Skip to main content
SpringerLink
Log in

Metagenomics of Plant Rhizosphere and Endophytic Association: Concepts and Applications

  • Chapter
  • First Online:
Plant, Soil and Microbes in Tropical Ecosystems

Part of the book series: Rhizosphere Biology ((RHBIO))

  • 806 Accesses

Abstract

Microbes in the rhizosphere influence plant growth, productivity, susceptibility, and resistance to biotic and abiotic stresses. Various studies have been reported to show diversity and activity of microbes are as high in plants as in endophytes and rhizosphere. The roots harbor more diverse microbes than any other part of the plant. The soil type and its management also influence the microbial diversity. The microbial communities can enhance and facilitate pathogen defense and their role in environmental remediation through different mechanisms. Metagenomics is a growing field that helps understand the genomes in the microbial communities. The high resolution of uncultured microbes and the correlation of the function with the environment can be achieved using functional metagenomics. New emerging subdisciplines of metagenomics are Metatranscriptomics and Metaproteomics, which provide further functional analysis of microbial communities. Integrative metagen“omics” approach results in comprehensive information for the community from genes to RNA to proteins and metabolites. In this chapter, we discuss the plant rhizosphere; types of metagenomics analysis such as 16S (for bacteria), whole metagenomics, and 18S/ITS (for fungus); and application of metagenome associated with rhizosphere and endophytes.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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

  • Abd-Elsalam KA, Almohimeed I, Moslem MA, Bahkali AH (2010) M13-microsatellite PCR and rDNA sequence markers for identification of Trichoderma (Hypocreaceae) species in Saudi Arabian soil. Genet Mol Res 9(4):2016–2024

    Article  CAS  PubMed  Google Scholar 

  • Afiahayati, Sato K, Sakakibara Y (2015) MetaVelvet-SL: an extension of the velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res 22(1):69–77

    Google Scholar 

  • Aira M, Gómez-Brandón M, Lazcano C, Bååth E, Domínguez J (2010) Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities. Soil Biol Biochem 42(12):2276–2281

    Article  CAS  Google Scholar 

  • Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R (2017) Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2(2):e00191–e00116

    PubMed  PubMed Central  Google Scholar 

  • Anslan S, Bahram M, Hiiesalu I, Tedersoo L (2017) PipeCraft: flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data. Mol Ecol Resour 17(6):e234–e240

    Article  CAS  PubMed  Google Scholar 

  • Balvočiūtė M, Huson DH (2017) SILVA, RDP, greengenes, NCBI and OTT - how do these taxonomies compare? BMC Genomics 18(Suppl 2):114

    Article  PubMed  PubMed Central  Google Scholar 

  • Barra PJ, Inostroza NG, Acuña JJ, Mora ML, Crowley DE, Jorquera MA (2016) Formulation of bacterial consortia from avocado (Persea americana Mill.) and their effect on growth, biomass and superoxide dismutase activity of wheat seedlings under salt stress. Appl Soil Ecol 102:80–91

    Article  Google Scholar 

  • Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) The Pfam protein families database. Nucleic Acids Res 32:D138–D141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bazghaleh N, Hamel C, Gan Y, Tar’an B, Knight JD (2015) Genotype-specific variation in the structure of root fungal communities is related to chickpea plant productivity. Appl Environ Microbiol 81(7):2368–2377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17(8):478–486

    Article  CAS  PubMed  Google Scholar 

  • Berlanas C, Berbegal M, Elena G, Laidani M, Cibriain JF, Sagües A, Gramaje D (2019) The fungal and bacterial rhizosphere microbiome associated with grapevine rootstock genotypes in mature and young vineyards. Front Microbiol 10:1142

    Article  PubMed  PubMed Central  Google Scholar 

  • Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J (2012) Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol 13(12):R122

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (2008) Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol 74(3):738–744

