Skip to main content

Application of Molecular Ecology Approaches in Sustainable Agriculture for a Better Understanding of Plant–Microbiome Interactions

  • Chapter
  • First Online:
Rhizosphere Microbes

Abstract

Plants are exposed to a natural habitat where the plants interact in diverse ways with their natural environment. To study the mechanisms of defense in the plants, microbes and their communities are given positive responses on the host. These beneficial responses include nutrient acquisition, resistance against plant pathogens, abiotic stress like drought, salinity, heat, and accelerated plant growth. Incredibly, in beneficial and pathogenic microbes, most of the other signals that induce plant immune responses are remarkably molecularly similar and sometimes identical. Therefore, it is uncertain which influences the results of direct interactions between the microbe and host, and the variables that allow plants to differentiate benefits from pathogens. Comprehensive approaches to empirical systems biology would be required to uncover the dynamic network of microbial, genetic, and metabolic interactions, such as the signaling pathways resolving microbe–host interactions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abdelfattah A, Li Destri Nicosia MG, Cacciola SO et al (2015) Metabarcoding analysis of fungal diversity in the phyllosphere and carposphere of olive (Olea europaea). PLoS One 10:e0131069

    Article  PubMed  PubMed Central  Google Scholar 

  • Ali Z, Ali S, Tashkandi M, Syed-Shan-e-Ali Z, Mahfouz MM (2016) CRISPR/Cas9-mediated immunity to Gemini viruses. Sci Rep 6:26912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Allen-Austin D, Austin B, Colwell RR (1984) Survival of Aeromonas sabnonicida in river water. FEMS Microbiol Lett 21:143–146

    Article  Google Scholar 

  • Baker K, Cook RJ (1974) Biological control of plant pathogens. WH Freeman, New York, p 433

    Google Scholar 

  • Barac T et al (2004) Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotechnol 22:583–588

    Article  CAS  PubMed  Google Scholar 

  • Bouffaud ML, Poirier MA, Muller D, Moenne-Loccoz Y (2014) Root microbiome relates to plant host evolution in maize and other Poaceae. Environ Microbiol 16:2804–2814

    Article  PubMed  Google Scholar 

  • Bulgarelli D, Schlaeppi K, Spaepen S, Van Themaat EVL, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Droge J, Pan Y, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17(3):392–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Byrd JJ, Xu HS, Colwell RR (1901) Viable but nonculturable bacteria in drinking water. Appl Environ Microbiol 57(875):878

    Google Scholar 

  • Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken L, Baylis M, Webster NS (2019) Scientists’ warning to humanity: microorganisms and climate change. Nat Rev Microbiol 17(9):569–586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Pachter L (2005) Bioinformatics for whole genome shotgun sequencing of microbial communities. PLoS Comput Biol 1:106–112

    Article  CAS  PubMed  Google Scholar 

  • Chen K, Wang Y, Zhang R, Zhang H, Gao C (2019a) CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu Rev Plant Biol 70:667–697

    Article  CAS  PubMed  Google Scholar 

  • Chen L, Wang WS, Wang T, Meng XF, Chen TT, Huang XX, Li YJ, Hou BK (2019b) Methyl salicylate glycosylation regulates plant defense signaling and systemic acquired resistance. Plant Physiol 180(4):2167–2181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chesson P (2003) Mechanisms of maintenance of species diversity. Annu Rev Ecol Syst 31(1):343–366

    Article  Google Scholar 

  • Colwell RR, Brayton PR, Grimes DJ, Roszak DB, Huq SA, Palmer LM (1985) Viable but nonculturable Vibrio cholerae and related pathogens in the environment: implications for release of genetically engineered microorganisms. BioTechnology 3:817–821

    Google Scholar 

  • Colwell RR, Knight IT, Sommerville Shults S, Casper CW (1989) Viable but non-culturable phenomenon in relationship to starvation/survival, “Injury”, and strategies for survival of bacteria in the environment. In: Hattori T, Ishida Y, Maruyama Y, Morita RY, Uchida A (eds) Recent advances in microbial ecology. Japanese Scientific Society Press, Tokyo, pp 85–88

