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References

  • Alexander M (1977) Introduction to Soil Microbiology. John Wiley & Sons Inc., New York.
  • Ariefdjohan MW, Savaiano DA & Nakatsu CH (2010) Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr J 9: 23.
  • Bakken LR (1985) Separation and purification of bacteria from soil. Appl Environ Microbiol 49: 14821487.
  • Biggerstaff J, Weidow B, Amirkhosravi A & Francis JL (2006) Enumeration of leukocyte infiltration in solid tumors by confocal laser scanning microscopy. BMC Immunol 7: 16.
  • 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: 955964.
  • Claesson MJ, O'Sullivan O, Wang Q, Nikkila J, Marchesi JR, Smidt H, de Vos WM, Ross RP & O'Toole PW (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4: e6669.
  • Cole JR, Wang Q, Cardenas E et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141D145.
  • Curtis TP, Sloan WT & Scannell JW (2002) Estimating prokaryotic diversity and its limits. P Natl Acad Sci USA 99: 1049410499.
  • de Lipthay JR, Enzinger C, Johnsen K, Aamand J & Sorensen SJ (2004) Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biol Biochem 36: 16071614.
  • Dolezel J, Bartos J, Voglmayr H & Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry A 51: 127129.
  • Ellenbroek FM & Cappenberg TE (1991) DNA-synthesis and tritiated-thymidine incorporation by heterotrophic fresh-water bacteria in continuous culture. Appl Environ Microbiol 57: 16751682.
  • Farrelly V, Rainey FA & Stackebrandt E (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S ribosomal-RNA genes from a mixture of bacterial species. Appl Environ Microbiol 61: 27982801.
  • Feinstein LM, Sul WJ & Blackwood CB (2009) Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl Environ Microbiol 75: 54285433.
  • Ferris MJ, Muyzer G & Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62: 340346.
  • Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA & Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74: 24612470.
  • Gilichinsky DA, Wilson GS, Friedmann EI et al. (2007) Microbial populations in antarctic permafrost: biodiversity, state, age, and implication for astrobiology. Astrobiology 7: 275311.
  • Gilichinsky D, Vishnivetskaya T, Petrova M, Spirina E, Mamikin V & Rivkina E (2008) Bacteria in Permafrost. Psychrophiles: From Biodiversity to Biotechnology (Margesin R, Schinner F, Marx J-C & Gerday C, eds), pp. 83102. Springer-Verlag, Berlin.
  • Hansen AA, Herbert RA, Mikkelsen K, Jensen LL, Kristoffersen T, Tiedje JM, Lomstein BA & Finster KW (2007) Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway. Environ Microbiol 9: 28702884.
  • Harms G, Layton AC, Dionisi HM, Gregory IR, Garrett VM, Hawkins SA, Robinson KG & Sayler GS (2003) Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37: 343351.
  • Hazen TC, Rocha AM & Techtmann SM (2013) Advances in monitoring environmental microbes. Curr Opin Biotechnol 24: 526533.
  • Klappenbach JA, Saxman PR, Cole JR & Schmidt TM (2001) RRNDB: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29: 181184.
  • Kobabe S, Wagner D & Pfeiffer EM (2004) Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation. FEMS Microbiol Ecol 50: 1323.
  • Lagendijk EL, Validov S, Lamers GE, de Weert S & Bloemberg GV (2010) Genetic tools for tagging Gram-negative bacteria with mCherry for visualization in vitro and in natural habitats, biofilm and pathogenicity studies. FEMS Microbiol Let 305: 8190.
  • Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics (Stackebrandt E & Goodfellow M, eds), pp. 15176. John Wiley & Sons, Chichester, New York.
  • Layton A, McKay L, Williams D, Garrett V, Gentry R & Sayler G (2006) Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl Environ Microbiol 72: 42144224.
  • Lemos LN, Fulthorpe RR & Roesch LFW (2012) Low sequencing efforts bias analyses of shared taxa in microbial communities. Folia Microbiol 57: 409413.
  • Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM & Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480: 368371.
  • Martineau C, Whyte LG & Greer CW (2010) Stable isotope probing analysis of the diversity and activity of methanotrophic bacteria in soils from the Canadian High Arctic. Appl Environ Microbiol 76: 57735784.
  • Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G & Catroux G (2001) DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 67: 23542359.
  • Meyer F, Paarmann D, D'Souza M et al. (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
  • Ogram A, Sayler GS & Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7: 5766.
  • Ozerskaya S, Kochkina G, Ivanushkina N & Gilichinsky D (2009) Fungi in permafrost. Permafrost Soils (Margesin R, ed.), pp. 8595. Springer-Verlag, Berlin, Heidelberg.
  • Parks DH & Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715721.
  • Pilloni G, Granitsiotis MS, Engel M & Lueders T (2012) Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS One 7: e40467.
  • Pinto AJ & Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7: e43093.
  • Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 75377541.
  • Steven B, Briggs G, McKay CP, Pollard WH, Greer CW & Whyte LG (2007) Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods. FEMS Microbiol Ecol 59: 513523.
  • Steven B, Niederberger TD & Whyte LG (2009) Bacterial and archaeal diversity in permafrost. Permafrost Soils (Margesin R, ed.), pp. 5972. Springer-Verlag, Berlin, Heidelberg.
  • Torsvik V, Goksoyr J & Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782787.
  • Vishnivetskaya T, Kathariou S, McGrath J, Gilichinsky D & Tiedje JM (2000) Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles 4: 165173.
  • Vishnivetskaya TA, Petrova MA, Urbance J, Ponder M, Moyer CL, Gilichinsky DA & Tiedje JM (2006) Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology 6: 400414.
  • Vorobyova E, Soina V, Gorlenko M, Minkovskaya N, Zalinova N, Mamukelashvili A, Gilichinsky D, Rivkina E & Vishnivetskaya T (1997) The deep cold biosphere: facts and hypothesis. FEMS Microbiol Rev 20: 277290.
  • Wagner D, Kobabe S & Liebner S (2009) Bacterial community structure and carbon turnover in permafrost-affected soils of the Lena Delta, northeastern Siberia. Can J Microbiol 55: 7383.
  • Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 52615267.
  • Wilhelm RC, Niederberger TD, Greer C & Whyte LG (2011) Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic. Can J Microbiol 57: 303315.
  • Yang ZH, Xiao Y, Zeng GM, Xu ZY & Liu YS (2007) Comparison of methods for total community DNA extraction and purification from compost. Appl Microbiol Biotechnol 74: 918925.
  • Yergeau E, Schoondermark-Stolk SA, Brodie EL, Dejean S, DeSantis TZ, Goncalves O, Piceno YM, Andersen GL & Kowalchuk GA (2009) Environmental microarray analyses of Antarctic soil microbial communities. ISME J 3: 340351.
  • Yergeau E, Hogues H, Whyte LG & Greer CW (2010) The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J 4: 12061214.
  • Zhang T, Barry RG, Knowles K, Heginbottom JA & Brown J (2008) Statistics and characteristics of permafrost and ground-ice distribution in the Northern Hemisphere. Polar Geog 31: 4768.
  • Zhou J, Bruns M & Tiedje J (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316322.
  • Zhou JZ, Davey ME, Figueras JB, Rivkina E, Gilichinsky D & Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology 143: 39133919.
  • Zhou JZ, Wu LY, Deng Y et al. (2011) Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5: 13031313.