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Rhizosphere Microbiome Metagenomics: Elucidating the Abditive Microflora

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Mining of Microbial Wealth and MetaGenomics

Abstract

The rhizosphere is a zone of biological activity between plant roots and soil harboring a plethora of microorganisms. The key interactions among a multitude of microorganisms in the rhizosphere have a direct or indirect effect on the plant. Being versatile and intriguingly complex, a comprehension regarding the elementary principles of microbial ecology and functioning is significant to enhance the plant productivity and agroecosystem working. The interplay between plant roots and the associated microbes is regulated by profound chemical signaling. Most of the known facts about these interactions till recently have been derived through the studies based on culturing the microbes; however, it is an established fact that majority of the microbes are uncultivable. Novel insights into enhancing our ability to unravel the quintessential factors determining the rhizosphere microbiome could offer the progress towards the development of sustainable agriculture. We now have the opportunity to utilize the advanced culture independent techniques to have an insight into the intriguing plant-microbe interplay. Metagenomic studies present a strong mandate to understand the enormous richness and diversity of rhizosphere microbiome as well as the key biological processes.

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References

  • Aakvik T, Lale R, Liles M, Valla S (2011) Metagenomic libraries for functional screening. In: de Brujin FJ (ed) Handbook of molecular microbial ecology I: metagenomics and complementary approaches. Wiley, Hoboken, pp 171–181. isbn 978-11-180-1051-8. doi: 10.1002/9781118010518.ch22

  • Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71:8966–8966. doi:10.1128/AEM.71.12.8966-8969.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amann RI (1995) Fluorescently labeled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol Ecol 4:543–553

    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 

  • Amorim JH, Macena TN, Lacerda-Junior GV, Rezende RP, Dias JC, Brendel M, Cascardo JC (2008) An improved extraction protocol for metagenomic DNA from a soil of the Brazilian Atlantic Rainforest. Genet Mol Res 7:1226–1232. doi:10.4238/vol7-4gmr509

    Article  CAS  PubMed  Google Scholar 

  • Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32:666–681. doi:10.1111/j.1365-3040.2009.01926.x

    Article  CAS  PubMed  Google Scholar 

  • Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266. doi:10.1146/annurev.arplant.57.032905.105159

    Article  CAS  PubMed  Google Scholar 

  • Bao Z, Okubo T, Kubota K, Kasahara Y, Tsurumaru H, Anda M, Ikeda S, Minamisawa K (2014) Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants. Appl Environ Microbiol 80:5043–5052. doi:10.1128/AEM.00969-14

    Article  PubMed  PubMed Central  Google Scholar 

  • Bastida F, Algora C, Hernandez T, Garcia C (2012) Feasibility of a cell separation–proteomic based method for soils with different edaphic properties and microbial biomass. Soil. Biol Biochem 45:136–138. doi:10.1016/j.soilbio.2011.10.017

    Article  CAS  Google Scholar 

  • Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917. doi:10.1038/ismej.2010.171

    Article  CAS  PubMed  Google Scholar 

  • Becher D, Bernhardt J, Fuchs S, Riedel K (2013) Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics 13:2895–2909. doi:10.1002/pmic.201300095

    CAS  PubMed  Google Scholar 

  • Beneduzi A, Ambrosini A, Passaglia LM (2012) Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents. Genet Mol Biol 35:1044–1051. doi:10.1590/S1415-47572012000600020. PMC: PMC3571425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown OG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM et al (2008) Accurate whole genome human sequencing using reversible terminator chemistry. Nature 456:53–59. doi:10.1038/nature07517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berendsen RL, Pieterse CMJ, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486. doi:10.1016/j.tplants.2012.04.001

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Opelt K, Zachow C, Lottmann J, Gotz M, Costa R, Smalla K (2006) The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs depending on plant species and site. FEMS Microbiol Ecol 56:250–261. doi:10.1111/j.1574-6941.2005.00025.x

    Article  CAS  PubMed  Google Scholar 

  • Bertin C, Yang X, Weston LA (2003) The role of root exudates and allelochemicals in the rhizosphere. Plant Soil 256:67–83. doi:10.1023/A:1026290508166

