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Metagenomics as a Tool to Explore New Insights from Plant-Microbe Interface

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Abstract

Microbial communities colonizing in and around the plants are essential for their survival and act as key determinants for plant’s holistic health to make the dynamic plant microbiome. The microbiome comprises of trillions of bacteria, fungi, viruses and other microorganisms interacting with each other as well as with the plants. Metagenomics is a powerful tool that enables rapid analysis of microbial heterogenicity, thus helping us to understand the association of microorganisms within their environment and the overall functioning of microbiome. Herein, an overview of culture-independent methods to explore the unculturable/yet to culture microbial diversity of plant microbiome is addressed. This chapter focuses on the different constituents of plant-microbe interface and the metagenomic studies related to them.

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References

  • 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 93:113–120

    Article  CAS  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  PubMed  PubMed Central  Google Scholar 

  • Baldotto LEB, Olivares FL (2008) Phylloepiphytic interaction between bacteria and different plant species in a tropical agricultural system. Can J Microbiol 54:918–931

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193:96–102

    Article  Google Scholar 

  • Bhatia S, Batra N, Pathak A, Green SJ, Joshi A, Chauhan A (2015) Metagenomic evaluation of bacterial and archaeal diversity in the geothermal hot springs of Manikaran, India. Genome Announc 3:e01544–e01514

    Article  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  Google Scholar 

  • Cocking EC (2003) Endophytic colonization of plant roots by nitrogen-fixing bacteria. Plant Soil 252:169–175

    Article  CAS  Google Scholar 

  • Compant S, Clément 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 

  • Corneo PE, Suenaga H, Kertesz MA, Dijkstra FA (2016) Effect of twenty four wheat genotypes on soil biochemical and microbial properties. Plant Soil 404(1–2):141–155

    Article  CAS  Google Scholar 

  • Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G et al (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69:49–55

    Article  CAS  Google Scholar 

  • Crump BC, Koch EW (2008) Attached bacterial populations shared by four species of aquatic angiosperms. Appl Environ Microbiol 74:5948–5957

    Article  CAS  Google Scholar 

  • De Kempeneer L, Sercu B, Vanbrabant W, Van Langenhove H, Verstraete W (2004) Bioaugmentation of the phyllosphere for the removal of toluene from indoor air. Appl Microbiol Biotechnol 64:284–288

    Article  Google Scholar 

  • Degnan PH, Ochman H (2012) Illumina-based analysis of microbial community diversity. ISME J 6(1):183

    Article  CAS  Google Scholar 

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106:16428–16433

    Article  CAS  Google Scholar 

  • Dennis PG, Miller AJ, Hirsch PR (2010) Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol 72:313–327

    Article  CAS  Google Scholar 

  • Donn S, Kirkegaard JA, Perera G, Richardson AE, Watt M (2015) Evolution of bacterial communities in the wheat crop rhizosphere. Environ Microbiol 17:610–621

    Article  Google Scholar 

  • Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A 112:E911–E920

    Article  CAS  Google Scholar 

  • El-Badry MA (2016) Bacterial community metagenomic and variation of some medicinal plant rhizosphere collected form Sinai. SCIREA J Agric 1(1):16

    Google Scholar 

  • Fahimipour AK, Kardish MR, Lang JM, Green JL, Eisen JA, Stachowicz JJ (2017) Global-scale structure of the eelgrass microbiome. Appl Environ Microbiol. https://doi.org/10.1128/AEM.03391-16

  • Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6(5):1007–1017

    Article  CAS  Google Scholar 

  • Filippidou S, Junier T, Wunderlin T, Lo CC, Li PE, Chain PS, Junier P (2015) Under-detection of endospore-forming firmicutes in metagenomic data. Comput Struct Biotechnol J 13:299–306

    Article  CAS  Google Scholar 

  • Finkel OM, Burch AY, Lindow SE, Post AF, Belkin S (2011) Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree. Appl Environ Microbiol 77:7647–7655

    Article  CAS  Google Scholar 

  • Gadhave KR, Devlin PF, Ebertz A, Ross A, Gange AC (2018) Soil inoculation with Bacillus spp. modifies root endophytic bacterial diversity, evenness, and community composition in a context-specific manner. Microb Ecol 76:741–750

    Article  CAS  Google Scholar 

  • Gang GH, Cho G, Kwak YS, Park EH (2017) Distribution of rhizosphere and endosphere fungi on the first-class endangered plant Cypripedium japonicum. Mycobiology 45:97–100

    Article  Google Scholar 

  • Gkarmiri K, Mahmood S, Ekblad A, Alström S, Högberg N, Finlay R (2017) Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape. Appl Environ Microbiol. https://doi.org/10.1128/AEM.01938-17

  • Glass GV (1976) Primary, secondary, and meta-analysis of research. Educ Res 5:3–8

    Article  Google Scholar 

  • Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M et al (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944

