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Microbial Genome Diversity and Microbial Genome Sequencing

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Microbial Genomics in Sustainable Agroecosystems

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Abstract

The role of microbiome in agroecosystems has evolved due to improvements in microbial diversity analysis methods. The journey of microbial diversity estimation progressed from culture-dependent to culture-independent methods. The culture-dependent methods are important in finding the microbial diversity of different environments; however, they are immensely biased toward the dominant microorganisms present in a community. With the advancement in sequencing techniques and genomics, the community exploration using culture-independent methods has commenced a new understanding of microbial interactions with their surroundings. Molecular studies of different environmental communities have uncovered <1% of the total number of prokaryotic species representing the cultivable fraction. This chapter summarizes the different methods to acquire a microbial diversity that may eventually enhance plant growth in sustainable agriculture and may often play a role in the management of environmental problems. The merits and demerits of the commonly used molecular methods to investigate microbial communities are discussed. The potential applications of next-generation sequencing techniques for a comprehensive assessment of microbial diversity have been illustrated.

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References

  • Abubucker S et al (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8:e1002358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Allen EE, Banfield JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3:489

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J (2016) High throughput sequencing: an overview of sequencing chemistry. Indian J Microbiol 56:394–404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arnold AE, Mejía LC, Kyllo D, Rojas EI, Maynard Z, Robbins N, Herre EA (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci 100:15649–15654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ashburner M et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ashelford K et al (2011) Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol 12:R28

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Azam S et al (2012) Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. Am J Bot 99:186–192

    Article  CAS  PubMed  Google Scholar 

  • Bååth E, Díaz-Raviña M, Frostegård Å, Campbell CDJA (1998) Effect of metal-rich sludge amendments on the soil microbial community. Appl Environ Microbiol 64:238–245

    PubMed  PubMed Central  Google Scholar 

  • Bae J-W et al (2005) Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl Environ Microbiol 71:8825–8835

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Banowetz GM, Whittaker GW, Dierksen KP, Azevedo MD, Kennedy AC, Griffith SM, Steiner JJ (2006) Fatty acid methyl ester analysis to identify sources of soil in surface water. J Environ Qual 35:133–140

    Article  CAS  PubMed  Google Scholar 

  • Bartram A, Lynch M, Stearns J, Moreno-Hagelsieb G, Neufeld J (2011) Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol 77(11):3846–3852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Behie SW, Moreira CC, Sementchoukova I, Barelli L, Zelisko PM, Bidochka MJ (2017) Carbon translocation from a plant to an insect-pathogenic endophytic fungus. Nat Commun 8:14245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bentley DR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63:2647–2653

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bowers J et al (2009) Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6:593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buggs RJ et al (2012) Next-generation sequencing and genome evolution in allopolyploids. Am J Bot 99:372–382

    Article  PubMed  Google Scholar 

  • Calvo P, Nelson L, Kloepper JW (2014) Agricultural uses of plant biostimulants. Plant Soil 383:3–41

    Article  CAS  Google Scholar 

  • Clarholm M (1994) The microbial loop in soil. In: Ritz K, Dighton J, Giller KE (eds) Beyond the biomass. Wiley-Sayce, Chichester, pp 221–230

    Google Scholar 

  • Clarke J, Wu H-C, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265

    Article  CAS  PubMed  Google Scholar 

  • Clegg CD, Ritz K, Griffiths BS (2000) % G+ C profiling and cross hybridisation of microbial DNA reveals great variation in below-ground community structure in UK upland grasslands. Appl Soil Ecol 14:125–134

    Article  Google Scholar 

  • Colwell RK (2009) Biodiversity: concepts, patterns, and measurement. In: Levin SA (ed) The Princeton guide to ecology. Princeton University Press, Princeton, NJ, pp 257–263

    Chapter  Google Scholar 

  • Cook H, Ussery DW (2013) Sigma factors in a thousand E. coli genomes. Environ Microbiol 15:3121–3129

    Article  CAS  PubMed  Google Scholar 

  • Derry A, Staddon W, Kevan P, Trevors J (1999) Functional diversity and community structure of micro-organisms in three arctic soils as determined by sole-carbon-source-utilization. Biodivers Conserv 8:205–221

    Article  Google Scholar 

  • Deschamps S, Campbell MA (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Mol Breed 25:553–570

    Article  CAS  Google Scholar 

  • Đokić L, Savić M, Narančić T, Vasiljević B (2010) Metagenomic analysis of soil microbial communities. Arch Biol Sci 62:559–564

