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Application of Molecular and Sequencing Techniques in Analysis of Microbial Diversity in Agroecosystem

  • Shobhika Parmar
  • Vijay Kumar Sharma
  • Jitendra Kumar
Chapter

Abstract

Ecological role of majority of microorganisms including bacteria, archaea and fungi, as well as viruses, is so important that life on Earth would not be possible without them. These microbes interact together with their environment in a very complex way that often defines the community structure and their ecological function. Further due to their extremely small size, there is a huge gap between the present knowledge and predictions. Recent advances in molecular biology especially in the DNA sequencing technology have provided more opportunities for comprehensive studies of these multifaceted microbes in agroecosystems. This chapter focuses on various recent molecular and sequencing techniques used to study microbial diversity.

Keywords

DNA sequencing technology Microbial diversity Microbial interactions Microbial community analysis Techniques and methods Agroecosystem 

References

  1. Abed RM, Al-Kharusi S, Prigent S, Headley T (2014) Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial mats from a constructed wetland. PLoS One 9(12):e114570PubMedPubMedCentralCrossRefGoogle Scholar
  2. Adil E (2015) Corrective measures of denaturing gradient gel electrophoresis limitations. J Environ Sci Technol 8(1):1–12CrossRefGoogle Scholar
  3. Agasti SS, Liong M, Peterson VM, Lee H, Weissleder R (2012) Photocleavable DNA barcode–antibody conjugates allow sensitive and multiplexed protein analysis in single cells. J Am Chem Soc 134(45):18499–18502PubMedPubMedCentralCrossRefGoogle Scholar
  4. Agrawal PK, Agrawal S, Shrivastava R (2015) Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem. 3 Biotech 5(6):853–866PubMedPubMedCentralCrossRefGoogle Scholar
  5. Ainsworth TD, Fine M, Blackall LL, Hoegh-Guldberg O (2006) Fluorescence in situ hybridization and spectral imaging of coral-associated bacterial communities. Appl Environ Microbiol 72(4):3016–3020PubMedPubMedCentralCrossRefGoogle Scholar
  6. Al-Bulushi IM, Bani-Uraba MS, Guizani NS, Al-Khusaibi MK, Al-Sadi AM (2017) Illumina MiSeq sequencing analysis of fungal diversity in stored dates. BMC Microbiol 17(1):72PubMedPubMedCentralCrossRefGoogle Scholar
  7. Alemzadeh E, Haddad R, Ahmadi AR (2014) Phytoplanktons and DNA barcoding: characterization and molecular analysis of phytoplanktons on the Persian Gulf. Iranian journal of microbiology 6(4):296PubMedPubMedCentralGoogle Scholar
  8. Alzubaidy H, Essack M, Malas TB, Bokhari A, Motwalli O, Kamanu FK et al (2016) Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea. Gene 576(2):626–636PubMedCrossRefPubMedCentralGoogle Scholar
  9. Amann R, Fuchs BM (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6(5):339PubMedCrossRefPubMedCentralGoogle Scholar
  10. Anderson TH (2003) Microbial eco-physiological indicators to asses soil quality. Agric Ecosyst Environ 98(1–3):285–293CrossRefGoogle Scholar
  11. Antonella P, Luca G (2013) The quantitative real-time PCR applications in the monitoring of marine harmful algal bloom (HAB) species. Environ Sci Pollut Res 20(10):6851–6862CrossRefGoogle Scholar
  12. Aquilanti L, Favilli F, Clementi F (2004) Comparison of different strategies for isolation and preliminary identification of Azotobacter from soil samples. Soil Biol Biochem 36(9):1475–1483CrossRefGoogle Scholar
  13. Arnot DE, Roper C, Bayoumi RA (1993) Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circumsporozoite gene can genetically barcode isolates. Mol Biochem Parasitol 61(1):15–24PubMedCrossRefPubMedCentralGoogle Scholar
  14. Avaniss-Aghajani E, Jones K, Holtzman A, Aronson T, Glover N, Boian M et al (1996) Molecular technique for rapid identification of mycobacteria. J Clin Microbiol 34(1):98–102PubMedPubMedCentralGoogle Scholar
  15. Barea JM (2015) Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions. J Soil Sci Plant Nutr 15(2):261–282Google Scholar
  16. Barea JM, Pozo MJ, Azcon R, Azcon-Aguilar C (2005) Microbial co-operation in the rhizosphere. J Exp Bot 56(417):1761–1778PubMedCrossRefPubMedCentralGoogle Scholar
  17. Beaulieu R, López-Mondéjar R, Tittarelli F, Ros M, Pascual JA (2011) qRT-PCR quantification of the biological control agent Trichoderma harzianum in peat and compost-based growing media. Bioresour Technol 102(3):2793–2798PubMedCrossRefPubMedCentralGoogle Scholar
  18. Blackwood CB, Marsh T, Kim SH, Paul EA (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 69(2):926–932PubMedPubMedCentralCrossRefGoogle Scholar
  19. Bohorquez LC, Delgado-Serrano L, López G, Osorio-Forero C, Klepac-Ceraj V, Kolter R et al (2012) In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes. Microb Ecol 63(1):103–115PubMedCrossRefPubMedCentralGoogle Scholar