    Google Scholar 

  • Crandall SG, Gold KM, Jiménez-Gasco MDM, Filgueiras CC, Willett DS (2020) A multi-omics approach to solving problems in plant disease ecology. PLoS One 15(9):e0237975. Published 2020 Sep 22. https://doi.org/10.1371/journal.pone.0237975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Toledo Thomazella DP, Brail Q, Dahlbeck D, Staskawicz B (2016) CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. BioRxiv:064824

    Google Scholar 

  • Dean JV, Shah RP, Mohammed LA (2003) Formation and vacuolar localization of salicylic acid glucose conjugates in soybean cell suspension cultures. Physiol Plant 118(3):328–336

    Article  CAS  Google Scholar 

  • Dean JV, Mohammed LA, Fitzpatrick T (2005) The formation, vacuolar localization, and tonoplast transport of salicylic acid glucose conjugates in tobacco cell suspension cultures. Planta 221:287–296. https://doi.org/10.1007/s00425-004-1430-3

    Article  CAS  PubMed  Google Scholar 

  • Dessaux Y, Grandclément C, Faure D (2016) Engineering the rhizosphere. Trends Plant Sci 21(3):266–278

    Article  CAS  PubMed  Google Scholar 

  • Ding P, Ding Y (2020) Stories of salicylic acid: a plant defense hormone. Trends Plant Sci 25(6):549–565

    Article  CAS  PubMed  Google Scholar 

  • Drahos DJ (1991) Current practices for monitoring genetically engineered microbes in the environment. Ag Biotech News lnf 3:39–48

    Google Scholar 

  • Duan L, Liu H, Li X, Xiao J, Wang S (2014) Multiple phytohormones and phytoalexins are involved in disease resistance to Magnaporthe oryzae invaded from roots in rice. Physiol Plant 152(3):486–500

    Article  CAS  PubMed  Google Scholar 

  • Eoh J, Gu L (2019) Biomaterials as vectors for the delivery of CRISPR–Cas9. Biomater Sci 7(4):1240–1261

    Article  CAS  PubMed  Google Scholar 

  • Erb M, Lenk C, Degenhardt J, Turlings TC (2009) The underestimated role of roots in defense against leaf attackers. Trends Plant Sci 14:653–659

    Article  CAS  PubMed  Google Scholar 

  • Fadiji AE, Babalola OO (2020) Elucidating mechanisms of endophytes used in plant protection and other bioactivities with multifunctional prospects. Front Bioeng Biotechnol 8:467

    Article  PubMed  PubMed Central  Google Scholar 

  • Fang Y, Tyler BM (2016) Efficient disruption and replacement of an effectors gene in the oomycete Phytophthora sojae using CRISPR/Cas9. Mol Plant Pathol 17(1):127–139

    Article  CAS  PubMed  Google Scholar 

  • Fister AS, Landherr L, Maximova SN, Guiltinan MJ (2018) Transient expression of CRISPR/Cas9 machinery targeting TcNPR3 enhances defense response in Theobroma cacao. Front Plant Sci 9:268

    Article  PubMed  PubMed Central  Google Scholar 

  • Fry JC, Day MJ (1990) Bacterial genetics in natural environments. Chapman and Hall, London

    Book  Google Scholar 

  • Fu F, Liu X, Wang R, Zhai C, Peng G, Yu F, Fernando WGD (2019) Fine mapping of Brassica napus blackleg resistance gene Rlm1 through bulked segregate RNA sequencing. Sci Rep 9:14600

    Article  PubMed  PubMed Central  Google Scholar 

  • Gaiero JR et al (2013) Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am J Bot 100:1738–1750

    Article  PubMed  Google Scholar 

  • Gilbert GS, Parker IM (2016) The evolutionary ecology of plant disease: a phylogenetic perspective. Annu Rev Phytopathol 54:549–578

    Article  CAS  PubMed  Google Scholar 

  • Guerrieri R, Vanguelova E, Michalski G et al (2015) Isotopic evidence for the occurrence of biological nitrification and nitrogen deposition processing in forest canopies. Glob Chang Biol 21:4613–4626