    Article  Google Scholar 

  • Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Am J Bot 99:175–185

    Article  CAS  PubMed  Google Scholar 

  • Eid J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  • El-Metwally S, Hamza T, Zakaria M, Helmy M (2013) Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol 9:e1003345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fakruddin M, Mannan KSB (2012) Next generation sequencing technologies-principles and prospects. Res Rev Biosci 6:240–247

    Google Scholar 

  • Fakruddin M, Mannan K (2013) Methods for analyzing diversity of microbial communities in natural environments. Ceylon J Sci 42

    Google Scholar 

  • Fisher MM, Triplett EWA (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fleischmann RD et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    Article  CAS  PubMed  Google Scholar 

  • Fraser CM et al (1995) The minimal gene complement of mycoplasma genitalium. Science 270:397–404

    Article  CAS  PubMed  Google Scholar 

  • Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK (2015) Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. Plant Methods 11:19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghazanfar S, Azim A, Ghazanfar MA, Anjum M, Begum I (2010) Metagenomics and its application in soil microbial community studies: biotechnological prospects. J Anim Plant Sci 6:611–622

    Google Scholar 

  • Giovannoni SJ, Britschgi TB, Moyer CL, Field KGJN (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60

    Article  CAS  PubMed  Google Scholar 

  • Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S (2010) METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics. Bioinformatics 26:2631–2632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goodfellow M, O’Donnell AG (1993) Handbook of new bacterial systematics. Academic Press, London/San Diego

    Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  PubMed  Google Scholar 

  • Greene EA, Voordouw G (2003) Analysis of environmental microbial communities by reverse sample genome probing. J Microbiol Methods 53:211–219

    Article  CAS  PubMed  Google Scholar 

  • Guo J et al (2008) Four-color DNA sequencing with 3′-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci 105:9145–9150

    Article  PubMed  PubMed Central  Google Scholar 

  • Harpole W (2010) Neutral theory of species diversity. Nat Educ Knowl 3(10):60

    Google Scholar 

  • Harris TD et al (2008) Single-molecule DNA sequencing of a viral genome. Science 320:106–109

    Article  CAS  PubMed  Google Scholar 

  • He R et al (2012) Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity. Am J Bot 99:232–247

    Article  CAS  PubMed  Google Scholar 

  • Hill G et al (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15:25–36

    Article  Google Scholar 

  • Howorka S, Cheley S, Bayley H (2001) Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotechnol 19:636

    Article  CAS  PubMed  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    CAS  PubMed  PubMed Central  Google Scholar 

  • Huse SM, Welch DBM, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML (2014) VAMPS: a website for visualization and analysis of microbial population structures. BMC bioinformatics 15:41

    Article  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome research: gr. 120618.120111

    Google Scholar 

  • Ilut DC, Coate JE, Luciano AK, Owens TG, May GD, Farmer A, Doyle JJ (2012) A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. Am J Bot 99:383–396

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kauppinen J, Pelkonen J, Katila M-L (1994) RFLP analysis of Mycobacterium malmoense strains using ribosomal RNA gene probes: an addition tool to examine intraspecies variation. J Microbiol Methods 19:261–267

    Article  CAS  Google Scholar 

  • Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58:169–188

    Article  CAS  PubMed  Google Scholar 

  • Lagesen K, Ussery DW, Wassenaar TM (2010) Genome update: the 1000th genome–a cautionary tale. Microbiology 156:603–608

    Article  CAS  PubMed  Google Scholar 

  • Lagier J-C et al (2018) Culturing the human microbiota and culturomics. Nat Rev Microbiol:1

    Google Scholar 

  • Lai Z et al (2012) Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am J Bot 99:209–218

    Article  CAS  PubMed  Google Scholar 

  • Landegren U, Kaiser R, Sanders J, Hood L (1988) A ligase-mediated gene detection technique. Science 241:1077–1080

    Article  CAS  PubMed  Google Scholar 

  • Langille MG et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686

    Article  CAS  PubMed  Google Scholar 

  • Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M (2010) Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 132:17961–17972

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lingner T, Aßhauer KP, Schreiber F, Meinicke P (2011) CoMet—a web server for comparative functional profiling of metagenomes. Nucleic Acids Res 39:W518–W523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu W-T, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522

    CAS  PubMed  PubMed Central  Google Scholar 

  • MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang Y-J, White DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65:3566–3574

    CAS  PubMed  PubMed Central  Google Scholar 

  • Markowitz VM et al (2011) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122

