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Rhizosphere Microbiomes and Their Potential Role in Increasing Soil Fertility and Crop Productivity

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Current Trends in Microbial Biotechnology for Sustainable Agriculture

Part of the book series: Environmental and Microbial Biotechnology ((EMB))

Abstract

Plant microbiome in rhizosphere plays the most critical role in plant growth promoting (PGP), development, and fertilization of soil. Plants and rhizospheric soil are natural resources that harbor microorganisms, and this plays important roles in the maintenance of nutrient balance and ecosystem function. The diverse group of microbes is significant components of soil plant systems, where they are bound in an intense network of interactions within the (rhizosphere-phyllospheric-endophytic). The microbes with PGP attributes have emerged as an important and promising tool for sustainable agriculture. PGP microbes promote plant growth directly or indirectly either by releasing plant growth phytohormones; solubilization of phosphorus, potassium, and zinc; and biological process such as nitrogen fixation or by producing siderophore, ammonia, and other secondary metabolites which have antagonistic activity against pathogenic microbes. The PGP microbes belong to different phylum of archaea (Euryarchaeota), bacteria (Acidobacteria, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Firmicutes, and Proteobacteria), and fungi (Ascomycota and Basidiomycota).

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References

  • Abhilash P, Powell JR, Singh HB, Singh BK (2012) Plant–microbe interactions: novel applications for exploitation in multipurpose remediation technologies. Trends Biotechnol 30:416–420

    Article  CAS  PubMed  Google Scholar 

  • Abo Nouh FA (2019) Endophytic fungi for sustainable agriculture. Microb Biosyst 4(1):31–44. https://doi.org/10.21608/MB.2019.38886

    Article  Google Scholar 

  • Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ Sci 26:1–20

    Article  Google Scholar 

  • Ahmad P, Hashem A, Abd-Allah EF, Alqarawi AA, John R, Egamberdieva D, Gucel S (2015) Role of Trichoderma harzianum in mitigating NaCl stress in Indian mustard (Brassica juncea L) through antioxidative defense system. Front Plant Sci 6:868

    Google Scholar 

  • Akram MS, Shahid M, Tahir M, Mehmood F, Ijaz M (2017) Plant-microbe interactions: current perspectives of mechanisms behind symbiotic and pathogenic associations. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives. Springer International Publishing AG, Singapore, pp 97–196. https://doi.org/10.1007/978-981-10-5813-4

    Chapter  Google Scholar 

  • Altomare C, Norvell WA, Björkman T, Harman GE (1999) Solubilization of phosphates and micronutrients by the plant growth-promoting and biocontrol fungus Trichoderma harzianum Rifai 1295-22. Appl Environ Microbiol 65:2926–2933

    Google Scholar 

  • Atieno M, Hermann L, Okalebo R, Lesueur D (2012) Efficiency of different formulations of Bradyrhizobium japonicum and effect of coinoculation of Bacillus subtilis with two different strains of Bradyrhizobium japonicum. World J Microbiol Biotechnol 28:2541–2550

    Google Scholar 

  • Badawi F, Sh F, Biomy AMM, Desoky AH (2011) Peanut plant growth and yield as influenced by co-inoculation with Bradyrhizobium and some rhizo-microorganisms under sandy loam soil conditions. Ann Agrar Sci 56:17–25

    Article  Google Scholar 

  • Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009) Rhizosphere chemical dialogues: plant–microbe interactions. Curr Opin Biotechnol 20:642–650

    Article  CAS  PubMed  Google Scholar 

  • Barazani O, Benderoth M, Groten K, Kuhlemeier C, Baldwin IT (2005) Piriformospora indica and Sebacina vermifera increase growth performance at the expense of herbivore resistance in Nicotiana attenuata. Oecologia 146:234–243

    Google Scholar 

  • Barea JM, Azcón R, Azcón-Aguilar C (2004) Mycorrhizal fungiand plant growth promoting rhizobacteria. In: Varma A, Abbott L, Werner D, Hampp R (eds) Plant surface microbiology. Springer-Verlag, Heidelberg, pp 351–371

    Google Scholar 

  • Barea JM, Pozo MJ, Azcon R, Azcon Aguilar C (2005) Microbial co-operation in the rhizosphere. J Exp Bot 56(417):1761–1778

    Article  CAS  PubMed  Google Scholar 

  • Berendsen RL, Pieterse CMJ, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13

    Article  CAS  PubMed  Google Scholar 

  • Bertin C, Yang X, Weston LA (2003) The role of root exudates and allelochemicals in the rhizosphere. Plant Soil 256:67–83

    Article  CAS  Google Scholar 

  • Bowen GD, Rovira AD (1999) The rhizosphere and its management to improve plant growth. Adv Agron 66:1–102

    Article  Google Scholar 

  • Chadha N, Mishra M, Prasad R, Varma A (2014) Root endophytic fungi: research update. J Biol Life Sci USA 5:135–158

    Article  Google Scholar 

  • Chauhan A, Guleria S, Walia A, Mahajan R, Verma S, Shirkot CK (2014) Isolation and characterization of Bacillus sp. with their effect on growth of tomato seedlings. Indian J Agric Biochem 27(2):193–201

