TY - JOUR
T1 - A newly designed degenerate PCR primer based on pmoA gene for detection of nitrite-dependent anaerobic methane-oxidizing bacteria from different ecological niches
AU - Han, Ping
AU - Gu, Ji Dong
N1 - Funding Information:
Acknowledgments This research project was supported in part by a Ph.D. studentship from The University of Hong Kong (PH) and additional financial support of Environmental Toxicology Education and Research Fund of this laboratory. Ms. Jessie Lai and Ms. Kelly Lau were thanked for their laboratory assistance.
PY - 2013/12
Y1 - 2013/12
N2 - A new pmoA gene-based PCR primer set was designed for detection of nitrite-dependent anaerobic oxidation of methane (n-damo) bacteria from four different ecosystems, namely rice paddy soil, freshwater reservoir, reed bed, and sludge from wastewater treatment plant. This primer set showed high specificity and efficiency in recovering n-damo bacteria from these diverse samples. The obtained sequences showed 88-94 and 90-96 % similarity to nucleotide and amino acid sequences, respectively, with the known NC10 phylum bacterium. According to the UniFrac principal coordinates analysis (PCoA), DNA sequences retrieved by the new PCR primer set in this study formed a separate group from the reported sequences, indicating higher diversity of n-damo in the environment. This newly designed PCR primer is capable of amplifying not only the currently known n-damo bacteria but also those that have not been reported, providing new information on the ecological diversity and distribution of this group of microorganisms in the ecosystem.
AB - A new pmoA gene-based PCR primer set was designed for detection of nitrite-dependent anaerobic oxidation of methane (n-damo) bacteria from four different ecosystems, namely rice paddy soil, freshwater reservoir, reed bed, and sludge from wastewater treatment plant. This primer set showed high specificity and efficiency in recovering n-damo bacteria from these diverse samples. The obtained sequences showed 88-94 and 90-96 % similarity to nucleotide and amino acid sequences, respectively, with the known NC10 phylum bacterium. According to the UniFrac principal coordinates analysis (PCoA), DNA sequences retrieved by the new PCR primer set in this study formed a separate group from the reported sequences, indicating higher diversity of n-damo in the environment. This newly designed PCR primer is capable of amplifying not only the currently known n-damo bacteria but also those that have not been reported, providing new information on the ecological diversity and distribution of this group of microorganisms in the ecosystem.
KW - Anaerobic methane oxidation
KW - PCR primer
KW - n-damo
KW - pmoA gene
UR - http://www.scopus.com/inward/record.url?scp=84888203780&partnerID=8YFLogxK
U2 - 10.1007/s00253-013-5260-8
DO - 10.1007/s00253-013-5260-8
M3 - 文章
C2 - 24201910
AN - SCOPUS:84888203780
SN - 0175-7598
VL - 97
SP - 10155
EP - 10162
JO - Applied Microbiology and Biotechnology
JF - Applied Microbiology and Biotechnology
IS - 23
ER -
