基于数据库分析不同类型生境中厌氧氨氧化细菌的多样性分布特征
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摘要
【目的】厌氧氨氧化过程是一种能在厌氧条件下氧化NH4+同时还原NO2–或者NO3–生成N2的过程,是氮素循环过程的重要途径之一。厌氧氨氧化过程由厌氧氨氧化细菌催化完成,目前通过分子生物学的手段已证实了厌氧氨氧化细菌存在于多种类型的生境中,本文对厌氧氨氧化细菌在不同类型生境中的多样性分布规律进行了系统分析。【方法】基于NCBI数据库中厌氧氨氧化细菌的16SrRNA基因序列,利用Mothur分析平台系统分析了厌氧氨氧化细菌在不同生境中的多样性分布规律和特征。【结果】分析表明,海洋环境中Ca. Scalindua属的厌氧氨氧化细菌占绝对主导;淡水和农业土壤中Ca. Brocadia属的厌氧氨氧化细菌占优势;工程系统中普遍存在Ca. Brocadia和Ca. Kuenenia属的厌氧氨氧化细菌;而湿地和河口环境中厌氧氨氧化细菌多样性最高,Ca. Scalindua、Ca. Brocadia和Ca. Kuenenia属的厌氧氨氧化细菌均有较高的相对丰度,显示出了陆地与海洋交汇的显著特征。【结论】本研究系统展示了不同的生境中厌氧氨氧化细菌的多样性群落结构生境分布特征,表明环境特征差异直接影响了厌氧氨氧化细菌的种群分布和系统演化。
[Objective] Anaerobic ammonium oxidation is a biogeochemical process of oxidizing ammonium and reducing nitrite or nitrate to produce N2 by anaerobic ammonium-oxidizing bacteria under anaerobic conditions,which is an important process for removing fixed nitrogen from global ecosystem. The objective of this study is to demonstrate the biogeography patterns of ammonium-oxidizing bacteria in diverse habitats. [Methods] Based on the 16 S rRNA gene sequences of ammonium-oxidizing bacteria from national center for biotechnology information database, we analyzed the distribution and diversity of ammonium-oxidizing bacteria in different habitat by Mothur Software. [Results] Results showed that Ca. Scalindua dominated in marine environment. Ca. Brocadia had broad distribution in both freshwater and agricultural soils ecosystem, and it was also dominant in engineered reactors,showing the higher concentration inorganic nitrogen may facilitate Ca. Brocadia existence. Wetland and estuary ecosystem had the highest diversity of ammonium-oxidizing bacteria in which Ca. Scalindua, Ca. Brocadia and Ca.Kuenenia all had relative higher abundance. [Conclusion] This study demonstrated the community structure and distribution characteristics of ammonium-oxidizing bacteria in different habitat, suggesting that different environmental factors in different habitat affect the population distribution and phylogenetic evolution of ammonium-oxidizing bacteria.
[Objective] Anaerobic ammonium oxidation is a biogeochemical process of oxidizing ammonium and reducing nitrite or nitrate to produce N2 by anaerobic ammonium-oxidizing bacteria under anaerobic conditions,which is an important process for removing fixed nitrogen from global ecosystem. The objective of this study is to demonstrate the biogeography patterns of ammonium-oxidizing bacteria in diverse habitats. [Methods] Based on the 16 S rRNA gene sequences of ammonium-oxidizing bacteria from national center for biotechnology information database, we analyzed the distribution and diversity of ammonium-oxidizing bacteria in different habitat by Mothur Software. [Results] Results showed that Ca. Scalindua dominated in marine environment. Ca. Brocadia had broad distribution in both freshwater and agricultural soils ecosystem, and it was also dominant in engineered reactors,showing the higher concentration inorganic nitrogen may facilitate Ca. Brocadia existence. Wetland and estuary ecosystem had the highest diversity of ammonium-oxidizing bacteria in which Ca. Scalindua, Ca. Brocadia and Ca.Kuenenia all had relative higher abundance. [Conclusion] This study demonstrated the community structure and distribution characteristics of ammonium-oxidizing bacteria in different habitat, suggesting that different environmental factors in different habitat affect the population distribution and phylogenetic evolution of ammonium-oxidizing bacteria.
引文
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[13]Borin S,Mapelli F,Rolli E,Song B,Tobias C,Schmid MC,De Lange GJ,Reichart GJ,Schouten S,Jetten M,Daffonchio D.Anammox bacterial populations in deep marine hypersaline gradient systems.Extremophiles,2013,17(2):289-299.
