Abstract
The natural association between plants and microorganisms has historically been linked to improved plant growth, nutrition and health. Rhizospheric and phyllospheric microorganisms have received much attention due to their applications in improved nutrient acquisition, enhanced water sequestration, induced systemic resistance, competitive exclusion of plant pathogens and remediation of environmental pollutants. Such beneficial attributes have motivated the adoption of these plant–microbe interactions in agro-ecosystems to improve productivity. The application of commercially available plant beneficial microorganisms (CAPBM) in agro-ecosystems is largely due to their compatibility and complementarity with natural processes of nutrient cycling, plant protection and other related biological processes. While numerous studies have reported the huge potential of the use of plant beneficial microorganisms in agro-ecosystems, wide-scale commercialization of microbial products are still lagging. Hurdles in the commercialization of CAPBM range from lack of awareness and regulatory framework to inaccurate product selection. The future prospects of the application of CAPBM will be determined by the adoption of new technologies that include multi-omics approach for improving the quality as well as applicability of these beneficial microorganisms in agro-ecosystems. Furthermore, government intervention is of utmost importance to ensure that the necessary regulatory framework is in place, thereby ensuring high quality of products. High-quality products will improve adoption rate, which would have downstream influences on job creation in the CAPBM and agricultural industries.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abdullahi R, Lihan S, Edward R (2015) Effect of arbuscular mycorrhizal fungi and poultry manure on growth and nutrients uptake by maize under field condition. Int J Agric Innov Res 4:158–163. ISSN (online): 2319-1473
Acioli-Santos B, Vieira HEE, Lima CE, Maia LC (2011) The molecular ectomycorrhizal fungus essence in association: a review of differentially expressed fungal genes during symbiosis formation. In: Diversity and biotechnology of ectomycorrhizae. Springer, Berlin/Heidelberg, pp 87–121. https://doi.org/10.1007/978-3-642-15196-5_5
Adeleke RA (2014) Getting rid of the unwanted: highlights of developments and challenges of biobeneficiation of iron ore minerals—a review. J Industrial Microbiol Biotechnol 41(12):1731–1741. https://doi.org/10.1007/s10295-014-1514-4
Adeleke RA, Cloete TE, Bertrand A, Khasa DP (2012) Iron ore weathering potentials of ectomycorrhizal plants. Mycorrhiza 22(7):535–544. https://doi.org/10.1007/s00572-012-0431-5
Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. JKSUS 26(1):1–20. https://doi.org/10.1016/j.jksus.2013.05.001
Ahmed E, Holmström SJ (2015) Siderophore production by microorganisms isolated from a podzol soil profile. Geomicrobiol J 32(5):397–411. https://doi.org/10.1080/01490451.2014.925011
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 Manag 93(1):113–120
Aroca R, Vernieri P, Ruiz-Lozano JM (2008) Mycorrhizal and non-mycorrhizal Lactuca sativa plants exhibit contrasting responses to exogenous ABA during drought stress and recovery. J Exp Bot 59:2029–2041. https://doi.org/10.1093/jxb/ern057
Augé RM (2001) Water relations, drought and vesicular-arbuscular mycorrhizal symbiosis. Mycorrhiza 11(1):3–42. https://doi.org/10.1007/s005720100097
Augé RM (2004) Arbuscular mycorrhizae and soil/plant water relations. Can J Soil Sci 84(4):373–381. https://doi.org/10.4141/S04-002
Augé RM, Sylvia DM, Park S, Buttery BR, Saxton AM, Moore JL, Cho K (2004) Partitioning mycorrhizal influence on water relations of Phaseolus vulgaris into soil and plant components. Can J Bot 82(4):503–514. https://doi.org/10.1139/b04-020
Al-Awadhi H, El-Nemr I, Mahmoud H, Sorkhoh NA, Radwan SS (2009) Plant-associated bacteria as tools for the phytoremediation of oily nitrogen-poor soils. Int J Phytoremediation 11(1):11–27. https://doi.org/10.1080/15226510802363261
Andrews JH, Harris RF (2000) The ecology and biogeography of microorganisms on plant surfaces. Annu Rev Phytopathol 38(1):145–180. https://doi.org/10.1146/annurev.phyto.38.1.145
Babu AN, Jogaiah S, Ito SI, Nagaraj AK, Tran LSP (2015) Improvement of growth, fruit weight and early blight disease protection of tomato plants by rhizosphere bacteria is correlated with their beneficial traits and induced biosynthesis of antioxidant peroxidase and polyphenol oxidase. Plant Sci 231:62–73
Baum C, El-Tohamy W, Gruda N (2015) Increasing the productivity and product quality of vegetable crops using arbuscular mycorrhizal fungi: a review. Sci Hort 187:131–141. https://doi.org/10.1016/j.scienta.2015.03.002
Becerra A, Bartoloni N, Cofré N, Soteras F, Cabello M (2014) Arbuscular mycorrhizal fungi in saline soils: vertical distribution at different soil depth. Braz J Microbiol 45(2):585–594