    CAS  Google Scholar 

  • Chhipa H, Deshmukh SK (2019) Fungal endophytes: rising tools in sustainable agriculture production. In: Jha S (ed) Endophytes and secondary metabolites. Springer International Publishing AG, Cham, pp 1–24

    Google Scholar 

  • Cohen AC, Travaglia CN, Bottini R, Piccoli PN (2009) Participation of abscisic acid and gibberellins produced by endophytic Azospirillum in the alleviation of drought effects in maize. Botany 87:455–462

    Article  CAS  Google Scholar 

  • Dakora FD, Phillips DA (2002) Root exudates as mediators of mineral acquisition in low-nutrient environments. In: Food security in nutrient-stressed environments: exploiting plants’ genetic capabilities. Springer, Dordrecht, pp 201–213

    Chapter  Google Scholar 

  • Dheeman S, Maheshwari DK, Baliyan N (2017) Bacterial endophytes for ecological intensification of agriculture. In: Maheshwari DK (ed) Endophytes: biology and biotechnology, sustainable development and biodiversity, vol 15. Springer International Publishing AG, Cham, pp 193–231. https://doi.org/10.1007/978-3-319-66541-2_1

    Chapter  Google Scholar 

  • Doley P, Jha DK (2010) Endophytic fungal assemblages from ethnomedicinal plant Rauwolfia serpentina (L) Benth. J Plant Pathol Microbiol 40(1):44–48

    Google Scholar 

  • Duy MV, Hoi NT, Ve NB, Thuc LV, Trang NQ (2015) Influence of Cellulomonas flavigena, Azospirillum sp. and Pseudomonas sp. on rice growth and yield grown in submerged soil amended with rice straw. Recent trends PGPR research for sustainable crop productivity 4th Asian PGPR conference Proceeding, HaNoi, VietNam

    Google Scholar 

  • Efthymiou A, Grønlund M, Müller-Stover DS, Jakobsen I (2018) Augmentation of the phosphorus fertilizer value of biochar by inoculation of wheat with selected Penicillium strains. Soil Biol Biochem 116:139–147

    Article  CAS  Google Scholar 

  • Egamberdieva D, Kamilova F, Validov S, Gafurova L, Kucharova Z, Lugtenberg B (2008) High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan. Environ Microbiol 10:1–9

    CAS  PubMed  Google Scholar 

  • Fakhro A, Andrade-Linares DR, von Bargen S, Bandte M, Büttner C, Grosch R, Schwarz D, Franken P (2010) Impact of Piriformospora indica on tomato growth and on interaction with fungal and viral pathogens. Mycorrhiza 20(3):191–200

    Article  PubMed  Google Scholar 

  • Franco-Correa M, Quintana A, Duque C, Suarez C, Rodríguez MX, Barea JM (2010) Evaluation of actinomycete strains for key traits related with plant growth promotion and mycorrhiza helping activities. Appl Soil Ecol 45:209–217

    Article  Google Scholar 

  • Gaba S, Singh RN, Abrol S, Yadav AN, Saxena AK et al (2017) Draft genome sequence of Halolamina pelagica CDK2 isolated from natural salterns from Rann of Kutch, Gujarat, India. Genome Announc 5(6):1–2

    Article  Google Scholar 

  • Garcia de Salamone IE, Hynes RK, Nelson LM (2001) Cytokinin production by plant growth promoting rhizobacteria and selected mutants. Can J Microbiol 47(5):404–411

    Article  CAS  PubMed  Google Scholar 

  • Garg N, Singla P (2012) The role of Glomus mosseae on key physiological and biochemical parameters of pea plants grown in arsenic contaminated soil. Sci Hortic 143:92–101

    Google Scholar 

  • Gehring CA, Mueller RC, Whitham TG (2006) Environmental and genetic effects on the formation of ectomycorrhizal and arbuscular mycorrhizal associations in cottonwoods. Oecologia 149:158–164

    Article  PubMed  Google Scholar 

  • Giri B, Giang PH, Kumari R, Prasad R, Varma A (2005) Microbial diversity in soils. In: Buscot F, Varma S (eds) Microorganisms in soils: roles in genesis and functions. Springer-Verlag, Heidelberg, pp 195–212

    Google Scholar 

  • Gopalakrishnan S, Sathya A, Vijayabharathi R, Varshney RK, Gowda CL, Krishnamurthy L (2015) Plant growth promoting rhizobia: challenges and opportunities. 3 Biotech 5:355–377

    Article  PubMed  Google Scholar 

  • Gray E, Smith D (2005) Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes. Soil Biol Biochem 37:395–412

    Article  CAS  Google Scholar 

  • Gutjahr C, Parniske M (2013) Cell and developmental biology of the arbuscular mycorrhiza symbiosis. Annu Rev Cell Dev Biol 29:593–617

    Article  CAS  PubMed  Google Scholar 

  • Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312:7–14

    Article  CAS  Google Scholar 

  • Hasan HAH (2002) Gibberellin and auxin production by plant root fungi and their biosynthesis under salinity-calcium interaction. Rostlinná Výroba 48:101–106

