Sự đồng tồn tại của quá trình oxy hóa amoni nitrit phụ thuộc yếm khí và oxy hóa metan trong đất rừng axit cận nhiệt đới

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093/nar/25.17.3389 Beer C, Reichstein M, Tomelleri E, Ciais P, Jung M, Carvalhais N, Rödenbeck C, Arain M, Baldocchi D, Bonan GB, Bondeau A, Cescatti A, Lasslop G, Lindroth A, Lomas M, Luyssaert S, Margolis H, Oleson K, Roupsard O, Veenendaa E, Viovy N, Williams C, Woodward F, Papale D (2010) Terrestrial gross carbon dioxide uptake: global distribution and covariation with climate. Science 329:834–838. doi:10.1126/science Byrne N, Strous M, Crépeau V, Kartal B, Birrien JL, Schmid M, Lesongeur F, Schouten S, Jaeschke A, Jetten M (2009) Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents. ISME J 3:117–123. doi:10.1038/ismej.2008.72 Chamchoi N, Nitisoravut S (2007) Anammox enrichment from different conventional sludges. Chemosphere 66:2225–2232. doi:10.1016/j.chemosphere.2006.09.036 Chan HW, Meng H, Gu J-D (2016) Anamox bacteria detected in fish intestinal tract systems. Appl Environ Biotechnol 1(1):13–18. doi:10.18063/AEB.2016.01.010 Chen J, Zhou ZC, Gu J-D (2014) Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes. Appl Microbiol Biotechnol 98:5685–5696. doi:10.1007/s00253-014-5733-4 Chen J, Zhou ZC, Gu J-D (2015) Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes. Appl Microbiol Biotechnol 99:1463–1473. doi:10.1007/s00253-014-6051-6 Dalsgaard T, Canfield DE, Petersen J, Thamdrup B, Acuña-González J (2003) N2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature 422:606–608. doi:10.1038/nature01526 Dalsgaard T, Thamdrup B, Canfield DE (2005) Anaerobic ammonium oxidation (anammox) in the marine environment. Res Microbiol 156(4):457–464 Egli K, Fanger U, Alvarez PJJ, Siegrist H, van der Meer JR, Zehnder AJB (2001) Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate. Arch Microbiol 175:198–207. doi:10.1007/s002030100255 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 75:3656–3662. doi:10.1128/AEM.00067-09 Gan XH, Zhang FQ, Gu J-D, Guo YD, Li ZQ, Zhang WQ, Xu XY, Zhou Y, Wen XY, Xie GG, Wang YF (2015) Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China. Antonie van Leeuwenhoek 109(2):237–251. doi:10.1007/s10482-015-0627-8 Güven D, Dapena A, Kartal B, Schmid MC, Maas B, van de Pas-Schoonen K, Sozen S, Mendez R, den Camp HJO, Jetten MS (2005) Propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria. Appl Environ Microbiol 71:1066–1071. doi:10.1128/AEM.71.2.1066-1071.2005 Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series 41:95–98 Hammer Ø (2012) PAST: PAleontological STatistics. Version 3.0. University of Oslo, Norway Han P, Gu J-D (2013) More refined diversity of anammox bacteria recovered and distribution in different ecosystems. Appl Microbiol Biotechnol 97:3653–3663. doi:10.1007/s00253-013-4756-6 Haroon MF, Hu S, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567–570. doi:10.1038/nature12375 Humbert S, Tarnawski S, Fromin N, Mallet MP, Aragno M, Zopfi J (2010) Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity. ISME J 4:450–454. doi:10.1038/ismej.2009.125 Humbert S, Zopfi J, Tarnawski SE (2012) Abundance of anammox bacteria in different wetland soils. Environ Microbiol Rep 4:484–490. doi:10.1111/j.1758-2229.2012.00347.x Jaeschke A, den Camp HJO, Harhangi H, Klimiuk A, Hopmans EC, Jetten MS, Schouten S, Damsté JSS (2009) 16S rRNA gene and lipid biomarker evidence for anaerobic ammonium-oxidizing bacteria (anammox) in California and Nevada hot springs. FEMS Microbiol Ecol 67:343–350. doi:10.1111/j.1574-6941.2008.00640.x Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ (2009) Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 44:65–84. doi:10.1080/10409230902722783 Jetten MSM (2001) New pathways for ammonia conversion in soil and aquatic systems. Plant Soil 230:9–19. doi:10.1023/A:1004683807250 Kartal B, Geerts W, Jetten MSM (2011) Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. Method Enzymol 486:89–108. doi:10.1016/B978-0-12-381294-0.00004-3 Kartal B, Rattray J, van Niftrik LA, van de Vossenberg J, Schmid MC, Webb RI, Schouten S, Fuerst JA, Damste JSS, Jetten MSM, Strous M (2007) Candidatus “Anammoxoglobus propionicus” a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria. Syst Appl Microbiol 30:39–49. doi:10.1016/j.syapm.2006.03.004 Kartal B, Van Niftrik L, Rattray J, Van De Vossenberg JL, Schmid MC, Damsté JS, Jetten MS, Strous M (2008) Candidatus ‘Brocadia fulgida’: an autofluorescent anaerobic ammonium oxidizing bacterium. FEMS Microbiol Ecol 63:46–55. doi:10.1111/j.1574-6941.2007.00408.x Kindaichi T, Tsushima I, Ogasawara Y, Shimokawa M, Ozaki N, Satoh H, Okabe S (2007) In situ activity and spatial organization of anaerobic ammonium-oxidizing (anammox) bacteria in biofilms. Appl Environ Microb 73:4931–4939. doi:10.1128/Aem.00156-07 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 35:233–238. doi:10.1016/j.syapm.2012.03.005 Li H, Chen S, Mu BZ, Gu J-D (2010) Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs. Microb Ecol 60:771–783. doi:10.1007/s00248-010-9733-3 Li L, He C, Ji G, Zhi W, Sheng L (2015) Nitrogen removal pathways in a tidal flow constructed wetland under flooded time constraints. Ecol Eng 81:266–271. doi:10.1016/j.ecoleng.2015.04.073 Li M, Gu J-D (2016) Molecular evidence of the existence of anaerobic ammonia oxidation bacteria in the gut of polychaete (Neanthes glandicincta). Appl Environ Biotechnol 1(1):19–29. doi:10.18063/AEB.2016.01.011 Liu Y, Zhang J, Zhao L, Li Y, Yang Y, Xie S (2015) Aerobic and nitrite-dependent methane-oxidizing microorganisms in sediments of freshwater lakes on the Yunnan Plateau. Appl Microbiol Biotechnol 99:2371–2381. doi:10.1007/s00253-014-6141-5 Long A, Heitman J, Tobias C, Philips R, Song B (2013) Co-occurring anammox, denitrification, and codenitrification in agricultural soils. Appl Environmental Microbiol 79:168–176. doi:10.1128/AEM.02520-12 Luesken FA, Sánchez J, van Alen TA, Sanabria J, den Camp HJO, Jetten MS, Kartal B (2011a) Simultaneous nitrite-dependent anaerobic methane and ammonium oxidation processes. Appl Environmental Microbiol 77:6802–6807. doi:10.1128/AEM.05539-11 Luesken FA, Zhu BL, van Alen TA, Butler MK, Diaz MR, Song B, den Camp HJMO, Jetten MSM, Ettwig KF (2011b) pmoA primers for detection of anaerobic methanotrophs. Appl Environ Microbiol 77:3877–3880. doi:10.1128/AEM.02960-10 Moore TA, Xing Y, Lazenby B, Lynch MD, Schiff S, Robertson WD, Timlin R, Lanza S, Ryan MC, Aravena R (2011) Prevalence of anaerobic ammonium-oxidizing bacteria in contaminated groundwater. Environ Sci Technol 45:7217–7225. doi:10.1021/es201243t Mulder A, Graaf A, Robertson L, Kuenen J (1995) Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor. FEMS Microbiol Ecol 16:177–184. doi:10.1016/0168-6496(94)00081-7 Quan ZX, Rhee SK, Zuo JE, Yang Y, Bae JW, Park JR, Lee ST, Park YH (2008) Diversity of ammonium-oxidizing bacteria in a granular sludge anaerobic ammonium-oxidizing (anammox) reactor. Environ Microbiol 10:3130–3139. doi:10.1111/j.1462-2920.2008.01642.x Raghoebarsing AA, Pol A, Van de Pas-Schoonen KT, Smolders AJ, Ettwig KF, Rijpstra WIC, Schouten S, Damsté JSS, den Camp HJO, Jetten MS (2006) A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918–921. doi:10.1038/nature04617 Reichle DE (1981) Dynamic properties of forest ecosystems. Cambridge University Press, New York Rysgaard S, Glud RN, Sejr MK, Blicher ME, Stahl HJ (2008) Denitrification activity and oxygen dynamics in Arctic Sea ice. Polar Biol 31:527–537. doi:10.1007/s00300-007-0384-x Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541. doi:10.1128/AEM.01541-09 Schmid M, Twachtmann U, Klein M, Strous M, Juretschko S, Jetten M, Metzger JW, Schleifer K-H, Wagner M (2000) Molecular evidence for genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst Appl Microbiol 23:93–106. doi:10.1016/S0723-2020(00)80050-8 Schmid M, Walsh K, Webb R, Rijpstra WI, van de Pas-Schoonen K, Verbruggen MJ, Hill T, Moffett B, Fuerst J, Schouten S (2003) Candidatus “Scalindua brodae”, sp. nov., Candidatus “Scalindua wagneri”, sp. nov., two new species of anaerobic ammonium oxidizing bacteria. Syst Appl Microbiol 26:529–538. doi:10.1078/072320203770865837 Schubert CJ, Durisch-Kaiser E, Wehrli B, Thamdrup B, Lam P, Kuypers MM (2006) Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika). Environ Microbiol 8:1857–1863. doi:10.1111/j.1462-2920.2006.01074.x Sedjo RA (1993) The carbon cycle and global forest ecosystem. Water Air Soil Poll 70:295–307. doi:10.1007/BF01105003 Shen LD, Liu S, He ZF, Lian X, Huang Q, He YF, Lou LP, Xu XY, Zheng P, Hu BL (2015) Depth-specific distribution and importance of nitrite-dependent anaerobic ammonium and methane-oxidising bacteria in an urban wetland. Soil Biol Biochem 83:43–51. doi:10.1016/j.soilbio.2015.01.010 Shen LD, Liu S, Huang Q, Lian X, He ZF, Geng S, Jin RC, He YF, Lou LP, Xu XY (2014a) Evidence for the cooccurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field. Appl Environmental Microbiol 80:7611–7619. doi:10.1128/AEM.02379-14 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-oxidizing bacteria in the sediments of the Qiantang River. Microb Ecol 67:341–349. doi:10.1007/s00248-013-0330-0 Strous M, Fuerst JA, Kramer EHM, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG, Jetten MSM (1999) Missing lithotroph identified as new planctomycete. Nature 400:446–449. doi:10.1038/22749 Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790–794. doi:10.1038/Nature04647 Tang CJ, Zheng P, Zhang L, Chen JW, Mahmood Q, Chen XG, Hu BL, Wang CH, Yu Y (2010) Enrichment features of anammox consortia from methanogenic granules loaded with high organic and methanol contents. Chemosphere 79:613–619. doi:10.1016/j.chemosphere.2010.02.045 Ter Braak CJ, Smilauer P (2012) Canoco reference manual and user’s guide: software for ordination, version 5.0. Microcomputer Power, Ithaca Thompson JD, Gibson T, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2.3. 1–2.3. 22. Wiley, New York US Department of Agriculture (1999) Soil taxonomy—a basic system of soil classification for making and interpreting soil surveys. USDA, Washington Van de Graaf AA, de Bruijn P, Robertson LA, Jetten MS, Kuenen JG (1996) Autotrophic growth of anaerobic ammonium-oxidizing micro-organisms in a fluidized bed reactor. Microbiol 142:2187–2196. doi:10.1099/13500872-142-8-2187 Van de Graaf AA, Mulder A, de Bruijn P, Jetten M, Robertson LA, Kuenen JG (1995) Anaerobic oxidation of ammonium is a biologically mediated process. Appl Environmental Microbiol 61:1246–1251 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. doi:10.1007/s00253-012-4036-x Wang Y, Zhu G, Harhangi HR, Zhu B, Jetten MS, Yin C, den Camp HJO (2012) Co-occurrence and distribution of nitrite-dependent anaerobic ammonium and methane-oxidizing bacteria in a paddy soil. FEMS Microbiol Lett 336:79–88. doi:10.1111/j.1574-6968.2012.02654.x Wright ES, Yilmaz LS, Noguera DR (2012) DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environmental Microbiol 78:717–725. doi:10.1128/AEM.06516-11 Wu L, Zhang L, Shi X, Liu T, Peng Y, Zheng J (2015) Analysis of the impact of reflux ratio on coupled partial nitrification-anammox for co-treatment of mature landfill leachate and domestic wastewater. Bioresource Technol 198:207–214. doi:10.1016/j.biortech.2015.08.072 Yang J, Jiang H, Wu G, Hou W, Sun Y, Lai Z, Dong H (2012) Co-occurrence of nitrite-dependent anaerobic methane oxidizing and anaerobic ammonia oxidizing bacteria in two Qinghai-Tibetan saline lakes. Front Earth Sci 6:383–391. doi:10.1007/s11707-012-0336-9 Zhang Y, Ruan XH, Op den Camp HJ, Smits TJ, Jetten MS, Schmid MC (2007) Diversity and abundance of aerobic and anaerobic ammonium-oxidizing bacteria in freshwater sediments of the Xinyi River (China). Environ Microbiol 9:2375–2382. doi:10.1111/j.1462-2920.2007.01357.x Zhou LL, Wang Y, Long XE, Guo JH, Zhu GB (2014) High abundance and diversity of nitrite-dependent anaerobic methane-oxidizing bacteria in a paddy field profile. FEMS Microbiol Lett 360:33–41. doi:10.1111/1574-6968.12567 Zhu G, Wang S, Wang Y, Wang C, Risgaard-Petersen N, Jetten MS, Yin C (2011) Anaerobic ammonia oxidation in a fertilized paddy soil. ISME J 5:1905–1912. doi:10.1038/ismej.2011.63 Zhu GB, Zhou LL, Wang Y, Wang SY, Guo JH, Long XE, Sun XB, Jiang B, Hou QY, Jetten MSM, Yin CQ (2015) Biogeographical distribution of denitrifying anaerobic methane oxidizing bacteria in Chinese wetland ecosystems. Env Microbiol Rep 7:128–138. doi:10.1111/1758-2229.12214