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Microbiomics: An Approach to Community Microbiology

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PlantOmics: The Omics of Plant Science

Abstract

Many biologists have known that there are many groups of microorganisms that, although they cannot be cultured, do exist and influence the life of mammals, plants, and other small multicellular organisms. Nowadays, many new sequencing techniques have been developed that, with very high precision, can identify the presence of these microorganisms and how they affect others. The microbiota of humans and plants can be studied, and their effects on health and growth are becoming known using the transcriptome analysis of interaction. Life on earth has evolved over billions of years, and its most initial form—the microorganism—has evolved in gradually changing environmental conditions. They are present everywhere: from high temperatures to freezing conditions, in water and in air, on surfaces and in inner cavities. Despite centuries of research, the world of microorganisms is not fully known, as only a fraction (0.001) of it is able to be cultured, thus leaving a world little known to us. Initially, polymerase chain reaction (PCR)-based techniques, and later 16S ribosomal RNA (rRNA) sequences, allowed a view into this hidden microbial diversity and provided knowledge about uncultured microbes. Microbiomic analyses made it possible to know about and culture members of previously unknown groups of certain microbiomes. Similarly, nucleic acid probes with fluorescent labels can identify even single cells in situ, and sequence-based analyses using random sequencing, as well as cloning of complete microbiomes, has facilitated the reconstruction of genomes. Transcriptomes and proteomes of microbiomes have provided microbiologists with opportunities to switch from diversity studies to that of functional microbiomics. Soil, which is essential for plants, is an ocean of microorganisms that affect plants largely through roots and on aerial surrounds. The study of microbiomics helps in the identification of new groups involved in plant diseases from the rhizosphere microbiome. The application of new groups of microorganisms and their interactions are enormous in the fields of food, human health, and plant health.

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References

  • Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431–440. doi:10.1038/nrmicro1872

    CAS  PubMed  Google Scholar 

  • Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci U S A 105:11512–11519

    PubMed Central  CAS  PubMed  Google Scholar 

  • Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762–770

    PubMed Central  CAS  PubMed  Google Scholar 

  • Bakker PAHM, Berendsen RL, Doornbos RF, Wintermans PCA, Pieterse CM (2013) The rhizosphere revisited: root microbiomics. Front Plant Sci 165:1–7

    Google Scholar 

  • Barata A, Malfeito-Ferreira M, Loureiro V (2012) The microbial ecology of wine grape berries. Int J Food Microbiol 153:243–259

    CAS  PubMed  Google Scholar 

  • Barret M, Frey-Klett P, Guillerm-Erckelboudt AV, Boutin M, Guernec G, Sarniguet A (2009) Effect of wheat roots infected with the pathogenic fungus Gaeumannomyces graminis var. tritici on gene expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp. Mol Plant Microbe Interact 22:1611–1623

    CAS  PubMed  Google Scholar 

  • Bartowski EJ (2009) Bacterial spoilage of wine and approaches to minimize it. Lett Appl Microbiol 48:149–156

    Google Scholar 

  • Behar A, Jurkevitch E, Yuval B (2008) Bringing back the fruit into fruit fly – bacteria interactions. Mol Ecol 17:1375–1386

    CAS  PubMed  Google Scholar 

  • Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411:786–789

    CAS  PubMed  Google Scholar 

  • Berry AE, Chiocchini C, Selby T, Sosio M, Wellington EM (2003) Isolation of high molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol Lett 223:15–20

    CAS  PubMed  Google Scholar 

  • Bohlool BB, Brock TD (1974) Immunofluorescence approach to the study of the ecology of Thermoplasma acidophilum in coal refuse material. Appl Microbiol 28:11–16

    PubMed Central  CAS  PubMed  Google Scholar 

  • Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M et al (2010) Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol 76:5533–5540

    PubMed Central  CAS  PubMed  Google Scholar 

  • Borody TJ (2000) “Flora Power” – fecal bacteria cure chronic C. difficile diarrhea. Am J Gastroenterol 95:3028–3029. doi:10.1111/j.1572-0241.2000.03277.x

