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Volumn 10, Issue 7, 2015, Pages

Back to basics - The influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PRIMER DNA; RNA 16S; SEWAGE;

EID: 84941331779     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0132783     Document Type: Article
Times cited : (412)

References (50)
  • 1
    • 84861997084 scopus 로고    scopus 로고
    • Microbial communities involved in enhanced biological phosphorus removal from wastewater-A model system in environmental biotechnology
    • Nielsen PH, Saunders AM, Hansen AA, Larsen P, Nielsen JL. Microbial communities involved in enhanced biological phosphorus removal from wastewater-a model system in environmental biotechnology. Curr Opin Biotechnol. 2012; 10: 452-9.
    • (2012) Curr Opin Biotechnol , vol.10 , pp. 452-459
    • Nielsen, P.H.1    Saunders, A.M.2    Hansen, A.A.3    Larsen, P.4    Nielsen, J.L.5
  • 2
    • 84897943415 scopus 로고    scopus 로고
    • A hundred years of activated sludge: Time for a rethink
    • Sheik AR, Muller EEL, Wilmes P. A hundred years of activated sludge: time for a rethink. Front Microbiol. 2014; 5: a47.
    • (2014) Front Microbiol , vol.5 , pp. a47
    • Sheik, A.R.1    Muller, E.E.L.2    Wilmes, P.3
  • 3
    • 84863981120 scopus 로고    scopus 로고
    • Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    • 22402401
    • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6: 1621-4. doi: 10.1038/ismej.2012.8 PMID: 22402401
    • (2012) ISME J , vol.6 , pp. 1621-1624
    • Caporaso, J.G.1    Lauber, C.L.2    Walters, W.A.3    Berg-Lyons, D.4    Huntley, J.5    Fierer, N.6
  • 5
    • 0032869809 scopus 로고    scopus 로고
    • Killing two birds with one stone: Simultaneous extraction of DNA and RNA from activated sludge biomass
    • Yu Z, Mohn WW. Killing two birds with one stone: simultaneous extraction of DNA and RNA from activated sludge biomass. Can J Microbiol. 1999 45: 269-272.
    • (1999) Can J Microbiol , vol.45 , pp. 269-272
    • Yu, Z.1    Mohn, W.W.2
  • 6
    • 0037447816 scopus 로고    scopus 로고
    • Efficient recovery of environmental DNA for expression cloning by indirect extraction methods
    • 19719633
    • Gabor EM, de Vries EJ, Janssen DB. Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiol Ecol. 2003; 44: 153-63. doi: 10.1016/S0168-6496(02) 00462-2 PMID: 19719633
    • (2003) FEMS Microbiol Ecol , vol.44 , pp. 153-163
    • Gabor, E.M.1    De Vries, E.J.2    Janssen, D.B.3
  • 7
    • 0037343410 scopus 로고    scopus 로고
    • A novel approach for extraction of PCR-compatible DNA from activated sludge samples collected from different biological effluent treatment plants
    • 12531500
    • Purohit HJ, Kapley A, Moharikar AA, Narde G. A novel approach for extraction of PCR-compatible DNA from activated sludge samples collected from different biological effluent treatment plants. J Microbiol Methods. 2003; 52: 315-23. PMID: 12531500
    • (2003) J Microbiol Methods , vol.52 , pp. 315-323
    • Purohit, H.J.1    Kapley, A.2    Moharikar, A.A.3    Narde, G.4
  • 8
    • 33748374452 scopus 로고    scopus 로고
    • Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples
    • 16943632
    • Roh C, Villatte F, Kim B-G, Schmid RD. Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples. Appl Biochem Biotechnol. 2006; 134: 97-112. PMID: 16943632
    • (2006) Appl Biochem Biotechnol , vol.134 , pp. 97-112
    • Roh, C.1    Villatte, F.2    Kim, B.-G.3    Schmid, R.D.4
  • 9
    • 37849020981 scopus 로고    scopus 로고
    • Purification of total DNA extracted from activated sludge
    • Shan G, Jin W, Lam EKH, Xing X. Purification of total DNA extracted from activated sludge. J Environ Sci. 2008; 20: 80-7.
