Skip to main content
SpringerLink
Log in

Plant and Microbial Genomics in Crop Improvement

  • Chapter
  • First Online:
Microbial Genomics in Sustainable Agroecosystems

Abstract

Classical soil science approaches have enabled us to establish basic principles of how the soil system functions and have answered numerous practical agricultural application questions. In recent years, efforts have been refocused on better understanding, managing, and benefiting from this system that contains one of the most complex biological communities of the planet. Soil biology is seen as being at the center of scientific research of this century with novel research objectives and goals being set. Genomics and metagenomics along with microbiological techniques are contributing greatly to advances in our understanding of living systems that exist in the soil and their interaction with plants. For its part, molecular plant nutrition has made significant progress in understanding the use of nutrients by plant cells and has identified molecular mechanisms that can improve nutrient use efficiency. Together, molecular soil microbiology and molecular plant nutrition are projected to be a driving force in agriculture and sustainable food production in the coming years.

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

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

  • Akiyama K, Matsuzaki K, Hayashi H (2005) Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435:824–827

    Article  CAS  PubMed  Google Scholar 

  • Andrade AE, Silva LP, Pereira JL, Noronha EF, Reis FB Jr, Bloch CJ, Marise J, Dos B, Domont L, Mehta FA (2008) In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea. FEMS Microbiol Lett 281:167–174

    Article  CAS  PubMed  Google Scholar 

  • Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J et al (2001) Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci USA 98:9883–9888

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ben Abdallah D, Frikha-Gargouri O, Tounsi S (2015) Bacillus amyloliquefaciens strain 32a as a source of lipopeptides for biocontrol of Agrobacterium tumefaciens strains. J Appl Microbiol 119:196–207

    Article  CAS  PubMed  Google Scholar 

  • Bolton MD, van Esse HP, Vossen JH, de Jonge R, Stergiopoulos I, Stulemeijer I et al (2008) The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species. Mol Microbiol 69(1):119–136

    Article  CAS  PubMed  Google Scholar 

  • Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis. Nat Commun 1:48

    Article  PubMed  CAS  Google Scholar 

  • Campo S, Carrascal M, Coca M, Abian J, Segundo BS (2004) The defense response of germinating maize embryos against fungal infection: a proteomics approach. Proteomics 4:383–396

    Article  CAS  PubMed  Google Scholar 

  • Cao Y, Xu Z, Ling N, Yuan Y, Yang X, Chen L, Shen B, Shen Q (2012) Isolation and identification of lipopeptides produced by B. subtilis SQR 9 for suppressing Fusarium wilt of cucumber. Sci Hortic 135:32–39

    Article  CAS  Google Scholar 

  • Chen M, Arato M, Borghi L, Nouri E, Reinhardt D (2018) Beneficial services of arbuscular mycorrhizal fungi- from ecology to application. Front Plant Sci 9:1270

    Article  PubMed  PubMed Central  Google Scholar 

  • Chowdhury SP, Hartmann A, Gao X, Borriss R (2015) Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42–a review. Front Microbiol 6:780

    Article  PubMed  PubMed Central  Google Scholar 

  • Compant S, Clement C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678

    Article  CAS  Google Scholar 

  • Curto M, Camafeita E, Lopez JA, Maldonado AM, Rubiales D, Jorrin JV (2006) A proteomic approach to study pea (Pisum sativum) responses to powdery mildew (Erysiphe pisi). Proteomics 6:S163–S174

    Article  PubMed  Google Scholar 

  • Daranas N, Rosello G, Cabrefiga J, Donati I et al (2019) Biological control of bacterial plant diseases with Lactobacillus plantarum strains selected for their broad-spectrum activity. Ann Appl Biol 174:92–105

    Article  PubMed  Google Scholar 

  • De Carvalho-Niebel F, Timmers AC, Chabaud M, Defaux-Petras A, Barker DG (2002) The Nod factor-elicited annexin MtAnn1 is preferentially localized at the nuclear periphery in symbiotically activated root tissues of Medicago truncatula. Plant J 32:343–352

