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Perceptions of Microbe–Microbe and Plant–Microbiome Interfaces: The Metagenomic Maneuver

  • Nikhi Verma
  • Vivek Kumar
Chapter

Abstract

The interactive relationship between plant and microbe starts on the surface of the plant, such as on the roots, leaves, or other parts. Various different types of microbes thrive on different parts of the plant. Microbes may also enter plant cells and are then known as endophytes; this relationship consists of an intricate interaction between plant and microbe. This intricate interaction occurs also at a genomic level. The plant–microbiome interaction may be beneficial or harmful for both, and sometimes it may be neutral. The presence of another microbe in the vicinity also changes the relationship between a microbe and its host. Now we understand that this type of communication or interface is very complicated, and, to understand this scenario, we need the help of modern techniques such as a metagenomic approach or next-generation sequencing. The soil and plant microbiome community plays a significant role in providing essential nutrients to the host plant and also in recycling nutrients and carbon in the environment. On the other hand, we do not know much about novel or nonisolated soil microbes; therefore, their functions are unknown to us. Using a metagenomic approach we can reveal the identity of an unknown soil microbe along with its functional gene information. Most of these associate microbes that enter into plant tissues communicate with their host very closely. This interaction influences metabolic aspects, nutritional uptake potential and transport, signaling of hormones, and stress mitigation, ultimately resulting in plant growth and development. In this respect, a metagenomic approach can be proficiently linked to other omics techniques to offer a multifarious picture of in-progress occurrences that exploit the communication between the plant and its total microbiome. The applied and practical purposes of these metagenomic studies, apart from providing a clearer vision of ecological biological diversity and ecological aspects of microbes, is to provide detailed and valuable tactics for enhancing crop production and protection against host pathogens.

Keywords

Microbe Interaction Metagenomics Plant Sequencing 

References

  1. Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M (2003) The isotope array, a new tool that employs substrate-mediated labelling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69:6875–6887PubMedPubMedCentralCrossRefGoogle Scholar
  2. Akiyama K, Matsuzaki K, Hayashi H (2005) Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435:824–827PubMedPubMedCentralCrossRefGoogle Scholar
  3. An D, Parsek MR (2007) The promise and peril of transcriptional profiling in biofilm communities. Curr Opin Microbiol 3:292–296CrossRefGoogle Scholar
  4. Andersson AF, Lundgren M, Eriksson S, Rosenlund M, Bernander R, Nilsson P (2006) Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol 7(10):R99.  https://doi.org/10.1186/gb-2006-7-10-r99 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Aneja MK, Sharma S, Mayer J, Schloter M, Munch JC (2004) RNA fingerprinting—a new method to screen for differences in plant litter degrading microbial communities. J Microbiol Methods 59:223–231PubMedCrossRefGoogle Scholar
  6. Badri DV, Quintana N, El Kassis EG, Kim HK, Choi YH, Sugiyama A, Verpoorte R, Martinoia E, Manter DK, Vivanco JM (2009) An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol 151:2006–2017PubMedPubMedCentralCrossRefGoogle Scholar
  7. Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288:4502–4512PubMedPubMedCentralCrossRefGoogle Scholar
  8. Bae JW, Rhee SK, Park JR, Chung WH, Nam YD, Lee I, Kim H, Park YH (2005) Development and evaluation of genome probing microarrays for monitoring lactic acid bacteria. Appl Environ Microbiol 71:8825–8835PubMedPubMedCentralCrossRefGoogle Scholar
