Abstract
Global demands for agricultural produce will increase up to 70% by the next two decades. To meet this goal, the productivity of crops needs to be increased under harsher climate conditions and with declining soil and water quality. In addition to this, widespread emergence of new pathogens and pests is posing a serious threat to agricultural produce. Plant-microbe interactions may have a beneficial, neutral, or negative effect on one or both partners. The whole world needs to address climate change scenario, by enabling agriculture to adopt climate-friendly practices. Plants host a rich microbiota, which supports plants in nutrition uptake and health management. Phytomicrobiome represents a great reservoir, which can be harnessed to improve the productivity of crops and food quality. A systematic research focused on the understanding of structure and function of phytomicrobiome driven by crop management and environmental factors is critical for devising reliable strategies to improve crop health and productivity in a sustainable way, by reducing chemical inputs and emissions of greenhouse gases. Microbial diversity associated with plants is highly underestimated, as the data generated by next-generation sequencing technologies have exhibited that only a small portion of microorganisms could be cultivated until now. Recently, the high-throughput microbial cultivation approach “culturomics” in conjunction with high-speed and low-cost identification technique based on MALDI-TOF MS has offered an opportunity to cultivate the not-yet-cultivated microorganisms and harness them to manipulate the crop phytomicrobiome. In this chapter, we discussed various aspects of phytomicrobiome, like beneficial and harmful effects of its members and colonization in rhizosphere and phyllosphere.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akiyama K, Matsuzaki K, Hayashi H (2005) Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435:824–827. doi:10.1038/nature03608
Al-Awadhi H, Al-Mailem D, Dashti N, Hakam L, Eliyas M, Radwan S (2012) The abundant occurrence of hydrocarbon-utilizing bacteria in the phyllospheres of cultivated and wild plants in Kuwait. Int Biodeterior Biodegrad 73:73–79. doi:10.1016/j.ibiod.2012.05.016
Ali N, Sorkhoh N, Salamah S, Eliyas M, Radwan S (2012) The potential of epiphytic hydrocarbon-utilizing bacteria on legume leaves for attenuation of atmospheric hydrocarbon pollutants. J Environ Manage 93:113–120. doi:10.1016/j.jenvman.2011.08.014
Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P (2004) Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol Evol 19:535–544. doi:10.1016/j.tree.2004.07.021
Arruda L, Beneduzi A, Martins A, Lisboa B, Lopes C, Bertolo F, Passaglia LMP, Vargas LK (2013) Screening of rhizobacteria from maize (Zea mays L.) in Rio Grande do Sul State (South Brazil) and analysis of their potential to improve plant growth. Appl Soil Ecol 63:15–22. doi:10.1016/j.apsoil.2012.09.001
Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266. doi:10.1146/annurev.arplant.57.032905.105159
Barak JD, Schroeder BK (2012) Interrelationships of food safety and plant pathology: the life cycle of human pathogens on plants. Annu Rev Phytopathol 50:241–266. doi:10.1146/annurev-phyto-081211-172936
Bascom-Slack CA, Arnold AE, Strobel SA (2012) Student-directed discovery of the plant microbiome and its products. Science 338:485–486. doi:10.1126/science.1215227
Bender SF, Wagg C, van der Heijden MGA (2016) An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends Ecol Evol 31:440–452. doi:10.1016/j.tree.2016.02.016
Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486. doi:10.1016/j.tplants.2012.04.001
Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193:96–102. doi:10.1016/j.plantsci.2012.05.010
Bourke PMA (1964) Emergence of potato blight, 1843-46. Nature 203:805–808. doi:10.1038/203805a0