Bello-Akinosho M (2018) Biodegradation of polycyclic aromatic hydrocarbons in contaminated soils using a tripartite association of ectomycorrhizal fungi, pine plant and their rhizosphere bacteria. Philosophiae Doctor (Microbiology). University of Pretoria, Pretoria, South Africa
Bello-Akinosho M, Makofane R, Adeleke R, Thantsha M, Pillay M, Chirima GJ (2016) Potential of polycyclic aromatic hydrocarbon-degrading bacterial isolates to contribute to soil fertility. Biomed Res Int 2016. https://doi.org/10.1155/2016/5798593
Bello-Akinosho M, Adeleke R, Thantsha MS, Maila M (2017) Pseudomonas sp. (strain 10–1B): a potential inoculum candidate for green and sustainable remediation. Remed J 27(3):75–79. https://doi.org/10.1002/rem.21521
Beneduzi A, Ambrosini A, Passaglia LM (2012) Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents. Genet Mol Biol 35(4):1044–1051
Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193:96–102. https://doi.org/10.1016/j.plantsci.2012.05.010
Berruti A, Lumini E, Balestrini R, Bianciotto V (2016) Arbuscular mycorrhizal fungi as natural biofertilizers: Let’s benefit from past successes. Front Microbiol 6:1559. https://doi.org/10.3389/fmicb.2015.01559
Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28(4):1327–1350. https://doi.org/10.1007/s11274-011-0979-9
Bitterlich M, Franken P, Graefe J (2018) Arbuscular mycorrhiza improves substrate hydraulic conductivity in the plant available moisture range under root growth exclusion. Front Plant Sci 9:301. https://doi.org/10.3389/fpls.2018.00301
Bojarczuk K, Kieliszewska-Rokicka B (2010) Effect of ectomycorrhiza on Cu and Pb accumulation in leaves and roots of silver birch (Betula pendula Roth.) seedlings grown in metal-contaminated soil. Water Air Soil Pollut 207(1–4):227–240. https://doi.org/10.1007/s11270-009-0131-8
Bonfante P, Desirò A (2015) Arbuscular mycorrhizas: the lives of beneficial fungi and their plant hosts. Principles of plant-microbe interactions. Springer, Cham, pp 235–245. https://doi.org/10.1007/978-3-319-08575-3_25
Brandl H, Bosshard R, Wegmann M (2001) Computer-munching microbes: metal leaching from electronic scrap by bacteria and fungi. Hydrometallurgy 59(2–3):319–326. https://doi.org/10.1016/S0304-386X(00)00188-2
Bradáčová K, Weber NF, Morad-Talab N, Asim M, Imran M, Weinmann M, Neumann G (2016) Micronutrients (Zn/Mn), seaweed extracts, and plant growth-promoting bacteria as cold-stress protectants in maize. Chem Biol Technol Agric 3(1):19. https://doi.org/10.1186/s40538-016-0069-1
Brearley FQ (2011) The importance of ectomycorrhizas for the growth of dipterocarps and the efficacy of ectomycorrhizal inoculation schemes. In: Diversity and biotechnology of ectomycorrhizae. Springer, Berlin/Heidelberg, pp 3–17. https://doi.org/10.1007/978-3-642-15196-5_1
Brundrett M (2002) Coevolution of roots and mycorrhizas of land plants. New Phytol 154:275–304. https://doi.org/10.1046/j.1469-8137.2002.00397.x
Brundrett M (2004) Diversity and classification of mycorrhizal associations. Biol Rev 79(3):473–495. https://doi.org/10.1017/S1464793103006316
Bruns TD, Bidartondo MI, Taylor LD (2002) Host specificity in ectomycorrhizal communities: what do the exceptions tell us? Integr Comp Biol 42(2):352–359. https://doi.org/10.1093/icb/42.2.352
Bücking H (2011) Ectomycoremediation: an eco-friendly technique for the remediation of polluted sites in: diversity and biotechnology of ectomycorrhizae. Springer, Berlin, Heidelberg, pp 209–229. https://link.springer.com/book/10.1007/978-3-642-15196-5
Bücking H, Liepold E, Ambilwade P (2012) The role of the Mycorrhizal symbiosis in nutrient uptake of plants and the regulatory mechanisms underlying these transport processes in: Plant Science, Intech Open. https://doi.org/10.5772/52570
Cairney JW, Meharg AA (2002) Interactions between ectomycorrhizal fungi and soil saprotrophs: implications for decomposition of organic matter in soils and degradation of organic pollutants in the rhizosphere. Can J Bot 80(8):803–809. https://doi.org/10.1139/b02-072
Caldwell BA, Jumpponen A, Trappe JM (2000) Utilization of major detrital substrates by dark-septate, root endophytes. Mycologia 92(2):230–232. https://doi.org/10.2307/3761555
Chalot M, Brun A (1998) Physiology of organic nitrogen acquisition by ectomycorrhizal fungi and ectomycorrhizas. FEMS Microbiol Rev 22(1):21–44. https://doi.org/10.1111/j.1574-6976.1998.tb00359.x
Chambers, D (2018) Drought has cut Western cape farm production by 20%‚ says finance MEC. Sunday Times, 7 March 2018. https://www.timeslive.co.za/news/south-africa/2018-03-07-drought-has-cut-western-cape-farm-production-by-20-says-finance-mec/
Conway GR (1986) Agroecosystem analysis for research and development. Winrock International Institute for Agricultural Development Bangkok: 19–35
Compant S, Reiter B, Sessitsch A, Nowak J, Clément C, Barka EA (2005) Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN. Appl Environ Microbiol 71(4):1685–1693. https://doi.org/10.1128/AEM.71.4.1685-1693.2005