  9. Bailly J, Fraissinet-Tachet L, Verner MC, Debaud JC, Lemaire M, Wésolowski-Louvel M, Marmeisse R (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 7:632–642CrossRefGoogle Scholar
  10. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O’Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59PubMedPubMedCentralCrossRefGoogle Scholar
  11. Berendsen RL, Pieterse CMJ, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486CrossRefGoogle Scholar
  12. Berg G, Rybakova D, Grube M, Koberl M (2016) The plant microbiome explored: implications for experimental botany. J Exp Bot 67:995–1002PubMedCrossRefGoogle Scholar
  13. Bertin C, Yang XH, Weston LA (2003) The role of root exudates and allelochemicals in the rhizosphere. Plant Soil 256:67–83CrossRefGoogle Scholar
  14. Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:245–254PubMedCrossRefGoogle Scholar
  15. Bodrossy L, Stralis-Pavese N, Konrad-Köszler M, Weilharter A, Reichenauer TG, Schöfer D, Sessitsch A (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72:1672–1676PubMedPubMedCentralCrossRefGoogle Scholar
  16. Bolan NS (1991) A critical review on the role of mycorrhizal fungi in the uptake of phosphorus by plants. Plant Soil 134:189–207CrossRefGoogle Scholar
  17. Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (2008) Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol 74:738–744CrossRefGoogle Scholar
  18. Brzostowicz PC, Walters DM, Thomas SM, Nagarajan V, Rouvière PE (2003) mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species. Appl Environ Microbiol 69:334–342PubMedPubMedCentralCrossRefGoogle Scholar
  19. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner FO, Amann R, Eickhorst T, Schulze-Lefert P (2012) Revealing structure and assembly cues for Arabidopsis root–inhabiting bacterial microbiota. Nature 488:91–95PubMedPubMedCentralCrossRefGoogle Scholar
  20. Bürgmann H, Widmer F, Sigler WV, Zeyer J (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69:1928–1935PubMedPubMedCentralCrossRefGoogle Scholar
  21. Cavalieri D, Grosu P (2004) Integrating whole-genome expression results into metabolic networks with pathway processor. Curr Protoc Bioinformatics. Chapter 7: Unit 7.6.  https://doi.org/10.1002/0471250953.bi0706s05
  22. Chaparro JM, Sheflin AM, Manter DK, Vivanco JM (2012) Manipulating the soil microbiome to increase soil health and plant fertility. Biol Fertil Soils 48:489–499CrossRefGoogle Scholar
  23. Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8:10PubMedCentralCrossRefGoogle Scholar
  24. 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 42:669–678CrossRefGoogle Scholar
  25. Conrad R, Erkel C, Liesack W (2006) Rice cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 17:262–267PubMedCrossRefGoogle Scholar
  26. Dakora FD (2003) Defining new roles for plant and rhizobial molecules in sole and mixed plant cultures involving symbiotic legumes. New Phytol 158:39–49CrossRefGoogle Scholar
  27. Damiani I, Baldacci-Cresp F, Hopkins J, Andrio E, Balzergue S, Lecomte P, Puppo A, Abad P, Favery B, Herouart D (2012) Plant genes involved in harbouring symbiotic rhizobia or pathogenic nematodes. New Phytol 194:511–522PubMedCrossRefGoogle Scholar
  28. DeLong EF (2006) Archaeal mysteries of the deep revealed. Proc Natl Acad Sci U S A 103:6417–6418PubMedPubMedCentralCrossRefGoogle Scholar
  29. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F (2008) Functional metagenomic profiling of nine biomes. Nature 452:629–632CrossRefGoogle Scholar
  30. Dobrovolskaya T, Khusnetdinova K, Manucharova N, Golovchenko A (2017) Structure of epiphytic bacterial communities of weeds. Microbiology 86(2):257–263CrossRefGoogle Scholar
  31. Egert M, de Graaf AA, Smidt H, de Vos WM, Venema K (2006) Beyond diversity: functional microbiomics of the human colon. Trends Microbiol 14:86–91PubMedCrossRefGoogle Scholar