    Article  CAS  Google Scholar 

  • Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914

    Article  CAS  Google Scholar 

  • Innerebner G, Knief C, Vorholt JA (2011) Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl Environ Microbiol 77:3202–3210

    Article  CAS  Google Scholar 

  • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719–1728

    Article  CAS  Google Scholar 

  • Jumpponen A, Jones KL (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184:438–448

    Article  CAS  Google Scholar 

  • Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–236

    Article  CAS  Google Scholar 

  • Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:216–239

    Article  Google Scholar 

  • Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, Von Mering C, Vorholt JA (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378–1390

    Article  CAS  Google Scholar 

  • Kumar V, AlMomin S, Al-Aqeel H, Al-Salameen F, Nair S, Shajan A (2018) Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. PLoS One 13:e0202127

    Article  Google Scholar 

  • Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RL, Knight R, Beiko RG (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821

    Article  CAS  Google Scholar 

  • Larkin RP, Hopkins DL, Martin FN (1993) Effect of successive watermelon plantings on Fusarium oxysporum and other microorganisms in soils suppressive and conducive to fusarium wilt of watermelon. Phytopathology 83:1097–1105

    Article  Google Scholar 

  • Lauber CL, Strickland MS, Bradford MA, Fierer N (2008) The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 40:2407–2415

    Article  CAS  Google Scholar 

  • Leveau JHJ, Tech JJ (2010) Grapevine microbiomics: bacterial diversity on grape leaves and berries revealed by high-throughput sequence analysis of 16S rRNA amplicons. In: International symposium on biological control of postharvest diseases: challenges and opportunities, vol 90, pp 31–42

    Google Scholar 

  • Li JG, Shen MC, Hou JF, Li L, Wu JX, Dong YH (2016) Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce. Sci Rep 6:25305–25314

    Article  CAS  Google Scholar 

  • Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883

    Article  CAS  Google Scholar 

  • Lopez-Velasco G, Welbaum GE, Boyer RR, Mane SP, Ponder MA (2011) Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons. J Appl Microbiol 110:1203–1214

    Article  CAS  Google Scholar 

  • Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90

    Article  CAS  Google Scholar 

  • Mendes R, Kruijt M, De Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332(6033):1097–1100

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Mirete S, De Figueras CG, González-Pastor JE (2007) Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl Environ Microbiol 73:6001–6011

    Article  CAS  Google Scholar 

  • Montarry J, Cartolaro P, Delmotte F, Jolivet J, Willocquet L (2008) Genetic structure and aggressiveness of Erysiphe necator populations during grapevine powdery mildew epidemics. Appl Environ Microbiol 74:6327–6332

    Article  CAS  Google Scholar 

  • Müller T, Ruppel S (2014) Progress in cultivation-independent phyllosphere microbiology. FEMS Microbiol Ecol 87:2–17

    Article  Google Scholar 

  • Nakashima Y, Egami Y, Kimura M, Wakimoto T, Abe I (2016) Metagenomic analysis of the sponge Discodermia reveals the production of the cyanobacterial natural product kasumigamide by ‘Entotheonella’. PLoS One 11:e0164468

    Article  Google Scholar 

  • Newton AC, Gravouil C, Fountaine JM (2010) Managing the ecology of foliar pathogens: ecological tolerance in crops. Ann Appl Biol 157:343–359

    Article  Google Scholar 

  • Ofaim S, Ofek-Lalzar M, Sela N, Jinag J, Kashi Y, Minz D, Freilich S (2017) Analysis of microbial functions in the rhizosphere using a metabolic-network based framework for metagenomics interpretation. Front Microbiol 8:1606–1620

    Article  Google Scholar 

  • Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos L (2015) Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinf Biol Insights 9:75–88

    Article  CAS  Google Scholar 

  • Padhi L, Mohanta YK, Panda SK (2013) Endophytic fungi with great promises: a review. J Adv Pharm Educ Res 3:152–170

    Google Scholar 

  • Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A 110(16):6548–6553

    Article  CAS  Google Scholar 

  • Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799

    Article  CAS  Google Scholar 

  • Prasad R, Kumar M, Varma A (2015) Role of PGPR in soil fertility and plant health. In: Egamberdieva D, Shrivastava S, Varma A (eds) Plant growth-promoting rhizobacteria (PGPR) and medicinal plants. Springer International Publishing, Cham, pp 247–260

    Chapter  Google Scholar 

  • Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321:341–361

    Article  CAS  Google Scholar 

  • Rahman MM, Flory E, Koyro HW, Abideen Z, Schikora A, Suarez C, Schnell S, Cardinale M (2018) Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.). Syst Appl Microbiol 41:386–398

    Article  Google Scholar 

  • Rastogi G, Sbodio A, Tech JJ, Suslow TV, Coaker GL, Leveau JH (2012) Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J 6:1812–1822