da Costa PB, Granada CE, Ambrosini A, Moreira F, de Souza R, dos Passos JFM, Arruda L, Passaglia LM (2014) A model to explain plant growth promotion traits: a multivariate analysis of 2,211 bacterial isolates. PLoS One 9(12):e116020. https://doi.org/10.1371/journal.pone.0116020
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(2):284–288. https://doi.org/10.1007/s00253-003-1415-3
Dittmann J, Heyser W, Bücking H (2002) Biodegradation of aromatic compounds by white rot and ectomycorrhizal fungal species and the accumulation of chlorinated benzoic acid in ectomycorrhizal pine seedlings.Chemosphere 49(3):297–306. https://doi.org/10.1016/S0045-6535(02)00323-5
Divito GA, Sadras VO (2014) How do phosphorus, potassium and Sulphur affect plant growth and biological nitrogen fixation in crop and pasture legumes? A meta-analysis. Field Crops Res 156:161–171. https://doi.org/10.1016/j.fcr.2013.11.004
Dunham SM, Larsson KH, Spatafora JW (2007) Species richness and community composition of mat-forming ectomycorrhizal fungi in old-and second-growth Douglas-fir forests of the HJ Andrews Experimental Forest, Oregon, USA. Mycorrhiza 17(8): 633–645. https://doi.org/10.1007/s00572-007-0141-6
Durand N, Monger HC, Canti MG, Verrecchia EP (2018) Calcium carbonate features. In: Interpretation of micromorphological features of soils and regoliths. Elsevier, pp 205–258. https://doi.org/10.1016/B978-0-444-63522-8.00009-7
Egger KN (1986) Substrate hydrolysis patterns of post-fire ascomycetes (Pezizales). Mycologia 78(5):771–780
Entry JA, Donnelly PK, Cromack K (1991) Influence of ectomycorrhizal mat soils on lignin and cellulose degradation. Biol Fertil Soils 11(1):75–78. https://doi.org/10.1007/BF00335839
Ercoli L, Schüßler A, Arduini I, Pellegrino E (2017) Strong increase of durum wheat iron and zinc content by field-inoculation with arbuscular mycorrhizal fungi at different soil nitrogen availabilities. Plant Soil 419:153–167. https://doi.org/10.1007/s11104-017-3319-5
Etesami H, Emami S, Alikhani HA (2017) Potassium solubilizing bacteria (KSB): mechanisms, promotion of plant growth, and future prospects: a review. J Soil Sci Plant Nutr 17(4):897–911. https://doi.org/10.4067/S0718-95162017000400005
Fahad S, Hussain S, Bano A, Saud S, Hassan S, Shan D, Tabassum MA (2015) Potential role of phytohormones and plant growth-promoting rhizobacteria in abiotic stresses: consequences for changing environment. Environ Sci Pollut R 22(7):4907–4921. https://doi.org/10.1007/s11356-014-3754-2
Farré-Armengol G, Filella I, Llusia J, Peñuelas J (2016) Bidirectional interaction between phyllospheric microbiotas and plant volatile emissions. Trends Plant Sci 21(10):854–860. https://doi.org/10.1016/j.tplants.2016.06.005
Finlay R, Söderström B (1992) Mycorrhiza and carbon flow to the soil in mycorrhizal functioning. Chapman & Hall, New York, pp 134–160. https://doi.org/10.1007/978-3-319-08575-3_3
Fokkema NJ, Van der Meulen F (1976) Antagonism of yeastlike phyllosphere fungi against Septoria nodorum on wheat leaves. Neth J Plant Pathol 82(1):13–16. https://doi.org/10.1007/BF01977343
Freiberg E (1998) Microclimatic parameters influencing nitrogen fixation in the phyllosphere in a Costa Rican premontane rain forest. Oecologia 117(1–2):9–18. https://doi.org/10.1007/s004420050625
Friberg S (2001) Distribution and diversity of arbuscular mycorrhizal fungi in traditional agriculture on the Niger inland delta, Mali, West Africa. CBM: s Skriftserie 3:53–80
Fürnkranz M, Wanek W, Richter A, Abell G, Rasche F, Sessitsch A (2008) Nitrogen fixation by phyllosphere bacteria associated with higher plants and their colonizing epiphytes of a tropical lowland rainforest of Costa Rica. ISME J 2(5):561. https://doi.org/10.1038/ismej.2008.14
Gardes M, Dahlberg A (1996) Mycorrhizal diversity in arctic and alpine tundra: an open question. New Phytol 133(1):147–157
Genney DR, Alexander IJ, Killham K, Meharg AA (2004) Degradation of the polycyclic aromatic hydrocarbon (PAH) fluorene is retarded in a Scots pine ectomycorrhizosphere. New Phytol 163(3):641–649. https://doi.org/10.1111/j.1469-8137.2004.01131.x
Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169(1):30–39. https://doi.org/10.1016/j.micres.2013.09.009
Gnanamanickam SS, Priyadarisini VB, Narayanan NN, Vasudevan P, Kavitha S (1999) An overview of bacterial blight disease of rice and strategies for its management. Curr Sci 77:1435–1444. https://www.jstor.org/stable/24105230
Göltenboth F, Langenberger G, Widmann P (2006) Tropical lowland evergreen rainforest. In: Ecology of insular Southeast Asia, pp 297–383
Goswami D, Thakker JN, Dhandhukia PC (2016) Portraying mechanics of plant growth promoting rhizobacteria (PGPR): a review. Cogent Food Agric 2(1):1127500. https://doi.org/10.1080/23311932.2015.1127500
Gouda S, Kerry RG, Das G, Paramithiotis S, Shin HS, Patra JK (2017) Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiol Res 206:131–140. https://doi.org/10.1016/j.micres.2017.08.016
