New PCR primers based on mcrA gene for retrieving more anaerobic methanotrophic archaea from coastal reedbed sediments

TY - JOUR

T1 - New PCR primers based on mcrA gene for retrieving more anaerobic methanotrophic archaea from coastal reedbed sediments

AU - Zhou, Zhichao

AU - Han, Ping

AU - Gu, Ji Dong

N1 - Funding Information: Acknowledgements This project was supported with a University Foundation Ph.D. Fellowship from the Graduate School, The University of Hong Kong (ZZ) and NSFC/RGC project N_HKU 718/11 (J-DG). We thank Ms. Kelly Lau for supportive technical assistance in laboratory.

PY - 2014/5

Y1 - 2014/5

N2 - Two pairs of PCR primes ANMEallF/R and ANME23F/R were designed by Codehop method based on sequences available to retrieve more anaerobic methanotrophic (ANME) archaea mcrA gene sequences and ANME 2 and 3 subtypes from reedbed in two seasons. Overall, the PCR primers showed slightly favor for ANME group mcrA gene sequences. Due to the predominance of methanogens mainly affiliated to Methanomicrobiales in the samples, a large portion of mcrA gene sequences amplified in the clone libraries belonged to methanogens. Differences in PCR primers and performance affected the mcrA gene-PCR-amplified community composition to a minor extent. PCR primers targeting ANME mcrA group g-h were designed to apply real-time PCR for quantifying more groups of mcrA gene-affiliated ANME archaea and tested with these same samples, and the most abundant group in the whole ANME mcrA community was ANME group g-h. In addition, a stable mcrA gene-harboring archaeal community pattern was detected in the reedbed sediment samples collected from two distinctively different seasons. The PCR and qPCR primers designed in this study can expand our knowledge on the distribution of ANME mcrA genes and community composition in the ecosystem to better understand the carbon cycle.

AB - Two pairs of PCR primes ANMEallF/R and ANME23F/R were designed by Codehop method based on sequences available to retrieve more anaerobic methanotrophic (ANME) archaea mcrA gene sequences and ANME 2 and 3 subtypes from reedbed in two seasons. Overall, the PCR primers showed slightly favor for ANME group mcrA gene sequences. Due to the predominance of methanogens mainly affiliated to Methanomicrobiales in the samples, a large portion of mcrA gene sequences amplified in the clone libraries belonged to methanogens. Differences in PCR primers and performance affected the mcrA gene-PCR-amplified community composition to a minor extent. PCR primers targeting ANME mcrA group g-h were designed to apply real-time PCR for quantifying more groups of mcrA gene-affiliated ANME archaea and tested with these same samples, and the most abundant group in the whole ANME mcrA community was ANME group g-h. In addition, a stable mcrA gene-harboring archaeal community pattern was detected in the reedbed sediment samples collected from two distinctively different seasons. The PCR and qPCR primers designed in this study can expand our knowledge on the distribution of ANME mcrA genes and community composition in the ecosystem to better understand the carbon cycle.

KW - Anaerobic methane oxidation

KW - Carbon cycle

KW - Methanogenesis and methane oxidation

KW - PCR detection

KW - mcrA gene

KW - qPCR

UR - http://www.scopus.com/inward/record.url?scp=84900822135&partnerID=8YFLogxK

U2 - 10.1007/s00253-014-5599-5

DO - 10.1007/s00253-014-5599-5

M3 - 文章

C2 - 24639204

AN - SCOPUS:84900822135

SN - 0175-7598

VL - 98

SP - 4663

EP - 4670

JO - Applied Microbiology and Biotechnology

JF - Applied Microbiology and Biotechnology

IS - 10

ER -