    Article  CAS  Google Scholar 

  • Remus-Emsermann MN, Tecon R, Kowalchuk GA, Leveau JH (2012) Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere. ISME J 6:756–765

    Article  CAS  Google Scholar 

  • Rosenblueth M, Martínez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant-Microbe Interact 19:827–837

    Article  CAS  Google Scholar 

  • Saito A, Ikeda S, Ezura H, Minamisawa K (2007) Microbial community analysis of the phytosphere using culture-independent methodologies. Microbes Environ 22:93–105

    Article  Google Scholar 

  • Sandhu A, Halverson LJ, Beattie GA (2007) Bacterial degradation of airborne phenol in the phyllosphere. Environ Microbiol 9:383–392

    Article  CAS  Google Scholar 

  • Schlaeppi K, Dombrowski N, Oter RG, van Themaat EVL, Schulze-Lefert P (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci U S A 111:585–592

    Article  CAS  Google Scholar 

  • Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J et al (2013) A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PLoS One 8:e76382

    Article  CAS  Google Scholar 

  • Shrivastava S, Prasad R, Varma A (2014) Anatomy of root from eyes of a microbiologist. In: Morte A, Varma A (eds) Root engineering, vol 40. Springer, Berlin, pp 3–22

    Chapter  Google Scholar 

  • Singh D, Raina TK, Kumar A, Singh J, Prasad R (2019) Plant microbiome: a reservoir of novel genes and metabolites. Plant Gene. https://doi.org/10.1016/j.plgene.2019.100177

    Article  CAS  Google Scholar 

  • Suman A, Shasany AK, Singh M, Shahi HN, Gaur A, Khanuja SPS (2001) Molecular assessment of diversity among endophytic diazotrophs isolated from subtropical Indian sugarcane. World J Microbiol Biotechnol 17:39–45

    Article  CAS  Google Scholar 

  • Teplitski M, Warriner K, Bartz J, Schneider KR (2011) Untangling metabolic and communication networks: interactions of enterics with phytobacteria and their implications in produce safety. Trends Microbiol 19:121–127

    Article  CAS  Google Scholar 

  • Thomas P (2017) Potential applications of endophytic microorganisms in agriculture. Biotechnol Dev 19:3–23

    Google Scholar 

  • Toju H, Tanabe AS, Yamamoto S, Sato H (2012) High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS One 7:e40863

    Article  CAS  Google Scholar 

  • Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep 7:40–50

    Article  Google Scholar 

  • Uroz S, Buée M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288

    Article  CAS  Google Scholar 

  • Varon-Lopez M, Dias ACF, Fasanella CC, Durrer A, Melo IS, Kuramae EE, Andreote FD (2014) Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments. Environ Microbiol 16:845–855

    Article  CAS  Google Scholar 

  • Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840

    Article  CAS  Google Scholar 

  • Whipps J, Hand P, Pink D, Bending GD (2008) Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbiol 105:1744–1755

    Article  CAS  Google Scholar 

  • Yadav AN, Kumar V, Dhaliwal HS, Prasad R, Saxena AK (2018) Microbiome in crops: diversity, distribution, and potential role in crop improvements. In: Prasad R, Gill SS, Tuteja N (eds) Crop improvement through microbial biotechnology. Elsevier, pp 303–327

    Google Scholar 

  • Zhang Y, Xu J, Riera N, Jin T, Li J, Wang N (2017) Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome. Microbiome 5:97–114

    Article  CAS  Google Scholar 

  • Zhou Y, Qiao X, Li W, Xu J, Wang W, Chen X (2011) Phyllosphere bacterial communities associated with the degradation of acetamiprid in Phaseolus vulgaris. Afr J Biotechnol 10:3809–3817

    Article  CAS  Google Scholar 

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Acknowledgement

PB thanks DST-SERB: SB/YS/LS-213/2013 for financial support.

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Authors and Affiliations

  1. Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India

    Prachi Bhargava, Ankit Verma, Anushka Singh, Sukriti Singh & Siddharth Vats

  2. Central Food and Technological Research Institute, Lucknow, Uttar Pradesh, India

    Mahejibin Khan

  3. Department of Microbiology, College of Basic Sciences and Humanities, GBPUA&T, Pantnagar, Uttarakhand, India

    Reeta Goel

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  1. Prachi Bhargava
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  2. Mahejibin Khan
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  3. Ankit Verma
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  4. Anushka Singh
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  5. Sukriti Singh
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  6. Siddharth Vats
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  7. Reeta Goel
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Editors and Affiliations

  1. Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India

    Ajit Varma

  2. Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India

    Swati Tripathi

  3. Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India

    Ram Prasad

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Bhargava, P. et al. (2019). Metagenomics as a Tool to Explore New Insights from Plant-Microbe Interface. In: Varma, A., Tripathi, S., Prasad, R. (eds) Plant Microbe Interface. Springer, Cham. https://doi.org/10.1007/978-3-030-19831-2_12

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