PL EN


Preferences help
enabled [disable] Abstract
Number of results
2015 | 62 | 1 | 151-160
Article title

Sampling, metadata and DNA extraction - important steps in metagenomic studies

Content
Title variants
Languages of publication
EN
Abstracts
EN
Metagenomic studies have become increasingly popular. They allow for the estimation of biodiversity in complex populations. This diversity presents an enormous but largely unexpected genetic and biological pool and can be exploited for the recovery of novel genes, entire metabolic pathways and their products. Generally metagenomic study is a genomic analysis of organisms by direct extraction and cloning of DNA from their natural environment. The most common problems of modern metagenomics are as follows: majority of the microorganisms present in the environment cannot be cultivated by standard techniques, DNA extraction methods are not very effective, isolated DNA is contaminated with various compounds, a choice for a screening method is not obvious.
Publisher

Year
Volume
62
Issue
1
Pages
151-160
Physical description
Dates
published
2015
received
2014-10-10
revised
2014-10-30
accepted
2014-11-12
online
2015-02-13
Contributors
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
author
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
References
  • Akarsubasi AT, Ince O, Oz NA, Kirdar B, Ince BK (2006) Evaluation of performance, acetoclastic methanogenic activity and archaeal composi- tion of full-scale UASB reactors treating alcohol distillery wastewaters. Process Biochem 41: 28-35.
  • Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.
  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
  • Amos GC, Zhang L, Hawkey PM, Gaze W, Wellington EM (2014) Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes. Vet Microbiol 171: 441-447.
  • Bai Y, Liu R, Liang J, Qu J (2013) Integrated metagenomic and physiochemical analyses to evaluate the potential role of microbes in the sand filter of a drinking water treatment system. PLoS One 8: e61011.
  • Barrett T, Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, Kimelman M, Pruitt K D, Resenchuk S, Tatusova T, Yaschenko E, Ostell J (2012) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res 40: D57-D63.
  • Bernhard AE, Field KG (1999) Identification of nonpoint sources of fecal pollution in coastal waters by using host specific 16s ribosomal dna genetic markers from fecal anaerobes. Appl Environ Microbiol 66: 1587-1594.
  • Błaszczyk D, Bednarek I, Machnik G, Sypniewski D, Sołtysik D, Loch T, Gałka S (2011) Amplified ribosomal dna restriction analysis (ardra) as a screening method for normal and bulking activeted sludge sample differentation. Polish J Environ Stud 20: 29-36.
  • Boccuzzi VM, Straube WL, Ravel J, Colwell RR, Hilla RT (1998) Preparation of DNA extracted from environmental water samples for PCR amplification. J Microbiol Methods 31: 193-199.
  • Buzzini AP, Sakamoto IK, Varesche MB, Pires EC (2006) Evaluation of the microbial diversity in an UASB reactor treating wastewater from an unbleached pulp plant. Process Biochem 41: 168-176.
  • Cai H, Archambault M, Prescott JF (2003) 16S ribosomal RNA sequence-based identification of veterinary clinical bacteria. J Vet Diagn Invest 15: 465-469.
  • Carrigg C, Rice O, Kavanagh S, Collins G, O'Flaherty V (2007) DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol 77: 955-964.
  • Chan OC, Liu WT, Fang HH (2001) Study of microbial community of brewery-treating granular sludge by denaturing gradient gel electrophor- esis of 16S rRNA gene. Water Sci Technol 43: 77-82.
  • Chao Y, Ma L, Yang Y, Ju F, Zhang X, Wu W, Zhang T (2013) Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment. Sci Rep 3: 3550.
  • Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7: 1104-1115.
  • Courtois S, Frostegård A, Goransson P, Depret G, Jeannin P, Simonet P (2001) Quantification of bacterial subgroups in soil: comprasion of DNA Extracted Directly from soil or from cells previously released by density gradient Centrifugation. Environ Microbiol 3: 431-439.
  • Cruds CR (1975) Protoza, Curds CR, Hawkes HA eds, Ecological Aspects of Used-water Treatment: vol 1, pp 203-268. The Organisms and Their Ecology. Academic Press, London.
  • Crump BC, Armbrust EV, Baross JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 65: 3192-3204.
  • Cullen DW, Hirsch PR (1998) Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol Biochem 30: 983-993.
  • Daims H, Taylor MW, Wagner M (2006) Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24: 483-489.
  • Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3: 470-478.
  • Debroas D, Humbert J, Enault F, Bronner G, Faubladier M, Cornillot E (2009) Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget - France). Environ Microbiol 11: 2412-2424.