  20. Bora N (2015) Actinobacterial diversity and dynamics as revealed by denaturing gradient gel electrophoresis. In: Diversity, dynamics and functional role of actinomycetes on European smear ripened cheeses. Springer, Cham, pp 103–136Google Scholar
  21. Bourgeois E, Dequiedt S, Lelièvre M, Van Oort F, Lamy I, Maron PA, Ranjard L (2015) Positive effect of the Miscanthus bioenergy crop on microbial diversity in wastewater-contaminated soil. Environ Chem Lett 13(4):495–501CrossRefGoogle Scholar
  22. Brandt ME, Padhye AA, Mayer LW, Holloway BP (1998) Utility of random amplified polymorphic DNA PCR and TaqMan automated detection in molecular identification of Aspergillus fumigatus. J Clin Microbiol 36(7):2057–2062PubMedPubMedCentralGoogle Scholar
  23. Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7(9):1466–1479PubMedCrossRefPubMedCentralGoogle Scholar
  24. Brussaard L, De Ruiter PC, Brown GG (2007) Soil biodiversity for agricultural sustainability. Agric Ecosyst Environ 121(3):233–244CrossRefGoogle Scholar
  25. Caffaro-Filho RA, Fantinatti-Garboggini F, Durrant LR (2007) Quantitative analysis of Terminal Restriction Fragment Length Polymorphism (T-RFLP) microbial community profiles: peak height data showed to be more reproducible than peak area. Braz J Microbiol 38(4):736–738CrossRefGoogle Scholar
  26. Cartwright J, Dzantor EK, Momen B (2016) Soil microbial community profiles and functional diversity in limestone cedar glades. Catena 147:216–224CrossRefGoogle Scholar
  27. Castiglioni B, Rizzi E, Frosini A, Sivonen K, Rajaniemi P, Rantala A et al (2004) Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol 70(12):7161–7172PubMedPubMedCentralCrossRefGoogle Scholar
  28. Chandra S, Nalapeta S, Nehra S, Varshney AK, Mathur N, Trivedi PC, Medicherla KM (2010) The diversity analysis of the microbial community in wastewater by Amplified rDNA Restriction Analysis (ARDRA). J Ecobiotechnol 2(4):51–55Google Scholar
  29. Cho JC, Tiedje JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67(8):3677–3682PubMedPubMedCentralCrossRefGoogle Scholar
  30. Choudhary M, Jat HS, Datta A, Yadav AK, Sapkota TB, Mondal S et al (2018) Sustainable intensification influences soil quality, biota, and productivity in cereal-based agroecosystems. Appl Soil Ecol 126:189–198CrossRefGoogle Scholar
  31. Chourasiya D, Sharma MP, Maheshwari HS, Ramesh A, Sharma SK, Adhya TK (2017) Microbial diversity and soil health in tropical agroecosystems. In: Advances in soil microbiology: recent trends and future prospects. Springer, Singapore, p 19–35CrossRefGoogle Scholar
  32. Classen AT, Boyle SI, Haskins KE, Overby ST, Hart SC (2003) Community-level physiological profiles of bacteria and fungi: plate type and incubation temperature influences on contrasting soils. FEMS Microbiol Ecol 44(3):319–328PubMedCrossRefPubMedCentralGoogle Scholar
  33. Cowan RS, Chase MW, Kress WJ, Savolainen V (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55(3):611–616CrossRefGoogle Scholar
  34. Cristescu ME (2014) From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol 29(10):566–571PubMedCrossRefPubMedCentralGoogle Scholar
  35. Croes S, Weyens N, Colpaert J, Vangronsveld J (2015) Characterization of the cultivable bacterial populations associated with field grown B rassica napus L.: an evaluation of sampling and isolation protocols. Environ Microbiol 17(7):2379–2392PubMedCrossRefPubMedCentralGoogle Scholar
  36. Cummings PJ, Ahmed R, Durocher JA, Jessen A, Vardi T, Obom KM (2013) Pyrosequencing for microbial identification and characterization. JoVE (J Visualized Exp) 78:e50405Google Scholar
  37. Daquiado AR, Kuppusamy S, Kim SY, Kim JH, Yoon YE, Kim PJ et al (2016) Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil. Appl Soil Ecol 108:84–91CrossRefGoogle Scholar
  38. Das B, Chakrabarti K (2013) Assessment of community level physiological profiles and molecular diversity of soil bacteria under different cropping systems. Turk J Agric For 37(4):468–474CrossRefGoogle Scholar
  39. de Vere N, Rich TC, Ford CR, Trinder SA, Long C, Moore CW et al (2012) DNA barcoding the native flowering plants and conifers of Wales. PLoS One 7(6):e37945PubMedPubMedCentralCrossRefGoogle Scholar
  40. De Vrieze J, Ijaz UZ, Saunders AM, Theuerl S (2018) Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion. Sci Rep 8(1):16818PubMedPubMedCentralCrossRefGoogle Scholar
  41. DeCoste NJ, Gadkar VJ, Filion M (2011) Relative and absolute quantitative real-time PCR-based quantifications of hcnC and phlD gene transcripts in natural soil spiked with Pseudomonas sp. strain LBUM300. Appl Environ Microbiol 77(1):41–47PubMedCrossRefPubMedCentralGoogle Scholar
  42. Delgado S, Mayo B (2004) Phenotypic and genetic diversity of Lactococcus lactis and Enterococcus spp. strains isolated from Northern Spain starter-free farmhouse cheeses. Int J Food Microbiol 90(3):309–319PubMedCrossRefPubMedCentralGoogle Scholar