    CAS  PubMed  Google Scholar 

  • Bott TL, Brock TD (1969) Bacterial growth rates above 90 degrees C in Yellowstone hot springs. Science 164:1411–1412

    CAS  Google Scholar 

  • Brock TD (1967) Life at high temperatures. Science 158:1012–1019

    CAS  PubMed  Google Scholar 

  • Brock TD, Brock ML (1968) Measurement of steady-state growth rates of a thermophilic alga directly in nature. J Bacteriol 95:811–815

    PubMed Central  CAS  PubMed  Google Scholar 

  • Buckley MJM, O’Morain CA (1998) Helicobacter biology discovery. Br Med Bull 54:7–16

    CAS  PubMed  Google Scholar 

  • Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95. doi:10.1038/nature11336

    CAS  PubMed  Google Scholar 

  • Carvalhais LC, Dennis PG, Badri DV, Tyson GW, Vivanco JM, Schenk PM (2013) Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS One 8:e56457. doi:10.1371/journal.pone.0056457

    PubMed Central  CAS  PubMed  Google Scholar 

  • Chen K, Pachter L (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 1:106–112. doi:10.1371/journal.pcbi.0010024

    CAS  PubMed  Google Scholar 

  • Cho JC, Giovannoni SJ (2004) Cultivation and growth characteristics of a diverse group of oligotrophic marine gammaproteobacteria. Appl Environ Microbiol 70:432–440

    PubMed Central  CAS  PubMed  Google Scholar 

  • Colwell RR, Grimes DJ (eds) (2000) Nonculturable microorganisms in the environment. ASM Press, Washington, DC

    Google Scholar 

  • Colwell RR, Tamplin ML, Brayton PR, Gauzens AL, Tall BD, Harrington D, Levine MM, Hall S, Huq A, Sack DA (1990) Environmental aspects of V. cholerae in transmission of cholera. In: Sack RB, Zinnaka Y (eds) Advances in research on cholera and related diarrhoeas, 7th edn. KTK Scientific Publications, Tokyo, pp 327–343

    Google Scholar 

  • Cortesi P, Bisiach M, Ricciolini M, Gadoury DM (1997) Cleistothecia of Uncinula necator – an additional source of inoculum in Italian vineyards. Plant Dis 81:922–926

    Google Scholar 

  • Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guerineau M, Jeannin P, Simonet P, Pernodet JL (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69:49–55

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cupples AM, Sanford RA, Sims GK (2005) Dehalogenation of bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) and ioxynil (3,5-diiodino-4-hydroxybenzonitrile) by desulfitobacterium chlororespirans. Appl Environ Microbiol 71(7):3741–3746

    PubMed Central  CAS  PubMed  Google Scholar 

  • Dahl Sawyer CA, Pestka JJ (1985) Foodservice systems: presence of injured bacteria in foods during food product flow. Annu Rev Microbiol 39:51–67

    Google Scholar 

  • DeCoste NJ, Gadkar VJ, Filion M (2010) Verticillium dahliae alters Pseudomonas spp. populations and HCN gene expression in the rhizosphere of strawberry. Can J Microbiol 56:906–915. doi:10.1139/ W10-080

    CAS  Google Scholar 

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

    Google Scholar 

  • Dethlefsen L, Relman DA (2010) Microbes and health sackler colloquium: incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. doi:10.1073/pnas.1000087107

    PubMed Central  PubMed  Google Scholar 

  • Dimakopoulou M, Tjamos SE, Antoniou PP, Pietri A, Battilani P, Avramidis N, Markakis EA, Tjamos EC (2008) Phyllosphere grapevine yeast Aureobasidium pullulans reduces Aspergillus carbonarius (sour rot) incidence in wine-producing vineyards in Greece. Biol Control 46:158–165