    Article  PubMed  Google Scholar 

  • de Melo FMPD, Fiore MF, Moraes LABD, Silva-Stenico ME, Scramin S, Teixeira MDA, Melo ISD (2009) Antifungal compound produced by the cassava endophyte Bacillus pumilus MAIIIM4A. Sci Agric 66:583–559

    Article  Google Scholar 

  • Delmotte N, Ahrens CH, Knief C, Qeli E, Koch M, Fischer HM, Vorholt JA, Hennecke H, Pessi G (2010) An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 10:1391–1400

    Article  CAS  PubMed  Google Scholar 

  • Etchegaray A, de Castro Bueno C, de Melo IS, Tsai SM, de Fátima Fiore M, SilvaStenico ME, de Moraes LAB, Teschke O (2008) Effect of a highly concentrated lipopeptide extract of Bacillus subtilis on fungal and bacterial cells. Arch Microbiol 190:611–622

    Article  CAS  PubMed  Google Scholar 

  • Falardeau J, Wise C, Novitsky L, Avis TJ (2013) Ecological and mechanistic insights into the direct and indirect antimicrobial properties of Bacillus subtilis lipopeptides on plant pathogens. J Chem Ecol 39:869–878

    Article  CAS  PubMed  Google Scholar 

  • Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X (1997) Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394–401

    Article  CAS  PubMed  Google Scholar 

  • Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P et al (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668–672

    Article  CAS  PubMed  Google Scholar 

  • Ganeshan G, Kumar AM (2005) Pseudomonas fluorescens, a potential bacterial antagonist to control plant diseases. J Plant Interact 1:123–134

    Article  CAS  Google Scholar 

  • Garcia-Garrido JM, Ocampo JA (2002) Regulation of the plant defence response in arbuscular mycorrhizal symbiosis. J Exp Bot 53:1377–1386

    Article  CAS  PubMed  Google Scholar 

  • Giraud E, Moulin L, Vallenet D, Barbe V, Cytryn E, Avarre JC, Jaubert M, Simon D, Cartieaux F, Prin Y et al (2007) Legumes symbioses: absence of Nod genes in photosynthetic Bradyrhizobia. Science 316:1307–1312

    Article  PubMed  Google Scholar 

  • Greenberg EP (1997) Quorum sensing in gram-negative bacteria. ASM News 63:371–377

    Google Scholar 

  • Harrison MJ (2005) Signaling in the arbuscular mycorrhizal symbiosis. Annu Rev Microbiol 59:19–42

    Article  CAS  PubMed  Google Scholar 

  • Hass D, Defago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307–319

    Article  CAS  Google Scholar 

  • Hsieh FC, Lin TC, Meng M, Kao SS (2008) Comparing methods for identifying Bacillus strains capable of producing the antifungal lipopeptide iturin A. Curr Microbiol 56:1–5

    Article  CAS  PubMed  Google Scholar 

  • Jacoby R, Peukert M, Succurro A, Koprivova A, Kopriva S (2017) The role of soil microorganisms in plant mineral nutrition-current knowledge and future directions. Front Plant Sci 8:1617

    Article  PubMed  PubMed Central  Google Scholar 

  • Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Iriguchi M, Kawashima K et al (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9:189–197

    Article  PubMed  Google Scholar 

  • Karunakaran R, Ramachandran VK, Seaman JC, East AK, Mouhsine B, Mauchline TH, Mauchline TH, Skeffington JPA, Poole PS (2009) Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J Bacteriol 191:4002–4014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kloepper JW, Metting Jr FB (1992) Plant growth-promoting rhizobacteria as biological control agents. In: Soil microbial ecology, pp 255–274

    Google Scholar 

  • Kwon YS, Lee DY, Rakwal R, Baek SB, Lee JH, Kwak YS, Seo JS, Chung WS, Bae DW, Kim SG (2016) Proteomic analyses of the interaction between the plant-growth promoting rhizobacterium Paenibacillus polymyxa E681 and Arabidopsis thaliana. Proteomics 16:122–135