    Article  CAS  Google Scholar 

  • Braker G, Zhou J, Wu L, Devol AH, Tiedje JM (2000) Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl Environ Microbiol 66:2096–2104. doi:10.1128/AEM.66.5.2096-2104.2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu TS, Schadt CW, Doktycz MJ, Pelletier DA (2012) Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol 194:5991–5993. doi:10.1128/JB.01243-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buckling A, Harrison F, Vos M, Brockhurst MA, Gardner A, West SA, Griffin A (2007) Siderophore-mediated cooperation and virulence in Pseudomonas aeruginosa. FEMS Microbiol Ecol 62:135–141. doi:10.1111/j.1574-6941.2007.00388.x

    Article  CAS  PubMed  Google Scholar 

  • Buee M, Reich M, Murat C, Martin FM (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456. doi:10.1111/j.1469-8137.2009.03003.x

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Spaepen SS, Themaat EVL, Shulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838. doi:10.1146/annurev-arplant-050312-120106

    Article  CAS  PubMed  Google Scholar 

  • Caracciolo AB, Bottoni P, Grenni P (2010) Fluorescence in situ hybridization in soil and water: a useful method for studying the effect of xenobiotics on bacterial community structure. Toxicol Environ Chem 92:567–579. doi:10.1080/02772241003620244

    Article  CAS  Google Scholar 

  • Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2012) Application of metatranscriptomics to soil environments. J Microbiol Methods 91:246–251. doi:10.1016/j.mimet.2012.08.011

    Article  CAS  PubMed  Google Scholar 

  • Carvalhais, LC, Dennis PG, Tyson GW, Schenk PM (2013) Rhizosphere metatranscriptomics: challenges and opportunities. In: de Brujin FJ (ed) Molecular microbial ecology of the rhizosphere. Wiley, Honboken, pp 1137–1144. doi: 10.1002/9781118297674.ch109. isbn (Print) 978-11-182-9617-2; (Online) 978-11-182-9767-4

    Google Scholar 

  • Chaudhary V, Rehman A, Mishra A, Chauhan PS, Nautiyal CS (2012) Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb Ecol 64:450–460. doi:10.1007/s00248-012-0025-y

  • Chauhan PS, Chaudhry V, Mishra S, Nautiyal CS (2011) Uncultured bacterial diversity in tropical maize (Zea mays L.) rhizosphere. J Basic Microbiol 51(1):15–32. doi:10.1002/jobm.20100017

  • Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41:252–263. doi:10.1007/s002480000087

    Article  CAS  PubMed  Google Scholar 

  • Costa R, Gotz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56:236–249. doi:10.1111/j.1574-6941.2005.00026.x

    Article  CAS  PubMed  Google Scholar 

  • Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478. doi:10.1038/nrmicro1160

    Article  CAS  PubMed  Google Scholar 

  • David DM, Lydia HZ, Janet KJ (2013) The potential of metagenomic approaches for understanding soil microbial processes. Soil Sci Soc Am J 78:3–10. doi:10.2136/sssaj2013.07.0287dgs

    Google Scholar 

  • De Vleesschauwer D, Hofte M (2009) Rhizobacteria-induced systemic resistance. Adv Bot Res 51:223–281. doi:10.1016/S0065-2296(09)51006-3

    Article  Google Scholar 

  • de Weert S, Dekkers LC, Bitter W, Tuinman S, Wijfjes AH, Boxtel RV, Lugtenberg BJ (2006) The two-component colR/S system of Pseudomonas fluorescensWCS365 plays a role in rhizosphere competence through maintaining the structure and function of the outermembrane. FEMS Microbiol Ecol 58:205–213. doi:10.1111/j.1574-6941.2006.00158.x

    Article  PubMed  Google Scholar 

  • Dobbelaere S, Vanderleyden J, Okon Y (2003) Plant growth-promoting effects of diazotrophs in the rhizosphere. CRC Crit Rev Plant Sci 22:107–149. doi:10.1080/713610853

    Article  CAS  Google Scholar 

  • Dokic L, Savic M, Narancic T, Vasiljevic B (2010) Metagenomic analysis of soil microbial communities. Arch Biol Sci 62:559–564. doi:10.2298/ABS1003559D

    Article  Google Scholar 

  • Doornbos RF, Van Loon LC, Bakker PA (2012) Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. Agron Sustain Dev 32:227–243. doi:10.1007/s13593-011-0028-y

    Article  Google Scholar 

  • Dube HC, Yeole RD (1999) Modern approaches and innovations in soil management. Rastogi Publications, Meerut, 33p