Bringel F, Couée I (2015) Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front Microbiol 6:486. doi:10.3389/fmicb.2015.00486
Brusamarello-Santos LC, Gilard F, Brulé L, Quilleré I, Gourion B, Ratet P, de Souza EM, Lea PJ, Hirel B (2017) Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense. PLoS One 12(3):e0174576. doi:10.1371/journal.pone.0174576
Bulgarelli D, Rott M, Schlaeppi K, van Themaat EVL, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner FO, Amann R, Eickhorst T, Schulze-Lefert P (2012) Revealing structure and assembly cues for Arabidopsis root-inhibiting bacterial microbiota. Nature 488:91–95. doi:10.1038/nature11336
Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EV, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838. doi:10.1146/annurev-arplant-050312-120106
Burgess TI, Scott JK, Mcdougall KL, Stukely MJC, Crane C, Dunstan WA, Brigg F, Andjic V, White D, Rudman T, Arentz F, Ota N, Hardy GESJ (2017) Current and projected global distribution of Phytophthora cinnamomi, one of the world’s worst plant pathogens. Glob Chang Biol 23:1661–1674. doi:10.1111/gcb.13492
Cappellazzo G, Lanfranco L, Fitz M, Wipf D, Bonfante P (2008) Characterization of an amino acid permease from the endomycorrhizal fungus Glomus mosseae. Plant Physiol 147:429–437
Chaparro JM, Badri VD, Vivanco MJ (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803. doi:10.1038/ismej.2013.196
Charpentier M, Oldroyd G (2010) How close are we to nitrogen-fixing cereals? Curr Opin Plant Biol 13:556–564. doi:10.1016/j.pbi.2010.08.003
De Kempeneer L, Sercu B, Vanbrabant W, Van Langenhove H, Verstraete W (2004) Bioaugmentation of the phyllosphere for the removal of toluene from indoor air. Appl Microbiol Biotechnol 64:284–288. doi:10.1007/s00253-003-1415-3
Defez R, Andreozzi A, Bianco C (2017) The overproduction of indole-3-acetic acid (IAA) in endophytes upregulates nitrogen fixation in both bacterial cultures and inoculated rice plants. Microb Ecol (in press). doi:10.1007/s00248-017-0948-4
Dickson I (2017) Gut microbiota: culturomics: illuminating microbial dark matter. Nat Rev Gastroenterol Hepatol 4:3. doi:10.1038/nrgastro.2016.189
Dubourg G, Lagier JC, Robert C, Armougom F, Hugon P, Metidji S, Dione N, Dangui NP, Pfleiderer A, Abrahao J, Musso D, Papazian L, Brouqui P, Bibi F, Yasir M, Vialettes B, Raoult D (2014) Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics. Int J Antimicrob Agents 44:17–124. doi:10.1016/j.ijantimicag.2014.04.020
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A 112:E911–E920. doi:10.1073/pnas.1414592112
Erickson MC, Webb CC, Diaz-Perez JC, Phatak SC, Silvoy JJ, Davey L, Payton AS, Liao J, Ma L, Doyle MP (2010) Infrequent internalization of Escherichia coli O157:H7 into field-grown leafy greens. J Food Prot 73:500–506. doi:10.4315/0362-028X-73.3.500
Farrar K, Bryant D, Cope-Selby N (2014) Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops. Plant Biotechnol J 12:1193–1206. doi:10.1111/pbi.12279
Fravel D, Olivain C, Alabouvette C (2003) Fusarium oxysporum and its biocontrol. New Phytol 157:493–502. doi:10.1046/j.1469-8137.2003.00700.x
Gallegos-Robles MA, Morales-Loredo A, Alvarez-Ojeda G, Vega PA, Chew MY, Velarde S, Fratamico P (2008) Identification of Salmonella serotypes isolated from cantaloupe and Chile pepper production systems in Mexico by PCR-restriction fragment length polymorphism. J Food Prot 71:2217–2222. doi:10.4315/0362-028X-71.11.2217
Gandolfi I, Canedoli C, Imperato V, Tagliaferri I, Gkorezis P, Vangronsveld J, Schioppa EP, Papacchini M, Bestetti G, Franzetti A (2017) Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area. Environ Pollut 220:650–658. doi:10.1016/j.envpol.2016.10.022
Garbeva P, Postma J, van Veen JA, van Elsas JD (2006) Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3. Environ Microbiol 8:233–246. doi:10.1111/j.1462-2920.2005.00888.x