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[18]Hu BL,Shen LD,Liu S,Cai C,Chen TT,Kartal B,Harhangi HR,Op den Camp HJM,Lou LP,Xu XY,Zheng P,Jetten MSM.Enrichment of an anammox bacterial community from a flooded paddy soil.Environmental Microbiology Reports,2013,5(3):483-489.
[19]Hong YG,Li M,Cao HL,Gu JD.Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea:analyses of marker gene abundance with physical chemical parameters.Microbial Ecology,2011,62(1):36-47.
[20]Hendrickx TLG,Kampman C,Zeeman G,Temmink H,Hu ZY,Kartal B,Buisman CJN.High specific activity for anammox bacteria enriched from activated sludge at 10°C.Bioresource Technology,2014,163:214-221.
[21]Wang J,Gu JD.Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China.Applied Microbiology and Biotechnology,2013,97(4):1785-1798.
[22]Ali M,Oshiki M,Awata T,Isobe K,Kimura Z,Yoshikawa H,Hira D,Kindaichi T,Satoh H,Fujii T,Okabe S.Physiological characterization of anaerobic ammonium oxidizing bacterium‘Candidatus Jettenia caeni’.Environmental Microbiology,2015,17(6):2172-2189.
[23]Kartal B,Koleva M,Arsov R,van der Star W,Jetten MSM,Strous M.Adaptation of a freshwater anammox population to high salinity wastewater.Journal of Biotechnology,2006,126(4):546-553.
[24]Hou LJ,Zheng YL,Liu M,Gong J,Zhang XL,Yin GY,You L.Anaerobic ammonium oxidation(anammox)bacterial diversity,abundance,and activity in marsh sediments of the Yangtze Estuary.Journal of Geophysical Research Biogeosciences,2013,118(3):1237-1246.
[25]Koop-Jakobsen K,Giblin AE.Anammox in tidal marsh sediments:the role of salinity,nitrogen loading,and marsh vegetation.Estuaries and Coasts,2009,32(2):238-245.
[26]Shao SD,Luan XW,Dang HY,Zhou HX,Zhao YK,Liu HT,Zhang YB,Dai LQ,Ye Y,Klotz MG.Deep-sea methane seep sediments in the Okhotsk Sea sustain diverse and abundant anammox bacteria.FEMS Microbiology Ecology,2014,87(2):503-516.
[27]van de Vossenberg J,Woebken D,Maalcke WJ,Wessels HJCT,Dutilh BE,Kartal B,Janssen-Megens EM,Roeselers G,Yan J,Speth D,Gloerich J,Geerts W,van der Biezen E,Pluk W,Francoijs KJ,Russ L,Lam P,Malfatti SA,Tringe SG,Haaijer SCM,Op den Camp HJM,Stunnenberg HG,Amann R,Kuypers MMM,Jetten MSM.The metagenome of the marine anammox bacterium‘Candidatus Scalindua profunda’illustrates the versatility of this globally important nitrogen cycle bacterium.Environmental Microbiology,2013,15(5):1275-1289.
[28]Sun W,Xu MY,Wu WM,Guo J,Xia CY,Sun GP,Wang AJ.Molecular diversity and distribution of anammox community in sediments of the Dongjiang River,a drinking water source of Hong Kong.Journal of Applied Microbiology,2014,116(2):464-476.
[29]Sonthiphand P,Neufeld JD.Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.PLoS One,2013,8(3):e57242.
[30]Moore TA,Xing YP,Lazenby B,Lynch MDJ,Schiff S,Robertson WD,Timlin R,Lanza S,Ryan MC,Aravena R,Fortin D,Clark ID,Neufeld JD.Prevalence of anaerobic ammonium-oxidizing bacteria in contaminated groundwater.Environmental Science&Technology,2011,45(17):7217-7225.
[31]Sher Y,Baram S,Dahan O,Ronen Z,Nejidat A.Ammonia transformations and abundance of ammonia oxidizers in a clay soil underlying a manure pond.FEMS Microbiology Ecology,2012,81(1):145-155.
[32]Zhu GB,Wang SY,Wang Y,Wang CX,Risgaard-Petersen N,Jetten MSM,Yin CQ.Anaerobic ammonia oxidation in a fertilized paddy soil.The ISME Journal,2011,5(12):1905-1912.
[33]Oshiki M,Shimokawa M,Fujii N,Satoh H,Okabe S.Physiological characteristics of the anaerobic ammonium-oxidizing bacterium‘Candidatus Brocadia sinica’.Microbiology,2011,157:1706-1713.