    CAS  Google Scholar 

  • Hassan MK, McInroy JA, Jones J, Shantharaj D, Liles MR, Kloepper JW (2019a) Pectin-rich amendment enhances soybean growth promotion and nodulation mediated by Bacillus Velezensis strains. Plan Theory 8:120

    CAS  Google Scholar 

  • Hassan MK, Mcinroy JA, Kloepper JW (2019b) The interactions of rhizo deposits with plant growth-promoting rhizobacteria in the rhizosphere: a review. Agric J 9:142

    CAS  Google Scholar 

  • Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152

    Article  CAS  Google Scholar 

  • Jain P, Pundir RK (2017) Potential role of endophytes in sustainable agriculture-recent developments and future prospects. In: Maheshwari DK (ed) Endophytes: biology and biotechnology, sustainable development and biodiversity, vol 15. Springer International Publishing AG, Cham, pp 145–160. https://doi.org/10.1007/978-3-319-66541-2_1

    Chapter  Google Scholar 

  • Jha B, Gontia I, Hartmann A (2012) The roots of the halophyte Salicornia brachiata are a source of new halo tolerant diazotrophic bacteria with plant growth-promoting potential. Plant Soil 356:265–277

    Google Scholar 

  • Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  Google Scholar 

  • Kang BG, Kim WT, Yun HS, Chang SC (2010) Use of plant growth-promoting rhizobacteria to control stress responses of plant roots. Plant Biotechnol Rep 4:179–183

    Article  Google Scholar 

  • Karagiannidis N, Bletsos F, Stavropoulos N (2002) Effect of Verticillium wilt (Verticillium dahliae Kleb.) and mycorrhiza (Glomus mosseae) on root colonization, growth and nutrient uptake in tomato and eggplant seedlings. Sci Hortic 94:145–156

    Article  CAS  Google Scholar 

  • Khan AL, Hamayun M, Ahmad N, Waqas M, Kang SM, Kim YH, Lee IJ (2011) Exophiala sp. LHL08 reprograms Cucumis sativus to higher growth under abiotic stresses. Physiol Plant 143(4):329–343

    Article  CAS  PubMed  Google Scholar 

  • Khare E, Mishra J, Arora NK (2018) Multifaceted interactions between endophytes and plant: developments and prospects. Front Microbiol 9(2732):1–12

    Google Scholar 

  • Kloepper JW, Ryu CM, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94:1259–1266

    Article  CAS  PubMed  Google Scholar 

  • Kobra N, Jalil K, Youbert G (2011) Arbuscular mycorrhizal fungi and biological control of Verticillium wilted cotton plants. Arch Phytopathol Plant Protect 44(10):933–942

    Article  Google Scholar 

  • Kour D, Rana KL, Verma P, Yadav AN, Kumar V (2017) Biofertilizers: eco-friendly technologies and bioresources for sustainable agriculture. In Proceeding of International Conference on Innovative Research in Engineering Science and Technology, IREST/PP/014

    Google Scholar 

  • Kour D, Rana KL, Yadav AN, Yadav N, Kumar M, Kumar V et al (2020) Microbial biofertilizers: bioresources and eco-friendly technologies for agricultural and environmental sustainability. Biocatal Agric Biotechnol 23:101487. https://doi.org/10.1016/j.bcab.2019.101487

    Article  Google Scholar 

  • Kour D, Rana KL, Yadav AN, Yadav N, Kumar V, Kumar A et al (2019a) Drought-tolerant phosphorus-solubilizing microbes: biodiversity and biotechnological applications for alleviation of drought stress in plants. In: Sayyed RZ, Arora NK, Reddy MS (eds) Plant growth promoting rhizobacteria for sustainable stress management, Rhizobacteria in abiotic stress management, vol 1. Springer, Singapore, pp 255–308. https://doi.org/10.1007/978-981-13-6536-2_13

    Chapter  Google Scholar 

  • Kour D, Rana KL, Yadav N, Yadav AN, Kumar A, Meena VS et al (2019b) Rhizospheric microbiomes: biodiversity, mechanisms of plant growth promotion, and biotechnological applications for sustainable agriculture. In: Kumar A, Meena VS (eds) Plant growth promoting Rhizobacteria for agricultural sustainability: from theory to practices. Springer, Singapore, pp 19–65. https://doi.org/10.1007/978-981-13-7553-8_2

    Chapter  Google Scholar 

  • Kucey RMN (1983) Phosphate solubilizing bacteria and fungi in various cultivated and virgin Alberta soils. Can J Soil Sci 63:671–678

    Article  CAS  Google Scholar 

  • Kumar M, Kour D, Yadav AN, Saxena R, Rai PK, Jyoti A et al (2019a) Biodiversity of methylotrophic microbial communities and their potential role in mitigation of abiotic stresses in plants. Biologia 74:287–308. https://doi.org/10.2478/s11756-019-00190-6

    Article  CAS  Google Scholar 

  • Kumar M, Yadav V, Tuteja N (2009) Antioxidant enzyme activities in maize plants colonized with Piriformospora indica. Microbiology 155:780–790

