated biphenyls in a contaminated soil augmented with Sinorhizobium meliloti. Process Biochem 37:955–963
Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663
Narasimhan K (2003) Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 32:146–153
Naveed M, Hussain MB, Zahir ZA, Mitter B, Sessitsch A (2014) Drought stress amelioration in wheat through inoculation with Burkholderia phytofirmans strain PsJN. Plant Growth Regul 73:121–131
Ngumbi E, Kloepper J (2016) Bacterial-mediated drought tolerance: current and future prospects. Appl Soil Ecol 105:109–225
Nielsen P, Sørensen J (1997) Multi-target and medium-independent fungal antagonism by hydrolytic enzymes in Paenibacillus polymyxa and Bacillus pumilus strains from barley rhizosphere. FEMS Microbiol Ecol 22:183–192
Niu B, Paulson JN, Zheng X, Kolter R (2017) Simplified and representative bacterial community of maize roots. PNAS 114:2450–2459
Nizzetto L, Perlinger JA (2012) Climatic, biological, and land cover controls on the exchange of gas-phase semivolatile chemical pollutants between forest canopies and the atmosphere. Environ Sci Technol 46:2699–2707
O’Sullivan G, Sandau C (eds) (2014) Environmental forensics for persistent organic pollutants. Elsevier, Amsterdam
Ouyang Y (2002) Phytoremediation: modeling plant uptake and contaminant transport in the soil–plant–atmosphere continuum. J Hydrol 266:66–82
Ouyang Y (2008) Modeling the mechanisms for uptake and translocation of dioxane in a soil-plant ecosystem with STELLA. J Contam Hydrol 95:17–29
Paasivirta J, Sinkkonen SI (2009) Environmentally relevant properties of all 209 polychlorinated biphenyl congeners for modeling their fate in different natural and climatic conditions. J Chem Eng Data 54:1189–1213
Passatore L, Rossetti S, Juwarkar AA, Massacci A (2014) Phytoremediation and bioremediation of polychlorinated biphenyls (PCBs): State of knowledge and research perspectives. J Hazard Mater 278:189–202
Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plant 118:10–15
Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799
Qin H, Brookes PC, Xu J (2014) Cucurbita spp. and Cucumis sativus enhance the dissipation of polychlorinated biphenyl congeners by stimulating soil microbial community development. Environ Pollut 184:306–312
Qin Y, Druzhinina IS, Pan X, Yuana Z (2016) Microbially mediated plant salt tolerance and microbiome-based solutions for saline agriculture. Biotechnol Adv 34:1245–1259
Rahman SFS, Singh E, Pieterse CMJ, Schenk PM (2018) Emerging microbial biocontrol strategies for plant pathogens. Plant Sci 267:102–111
Rolli E, Marasco R, Vigani G, Ettoumi B, Mapelli F, Deangelis ML, Pierotti Cei F (2014) Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environ Microbiol 17:316–331
Santaella C, Schue M, Berge O, Heulin T, Achouak W (2008) The exopolysaccharide of Rhizobium sp. YAS34 is not necessary for biofilm formation on Arabidopsis thaliana and Brassica napus roots but contributes to root colonization. Environ Microbiol 10:2150–2163
Schwitzguébel J-P (2017) Phytoremediation of soils contaminated by organic compounds: hype, hope and facts. J Soils Sediments 17:1492–1502
Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56
Shen C, Tang X, Cheema SA, Zhang C, Khan MI, Liang F, Chen X, Zhu Y, Lin Q, Chen Y (2009) Enhanced phytoremediation potential of polychlorinated biphenyl contaminated soil from e-waste recycling area in the presence of randomly methylated-β-cyclodextrins. J Hazard Mater 172:1671–1676
Slater H, Gouin T, Leigh MB (2011) Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native tree species. Chemosphere 84:199–206
Soussi A, Ferjani R, Marasco R, Guesmi A, Cherif H, Rolli E, Mapelli F, Ouzari H, Daffonchio D, Cherif A (2016) Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential. Plant Soil:357–370
Sparks T (ed) (2000) Statistics in ecotoxicology, Ecological and environmental toxicology series. Wiley, Chichester/New York. 300p
Teng Y, Luo Y, Sun X, Tu C, Xu L, Liu W, Li Z, Christie P (2010) influence of arbuscular mycorrhiza and rhizobium on phytoremediation by alfalfa of an agricultural soil contaminated with weathered PCBs: a field study. Int J Phytoremediation 12:516–533
