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

Tae Gwan Kim, So Yeon Jeong, Kyung Suk Cho

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12 Scopus citations

Abstract

Two different quantitative PCR platforms, droplet digital PCR (dd-PCR) and quantitative real-time PCR (qPCR), were compared in a mcrA-based methanogen community assay that quantifies ten methanogen sub-groups. Both technologies exhibited similar PCR efficiencies over at least four orders of magnitude and the same lower limits of detection (8 copiesmL-DNA extract-1). The mcrA-based methanogen communities in three full-scale anaerobic digesters were examined using the two technologies. dd-PCR detected seven groups from the digesters, while qPCR did five groups, indicating that dd-PCR is more sensitive for DNA quantification. Linear regression showed quantitative agreements between both of the technologies (R2 = 0.59-0.98) in the five groups that were concurrently detected. Principal component analysis from the two datasets consistently indicated a substantial difference in the community composition among the digesters and revealed similar levels of differentiation among the communities. The combined results suggest that dd-PCR is more promising for examining methanogenic archaeal communities in biotechnological processes.

Original languageEnglish
Pages (from-to)1-4
Number of pages4
JournalBiotechnology Reports
Volume4
Issue number1
DOIs
StatePublished - 1 Dec 2014

Keywords

  • Anaerobic digester
  • Droplet-digital PCR
  • mcrA
  • Methanogen community
  • Quantitative real-time PCR

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