    Google Scholar 

  • Kumar V, Joshi S, Pant NC, Sangwan P, Yadav AN, Saxena A et al (2019b) Molecular approaches for combating multiple abiotic stresses in crops of arid and semi-arid region. In: Singh SP, Upadhyay SK, Pandey A, Kumar S (eds) Molecular approaches in plant biology and environmental challenges. Springer, Singapore, pp 149–170. https://doi.org/10.1007/978-981-15-0690-1_8

    Chapter  Google Scholar 

  • Larsen J, Bødker L (2001) Interactions between pea root-inhabiting fungi examined using signature fatty acids. New Phytol 149:487–493

    Article  CAS  PubMed  Google Scholar 

  • Lata R, Chowdhury S, Gond S, White JF (2018) Induction of abiotic stress tolerance in plants by endophytic microbes. Appl Microbiol 66(4):268–276

    Article  CAS  Google Scholar 

  • Li JY, Strobel GA, Harper JK, Lobkovsky E, Clardy J (2000) Cryptocin, a potent tetramic acid antimycotic from the endophytic fungus Cryptosporiopsis quercina. Org Lett 2:767–770

    Google Scholar 

  • Lins MRCR, Fontes JM, Vasconcelos NM, Santos DMS, Ferreira OE, Ribeiro MRC, Azevedo JL, Araújo JM, GMS L (2014) Plant growth promoting potential of endophytic bacteria isolated from cashew leaves. Afr J Biotechnol 13:3360–3365

    Article  Google Scholar 

  • Liu H, Carvalhais LC, Crawford M, Singh E, Dennis PG, Pieterse CMJ, Schenk PM (2017) Inner plant values: diversity, colonization and benefits from endophytic bacteria. Front Microbiol 8:2552

    Article  PubMed  PubMed Central  Google Scholar 

  • Lugtenberg BJJ, Caradus JR, Johnson LJ (2016) Fungal endophytes for sustainable crop production. FEMS Microbiol Ecol 92(12):1–17

    Article  CAS  Google Scholar 

  • Lynch J, Whipps J (1991) Substrate flow in the rhizosphere. In: The rhizosphere and plant growth. Springer, Dordrecht, pp 15–24

    Chapter  Google Scholar 

  • Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, et al. (2017) Abiotic stress responses and microbe mediated mitigation in plants: the omics strategies. Front Plant Sci 8:172

    Google Scholar 

  • Mehta P, Walia A, Shirkot CK (2015) Functional diversity of phosphate solubilizing plant growth promoting Rhizobacteria isolated from apple trees in the trans Himalayan Region of Himachal Pradesh, India. Biol Agri Hort 31(4):265–288

    Article  Google Scholar 

  • Mehta P, Sharma P, Putatunda C, Walia A (2019) Endophytic fungi: role in phosphate solubilization. In: Singh BP (ed) Advances in endophytic fungal research. Cham, Springer Nature Switzerland AG, pp 183–209. https://doi.org/10.1007/978-3-030-03589-1

    Chapter  Google Scholar 

  • Qiu M, Li S, Zhou X, Cui X, Vivanco JM, Zhang N, Shen Q, Zhang R (2014) De-coupling of root microbiome associations followed by antagonist inoculation improves rhizosphere soil suppressiveness. Biol Fertil Soils 50:217–224. https://doi.org/10.1007/s00374-013-0835-1

    Article  CAS  Google Scholar 

  • Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, et al. (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100

    Google Scholar 

  • Mirza MS, Ahmad W, Latif F, Haurat J, Bally R, Normand P, Malik KA (2001) Isolation partial characterization and the effect of plant growth-promoting bacteria (PGPB) on micro propagated sugarcane in vitro. Plant Soil 237(1):47–54

    Article  CAS  Google Scholar 

  • Mohanram S, Kumar P (2019) Rhizosphere microbiome: revisiting the synergy of plant-microbe interactions. Ann Microbiol 69:307–320

    Article  Google Scholar 

  • Momotaz R, Alam MM, Islam MN, Alam KM, Rahman MZ (2015) Management of the root-knot nematode of tomato by inoculation with Arbuscular Mycorrhizal fungi. Int J Sustain Crop Prod 10(2):48–54

    Google Scholar 

  • Mondal S, Halder SK, Yadav AN, Mondal KC (2020) Microbial consortium with multifunctional plant growth promoting attributes: future perspective in agriculture. In: Yadav AN, Rastegari AA, Yadav N, Kour D (eds) Advances in plant microbiome and sustainable agriculture, Functional annotation and future challenges, vol 2. Springer, Singapore, pp 219–254. https://doi.org/10.1007/978-981-15-3204-7_10

    Chapter  Google Scholar 

  • Murphy BR, Doohan FM, Hodkinson TR (2015) Fungal root endophytes of a wild barley species increase yield in a nutrient-stressed barley cultivar. Symbiosis 65(1):1–7

    Article  CAS  Google Scholar 

  • Nath R, Sharma GD, Barooah M (2012) Efficiency of tricalcium phosphate solubilization by two different endophytic Penicillium sp. isolated from tea (Camelia sinensis L) Er. J Exp Biol 2(4):1354–1358