Gulati A, Sharma N, Vyas P, Sood S, Rahi P, Pathania V, Prasad R (2010) Organic acid production and plant growth promotion as a function of phosphate solubilization by Acinetobacter rhizosphaerae strain BIHB 723 isolated from the cold deserts of the trans-Himalayas. Arch Microbiol 192:975–983. doi:10.1007/s00203-010-0615-3
Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307–319. doi:10.1038/nrmicro1129
Han S, Micallef SA (2016) Environmental metabolomics of the tomato plant surface provides insights on Salmonella enterica colonization. Appl Environ Microbiol 82:3131–3142. doi:10.1128/AEM.00435-16
Hariprasad P, Niranjana SR (2009) Isolation and characterization of phosphate solubilizing rhizobacteria to improve plant health of tomato. Plant Soil 316:13–24. doi:10.1007/s11104-008-9754-6
Harman GE, Howell CR, Viterbo A, Chet I, Lorito M (2004) Trichoderma species: opportunistic, avirulent plant symbionts. Nat Rev Microbiol 2:43–56. doi:10.1038/nrmicro797
Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312:7–14. doi:10.1007/s11104-007-9514-z
Hiltner L (1904) Ueber neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie und unter besonderer BerUcksichtigung der Grundungung und Brache. Arb Deut Landw Gesell 98:59–78
Hirsch PR, Mauchline TH (2012) Who’s who in the plant root microbiome? Nat Biotechnol 30:961–962. doi:10.1038/nbt.2387
Hofmann A, Fischer D, Hartmann A, Schmid M (2014) Colonization of plants by human pathogenic bacteria in the course of organic vegetable production. Front Microbiol 5:191. doi:10.3389/fmicb.2014.00191
Ibenyassine K, Mhand RA, Karamoko Y, Anajjar B, Chouibani MM, Ennaji M (2007) Bacterial pathogens recovered from vegetables irrigated by wastewater in Morocco. J Environ Health 69:47–51
Islam M, Morgan J, Doyle MP, Phatak SC, Millner P, Jiang X (2004) Persistence of Salmonella enterica serovar Typhimurium on lettuce and parsley and in soils on which they were grown in fields treated with contaminated manure composts or irrigation water. Foodborne Pathog Dis 1:27–35. doi:10.1089/153531404772914437
Johnson NC, Angelard C, Sanders IR, Kiers ET (2013) Predicting community and ecosystem outcomes of mycorrhizal responses to global change. Ecol Lett 16:140–153. doi:10.1111/ele.12085
Karlsson I, Friberg H, Kolseth A-K, Steinberg C, Persson P (2017) Organic farming increases richness of fungal taxa in the wheat phyllosphere. Mol Ecol (in press). doi:10.1111/mec.14132
Kembel SW, O’Connor TK, Arnold HK, Hubbell SP, Wright SJ, Green JL (2014) Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc Natl Acad Sci 111:13715–13720. doi:10.1073/pnas.1216057111
Koukkidis G, Haigh R, Allcock N, Jordan S, Freestone P (2017) Salad leaf juices enhance Salmonella growth, colonization of fresh produce, and virulence. Appl Environ Microbiol 83:e02416–e02416. doi:10.1128/AEM.02416-16
Kuan KB, Othman R, Abdul Rahim K, Shamsuddin ZH (2016) Plant growth-promoting rhizobacteria inoculation to enhance vegetative growth, nitrogen fixation and nitrogen remobilisation of maize under greenhouse conditions. PLoS One 11(3):e0152478. doi:10.1371/journal.pone.0152478
Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. J Plant Nutr Soil Sci 163:421–431. doi:10.1002/1522-2624
Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, Caputo A, Cadoret F, Traore SI, Seck EH, Dubourg G, Durand G, Mourembou G, Guilhot E, Togo A, Bellali S, Bachar D, Cassir N, Bittar F, Delerce J, Mailhe M, Ricaboni D, Bilen M, Dangui Nieko NP, Dia Badiane NM, Valles C, Mouelhi D, Diop K, Million M, Musso D, Abrahão J, Azhar EI, Bibi F, Yasir M, Diallo A, Sokhna C, Djossou F, Vitton V, Robert C, Rolain JM, La Scola B, Fournier PE, Levasseur A, Raoult D (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 1:16203. doi:10.1038/nmicrobiol.2016.203