    • (2008) J Environ Sci , vol.20 , pp. 80-87
    • Shan, G.1    Jin, W.2    Lam, E.K.H.3    Xing, X.4
  • 10
    • 77955848942 scopus 로고    scopus 로고
    • Bacterial community analysis of activated sludge: An evaluation of four commonly used DNA extraction methods
    • 20652692
    • Vanysacker L, Declerck SAJ, Hellemans B, De Meester L, Vankelecom I, Declerck P. Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods. Appl Microbiol Biotechnol. 2010; 88: 299-307. doi: 10.1007/s00253-010-2770-5 PMID: 20652692
    • (2010) Appl Microbiol Biotechnol , vol.88 , pp. 299-307
    • Vanysacker, L.1    Declerck, S.A.J.2    Hellemans, B.3    De Meester, L.4    Vankelecom, I.5    Declerck, P.6
  • 11
    • 72649093145 scopus 로고    scopus 로고
    • Extracting nucleic acids from activated sludge which reflect community population diversity
    • 19768568
    • McIlroy SJ, Porter K, Seviour RJ, Tillett D. Extracting nucleic acids from activated sludge which reflect community population diversity. Antonie van Leeuwenhoek. 2009; 96: 593-605. doi: 10.1007/s10482-009-9374-z PMID: 19768568
    • (2009) Antonie Van Leeuwenhoek , vol.96 , pp. 593-605
    • McIlroy, S.J.1    Porter, K.2    Seviour, R.J.3    Tillett, D.4
  • 12
    • 84877765843 scopus 로고    scopus 로고
    • Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing
    • 22760785
    • Guo F, Zhang T. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl Microbiol Biotechnol. 2013; 97: 4607-16. doi: 10.1007/s00253-012-4244-4 PMID: 22760785
    • (2013) Appl Microbiol Biotechnol , vol.97 , pp. 4607-4616
    • Guo, F.1    Zhang, T.2
  • 13
    • 84872323101 scopus 로고    scopus 로고
    • Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets
    • 23341963
    • Cai L, Ye L, Tong AHY, Lok S, Zhang T. Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One. 2013: 8: e53649. doi: 10.1371/journal.pone.0053649 PMID: 23341963
    • (2013) PLoS One , vol.8 , pp. e53649
    • Cai, L.1    Ye, L.2    Tong, A.H.Y.3    Lok, S.4    Zhang, T.5
  • 14
    • 84885796893 scopus 로고    scopus 로고
    • Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment
    • 24146837
    • Guo F, Ju F, Cai L, Zhang T. Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PLoS One. 2013; 8: e76185. doi: 10.1371/journal.pone.0076185 PMID: 24146837
    • (2013) PLoS One , vol.8 , pp. e76185
    • Guo, F.1    Ju, F.2    Cai, L.3    Zhang, T.4
  • 15
    • 84871808499 scopus 로고    scopus 로고
    • Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
    • 22933715
    • 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. Nucleic Acids Res. 2013; 41: e1. doi: 10.1093/nar/gks808 PMID: 22933715
    • (2013) Nucleic Acids Res , vol.41 , pp. e1
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Peplies, J.4    Quast, C.5    Horn, M.6
  • 16
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki MT, Giovannoni SJ. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environl Microbiol. 1996 62: 625-30.