Goudjal Y, Toumatia O, Yekkour A, Sabaou N, Mathieu F, Zitouni A (2014) Biocontrol of Rhizoctonia solani damping-off and promotion of tomato plant growth by endophytic actinomycetes isolated from native plants of Algerian Sahara. Microbiol Res 169(1):59–65. https://doi.org/10.1016/j.micres.2013.06.014
Gunderson JJ, Knight JD, Van Rees KCJ (2007) Impact of ectomycorrhizal colonization of hybrid poplar on the remediation of diesel-contaminated soil. J Environ Qual 36(4):927–934. https://doi.org/10.2134/jeq2006.0260
Gupta N, Sahoo D (2010) Evaluation of in vitro solubilization potential of phosphate solubilising Streptomyces isolated from phyllosphere of Heritiera fomes (mangrove). Afr J Microbial Res 4(3):136–142
Gupta M, Kiran S, Gulati A, Singh B, Tewari R (2012) Isolation and identification of phosphate solubilizing bacteria able to enhance the growth and aloin-A biosynthesis of Aloe barbadensis Miller. Microbiol Res 167(6):358–363. https://doi.org/10.1016/j.micres.2012.02.004
Gupta G, Parihar SS, Ahirwar NK, Snehi SK, Singh V (2015) Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol 7(2):096–102. https://doi.org/10.4172/1948-5948.1000188
Hallett PD, Feeney DS, Bengough AG, Rillig MC, Scrimgeour CM, Young IM (2009) Disentangling the impact of AM fungi versus roots on soil structure and water transport. Plant Soil 314:183–196. https://doi.org/10.1007/s11104-008-9717-y
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. https://doi.org/10.1016/j.tim.2008.07.008
Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293:1129–1133. https://doi.org/10.1126/science.1061457
Helgason T, Fitter AH (2009) Natural selection and the evolutionary ecology of the arbuscular mycorrhizal fungi (Phylum Glomeromycota). J Exp Bot 60:2465–2480. https://doi.org/10.1093/jxb/erp144
Hiltunen LH, Ojanperä T, Kortemaa H, Richter E, Lehtonen MJ, Valkonen JPT (2009) Interactions and biocontrol of pathogenic Streptomyces strains co-occurring in potato scab lesions. J Appl Microbiol 106(1):199–212. https://doi.org/10.1111/j.1365-2672.2008.03992.x
Hirano SS, Upper CD (2000) Bacteria in the leaf ecosystem with emphasis onPseudomonas syringae—a pathogen, ice nucleus, and epiphyte. Microbiol Mol Biol Rev 64(3):624–653. https://doi.org/10.1128/MMBR.64.3.624-653.2000
Horton TR, Bruns TD (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol Ecol 10(8):1855–1871. https://doi.org/10.1046/j.0962-1083.2001.01333.x
Hosny M, Van Tuinen D, Jacquin F, Füller P, Zhao B, Gianinazzi-Pearson V, Franken P (1999) Arbuscular mycorrhizal fungi and bacteria: how to construct prokaryotic DNA-free genomic libraries from the Glomales. FEMS Microbiol Lett 170(2):425–430. https://doi.org/10.1111/j.1574-6968.1999.tb13404.x
Hristozkova M, Gigova L, Geneva M, Stancheva I, Velikova V, Marinova G (2018) Influence of mycorrhizal Fungi and microalgae dual inoculation on basil plants performance. Gesunde Pflanzen 70(2):99–107. https://doi.org/10.1007/s10343-018-0420-5
Isaac S (1991) Fungal-plant interactions. Springer, Dordrecht
Jahromi F, Aroca R, Porcel R, Ruiz-Lozano JM (2008) Influence of salinity on the in vitro development of Glomus intraradices and on the in vivo physiological and molecular responses of mycorrhizal lettuce plants. Microb Ecol 55:45. https://doi.org/10.1007/s00248-007-9249-7
Jentschke G, Godbold DL (2000) Metal toxicity and ectomycorrhizas. Physiol Plant 109(2):107–116. https://doi.org/10.1034/j.1399-3054.2000.100201.x
Johnson KB, Stockwell VO (1998) Management of fire blight: a case study in microbial ecology. Annu Rev Phytopathol 36(1):227–248. https://doi.org/10.1146/annurev.phyto.36.1.227
Joner EJ, Leyval C, Colpaert JV (2006) Ectomycorrhizas impede phytoremediation of polycyclic aromatic hydrocarbons (PAHs) both within and beyond the rhizosphere. Environ Pollut 142(1):34–38. https://doi.org/10.1016/j.envpol.2005.09.007
Jung SC, Martinez-Medina A, Lopez-Raez JA, Pozo MJ (2012) Mycorrhiza-induced resistance and priming of plant defenses. J Chem Ecol 38:651–664. https://doi.org/10.1007/s10886-012-0134-6
Junker RR, Loewel C, Gross R, Dötter S, Keller A, Blüthgen N (2011) Composition of epiphytic bacterial communities differs on petals and leaves. Plant Biol 13(6):918–924. https://doi.org/10.1111/j.1438-8677.2011.00454.x
Kaewchai S, Soytong K, Hyde K (2009) Mycofungicides and fungal biofertilizers. Fungal Divers 38:25–50
Kaymak HC (2010) Potential of PGPR in agricultural innovations. In: plant growth and health promoting bacteria. Springer, Berlin/Heidelberg, pp 45–79. https://doi.org/10.1007/978-3-642-13612-2_3
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(38):13715–13720. https://doi.org/10.1073/pnas.1216057111
Kennedy C, Bishop P (2004) Genetics of nitrogen fixation and related aspects of metabolism in species of Azotobacter: history and current status. In: Genetics and regulation of nitrogen fixation in free-living bacteria. Springer, Dordrecht, pp 27–52. https://doi.org/10.1007/1-4020-2179-8_2
Kenrick P, Strullu-Derrien C (2014) The origin and early evolution of roots. Plant Physiol:114. https://doi.org/10.1104/pp.114.244517