Laranjo M, Alexandre A, Oliveira S (2014) Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus. Microbiol Res 169:2–17. doi:10.1016/j.micres.2013.09.012
Lareen A, Burton F, Schafer P (2016) Plant root-microbe communication in shaping root microbiomes. Plant Mol Biol 90:575–587. doi:10.1007/s11103-015-0417-8
Larousse M, Galiana E (2017) Microbial partnerships of pathogenic oomycetes. PLoS Pathog 13:e1006028. doi:10.1371/journal.ppat.1006028
Latz E, Eisenhauer N, Scheu S, Jousset A (2015) Plant identity drives the expression of biocontrol factors in a rhizosphere bacterium across a plant diversity gradient. Funct Ecol 29:1225–1234. doi:10.1111/1365-2435.12417
Latz E, Eisenhauer N, Rall BC, Scheu S, Jousset A (2016) Unravelling linkages between plant community composition and the pathogen-suppressive potential of soils. Sci Rep 6:23584. doi:10.1038/srep23584
Lecomte C, Alabouvette C, Edel-Hermann V, Robert F, Steinberg C (2016) Biological control of ornamental plant diseases caused by Fusarium oxysporum: a review. Biol Control 101:17–30. doi:10.1016/j.biocontrol.2016.06.004
Lopez-Pedrosa A, Gonzalez-Guerrero M, Valderas A, Azcon-Aguilar C, Ferrol N (2006) GintAMT1 encodes a functional high-affinity ammonium transporter that is expressed in the extra radical mycelium of Glomus intraradices. Fungal Genet Biol 43:102–110. doi:10.1016/j.fgb.2005.10.005
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root. Nature 488:86–90. doi:10.1038/nature11237
Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow M, Verdier V, Beer SV, Machado MA, Toth I, Salmond G, Foster GD (2012) Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol 13:614–629. doi:10.1111/J.1364-3703.2012.00804.X
Melotto M, Panchal S, Roy D (2014) Plant innate immunity against human bacterial pathogens. Front Microbiol 5:411. doi:10.3389/fmicb.2014.00411
Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100. doi:10.1126/science.1203980
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. doi:10.1111/1574-6976.12028
Montañez A, Abreu C, Gill PR, Hardarson G, Siracdi M (2009) Biological nitrogen fixation in maize (Zea mays L.) by 15N isotope-dilution and identification of associated culturable diazotrophs. Biol Fertil Soils 45:253–263. doi:10.1007/s00374-008-0322-2
Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS One 7:e35498. doi:10.1371/journal.pone.0035498
Newton AC, Gravouil C, Fountaine JM (2010) Managing the ecology of foliar pathogens: ecological tolerance in crops. Ann Appl Biol 157:343–359. doi:10.1111/j.1744-7348.2010.00437.x
Nicholson AM, Gurtler JB, Bailey RB, Niemira BA, Douds DD (2015) Influence of mycorrhizal fungi on fate of E. coli O157:H7 and Salmonella in soil and internalization into Romaine lettuce plants. Int J Food Microbiol 192:95–102. doi:10.1016/j.ijfoodmicro.2014.10.001
Norman JS, Hare JR, Friesen ML (2017) Comment: isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of maize seedlings in greenhouses. Front Plant Sci 8:212. doi:10.3389/fpls.2017.00212
Oldroyd GED (2013) Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat Rev Microbiol 11:252–263. doi:10.1038/nrmicro2990
Ongeng D, Haberbeck LU, Mauriello G, Ryckeboer J, Springael D, Geeraerd AH (2014) Modeling the fate of Escherichia coli O157:H7 and Salmonella enterica in the agricultural environment: current perspective. J Food Sci 79:R421–R427. doi:10.1111/1750-3841.12392
Ortega RA, Mahnert A, Berg C, Müller H, Berg G (2016) The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals. FEMS Microbiol Ecol 92:fiw173. doi:10.1093/femsec/ fiw173
Oteino N, Lally RD, Kiwanuka S, Lloyd A, Ryan D, Germaine KJ, Dowling DN (2015) Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microbiol 6:745. doi:10.3389/fmicb.2015.00745
Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol 6:763–775. doi:10.1038/nrmicro1987
Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14:257–263. doi:10.1016/j.tim.2006.04.007