  43. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243(4896):1360–1363PubMedCrossRefPubMedCentralGoogle Scholar
  44. Demidenko NV, Penin AA (2012) Comparative analysis of gene expression level by quantitative real-time PCR has limited application in objects with different morphology. PLoS One 7(5):e38161PubMedPubMedCentralCrossRefGoogle Scholar
  45. Derveaux S, Vandesompele J, Hellemans J (2010) How to do successful gene expression analysis using real-time PCR. Methods 50(4):227–230PubMedCrossRefPubMedCentralGoogle Scholar
  46. Dhal PK, Islam E, Kazy SK, Sar P (2011) Culture-independent molecular analysis of bacterial diversity in uranium-ore/-mine waste-contaminated and non-contaminated sites from uranium mines. 3 Biotech 1(4):261–272PubMedPubMedCentralCrossRefGoogle Scholar
  47. Doi H, Takahara T, Minamoto T, Matsuhashi S, Uchii K, Yamanaka H (2015) Droplet digital polymerase chain reaction (PCR) outperforms real-time PCR in the detection of environmental DNA from an invasive fish species. Environ Sci Technol 49(9):5601–5608PubMedCrossRefPubMedCentralGoogle Scholar
  48. Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15(1):3–11CrossRefGoogle Scholar
  49. Dunbar J, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66(7):2943–2950PubMedPubMedCentralCrossRefGoogle Scholar
  50. Eevers N, Hawthorne JR, White JC, Vangronsveld J, Weyens N (2016) Exposure of Cucurbita pepo to DDE-contamination alters the endophytic community: a cultivation dependent vs a cultivation independent approach. Environ Pollut 209:147–154PubMedCrossRefPubMedCentralGoogle Scholar
  51. Eichner CA, Erb RW, Timmis KN, Wagner-Döbler I (1999) Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community. Appl Environ Microbiol 65(1):102–109PubMedPubMedCentralGoogle Scholar
  52. Fierer N, Jackson JA, Vilgalys R, Jackson RB (2005) Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71(7):4117–4120PubMedPubMedCentralCrossRefGoogle Scholar
  53. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65(10):4630–4636PubMedPubMedCentralGoogle Scholar
  54. Frąc M, Oszust K, Lipiec J (2012) Community level physiological profiles (CLPP), characterization and microbial activity of soil amended with dairy sewage sludge. Sensors 12(3):3253–3268PubMedCrossRefPubMedCentralGoogle Scholar
  55. Franklin RB, Taylor DR, Mills AL (1999) Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD). J Microbiol Methods 35(3):225–235PubMedCrossRefPubMedCentralGoogle Scholar
  56. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci 103(35):13104–13109PubMedCrossRefPubMedCentralGoogle Scholar
  57. Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, Brown JH (2008) A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci 105(22):7774–7778PubMedCrossRefPubMedCentralGoogle Scholar
  58. Gao W, Zhang W, Meldrum DR (2011) RT-qPCR based quantitative analysis of gene expression in single bacterial cells. J Microbiol Methods 85(3):221–227PubMedCrossRefPubMedCentralGoogle Scholar
  59. Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57(8):2351–2359PubMedPubMedCentralGoogle Scholar
  60. Genney DR, Anderson IC, Alexander IJ (2006) Fine-scale distribution of pine ectomycorrhizas and their extramatrical mycelium. New Phytol 170(2):381–390PubMedCrossRefPubMedCentralGoogle Scholar
  61. Gentry TJ, Pepper IL, Pierson LS III (2015) Microbial diversity and interactions in natural ecosystems, Environmental microbiology. Academic, pp 441–460Google Scholar
  62. Ghosh S, Bagheri B, Morgan HH, Divol B, Setati ME (2015) Assessment of wine microbial diversity using ARISA and cultivation-based methods. Ann Microbiol 65(4):1833–1840CrossRefGoogle Scholar
  63. Gómez-Villalba B, Calvo C, Vilchez R, González-López J, Rodelas B (2006) TGGE analysis of the diversity of ammonia-oxidizing and denitrifying bacteria in submerged filter biofilms for the treatment of urban wastewater. Appl Microbiol Biotechnol 72(2):393–400PubMedCrossRefPubMedCentralGoogle Scholar
  64. Haack SK, Garchow H, Klug MJ, Forney LJ (1995) Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns. Appl Environ Microbiol 61(4):1458–1468PubMedPubMedCentralGoogle Scholar
  65. Hadrys H, Balick M, Schierwater B (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol 1(1):55–63PubMedCrossRefPubMedCentralGoogle Scholar
  66. Haegeman B, Hamelin J, Moriarty J, Neal P, Dushoff J, Weitz JS (2013) Robust estimation of microbial diversity in theory and in practice. ISME J 7(6):1092PubMedPubMedCentralCrossRefGoogle Scholar
  67. Hall V, Talbot PR, Stubbs SL, Duerden BI (2001) Identification of clinical isolates of actinomyces species by amplified 16S ribosomal DNA restriction analysis. J Clin Microbiol 39(10):3555–3562PubMedPubMedCentralCrossRefGoogle Scholar