Khan MMA, Haque E, Paul NC, Khaleque MA, Al-Garni SMS, Rahman M, Islam MT (2017) Enhancement of growth and grain yield of Rice in nutrient deficient soils by Rice probiotic Bacteria. Rice Sci 24:264–273. https://doi.org/10.1016/j.rsci.2017.02.002
Kirschner R (2015) Fungi on the leaf—a contribution towards a review of phyllosphere microbiology from the mycological perspective. In: Biodiversity and ecology of fungi, lichens and mosses—Kerner von Marilaun workshop, pp 426–441
Knief C, Delmotte N, Vorholt JA (2011) Bacterial adaptation to life in association with plants–a proteomic perspective from culture to in situ conditions. Proteomics 11(15):3086–3105. https://doi.org/10.3389/fpls.2014.00216
Kumar AS, Sridar R, Uthandi S (2017) Mitigation of drought in rice by a phyllosphere bacterium Bacillus altitudinis FD48. Afr J Microbiol Res 11(45):1614–1625
Kwak MJ, Jeong H, Madhaiyan M, Lee Y, Sa TM, Oh TK, Kim JF (2014) Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS One 9(9):e106704
Landeweert R, Hoffland E, Finlay RD, Kuyper TW, van Breemen N (2001) Linking plants to rocks: ectomycorrhizal fungi mobilize nutrients from minerals. Trends Ecol Evol 16(5):248–254. https://doi.org/10.1016/S0169-5347(01)02122-X
Lindow SE, Leveau JH (2002) Phyllosphere microbiology. Curr Opin Biotechnol 13(3):238–243. https://doi.org/10.1016/S0958-1669(02)00313-0
Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69(4):1875–1883. https://doi.org/10.1128/AEM.69.4.1875-1883.2003
Liu YH, Huang CJ, Chen CY (2010) Identification and transcriptional analysis of genes involved in Bacillus cereus-induced systemic resistance. Lilium. Biol Plantarum 54(4):697–702. https://doi.org/10.1007/s10535-010-0123-y
Liu D, Lian B, Dong H (2012) Isolation of Paenibacillus sp. and assessment of its potential for enhancing mineral weathering. Geomicrobiol J 29(5):413–421. https://doi.org/10.1080/01490451.2011.576602
Lodge DJ (2000) Ecto- or arbuscular mycorrhizas – which are best? New Phytol 146(3):353–354. https://doi.org/10.1046/j.1469-8137.2000.00668.x
López-Mondéjar R, Kostovčík M, Lladó S, Carro L, García-Fraile P (2017) Exploring the plant microbiome through multi-omics approaches. In: Probiotics in agroecosystem. Springer, Singapore, pp 233–268. https://doi.org/10.1007/978-981-10-4059-7_13
Lugtenberg B (2015) Life of microbes in the rhizosphere. In: Principles of plant-microbe interactions: microbes for sustainable agriculture. Springer, Cham, pp 7–15. https://www.springer.com/gp/book/9783319085746
Malusà E, Pinzari F, Canfora L (2016) Efficacy of biofertilizers: challenges to improve crop production. In: Microbial inoculants in sustainable agricultural productivity. Springer, New Delhi, pp 17–40. https://doi.org/10.1007/978-81-322-2644-4_2
Martin F, Díez J, Dell B, Delaruelle C (2002) Phylogeography of the ectomycorrhizal Pisolithus species as inferred from nuclear ribosomal DNA ITS sequences. New Phytol 153(2):345–357. https://doi.org/10.1046/j.0028-646X.2001.00313.x
Martin BC, George SJ, Price CA, Ryan MH, Tibbett M (2014) The role of root exuded low molecular weight organic anions in facilitating petroleum hydrocarbon degradation: current knowledge and future directions. Sci Tot Environ 472:642–653. https://doi.org/10.1016/j.scitotenv.2013.11.050
Marx DH, Artman JD (1979) Pisolithus tinctorius ectomycorrhizae improve survival and growth of pine seedlings on acid coal spoils in Kentucky and Virginia. Reclam Rev 2:23–31
Marx DH, Daniel WJ (1976) Maintaining cultures of ectomycorrhizal and plant pathogenic fungi in sterile water cold storage. Can J Microbiol 22(3):338–341
Mashiane RA, Ezeokoli OT, Adeleke RA, Bezuidenhout CC (2017) Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa. World J Microbiol Biotechnol 33(4):80. https://doi.org/10.1007/s11274-017-2249-y
Mashiane RA, Adeleke RA, Bezuidenhout CC, Chirima GJ (2018) Community composition and functions of endophytic bacteria of Bt maize. S Afr J Sci 114(7–8):88–97. https://doi.org/10.17159/sajs.2018/20170018
Meena VS, Maurya BR, Verma JP, Meena RS (eds) (2016) Potassium solubilizing microorganisms for sustainable agriculture. Springer
Meharg AA, Cairney JW, Maguire N (1997) Mineralization of 2, 4-dichlorophenol by ectomycorrhizal fungi in axenic culture and in symbiosis with pine. Chemosphere 34(12):2495–2504. https://doi.org/10.1016/S0045-6535(97)00005-2
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. https://doi.org/10.1111/1574-6976.12028
Minuto A, Spadaro D, Garibaldi A, Gullino ML (2006) Control of soilborne pathogens of tomato using a commercial formulation of Streptomyces griseoviridis and solarization. Crop Protect 25(5):468–475. https://doi.org/10.1016/j.cropro.2005.08.001
Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA (2017) Archaea are interactive components of complex microbiomes. Trends Microbiol 26(1):70–85
Molina R, Trappe J (1982) Lack of mycorrhizal specificity in the ericaceous hosts Arbutus menziessi and Arctostaphylos uva-ursi. New Phytol 90:495–509. https://doi.org/10.1111/j.1469-8137.1982.tb04482.x