    Google Scholar 

  • Naveed M, Qureshi MA, Zahir ZA, Hussain MB, Sessitsch A, Mitter B (2015) L-tryptophan- dependent biosynthesis of indole-3-acetic acid (IAA) improves plant growth and colonization of maize by Burkholderia phytofirmans PsJN. Ann Microbiol 65:1391–1389

    Google Scholar 

  • Niste M, Vidican R, Pop R, Rotar I (2013) Stress factors affecting symbiosis activity and nitrogen fixation by Rhizobium cultured in vitro. ProEnvironment 6(13):42–45

    Google Scholar 

  • Oelmüller R, Sherameti I, Tripathi S, Varma A, Jena F, Botanik A, Str D (2009) Piriformospora indica, a cultivable root endophyte with multiple biotechnological applications. Symbiosis 49:1–17

    Google Scholar 

  • Oldroyd GE, Murray JD, Poole PS, Downie JA (2011) The rules of engagement in the legume rhizobial symbiosis. Annu Rev Genet 45:119–144

    Article  CAS  PubMed  Google Scholar 

  • Olivares J, Bedmar EJ, Sanjuán J (2013) Biological nitrogen fixation in the context of global change. Mol Plant Microb Int 26(5):486–494

    Article  CAS  Google Scholar 

  • Pandey KK, Upadhyay JP (2000) Microbial population from rhizosphere and non-rhizosphere soil of pigeon pea. J Mycol Plant Pathol 30(1):7–10

    Google Scholar 

  • Park Y, Mishra RC, Yoon S, Kim H, Park C, Seo S, Bae H (2018) Endophytic Trichoderma citrinoviride isolated from mountain-cultivated ginseng (Panax ginseng) has great potential as a biocontrol agent against ginseng pathogens. J Ginseng Res 43:408–420

    Google Scholar 

  • Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol 6(10):763–775

    Article  CAS  PubMed  Google Scholar 

  • de Paula TJ, Rotter C, Han B (2001) Effect of soil moisture and panting date on Rhizoctonia root rot of beans and its control Journal of American Science by Trichoderma harizanum. Bulletin OILB/SROP 24(3):99–10

    Google Scholar 

  • Prasad K (2017) Biology, diversity and promising role of mycorrhizal endophytes for Green Technology. In: Maheshwari DK (ed) Endophytes: biology and biotechnology, sustainable development and biodiversity, vol 15. Springer International Publishing AG, Cham, pp 267–302. https://doi.org/10.1007/978-3-319-66541-2_1

    Chapter  Google Scholar 

  • Prashar P, Kapoor N, Sachdeva S (2014) Rhizosphere: its structure, bacterial diversity and significance. Rev Environ Sci Biotechnol 13:63–77

    Article  CAS  Google Scholar 

  • Priyadharsini P, Muthukumar T (2017) The root endophytic fungus Curvularia geniculate from Parthenium hysterophorus roots improves plant growth through phosphate solubilization and phytohormone production. Fungal Ecol 27:69–77

    Google Scholar 

  • Raghuwanshi R (2018) Fungal community in mitigating impacts of drought in plants. In: Gehlot P, Singh J (eds) Fungi and their role in sustainable development: current perspectives. Springer Nature Singapore Pvt Ltd, Singapore, pp 267–382. https://doi.org/10.1007/978-981-13-0393-7_15

    Chapter  Google Scholar 

  • Rai PK, Singh M, Anand K, Saurabhj S, Kaur T, Kour D et al (2020) Role and potential applications of plant growth promotion rhizobacteria for sustainable agriculture. In: Rastegari AA, Yadav AN, Yadav N (eds) Trends of microbial biotechnology for sustainable agriculture and biomedicine systems: diversity and functional perspectives. Elsevier, Amsterdam, pp 49–60. https://doi.org/10.1016/B978-0-12-820526-6.00004-X

    Chapter  Google Scholar 

  • Rana KL, Kour D, Kaur T, Devi R, Yadav AN, Yadav N et al (2020a) Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability. Antonie Van Leeuwenhoek. https://doi.org/10.1007/s10482-020-01429-y

  • Rana KL, Kour D, Kaur T, Sheikh I, Yadav AN, Kumar V et al (2020b) Endophytic microbes from diverse wheat genotypes and their potential biotechnological applications in plant growth promotion and nutrient uptake. Proc Natl Acad Sci India B. https://doi.org/10.1007/s40011-020-01168-0

  • Rana KL, Kour D, Yadav AN (2019) Endophytic microbiomes: biodiversity, ecological significance and biotechnological applications. Res J Biotechnol 14:142–162

    Google Scholar 

  • Rashid MA, Mujawar LH, Shahzad T, Almeelbi T, Ismail IMI, Oves M (2016) Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils. Microbiol Res 183:26–41

    Article  CAS  PubMed  Google Scholar 

  • Rastegari AA, Yadav AN, Yadav N (2020) New and future developments in microbial biotechnology and bioengineering: Trends of microbial biotechnology for sustainable agriculture and biomedicine systems: diversity and functional perspectives. Elsevier, Amsterdam

