title: Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments.
abstract: Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.
authors.affiliation: Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.|School of Life Sciences, University of Warwick, Coventry, UK.
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.affiliation: School of Environment and Natural Resources, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Dick
authors.affiliation: Institute of Environmental Engineering, National Chiao Tung University, Hsinchu, 30010, Taiwan.
authors.forename: Jih-Gaw
authors.initials: JG
authors.lastname: Lin
authors.affiliation: Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China. jdgu@hku.hk.
authors.forename: Ji-Dong
authors.identifier: http://orcid.org/0000-0002-7082-9784
authors.initials: JD
authors.lastname: Gu
mesh_terms: D001421:Bacteria, Anaerobic / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D004783:Environmental Microbiology; D008772:Methylococcaceae / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D008828:Microbiological Techniques / Q000379:methods; D009573:Nitrites / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D009573:Nitrites
keywords: Anaerobic methane oxidation; Denitrification; Methylomirabilis oxyfera-like bacteria; Molecular detection; N-damo; PCR primer; pmoA gene