    • (1996) Appl Environl Microbiol , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 17
    • 84865060813 scopus 로고    scopus 로고
    • PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
    • 22905208
    • Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 2012; 7: e43093. doi: 10.1371/journal.pone.0043093 PMID: 22905208
    • (2012) PLoS One , vol.7 , pp. e43093
    • Pinto, A.J.1    Raskin, L.2
  • 19
    • 84907033647 scopus 로고    scopus 로고
    • Dead or alive: Molecular assessment of microbial viability
    • 25038100
    • Cangelosi GA, Meschke JS. Dead or alive: molecular assessment of microbial viability. Appl Environ Microbiol. 2014; 80: 5884-91. doi: 10.1128/AEM.01763-14 PMID: 25038100
    • (2014) Appl Environ Microbiol , vol.80 , pp. 5884-5891
    • Cangelosi, G.A.1    Meschke, J.S.2
  • 21
    • 77955659296 scopus 로고    scopus 로고
    • The biofilm matrix
    • 20676145
    • Flemming HC, Wingender J. The biofilm matrix. Nat Rev Microbiol. 2010; 8: 623-33. doi: 10.1038/nrmicro2415 PMID: 20676145
    • (2010) Nat Rev Microbiol , vol.8 , pp. 623-633
    • Flemming, H.C.1    Wingender, J.2
  • 22
    • 79952085066 scopus 로고    scopus 로고
    • Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms
    • 21118344
    • Dominiak DM, Nielsen JL, Nielsen PH. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms. Environ Microbiol. 2011; 13: 710-21. doi: 10.1111/j.1462-2920. 2010.02375.x PMID: 21118344
    • (2011) Environ Microbiol , vol.13 , pp. 710-721
    • Dominiak, D.M.1    Nielsen, J.L.2    Nielsen, P.H.3
  • 23
    • 33645052196 scopus 로고    scopus 로고
    • A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms
    • 16430688
    • Allesen-Holm M, Barken KB, Yang L, Klausen M, Webb JS, Kjelleberg S, et al. A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms. Mol Microbiol. 2006; 59: 1114-28. PMID: 16430688
    • (2006) Mol Microbiol , vol.59 , pp. 1114-1128
    • Allesen-Holm, M.1    Barken, K.B.2    Yang, L.3    Klausen, M.4    Webb, J.S.5    Kjelleberg, S.6
  • 24
    • 84862192626 scopus 로고    scopus 로고
    • Evaluation of 16S rDNA-based community profiling for human microbiome research
    • 22720093
    • Jumpstart Consortium Human Microbiome Project Data Generation Working Group. Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One.2012; 7: e39315. doi: 10.1371/journal.pone.0039315 PMID: 22720093
    • (2012) PLoS One , vol.7 , pp. e39315
  • 25
    • 77957319103 scopus 로고    scopus 로고
    • A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants
    • 20723961
    • Nielsen PH, Mielczarek AT, Kragelund C, Nielsen JL, Saunders AM, Kong Y, et al. A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. Water Res. 2010; 44: 5070-88. doi: 10.1016/j.watres.2010.07.036 PMID: 20723961
    • (2010) Water Res , vol.44 , pp. 5070-5088
    • Nielsen, P.H.1    Mielczarek, A.T.2    Kragelund, C.3    Nielsen, J.L.4    Saunders, A.M.5    Kong, Y.6
  • 26
    • 38949130743 scopus 로고    scopus 로고
    • Characterization of the loosely attached fraction of activated sludge bacteria
    • 17889248
    • Morgan-Sagastume F, Larsen P, Nielsen JL, Nielsen PH. Characterization of the loosely attached fraction of activated sludge bacteria. Water Res. 2008; 42: 843-54. PMID: 17889248
    • (2008) Water Res , vol.42 , pp. 843-854
    • Morgan-Sagastume, F.1    Larsen, P.2    Nielsen, J.L.3    Nielsen, P.H.4
  • 28
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • 22388286
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9: 357-9. doi: 10.1038/nmeth.1923 PMID: 22388286
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 29
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • 21903629
    • Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011; 27: 2957-63. doi: 10.1093/bioinformatics/btr507 PMID: 21903629
    • (2011) Bioinformatics , vol.27 , pp. 2957-2963
    • Magoč, T.1    Salzberg, S.L.2
  • 30
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate OTU sequences from microbial amplicon reads
    • 23955772
    • Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013; 10: 996-998. doi: 10.1038/nmeth.2604 PMID: 23955772
    • (2013) Nat Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 31
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • 17586664
    • Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73: 5261-7. PMID: 17586664
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 34
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013; 41: 590-596.
    • (2013) Nucleic Acids Res , vol.41 , pp. 590-596
    • Quast, C.1    Pruesse, E.2    Yilmaz, P.3    Gerken, J.4    Schweer, T.5    Yarza, P.6
  • 35
    • 84863304598 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria
    • R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/. 2015.