  68. Harry M, Jusseaume N, Gambier B, Garnier-Sillam E (2001) Use of RAPD markers for the study of microbial community similarity from termite mounds and tropical soils. Soil Biol Biochem 33(4–5):417–427CrossRefGoogle Scholar
  69. Hebert PD, Cywinska A, Ball SL, Dewaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond Ser B Biol Sci 270(1512):313–321CrossRefGoogle Scholar
  70. Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63(8):3233–3241PubMedPubMedCentralGoogle Scholar
  71. Higuchi R, Dollinger G, Walsh PS, Griffith R (1992) Simultaneous amplification and detection of specific DNA sequences. Bio/Technology 10(4):413–417PubMedCrossRefGoogle Scholar
  72. Hoshino T, Terahara T, Yamada K, Okuda H, Suzuki I, Tsuneda S et al (2006) Long-term monitoring of the succession of a microbial community in activated sludge from a circulation flush toilet as a closed system. FEMS Microbiol Ecol 55(3):459–470PubMedCrossRefPubMedCentralGoogle Scholar
  73. Ibáñez F, Angelini J, Taurian T, Tonelli ML, Fabra A (2009) Endophytic occupation of peanut root nodules by opportunistic Gammaproteobacteria. Syst Appl Microbiol 32(1):49–55PubMedCrossRefPubMedCentralGoogle Scholar
  74. Insam H (1997) A new set of substrates proposed for community characterization in environmental samples. In: Microbial communities: functional versus structural approaches, pp 259–260CrossRefGoogle Scholar
  75. Jackson CR, Randolph KC, Osborn SL, Tyler HL (2013) Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol 13(1):274PubMedPubMedCentralCrossRefGoogle Scholar
  76. Jami E, Shterzer N, Mizrahi I (2014) Evaluation of automated ribosomal intergenic spacer analysis for bacterial fingerprinting of rumen microbiome compared to pyrosequencing technology. Pathogens 3(1):109–120PubMedPubMedCentralCrossRefGoogle Scholar
  77. Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A et al (2013) Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett 16(10):1245–1257PubMedCrossRefPubMedCentralGoogle Scholar
  78. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci 92(10):4487–4491PubMedCrossRefPubMedCentralGoogle Scholar
  79. Johnson D, Vandenkoornhuyse PJ, Leake JR, Gilbert L, Booth RE, Grime JP et al (2004) Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosms. New Phytol 161(2):503–515CrossRefGoogle Scholar
  80. Kabeer FA, Jabir T, Krishnan KP, Abdulla MH (2019) Metagenomic data of fungal community in Kongsfjorden, Arctic using Illumina next generation sequencing. Data Brief 22:195–198PubMedCrossRefPubMedCentralGoogle Scholar
  81. Kadali K, Shahsavari E, Simons K, Sheppard P, Ball A (2015) RNA-TGGE, a tool for assessing the potential for bioremediation in impacted marine ecosystems. J Mar Sci Eng 3(3):968–980CrossRefGoogle Scholar
  82. Kamo T, Kusumoto Y, Tokuoka Y, Okubo S, Hayakawa H, Yoshiyama M, Kimura K, Konuma A (2018) A DNA barcoding method for identifying and quantifying the composition of pollen species collected by European honeybees, Apis mellifera (Hymenoptera: Apidae). Appl Entomol Zool 53(3):353–361PubMedPubMedCentralCrossRefGoogle Scholar
  83. Karczewski K, Riss HW, Meyer EI (2017) Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems. Limnologica 67:45–53CrossRefGoogle Scholar
  84. Kari A, Nagymáté Z, Romsics C, Vajna B, Kutasi J, Puspán I et al (2019) Monitoring of soil microbial inoculants and their impact on maize (Zea mays L.) rhizosphere using T-RFLP molecular fingerprint method. Appl Soil Ecol 138:233–244CrossRefGoogle Scholar
  85. Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170(1):75–86CrossRefGoogle Scholar
  86. Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56(1):211–236PubMedCrossRefPubMedCentralGoogle Scholar
  87. 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(2):169–188PubMedCrossRefPubMedCentralGoogle Scholar
  88. Kjelleberg S (2002) Environmental biotechnology. Curr Opin Biotechnol 13(3):199PubMedCrossRefPubMedCentralGoogle Scholar
  89. Kredics L, Chen L, Kedves O, Büchner R, Hatvani L, Allaga H et al (2018) Molecular tools for monitoring Trichoderma in agricultural environments. Front Microbiol 9:1599PubMedPubMedCentralCrossRefGoogle Scholar
  90. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci 102(23):8369–8374PubMedCrossRefPubMedCentralGoogle Scholar
  91. Kress WJ, García-Robledo C, Uriarte M, Erickson DL (2015) DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 30(1):25–35PubMedCrossRefPubMedCentralGoogle Scholar
  92. Kumar NS, Gurusubramanian G (2011) Random amplified polymorphic DNA (RAPD) markers and its applications. Sci Vis 11(3):116–124Google Scholar
  93. Lagomarsino A, Knapp BA, Moscatelli MC, De Angelis P, Grego S, Insam H (2007) Structural and functional diversity of soil microbes is affected by elevated [CO 2] and N addition in a poplar plantation. J Soils Sediments 7(6):399–405CrossRefGoogle Scholar