Molina R, Massicotte H, Trappe JM (1992) Specificity phenomena in mycorrhizal symbioses: community-ecological consequences and practical implications. In: Mycorrhizal functioning: an integrative plant-fungal process, pp 357–423
Morton JB (1990) Evolutionary relationships among arbuscular mycorrhizal Fungi in the Endogonaceae. Mycologia 82(2):192–207. https://doi.org/10.1080/00275514.1990.12025865
Muchovej RM (2004) Importance of mycorrhizae for agricultural crops. Institute of Food and Agricultural Sciences (IFAS), University of Florida. SS-AGR-170, Gainesville, FL
Müller T, Behrendt U, Ruppel S, von der Waydbrink G, Müller ME (2016) Fluorescent pseudomonads in the phyllosphere of wheat: potential antagonists against fungal phytopathogens. Curr Microbiol 72(4):383–389
Ochieng JRA (2015) Towards a regulatory framework for increased and sustainable use of bio-fertilizers in Kenya, MA thesis, Centre for Advanced Studies in Environmental Law and Policy (CASELAP), University of Nairobi
Osono T (2006) Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Can J Microbiol 52(8):701–716. https://doi.org/10.1139/w06-023
Peixoto RS, Vermelho AB, Rosado AS (2011) Petroleum-degrading enzymes: bioremediation and new prospects. Enzyme Res 2011. https://doi.org/10.4061/2011/475193
Pieterse CMJ, Vanwees SCM (2014) Induced disease resistance. In: Lugtenberg B (ed) Principles of plant-microbe interactions: microbes for sustainable agriculture, Cham, Springer, pp 123–134
Pieterse CM, Zamioudis C, Berendsen RL, Weller DM, Van Wees SC, Bakker PA (2014) Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol 52. https://doi.org/10.1146/annurev-phyto-082712-102340
Pozo MJ, Azcón-Aguilar C (2007) Unraveling mycorrhiza-induced resistance. Curr Opin Plant Biol 10:393–398. https://doi.org/10.1016/j.pbi.2007.05.004
Pringle A, Moncalvo JM, Vilgalys R (2000) High levels of variation in ribosomal DNA sequences within and among spores of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica. Mycologia 92(2):259–268. https://doi.org/10.2307/3761559
Querejeta J (2017) Soil water retention and availability as influenced by mycorrhizal symbiosis: consequences for individual plants, communities, and ecosystems. Mycorrhizal Mediation of Soil. Elsevier, pp 299–317. https://doi.org/10.1016/B978-0-12-804312-7.00017-6
Radwan SS, Sorkhoh NA, Fardoun F, Al-Hasan RH (1995) Soil management enhancing hydrocarbon biodegradation in the polluted Kuwaiti desert. Appl Microbiol Biotechnol 44(1–2):265–270. https://doi.org/10.1007/BF00164513
Rastogi G, Coaker GL, Leveau JH (2013) New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 348(1):1–10. https://doi.org/10.1111/1574-6968.12225
Remus-Emsermann MN, Schlechter RO (2018) Phyllosphere microbiology: at the interface between microbial individuals and the plant host. New Phytol 218(4):1327–1333. https://doi.org/10.1111/nph.15054
Rodrigues K & Rodrigues B (2017) Development of carrier based in vitro produced arbuscular mycorrhizal (AM) fungal inocula for organic agriculture. AOAS. 1(1): 26-37. http://irgu.unigoa.ac.in/drs/handle/unigoa/4909
Rostami M, Hasanzadeh N, Khodaygan P, Riahi-Madvar A (2018) Ice nucleation active bacteria from pistachio in Kerman Province, Iran. JPP 100(1):51–58
Roossinck MJ (2011) The good viruses: viral mutualistic symbioses. Nat Rev Microbiol 9:99. https://doi.org/10.1038/nrmicro2491
Rouphael Y, Franken P, Schneider C, Schwarz D, Giovannetti M, Agnolucci M, De Pascale S, Bonini P, Colla G (2015) Arbuscular mycorrhizal fungi act as biostimulants in horticultural crops. Sci Hort 196:91–108. https://doi.org/10.1016/j.scienta.2015.09.002
Sanders IR, Croll D (2010) Arbuscular mycorrhiza: the challenge to understand the genetics of the fungal partner. Annu Rev Genet 44:271–292. https://doi.org/10.1146/annurev-genet-102108-134239
Sandhu A, Halverson LJ, Beattie GA (2007) Bacterial degradation of airborne phenol in the phyllosphere. Environ Microbiol 9:383–392
Sangthong S, Suksabye P, Thiravetyan P (2016) Air-borne xylene degradation by Bougainvillea buttiana and the role of epiphytic bacteria in the degradation. Ecotoxicol Environ Saf 126:273–280. https://doi.org/10.1016/j.ecoenv.2015.12.017
Sarand I, Timonen S, Koivula T, Peltola R, Haahtela K, Sen R, Romantschuk M (1999) Tolerance and biodegradation of m-toluate by Scots pine, a mycorrhizal fungus and fluorescent pseudomonads individually and under associative conditions. J Appl Microbiol 86(5):817–826. https://doi.org/10.1046/j.1365-2672.1999.00731.x
Sartori M, Nesci A, García J, Passone MA, Montemarani A, Etcheverry M (2017) Efficacy of epiphytic bacteria to prevent northern leaf blight caused by Exserohilum turcicum in maize. Rev Argent Microbiol 49(1):75–82
Sayyed RZ, Chincholkar SB, Reddy MS, Gangurde NS, Patel PR (2013) Siderophore producing PGPR for crop nutrition and phytopathogen suppression. In: Bacteria in agrobiology: disease management. Springer, Berlin/Heidelberg, pp 449–471. https://doi.org/10.1007/978-3-642-33639-3_17