  32. El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69:2377–2382PubMedPubMedCentralCrossRefGoogle Scholar
  33. Eyers L, George I, Schuler L, Stenuit B, Agathos SN, Fantroussi SEI (2004) Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl Environ Microbiol 66:123–130Google Scholar
  34. Ferrer M, Beloqui A, Timmis KN, Golyshin PN (2008) Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 16:109–123PubMedCrossRefGoogle Scholar
  35. Fischer D, Pfitzner B, Schmid M, Simões-Araújo JL, Reis VM, Pereira W, Ormeño-Orrillo E, Hai B, Hofmann A, Schloter M, Martinez-Romero E, Baldani JI, Hartmann A (2012) Molecular characterisation of the diazotrophic bacterial community in uninoculated and inoculated field-grown sugarcane (Saccharum sp.). Plant Soil 356:83–99CrossRefGoogle Scholar
  36. Fleming JT, Yao WH, Sayler GS (1998) Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms. Appl Environ Microbiol 64:3698–3706PubMedPubMedCentralGoogle Scholar
  37. Galbally IE, Kirstine W (2002) The production of methanol by flowering plants and the global cycle of methanol. J Atmos Chem 43:195–229CrossRefGoogle Scholar
  38. Galbraith EA, Antonopoulos DA, White BA (2004) Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ Microbiol 6:928–937PubMedCrossRefGoogle Scholar
  39. Gao H, Yang ZK, Gentry TJ, Wu L, Schadt CW, Zhou J (2006) Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol 2:563–571Google Scholar
  40. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO, Klenk HP, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R (2010) The Earth Microbiome Project: meeting report of the “1st EMP Meeting on Sample Selection and Acquisition” at Argonne National Laboratory October 6 2010. Stand Genomic Sci 3:249–253PubMedPubMedCentralCrossRefGoogle Scholar
  41. Glick BR (2005) Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. FEMS Microbiol Lett 251:1–7PubMedPubMedCentralCrossRefGoogle Scholar
  42. Haichar FEZ, Achouak W, Christen R, Heulin T, Marol C, Marais MF, Mougel C, Ranjard L, Balesdent J, Berge O (2007) Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 9:625–634PubMedCrossRefPubMedCentralGoogle Scholar
  43. Hiltner L (1904) Über neuere Erfahrungen und Probleme auf dem Gebiet der Bodenbakteriologie und unter besonderer Berücksichtigung der Grüdungen und Brache. Arbeiten der Deutschen Landwirtschafts-Gesellschaft H 98:59–78Google Scholar
  44. Hoheisel JD (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet 7:200–210PubMedCrossRefPubMedCentralGoogle Scholar
  45. Hong SH, Bunge J, Leslin C, Jeon S, Epstein SS (2009) Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J 3:1365–1373CrossRefGoogle Scholar
  46. Inceoglu O, Abu Al-Soud W, Salles JF, Semenov AV, van Elsas JD (2011) Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS One 6:11CrossRefGoogle Scholar
  47. James EK (2000) Nitrogen fixation in endophytic and associative symbiosis. Field Crop Res 65:197–209CrossRefGoogle Scholar
  48. Kniskern JM, Traw MB, Bergelson J (2007) Salicylic acid and jasmonic acid signalling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol Plant-Microbe Interact 20:1512–1522PubMedCrossRefGoogle Scholar
  49. Lemarchand K, Masson L, Brousseau R (2004) Molecular biology and DNA microarray technology for microbial quality monitoring of water. Crit Rev Microbiol 30:145–172PubMedCrossRefGoogle Scholar
  50. Lian J, Wang Z, Zhou S (2008) Response of endophytic bacterial communities in banana tissue culture plantlets to Fusarium wilt pathogen infection. J Gen Appl Microbiol 54(2):83–92PubMedCrossRefGoogle Scholar
  51. Liang P, Pardee AB (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:971–976CrossRefGoogle Scholar
  52. Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883PubMedPubMedCentralCrossRefGoogle Scholar