  94. Lehman RM, Colwell FS, Ringelberg DB, White DC (1995) Combined microbial community-level analyses for quality assurance of terrestrial subsurface cores. J Microbiol Methods 22(3):263–281CrossRefGoogle Scholar
  95. Lenaerts J, Lappin-Scott HM, Porter J (2007) Improved fluorescent in situ hybridization method for detection of bacteria from activated sludge and river water by using DNA molecular beacons and flow cytometry. Appl Environ Microbiol 73(6):2020–2023PubMedPubMedCentralCrossRefGoogle Scholar
  96. Li Y, Chen L, Wen H, Zhou T, Zhang T, Gao X (2014) 454 Pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas. J Microbiol Biotechnol 24(3):313–323PubMedCrossRefPubMedCentralGoogle Scholar
  97. Li Q, Chen C, Penttinen P, Xiong C, Zheng L, Huang W (2016) Microbial diversity associated with Tricholoma matsutake fruiting bodies. Microbiology 85(5):531–539CrossRefGoogle Scholar
  98. Liebich J, Schloter M, Schäffer A, Vereecken H, Burauel P (2007) Degradation and humification of maize straw in soil microcosms inoculated with simple and complex microbial communities. Eur J Soil Sci 58(1):141–151CrossRefGoogle Scholar
  99. Lima-Bittencourt CI, Astolfi-Filho S, Chartone-Souza E, Santos FR, Nascimento AM (2007) Analysis of Chromobacterium sp. natural isolates from different Brazilian ecosystems. BMC Microbiol 7(1):58PubMedPubMedCentralCrossRefGoogle Scholar
  100. Liu WT, 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(11):4516–4522PubMedPubMedCentralGoogle Scholar
  101. Liu Y, Wu L, Wu X, Li H, Liao Q, Zhang X et al (2017) Analysis of microbial diversity in soil under ginger cultivation. Scientifica 2017:8256865PubMedPubMedCentralCrossRefGoogle Scholar
  102. Lladó S, Baldrian P (2017) Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments. PLoS One 12(2):e0171638PubMedPubMedCentralCrossRefGoogle Scholar
  103. Maron PA, Mougel C, Ranjard L (2011) Soil microbial diversity: methodological strategy, spatial overview and functional interest. C R Biol 334(5–6):403–411PubMedCrossRefPubMedCentralGoogle Scholar
  104. Massol-Deya AA, Odelson DA, Hickey RF, Tiedje JM (1995) Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis (ARDRA). In: Molecular microbial ecology manual. Springer, Dordrecht, p 289–296CrossRefGoogle Scholar
  105. Miller KM, Ming TJ, Schulze AD, Withler RE (1999) Denaturing gradient gel electrophoresis (DGGE): a rapid and sensitive technique to screen nucleotide sequence variation in populations. BioTechniques 27(5):1016–1030PubMedCrossRefPubMedCentralGoogle Scholar
  106. Mohapatra BR, La Duc MT (2012) Evaluation of fluorescence in situ hybridization to detect encapsulated Bacillus pumilus SAFR-032 spores released from poly (methyl methacrylate). Microbiol Immunol 56(1):40–47PubMedCrossRefPubMedCentralGoogle Scholar
  107. Moscatelli MC, Secondi L, Marabottini R, Papp R, Stazi SR, Mania E, Marinari S (2018) Assessment of soil microbial functional diversity: land use and soil properties affect CLPP-MicroResp and enzymes responses. Pedobiologia 66:36–42CrossRefGoogle Scholar
  108. Moter A, Göbel UB (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85–112PubMedCrossRefPubMedCentralGoogle Scholar
  109. Moura JBD, Ventura MVA, Junior V, Gonçalves W, Souza RF, Lopes Filho LC et al (2018) Microbial diversity as a soil quality indicator in agroecosystems in Brazilian savannas. Afr J Agric Res 13(25):1306–1310CrossRefGoogle Scholar
  110. Mukherjee S, Kumar D, Chakraborty R (2016) Bacterial diversity in sediments of river Mahananda (Siliguri) as determined by 16S rRNA gene analysis. Indian J Biotechnol 15:201–209Google Scholar
  111. Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2(3):317–322PubMedCrossRefPubMedCentralGoogle Scholar
  112. Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695–700PubMedPubMedCentralGoogle Scholar
  113. Myrold DD, Zeglin LH, Jansson JK (2014) The potential of metagenomic approaches for understanding soil microbial processes. Soil Sci Soc Am J 78(1):3–10CrossRefGoogle Scholar
  114. Nakatsu CH (2007) Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Sci Soc Am J 71(2):562–571CrossRefGoogle Scholar
  115. Natsir A, Nadir M, Syahrir S, Mujnisa A, Purnomo N, Egan AR, Leury BJ (2016) Amplified ribosomal DNA restriction analysis method to assess rumen microbial diversity of ruminant. Int J Biol Life Agric Sci 10(12):865–871Google Scholar
  116. Nielsen MN, Winding A (2002) Microorganisms as indicators of soil health. National Environmental Research Institute (NERI), Technical Report no. 388. https://www.dmu.dk/1_Viden/2_Publikationer/3_Fagrapporter/rapporter/FR388.pdf
  117. Novinscak A, Filion M (2011) Effect of soil clay content on RNA isolation and on detection and quantification of bacterial gene transcripts in soil by quantitative reverse transcription-PCR. Appl Environ Microbiol 77(17):6249–6252PubMedPubMedCentralCrossRefGoogle Scholar