[34]van der Star WRL,Miclea AI,van Dongen UGJM,Muyzer G,Picioreanu C,van Loosdrecht MCM.The membrane bioreactor:a novel tool to grow anammox bacteria as free cells.Biotechnology and Bioengineering,2008,101(2):286-294.
[2]Broda E.Two kinds of lithotrophs missing in nature.Zeitschrift für Allgemeine Mikrobiologie,1977,17(6):491-493.
[3]Mulder A,van de Graaf AA,Robertson L A,Kuenen JG.Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor.FEMS Microbiology Ecology,1995,16(3):177-184.
[4]Lotti T,Kleerebezem R,Lubello C,van Loosdrecht MCM.Physiological and kinetic characterization of a suspended cell anammox culture.Water Research,2014,60:1-14.
[5]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 HJ,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 MS,Wagner M,Le Paslier D.Deciphering the evolution and metabolism of an anammox bacterium from a community genome.Nature,2006,440(7085):790-794.
[6]Mao NJ,Ren HQ,Geng JJ,Ding LL,Xu K.Engineering application of anaerobic ammonium oxidation process in wastewater treatment.World Journal of Microbiology and Biotechnology,2017,33(8):153.
[7]Schmid MC,Maas B,Dapena A,van de Pas-Schoonen K,van de Vossenberg J,Kartal B,van Niftrik L,Schmidt I,Cirpus I,Kuenen JG,Wagner M,DamstéJSS,Kuypers M,Revsbech NP,Mendez R,Jetten MSM,Strous M.Biomarkers for in situ detection of anaerobic ammonium-oxidizing(anammox)bacteria.Applied and Environmental Microbiology,2005,71(4):1677-1684.
[8]Thamdrup B,Dalsgaard T.Production of N2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments.Applied and Environmental Microbiology,2002,68(3):1312-1318.
[9]Song B,Buckner CT,Hembury DJ,Mills RA,Palmer MR.Impact of volcanic ash on anammox communities in deep sea sediments.Environmental Microbiology Reports,2014,6(2):159-166.
[10]Zhu GB,Wang SY,Wang WD,Wang Y,Zhou LL,Jiang B,Op den Camp HJM,Risgaard-Petersen N,Schwark L,Peng YZ,Hefting MM,Jetten MSM,Yin CQ.Hotspots of anaerobic ammonium oxidation at land-freshwater interfaces.Nature Geoscience,2013,6(2):103-107.
[11]Humbert S,Tarnawski S,Fromin N,Mallet MP,Aragno M,Zopfi J.Molecular detection of anammox bacteria in terrestrial ecosystems:distribution and diversity.The ISMEJournal,2010,4(3):450-454.
[12]Russ L,Kartal B,op den Camp HJM,Sollai M,Le Bruchec J,Caprais JC,Godfroy A,DamstéJSS,Jetten MSM.Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin.Frontiers in Microbiology,2013,4(1):219.
[13]Borin S,Mapelli F,Rolli E,Song B,Tobias C,Schmid MC,De Lange GJ,Reichart GJ,Schouten S,Jetten M,Daffonchio D.Anammox bacterial populations in deep marine hypersaline gradient systems.Extremophiles,2013,17(2):289-299.
[14]Rysgaard S,Glud RN.Anaerobic N2 production in Arctic sea ice.Limnology and Oceanography,2004,49(1):86-94.
[15]Penton CR,Devol AH,Tiedje JM.Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments.Applied and Environmental Microbiology,2006,72(10):6829-6832.
[16]Shartau SLC,Yurkiw M,Lin SP,Grigoryan AA,Lambo A,Park HS,Lomans BP,van der Biezen E,Jetten MSM,Voordouw G.Ammonium concentrations in produced waters from a mesothermic oil field subjected to nitrate injection decrease through formation of denitrifying biomass and anammox activity.Applied and Environmental Microbiology,2010,76(15):4977-4987.
[17]Strous M,Fuerst JA,Kramer EHM,Logemann S,Muyzer G,van de Pas-Schoonen KT,Webb R,Kuenen JG,Jetten MSM.Missing lithotroph identified as new planctomycete.Nature,1999,400(6743):446-449.
[18]Hu BL,Shen LD,Liu S,Cai C,Chen TT,Kartal B,Harhangi HR,Op den Camp HJM,Lou LP,Xu XY,Zheng P,Jetten MSM.Enrichment of an anammox bacterial community from a flooded paddy soil.Environmental Microbiology Reports,2013,5(3):483-489.