Scheublin TR, Deusch S, Moreno-Forero SK, Müller JA, van der Meer JR, Leveau JH (2014) Transcriptional profiling of G ram-positive a rthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds. Environ Microbiol 16(7):2212–2225. https://doi.org/10.1111/1462-2920.12375
Schouteden N, De Waele D, Panis B, Vos CM (2015) Arbuscular mycorrhizal fungi for the biocontrol of plant-parasitic nematodes: a review of the mechanisms involved. Front Microbiol 6(1280). https://doi.org/10.3389/fmicb.2015.01280
Senthilkumar M, Krishnamoorthy R (2017) Isolation and characterization of tomato leaf Phyllosphere Methylobacterium and their effect on plant growth. Int J Curr Microbiol App Sci 6(11):2121–2136
Shamseldin A (2013) The role of different genes involved in symbiotic nitrogen fixation—review. Globl J Biotechnol Bioch 8(4):84–94. https://doi.org/10.5829/idosi.gjbb.2013.8.4.82103
Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. Springer Plus 2(587):1–14. https://doi.org/10.1186/2193-1801-2-587
Shen J, Yuan L, Zhang J, Li H, Bai Z, Chen X, Zhang W, Zhang F (2011) Phosphorus dynamics: from soil to plant. Plant Physiol 156(3):111. https://doi.org/10.1104/pp.111.175232
Sihi D, Dari B, Sharma DK, Pathak H, Nain L, Sharma OP (2017) Evaluation of soil health in organic vs. conventional farming of basmati rice in North India. J Plant Nutr Soil Sci 180:389–406. https://doi.org/10.1002/jpln.201700128
Singh R, Kothari R (2017) The omics era and host microbiomes. In: Understanding host-microbiome interactions-an omics approach. Springer, Singapore, pp 3–12. https://doi.org/10.1007/978-981-10-5050-3_1
Skirvin RM, Kohler E, Steiner H, Ayers D, Laughnan A, Norton MA, Warmund M (2000) The use of genetically engineered bacteria to control frost on strawberries and potatoes. Whatever happened to all of that research? Sci Hortic 84(1–2):179–189. https://doi.org/10.1016/S0304-4238(99)00097-7
Smith SE, Read D (2008) Mycorrhizal Symbiosis, 3rd edn. Academic, London
Smith SE, Jakobsen I, Grønlund M, Smith FA (2011) Roles of arbuscular mycorrhizas in plant phosphorus (P) nutrition: interactions between pathways of P uptake in arbuscular mycorrhizal (AM) roots have important implications for understanding and manipulating plant P acquisition. Plant Physiol 156(3):111. https://doi.org/10.1104/pp.111.174581
Song YY, Cao M, Xie LJ, Liang XT, Zeng RS, Su YJ, Huang JH, Wang RL, Luo SM (2011) Induction of DIMBOA accumulation and systemic defense responses as a mechanism of enhanced resistance of mycorrhizal corn (Zea mays L.) to sheath blight. Mycorrhiza 21:721–731. https://doi.org/10.1007/s00572-011-0380-4
Song Y, Chen D, Lu K, Sun Z, Zeng R (2015) Enhanced tomato disease resistance primed by arbuscular mycorrhizal fungus. Front Plant Sci 6:786. https://doi.org/10.3389/fpls.2015.00786
Sorkhoh NA, Ali N, Al-Awadhi H, Dashti N, Al-Mailem DM, Eliyas M, Radwan SS (2010) Phytoremediation of mercury in pristine and crude oil contaminated soils: contributions of rhizobacteria and their host plants to mercury removal. Ecotoxicol Environ Saf 73(8):1998–2003. https://doi.org/10.1016/j.ecoenv.2010.08.033
Souza R, Ambrosini A, Passaglia LM (2015) Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol 38(4):401–419. https://doi.org/10.1590/S1415-475738420150053
Subudhi E, Sahoo RK, Dey S, Das A, Sahoo K (2018) Unraveling plant-endophyte interactions: an omics insight. In: Endophytes and secondary metabolites. Springer, Cham, pp 1–19. https://doi.org/10.1007/978-3-319-76900-4_2-1
Suhag M (2016) Potential of biofertilizers to replace chemical fertilizers. Int Adv Res J Sci Eng Technol 3:163–167. ISSN (Online): 2393-8021
Sy A, Timmers AC, Knief C, Vorholt JA (2005) Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microb 71(11):7245–7252
Tam PC (1995) Heavy metal tolerance by ectomycorrhizal fungi and metal amelioration by Pisolithus tinctorius. Mycorrhiza 5(3):181–187. https://doi.org/10.1007/BF00203335
Thomson BD, Grove TS, Malajczuk N, Hardy GSJ (1994) The effectiveness of ectomycorrhizal fungi in increasing the growth of Eucalyptus globulus Labill. In relation to root colonization and hyphal development in soil. New Phytol 126(3):517–524
Tian C, Shi Z, Chen Z, Feng G (2006) Arbuscular mycorrhizal associations in the Gurbantunggut Desert. Chin Sci Bull 51(1):140–146. https://doi.org/10.1007/s11434-006-8218-8
Timmusk S, Behers L, Muthoni J, Muraya A, Aronsson AC (2017) Perspectives and challenges of microbial application for crop improvement. Front Plant Sci 8:49. https://doi.org/10.3389/fpls.2017.00049
Tokala RK, Strap JL, Jung CM, Crawford DL, Salove MH, Deobald LA, Morra MJ (2002) Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum). Appl Environ Microbiol 68(5):2161–2171. https://doi.org/10.1128/AEM.68.5.2161-2171.2002
Tyagi S, Singh R, Javeria S (2014) Effect of climate change on plant-microbe interaction: an overview. Eur J Mol Biotech (3):149–156