  118. Oberauner L, Zachow C, Lackner S, Högenauer C, Smolle KH, Berg G (2013) The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing. Sci Rep 3:1413PubMedPubMedCentralCrossRefGoogle Scholar
  119. Orlewska K, Piotrowska-Seget Z, Bratosiewicz-Wąsik J, Cycoń M (2018) Characterization of bacterial diversity in soil contaminated with the macrolide antibiotic erythromycin and/or inoculated with a multidrug-resistant Raoultella sp. strain using the PCR-DGGE approach. Appl Soil Ecol 126:57–64CrossRefGoogle Scholar
  120. 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(1):39–50PubMedCrossRefPubMedCentralGoogle Scholar
  121. Osborne CA, Rees GN, Bernstein Y, Janssen PH (2006) New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol 72(2):1270–1278PubMedPubMedCentralCrossRefGoogle Scholar
  122. Øvreås L, Torsvik V (1998) Microbial diversity and community structure in two different agricultural soil communities. Microb Ecol 36(3–4):303–315PubMedPubMedCentralGoogle Scholar
  123. Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A (2014) A survey of tools for the analysis of quantitative PCR (qPCR) data. Biomol Detect Quantif 1(1):23–33PubMedPubMedCentralCrossRefGoogle Scholar
  124. Piveteau P, Depret G, Pivato B, Garmyn D, Hartmann A (2011) Changes in gene expression during adaptation of Listeria monocytogenes to the soil environment. PLoS One 6(9):e24881PubMedPubMedCentralCrossRefGoogle Scholar
  125. Porcellato D, Brighton C, McMahon DJ, Oberg CJ, Lefevre M, Broadbent JR, Steele JL (2014) Application of ARISA to assess the influence of salt content and cation type on microbiological diversity of Cheddar cheese. Lett Appl Microbiol 59(2):207–216PubMedCrossRefPubMedCentralGoogle Scholar
  126. Pudasaini S, Wilson J, Ji M, van Dorst J, Snape I, Palmer AS et al (2017) Microbial diversity of browning Peninsula, eastern Antarctica revealed using molecular and cultivation methods. Front Microbiol 8:591PubMedPubMedCentralCrossRefGoogle Scholar
  127. Purahong W, Stempfhuber B, Lentendu G, Francioli D, Reitz T, Buscot F, Schloter M, Krüger D (2015) Influence of commonly used primer systems on automated ribosomal intergenic spacer analysis of bacterial communities in environmental samples. PLoS One 10(3):e0118967PubMedPubMedCentralCrossRefGoogle Scholar
  128. Raeymaekers L (2000) Basic principles of quantitative PCR. Mol Biotechnol 15(2):115–122PubMedCrossRefPubMedCentralGoogle Scholar
  129. Ramakrishnan B, Lueders T, Conrad R, Friedrich M (2000) Effect of soil aggregate size on methanogenesis and archaeal community structure in anoxic rice field soil. FEMS Microbiol Ecol 32(3):261–270PubMedCrossRefPubMedCentralGoogle Scholar
  130. Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67(10):4479–4487PubMedPubMedCentralCrossRefGoogle Scholar
  131. Remus-Emsermann MN, Lücker S, Müller DB, Potthoff E, Daims H, Vorholt JA (2014) Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization. Environ Microbiol 16(7):2329–2340PubMedCrossRefPubMedCentralGoogle Scholar
  132. Rick WY, Wang T, Bedzyk L, Croker KM (2001) Applications of DNA microarrays in microbial systems. J Microbiol Methods 47(3):257–272CrossRefGoogle Scholar
  133. Riesner D, Steger G, Zimmat R, Owens RA, Wagenhöfer M, Hillen W et al (1989) Temperature-gradient gel electrophoresis of nucleic acids: analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 10(5–6):377–389PubMedCrossRefPubMedCentralGoogle Scholar
  134. Roger-Estrade J, Anger C, Bertrand M, Richard G (2010) Tillage and soil ecology: partners for sustainable agriculture. Soil Tillage Res 111(1):33–40CrossRefGoogle Scholar
  135. Rogers SW, Moorman TB, Ong SK (2007) Fluorescent in situ hybridization and micro-autoradiography applied to ecophysiology in soil. Soil Sci Soc Am J 71(2):620–631CrossRefGoogle Scholar
  136. Roh SW, Abell GC, Kim KH, Nam YD, Bae JW (2010) Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol 28(6):291–299PubMedCrossRefPubMedCentralGoogle Scholar
  137. Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM, Trevors JT (2005) Microbial gene expression in soil: methods, applications and challenges. J Microbiol Methods 63(1):1–19PubMedCrossRefPubMedCentralGoogle Scholar
  138. Salgado-Salazar C, Bauchan GR, Wallace EC, Crouch JA (2018) Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH). Plant Methods 14(1):92PubMedPubMedCentralCrossRefGoogle Scholar
  139. Sánchez-López AS, Thijs S, Beckers B, González-Chávez MC, Weyens N, Carrillo-González R, Vangronsveld J (2018) Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of Crotalaria pumila growing on metal mine residues. Plant Soil 422(1–2):51–66CrossRefGoogle Scholar
  140. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R (2005) Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philos Trans R Soc B: Biol Sci 360(1462):1805–1811CrossRefGoogle Scholar