Peñuelas J, Terradas J (2014) The foliar microbiome. Trends Plant Sci 19:278–280. doi:10.1016/j.tplants.2013.12.007
Piromyou P, Buranabanyat B, Tantasawat P, Tittabutr P, Boonkerd N, Teaumroong N (2011) Effect of plant growth promoting rhizobacteria (PGPR) inoculation on microbial community structure in rhizosphere of forage corn cultivated in Thailand. Eur J Soil Biol 47:44–54. doi:10.1016/j.ejsobi.2010.11.004
Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361. doi:10.1007/s11104-008-9568-6
Rahi P, Kapoor R, Young JPW, Gulati A (2012) A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas. Mol Ecol 21(1):145–159. doi:10.1111/j.1365-294X.2011.05368.x
Rahi P, Sharma OP, Shouche YS (2016) Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) based microbial identifications: challenges and scopes for microbial ecologists. Front Microbiol 7:1359. doi:10.3389/fmicb.2016.01359
Rangel de Souza ALS, De Souza SA, De Oliveira MVV, Ferraz TM, Figueiredo FAMMA, Da Silva ND, Rangel PL, Panisset CRS, Olivares FL, Campostrini E, De Souza FGA (2016) Endophytic colonization of Arabidopsis thaliana by Gluconacetobacter diazotrophicus and its effect on plant growth promotion, plant physiology, and activation of plant defense. Plant Soil 399:257–270. doi:10.1007/s11104-015-2672-5
Rascovan N, Carbonetto B, Perrig D, Díaz M, Canciani W, Abalo M, Alloati J, González-Anta G, Vazquez MP (2016) Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Sci Rep 6:28084. doi:10.1038/srep28084
Rastogi G, Coaker GL, Leveau JHJ (2013) New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 348:1–10. doi:10.1111/1574-6968.12225
Redford AJ, Fierer N (2009) Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb Ecol 58:189. doi:10.1007/s00248-009-9495-y
Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol 53:403–424. doi:10.1146/annurev-phyto-082712-102342
Richardson A, Barea J-M, McNeill A, Prigent-Combaret C (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 321:305–339. doi:10.1007/s11104-009-9895-2
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu W-T, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437. doi:10.1038/nature12352
Saleem M, Meckes N, Pervaiz ZH, Traw MB (2017) Microbial interactions in the phyllosphere increase plant performance under herbivore biotic stress. Front Microbiol 8:41. doi:10.3389/fmicb.2017.00041
Samad A, Trognitz F, Compant S, Antonielli L, Sessitsch A (2017) Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants. Environ Microbiol 19:1407–1424. doi:10.1111/1462-2920.13618
Sandhu A, Halverson LJ, Beattie GA (2007) Bacterial degradation of airborne phenol in the phyllosphere. Environ Microbiol 9:383–392. doi:10.1111/j.1462-2920.2006.01149.x
Sangthong S, Suksabye P, Thiravetyan P (2016) Air-borne xylene degradation by Bouganvillea buttiana and the role of epiphytic bacteria in the degradation. Ecotoxicol Environ Saf 126:273–280. doi:10.1016/j.ecoenv.2015.12.017
Saville AC, Martin MD, Ristaino JB (2016) Historic late blight outbreaks caused by a widespread dominant lineage of Phytophthora infestans (Mont.) de Bary. PLoS One 11(12):e0168381. doi:10.1371/journal.pone.0168381
Scheublin TR, Deusch S, Moreno-Forero SK, Müller JA, van der Meer JR, Leveau JHJ (2014) Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds. Environ Microbiol 16:2212–2225. doi:10.1111/1462-2920.12375
Sheldrake M, Rosenstock NP, Revillini D, Olsson PA, Mangan S, Sayer EJ, Wallander H, Turner BL, Tanner EVJ (2017) Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest. New Phytol 214:455–467. doi:10.1111/nph.14384
Singh BK, Munro S, Potts JM, Millard P (2007) Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl Soil Ecol 36:147–155. doi:10.1016/j.apsoil.2007.01.004
Smith SE, Smith FA (2012) Fresh perspectives on the roles of arbuscular mycorrhizal fungi in plant nutrition and growth. Mycologia 104:1–13. doi:10.3852/11-229