  • Drzewicki A (2004) Evaluation of fauna as bio-indicator in activated sludge proces. Gas Wat Saint Eng 10: 359.
  • Eikelboom DH (1975) Filamentous organisms observed in activated sludge. Water Res 9: 365-388.
  • Ferreira A et al. (2014) Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. PLoS One 9: e97338.
  • Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft R, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li L, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone S-A, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, Gil IS, Wilson G, Wipat A (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26: 541-547.
  • Fuhrma JA, Comeau DE, Hagstrom A, Chan AM (1988) Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies. Appl Environ Microbiol 54: 1426-1429.
  • Ghai R, Rodrıguez-Valera F, McMahon KD, Toyama D, Rinke R, Souza de Oliveir TC, Garcia JW, Pellon de Miranda F, Henrique-Silva F (2011) Metagenomics of the water column in the pristine upper course of the Amazon River. PLoS One 6: e23785.
  • Ghai R, Hernandez CM, Picazo A, Mizuno CM, Ininbergs K, Díez B, Valas R, DuPont CL, McMahon KD, Camacho A, Rodriguez-Valera F (2012) Metagenomes of mediterranean coastal lagoons. Sci Rep 2 490.
  • Giger W, Roberts PV (1978) Characterization of persistent organic carbon, In Water Pollution Microbiology. Mitchell R ed, 2, 135-175. John Wiley & Sons, New York.
  • Gilbride KA, Lee DY, Beaudette LA (2006) Molecular techniques in wastewater: Understanding microbial communities, detecting pathogens, and real-time proces control. J Microbiol Methods 66: 1-20.
  • Hammes F, Boon N, Clement G, de Villiers J, Siciliano SD, Verstraete W (2003) Molecular, biochemical and ecological characterisation of a bio-catalytic calcification reactor. Appl Microbiol Biotechnol 62: 191-201.
  • Handelsman J et al. (2007) (Committee on Metagenomics: Challenges and Functional Applications, National Research Council). The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet; The National Academies Press, Washington, DC, USA.
  • Harry M, Gambier B, Bourezgui Y, Garnier-Sillam E (1999) Evaluation of puricication procedures for DNA extracted from organic rich samples: interference with humic substances. Analysis 27: 439-442.
  • Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific Microorganisms in the soil bacterial community. Appl Environ Microbiol 54: 703-711.
  • Hu Y, Liu Z, Yan J, Qi X, Li J, Zhong S, Yu J, Liu Q (2010) A developed DNA extraction method for different soil samples. J Basic Microbiol 50: 401-407.
  • 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.
  • Ito T, Okabe S, Satoh H, Watanabe Y (2002) Successional development of sulfate-reducing bacterial populations and their activities in a wastewater biofilm growing under microaerophilic conditions. Appl Environ Microbiol 68: 1392-1402.
  • Jiménez DJ, Andreote FD, Chaves D, Montaña JS, Osorio-Forero C, Junca H, Zambrano MM, Baena S (2012) Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes. PLoS One 7: e52069.
  • Kapardar RK, Ranjan R, Grover A, Puri M, Sharma R (2010) Identification and characterization of genes conferring salt tolerance to Escherichia coli from pond water metagenome. Bioresour Technol 101: 3917-3924.
  • Kim KH, Bae JW (2011) Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 77: 7663-7668.
  • Kozdrój J (2010) Isolation of nucleic acids from the environment. Kosmos 59: 141-149.
  • Krsek M, Wellington EM (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Methods 39: 1-16.
  • Kumaran P, Shivaraman N (1988) Biological treatment of toxic industrial wastes, In Biotreament Systems, Wise DL ed, pp 227-283. CRC Press, Boca Raton, FL.
  • Lakay FM, Botha A, Prior BA (2007) Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. J Appl Microbiol 102: 265-273.
  • Maarit Niemi R, Heiskanen I, Wallenius K, Lindstrom K (2001) Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods 45: 155-165.
  • Martins AM, Pagilla K, Heijnen JJ, Van Loosdrecht MC (2004) Filamentous bulking sludge - a critical review. Water Res 38: 793-817.
  • McDonald RM (1986) Sampling soil microfloras: dispersion of soil by ion exchange and extraction of specific Microorganisms from suspension by elutriation. Soil Biol Biochem 18: 309-406.
  • Metcalf and Eddy (1991) In Wastewater Engineering: Treatment, Disposal and Reuse, 3rd edn, McGraw - Hill, New York.
  • Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715-4724.
  • Miller DN (2001) Evaluation of gel filtration resins for removal of PCR inhibitors substances from soils and sediments. J Microbiol Methods 44: 49-58.
  • Milling A, Gomes NCM, Oros-Sicher M, Gotz M, Smalla K (2005) Nucleic acids extraction from environmental samples. In Molecular microbial ecology; Osborn AM, Smith CJ ed, pp 1-24. Taylor & Francis, New York.
  • Mohamed YM, Ghazy MA, Sayed A, Ouf A, El-Dorry H, Siam R (2013) Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool. Sci Rep 3 3358.
  • More MI, Herrick JB, Silva MC, Ghiorse WC, Madsen EL (1994) Quantitative cell lysis of indigenous microorganism and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol 60: 1572-1580.
  • Morgan JL, Darling AE, Eisen JA (2010) Metagenomic Sequencing of an In Vitro-Simulated Microbial Community. PLoS One 5: e10209.
  • Ocepek M, Pate M, Kušar D, Hubad B, Avberšek J, Logar K, Lapanje A, Zrimec A (2011) Comparison of DNA extraction methods to detect Salmonella spp. in tap water. Slov Vet Zb 48: 93-98.
  • Ogarm A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7: 57-66.
  • Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo C, Poretsky R, Konstantinidis KT (2011) Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of lake lanier, a temperate freshwater ecosystem. Appl Environ Microbiol 77: 6000-6011.
  • Onda S, Hiraishi A, Matsuo Y, Takii S (2002) Polyphasic approaches to the identification of predominant polyphosphate-accumulating organisms in a laboratory-scale anaerobic/aerobic activated sludge system. J Gen Appl Microbiol 48: 43-54.
  • Orsini M, Romano-Spica V (2001) A microwave-based method for nucleic acid isolation from environmental saples. Lett Appl Method 33: 17-21.
  • Painter HA, Viney M (1959) Composition of domestic sewage . J Biochem Microbiol Technol 1: 143-162.
  • Parker DS, Jenkins D, Kaufman WJ (1971) Physical conditioning of the activated sludge. J Water Pollut Control Fed 43: 1971.
  • Parsley LC, Consuegra EJ, Kakirde KS, Land AM, Harper WF Jr, Liles MR (2010) Identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage. Appl Environ Microbiol 76: 3753-3757.
  • Paul EA, Clark FE (1989) Soil microbiology and biochemistry, 3. Academic Press, San Diego 3.
  • Peršoh D, Theuerl S, Buscot F, Rambold G (2008) Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J Microbiol Methods 75: 19-24.
  • 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.
  • Pillai SD, Josephson KL, Bailey RL, Gerba CP, Pepper IL (1991) Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences. Appl Environ Microbiol 57: 2283-2286.
  • Porteous LA, Seider RJ, Watrud LS (1997) An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications. Mol Ecol 6: 787-791.
  • Ranjan R, Grover A, Kapardar RK, Sharma R (2005) Isolation of novel lipolytic genes from uncultured bacteria of pond water. Biochem Biophys Res Commun 335: 57-65.
  • Rivera IN, Lipp EK, Gil A, Choopun N, Huq A, Colwell RR (2003) Method of DNA extraction and application of multiplex polymerase chain reaction to detect toxigenic Vibrio cholera O1 and O139 from aquatic ecosystems. Environ Microbiol 5: 599-606.
  • Robe P, Nalin R, Capella C, Vogel TM, Simonet P (2003) Extracion of DNA from soil. Eur J Soil Biol 39: 183-190.
  • Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M (2009) Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11: 2806-2820.
  • Rossello-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39-76.
  • Saano A, Tas E, Pippola S, Lidstorm K, Van Elsas JD (1995) Extraction and analysis of microbial DNA from soil, In Nucleic Acids in the Environmental: Methods and Applications, van Elsas JD, Trevors JT eds, pp 49-67. Springer-Verlag, Heidelberg, Germany.
  • Sabree ZL, Rondon MR, Handelsman J (2009) Metagenomics. In Encyclopedia of Microbiology, 3rd edn, pp. 622-632. Academic Press.
  • Santegoeds CM, Ferdelman TG, Muyzer G, de Beer D (1998) Structural and functional dynamics of sulfate-reducing populations in bacterial bio- films. Appl Environ Microbiol 64: 3731-3739.
  • Sanz JL, Köchling T (2007) Molecular biology used in wastewater treatment: An overview. Process Biochem 42: 119-133.