  141. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467–470PubMedCrossRefPubMedCentralGoogle Scholar
  142. Seumahu CA, Suwanto A, Rusmana I, Solihin DD (2013) Bacterial and fungal communities in tempeh as reveal by amplified ribosomal intergenic sequence analysis. HAYATI J Biosci 20(2):65–71CrossRefGoogle Scholar
  143. Sharkey FH, Banat IM, Marchant R (2004) Detection and quantification of gene expression in environmental bacteriology. Appl Environ Microbiol 70(7):3795–3806PubMedPubMedCentralCrossRefGoogle Scholar
  144. Sharma VK, Li XY, Wu GL, Bai WX, Parmar S, White JF Jr, Li HY (2019) Endophytic community of Pb-Zn hyperaccumulator Arabis alpina and its role in host plants metal tolerance. Plant Soil:1–15Google Scholar
  145. Shi Y, Yang H, Zhang T, Sun J, Lou K (2014) Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain. Appl Microbiol Biotechnol 98(14):6375–6385PubMedCrossRefPubMedCentralGoogle Scholar
  146. Siddique AB, Unterseher M (2016) A cost-effective and efficient strategy for Illumina sequencing of fungal communities: a case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition. Fungal Ecol 20:175–185CrossRefGoogle Scholar
  147. Silawat N, Chouhan S, Sairkar P, Garg RK, Vijay N, Mehrotra NN (2010) Estimation of bacterial diversity in soil and vermi compost using sole source carbon utilization (SSCU) profile. Afr J Microbiol Res 4(4):255–266Google Scholar
  148. Sirohi SK, Singh N, Dagar SS, Puniya AK (2012) Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 95(5):1135–1154PubMedCrossRefPubMedCentralGoogle Scholar
  149. Smit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23(3):249–261CrossRefGoogle Scholar
  150. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR et al (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci 103(32):12115–12120PubMedCrossRefPubMedCentralGoogle Scholar
  151. Solomon L, Ogugbue CJ, Okpokwasili GC (2018) Influence of biostimulation treatment using composted plant biomass on bacterial diversity of an aged petroleum contaminated soil as determined by culture-dependent and 16S rRNA gene PCR-DGGE based identification methods. S Asian J Res Microbiol 1–16Google Scholar
  152. Stefani FO, Bell TH, Marchand C, Ivan E, El Yassimi A, St-Arnaud M, Hijri M (2015) Culture-dependent and-independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. PLoS One 10(6):e0128272PubMedPubMedCentralCrossRefGoogle Scholar
  153. Sun S, Guo Z, Yang R, Sheng Z, Cao P (2013) Analysis of microbial diversity in tomato paste wastewater through PCR-DGGE. Biotechnol Bioprocess Eng 18(1):111–118CrossRefGoogle Scholar
  154. Tan B, Ng CM, Nshimyimana JP, Loh LL, Gin KYH, Thompson JR (2015) Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front Microbiol 6:1027PubMedPubMedCentralGoogle Scholar
  155. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69(2):1159–1171PubMedPubMedCentralCrossRefGoogle Scholar
  156. Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 12(3):377–388PubMedCrossRefPubMedCentralGoogle Scholar
  157. Taylor MW, Tsai P, Anfang N, Ross HA, Goddard MR (2014) Pyrosequencing reveals regional differences in fruit-associated fungal communities. Environ Microbiol 16(9):2848–2858PubMedPubMedCentralCrossRefGoogle Scholar
  158. Thakur VV, Tiwari S, Tripathi N, Tiwari G, Sapre S (2016) DNA barcoding and phylogenetic analyses of mentha species using rbcL sequences. Ann Phytomedicine 5(1):59–62Google Scholar
  159. Terrat S, Christen R, Dequiedt S, Lelièvre M, Nowak V, Regnier T et al (2012) Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure. Microb Biotechnol 5(1):135–141PubMedCrossRefPubMedCentralGoogle Scholar
  160. Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26(1):37–57PubMedCrossRefPubMedCentralGoogle Scholar
  161. Thimm T, Tebbe CC (2003) Protocol for rapid fluorescence in situ hybridization of bacteria in cryosections of microarthropods. Appl Environ Microbiol 69(5):2875–2878PubMedPubMedCentralCrossRefGoogle Scholar
  162. Tiedje JM, Cho JC, Murray A, Treves D, Xia B, Zhou J (2001) Soil teeming with life: new frontiers for soil science. In: Sustainable management of soil organic matter. CAB International, Wallingford, pp 393–412Google Scholar
  163. Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5(3):240–245CrossRefGoogle Scholar
  164. Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56(3):782–787PubMedPubMedCentralGoogle Scholar
  165. Valasek MA, Repa JJ (2005) The power of real-time PCR. Adv Physiol Educ 29(3):151–159PubMedCrossRefPubMedCentralGoogle Scholar
  166. Valones MAA, Guimarães RL, Brandão LAC, Souza PRED, Carvalho ADAT, Crovela S (2009) Principles and applications of polymerase chain reaction in medical diagnostic fields: a review. Braz J Microbiol 40(1):1–11PubMedPubMedCentralCrossRefGoogle Scholar