    Google Scholar 

  • Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar M, Alexander S, Alexander IE, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57–70. doi:10.1186/1471-2164-7-57

    Article  PubMed  PubMed Central  Google Scholar 

  • Egamberdieva D, Kamilova F, Validov S, Gafurova L, Kucharova Z, Lugtenberg B (2008) High incidence of plant growth stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan. Environ Microbiol 10:1–9. doi:10.1111/j.1462-2920.2007.01424.x

    CAS  PubMed  Google Scholar 

  • Gams W (2007) Biodiversity of soil-inhabiting fungi. Biodivers Conserv 16:69–72. doi:10.1007/s10531-006-9121-y

    Article  Google Scholar 

  • Gianfreda L (2015) Enzymes of importance to rhizosphere processes. J Soil Sci Plant Nutr 15:283–306. doi:10.4067/S0718-95162015005000022

    CAS  Google Scholar 

  • Gray EJ, Smith DL (2005) Intracellular and extracellular PGPR: commonalities and distinctions in the plant-bacterium signaling processes. Soil Biol Biochem 37:395–412. doi:10.1016/j.soilbio.2004.08.030

    Article  CAS  Google Scholar 

  • Grayston SJ, Vaughan D, Jones D (1997) Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Appl Soil Ecol 5:29–56. doi:10.1016/s0929-1393(96)00126-6

    Article  Google Scholar 

  • Guazzaroni ME, Golyshin PN, Ferrer M (2010) Analysis of complex microbial community through metagenomic survey. In: Marco D (ed) Metagenomics: theory, methods and application. Caister Academic Press, Argentina, pp 55–77. isbn 978-1-904455-54-7

    Google Scholar 

  • Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10:R32. doi:10.1186/gb-2009-10-3-r32

    Article  PubMed  PubMed Central  Google Scholar 

  • Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312:7–14. doi:10.1007/s11104-007-9514-z

    Article  CAS  Google Scholar 

  • Hawkes CV, DeAngelis KM, Firestone MK (2007) Root interactions with soil microbial communities and processes. In: Cardon Z, Whitbeck J (ed) The rhizosphere. Elsevier, pp 1–29. doi: 10.1016/B978-012088775-0/50003-3. isbn 978-0-12-088775-0

  • Hein JW, Wolfe GV, Blee KA (2008) Comparison of rhizosphere bacterial communities in Arabidopsis thaliana mutants for systemic acquired resistance. Microb Ecol 55:333–343. doi:10.1007/s00248-007-9279-1

    Article  CAS  PubMed  Google Scholar 

  • Hider RC, Kong X (2010) Chemistry and biology of siderophores. Nat Prod Rep 27:637–657. doi:10.1039/b906679a

    Article  CAS  PubMed  Google Scholar 

  • Hikaru S (2012) Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ Microbiol 14:13–22. doi:10.1111/j.1462-2920.2011.02438.x

    Article  Google Scholar 

  • Hogberg MN, Hogberg P, Myrold DD (2006) Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three? Oecologia 150:590–601. doi:10.1007/s00442-006-0562-5

    Article  PubMed  Google Scholar 

  • Hong SH, Bunge J, Jeon SO, Epstein SS (2006) Predicting microbial species richness. Proc Natl Acad Sci U S A 103:117–122. doi:10.1073/pnas.0507245102

    Article  CAS  PubMed  Google Scholar 

  • Jaya KA, Kumarapillai H (2011) Metagenomic analysis of bacterial diversity in the rice rhizosphere soil microbiome. Biotechnol Bioinformatics Bioeng 1:361–367

    Google Scholar 

  • Johri BN, Sharma A, Virdi JS (2003) Rhizobacterial diversity in India and its influence on soil and plant health. Adv Biochem Eng Biotechnol 84:49–89. doi:10.1007/b11036

    CAS  PubMed  Google Scholar 

  • Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329. doi:10.1038/nature05286

    Article  CAS  PubMed  Google Scholar 

  • Jones DL, Hodge A, Kuzyakov Y (2004) Plant and mycorrhizal regulation of rhizodeposition. New Phytol 163:459–480. doi:10.1111/j.1469-8137.2004.01130.x

    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. doi:10.1146/annurev.micro.56.012302.161120

    Article  CAS  PubMed  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. doi:10.1038/ismej.2011.192

    Article  CAS  PubMed  Google Scholar 

  • Kuklinsky-Sobral J, Araujo WL, Mendes R, Geraldi IO, Pizzirani-Kleiner AA, Azevedo JL (2004) Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environ Microbiol 6:1244–1251. doi:10.1111/j.1462-2920.2004.00658.x

    Article  CAS  PubMed  Google Scholar 

  • Lagos L, Navarrete O, Maruyama F (2014) Bacterial community structures in rhizosphere microsites of ryegrass (Lolium perenne var. Nui) as revealed by pyrosequencing. Biol Fertil Soils 50:1253–1266. doi:10.1007/s00374-014-0939-2

    Article  Google Scholar 

  • Lee SA, Park J, Chu B, Kim JM, Joa JH, Sang MK, Song J, Weon HY (2016) Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches. J Microbiol 54:823–831. doi:10.1007/s12275-016-6410-3

    Article  CAS  PubMed  Google Scholar 

  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809. doi:10.1038/nature04983

    Article  CAS  PubMed  Google Scholar 

  • Lesuffleur F, Paynel F, Bataille MP, Deunff E, Cliquet JB (2007) Root amino acid exudation: measurement of high efflux rates of glycine and serine from six different plant species. Plant Soil 294:235–246. doi:10.1007/s11104-007-9249-x

    Article  CAS  Google Scholar 

  • Leveau JH, Uroz S, de Boer W (2010) The bacterial genus Collimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments. Environ Microbiol 12:281–292. doi:10.1111/j.1462-2920.2009.02010.x

    Article  CAS  PubMed  Google Scholar 

  • Li T, Wu TD, Mazeas L, Toffin L, Guerquin-Kern JL, Leblon G, Bouchez T (2008) Simultaneous analysis of microbial identity and function using NanoSIMS. Environ Microbiol 10:580–588. doi:10.1111/j.1462-2920.2007.01478.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lopes LD, Pereira e Silva MC, Andreote FD (2016) Bacterial abilities and adaptation toward the rhizosphere colonization. Front Microbiol 7:1341. doi:10.3389/fmicb.2016.01341

    Article  PubMed  PubMed Central  Google Scholar 

  • Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556. doi:10.1146/annurev.micro.62.081307.162918

    Article  CAS  PubMed  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, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90. doi:10.1038/nature11237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mapelli F, Marasco R, Balloi A, Rolli E, Cappitelli F, Daffonchio D, Borin S (2012) Mineral-microbe interactions: biotechnological potential of bioweathering. J Biotechnol 157:473–481. doi:10.1016/j.jbiotec.2011.11.013

    Article  CAS  PubMed  Google Scholar 

  • Mendes R, Krujit M, de Bruijn I, Raajimakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Sci 332:1097–1100. doi:10.1126/science.1203980

    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. doi:10.1111/1574-6976.12028

    Article  CAS  PubMed  Google Scholar 

  • Mendes LW, Kuramae EE, Navarrete AA, van Veen JA, Tsai SM (2014) Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 8:1577–1587. doi:10.1038/ismej.2014.17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Micallef SA, Shiaris MP, Colon-Carmona A (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60:1729–1742. doi:10.1093/jxb/erp053

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Myrold DD, Nannipieri P (2014) Classical techniques versus omics approaches. In: Nannipieri P, Pietramellara G, Renella G (eds) Omics in soil science. Caister Academic Press, Haverhill, pp 179–187. isbn 978-1-908230-94-2. doi: 10.1.1.718.6012

    Google Scholar 

  • Nautiyal CS, Srivastava S, Chauhan PS (2008) Rhizosphere colonization: molecular determinants from plant-microbe coexistence perspective. In: Nautiyal CS, Dion P (eds) Molecular mechanisms of plant and microbe coexistence. Springer, Berlin, pp 99–123. isbn:978-3-540-75575-3

    Google Scholar 

  • Nautiyal CS, Chauhan PS, Bhatia CR (2010) Changes in soil physicochemical properties and microbial functional diversity due to 14 years of conversion of grassland to organic agriculture in semi-arid agroecosystem. Soil Tillage Res 109:55–60. doi:10.1016/j.still.2010.04.008

    Article  Google Scholar 

  • Neufeld JD, Chen Y, Dumont MG, Murrell JC (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Microbiology 10:1526–1535. doi:10.1111/j.1462-2920-2008.01568.x