    Google Scholar 

  • Roberts E, Lindow S (2014) Loline alkaloid production by fungal endophytes of Fescue species select for particular epiphytic bacterial microflora. ISME J 8:359–368

    Google Scholar 

  • Rodriguez R, Redman R (2008) More than 400 million years of evolution and some plants still can’t make it on their own : plant stress tolerance via fungal symbiosis. J Exp Botany 59(5):1109–1114

    Article  CAS  Google Scholar 

  • Rodriguez RJ, White JF, Arnold AE, Redman RS et al (2009) Fungal endophytes: diversity and functional roles. New Phytol 182:314–330

    Article  CAS  PubMed  Google Scholar 

  • Saba H, Vibhash D, Manisha M, Prashant KS, Farhan H, Tauseef A (2012) Trichoderma a promising plant growth stimulator and biocontrol agent. Mycosphere 3(4):524–531. https://doi.org/10.5943/mycosphere/3/4/14

  • Sahu PK, Gupta A, Lavanya G, Bakade R, Singh DP (2017) Bacterial endophytes: potential candidates for plant growth promotion. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives. Springer International Publishing AG, Singapore, pp 611–632. https://doi.org/10.1007/978-981-10-5813-4

    Chapter  Google Scholar 

  • Sen S, Chandrasekhar CN (2014) Effect of PGPR on growth promotion of rice (Oryza sativa L) under salt stress. Asian J Plant Sci Res 4:62–67

    Google Scholar 

  • Shaikh S, Wani S, Sayyed R (2018) Impact of interactions between rhizosphere and rhizobacteria: a review. J Bacteriol Mycol 5:1058

    Google Scholar 

  • Sharaff MS, Subrahmanyam G, Kumar A, Yadav AN (2020) Mechanistic understanding of root-microbiome interaction for sustainable agriculture in polluted soils. In: Rastegari AA, Yadav AN, Yadav N (eds) Trends of microbial biotechnology for sustainable agriculture and biomedicine systems: diversity and functional perspectives. Elsevier, Amsterdam, pp 61–84. https://doi.org/10.1016/B978-0-12-820526-6.00005-1

    Chapter  Google Scholar 

  • Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus 2:587

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Singh A, Kumar R, Yadav AN, Mishra S, Sachan S, Sachan SG (2020) Tiny microbes, big yields: microorganisms for enhancing food crop production sustainable development. In: Rastegari AA, Yadav AN, Yadav N (eds) Trends of microbial biotechnology for sustainable agriculture and biomedicine systems: diversity and functional perspectives. Elsevier, Amsterdam, pp 1–15. https://doi.org/10.1016/B978-0-12-820526-6.00001-4

    Chapter  Google Scholar 

  • 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. https://doi.org/10.1016/j.apsoil.2007.01.004

    Article  Google Scholar 

  • Singh A, Sharma J, Rexer KH, Varma A (2000) Plant productivity determinants beyond minerals, water and light: Piriformospora indica—a revolutionary plant growth promoting fungus. Curr Sci 79:1548–1554

    Google Scholar 

  • Sirrenberg A, Göbel C, Grond S, Czempinski N, Ratzinger A, Karlovsky P, et al. (2007) Piriformospora indica affects plant growth by auxin production. Physiol Plant 131(4):581–589

    Google Scholar 

  • Sivakumar PV, Thamizhiniyan P (2012) Enhancement in growth and yield of tomato by using AM fungi and Azospirillum. Int J Environ Biol 2(3):137–141

    Google Scholar 

  • Sorty AM, Meena KK, Choudhary K, Bitla UM, Minhas PS, Krishnani KK (2016) Effect of plant growth promoting bacteria associated with halophytic weed (Psoralea corylifolia L) on germination and seedling growth of wheat under saline conditions. Appl Biochem Biotechnol 180:872–882

    Google Scholar 

  • Souza R, Beneduzi A, Ambrosini A, Costa PB, Meyer J, Vargas LK, Schoenfeld R, Passaglia LMP (2013) The effect of plant growth-promoting rhizobacteria on the growth of rice (Oryza sativa L) cropped in southern Brazilian fields. Plant Soil 366(1):585–603

    Google Scholar 

  • Srivastav S, Yadav KS, Kundu BS (2004) Prospects of using phosphate solubilizing Pseudomonas as biofungicide. Indian J Microbiol 44:91–94

    Google Scholar 

  • Subrahmanyam G, Kumar A, Sandilya SP, Chutia M, Yadav AN (2020) Diversity, plant growth promoting attributes, and agricultural applications of rhizospheric microbes. In: Yadav AN, Singh J, Rastegari AA, Yadav N (eds) Plant microbiomes for sustainable agriculture. Springer, Cham, pp 1–52. https://doi.org/10.1007/978-3-030-38453-1_1

    Chapter  Google Scholar 

  • Suman A, Yadav AN, Verma P (2016) Endophytic microbes in crops: diversity and beneficial impact for sustainable agriculture. In: Singh DP, Abhilash PC, Prabha R (eds) Microbial inoculants in sustainable agricultural productivity, research perspectives. Springer-Verlag, New Delhi, pp 117–143