    • (2015) R: A Language and Environment for Statistical Computing
  • 36
    • 84876427223 scopus 로고    scopus 로고
    • Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
    • 23630581
    • McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013; 8: e61217. doi: 10.1371/journal.pone.0061217 PMID: 23630581
    • (2013) PLoS One , vol.8 , pp. e61217
    • McMurdie, P.J.1    Holmes, S.2
  • 38
    • 37249026668 scopus 로고    scopus 로고
    • Reshaping data with the reshape package
    • 2007
    • Wickham H (2007). Reshaping Data with the reshape Package. J Stat Softw. 2007; 21: 1-20.
    • (2007) J Stat Softw. , vol.21 , pp. 1-20
    • Wickham, H.1
  • 41
    • 85055520225 scopus 로고    scopus 로고
    • Knitr: A comprehensive tool for reproducible research in R
    • Stodden Victoria, Leisch Friedrich and Peng Roger D., eds.,. Chapman and Hall/CRC
    • Xie Y. knitr: A Comprehensive Tool for Reproducible Research in R. In Stodden Victoria, Leisch Friedrich and Peng Roger D., eds., Implementing Reproducible Computational Research. Chapman and Hall/CRC. ISBN 978-1466561595. 2014.
    • (2014) Implementing Reproducible Computational Research
    • Xie, Y.1
  • 44
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
    • 25516281
    • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 2014; 15: 550. PMID: 25516281
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 47
    • 77649110123 scopus 로고    scopus 로고
    • Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent
    • 19840106
    • McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol. 2010; 12, 378-92. doi: 10.1111/j.1462-2920.2009.02075.x PMID: 19840106
    • (2010) Environ Microbiol , vol.12 , pp. 378-392
    • McLellan, S.L.1    Huse, S.M.2    Mueller-Spitz, S.R.3    Andreishcheva, E.N.4    Sogin, M.L.5
  • 48
    • 84861346969 scopus 로고    scopus 로고
    • A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal
    • 22170425
    • Albertsen M, Hansen LBS, Saunders AM, Nielsen PH, Nielsen KL. A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J. 2012; 6: 1094-106. doi: 10.1038/ismej.2011.176 PMID: 22170425
    • (2012) ISME J , vol.6 , pp. 1094-1106
    • Albertsen, M.1    Hansen, L.B.S.2    Saunders, A.M.3    Nielsen, P.H.4    Nielsen, K.L.5
  • 49
    • 79955658957 scopus 로고    scopus 로고
    • Eikelboom's morphotype 0803 in activated sludge belongs to genus Caldilinea in the phylum Chloroflexi
    • 21299573
    • Kragelund C, Thomsen TR, Mielczarek AT, Nielsen PH. Eikelboom's morphotype 0803 in activated sludge belongs to genus Caldilinea in the phylum Chloroflexi. FEMS Microbiol Ecol. 2011; 76: 451-462. doi: 10.1111/j.1574-6941.2011.01065.x PMID: 21299573
    • (2011) FEMS Microbiol Ecol , vol.76 , pp. 451-462
    • Kragelund, C.1    Thomsen, T.R.2    Mielczarek, A.T.3    Nielsen, P.H.4
  • 50
    • 84894334250 scopus 로고    scopus 로고
    • Candidatus competibacter-lineage genomes retrieved from metagenomes reveal functional metabolic diversity
    • 24173461
    • McIlroy SJ, Albertsen M, Andresen EK, Saunders AM, Kristiansen R, Stokholm-Bjerregaard M, et al. "Candidatus Competibacter"-lineage genomes retrieved from metagenomes reveal functional metabolic diversity. ISME J 2014; 8: 613-24. doi: 10.1038/ismej.2013.162 PMID: 24173461
    • (2014) ISME J , vol.8 , pp. 613-624
    • McIlroy, S.J.1    Albertsen, M.2    Andresen, E.K.3    Saunders, A.M.4    Kristiansen, R.5    Stokholm-Bjerregaard, M.6


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