    Article  PubMed  Google Scholar 

  • Gumtow R et al (2018) A Phytophthora palmivora extracellular cystatin-like protease inhibitor targets papain to contribute to virulence on papaya. Mol Plant Microbe Interact 31(3):363–373

    Article  CAS  PubMed  Google Scholar 

  • Handelsman J et al (2007) National Research Council Committee on metagenomics: challenges and functional applications. In: The new science of metagenomics: revealing the secrets of our microbial planet. The National Academies Press, Washington, DC

    Google Scholar 

  • Hassani MA, Durán P, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6(1):58

    Article  PubMed  PubMed Central  Google Scholar 

  • Holland M (2011) Nitrogen: give and take from phyllosphere microbes. In: Ploacco JC, Todd CD (eds) Ecological aspects of nitrogen metabolism in plants, 1st edn. Wiley, Hoboken, NJ, pp 217–230

    Google Scholar 

  • Hussong D, Colwell RR, O'Brien M, Weiss E, Pearson AD, Weiner RM, Burge WD (1987) Viable Legionella pneumophila not detectable by culture on agar media. BioTechnology 5(947):050

    Google Scholar 

  • Jia H et al (2017) Genome editing of the disease susceptibility gene CsLOB1 in citrus confers resistance to citrus canker. Plant Biotechnol J 15(7):817–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kashyap AS, Manzar N, Rajawat MVS, Kesharwani AK, Singh RP, Dubey SC, Pattanayak D, Dhar S, Lal SK, Singh D (2021) Screening and biocontrol potential of rhizobacteria native to gangetic plains and hilly regions to induce systemic resistance and promote plant growth in chilli against bacterial wilt disease. Plan Theory 10(10):2125. https://doi.org/10.3390/plants10102125

    Article  CAS  Google Scholar 

  • Kashyap AS, Manzar N, Nebapure SM, Rajawat MVS, Deo MM, Singh JP, Kesharwani AK, Singh RP, Dubey SC, Singh D (2022) Unraveling microbial volatile elicitors using a transparent methodology for induction of systemic resistance and regulation of antioxidant genes at expression levels in chili against bacterial wilt disease. Antioxidants 11(2):404. https://doi.org/10.3390/antiox11020404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Keeling PJ (2010) The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc B Biol Sci 365(1541):729–748

    Article  CAS  Google Scholar 

  • 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 U S A 111:13715–13720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khare E, Mishra J, Arora N (2018) Multifaceted interactions between endophytes and plant: developments and prospects. Front Microbiol 9:2732. PMID: 30498482. https://doi.org/10.3389/fmicb.2018.02732

    Article  PubMed  PubMed Central  Google Scholar 

  • Knott GJ, Doudna JA (2018) CRISPR-CAS guides the future of genetic engineering. Science 361(6405):866–869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kusajima M, Shima S, Fujita M, Minamisawa K, Che FS, Yamakawa H et al (2018) Involvement of ethylene signaling in Azospirillum sp. B510-induced disease resistance in rice. Biosci Biotechnol Biochem 82(9):1522–1526

    Article  CAS  PubMed  Google Scholar 

  • Lan L, Wang W, Huang Y, Zhao C, X. (2019) BuWNT7A overexpression inhibits growth and migration of hepatocellular carcinoma via the β-catenin independent pathway. Bio Med Res Int:36059502019

    Google Scholar 

  • Langner T, Kamoun S, Belhaj K (2018) CRISPR crops: plant genome editing toward disease resistance. Annu Rev Phytopathol 56:479–512

    Article  CAS  PubMed  Google Scholar 

  • Lee B, Lee S, Ryu CM (2012) Foliar aphid feeding recruits rhizosphere bacteria and primes plant immunity against pathogenic and non-pathogenic bacteria in pepper. Ann Bot 110:281–290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lerner A, Herschkovitz Y, Baudoin E, Nazaret S, Moenne-Loccoz Y, Okon Y et al (2006) Effect of Azospirillum brasilense inoculation on rhizobacterial communities analyzed by denaturing gradient gel electrophoresis and automated ribosomal intergenic spacer analysis. Soil Biol Biochem 38:1212–1218