  • Schmidt M, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173: 4371-4378.
  • Sekiguchi Y, Takahashi H, Kamagata Y, Ohashi A, Harada H (2001) In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I. Appl Environ Microbiol 67: 5740-5749.
  • Sharma PK, Capalash N, Kaur J (2007) An improved method for single step purification of metagenomic DNA. Mol Biotechnol 36: 61-63.
  • Shi P, Jia S, Zhang X, Zhang T, Cheng S, Li A (2013) Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water. Water Res 47: 111-120.
  • Simonet P, Capella A, Navarro E, Bardin R, Moiroud A (1984) An improved method for lysis of Frankia with achromopeptidase allows detection of new plasmids. Can J Microbiol 30: 1292-1295.
  • Snaidr J, Amann R, Huber I, Ludwig W, Schleifer KH (1997) Phylogenetic analysis and in situ identyfication of bacteria in activeted sludge. Appl Environ Microbiol 63: 2884-2896.
  • Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored ''rare biosphere''. Proc Natl Acad Sci 103: 12115-12120.
  • Somerville CC, Knight IT, Straube WL, Colwell RR (1989) Simple, rapid method for direct isolation of nucleic acids from Aquatic Environments. Appl Environ Microbiol 55: 548-554.
  • Steele H, Streit WR (2006) Metagenomics for the study of soil microbial communities. In Molecular approaches this soil rhizosphere and plant microorganism analysis. Cooper JE, Rao JR eds, pp 42-54. CAB International, Wallingford.
  • Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54: 2908-2915.
  • Stein JL, Marsh TL, Wu KY, Shizuya T, DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591-599.
  • Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA Extracted Directly from soil in detection and transforamation of receombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59: 2657-2665.
  • Tekere M, Lötter A, Olivier J, Jonker N, Venter S (2011) Metagenomic analysis of bacterial diversity of Siloam hot water spring, Limpopo, South Africa. Afr J Biotechnol 10: 18005-18012.
  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2: 3.
  • Torsvik V (1980) Isolation of bacterial DNA from soil. Soil Biol Biochem 12: 15-21.
  • Torsvik V, Sorheim R, Goksoyr R (1996) Total bacterial diversity in soil and sediment communities. J Ind Microbiol 17: 170-178.
  • Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes that ecosystems. Curr Opin Microbiol 5: 240-245.
  • Tsai YL, Park MJ, Olson BH (1991) Rapid method for direct extraction of mRNA from seeded soils. Appl Environ Microbiol 57: 765-768.
  • Ueda S, Earle RL (1972) Microflora of activated sludge. J Gen Appl Microbiol 18: 239-248.
  • Van Lubbe JGM (2012) Handbook of Biological Wastewater Treatment: Design and Optimisation of Activated Sludge Systems. 2nd edn, pp 26-31. London.
  • Venter JC et al. (2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 304: 66-74.
  • Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Delanghe J, Van Simaey LL, De Ganck K, Temmerman M, Vaneechoutte M (2004) Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol 4 16.
  • Wagner AM, Loete ET (2002) 16S rRNA Sequence analysis of bacteria present in foaming activited sludge. Syst Appl Microbiol 25: 434-439.
  • Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in natural community. Nature 345: 63-65.
  • Wellington EMH, Marsh P, Watts JEM, Burden J (1997) Indirect approaches for studying soil microorganism based on cell extraction and culturing. In Modern Soil Microbiology, van Elsas JD, Jansson JK, Trevors JT eds, CRC Press.
  • Wexler M, Bond PL, Richardson DJ, Johnston AW (2005) A wide host-range metagenomic library from a waste water treatment plant yield a novel alkohol/aldehyde dehydrogenase. Environ Microbiol 7: 1917-1926.
  • Wooley JC, Godzik A, Friedberg I (2010) A primer on Metagenomics. PLoS Comput Biol 6: e1000667.
  • Yu W, Su S, Lee C (2008) A novel retrieval system for nearly complete microbial genomic fragments from soil samples. J Microbiol Methods 72: 197-205.
  • Zhang C, Bennet GN (2005) Biodegradation of xenobiotics by anaerobic bacteria. Appl Microbiol Biotechnol 67: 600-618.
  • Zhongtang Y, Mohn WW (1999) Killing two birds with one stone: simultaneous extraction of DNA and RNA from activated sludge biomass. Can J Microbiol 45: 269-272.
  • Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soil of diverse composition. Appl Environ Microbiol 62: 316-322.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv62p151kz
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.