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Design and evaluation of universal 16S rRNA gene primers for high-throughput sequencing to simultaneously detect DAMO microbes and anammox bacteria

Lu, Yong-Ze, Ding, Zhao-Wei, Ding, Jing, Fu, Liang, Zeng, Raymond J.
Water research 2015 v.87 pp. 385-394
Archaea, DNA primers, anaerobic ammonium oxidation, community structure, data collection, denitrification, fermentation, freshwater, genes, high-throughput nucleotide sequencing, methane, nitrifying bacteria, oxidation, plant cultural practices, ribosomal RNA, sediments, wastewater treatment
To develop universal 16S rRNA gene primers for high-throughput sequencing for the simultaneous detection of denitrifying anaerobic methane oxidation (DAMO) archaea, DAMO bacteria, and anaerobic ammonium oxidation (anammox) bacteria, four published primer sets (PS2–PS5) were modified. The overall coverage of the four primer pairs was evaluated in silico with the Silva SSU r119 dataset. Based on the virtual evaluation, the two best primer pairs (PS4 and PS5) were selected for further verification. Illumina MiSeq sequencing of a freshwater sediment and a culture from a DAMO–anammox reactor using these two primer pairs revealed that PS5 (341b4F–806R) was the most promising universal primer pair. This pair of primers detected both archaea and bacteria with less bias than PS4. Furthermore, an anaerobic fermentation culture and a wastewater treatment plant culture were used to verify the accuracy of PS5. More importantly, it detected DAMO archaea, DAMO bacteria, and anammox bacteria simultaneously with no false positives appeared. This universal 16S rRNA gene primer pair extends the existing molecular tools for studying the community structures and distributions of DAMO microbes and their potential interactions with anammox bacteria in different environments.