    Google Scholar 

  • Doenges JL (1938) Spirochaetes in the gastric glands of Macacus rhesus and humans without definite history of related disease. Proc Soc Exp Biol Med 38:536–538

    Google Scholar 

  • Dominati E, Patterson M, Mackay A (2010) A framework for classifying and quantifying the natural capital and ecosystem services of soils. Ecol Econ 69:1858–1868

    Google Scholar 

  • Doornbos RF, VanLoon LC, Bakker PAHM (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

    Google Scholar 

  • Drews G (1999) Ferdinand Cohn: a promoter of modern microbiology. Nova Acta Leopold 80(130):13–14

    Google Scholar 

  • Fan B, Cravalhais LC, Becker A, Fedoseyenko D, VonWiren N, Borriss R (2012) Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiol 12:116. doi:10.1186/1471-2180-12-116

    PubMed Central  CAS  PubMed  Google Scholar 

  • Garrett WS, Gordon JI, Glimcher LH (2010) Homeostasis and inflammation in the intestine. Cell 140:859–870

    PubMed Central  CAS  PubMed  Google Scholar 

  • Geison GL (1981) Cohn, Ferdinand Julius. In: Gillispie CC (ed) Dictionary of scientific biography, vol 3. Scribner, New York

    Google Scholar 

  • Germida JJ, Siciliano SD, DeFreitas JR, Seib AM (1998) Diversity of root-associated bacteria associated with field grown canola (Brassica napus L.) and wheat(Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50. doi:10.1111/j.1574-6941.1998.tb01560.x

    CAS  Google Scholar 

  • Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J et al (2012) Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol 13:R23. doi:10.1186/gb-2012-13-3-r23

    PubMed Central  CAS  PubMed  Google Scholar 

  • Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO et al (2009) Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A 106:1374–1379. doi:10.1073/pnas.0808022106

    PubMed Central  CAS  PubMed  Google Scholar 

  • Grayston SJ, Wang S, Campbell CD, Edwards AC (1998) Selective in fluence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378. doi:10.1016/S0038-0717(97)00124-7

    CAS  Google Scholar 

  • Grimes DJ, Atwell RW, Brayton PR, Palmer LM, Rollins DM, Roszak DB, Singleton FL, Tamplin ML, Colwell RR (1986) The fate of enteric pathogenic bacteria in estuarine and marine environments. Microbiol Sci 3:324–329

    CAS  PubMed  Google Scholar 

  • Grove GG (2004) Perennation of Uncinula necator in vineyards of eastern Washington. Plant Dis 88:242–247

    Google Scholar 

  • Guarner F, Malagelada JR (2003) Gut flora in health and disease. Lancet 361:512–519

    PubMed  Google Scholar 

  • Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J et al (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230. doi:10.1038/ismej.2008.80

    CAS  PubMed  Google Scholar 

  • Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19:1141–1152. doi:10.1101/gr.085464.108

    PubMed Central  CAS  PubMed  Google Scholar 

  • Harmsen HJM, Welling GW (2002) Fluorescence in situ hybridization as a tool in intestinal bacteriology. In: Tannock GW (ed) Probiotics and prebiotics: where are we going? Caister Academic Press, Norfolk, pp 41–58

    Google Scholar 

  • Harmsen HJM, Raangs GC, He T, Degener JE, Welling GW (2002) Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 68:2982–2990

    PubMed Central  CAS  PubMed  Google Scholar 

  • Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, Lüscher P, Widmer F, Frey B (2014) Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J 8(1):226–244

    PubMed Central  CAS  PubMed  Google Scholar 

  • Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M et al (2010) Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464:908–912. doi:10.1038/nature08937

    CAS  PubMed  Google Scholar 

  • Heider J, Rabus R (2008) Genomic insights in the anaerobic biodegradation of organic pollutants. In: Diaz E (ed) Microbial degradation, Genomics and molecular biology. Caister Academic Press, Norfolk, pp 25–54. ISBN 978-1-904455-17-2