    Article  CAS  PubMed  Google Scholar 

  • Lardi M, Pessi G (2018) Functional genomics approaches to studying symbioses between legumes and nitrogen-fixing rhizobia. High Throughput 7:15

    Article  PubMed Central  CAS  Google Scholar 

  • Liang J, Hoffrichter A, Brachmann A, Marin M (2018) Complete genome of rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont. Stand Genomic Sci 13:36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Wei S, Wang F, James EK, Guo X, Zagar C, Xia LG, Dong X, Wang YP (2012) Burkholderia and Cupriavidus spp. are the preferred symbionts of Mimosa spp. in southern China. FEMS Microbiol Ecol 80:417–426

    Article  CAS  PubMed  Google Scholar 

  • MacLean AM, Finan TM, Sadowsky MJ (2007) Genomes of the symbiotic nitrogen-fixing bacteria of legumes. Plant Physiol 144:615–622

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maghari BM, Ardekani AM (2011) Genetically modified foods and social concerns. Avicenna J Med Biotechnol 3:109–117

    PubMed  PubMed Central  Google Scholar 

  • Meena KR, Kanwar SS (2015) Lipopeptides as the antifungal and antibacterial agents: applications in food safety and therapeutics. BioMed Res Int 9: https://doi.org/10.1155/2015/473050

    Article  CAS  Google Scholar 

  • Mhlongo MI, Piater LA, Madala NE, Labuschagne N, Dubery IA (2018) The chemistry of plant-microbe interactions in the rhizosphere and the potential for metabolomics to reveal signaling related to defense priming and induced systemic resistance. Front Plant Sci 9:112. https://doi.org/10.3389/fpls.2018.00112

    Article  PubMed  PubMed Central  Google Scholar 

  • Morrissey JP, Osbourn AE (1999) Fungal resistance to plant antibiotics as a mechanism of pathogenesis. Microbiol Mol Biol Rev 63:708–724

    CAS  PubMed  PubMed Central  Google Scholar 

  • Muthukumar A, Eswaran A, Sanjeevkumas K (2011) Exploitation of Trichoderma species on the growth of Pythium Aphanidermatum in Chilli. Braz J Microbiol 42:1598–1607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nester E, Gordon MP, Kerr A (2005) Agrobacterium tumefaciens: from plant pathology to biotechnology. APS Press, St. Paul

    Google Scholar 

  • Prabhukarthikeyan SR, Keerthana U, Raguchander T (2018) Antibiotic-producing Pseudomonas fluorescens mediates rhizome rot disease resistance and promotes plant growth in turmeric plants. Microbiol Res 210:65–73. https://doi.org/10.1016/j.micres.2018.03.009

    Article  CAS  PubMed  Google Scholar 

  • Ramachandran VK, East AK, Karunakaran R, Downie JA, Poole PS (2011) Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol 12:R106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rampitsch C, Bykova NV, McCallum B, Beimcik E, Ens W (2006) Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host pathogen interaction. Proteomics 6:1897–1907

    Article  CAS  PubMed  Google Scholar 

  • Sablok G, Rosselli R, Seeman T, van Velzen R, Polone E, Giacomini A, La Porta N, Geurts R, Muresu R, Squartini A (2017) Draft genome sequence of the nitrogen-fixing Rhizobium sullae type strain IS123T focusing on the key genes for symbiosis with its host Hedysarum coronarium L. Front Microbiol 8:1348

    Article  PubMed  PubMed Central  Google Scholar 

  • Sachdev S, Singh RP (2018) Root colonization: imperative mechanism for efficient plant protection and growth. MOJ Ecol Environ Sci 3:240–242

    Google Scholar 

  • Servin-Garciduenas LE, Guerrero G, Rogel-Hernandez MA, Martinez-Romero E (2019) Genome sequence of Rhizobium jaguaris CCGE525T, a strain isolated from Calliandra grandiflora nodules from a rain forest in Mexico. Microbiol Res Announc 8:e01584–e01518