    CAS  Google Scholar 

  • Palenik B, Ren Q, Tai V, Paulsen IT (2009) Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ Microbiol 11:349–359. doi:10.1111/j.1462-2920.2008.01772.x

    Article  CAS  PubMed  Google Scholar 

  • Pascual J, Blanco S, Garcia-Lopez M, Garcia-Salamanca A, Bursakov SA, Genilloud O, Bills GF, Ramos JL, van Dillewjin P (2016) Assessing bacterial diversity in the rhizosphere of Thymus zygis growing in the Sierra Nevada National Park (Spain) through culture-dependent and independent approaches. PLoS One 11:e0146558. doi:10.1371/journal.pone.0146558

    Article  PubMed  PubMed Central  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. doi:10.1038/nrmicro3109

    Article  CAS  PubMed  Google Scholar 

  • Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C (2015) Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process: a review. Biol Fertil Soils 5:403–415. doi:10.1007/s00374-015-0996-1

    Article  Google Scholar 

  • Pires AC, Cleary DF, Almeida A, Cunha A, Dealtry S, Mendonca-Hagler LC, Smalla K, Gomes NC (2012) Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Appl Environ Microbiol 78:5520–5528. doi:10.1128/AEM.00386-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prashar P, Kapoor N, Sachdeva S (2014) Rhizosphere: its structure, bacterial diversity and significance. Rev Environ Sci Biotechnol 13:63–77. doi:10.1007/s11157-013-9317-z

    Article  CAS  Google Scholar 

  • Raaijmakers JM, Weller DM (2001) Exploiting genotypic diversity of 2,4-diacetylphloroglucinol-producing Pseudomonas spp.: characterization of superior root-colonizing P. fluorescens strain Q8r1-96. Appl Environ Microbiol 67:2545–2554. doi:10.1128/AEM.67.6.2545-2554.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moenne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soil borne pathogens and beneficial microorganisms. Plant Soil 321:341–361. doi:10.1007/s11104-008-9568-6

    Article  CAS  Google Scholar 

  • Rawat S, Johri BN (2014) Thermophilic fungi: diversity and significance in composting. Kavaka 42:52–68

    Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552. doi:10.1146/annurev.genet.38.072902.091216

    Article  CAS  PubMed  Google Scholar 

  • Salles JF, van Veen JA, van Elsas JD (2004) Multivariate analyses of Burkholderia species in soil: effect of crop and land use history. Appl Environ Microbiol 70:4012–4020. doi:10.1128/AEM.70.7.4012-4020-2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmidt H, Eickhorst T (2014) Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition–fluorescence in situ hybridization. FEMS Microbiol Ecol 87:390–402. doi:10.1111/1574-6941.12232

    Article  CAS  PubMed  Google Scholar 

  • Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145. doi:10.1038/nbt1486

    Article  CAS  PubMed  Google Scholar 

  • Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77:1153–1161. doi:10.1128/AEM.02345-10

    Article  CAS  PubMed  Google Scholar 

  • Simons M, Permentier HP, de Weger LA, Wijffelman CA, Lugtenberg BJ (1997) Amino acid synthesis is necessary for tomato root colonization by Pseudomonas fluorescens strain WCS365. Mol Plant Microbe Interact 10:102–106. doi:10.1094/MPMI.1997.10.1.102

    Article  CAS  Google Scholar 

  • Singh BK, Munro S, Potts JM, Millard P (2007) Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl Soil Ecol 36:147–155. doi:10.1016/j.apsoil.2007.01.004

    Article  Google Scholar 

  • Singh BK, Campbell CD, Sorenson SJ, Zhou J (2009) Soil genomics. Nat Rev Microbiol 7:756. doi:10.1038/nrmicro2119-c1

    Article  CAS  PubMed  Google Scholar 

  • Sinha R, Goel R, Johri BN (2001) Molecular markers in rhizosphere microbiology. In: Maheshwari DK, Dubey RC (eds) Innovative approaches in microbiology. Bishen Singh Mahendra Pal Singh, Dehradun, p 255. isbn:978-81-211-0210-0

    Google Scholar 

  • Somers E, Vanderleyden J, Srinivasan M (2004) Rhizosphere bacterial signaling: a love parade beneath our feet. Crit Rev Microbiol 30:205–235. doi:10.1080/10408410490468786