    Google Scholar 

  • Heuer H, Smalla K (2012) Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 36:1083–1104

    CAS  PubMed  Google Scholar 

  • Heylen K, Hoefman S, Vekeman B, Peiren J, De Vos P (2012) Safeguarding bacterial resources promotes biotechnological innovation. Appl Microbiol Biotechnol 94:565–574

    CAS  PubMed  Google Scholar 

  • Hirsch PR, Mauchline TH (2012) Who’s who in the plant root microbiome? Nat Biotechnol 30:961–962. doi:10.1038/nbt.2387

    CAS  PubMed  Google Scholar 

  • Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD (2011) Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca species) phyllosphere. Appl Environ Microbiol 76:8117–8125

    Google Scholar 

  • Inceoglu O, VanOverbeek LS, Salles JF, Van Elsas JD (2013) The normal operating range of bacterial communities in soil used for potato cropping. Appl Environ Microbiol 79:1160–1170. doi:10.1128/AEM.02811-12

    PubMed Central  CAS  PubMed  Google Scholar 

  • Jansen GJ, Wildeboer-Veloo AC, Tonk RH, Franks AH, Welling GW (1999) Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria. J Microbiol Methods 37:215–221

    CAS  PubMed  Google Scholar 

  • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions acidobacteria, actinobacteria, proteobacteria, and verrucomicrobia. Appl Environ Microbiol 68:2391–2396

    PubMed Central  CAS  PubMed  Google Scholar 

  • Jansson JK, Neufeld JD, Moran MA, Gilbert JA (2012) Omics for understanding microbial functional dynamics. Environ Microbiol 14:1–3. doi:10.1111/j.1462-2920.2011.02518

    CAS  PubMed  Google Scholar 

  • Jia W, Li H, Zhao L, Nicholson JK (2008) Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 7:123–129. doi:10.1038/nrd2505

    CAS  PubMed  Google Scholar 

  • Johnson RA, Wichern DW (2007) Applied multivariate statistical analysis, 6th edn. Prentice Hall, Englewood Cliffs

    Google Scholar 

  • Jousset A, Rochat L, Lanoue A, Bonkowski M, Keel C, Scheu S (2011) Plants respond to pathogen infection by enhancing the antifungal gene expression of root-associated bacteria. Mol Plant Microbe Interact 24:352–358. doi:10.1094/MPMI-09-10-0208

    CAS  PubMed  Google Scholar 

  • Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ (2010) Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 44:354–360. doi:10.1097/MCG.0b013e3181c87e02

    PubMed  Google Scholar 

  • Kirk JL, Klironomos JN, Lee H, Trevors JT (2005) The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil. Environ Pollut 133:455–465. doi:10.1016/j.envpol.2004.06.002

    CAS  PubMed  Google Scholar 

  • Koch B, Worm J, Jensen LE, Hojberg O, Nybroe O (2001) Carbon limitation induces σs-dependent gene expression in Pseudomonas fluorescens in soil. Appl Environ Microbiol 67:3363–3370. doi:10.1128/AEM.67.8.3363-3370.2001

    PubMed Central  CAS  PubMed  Google Scholar 

  • Koukkou A-I, Vandera E (2011) Hydrocarbon-degrading soil bacteria: current research. In: Koukkou A-I (ed) Microbial bioremediation of non-metals: current research. Caister Academic Press, Norfolk, pp 93–117. ISBN 978-1-904455-83-7

    Google Scholar 

  • Kwak YS, Bonsall RF, Okubara PA, Paulitz TC, Thomashow LS, Weller DM (2012) Factors impacting the activity of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens against take-all of wheat. Soil Biol Biochem 54:48–56. doi:10.1016/j.soilbio.2012.05.012

    CAS  Google Scholar 

  • Kyselkova M, Kopecky J, Frapolli M, Defago G, Sagova-Mareckova M, Grundmann GL et al (2009) Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J 3:1127–1138. doi:10.1038/ismej.2009.61