    Article  CAS  PubMed Central  Google Scholar 

  • Masciarelli O, Llanes A, Luna V (2014) A new PGPR co-inoculated with Bradyrhizobium japonicum enhances soybean nodulation. Microbiol Res 169:609–615

    Article  CAS  PubMed  Google Scholar 

  • Matsen FA, Evans SN (2013) Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. Plos ONE 8:e56859

    Article  CAS  PubMed  Google Scholar 

  • McKain MR et al (2012) Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). Am J Bot 99:397–406

    Article  PubMed  Google Scholar 

  • McKernan K, Blanchard A, Kotler L, Costa G (2016) Reagents, methods, and libraries for bead-based sequencing. Google Patents

    Google Scholar 

  • Mende DR et al (2012) Assessment of metagenomic assembly using simulated next generation sequencing data. Plos one 7:e31386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mendes R et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science:1203980

    Google Scholar 

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31

    Article  CAS  PubMed  Google Scholar 

  • Meyer F et al (2008) The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinf 9:386

    Article  CAS  Google Scholar 

  • Mizrahi-Man O, Davenport ER, Gilad Y (2013) Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. Plos one 8:e53608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moorthie S, Mattocks CJ, Wright CF (2011) Review of massively parallel DNA sequencing technologies. HUGO J 5:1–12

    Article  PubMed  PubMed Central  Google Scholar 

  • Morris CE, Monier J-M (2003) The ecological significance of biofilm formation by plant-associated bacteria. Annu Rev Phytopathol 41:429–453

    Article  CAS  PubMed  Google Scholar 

  • Moyer CL, Dobbs FC, Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 60:871–879

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl Environ Microbiol 62:2501–2507

    CAS  PubMed  PubMed Central  Google Scholar 

  • Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317–322

    Article  CAS  PubMed  Google Scholar 

  • Myllykangas S, Buenrostro J, Ji HP (2012) Overview of sequencing technology platforms. In: Bioinformatics for high throughput sequencing. Springer, Berlin, pp 11–25

    Chapter  Google Scholar 

  • Narisawa K, Hambleton S, Currah RS (2007) Heteroconium chaetospira, a dark septate root endophyte allied to the Herpotrichiellaceae (Chaetothyriales) obtained from some forest soil samples in Canada using bait plants. Mycoscience 48:274–281

    Article  Google Scholar 

  • Naum M, Lampel KA (2011) Analytical methods | DNA-based assays. In: Fuquay JW, ed. Encyclopedia of dairy sciences, 2nd edn. Academic Press, San Diego pp 221–225

    Google Scholar 

  • NCBI (2018) National center for biotechnology information genome browser. https://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt. Accessed 2018

  • Nielsen HB et al (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 32:822

    Article  CAS  PubMed  Google Scholar 

  • Niemi RM, Heiskanen I, Wallenius K, Lindström K (2001) Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods 45:155–165

    Article  Google Scholar 

  • Ondov BD, Bergman NH, Phillippy AM (2011) Interactive metagenomic visualization in a Web browser. BMC bioinformatics 12:385

    Article  PubMed  PubMed Central  Google Scholar 

  • Orlando L et al (2011) True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res 21(10):1705–1719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Orlewska K, Piotrowska-Seget Z, Cycon M (2018) Use of the PCR-DGGE Method for the Analysis of the Bacterial Community Structure in Soil Treated With the Cephalosporin Antibiotic Cefuroxime and/or Inoculated With a Multidrug-Resistant Pseudomonas putida Strain MC1. Front Microbiol 9:1387

    Article  PubMed  PubMed Central  Google Scholar 

  • Osborn AM, Moore ER, Timmis KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50

    Article  CAS  PubMed  Google Scholar 

  • Ozsolak F et al (2009) Direct RNA sequencing. Nature 461:814

    Article  CAS  PubMed  Google Scholar 

  • Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52:413–435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pop M (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform 10:354–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  CAS  PubMed  Google Scholar 

  • Reysenbach A-L, Giver LJ, Wickham GS, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417–3418

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ronaghi M, Uhlén M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate. Science 281:363–365

    Article  CAS  PubMed  Google Scholar 

  • Rothberg JM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348

    Article  CAS  PubMed  Google Scholar 

  • Rudi K, Zimonja M, Trosvik P, Naes T (2007) Use of multivariate statistics for 16S rRNA gene analysis of microbial communities. Int J Food Microbiol 120:95–99