    Article  CAS  PubMed  Google Scholar 

  • Bromberg JS, Fricke WF, Brinkman CC, Simon T, Mongodin EF (2015) Microbiota—implications for immunity and transplantation. Nat Rev Nephrol 11(6):342–353

    Article  CAS  PubMed  Google Scholar 

  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13(7):581–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD (2016) The Metacyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 44(D1):D471–D480

    Article  CAS  PubMed  Google Scholar 

  • Chakravorty S, Helb D, Burday M, Connell N, Alland D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69(2):330–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chi F, Shen SH, Cheng HP, Jing YX, Yanni YG, Dazzo FB (2005) Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl Environ Microbiol 71(11):7271–7278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Claire Horner-Devine M, Leibold MA, Smith VH, Bohannan BJ (2003) Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett 6(7):613–622

    Article  Google Scholar 

  • Cochrane G, Karsch-Mizrachi I, Takagi T (2016) The international nucleotide sequence database collaboration. Nucleic Acids Res 44(D1):D48–D50

    Article  CAS  PubMed  Google Scholar 

  • Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35:D169–D172

    Article  CAS  PubMed  Google Scholar 

  • Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2014) Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633–D642

    Article  CAS  PubMed  Google Scholar 

  • Cuadros-Orellana S, Leite LR, Smith A, Medeiros JD, Badotti F, Fonseca PL, Vaz AB, Oliveira G, Góes-Neto A (2013) Assessment of fungal diversity in the environment using metagenomics: a decade in review. Fungal Genom Biol 3(2):1

    Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99(16):10494–10499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dilthey AT, Jain C, Koren S, Phillippy AM (2019) Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. Nat Commun 10(1):3066

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461

    Article  CAS  PubMed  Google Scholar 

  • Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10(10):996–998

    Article  CAS  PubMed  Google Scholar 

  • Edgar RC (2016) UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. BioRxiv. https://doi.org/10.1101/081257

  • Elias F, Woyessa D, Muleta D Phosphate solubilization potential of rhizosphere fungi isolated from plants in Jimma zone, Southwest Ethiopia. Int J Microbiol 2016, 2016:5472601

    Google Scholar 

  • Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D’Eustachio P (2016) The reactome pathway knowledgebase. Nucleic Acids Res 44(D1):D481–D487

    Article  CAS  PubMed  Google Scholar 

  • Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 105(10):3805–3810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gallart M, Adair KL, Love J, Meason DF, Clinton PW, Xue J, Turnbull MH (2018) Host genotype and nitrogen form shape the root microbiome of Pinus radiata. Microb Ecol 75(2):419–433

    Article  CAS  PubMed  Google Scholar 

  • Ghosh A, Mehta A, Khan AM (2019) Metagenomic analysis and its applications. Encyclop Bioinform Comput Biol 3:184–193

    Article  Google Scholar 

  • Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F (2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc (1):pdb.prot5368

    Google Scholar 

  • Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, Griffiths RI, Schonrogge K (2015) PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol Evol 6(8):973–980

    Article  PubMed  PubMed Central  Google Scholar 

  • Haft DH, Selengut JD, White O (2003) The TIGRFAMs database of protein families. Nucleic Acids Res 31(1):371–373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J (2014) LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2(1):30

    Article  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Weber N (2013) Microbial community analysis using MEGAN. Methods Enzymol 531:465–485

    Article  CAS  PubMed  Google Scholar 

  • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119

    Article  CAS  Google Scholar 

  • Jones P, Garcia BJ, Furches A, Tuskan GA, Jacobson D (2019) Plant host-associated mechanisms for microbial selection. Front Plant Sci 10:862

    Article  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109–D114

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428(4):726–731

    Article  CAS  PubMed  Google Scholar 

  • Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (2011) Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucl Acids Res 40(1):e9

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (2012) Gene prediction with glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res 40(1):e9

    Article  CAS  PubMed  Google Scholar 

  • Kim D, Song L, Breitwieser FP, Salzberg SL (2016) Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 26(12):1721–1729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AF, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiss M, Larsson KH (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22(21):5271–5277

