Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments
- 814 Downloads
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.
KeywordsN-damo Anaerobic methane oxidation Denitrification Methylomirabilis oxyfera-like bacteria Molecular detection PCR primer pmoA gene
This project was supported by Hong Kong PhD Fellowship (JC) and RGC GRF grant no. 701913 (J-DG). Additional financial support for this research project was from the laboratory fund.
Compliance with ethical standards
This study was funded by RGC GRF grant no. 701913 (J-DG) and a Hong Kong PhD Fellowship (JC).
Conflict of interest
All authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543–548CrossRefPubMedGoogle Scholar
- Gao J, Luo X, Wu G, Peng Y (2013) Occurrence of nitrite-dependent anaerobic methane oxidizing bacteria from different soil and wastewater sludge. NCBI Genbank web http://www.ncbinlmnihgov/nuccore/ Accessed 17 April 2014
- Han P, Gu J-D (2015) Further analysis of anammox bacterial community structures along an anthropogenic nitrogen-input gradient from the riparian sediments of the Pearl River Delta to the deep-ocean sediments of the South China Sea. Geomicrobiolgy. Journal 32:789–798Google Scholar
- Hu BL, Shen LD, Lian X, Zhu Q, Liu S, Huang Q, He ZF, Geng S, Cheng DQ, Lou LP, Xu XY, Zheng P, He YF (2014) Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands. Proc Natl Acad Sci U S A 111:4495–4500CrossRefPubMedPubMedCentralGoogle Scholar
- Juretschko S, Timmermann G, Schmid M, Schleifer KH, Pommerening-Roser A, Koops HP, Wagner M (1998) Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl Environ Microbiol 64:3042–3051PubMedPubMedCentralGoogle Scholar
- Kojima H, Tokizawa R, Kogure K, Kobayashi Y, Itoh M, Shiah FK, Okuda N, Fukui M (2014) Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer. Scientific Reports 4:5728CrossRefPubMedPubMedCentralGoogle Scholar
- Kool DM, Zhu BL, Rijpstra WIC, Jetten MSM, Ettwig KF, Damste JSS (2012) Rare branched fatty acids characterize the lipid composition of the intra-aerobic methane oxidizer “Candidatus Methylomirabilis oxyfera”. Appl Environ Microbiol 78:8650–8656Google Scholar
- Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp. 115–175Google Scholar
- Luesken FA, van Alen TA, van der Biezen E, Frijters C, Toonen G, Kampman C, Hendrickx TL, Zeeman G, Temmink H, Strous M, Op den Camp HJ, Jetten MS (2011b) Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge. Appl Microbiol Biotechnol 92:845–854CrossRefPubMedPubMedCentralGoogle Scholar
- Masashi, H, Masafumi, K, Masato, K, Takashi, Y (2013) Enrichment of denitrifying anaerobic methane oxidizing microorganisms using nitrate or nitrite as electron acceptor. NCBI Genbank web http://wwwncbinlmnihgov/nuccore/ Accessed 17 April 2014Google Scholar
- Mason I (1977) Methane as a carbon source in biological denitrification. Journal of Water Pollution Control Federation 49:855–857Google Scholar
- Raghoebarsing AA, Smolders AJ, Schmid MC, Rijpstra WI, Wolters-Arts M, Derksen J, Jetten MS, Schouten S, Sinninghe Damste JS, Lamers LP, Roelofs JG, Op den Camp HJ, Strous M (2005) Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436:1153–1156CrossRefPubMedGoogle Scholar
- Shen LD, Liu S, Huang Q, Lian X, He ZF, Geng S, Jin RC, He YF, Lou LP, Xu XY, Zheng P, Hu BL (2014a) Evidence for the cooccurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field. Appl Environ Microbiol 80:7611–7619CrossRefPubMedPubMedCentralGoogle Scholar
- Shen LD, Liu S, Zhu Q, Li XY, Cai C, Cheng DQ, Lou LP, Xu XY, Zheng P, Hu BL (2014b) Distribution and diversity of nitrite-dependent anaerobic methane-oxidising bacteria in the sediments of the Qiantang River. Microb Ecol 67:341–349Google Scholar
- Wu ML, Ettwig KF, Jetten MS, Strous M, Keltjens JT, van Niftrik L (2011) A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus ‘Methylomirabilis oxyfera’. Biochem Soc Trans 39:243–248Google Scholar
- Zhu Q, Shen LD, Hu BL, Lou LP, Cheng DQ (2013) Molecular detection of denitrifying anaerobic oxidizing bacteria in the sediment of West Lake, Hangzhou. Acta Sci Circumst 33:1321–1325Google Scholar