    Article  CAS  Google Scholar 

  • Li C, Hu W, Pan B, Liu Y, Yuan S, Ding Y et al (2017) Rhizobacterium Bacillus amyloliquefaciens strain SQRT3-mediated induced systemic resistance controls bacterial wilt of tomato. Pedosphere 27:1135–1146

    Article  CAS  Google Scholar 

  • Lindeberg M (2012) Genome-enabled perspectives on the composition, evolution, and expression of virulence determinants in bacterial plant pathogens. Annu Rev Phytopathol 50:111–132. https://doi.org/10.1146/annurev-phyto-081211-173022. PMID: 22559066

    Article  CAS  PubMed  Google Scholar 

  • Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS, Velasco R, Kanchiswamy CN (2016) DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front Plant Sci 7:1904

    Article  PubMed  PubMed Central  Google Scholar 

  • Manzar N, Singh Y, Kashyap AS, Sahu PK, Rajawat MVS, Bhowmik A, Sharma PK, Saxena AK (2020) Biocontrol potential of native Trichoderma spp. against anthracnose of great millet (Sorghum bicolour L.) from Tarai and hill regions of India. Biol Control 152:104474

    Article  Google Scholar 

  • Manzar N, Singh Y, Kashyap AS, Sahu PK, Rajawat MVS, Bhowmik A, Sharma PK, Saxena AK (2021) Biocontrol potential of native Trichoderma spp. against anthracnose of great millet (Sorghum bicolour L.) from Tarai and hill regions of India. Biol Control 152:104474. https://doi.org/10.1016/j.biocontrol.2020.104474. S1049964420307015 104474

    Article  CAS  Google Scholar 

  • Marques JM, da Silva TF, Vollu RE, Blank AF, Ding G-C, Seldin L et al (2014) Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 88:424–435

    Article  CAS  PubMed  Google Scholar 

  • Meireles JE, Cavender-Bares J, Townsend PA, Ustin S, Gamon JA, Schweiger AK et al (2020) Leaf reflectance spectra capture the evolutionary history of seed plants. New Phytol 228:485–493. https://doi.org/10.1111/nph.16771. PMID: 32579721

    Article  PubMed  PubMed Central  Google Scholar 

  • Miao J, Chi Y, Lin D, Tyler BM, Liu X (2018) Mutations in ORP1 conferring oxathiapiprolin resistance confirmed by genome editing using CRISPR/Cas9 in Phytophthora capsici and P. sojae. Phytopathology 108(12):1412–1419

    Article  CAS  PubMed  Google Scholar 

  • Molina L et al (2003) Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. FEMS Microbiol Ecol 45:71–81

    Article  CAS  PubMed  Google Scholar 

  • Monaghan J, Zipfel C (2012) Plant pattern recognition receptor complexes at the plasma membrane. Curr Opin Plant Biol 15:349–357

    Article  CAS  PubMed  Google Scholar 

  • Moon JY, Kim ST, Choi GJ, Kwon SY, Cho HS, Kim HS, Moon JS, Park JM (2020) Comparative proteomic analysis of host responses to Plasmodiophora brassicae infection in susceptible and resistant Brassica oleracea. Plant Biotechnol Rep 14:263–274

    Article  Google Scholar 

  • Muller DB, Vogel C, Bai Y, Vorholt JA (2016) The plant microbiota: systems-level insights and perspectives. Ann Rev Genet 50:211–234

    Article  CAS  PubMed  Google Scholar 

  • Negrão S, Schmöckel SM, Tester M (2017) Evaluating physiological responses of plants to salinity stress. Ann Bot 119(1):1–1

    Article  PubMed  Google Scholar 

  • Neik TX, Amas J, Barbetti M, Edwards D, Batley J (2020) Understanding host–pathogen interactions in Brassica napus in the omics era. Plan Theory 9:1336

