Comparison of droplet digital PCR and quantitative real-time PCR in mcrA-based methanogen community analysis

Demirel, 2008, The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review, Rev. Environ. Sci. Biotechnol., 7, 173, 10.1007/s11157-008-9131-1 Garcia, 2000, Taxonomic, phylogenetic, and ecological diversity of methanogenic archaea, Anaerobe, 6, 205, 10.1006/anae.2000.0345 Hayden, 2013, Comparison of droplet digital PCR to real-time PCR for quantitative detection of Cytomegalovirus, J. Clin. Microbiol., 51, 540, 10.1128/JCM.02620-12 Henrich, 2012, Low-level detection and quantitation of cellular HIV-1 DNA and 2-LTR circles using droplet digital PCR, J. Virol. Methods, 186, 68, 10.1016/j.jviromet.2012.08.019 Higuchi, 1993, Kinetic PCR analysis: real-time monitoring of DNA amplification reactions, Nat. Biotechnol., 11, 1026, 10.1038/nbt0993-1026 Hindson, 2011, High-throughput droplet digital PCR system for absolute quantitation of DNA copy number, Anal. Chem., 83, 8604, 10.1021/ac202028g Kelley, 2013, Detection of methicillin-resistant Staphylococcus aureus by a duplex droplet digital PCR assay, J. Clin. Microbiol., 51, 2033, 10.1128/JCM.00196-13 Kim, 2014, Comparison of droplet digital PCR and quantitative real-time PCR for examining population dynamics of bacteria in soil, Appl. Microbiol. Biotechnol., 98, 6105, 10.1007/s00253-014-5794-4 Kim, 2013, Use of artificial DNA with multiple probe sites as reference DNA templates for quantitative real-time PCR to examine methanogen communities, J. Environ. Sci. Health Part A, 48, 417, 10.1080/10934529.2013.728915 Leclerc, 2004, Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing, Environ. Microbiol., 6, 809, 10.1111/j.1462-2920.2004.00616.x Levén, 2007, Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste, FEMS Microbiol. Ecol., 59, 683, 10.1111/j.1574-6941.2006.00263.x Morisset, 2013, Quantitative analysis of food and feed samples with droplet digital PCR, PLoS One, 8, e62583, 10.1371/journal.pone.0062583 Pinheiro, 2012, Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification, Anal. Chem., 84, 1003, 10.1021/ac202578x Steinberg, 2009, mcrA-targeted real-time quantitative PCR method to examine methanogen communities, Appl. Environ. Microbiol., 75, 4435, 10.1128/AEM.02858-08 Strain, 2013, Highly precise measurement of HIV DNA by droplet digital PCR, PLoS One, 8, e55943, 10.1371/journal.pone.0055943 Stults, 2001, Application of the 5′ fluorogenic exonuclease assay (taqMan) for quantitative ribosomal DNA and rRNA analysis in sediments, Appl. Environ. Microbiol., 67, 2781, 10.1128/AEM.67.6.2781-2789.2001 Sundberg, 2013, 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters, FEMS Microbiol. Ecol., 85, 612, 10.1111/1574-6941.12148 ter Braak, 2002 Zielińska, 2013, Impact of temperature, microwave radiation and organic loading rate on methanogenic community and biogas production during fermentation of dairy wastewater, Bioresour. Technol., 129, 308, 10.1016/j.biortech.2012.11.093