A practical introduction to microbial community sequencing

Central European Journal of Biology - Tập 8 - Trang 399-409 - 2013
Dominika Chmolowska1
1Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland

Tóm tắt

The use of molecular methods is gaining popularity throughout the field of microbial community ecology studies thanks to their flexibility of application, which ranges from community structure to function and trait determination. Nonetheless, there are environmental microbiologists, who are new in the field and are just starting to get to grips with the genetic tool box. It is for them that this practitioner’s mini-review was compiled. The methods available for microbial community structure analysis are discussed, after which, the reader is introduced to sequencing, as this tool is the most appropriate and has seen the greatest development in recent years. A focus on the practical aspects of the methodology is maintained throughout. The sample preparation procedure from extraction to sequencing is described. Different applications and considerations of sequencing are briefly explained, including clone library sequencing vs. amplicon library sequencing, shotgun-metagenomics vs. metatranscriptomics and the ‘double RNA approach’.

Tài liệu tham khảo

Janssen P.H., Yates P.S., Grinton B.E., Taylor P.M., Sait M., Improved Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the Divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia, Appl. Environ. Microbiol., 2002, 68,5, 2391–2396 Nichols D., Cahoon N., Trakhtenberg E.M., Pham L., Mehta A, Belanger A., et al., Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species, Appl. Environ. Microbiol., 2010, 76, 2445–2450 Stefanowicz A., The Biolog Plates Technique as a Tool in Ecological Studies of Microbial Communities, Polish. Jour. Environ. Stud., 2006, 15, 669–676 Pinkart H.C., Ringelberg D.B., Piceno Y.M., MacNaughton S.J., White D.C., Biochemical Approaches to Biomass Measurements and Community Structure Analysis, In: Hurst C.J., Crawford R.L., Knudsen G.R., McInerney M.J., Stetzenbach L.D. (Eds.), Manual of Environmental Microbiology, ASM Press, Washington D.C., 2002 Olsson P., Signature fatty acids provide tools for determination of the distribution and interactions of mycorrhizal fungi in soil, FEMS Microbiol. Ecol., 1999, 29, 303–310 Frostegård Å., Tunlid A., Bååth E., Use and misuse of PLFA measurements in soils, Soil Biol. Biochem., 2011, 43, 1621–1625 Tyson G.W., Chapman J, Hugenholtz P, Allen E.E., Ram R.J., Richardson P.M., et al., Community structure and metabolism through reconstruction of microbial genomes from the environment, Nature, 2004, 428, 37–43 Simon C., Daniel R., Metagenomic analyses: past and future trends, Appl. Environ. Microbiol., 2011, 77, 1153–1161 Cantarel B.L., Erickson A.R., VerBerkmoes N.C., Erickson B.K., Carey P.A, Pan C., et al., Strategies for metagenomic-guided whole-community proteomics of complex microbial environments, PLoS One, 2011, 6, e27173 Huang W.E., Griffiths R.I., Thompson I.P., Bailey M.J., Whiteley A.S., Raman Microscopic Analysis of Single Microbial Cells, Anal. Chem., 2004, 76, 4452–4458 Harz M., Rösch P., Popp J., Vibrational spectroscopy-a powerful tool for the rapid identification of microbial cells at the single-cell level, Cytometry, 2009, 75A, 104–113 Adamczyk J., Hesselsoe M., Iversen N., Horn M., Lehner A., Nielsen P.H., et al., The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function, Appl. Environ. Microbiol., 2003, 69, 6875–6887 Okabe S., Kindaichi T., Ito T., MAR-FISH — An Ecophysiological Approach to Link Phylogenetic Affiliation and In Situ Metabolic Activity of Microorganisms at a Single-Cell Resolution, Microbes Environ., 2004, 19, 83–98 Musat N., Halm H., Winterholler B., Hoppe P., Peduzzi S., Hillion F., et al., A single-cell view on the ecophysiology of anaerobic phototrophic bacteria, Proc Natl Acad Sci USA, 2008, 105, 17861–17866 Schippers A., Neretin L.N., Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using realtime PCR, Environ. Microbiol., 2006, 8, 1251–1260 DeSantis T.Z., Brodie E.L., Moberg J.P., Zubieta I.X., Piceno Y.M., Andersen G.L., High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment, Microbial Ecol., 2007, 53, 371–383 He Z., Gentry T.J., Schadt C.W., Wu L., Liebich J., Chong S.C., et al., GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes, The ISME Journal, 2007, 1, 67–77 Wilson K.H., Wilson W.J., Jennifer L., Desantis T.Z., Viswanathan V.S., Kuczmarski T.A., et al., High-Density Microarray of Small-Subunit Ribosomal DNA Probes High-Density Microarray of Small-Subunit Ribosomal DNA Probes, Appl.Environ. Microbiol., 2002, 68, 2535–2541 Hazen T.C., Rocha A.M., Techtmann S.M., Advances in monitoring environmental microbes, Cur. Opin. Biotech., 2012, 24, 1–8 Zwart G., van