    CAS  Google Scholar 

  • O’Donnell ST, Ross RP, Stanton C (2020) The progress of multi-omics technologies: determining function in lactic acid bacteria using a systems level approach. Front Microbiol 10:3084

    Article  PubMed  PubMed Central  Google Scholar 

  • Pathak RK, Baunthiyal M, Pandey N, Pandey D, Kumar A (2017) Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in brassica. Sci Rep 7:16790

    Article  PubMed  PubMed Central  Google Scholar 

  • Peng A, Chen S, Lei T, Xu L, He Y, Wu L, Zou X (2017) Engineering cancer-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnol J 15(12):1509–1519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peyraud R, Mbengue M, Barbacci A, Raffaele S (2019) Intercellular cooperation in a fungal plant pathogen facilitates host colonization. Proc Natl Acad Sci U S A 116:3193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Redford AJ, Bowers RM, Knight R et al (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12:2885–2893

    Article  PubMed  PubMed Central  Google Scholar 

  • Rekhter D, Lüdke D, Ding Y, Feussner K, Zienkiewicz K, Lipka V, Wiermer M, Zhang Y, Feussner I (2019) Isochorismate-derived biosynthesis of the plant stress hormone salicylic acid. Science 365(6452):498–502

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez PA, Rothballer M, Chowdhury SP, Nussbaumer T, Gutjahr C, Falter-Braun P (2019) Systems biology of plant-microbiome interactions. Mol Plant 12(6):804–821

    Article  CAS  PubMed  Google Scholar 

  • Rollins RM, Colwell RR (1986) Viable but nonculturable stage of Campylobacter jejuni and its role in survival in the natural aquatic environment. Appl Environ Microbiol 52:531–538

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roszak DB, Grimes DJ, Colwell RR (1984) Viable but non-recoverable stage of Sabnonelkl enteritidis in aquatic systems. Can J Microbiol 30:334–338

    Article  CAS  PubMed  Google Scholar 

  • Ruinen J (1965) The phyllosphere—III. Nitrogen fixation in the phyllosphere. Plant and Soil 22:375–394

    Article  Google Scholar 

  • Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Pare PW et al (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci U S A 100:4927–4932. https://doi.org/10.1073/pnas.0730845100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sahu PK, Singh S, Gupta AR, Gupta A, Singh UB, Manzar N, Bhowmik A, Singh HV, Saxena AK (2020) Endophytic bacilli from medicinal-aromatic perennial Holy basil (Ocimum tenuiflorum L.) modulate plant growth promotion and induced systemic resistance against Rhizoctonia solani in rice (Oryza sativa L.). Biol Control 150:104353. https://doi.org/10.1016/j.biocontrol.2020.104353. S104996441930920X104353

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Saraf M et al (2014) Role of allelochemicals in plant growth promoting rhizobacteria for biocontrol of phytopathogens. Microbiol Res 169:18–29

    Article  CAS  PubMed  Google Scholar 

  • Sessitsch A et al (2013) The role of plant-associated bacteria in the mobilization and phytoextraction of trace elements in contaminated soils. Soil Biol Biochem 60:182–194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shelake RM, Pramanik D, Kim JY (2019) Exploration of plant-microbe interactions for sustainable agriculture in CRISPR era. Microorganisms 7(8):269

    Article  PubMed Central  Google Scholar 

  • Shine MB, Yang JW, El-Habbak M, Nagyabhyru P, Fu DQ, Navarre D, Ghabrial S, Kachroo P, Kachroo A (2016) Cooperative functioning between phenylalanine ammonia lyase and isochorismate synthase activities contributes to salicylic acid biosynthesis in soybean. New Phytol 212(3):627–636

    Article  CAS  PubMed  Google Scholar 

  • Siegel-Hertz K, Edel-Hermann V, Chapelle E, Terrat S, Raaijmakers JM, Steinberg C (2018) Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Chateaurenard region. Front Microbiol 9:568

    Article  PubMed  PubMed Central  Google Scholar 

  • Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K (2014) Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One 9:e100709