    Article  PubMed  CAS  Google Scholar 

  • Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R (2012) Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Microbiol. Chapter 1:Unit 1E.5

    Google Scholar 

  • Lakshmanan V, Selvaraj G, Bais HP (2014) Functional soil microbiome: belowground solutions to an aboveground problem. Plant Physiol 166(2):689–700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31(9):814–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu K, McInroy JA, Hu CH, Kloepper JW (2018) Mixtures of plant-growth-promoting rhizobacteria enhance biological control of multiple plant diseases and plant-growth promotion in the presence of pathogens. Plant Dis 102(1):67–72

    Article  PubMed  Google Scholar 

  • López MF, Ramirez-Saad HC, Martínez-Abarca F, Aguirre-Garrido JF, Toro N (2012) Rhizosphere metagenomics. In: Nelson KE (ed) Encyclopedia of metagenomics. Springer, New York, pp 1–8

    Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler [published correction appears in Gigascience. 2015;4:30]. Gigascience 1(1):18

    Article  PubMed  PubMed Central  Google Scholar 

  • Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Majeed A, Abbasi MK, Hameed S, Imran A, Rahim N (2015) Isolation and characterization of plant growth-promoting rhizobacteria from wheat rhi q zosphere and their effect on plant growth promotion. Front Microbiol 6:198

    Article  PubMed  PubMed Central  Google Scholar 

  • Marizzoni M, Gurry T, Provasi S, Greub G, Lopizzo N, Ribaldi F, Festari C, Mazzelli M, Mombelli E, Salvatore M, Mirabelli P, Franzese M, Soricelli A, Frisoni GB, Cattaneo A (2020) Comparison of bioinformatics pipelines and operating systems for the analyses of 16S rRNA gene amplicon sequences in human fecal samples. Front Microbiol 11:1262

    Article  PubMed  PubMed Central  Google Scholar 

  • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12

    Article  Google Scholar 

  • Massart S, Martinez-Medina M, Jijakli MH (2015) Biological control in the microbiome era: challenges and opportunities. Biol Control 89:98–108

    Article  Google Scholar 

  • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6(3):610–618

    Article  CAS  PubMed  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  PubMed  Google Scholar 

  • Menzel P, Ng KL, Krogh A (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun 7:11257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Namiki T, Hachiya T, Tanaka H, Sakakibara Y (2012) MetaVelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 40(20):e155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R (2013) Advancing our understanding of the human microbiome using QIIME. Methods Enzymol 531:371–444

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res 47(D1):D259–D264

    Article  CAS  PubMed  Google Scholar 

  • Noguchi H, Taniguchi T, Itoh T (2008) MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 15(6):387–396

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nurk S, Meleshko D, Korobeynikov A, Pevzner PA (2017) metaSPAdes: a new versatile metagenomic assembler. Genome Res 27(5):824–834

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27(1):29–34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ounit R, Wanamaker S, Close TJ, Lonardi S (2015) CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 16(1):236

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33(17):5691–5702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oyserman BO, Noguera DR, del Rio TG, Tringe SG, McMahon KD (2016) Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME J 10(4):810–822

    Article  CAS  PubMed  Google Scholar 

  • Palmer JM, Jusino MA, Banik MT, Lindner DL (2018) Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data. PeerJ 6:e4925

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Peng Y, Leung HC, Yiu SM, Chin FY (2011) Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27(13):i94–i101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng Y, Leung HC, Yiu SM, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11):1420–1428

    Article  CAS  PubMed  Google Scholar 

  • Petriz BA, Franco OL (2017) Metaproteomics as a complementary approach to gut microbiota in health and disease. Front Chem 5:4

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pevzner PA, Tang H, Waterman MS (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A 98(17):9748–9753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Plummer E, Twin J, Bulach DM, Garland SM, Tabrizi SN (2015) A comparison of three bioinformatics pipelines for the analysis of preterm gut microbiota using 16S rRNA gene sequencing data. J Proteom Bioinform 8(12):283–291