    Article  CAS  PubMed  Google Scholar 

  • Spiegelman D, Whissell G, Greer CW (2005) A survey of the methods for the characterization of microbial consortia and communities. Can J Microbiol 51:355–386. doi:10.1139/w05-003

    Article  CAS  PubMed  Google Scholar 

  • Thompson JR, Pacocha S, Pharino C, Klepac-Ceraj V, Hunt DE, Benoit J, Sarma-Rupavtarm R, Distel DL, Polz MF (2005) Genotypic diversity within a natural coastal bacterioplankton population. Sci 307:1311–1313. doi:10.1126/science.1106028

    Article  CAS  Google Scholar 

  • Torsten T, Jack G, Folker M (2012) Metagenomics–a guide from sampling to data analysis. Microb Inform Exp 2:3. doi:10.1186/2042-5783-2-3

    Article  Google Scholar 

  • Torsvik V, Overas L, Thingstad T (2002) Prokaryotic diversity magnitude dynamics, and controlling factors. Science 296:1064–1066. doi:10.1126/science.1071698

    Article  CAS  PubMed  Google Scholar 

  • Tringe SG, Von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P (2005) Comparative metagenomics of microbial communities. Sci 308:554–557. doi:10.1126/science.1107851

    Article  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43. doi:10.1038/nature02340

    Article  CAS  PubMed  Google Scholar 

  • Uroz S, Buee 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. doi:10.1111/j.1758-2229.2009.00117.x

    Article  CAS  PubMed  Google Scholar 

  • Velazquez-Sepulveda I, Orozco-Mosqueda MC, Prieto-Barajas CM, Santoyo G (2012) Bacterial diversity associated with the rhizosphere of wheat plants (Triticum aestivum): toward a metagenomic analysis. Phyton 81:81–87. doi: 10.1.1.472.577

    Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Sci 304:66–74. doi:10.1126/science.1093857

    Article  CAS  Google Scholar 

  • Walker TS, Bais HP, Grotewold E, Vivanco JM (2003) Root exudation and rhizosphere biology. Plant Physiol 132:44–51. doi:10.1104/pp.102.019661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang HB, Zhang ZX, Li H, Lin WX (2011) Characterization of metaproteomics in crop rhizospheric soil. J Proteome Res 10:932–940. doi:10.1021/pr100981r

    Article  CAS  PubMed  Google Scholar 

  • Wegley L, Mosier-Boss P, Lieberman S, Andrews J, Graff-Baker A, Rohwer F (2006) Rapid estimation of microbial numbers in water using bulk fluorescence. Environ Microbiol 8:1775–1782. doi:10.1111/j.1462-2920.2006.01062.x

    Article  CAS  PubMed  Google Scholar 

  • Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J (2005) Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 71:6335–6344. doi:10.1128/AEM.71.10.6335-6344.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zwirglmaier K (2005) Fluorescence in situ hybridization (FISH)-the next generation. FEMS Microbiol Lett 246:151–158. doi:10.1016/j.femsle.2005.04.015

    Article  CAS  PubMed  Google Scholar 

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Acknowledgment

The authors acknowledge the financial assistance provided by Uttarakhand State Biotechnology Department.

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Authors and Affiliations

  1. Department of Botany and Microbiology, H.N.B.G.U. (A Central University), Srinagar Garhwal, Uttarakhand, India

    Asifa Mushtaq & Seema Rawat

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  1. Asifa Mushtaq
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  2. Seema Rawat
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Correspondence to Seema Rawat .

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  1. Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India

    Vipin Chandra Kalia

  2. Microbial Culture Collection, National Centre for Cell Science, Pune, India

    Yogesh Shouche

  3. Environmental Biotechnology and Genomics Division, National Environmental Engineering Research Institute (CSIR), Nagpur, India

    Hemant J. Purohit

  4. Microbial Culture Collection, National Centre for Cell Science, Pune, India

    Praveen Rahi

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Mushtaq, A., Rawat, S. (2017). Rhizosphere Microbiome Metagenomics: Elucidating the Abditive Microflora. In: Kalia, V., Shouche, Y., Purohit, H., Rahi, P. (eds) Mining of Microbial Wealth and MetaGenomics. Springer, Singapore. https://doi.org/10.1007/978-981-10-5708-3_2

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