[19]Hong YG,Li M,Cao HL,Gu JD.Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea:analyses of marker gene abundance with physical chemical parameters.Microbial Ecology,2011,62(1):36-47.
[20]Hendrickx TLG,Kampman C,Zeeman G,Temmink H,Hu ZY,Kartal B,Buisman CJN.High specific activity for anammox bacteria enriched from activated sludge at 10°C.Bioresource Technology,2014,163:214-221.
[21]Wang J,Gu JD.Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China.Applied Microbiology and Biotechnology,2013,97(4):1785-1798.
[22]Ali M,Oshiki M,Awata T,Isobe K,Kimura Z,Yoshikawa H,Hira D,Kindaichi T,Satoh H,Fujii T,Okabe S.Physiological characterization of anaerobic ammonium oxidizing bacterium‘Candidatus Jettenia caeni’.Environmental Microbiology,2015,17(6):2172-2189.
[23]Kartal B,Koleva M,Arsov R,van der Star W,Jetten MSM,Strous M.Adaptation of a freshwater anammox population to high salinity wastewater.Journal of Biotechnology,2006,126(4):546-553.
[24]Hou LJ,Zheng YL,Liu M,Gong J,Zhang XL,Yin GY,You L.Anaerobic ammonium oxidation(anammox)bacterial diversity,abundance,and activity in marsh sediments of the Yangtze Estuary.Journal of Geophysical Research Biogeosciences,2013,118(3):1237-1246.
[25]Koop-Jakobsen K,Giblin AE.Anammox in tidal marsh sediments:the role of salinity,nitrogen loading,and marsh vegetation.Estuaries and Coasts,2009,32(2):238-245.
[26]Shao SD,Luan XW,Dang HY,Zhou HX,Zhao YK,Liu HT,Zhang YB,Dai LQ,Ye Y,Klotz MG.Deep-sea methane seep sediments in the Okhotsk Sea sustain diverse and abundant anammox bacteria.FEMS Microbiology Ecology,2014,87(2):503-516.
[27]van de Vossenberg J,Woebken D,Maalcke WJ,Wessels HJCT,Dutilh BE,Kartal B,Janssen-Megens EM,Roeselers G,Yan J,Speth D,Gloerich J,Geerts W,van der Biezen E,Pluk W,Francoijs KJ,Russ L,Lam P,Malfatti SA,Tringe SG,Haaijer SCM,Op den Camp HJM,Stunnenberg HG,Amann R,Kuypers MMM,Jetten MSM.The metagenome of the marine anammox bacterium‘Candidatus Scalindua profunda’illustrates the versatility of this globally important nitrogen cycle bacterium.Environmental Microbiology,2013,15(5):1275-1289.
[28]Sun W,Xu MY,Wu WM,Guo J,Xia CY,Sun GP,Wang AJ.Molecular diversity and distribution of anammox community in sediments of the Dongjiang River,a drinking water source of Hong Kong.Journal of Applied Microbiology,2014,116(2):464-476.
[29]Sonthiphand P,Neufeld JD.Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.PLoS One,2013,8(3):e57242.
[30]Moore TA,Xing YP,Lazenby B,Lynch MDJ,Schiff S,Robertson WD,Timlin R,Lanza S,Ryan MC,Aravena R,Fortin D,Clark ID,Neufeld JD.Prevalence of anaerobic ammonium-oxidizing bacteria in contaminated groundwater.Environmental Science&Technology,2011,45(17):7217-7225.
[31]Sher Y,Baram S,Dahan O,Ronen Z,Nejidat A.Ammonia transformations and abundance of ammonia oxidizers in a clay soil underlying a manure pond.FEMS Microbiology Ecology,2012,81(1):145-155.
[32]Zhu GB,Wang SY,Wang Y,Wang CX,Risgaard-Petersen N,Jetten MSM,Yin CQ.Anaerobic ammonia oxidation in a fertilized paddy soil.The ISME Journal,2011,5(12):1905-1912.
[33]Oshiki M,Shimokawa M,Fujii N,Satoh H,Okabe S.Physiological characteristics of the anaerobic ammonium-oxidizing bacterium‘Candidatus Brocadia sinica’.Microbiology,2011,157:1706-1713.
[34]van der Star WRL,Miclea AI,van Dongen UGJM,Muyzer G,Picioreanu C,van Loosdrecht MCM.The membrane bioreactor:a novel tool to grow anammox bacteria as free cells.Biotechnology and Bioengineering,2008,101(2):286-294.