    Article  Google Scholar 

  • Poudel R, Jumpponen A, Kennelly MM, Rivard CL, Gomez-Montano L, Garrett KA (2019) Rootstocks shape the rhizobiome: rhizosphere and endosphere bacterial communities in the grafted tomato system. Appl Environ Microbiol 85(2):e01765–e01718

    Article  PubMed  PubMed Central  Google Scholar 

  • Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res 40(Database issue):D284–D289

    Article  CAS  PubMed  Google Scholar 

  • Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 42(Database issue):D231–D239

    Article  CAS  PubMed  Google Scholar 

  • Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK (2019) Rhizosphere metagenomics of Paspalum scrobiculatum L. (Kodo millet) reveals rhizobiome multifunctionalities. Microorganisms 7(12):608

    Article  CAS  PubMed Central  Google Scholar 

  • Prodan A, Tremaroli V, Brolin H, Zwinderman AH, Nieuwdorp M, Levin E (2020) Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing. PLoS One 15(1):e0227434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40:D290–D301

    Article  CAS  PubMed  Google Scholar 

  • Qiao Q, Wang F, Zhang J, Chen Y, Zhang C, Liu G, Zhang H, Ma C, Zhang J (2017) The variation in the rhizosphere microbiome of cotton with soil type, genotype and developmental stage. Sci Rep 7(1):3940

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res 41(D1):D590–D596

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596

    Article  CAS  PubMed  Google Scholar 

  • Ramakrishnan J, Shunmugasundaram M, Narayanan M (2009) Streptomyces sp. SCBT isolated from rhizosphere soil of medicinal plants is antagonistic to pathogenic bacteria. Iran J Biotechnol 7(2):75–81

    CAS  Google Scholar 

  • Rascovan N, Carbonetto B, Perrig D, Díaz M, Canciani W, Abalo M, Alloati J, González-Anta G, Vazquez MP (2016) Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Sci Rep 6:28084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol 53:403–424

    Article  CAS  PubMed  Google Scholar 

  • Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38(20):e191

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG (2014) Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2:e545

    Article  PubMed  PubMed Central  Google Scholar 

  • Romero M, Gallego D, Blaz J, Lechuga A, Martínez JF, Barajas HR, Hayano-Kanashiro C, Peimbert M, Cruz-Ortega R, Molina-Freaner FE, Alcaraz LD (2019) Rhizosphere metagenomics of mine tailings colonizing plants: assembling and selecting synthetic bacterial communities to enhance in situ bioremediation. https://doi.org/10.1101/664805

  • Roumpeka DD, Wallace RJ, Escalettes F, Fotheringham I, Watson M (2017) A review of bioinformatics tools for bio-prospecting from metagenomic sequence data. Front Genet 8:23

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ryan PR, Dessaux Y, Thomashow LS, Weller DM (2009) Rhizosphere engineering and management for sustainable agriculture. Plant Soil 321(1–2):363–383

    Article  CAS  Google Scholar 

  • Sapkota R, Knorr K, Jørgensen LN, O’Hanlon KA, Nicolaisen M (2015) Host genotype is an important determinant of the cereal phyllosphere mycobiome. New Phytol 207(4):1134–1144

    Article  CAS  PubMed  Google Scholar 

  • Sato K, Sakakibara Y (2014) MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res 22(1):69–77

    PubMed  PubMed Central  Google Scholar 

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9(8):811–814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O (2007) TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35:D260–D264

    Article  CAS  PubMed  Google Scholar 

  • Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153–1161

    Article  CAS  PubMed  Google Scholar 

  • Soni R, Kumar V, Suyal DC, Jain L, Goel R (2017) Metagenomics of plant rhizosphere microbiome. In: Understanding host-microbiome interactions-an omics approach. Springer, Singapore, pp 193–205