  53. Liu WT, Zhu L (2005) Environmental microbiology-on-a-chip and its future impacts. Trends Biotechnol 23:174–179PubMedCrossRefGoogle Scholar
  54. Loy A, Kusel K, Lehner A, Drake HL, Wagner M (2004) Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal co-occurrence of recognized genera and novel lineages. Appl Environ Microbiol 70:6998–7009PubMedPubMedCentralCrossRefGoogle Scholar
  55. Lozupone CA, Knight R (2008) Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 32:557–578PubMedPubMedCentralCrossRefGoogle Scholar
  56. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90PubMedPubMedCentralCrossRefGoogle Scholar
  57. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedPubMedCentralCrossRefGoogle Scholar
  58. 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 332:1097–1100CrossRefGoogle Scholar
  59. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663PubMedPubMedCentralCrossRefGoogle Scholar
  60. Meyer JB, Song-Wilson Y, Foetzki A, Luginbuhl C, Winzeler M, Kneubühler Y, Matasci C, Mascher-Frutschi F, Kalinina O, Boller T, Keel C, Maurhofer M (2013) Does wheat genetically modified for disease resistance affect root-colonizing pseudomonads and arbuscular mycorrhizal fungi? PLoS One 8:12Google Scholar
  61. Micallef SA, Shiaris MPC-CA (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60:1729–1742PubMedPubMedCentralCrossRefGoogle Scholar
  62. Mitter B, Pfaffenbichler N, Flavell R, Compant S, Antonielli L (2017) A new approach to modify plant microbiomes and traits by introducing beneficial bacteria at flowering into progeny seeds. Front Microbiol 8:11.  https://doi.org/10.3389/fmicb.2017.00011 CrossRefPubMedPubMedCentralGoogle Scholar
  63. Monteiro RA, Balsanelli E, Wassem R, Marin AM, Brusamarello-Santos LCC, Schmidt MA, Tadra-Sfeir MZ, Pankievicz VCS, Cruz LM, Chubatsu LS, Pedrosa FO, Souza EM (2012) Herbaspirillum–plant interactions: microscopical, histological and molecular aspects. Plant Soil 356:175–196CrossRefGoogle Scholar
  64. Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Serra PR, Stevens R, Snape J, Brass A, Field D (2006) Annotation of environmental OMICS data: application to the transcriptomics domain. OMICS 2:172–178CrossRefGoogle Scholar
  65. Nygaard V, Hovig E (2006) Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res 34:996–1014PubMedPubMedCentralCrossRefGoogle Scholar
  66. Park SJ, Kang CH, Chae JC, Rhee SK (2008) Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol Lett 284:28–34PubMedCrossRefGoogle Scholar
  67. Philippot L, Hallin S, Borjesson G, Baggs EM (2009) Biochemical cycling in the rhizosphere having an impact on global change. Plant Soil 321:61–81CrossRefGoogle Scholar
  68. Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7:16Google Scholar
  69. Rebrikov DV, Desai SM, Siebert PD, Lukyanov SA (2004) Suppression subtractive hybridization. Methods Mol Biol 258:107–134PubMedGoogle Scholar
  70. Reinhold-Hurek B, Bunger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol 53:403–424PubMedCrossRefGoogle Scholar
  71. Rezzonico F, Binder C, Defago G, Moenne-Loccoz Y (2005) The type III secretion system of biocontrol Pseudomonas fluorescens KD targets the phytopathogenic chromista Pythium ultimum and promotes cucumber protection. Mol Plant-Microbe Interact 18:991–1001PubMedCrossRefGoogle Scholar
  72. Sebat JL, Colwell FS, Crawford RL (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol 8:4927–4934CrossRefGoogle Scholar
  73. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13:216–223PubMedPubMedCentralCrossRefGoogle Scholar
  74. Selvakumar G, Panneerselvam P, Ganeshamurthy AN, Maheshwari DK (2012) Bacterial mediated alleviation of abiotic stress in crops. In: Maheshwari DK (ed) Bacteria in agrobiology: stress management. Springer, New York, pp 205–224CrossRefGoogle Scholar
  75. Sessitsch A, Hardoim P, Doring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T, Sarkar A, Bodrossy L, vanOverbeek L, Brar D, van Elsas JD, Reinhold-Hurek B (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36PubMedCrossRefGoogle Scholar
