A newly designed degenerate PCR primer based on pmoA gene for detection of nitrite-dependent anaerobic methane-oxidizing bacteria from different ecological niches

Applied Microbiology and Biotechnology

Volumn 97, Issue 23, 2013, Pages 10155-10162

  Han, Ping ^a   Gu, Ji Dong ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Anaerobic methane oxidation; n damo; PCR primer; pmoA gene

Indexed keywords

ANAEROBIC METHANE OXIDATIONS; ANAEROBIC OXIDATION OF METHANES; FRESHWATER RESERVOIRS; METHANE-OXIDIZING BACTERIA; N-DAMO; PCR PRIMERS; PRINCIPAL COORDINATES ANALYSIS; WASTEWATER TREATMENT PLANTS;

AMINO ACIDS; ECOSYSTEMS; GENES; METHANE; POLYMERASE CHAIN REACTION;

BACTERIA;

METHANE; NITRITE;

AMINO ACID; DNA; GENE EXPRESSION; METHANOGENIC BACTERIUM; NICHE; NITRITE; POLYMERASE CHAIN REACTION; SAMPLING;

AMINO ACID SEQUENCE; ANAEROBIC BACTERIUM; ARTICLE; DNA SEQUENCE; ECOLOGICAL NICHE; ECOSYSTEM; FRESHWATER RESERVOIR; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLUM; POLYMERASE CHAIN REACTION; REED BED; RICE PADDY SOIL; SLUDGE; SOIL;

BACTERIA (MICROORGANISMS);

AMINO ACID SEQUENCE; ANAEROBIOSIS; BACTERIA; BACTERIAL PROTEINS; DNA PRIMERS; METHANE; MOLECULAR SEQUENCE DATA; NITRITES; OXIDATION-REDUCTION; OXYGENASES; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SOIL MICROBIOLOGY;

EID: 84888203780     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5260-8     Document Type: Article

References (32)

1. Chung CT, Niemela SL, Miller RH (1989) One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A 86(7):2172-2175
2. Ettwig KF, Shima S, van de Pas-Schoonen KT, Kahnt J, Medema MH, Op den Camp HJ, Jetten MS, Strous M (2008) Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea. Environ Microbiol 10(11):3164-3173
3. Ettwig KF, van Alen T, van de Pas-Schoonen KT, Jetten MS, Strous M (2009) Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum. Appl Environ Microbiol 75(11):3656-3662
4. 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(7288):543-548
5. Ettwig KF, Speth DR, Reimann J, Wu ML, Jetten MS, Keltjens JT (2012) Bacterial oxygen production in the dark. Front Microbiol 3:273
6. Friedrich A, George RL, Bridges CC, Prasad PD, Ganapathy V (2001) Transport of choline and its relationship to the expression of the organic cation transporters in a rat brain microvessel endothelial cell line (RBE4). Biochim Biophys Acta 1512(2):299-307
7. Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305(5689):1457-1462
8. Han P, Gu J-D (2013) More refined diversity of anammox bacteria recovered and distribution in different ecosystems. Appl Microbiol Biotechnol 97(8):3653-3663
9. Ho A, Vlaeminck SE, Ettwig KF, Schneider B, Frenzel P, Boon N (2013) Revisiting methanotrophic communities in sewage treatment plants. Appl Environ Microbiol 79(8):2841-2846
10. Holmes AJ, Costello A, Lidstrom ME, Murrell JC (1995) Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132(3):203-208
11. Hu SH, Zeng RJ, Burow LC, Lant P, Keller J, Yuan ZG (2009) Enrichment of denitrifying anaerobic methane oxidizing microorganisms. Env Microbiol Rep 1(5):377-384
12. Kampman C, Hendrickx TL, Luesken FA, van Alen TA, Op den Camp HJ, Jetten MS, Zeeman G, Buisman CJ, Temmink H (2012) Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment. J Hazard Mater 227-228:164-171
13. King GM, Nanba K (2008) Distribution of atmospheric methane oxidation and methanotrophic communities on Hawaiian volcanic deposits and soils. Microb Environ 23(4):326-330
14. Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol 69(11):6703-6714
15. Kojima H, Tsutsumi M, Ishikawa K, Iwata T, Mussmann M, Fukui M (2012) Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa. Syst Appl Microbiol 35(4):233-238
16. Kruger M, Meyerdierks A, Glockner FO, Amann R, Widdel F, Kube M, Reinhardt R, Kahnt J, Bocher R, Thauer RK, Shima S (2003) A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426(6968):878-881
17. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12):8228-8235
18. Luesken FA, Sanchez J, van Alen TA, Sanabria J, Op den Camp HJ, Jetten MS, Kartal B (2011a) Simultaneous nitrite-dependent anaerobic methane and ammonium oxidation processes. Appl Environ Microbiol 77(19):6802-6807
19. 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(4):845-854
20. Luesken FA, Zhu B, van Alen TA, Butler MK, Diaz MR, Song B, Op den Camp HJ, Jetten MS, Ettwig KF (2011c) pmoA primers for detection of anaerobic methanotrophs. Appl Environ Microbiol 77(11):3877-3880
21. Luke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P (2010) Biogeography of wetland rice methanotrophs. Environ Microbiol 12(4):862-872
22. McDonald IR, Bodrossy L, Chen Y, Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74(5):1305-1315
23. Raghoebarsing AA, Pol A, van de Pas-Schoonen KT, Smolders AJ, Ettwig KF, Rijpstra WI, Schouten S, Damste JS, Op den Camp HJ, Jetten MS, Strous M (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440(7086):918-921
24. Rose TM, Henikoff JG, Henikoff S (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res 31(13):3763-3766
25. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microb 71(3):1501-1506
26. Staheli JP, Boyce R, Kovarik D, Rose TM (2011) CODEHOP PCR and CODEHOP PCR primer design. Methods Mol Biol 687:57-73
27. Wang J, Gu J-D (2013) Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China. Appl Microbiol Biotechnol 97:1785-1798
28. Wang CC, Lee PH, Kumar M, Huang YT, Sung S, Lin JG (2010) Simultaneous partial nitrification, anaerobic ammonium oxidation and denitrification (SNAD) in a full-scale landfill-leachate treatment plant. J Hazard Mater 175(1-3):622-628
29. Wang Y, Zhu G, Harhangi HR, Zhu B, Jetten MS, Yin C, Op den Camp HJ (2012) Co-occurrence and distribution of nitrite-dependent anaerobic ammonium and methane-oxidizing bacteria in a paddy soil. FEMS Microbiol Lett 336(2):79-88
30. Wang J, Dong HL, Wang W-D, Gu J-D (2013) Reverse-transcriptional gene expression of anammox, AOA and AOB in soybean and paddy soils of Northern China. Appl Microbiol Biotechnol. doi: 10.1007/s00253-013-5242-x
31. Wu ML, van Alen TA, van Donselaar EG, Strous M, Jetten MS, van Niftrik L (2012) Co-localization of particulate methane monooxygenase and cd(1) nitrite reductase in the denitrifying methanotroph 'Candidatus Methylomirabilis oxyfera'. FEMS Microbiol Lett 333:49-56
32. Zhu B, Sanchez J, van Alen TA, Sanabria J, Jetten MS, Ettwig KF, Kartal B (2011) Combined anaerobic ammonium and methane oxidation for nitrogen and methane removal. Biochem Soc Trans 39(6):1822-1825