  167. Van Der Heijden MG, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11(3):296–310CrossRefGoogle Scholar
  168. Van Der Maarel MJ, Artz RR, Haanstra R, Forney LJ (1998) Association of marine archaea with the digestive tracts of two marine fish species. Appl Environ Microbiol 64(8):2894–2898PubMedPubMedCentralGoogle Scholar
  169. Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30(9):418–426PubMedCrossRefPubMedCentralGoogle Scholar
  170. van Elsas JD, Chiurazzi M, Mallon CA, Elhottovā D, Krištůfek V, Salles JF (2012) Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci 109(4):1159–1164PubMedCrossRefPubMedCentralGoogle Scholar
  171. Vaz-Moreira I, Egas C, Nunes OC, Manaia CM (2011) Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample. Antonie Van Leeuwenhoek 100(2):245–257PubMedCrossRefPubMedCentralGoogle Scholar
  172. Wagner M, Haider S (2012) New trends in fluorescence in situ hybridization for identification and functional analyses of microbes. Curr Opin Biotechnol 23(1):96–102PubMedCrossRefPubMedCentralGoogle Scholar
  173. Wang J, Ma T, Zhao L, Lv J, Li G, Zhang H et al (2008) Monitoring exogenous and indigenous bacteria by PCR-DGGE technology during the process of microbial enhanced oil recovery. J Ind Microbiol Biotechnol 35(6):619–628PubMedCrossRefPubMedCentralGoogle Scholar
  174. Wang W, Wu Y, Yan Y, Ermakova M, Kerstetter R, Messing J (2010) DNA barcoding of the Lemnaceae, a family of aquatic monocots. BMC Plant Biol 10(1):205PubMedPubMedCentralCrossRefGoogle Scholar
  175. Wang X, Hu M, Xia Y, Wen X, Ding K (2012) Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol 78(19):7042–7047PubMedPubMedCentralCrossRefGoogle Scholar
  176. Wang W, Zhai Y, Cao L, Tan H, Zhang R (2016) Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.). Microbiol Res 188:1–8PubMedCrossRefPubMedCentralGoogle Scholar
  177. Wang K, Mao H, Li X (2018) Functional characteristics and influence factors of microbial community in sewage sludge composting with inorganic bulking agent. Bioresour Technol 249:527–535PubMedCrossRefPubMedCentralGoogle Scholar
  178. Wintzingerode FV, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21(3):213–229CrossRefGoogle Scholar
  179. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP (1997a) Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22(1):130–138PubMedCrossRefPubMedCentralGoogle Scholar
  180. Wittwer CT, Ririe KM, Andrew RV, David DA, Gundry RA, Balis UJ (1997b) The LightCyclerTM: a microvolume multisample fluorimeter with rapid temperature control. BioTechniques 22(1):176–181PubMedCrossRefPubMedCentralGoogle Scholar
  181. Wong ML, Medrano JF (2005) Real-time PCR for mRNA quantitation. BioTechniques 39(1):75–85PubMedCrossRefPubMedCentralGoogle Scholar
  182. Xia X, Bollinger J, Ogram A (1995) Molecular genetic analysis of the response of three soil microbial communities to the application of 2, 4-D. Mol Ecol 4(1):17–28PubMedCrossRefPubMedCentralGoogle Scholar
  183. Yang YH, Yao J, Hu S, Qi Y (2000) Effects of agricultural chemicals on DNA sequence diversity of soil microbial community: a study with RAPD marker. Microb Ecol 39(1):72–79PubMedCrossRefPubMedCentralGoogle Scholar
  184. Yang F, Ding F, Chen H, He M, Zhu S, Ma X, et al, (2018a) Dna Barcoding for the identification and authentication of animal species in traditional medicine. Evid-Based Complement Alternat Med 2018Google Scholar
  185. Yang H, Peng C, Xiao Y, Wang X, Xu J (2018b) Study of conventional PCR and qRT-PCR detection methods for genetically modified soybean (Glycine max) SHZD32-1. J Agric Biotechnol 26(3):492–501Google Scholar
  186. Zahra NB, Shinwari ZK, Qaiser M (2016) Dna barcoding: a tool for standardization of Herbal Medicinal Products (HMPS) of Lamiaceae from Pakistan. Pak J Bot 48(5):2167–2174Google Scholar
  187. Zhang T, Fang HH (2006) Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 70(3):281–289PubMedCrossRefPubMedCentralGoogle Scholar
  188. Zhang X, Yan X, Gao P, Wang L, Zhou Z, Zhao L (2005) Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system. J Microbiol Methods 60(1):1–11PubMedCrossRefPubMedCentralGoogle Scholar
  189. Zhang L, Kang M, Huang Y, Yang L (2016) Fungal communities from the calcareous deep-sea sediments in the Southwest India ridge revealed by Illumina sequencing technology. World J Microbiol Biotechnol 32(5):78PubMedCrossRefPubMedCentralGoogle Scholar
  190. Zhao L, Ma Z, Luan Y, Lu A, Wang J, Pan L (2010) Molecular methods of studying microbial diversity in soil environments. In: International conference on computer and computing technologies in agriculture. Springer, Berlin, p 83–89CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Shobhika Parmar
    • 1
  • Vijay Kumar Sharma
    • 1
  • Jitendra Kumar
    • 1
  1. 1.Medical School of Kunming University of Science and TechnologyKunmingChina

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