    Article  CAS  PubMed  Google Scholar 

  • Sarethy IP, Pan S, Danquah MK (2014) Modern taxonomy for microbial diversity. In: Biodiversity-The dynamic balance of the planet. InTech Open, London

    Google Scholar 

  • Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310

    Article  CAS  PubMed  Google Scholar 

  • Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5:e75

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shendure J et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732

    Article  CAS  PubMed  Google Scholar 

  • Shulaev V et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Sørheim R, Torsvik VL, Goksøyr J (1989) Phenotypical divergences between populations of soil bacteria isolated on different media. Microb Ecol 17:181–192

    Article  PubMed  Google Scholar 

  • Steele PR, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack J, Pires JC (2012) Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae. Am J Bot 99:330–348

    Article  CAS  PubMed  Google Scholar 

  • Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for a nonmodel plant species1. Am J Bot 99:257–266

    Article  CAS  PubMed  Google Scholar 

  • Tabacchioni S, Chiarini L, Bevivino A, Cantale C, Dalmastri C (2000) Bias caused by using different isolation media for assessing the genetic diversity of a natural microbial population. Microb Ecol 40:169–176

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Theron J, Cloete T (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26:37–57

    Article  CAS  PubMed  Google Scholar 

  • Thompson JF, Steinmann KE (2010) Single molecule sequencing with a HeliScope genetic analysis system. Curr Protoc Mol Biol 92:7.10. 11–17.10. 14

    Google Scholar 

  • Tiedje JM, Asuming-Brempong S, Nüsslein K, Marsh TL, Flynn SJ (1999) Opening the black box of soil microbial diversity. Appl Soil Ecol 13:109–122

    Article  Google Scholar 

  • Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities—a review. J Ind Microbiol 17:170–178

    CAS  Google Scholar 

  • Torsvik V, Daae FL, Sandaa R-A, Øvreås L (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. J Biotechnol 64:53–62

    Article  CAS  PubMed  Google Scholar 

  • Trevors J (1998) Bacterial biodiversity in soil with an emphasis on chemically-contaminated soils. Water Air Soil Pollut 101:45–67

    Article  CAS  Google Scholar 

  • Tyson GW et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37

    Article  CAS  PubMed  Google Scholar 

  • Usuki F, Narisawa K (2007) A mutualistic symbiosis between a dark septate endophytic fungus, Heteroconium chaetospira, and a nonmycorrhizal plant, Chinese cabbage. Mycologia 99:175–184

    Article  CAS  PubMed  Google Scholar 

  • Van der Heijden MG et al (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396:69

    Article  CAS  Google Scholar 

  • von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  • Wu M, Scott AJ (2012) Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28:1033–1034

    Article  CAS  PubMed  Google Scholar 

  • Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227–239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zalapa JE et al (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193–208

    Article  CAS  PubMed  Google Scholar 

  • Zavala-Gonzalez EA et al (2017) Arabidopsis thaliana root colonization by the nematophagous fungus Pochonia chlamydosporia is modulated by jasmonate signaling and leads to accelerated flowering and improved yield. New Phytol 213:351–364

    Article  CAS  PubMed  Google Scholar 

  • Zeyaullah M et al (2009) Metagenomics-An advanced approach for noncultivable micro-organisms. Biotechnol Mol Biol Rev 4:49–54

    CAS  Google Scholar 

  • Zhao L et al (2012) Characterization of microbial diversity and community in water flooding oil reservoirs in China. World J Microbiol 28:3039–3052

    Article  Google Scholar 

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  1. School of Basic Sciences, Indian Institute of Technology (IIT), Mandi, Himachal Pradesh, India

    Aditi Jangid & Tulika Prakash

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  1. Aditi Jangid
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  2. Tulika Prakash
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Editors and Affiliations

  1. Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India

    Vijay Tripathi

  2. Department of Forestry, North Eastern Regional Institute of Science and Technology (Deemed To Be University-MHRD), Itanagar, Arunachal Pradesh, India

    Pradeep Kumar

  3. Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India

    Pooja Tripathi

  4. Department of Botany, Kamla Nehru P.G. College, Raebareli, Uttar Pradesh, India

    Amit Kishore

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Jangid, A., Prakash, T. (2019). Microbial Genome Diversity and Microbial Genome Sequencing. In: Tripathi, V., Kumar, P., Tripathi, P., Kishore, A. (eds) Microbial Genomics in Sustainable Agroecosystems. Springer, Singapore. https://doi.org/10.1007/978-981-13-8739-5_10

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