    PubMed  Google Scholar 

  • Lee B, Lee S, Ryu MR (2012) Foliar aphid feeding recruits rhizosphere bacteria and primes plant immunity against pathogenic and nonpathogenic bacteria in pepper. Ann Bot 110:281–290. doi:10.1093/aob/mcs055

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lemanceau P, Corberand T, Gardan L, Latour X, Laguerre G, Boeuf-gras J-M et al (1995) Effect of two plant species, flax (Linum usitatissimum L.) and tomato (Lycopersicon esculentum Mill.), on the diversity of soil borne populations of fluorescent pseudomonads. Appl Environ Microbiol 61:1004–1012

    PubMed Central  CAS  PubMed  Google Scholar 

  • Leveau JHJ (2009) Life on leaves. Nature 461:741

    CAS  PubMed  Google Scholar 

  • Leveau JHJ, Tech JJ (2011) Grapevine microbiomics: Bacterial diversity on grape leaves and berries revealed by high-throughput sequence analysis of 16S rRNA amplicons. Acta Horticult 905:31–42

    Google Scholar 

  • Ley RE (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26:5–11. doi:10.1097/MOG.0b013e328333d751

    PubMed  Google Scholar 

  • Li X, LeBlanc J, Truong A, Vuthoori R, Chen SS et al (2011) A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS One 6:e26542. doi:10.1371/journal.pone.0026542

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lorenz P, Liebeton K, Niehaus F, Eck J (2002) Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol 13:572–577

    CAS  PubMed  Google Scholar 

  • Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. doi:10.1128/AEM. 71.12.8228-8235.2005

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556. doi:10.1146/annurev.micro.62.081307

    CAS  PubMed  Google Scholar 

  • Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Victor 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(7409):86–90

    PubMed Central  CAS  PubMed  Google Scholar 

  • Mark GL, Dow JM, Kiely PD, Higgings H, Haynes J, Baysse C et al (2005) Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe plant interactions. Proc Natl Acad Sci U S A 102:17454–17459. doi:10.1073/pnas.0506407102

    PubMed Central  CAS  PubMed  Google Scholar 

  • Marshall BJ, McGechie DB, Rogers PA, Glancy RJ (1985a) Pyloric campylobacter infection and gastroduodenal disease. Med J Aust 142:439–444

    CAS  PubMed  Google Scholar 

  • Marshall BJ, Armstrong JA, McGechie DB, Glancy RJ (1985b) Attempt to fulfil Koch’s postulates for pyloric Campylobacter. Med J Aust 142:436–439

    CAS  PubMed  Google Scholar 

  • Martin FP, Wang Y, Sprenger N, Yap IK, Lundstedt T et al (2008) Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol 4:157. doi:10.1038/msb4100190

    PubMed Central  PubMed  Google Scholar 

  • Martins G, Lauga B, Miot-Sertier C, Mercier A, Lonvaud A, Soulas M-L, Soulas G, de Masneuf-Pomaré I (2013) Characterization of epiphytic bacterial communities from grape, leaves, bark and soil of grapevine plants grown, and their relation. PLoS One 8(8):1–9

    Google Scholar 

  • Mavrodi OV, Mavrodi DV, Parejko JA, Thomashow LS, Weller DM (2012) Irrigation differentially impacts populations of indigenous antibiotic producing Pseudomonas spp. in the rhizosphere of wheat. Appl Environ Microbiol 78:3214–3220. doi:10.1128/AEM. 07968-11

    PubMed Central  CAS  PubMed  Google Scholar 

  • Mazumdar PMH (1995) Species and specificity: an interpretation of the history of immunology. Cambridge University Press, New York

    Google Scholar 

  • Mazurier S, Corberand T, Lemanceau P, Raaijmakers JM (2009) Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt. ISME J 3:977–991. doi:10.1038/ismej.2009.33