    Google Scholar 

  • Shukla M, Al-Busaidi KT, Trivedi M, Tiwari RK (2018) Status of research, regulations and challenges for genetically modified crops in India. GM Crops Food 9:173–188

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh S, Dey SS, Bhatia R, Batley J, Kumar R (2018) Molecular breeding for resistance to black rot [Xanthomonas campestris pv. campestris (Pammel) Dowson] in Brassicas: recent advances. Euphytica 214:196. https://doi.org/10.1007/s10681-018-2275-3

    Article  CAS  Google Scholar 

  • Srivastava A, George J, Karuturi RKM (2019) Transcriptome analysis. In: Encyclopedia of bioinformatics and computational biology, vol. 3, pp 792–805

    Chapter  Google Scholar 

  • Steinkellner S, Lendzemo V, Langer I, Schweiger P, Khaosaad T, Toussaint J-P, Vierheilig H (2007) Flavonoids and strigolactones in root exudates as signals in symbiotic and pathogenic plant-fungus interactions. Molecules 12:1290–1306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stiens M, Schneiker S, Keller M, Kuhn S, Puhler A, Schlüter A (2006) Sequence analysis of the 144-kilobase accessory plasmid pSmeSM11a, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. Appl Environ Microbiol 72:3662–3672

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uchiumi T, Ohwada T, Itakura M, Mitsui H, Nukui N, Dawadi P, Kaneko T, Tabata S, Yokoyama T, Tejima K et al (2004) Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J Bacteriol 186:2439–2448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • War AR, Taggar GK, Hussain B, Taggar MS, Nair RM, Sharma HC (2018) Plant defense against herbivory and insect adaptations. AoB Plants 10:ply037. https://doi.org/10.1093/aobpla/ply037

    Article  CAS  Google Scholar 

  • Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS et al (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7:R34

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang C, Wohlhueter R, Zhang H (2016) Genetically modified foods: a critical review of their promise and problems. Food Sci Human Wellness 5:116–123

    Article  Google Scholar 

  • Zhang X, Zhang R, Gao J, Wang X, Fan F, Ma X et al (2017) Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria. Soil Biol Biochem 104:208–217

    Article  CAS  Google Scholar 

  • Zhou W, Kolb FL, Riechers DE (2005) Identification of proteins induced or upregulated by Fusarium head blight infection in the spikes of hexaploid wheat (Triticum aestivum). Genome 48:770–780

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India

    Indu Rialch

  2. Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India

    Saurabh Singh

  3. ICAR- Indian Agricultural Research Institute, Katrain, Kullu Valley, India

    Rajender Singh

  4. Department of Genetics & Plant Breeding, Govind Ballabh Pant University of Agriculture & Technology, Pantnagar, India

    Arun Kumar

Authors
  1. Indu Rialch
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Saurabh Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajender Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Arun Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Molecular and Cellular Engineering, Sam Higginbottom University of Agriculture Technology and Sciences, Allahabad, Uttar Pradesh, India

    Vijay Tripathi

  2. Department of Forestry, North Eastern Regional Institute of Science and Technology (NERIST), Nirjuli, Arunachal Pradesh, India

    Pradeep Kumar

  3. Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India

    Pooja Tripathi

  4. Department of Botany, Kamla Nehru P.G. College, Raebareli, Uttar Pradesh, India

    Amit Kishore

  5. Department of Forestry, North Eastern Regional Institute of Science and Technology (NERIST), Nirjuli, Arunachal Pradesh, India

    Madhu Kamle

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Rialch, I., Singh, S., Singh, R., Kumar, A. (2019). Plant and Microbial Genomics in Crop Improvement. In: Tripathi, V., Kumar, P., Tripathi, P., Kishore, A., Kamle, M. (eds) Microbial Genomics in Sustainable Agroecosystems. Springer, Singapore. https://doi.org/10.1007/978-981-32-9860-6_13

Download citation

Publish with us

Policies and ethics

Search

Navigation