Uribe D, Sánchez-Nieves J, Vanegas J (2010) Role of microbial biofertilizers in the development of a sustainable agriculture in the tropics. In: Dion P (ed) Soil biology and agriculture in the tropics. Springer, Berlin, pp 235–250. https://doi.org/10.1007/978-3-642-05076-3_11
van Der Heijden MG, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310. https://doi.org/10.1111/j.1461-0248.2007.01139.x
van Wezel GP, Vijgenboom E (2004) Novel aspects of signaling in Streptomyces development. Adv Appl Microbiol 56:65–88. https://doi.org/10.1016/S0065-2164(04)56002-1
Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10(12):828. https://doi.org/10.1038/nrmicro2910
Voříšková J, Baldrian P (2013) Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J 7(3):477. https://doi.org/10.1038/ismej.2012.116
Vurro M, Bonciani B, Vannacci G (2010) Emerging infectious diseases of crop plants in developing countries: impact on agriculture and socio-economic consequences. Food Secur 2:113–132. https://doi.org/10.1007/s12571-010-0062-7
Walker C, Schüßler A (2004) Nomenclatural clarifications and new taxa in the Glomeromycota. Mycol Res 108(9):981–982. https://doi.org/10.1017/S0953756204231173
Wallander H (2000a) Uptake of P from apatite by Pinus sylvestris seedlings colonised by different ectomycorrhizal fungi. Plant Soil 218(1–2):249–256. https://doi.org/10.1023/A:1014936217105
Wallander H (2000b) Use of strontium isotopes and foliar K content to estimate weathering of biotite induced by pine seedlings colonised by ectomycorrhizal fungi from two different soils. Plant Soil 222(1–2):215–229. https://doi.org/10.1023/A:1004756221985
Wallander H, Wickman T (1999) Biotite and microcline as potassium sources in ectomycorrhizal and non-mycorrhizal Pinus sylvestris seedlings. Mycorrhiza 9(1):25–32. https://doi.org/10.1007/s005720050259
Wang Q, Dodd IC, Belimov AA, Jiang F (2016) Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase growth and photosynthesis of pea plants under salt stress by limiting Na+ accumulation. Funct Plant Biol 43(2):161–172. https://doi.org/10.1071/FP15200
Whipps J, Hand P, Pink D, Bending GD (2008) Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbial 105(6):1744–1755. https://doi.org/10.1111/j.1365-2672.2008.03906.x
Wilson M, Hirano SS, Lindow SE (1999) Location and survival of leaf-associated bacteria in relation to pathogenicity and potential for growth within the leaf. Appl Environ Microbiol 65(4):1435–1443
Wu CH, Bernard SM, Andersen GL, Chen W (2009) Developing microbe–plant interactions for applications in plant-growth promotion and disease control, production of useful compounds, remediation and carbon sequestration. Microb Biotech 2(4):428–440. https://doi.org/10.1111/j.1751-7915.2009.00109.x
Wyss P, Boller T, Wiemken A (1991) Phytoalexin response is elicited by a pathogen (Rhizoctonia solani) but not by a mycorrhizal fungus (Glomus mosseae) in soybean roots. Exp 47:395–399. https://doi.org/10.1007/BF01972082
Xu C, Leskovar DI (2015) Effects of A. nodosum seaweed extracts on spinach growth, physiology and nutrition value under drought stress. Sci Hort 183:39–47. https://doi.org/10.1016/j.scienta.2014.12.004
Xu P, Chen F, Mannas JP, Feldman T, Sumner LW, Roossinck MJ (2008) Virus infection improves drought tolerance. New Phytol 180(4):911–921. https://doi.org/10.1111/j.1469-8137.2008.02627.x
Yao M, Desilets H, Charles M, Boulanger R, Tweddell R (2003) Effect of mycorrhization on the accumulation of rishitin and solavetivone in potato plantlets challenged with Rhizoctonia solani. Mycorrhiza 13:333–336. https://doi.org/10.1007/s00572-003-0267-0
Yu TE, Egger KN, Peterson LR (2001) Ectendomycorrhizal associations–characteristics and functions. Mycorrhiza 11(4):167–177. https://doi.org/10.1007/s005720100110
Zabinski CA, Bunn RA (2014) Function of mycorrhizae in extreme environments. In: Mycorrhizal Fungi: use in sustainable agriculture and land restoration. Springer, Berlin, Heidelberg, pp 201–214. https://doi.org/10.1007/978-3-662-45370-4_12
Zhang F, Zhang J, Chen L, Shi X, Lui Z, Li C (2015) Heterologous expression of ACC deaminase from Trichoderma asperellum improves the growth performance of Arabidopsis thaliana under normal and salt stress conditions. Plant Physiol Biochem 94:41–47. https://doi.org/10.1016/j.plaphy.2015.05.007
Zipfel C (2008) Pattern-recognition receptors in plant innate immunity. Curr Opin Immunol 20:10–16. https://doi.org/10.1016/j.coi.2007.11.003
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
Adeleke, R.A., Nunthkumar, B., Roopnarain, A., Obi, L. (2019). Applications of Plant–Microbe Interactions in Agro-Ecosystems. In: Kumar, V., Prasad, R., Kumar, M., Choudhary, D. (eds) Microbiome in Plant Health and Disease. Springer, Singapore. https://doi.org/10.1007/978-981-13-8495-0_1
Download citation
DOI: https://doi.org/10.1007/978-981-13-8495-0_1
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-8494-3
Online ISBN: 978-981-13-8495-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)