    CAS  PubMed  Google Scholar 

  • Mazzola M (2002) Mechanisms of natural soil suppressiveness to soil borne diseases. Antonie Van Leeuwenhoek 81:557–564. doi:10.1023/A:1020557523557

    CAS  PubMed  Google Scholar 

  • McLeod MP, Eltis LD (2008) Genomic insights into the aerobic pathways for degradation of organic pollutants. In: Diaz E (ed) Microbial degradation, Genomics and molecular biology. Caister Academic Press, Norfolk, pp 1–24. ISBN 978-1-904455-17-2

    Google Scholar 

  • Mendes R, Kruijt M, DeBruijn I, Dekkers E, VanderVoort M, Schneider JHM et al (2011) Deciphering the rhizosphere microbiome for disease suppressive bacteria. Science 332:1097–1100. doi:10.1126/science.1203980

    CAS  PubMed  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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Morgan C, Huttenhowr C (2012) Chapter 12: human microbiome analysis. PLoS Comput Biol. doi:10.1371/journal.pcbi.1002808

    PubMed Central  PubMed  Google Scholar 

  • Mosser JL, Bohlool BB, Brock TD (1974) Growth rates of Sulfolobus acidocaldarius in nature. J Bacteriol 118:1075–1081

    PubMed Central  CAS  PubMed  Google Scholar 

  • Munkvold GP, Marois JJ (1993) Efficacy of natural epiphytes and colonizers of grapevine pruning wounds for biological control of Eutypa dieback. Phytopathology 83:624–629

    Google Scholar 

  • Nasidze I, Li J, Quinque D, Tang K, Stoneking M (2009) Global diversity in the human salivary microbiome. Genome Res 19:636–643. doi:10.1101/gr.084616.108

    PubMed Central  CAS  PubMed  Google Scholar 

  • Nicholson JK, Holmes E, Wilson ID (2005) Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3:431–438. doi:10.1038/nrmicro1152

    CAS  PubMed  Google Scholar 

  • Okubara PA, Bonsall RF (2008) Accumulation of Pseudomonas-derived 2,4-diacetylphloroglucinol on wheat seedling roots is influenced by hostcultivar. Biol Control 46:322–331. doi:10.1016/j.biocontrol.2008.03.013

    CAS  Google Scholar 

  • Pearson RC, Goheen AC (eds) (2008) Compendium of grape diseases. APS Press, St. Paul

    Google Scholar 

  • Pechy-Tarr M, Borel N, Kupfer-Schmied P, Turner V, Binggeli O, Radovanovic D et al (2013) Control and host-dependent activation of insect toxin expression in a root-associated biocontrol pseudomonad. Environ Microbiol 15:736–750. doi:10.1111/1462-2920.12050

    CAS  PubMed  Google Scholar 

  • Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP et al (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11:1358–1375. doi:10.1111/j.1462-2920.2008.01863.x

    CAS  PubMed  Google Scholar 

  • Prakash O, Shouche Y, Jangid K, Kostka JE (2013) Microbial cultivation and the role of microbial resource centers in the omics era. Appl Microbiol Biotechnol 97:51–62

    CAS  PubMed  Google Scholar 

  • Raaijmakers JM, Weller DM (1998) Natural plant protection by 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline soils. Mol Plant Microbe Interact 11:144–152. doi:10.1094/MPMI.1998.11.2.144

    CAS  Google Scholar 

  • Rappe MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

    CAS  PubMed  Google Scholar 

  • Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12:2885–2893

    PubMed Central  PubMed  Google Scholar 

  • Rosenzweig N, Tiedje JM, Quensen JF III, Meng Q, Hao JJ (2012) Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Dis 96:718–725. doi:10.1094/PDIS-07-11-0571

    Google Scholar 

  • Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666

    CAS  PubMed  Google Scholar 

  • Schloss PD (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6:e1000844. doi:10.1371/journal.pcbi.1000844