  76. Sharma S, Aneja MK, Mayer J, Schloter M, Munch JC (2004) RNA fingerprinting of microbial community in the rhizosphere soil of grain legumes. FEMS Microbiol Lett 240:181–186PubMedCrossRefGoogle Scholar
  77. Stursova M, Zifcakova L, Leigh MB, Burgess R, Baldrian P (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80:735–746PubMedCrossRefGoogle Scholar
  78. Suman A, Yadav AN, Verma P (2016) Endophytic microbes in crops: diversity and beneficial impact for sustainable agriculture. In: Singh DP, Singh HB, Prabha R (eds) Microbial inoculants in sustainable agricultural productivity. Vol 1: research perspectives. Springer, Dordrecht, pp 117–143Google Scholar
  79. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69:1159–1171PubMedPubMedCentralCrossRefGoogle Scholar
  80. Teixeira L, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4:989–1001PubMedCrossRefGoogle Scholar
  81. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 36:664–675PubMedCrossRefGoogle Scholar
  82. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554–557PubMedCrossRefGoogle Scholar
  83. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804–810PubMedPubMedCentralCrossRefGoogle Scholar
  84. Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL (2005) E-predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol 9:R78CrossRefGoogle Scholar
  85. van der Heijden MGA, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310PubMedPubMedCentralCrossRefGoogle Scholar
  86. Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M (2009) Metagenomic approaches in systems microbiology. FEMS Microbiol Rev 33(1):236–255PubMedCrossRefPubMedCentralGoogle Scholar
  87. Vokou D, Vareli K, Zarali E, Karamanoli K, Constantinidou HIA, Monokrousos N, Halley JM, Sainis I (2012) Exploring biodiversity in the bacterial community of the Mediterranean phyllosphere and its relationship with airborne bacteria. Microb Ecol 64:714–724PubMedCrossRefPubMedCentralGoogle Scholar
  88. Walters DM, Russ R, Knackmuss H, Pouviere PE (2001) High-density sampling of a bacterial operon using mRNA differential display. Gene 273:305–315PubMedCrossRefPubMedCentralGoogle Scholar
  89. Ward BB, Eveillard D, Kirshtein JD, Nelson JD, Voytek MA, Jackson GA (2007) Ammonia oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ Microbiol 9:2522–2538PubMedCrossRefPubMedCentralGoogle Scholar
  90. Wrage N, Velthof GL, van Beusichem ML, Oenema O (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol Biochem 33:1723–1732CrossRefGoogle Scholar
  91. Wu L, Thompson DK, Liu X, Fields MW, Bagwell CE, Tiedje JM, Zhou J (2004) Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ Sci Technol 38:6775–6782PubMedCrossRefPubMedCentralGoogle Scholar
  92. Wu L, Liu X, Schadt CW, Zhou J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72 4931–4941PubMedPubMedCentralCrossRefGoogle Scholar
  93. Yakimov MM, Timmis KN, Golyshin PN (2007) Obligate oil degrading marine bacteria. Curr Opin Biotechnol 18:257–266CrossRefGoogle Scholar
  94. Zamioudis C, Pieterse CM (2012) Modulation of host immunity by beneficial microbes. Mol Plant-Microbe Interact 25:139–150PubMedPubMedCentralCrossRefGoogle Scholar
  95. Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207PubMedCrossRefGoogle Scholar
  96. Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294PubMedCrossRefGoogle Scholar
  97. Zhou J, Thompson DK (2004) Microarray technology and applications in environmental microbiology. Adv Agron 82:183–270CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Nikhi Verma
    • 1
  • Vivek Kumar
    • 2
  1. 1.Department of Medical Mycology, VP Chest InstituteUniversity of DelhiDelhiIndia
  2. 2.Himalayan School of BiosciencesSwami Rama Himalayan UniversityDehradunIndia

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