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Introduction to Modern Tools and Techniques to Understand Microbes

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Modern Tools and Techniques to Understand Microbes

Abstract

Microorganisms are omnipresent in the nature and having both positive and negative effects on various aspects of human life and society. To study their impact on environment and other associated fields, it is crucial to be able to cultivate the microbes under laboratory conditions and to detect and identify them quickly and accurately. However, difficulties in cultivating most of the microbes by standard traditional methods such as plate count, filteration, etc., limit our ability to study these tiny organisms. To enhance the microbial studies effectively particularly for microbes which are viable but non-culturable (VBNC), several modern approaches such as molecular methods are proving to be appreciated. The most appreciable modern molecular methods which are used to detect and identify organisms include rRNA or rDNA fingerprinting, probing, and sequencing.

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References

  • Arbeit RD (1995) Laboratory procedures for the epidemiologic analysis of microorganisms. In: Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH (eds) Manual of clinical microbiology, 6th edn. American Society of Microbiology, Washington, DC, pp 190–208

    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 3:133–140

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Borneman J, Triplett EC (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 

  • 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 

  • De Santis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53:371–383

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • 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 66:2943–2950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fakruddin M, Mannan MKSB (2013) Methods for analyzing diversity of microbial communities in natural environments. Ceylon J Sci (Bio Sci) 42:19–33

    Google Scholar 

  • 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 65:4630–4636

    CAS  PubMed  PubMed Central  Google Scholar 

  • Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-solecarbon-source utilization. Appl Environ Microbiol 57:2351–2359

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J (2006) Microarray applications in microbial ecology research. Microb Ecol 52:159–175

    Article  CAS  PubMed  Google Scholar 

  • Ghazanfar S, Azim A, Ghazanfar MA, Anjum MI, 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 KG (1990) Genetic diversity in Sargasso Sea Bacterioplankton. Nature 345:60–62

    Article  CAS  PubMed  Google Scholar 

  • Glynn B, Lahiff S, Wernecke M, Barry T, Smith TJ, Maher M (2006) Current and emerging molecular diagnostic technologies applicable to bacterial food safety. Int J Dairy Technol 59:126–139

    Article  CAS  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 

  • Gray PHH (1926) A method of staining bacterial flagella. J Bacteriol 12:273–274

    CAS  PubMed  PubMed Central  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 

  • Hagens S, Loessner MJ (2007) Application of bacteriophages for detection and control of foodborne pathogens. Appl Microbiol Biotechnol 76:513–519

    Article  CAS  PubMed  Google Scholar 

  • Holst-Jensen A, Rønning SB, Løvseth A, Berdal KG (2003) PCR technology for screening and quantification of genetically modified organisms (GMOs). Anal Bioanal Chem 375:985–993

    Article  CAS  PubMed  Google Scholar 

  • Kell DB, Kaprelyants AS, Weichart DH, Harwood CR, Barer MR (1998) Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Antonie Van Leeuwenhoek 73:169–187

    Article  CAS  PubMed  Google Scholar 

  • Kjoller R, Rosendahl S (2000) Detection of arbuscular mycorrhizal fungi (Glomales) in roots by nested PCR and SSCP (single stranded conformation polymorphism). Plant Soil 226:189–196

    Article  CAS  Google Scholar 

  • Kretzer JW, Lehmann R, Schmelcher M, Banz M, Kim K-P, Korn C, Loessner MJ (2007) Use of high-affinity cell wall-binding domains of bacteriophage endolysins for immobilization and separation of bacterial cells. Appl Environ Microbiol 73:1992–2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leifson E (1930) Staining, shape and arrangement of bacterial flagella. J Bacteriol 62:377–389

    Google Scholar 

  • 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 63:4516–4522

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lukow T, Dunfield PF, Liesack W (2000) Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol Ecol 32:241–247

    Article  CAS  Google Scholar 

  • Lyon H (1991) Theory and strategy in histochemistry. Springer, Berlin

    Book  Google Scholar 

  • Malorny B, Tassios PT, Rådström P, Cook N, Wagner M, Hoorfar J (2003) Standardization of diagnostic PCR for the detection of foodborne pathogens. Int J Food Microbiol 83:39–48

    Article  CAS  PubMed  Google Scholar 

  • 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 27:1016–1030

    CAS  PubMed  Google Scholar 

  • Minsky M (1988) Memoir on inventing the confocal microscope. Scanning 10:128–138

    Article  Google Scholar 

  • Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:3518–3525

    CAS  PubMed  PubMed Central  Google Scholar 

  • Monis PT, Giglio S (2006) Nucleic acid amplification-based technique for pathogen detection and identification. Infect Genet Evol 6:2–12