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun P, Tian QY, Zhao MG, Dai XY, Huang JH, Li LH, Zhang WH (2007) Aluminum-induced ethylene production is associated with inhibition of root elongation in Lotus japonicus L. Plant Cell Physiol 48:1229–1235

    Article  CAS  PubMed  Google Scholar 

  • Sussman M, Collins CA, Skinner FA, Stewart-Tull DE (1988) The release of genetically engineered micro-organisms. Academic Press, San Diego, CA

    Google Scholar 

  • Swarup R, Perry P, Hagenbeek D, Van Der Straeten D, Beemster GT, Sandberg G, Bhalerao R, Ljung K, Bennett MJ (2007) Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell 19(7):2186–2196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thrall PH, Hochberg ME, Burdon JJ, Bever JD (2007) Coevolution of symbiotic mutualists and parasites in a community context. Trends Ecol Evol 22(3):120–126

    Article  PubMed  Google Scholar 

  • Torrens-Spence MP, Bobokalonova A, Carballo V, Glinkerman CM, Pluskal T, Shen A, Weng JK (2019) PBS3 and EPS1 complete salicylic acid biosynthesis from isochorismate in Arabidopsis. Mol Plant 12(12):1577–1586

    Article  CAS  PubMed  Google Scholar 

  • Tortosa M, Cartea ME, Rodríguez VM, Velasco P (2018) Unraveling the metabolic response of Brassica oleracea exposed to Xanthomonas campestris pv. campestris. J Sci Food Agric 98:3675–3683

    Article  CAS  PubMed  Google Scholar 

  • Trivedi P, Delgado-Baquerizobc M, Trivedi C, Hamonts K, Anderson IC, Singh BK et al (2017) Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Soil Biol Biochem 111:10–14. https://doi.org/10.1016/j.soilbio.2017.03.013

    Article  CAS  Google Scholar 

  • Valladares F, Gianoli E, Gómez JM (2007) Ecological limits to plant phenotypic plasticity. New Phytol 176:749–763

    Article  PubMed  Google Scholar 

  • Verslues PE (2017) Time to grow: factors that control plant growth during mild to moderate drought stress. Plant Cell Environ 40:177–179

    Article  CAS  PubMed  Google Scholar 

  • Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828

    Article  CAS  PubMed  Google Scholar 

  • Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, Ley RE (2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci 115(28):7368–7373

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32(9):947–951

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Zhao K (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11(4):e0154027

    Article  PubMed  PubMed Central  Google Scholar 

  • Whitaker BK, Reynolds HL, Clay K (2018) Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switch grass). Ecology 99:2703–2711

    Article  PubMed  Google Scholar 

  • Xu HS, Roberts N, Singleton FL, Anwell RW, Grimes DJ, Colwell RR (1982) Survival and viability of non-culturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 8:313–323

    Article  CAS  PubMed  Google Scholar 

  • Yin K, Gao C, Qiu JL (2017) Progress and prospects in plant genome editing. Nat Plants 3(8):1–6

    Article  Google Scholar 

  • Zaidi SSEA, Mukhtar MS, Mansoor S (2018) Genome editing: targeting susceptibility genes for plant disease resistance. Trends Biotechnol 36(9):898–906

    Article  CAS  PubMed  Google Scholar 

  • Zaidi S, Se A, Mahas A, Vanderschuren H et al (2020) Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome Biol 21:289

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Bai Y, Wu G, Zou S, Chen Y, Gao C, Tang D (2017) Simultaneous modification of three homoeologs of TaEDR1 by genome editing enhances powdery mildew resistance in wheat. Plant J 91(4):714–724

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Manzar, N. et al. (2022). Application of Molecular Ecology Approaches in Sustainable Agriculture for a Better Understanding of Plant–Microbiome Interactions. In: Singh, U.B., Sahu, P.K., Singh, H.V., Sharma, P.K., Sharma, S.K. (eds) Rhizosphere Microbes. Microorganisms for Sustainability, vol 40. Springer, Singapore. https://doi.org/10.1007/978-981-19-5872-4_3

Download citation

Publish with us

Policies and ethics