Smith DL, Gravel V, Yergeau E (2017) Signalling in the phytomicrobiome: Understanding and harnessing the plant holobiont. Front Plant Sci 8:611. doi:10.3389/fpls.2017.00611
Solden L, Lloyd K, Wrighton K (2016) The bright side of microbial dark matter: lessons learned from the uncultivated majority. Cur Opin Microbiol 31(2):17–226. doi:10.1016/j.mib.2016.04.020
Sprent JI, Ardley J, James EK (2017) Biogeography of nodulated legumes and their nitrogen-fixing symbionts. New Phytol (in press). doi:10.1111/nph.14474
Stukenbrock EH, McDonald B (2009) The origins of plant pathogens in agroecosystems. Annu Rev Phytopathol 46:75–100. doi:10.1146/annurev.phyto.010708.154114
Teplitski M, Warriner K, Bartz J, Schneider KR (2011) Untangling metabolic and communication networks: interactions of enterics with phytobacteria and their implications in produce safety. Trends Microbiol 19:121–127. doi:10.1016/j.tim.2010.11.007
Vartoukian SR, Palmer RM, Wade WG (2010) Strategies for culture of ‘unculturable’ bacteria. FEMS Microbiol Let 309:1–7. doi:10.1111/j.1574-6968.2010.02000.x
Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840. doi:10.1038/nrmicro2910
Vuong HB, Thrall PH, Barrett LG (2017) Host species and environmental variation can influence rhizobial community composition. J Ecol 105:540–548. doi:10.1111/1365-2745.12687
Waight K, Pinyakong O, Luepromchai E (2007) Degradation of phenanthrene on plant leaves by phyllosphere bacteria. J Gen Appl Microbiol 53:265–272. doi:10.2323/jgam.53.265
Wallenstein MD (2017) Managing and manipulating the rhizosphere microbiome for plant health: a systems approach. Rhizo (in press). doi:10.1016/j.rhisph.2017.04.004
Weller DM, Raaijmakers JM, Gardener BBM, Thomashow LS (2002) Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol 40:309–348. doi:10.1146/annurev.phyto.40.030402.110010
Whipps JM, Hand P, Pink D, Bending GD (2008) Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbiol 105:1744–1755. doi:10.1111/j.1365-2672.2008.03906.x
Williams TR, Marco ML (2014) Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors. mBio 5:e01564-14. doi:10.1128/mBio.01564-14
Williams A, Manoharan L, Rosenstock NP, Olsson PA, Hedlund K (2017) Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange. New Phytol 213:874–885. doi:10.1111/nph.14196
Xiao X, Chen W, Zong L, Yang J, Jiao S, Lin Y, Wang E, Wei G (2017) Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments. Mol Ecol 26:1641–1651. doi:10.1111/mec.14027
Ximenes E, Hoagland L, Ku S, Li X, Ladisch M (2017) Human pathogens in plant biofilms: formation, physiology, and detection. Biotechnol Bioeng (in press). doi:10.1002/bit.26247
Yoon V, Tian G, Vessey JK, Macfie SM, Dangi OP, Kumer AK, Tian L (2016) Colonization efficiency of different sorghum genotypes by Gluconacetobacter diazotrophicus. Plant Soil 398:243–256. doi:10.1007/s11104-015-2653-8
Yutthammo C, Thongthammachat N, Pinphanichakarn P, Luepromchai E (2010) Diversity and activity of PAH-degrading bacteria in the phyllosphere of ornamental plants. Microb Ecol 59:357–368. doi:10.1007/s00248-009-9631-8
Acknowledgments
This work was supported by the Department of Biotechnology, Government of India (BT/Coord.II/01/03/2016), and Department of Science and Technology, Government of India (YSS/2015/000149).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Rahi, P. (2017). Phytomicrobiome: A Reservoir for Sustainable Agriculture. In: Kalia, V., Shouche, Y., Purohit, H., Rahi, P. (eds) Mining of Microbial Wealth and MetaGenomics. Springer, Singapore. https://doi.org/10.1007/978-981-10-5708-3_7
Download citation
DOI: https://doi.org/10.1007/978-981-10-5708-3_7
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-5707-6
Online ISBN: 978-981-10-5708-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)