    Article  CAS  PubMed  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 tetraneric restriction enzymes for studies of microbial diversity in Nature. Appl Environ Microbiol 62:2501–2507

    CAS  PubMed  PubMed Central  Google Scholar 

  • Muhling M, Woolven-Allen J, Murrell JC, Joint I (2008) Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J 2:379–392

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Pelczar JM, Chan ECS, Krieg R (1998) Noel microbiology, 5th edn. Tata McGraw-Hill Publishing Company Limited, New Delhi

    Google Scholar 

  • Peters S, Koschinsky S, Schwieger F, Tebbe CC (2000) Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism based genetic profiles of small-subunit rRNA genes. Appl Environ Microbiol 66:930–936

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prescott ML, Harley PJ, Klein AD (2005) Microbiology, 6th edn. McGraw-Hill Higher Education, New York

    Google Scholar 

  • Rodríguez-Lázaro D, Lombard B, Smith H, Rzezutka A, D’Agastino M, Helmuth R, Schroeter A, Malorny B, Miko A, Guerra B, Davison J, Kobilinsky A, Hernández M, Berhteau Y, Cook N (2007) Trends in analytical methodology in food safety and quality: monitoring microorganisms and genetically modified organisms. Trends Food Sci Technol 18:306–319

    Article  Google Scholar 

  • Royo JL, Hidalgo M, Ruiz A (2007) Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping. Nat Protoc 2:1734–1739

    Article  CAS  PubMed  Google Scholar 

  • Rudi K, Zimonja M, Trosvik P, Næs 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 

  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of ß-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354

    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 

  • Stach JEM, Bathe S, Clapp JP, Burns RG (2001) PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods. FEMS Microbiol Ecol 36:139–151

    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 

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

    Article  CAS  PubMed  Google Scholar 

  • Thies JE (2007) Soil microbial community analysis using terminal restriction fragment length polymorphisms. Soil Sci Soc Am J 71:579–591

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Tonin C, Vandenkoornhuyse P, Joner EJ, Straczek J, Leyval C (2001) Assessment of arbuscular mycorrhizal fungi diversity in the rhizosphere of Violoacalaminaria and effect of these fungi on heavy metal uptake by clover. Mycorrhiza 10:161–168

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Touron A, Berthe T, Pawlak B, Petit F (2005) Detection of Salmonella in environmental water and sediment by a nested-multiplex polymerase chain reaction assay. Res Microbiol 156:541–553

    Article  CAS  PubMed  Google Scholar 

  • Towner KJ, Cockayne A (1993) Molecular methods for microbial identification and typing, 1st edn. Chapman & Hall, London, pp. 1–202

    Book  Google Scholar 

  • Van den Bogert B, de Vos WM, Zoetendal EG, Kleerebezem M (2011) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77:2071–2080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

    CAS  PubMed  PubMed Central  Google Scholar 

  • Voutou B, Stefanaki E-C (2008) Electron microscopy: the basics. Physics of advanced materials winter school. Aristotle University of Thessaloniki, Greece

    Google Scholar 

  • Woeste S, Demchick P (1991) New version of the negative stain. Appl Environ Microbiol 57:1858–1859

    CAS  PubMed  PubMed Central  Google Scholar 

  • YashRoy RC (1990) Lamellar dispersion and phase separation of chloroplast membrane lipids by negative staining electron microscopy. J Biosci 15:93–98

    Article  CAS  Google Scholar 

  • Zernike F (1942) Phase contrast, a new method for the microscope observation of transparent objects. Physica 9:686–698

    Article  Google Scholar 

  • Zeyaullah M, Kamli MR, Islam B, Atif M, Benkhayal FA, Nehal M, Rizvi MA, Ali A (2009) Metagenomics—an advanced approach for noncultivable micro-organisms. Biotechnol Mol Bio Rev 4:49–54

    CAS  Google Scholar 

  • Zhao L, Ma T, Gao M, Gao P, Cao M, Zhu X, Li G (2012) Characterization of microbial diversity and community in water flooding oil reservoirs in China. World J Microbiol Biotechnol 28:3039–3052

    Article  PubMed  Google Scholar 

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Acknowledgment

Ajit Varma is thankful to Department of Science and Technology and Department of Biotechnology for partial financial funding and to DST-FIST for providing confocal microscope facility.

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Goyal, P., Bhola, D., Varma, A. (2017). Introduction to Modern Tools and Techniques to Understand Microbes. In: Varma, A., Sharma, A. (eds) Modern Tools and Techniques to Understand Microbes. Springer, Cham. https://doi.org/10.1007/978-3-319-49197-4_1

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