    PubMed Central  PubMed  Google Scholar 

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi:10.1128/AEM.01541-09

    PubMed Central  CAS  PubMed  Google Scholar 

  • Schreiner K, Hagn A, Kyselkova M, Moenne-Loccoz Y, Welzl G, Munch JC et al (2010) Comparison of barley succession and take-all disease as environmental factors shaping the rhizobacterial community during take-all decline. Appl Environ Microbiol 76:4703–4712. doi:10.1128/AEM.00481-10

    PubMed Central  CAS  PubMed  Google Scholar 

  • Schwiertz A, Le Blay G, Blaut M (2000) Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA targeted oligonucleotide probes. Appl Environ Microbiol 66:375–382

    PubMed Central  CAS  PubMed  Google Scholar 

  • Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224

    PubMed Central  CAS  PubMed  Google Scholar 

  • Shi Y, Tyson GW, DeLong EF (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459:266–269. doi:10.1038/nature08055

    CAS  PubMed  Google Scholar 

  • Simu K, Hagstrom A (2004) Oligotrophic bacterioplankton with a novel single-cell life strategy. Appl Environ Microbiol 70:2445–2451

    PubMed Central  CAS  PubMed  Google Scholar 

  • Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291

    PubMed Central  CAS  PubMed  Google Scholar 

  • Sogin ML, Morrison HG, Huber JA et al (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103(32):12115–12120

    PubMed Central  CAS  PubMed  Google Scholar 

  • Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346

    CAS  PubMed  Google Scholar 

  • Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment front a planktonic marine archaeon. J Bacteriol 178:591–599

    PubMed Central  CAS  PubMed  Google Scholar 

  • Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245

    CAS  PubMed  Google Scholar 

  • Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787

    PubMed Central  CAS  PubMed  Google Scholar 

  • Turnbaugh PJ, Gordon JI (2008) An invitation to the marriage of metagenomics and metabolomics. Cell 134:708–713. doi:10.1016/j.cell.2008.08.025

    CAS  PubMed  Google Scholar 

  • Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER et al (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031. doi:10.1038/nature05414

    PubMed  Google Scholar 

  • Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A et al (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484. doi:10.1038/nature07540

    PubMed Central  CAS  PubMed  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

    CAS  PubMed  Google Scholar 

  • van der Meer JR (2008) A genomic view on the evolution of catabolic pathways and bacterial adaptation to xenobiotic compounds. In: Diaz E (ed) Genomics and molecular biology. Caister Academic Press, Madrid, pp 219–269

    Google Scholar 

  • Van-Camp L, Bujarrabal B, Gentile AR, Jones RJA, Montanarella L, Olazabal C et al (2004) Reports of the technical working groups established under the thematic strategy for soil protection. Office for Official Publication of the European Communities, Luxembourg, p 872

    Google Scholar 

  • Varela C, Siebert T, Cozzolino D, Rose L, McLean H, Henschke PA (2009) Discovering a chemical basis for differentiating wines made by fermentation with ‘wild’ indigenous and inoculated yeasts: role of yeast volatile compounds. Aust J Grape Wine Res 15:238–248

    CAS  Google Scholar 

  • Vaughan EE, Schut F, Heilig GHJ, Zoetendal EG, de Vos WM, Akkermans ADL (2000) A molecular view of the intestinal ecosystem. Curr Issues Intest Microbiol 1:1–12

    CAS  PubMed  Google Scholar 

  • Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M et al (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3:179–189

    CAS  PubMed  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D et al (2004a) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. doi:10.1126/science.1093857

    CAS  PubMed  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 YH, Smith HO (2004b) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74

    CAS  PubMed  Google Scholar 

  • Verginer M, Leitner E, Berg G (2010) Production of volatile metabolites by grape associated microorganisms. J Agric Food Chem 58(14):8344–8350

    CAS  PubMed  Google Scholar 

  • Wallner G, Fuchs B, Spring S, Beisker W, Amann RI (1997) Flow sorting of micro organisms for molecular analysis. Appl Environ Microbiol 63:4223–4231