Terzaghi E, Morselli M, Semplice M, Cerabolini BEL, Jones KC, Freppaz M, Di Guardo A (2017) SoilPlusVeg: an integrated air-plant-litter-soil model to predict organic chemical fate and recycling in forests. Sci Total Environ 595:169–177
Terzaghi E, Zanardini E, Morosini C, Raspa G, Borin S, Mapelli F, Vergani L, Di Guardo A (2018) Rhizoremediation half-lives of PCBs: role of congener composition, organic carbon forms, bioavailability, microbial activity, plant species and soil conditions, on the prediction of fate and persistence in soil. Sci Total Environ 612:544–560
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
Tiwari S, Lata C, Chauhan PS, Nautiyal CS (2016) Pseudomonas putida attunes morphophysiological, biochemical and molecular responses in Cicer arietinum L. during drought stress and recovery. Plant Physiol Biochem 99:108–117
Topp E, Scheunert I, Attar A, Korte F (1986) Factors affecting the uptake of C-14-labeled organic chemicals by plants from soil. Ecotox Environ Safe 11:219–228
Trapp S (2015) calibration of a plant uptake model with plant- and site-specific data for uptake of chlorinated organic compounds into radish. Environ Sci Technol 49:395–402
Tu C, Teng Y, Luo Y, Sun X, Deng S, Li Z, Liu W, Xu Z (2011) PCB removal, soil enzyme activities, and microbial community structures during the phytoremediation by alfalfa in field soils. J Soils Sediments 11:649–656
Tu C, Ma L, Guo P, Song F, Teng Y, Zhang H, Luo Y (2017) Rhizoremediation of a dioxin-like PCB polluted soil by alfalfa: Dynamic characterization at temporal and spatial scale. Chemosphere 189:517–524
Van Aken B, Correa PA, Schnoor JL (2010) phytoremediation of polychlorinated biphenyls: new trends and promises. Environ Sci Technol 44:2767–2776
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
Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A (2016) Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria. Microbiol Res 184:13–24
Walker A (1974) A simulation model for prediction of herbicide persistence. J Environ Qual 3:396–401
Wania F, McLachlan MS (2001) Estimating the influence of forests on the overall fate of Semivolatile organic compounds using a multimedia fate model. Environ Sci Technol 35:582–590
Weyens N, van der Lelie D, Taghavi S, Newman L, Vangronsveld J (2009) Exploiting plant–microbe partnerships to improve biomass production and remediation. Trends Biotechnol 27:591–598
Whitfield Åslund ML, Zeeb B, Rutter A, Reimer K (2007) In situ phytoextraction of polychlorinated biphenyl – (PCB)contaminated soil. Sci Total Environ 374:1–12
Whitfield Åslund ML, Rutter A, Reimer KJ, Zeeb BA (2008) The effects of repeated planting, planting density, and specific transfer pathways on PCB uptake by Cucurbita pepo grown in field conditions. Sci Total Environ 405:14–25
Xu L, Teng Y, Li Z-G, Norton JM, Luo Y-M (2010) Enhanced removal of polychlorinated biphenyls from alfalfa rhizosphere soil in a field study: the impact of a rhizobial inoculum. Sci Total Environ 408:1007–1013
Yuan Z, Druzhinina IS, Labbé J, Redman R, Qin Y, Rodriguez R, Lin F (2016) Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity. Sci Rep 6:32467
Zolla G, Badri DV, Bakker MG, Manter DK, Vivanco JM (2013) Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis. Appl Soil Ecol 68:1–9
Acknowledgments
We thank the EU Horizon 2020 MADFORWATER project (GA No. 688320, www.madforwater.eu) and the collaboration of the “Caffaro Working Group”: Stefano Armiraglio, Simone Anelli, Vanna M. Sale, and Paolo Nastasio and the funding agency Ente Regionale per i Servizi all’Agricoltura e alle Foreste (ERSAF). DSAT of University of Insubria is also acknowledged for funding part of ET’s salary.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Riva, V. et al. (2019). Exploitation of Rhizosphere Microbiome Services. In: Reinhardt, D., Sharma, A. (eds) Methods in Rhizosphere Biology Research. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-13-5767-1_7
Download citation
DOI: https://doi.org/10.1007/978-981-13-5767-1_7
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-5766-4
Online ISBN: 978-981-13-5767-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)