Hannen E.J., Kamst-van Agterveld M.P., van der Gucht K., Lindström E.S., van Wichelen J., et al., Rapid screening for freshwater bacterial groups by using reverse line blot hybridization, Appl. Environ. Microbiol., 2003, 69, 5875–5883 Nocker A., Burr M., Camper A.K., Genotypic Microbial Community Profiling: A Critical Technical Review, Microb. Ecol., 2007, 54, 276–289 Schütte U.M.E., Abdo Z., Bent S.J., Shyu C., Williams C.J., Pierson J.D., Forney L.J., Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities, Appl. Microbiol. Biotechnol., 2008, 80, 365–380 Prosser J.I., Replicate or lie, Environ. Microbiol., 2010, 12, 1806–1810 Magurran E.E., McGill B.J., Biological diversity: frontiers in measurement and assessment, Oxford University Press, Oxford, 2011 Delmont T.O., Robe P., Cecillon S., Clark I.M., Constancias F., Simonet P., et al., Accessing the Soil Metagenome for Studies of Microbial Diversity, Appl. Env. Microbiol., 2011, 77, 1315–1324 Ovreas L., Curtis T.P., Microbial diversity and ecology, In: Magurran E.E., McGill B.J. (Eds.), Biological diversity: frontiers in measurement and assessment, Oxford University Press, Oxford, 2011 Simister R.L., Schmitt S., Taylor M.W., Evaluating methods for the preservation and extraction of DNA and RNA for analysis of microbial communities in marine sponges, J. Exp. Mar. Biol. Ecol., 2011, 397, 38–43 Masek T., Vopalensky V., Suchomelova P., Pospisek M., Denaturing RNA electrophoresis in TAE agarose gels, Anal. Biochem., 2005, 336, 46–50 Blagodatskaya E.V., Blagodatskiı S.A., Anderson T.H., Quantitative isolation of microbial DNA from the different types of soils of natural and agricultural ecosystems, Microbiology, 2003, 72, 840–846 Aoshima H., Kimura A., Shibutan A., Okada C., Matsumiya Y., Kubo M., Evaluation of soil bacterial biomass using environmental DNA extracted by slow-stirring method, Appl. Microbiol. Biotech., 2006, 71, 875–880 Wang Y., Qian P.-Y., Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies, PLoS One, 2009, 4, e7401 Klindworth A., Pruesse E., Schweer T., Peplies J., Quast C., Horn M., et al., Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucl. Acid Res., 2012, 1–11 Mao D-P., Zhou Q., Chen Ch-Y., Quan Z-X., Coverage evaluation of universal bacterial primers using the metagenomic datasets, BMC Microbiology, 2012, 12, 66 Walsh P.S., Erlich H.A., Higuchi R., Preferential PCR Amplification of Alleles: Mechanisms and Solutions, Genome Res., 1992, 1, 241–250 Abd-Elsalam K.A., Bioinformatic tools and guideline for PCR primer design, Afr. Jour. Biotech., 2003, 2, 91–95 Chen Z., Zhang Y., Dimethyl sulfoxide targets phage RNA polymerases to promote transcription, Biochem. Biophys. Res. Comm., 2005, 333, 664–670 Rapley R., Enhancing PCR Amplification and Sequencing Using DNA-Binding Proteins, Mol. Biotech., 1994, 2, 295–298 Sipos R., Székely A.J., Palatinszky M., Révész S., Márialigeti K., Nikolausz M., Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis, FEMS Microbiol. Ecol., 2007, 60, 341–350 Mardis E.R., A decade’s perspective on DNA sequencing technology, Nature, 2011, 470, 198–203 Glenn T.C., Field guide to next-generation DNA sequencers, Mol. Ecol. Res., 2011, 11, 759–769 Shokralla S., Spall J.L., Gibson J.F., Hajibabaei M., Next-generation sequencing technologies for environmental DNA research, Molecular Ecology, 2012, 21, 1794–1805 Ahmadian A., Ehn M., Hober S., Pyrosequencing: history, biochemistry and future, Clin. chim. acta, 2006, 363, 83–94 Margulies M., Egholm M., Altman W., Attiya S., Bader J.S., Bemben L.A., et al., Genome sequencing in microfabricated high-density picolitre reactors, Nature, 2005, 437, 376–380 Ronaghi M., Karamohamed S., Pettersson B., Uhlén M., Nyrén P., Real-time DNA sequencing using detection of pyrophosphate release, Anal. Biochem., 1996, 242, 84–89 Hamady M., Walker J.J., Harris J.K., Gold N.J., Knight R., Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex, Nat Methods, 2008, 5, 235–237 Kunin V., Copeland A., Lapidus A., Mavromatis K., Hugenholtz P., A bioinformatician’s guide to metagenomics, Microbiol. Mol. Biol. Rev., 2008, 72, 557–578 Wooley J.C., Godzik A., Friedberg I., A Primer on Metagenomics, PLoS Comput Biol, 2010, 6, e1000667 Moran M.A., Metatranscriptomics: Eavesdropping on Complex Microbial Communities, Microbe, 2009, 4, 329–335 Urich T., Lanzén A., Qi J., Huson, D.H., Schleper C., Schuster S.C., Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome, PLoS ONE, 2008, 3, e2527 Lanzén A., Jørgensen S.L., Bengtsson M.M., Jonassen I., Ovreas L., Urich T., Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA, FEMS Microbiol. Ecol., 2011, 77, 577–589 Gilbert M.T., Tomsho L.P., Rendulic S., Packard M., Drautz D.I., Sher A., et al., Whole-genome shotgun sequencing of mitochondria from ancient hair shafts, Science, 2007, 317, 1927–1930