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. doi:10.1128/AEM. 00062-07

    PubMed Central  CAS  PubMed  Google Scholar 

  • Weinert N, Piceno Y, Ding GC, Meincke R, Heuer H, Berg G et al (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar dependent taxa. FEMS Microbiol Ecol 75:497–506. doi:10.1111/j.1574-6941.2010.01025.x

    CAS  PubMed  Google Scholar 

  • Weller DM, Raaijmakers JM, McSpadden Gardener BB, Thomashow LS (2002) Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol 40:309–348. doi:10.1146/ annurev.phyto.40.030402.110010

    CAS  PubMed  Google Scholar 

  • Whang K, Hattori T (1988) Oligotrophic bacteria from rendzina forest soil. Antonie Van Leeuwenhoek 54:19–36

    CAS  PubMed  Google Scholar 

  • Widenfalk A, Bertilsson S, Sundh I, Goedkoop W (2008) Effects of pesticides on community composition and activity of sediment microbes–responses at various levels of microbial community organization. Environ Pollut 152(3):576–584

    CAS  PubMed  Google Scholar 

  • Yang JW, Yi HS, Kim H, Lee B, Lee S, Ghim SY, Ryu CM (2011) Whitefly infestation of pepper plants elicits defence responses against bacterial pathogens in leaves and roots and changes the below-ground microflora. J Ecol 99:46–56

    CAS  Google Scholar 

  • Zijnge V, van Leeuwen MB, Degener JE, Abbas F, Thurnheer T et al (2010) Oral biofilm architecture on natural teeth. PLoS One 5:e9321. doi:10.1371/journal.pone.0009321

    PubMed Central  PubMed  Google Scholar 

  • Zoetendal EG, Ben-Amor K, Harmsen HJM, Schut F, Akkermans ADL, de Vos WM (2002) Quantification of uncultured Ruminococcus obeum-like bacteria in human fecal samples by fluorescent in situ hybridization and flow cytometry using 16S rRNA-targeted probes. Appl Environ Microbiol 68:4225–4232

    PubMed Central  CAS  PubMed  Google Scholar 

  • Zysko A, Sanguin H, Hayes A, Wardleworth L, Zeef LAH, Sim A et al (2012) Transcriptional response of Pseudomonas aeruginosa to a phosphate-deficient Lolium perenne rhizosphere. Plant Soil 359:25–44. doi:10.1007/s11104-011-1060-z

    CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India

    Pankaj Sharma Ph.D.

  2. Toronto General Research Institute, University Health Network, Toronto, ON, Canada

    Vijaya Brahma Ph.D.

  3. Department of Dental Microbiology, Theerthankar Mahaveer University, Moradabad, Uttar Pradesh, India

    Anamika Sharma Ph.D.

  4. Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana, 141004, Punjab, India

    R. K. Dubey Ph.D.

  5. Schools of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India

    G. S. Sidhu Ph.D. & P. K. Malhotra Ph.D.

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  1. Pankaj Sharma Ph.D.
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  2. Vijaya Brahma Ph.D.
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  3. Anamika Sharma Ph.D.
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  4. R. K. Dubey Ph.D.
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  5. G. S. Sidhu Ph.D.
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  6. P. K. Malhotra Ph.D.
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Correspondence to R. K. Dubey Ph.D. .

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Editors and Affiliations

  1. Department of Genomics, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, West Bengal, India

    Debmalya Barh

  2. University of Agriculture, Centre of Biochemistry and Biotechnology, Faisalabad, Pakistan

    Muhammad Sarwar Khan

  3. Department of Plant Biology, North Carolina State University, Raleigh, North Carolina, USA

    Eric Davies

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Sharma, P., Brahma, V., Sharma, A., Dubey, R.K., Sidhu, G.S., Malhotra, P.K. (2015). Microbiomics: An Approach to Community Microbiology. In: Barh, D., Khan, M., Davies, E. (eds) PlantOmics: The Omics of Plant Science. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2172-2_22

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