    Chapter  Google Scholar 

  • Takishita Y, Charron JB, Smith DL (2018) Biocontrol rhizobacterium Pseudomonas sp. 23S induces systemic resistance in tomato (Solanum lycopersicum L) against bacterial canker Clavibacter michiganensis subsp michiganensis. Front Microbiol 9:2119

    Google Scholar 

  • Talapatra K, Das AR, Saha AK, Das P (2017) In vitro antagonistic activity of a root endophytic fungus towards plant pathogenic fungi. J Appl Biol Biotechnol 5(2):68–71

    Google Scholar 

  • Thakur N, Kaur S, Tomar P, Thakur S, Yadav AN (2020) Microbial biopesticides: current status and advancement for sustainable agriculture and environment. In: Rastegari AA, Yadav AN, Yadav N (eds) Trends of microbial biotechnology for sustainable agriculture and biomedicine systems: diversity and functional perspectives. Elsevier, Amsterdam, pp 243–282. https://doi.org/10.1016/B978-0-12-820526-6.00016-6

    Chapter  Google Scholar 

  • Theocharis A, Bordiec S, Fernandez O, Paquis S, Dhondt-Cordelier S, Baillieul F, Clément C, Barka EA (2012) Burkholderia phytofirmans PsJN primes Vitis vinifera L and confers a better tolerance to low nonfreezing temperatures. Mol Plant-Microbe Interact 25(2):241–249

    Google Scholar 

  • Tilak K, Ranganayaki N, Pal KK, De R, Saxena AK (2005) Diversity of plant growth and soil health supporting bacteria. Curr Sci 89(1):136–150

    CAS  Google Scholar 

  • Tiwari P, Bajpai M, Singh LK, Mishra S, Yadav AN (2020) Phytohormones producing fungal communities: metabolic engineering for abiotic stress tolerance in crops. In: Yadav AN, Mishra S, Kour D, Yadav N, Kumar A (eds) Agriculturally important fungi for sustainable agriculture, Perspective for diversity and crop productivity, vol 1. Springer, Cham, pp 56–86. https://doi.org/10.1007/978-3-030-45971-0_8

    Chapter  Google Scholar 

  • Torres-Barragán A, Zavale-Tamejia E, Gonzalez-Chavez C, Ferrera-Cerrato R (1996) The use of arbuscular mycorrhizae to control onion white rot (Sclerotium cepivorum) under field conditions. Mycorrhiza 6:253–257

    Google Scholar 

  • Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Uma Maheswari T, Anbukkarasi K, Hemalatha T, Chendrayan K (2013) Studies on phytohormone producing ability of indigenous endophytic bacteria isolated from tropical legume crops. Int J Curr Microbiol App Sci 2(6):127–136

    Google Scholar 

  • Uren NC (2000) Types amounts and possible functions of compounds released into the rhizosphere by soil-grown plants in the rhizosphere. CRC Press, Boca Raton, FL, pp 35–56

    Google Scholar 

  • Van der Heijden MGA, Streitwolf-Engel RR, Siegrist S, Neudecker A, Ineichen K, Boller T, Wiemken A, Sanders IR (2006) The mycorrhizal contribution to plant productivity, plant nutrition and soil structure in experimental grassland. New Phytol 172:739–752

    Article  PubMed  Google Scholar 

  • Varma A, Sudha S, Franken P (1999) Piriformospora indica-a cul-tivable plant growth promoting root endophyte with similari-ties to arbuscular mycorrhizal fungi. Appl Environ Microbiol 65:2741–2744

    Google Scholar 

  • Verma P, Yadav AN, Khannam KS et al (2016a) Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from the peninsular zone of India. Saudi J Biol Sci 26:1882–1895. https://doi.org/10.1016/j.sjbs.2016.01.042

    Article  PubMed  PubMed Central  Google Scholar 

  • Verma P, Yadav AN, Khannam KS, Kumar S, Saxena AK et al (2016b) Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India. J Basic Microbiol 56(1):44–58

    Article  CAS  PubMed  Google Scholar 

  • Verma P, Yadav AN, Khannam KS et al (2016c) Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from the peninsular zone of India. Saud J Biol Sci 26:1882–1895. https://doi.org/10.1016/j.sjbs.2016.01.042

    Article  Google Scholar 

  • Verma P, Yadav AN, Khannam KS, Panjiar N, Kumar S et al (2015) Assessment of genetic diversity and plant growth promoting attributes of psychotolerant bacteria allied with wheat (Triticum aestivum) from the northern hills zone of India. Ann Microbiol 65(4):1885–1899

    Google Scholar 

  • Verma P, Yadav AN, Kumar V, Singh DP, Saxena AK (2017) Beneficial plant-microbes interactions: biodiversity of microbes from diverse extreme environments and its impact for crop improvement. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives, Microbial interactions and agro-ecological impacts, vol 2. Springer, Singapore, pp 543–580. https://doi.org/10.1007/978-981-10-6593-4_22