    Chapter  Google Scholar 

  • Tartar A, Wheeler MM, Zhou X, Coy MR, Boucias DG, Scharf ME (2009) Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. Biotechnol Biofuels 2:25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278(5338):631–637

    Article  CAS  PubMed  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M (2013) MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol 14(1):R2

    Article  PubMed  PubMed Central  Google Scholar 

  • Tsurumaru H, Okubo T, Okazaki K, Hashimoto M, Kakizaki K, Hanzawa E, Takahashi H, Asanome N, Tanaka F, Sekiyama Y, Ikeda S, Minamisawa K (2015) Metagenomic analysis of the bacterial community associated with the taproot of sugar beet. Microbes Environ 30(1):63–69

    Article  PubMed  PubMed Central  Google Scholar 

  • Vega-Avila AD, Gumiere T, Andrade PA, Lima-Perim JE, Durrer A, Baigori M, Vazquez F, Andreote FD (2015) Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina. Antonie Van Leeuwenhoek 107(2):575–588

    Article  CAS  PubMed  Google Scholar 

  • Verma A, Kumar S, Kumar G, Saini JK, Agrawal R, Satlewal A, Ansari MW (2018) Rhizosphere metabolite profiling: an opportunity to understand plant-microbe interactions for crop improvement. In: Crop improvement through microbial biotechnology. Elsevier, Singapore, pp 343–361

    Google Scholar 

  • Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M (2009) Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 33(1):236–255

    Article  CAS  PubMed  Google Scholar 

  • Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, Paczian T, Trimble WL, Bagchi S, Grama A, Chaterji S, Meyer F (2016) The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Res 44(D1):D590–D594

    Article  CAS  PubMed  Google Scholar 

  • Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15(3):R46

    Article  PubMed  PubMed Central  Google Scholar 

  • Wood DE, Lu J, Langmead B (2019) Improved metagenomic analysis with Kraken 2. Genome Biol 20(1):257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res 42:D643–D648

    Article  CAS  PubMed  Google Scholar 

  • Yurgel SN, Nearing JT, Douglas GM, Langille MGI (2019) Metagenomic functional shifts to plant induced environmental changes. Front Microbiol 10:1682

    Article  PubMed  PubMed Central  Google Scholar 

  • Zampieri E, Chiapello M, Daghino S, Bonfante P, Mello A (2016) Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles. Sci Rep 6:25773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Sun J, Mu H, Lun JCY, Qiu JW (2017) Molecular pathology of skeletal growth anomalies in the brain coral Platygyra carnosa: a meta-transcriptomic analysis. Mar Pollut Bull 124(2):660–667

    Article  CAS  PubMed  Google Scholar 

  • Zhang Q, Acuña JJ, Inostroza NG, Mora ML, Radic S, Sadowsky MJ, Jorquera MA (2019) Endophytic bacterial communities associated with roots and leaves of plants growing in chilean extreme environments. Sci Rep 9(1):4950

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu W, Lomsadze A, Borodovsky M (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38(12):e132

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Eurofins Genomics India Pvt. Ltd., Bengaluru, Karnataka, India

    Arpita Ghosh & Ankita Rathore

  2. Elanco IAC, Bengaluru, Karnataka, India

    Balakuntla Jayanth

Authors
  1. Arpita Ghosh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ankita Rathore
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Balakuntla Jayanth
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, India

    Suresh Kumar Dubey

  2. Department of Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, India

    Satish Kumar Verma

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Ghosh, A., Rathore, A., Jayanth, B. (2021). Metagenomics of Plant Rhizosphere and Endophytic Association: Concepts and Applications. In: Dubey, S.K., Verma, S.K. (eds) Plant, Soil and Microbes in Tropical Ecosystems. Rhizosphere Biology. Springer, Singapore. https://doi.org/10.1007/978-981-16-3364-5_13

Download citation

Publish with us

Policies and ethics

Search

Navigation