    Chapter  Google Scholar 

  • Wahid OA, Mehana TA (2000) Impact of phosphate solubilizing fungi on the yield and phosphorus uptake by wheat and faba bean plants. Microbiol Res 155:221–227

    Article  CAS  PubMed  Google Scholar 

  • Wakelin SA, Warren RA, Harvey PR, Ryder MH (2004) Phosphate solubilization by Penicillium sp. closely associated with wheat roots. Biol Fertil Soils 40:36–43

    Google Scholar 

  • Waller F, Achatz B, Baltruschat H (2005) The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield. Proc Natl Acad Sci U S A 102:13386–13391

    Google Scholar 

  • Waqas M, Khan AL, Hamayun M, Shahzad R, Kang SM, Kim JG, Lee IJ (2015) Endophytic fungi promote plant growth and mitigate the adverse effects of stem rot: an example of Penicillium citrinum and Aspergillus terreus. J Plant Interact 10(1):280–287

    Google Scholar 

  • Waqas M, Khan AL, Kamran M, Hamayun M, Kang SM, Kim YH, Lee IJ (2012) Endophytic fungi produce gibberellins and indoleacetic acid and promotes hostplant growth during stress. Molecules 17:10754–10773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Werner D (2000) Organic signals between plants and microorganisms in the rhizosphere: biochemistry and organic substances at the soil–plant interface. Marcel Dekker, New York, NY, pp 197–222

    Google Scholar 

  • Yadav AN (2019) Endophytic fungi for plant growth promotion and adaptation under abiotic stress conditions. Acta Sci Agric 3(1):91–93

    CAS  Google Scholar 

  • Yadav AN (2017) Agriculturally important microbiomes: biodiversity and multifarious PGP attributes for amelioration of diverse abiotic stresses in crops for sustainable agriculture. Biomed J Sci Tech Res 1(4):861–864. https://doi.org/10.26717/BJSTR.2017.01.000321

    Article  Google Scholar 

  • Yadav AN, Sharma D, Gulati S, Singh S, Kaushik R (2015) Haloarchaea endowed with phosphorus solubilization attribute implicated in phosphorus cycle. Sci Rep 5:12293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yadav AN, Singh J, Rastegari AA, Yadav N (2020) Plant microbiomes for sustainable agriculture. Springer, Cham

    Book  Google Scholar 

  • Yadav AN, Verma P, Kaushik R, Dhaliwal HS, Saxena AK (2017a) Archaea endowed with plant growth promoting attributes. EC Microbiol 8(6):294–298

    Google Scholar 

  • Yadav AN, Verma P, Kour D, Rana K, Kumar V et al (2017b) Plant microbiomes and its beneficial multifunctional plant growth promoting attributes. Int J Environ Sci Nat Resour 3(1):1–8

    Google Scholar 

  • Yadav AN, Verma P, Kumar S, Kumar V, Kumar M, Kumari Sugitha TC et al (2018) Actinobacteria from rhizosphere: molecular diversity, distributions, and potential biotechnological applications. In: Singh BP, Gupta VK, Passari AK (eds) New and future developments in microbial biotechnology and bioengineering. Elsevier, Amsterdam, pp 13–41. https://doi.org/10.1016/B978-0-444-63994-3.00002-3

    Chapter  Google Scholar 

  • Zabalgogeazcoa I (2008) Fungal endophytes and their interaction with plant pathogens. Span J Agric Res 6:138–146

    Article  Google Scholar 

  • Zou WX, Meng JC, Lu H, Chen GX, Shi GX, Zhang TY, Tan RX (2000) Metabolites of Colletotrichum gloeosporioides, an endophytic fungus in Artemisia mongolica. J Nat Prod 63:1529–1530

    Google Scholar 

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Authors and Affiliations

  1. Botany Department, Faculty of Science, Arish University, North Sinai, Egypt

    Sara Atef Gezaf

  2. Zoology Department, Faculty of Science, University of Suez Canal, Ismailia, Egypt

    Hebtallah H. Abo Mahas

  3. Botany Department, Faculty of Science, University of Suez Canal, Ismailia, Egypt

    Ahmed M. Abdel-Azeem

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  1. Sara Atef Gezaf
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  2. Hebtallah H. Abo Mahas
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  3. Ahmed M. Abdel-Azeem
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Editors and Affiliations

  1. Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India

    Ajar Nath Yadav

  2. Department of Microbiology, Lovely Professional University, Phagwara, Punjab, India

    Joginder Singh

  3. Department of Environmental Microbiology, Babasaheb Ambedkar University, Lucknow, Uttar Pradesh, India

    Chhatarpal Singh

  4. Veer Bahadur Singh Purvanchal University, Jaunpur, Uttar Pradesh, India

    Neelam Yadav

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Gezaf, S.A., Abo Mahas, H.H., Abdel-Azeem, A.M. (2021). Rhizosphere Microbiomes and Their Potential Role in Increasing Soil Fertility and Crop Productivity. In: Yadav, A.N., Singh, J., Singh, C., Yadav, N. (eds) Current Trends in Microbial Biotechnology for Sustainable Agriculture . Environmental and Microbial Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-15-6949-4_8

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