典型湿地沉积物中硝酸盐异化还原成铵的细菌群落结构的研究
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摘要
为研究中国典型湿地沉积物硝酸盐异化还原成铵过程(Dissimilatory nitrate reduction to ammonium,DNRA)的群落组成,针对DNRA过程的功能基因nrfA进行高通量测序.选取中国典型湿地岸边带的表层沉积物8个样点,质控后每个样品得到60000条序列,在相似度≥90%得到279个OTUs进行生态学分析.由基因丰度值显示:8个湿地沉积物的丰度为(6.69±0.28)×10~7～(8.44±0.48)×10~8 copies g~(-1).多样性分析(OTUs水平)结果表明:本研究的湿地沉积物样点中,南方湿地沉积物样点的多样性要高于北方样点.对代表OTUs进行分类,共定义到8个门(Phylum),23个属(Genus).其中相对丰度最高的3个属为Anaeromyxobacter(24.71%)、Anaerolinea(9.70%)和Dokdonella(7.94%),表明三者在群落组成中占主导地位.PCoA分析(OTUs水平)表明南北方地区差异是导致中国湿地沉积物中DNRA菌群结构不同的最主要影响因素.结合沉积物理化因子分析,DNRA细菌的丰度与碳氮比、年平均降水量及年平均温度呈显著正相关.本研究在一定程度上揭示了中国典型湿地沉积物DNRA细菌的群落组成、多样性及其与环境因子的关系.
To investigate the community structure of dissimilatory nitrate reduction to ammonium(DNRA) process in wetland sediments of China, high-throughput sequencing was carried out for the functional gene nrfA of DNRA bacteria. A total of 8 samples of surface sediments from typical wetlands in China were selected. After quality control, 60000 sequences were obtained for each sample, and 279 OTUs were obtained for community analysis at 90% sequence similarity. The abundance of DNRA bacteria ranged from(6.69±0.28)×10~7～(8.44±0.48)×10~8 copies·g~(-1). Results of diversity analysis(OTUs level) show that the diversity of wetland sediment samples in the south was higher than that in the north. The representative OTUs was classified into 8 phyla and 23 genera. The three highest richness genera were Anaeromyxobacter(24.71%), Anaerolinea(9.70%) and Dokdonella(7.94%), indicating their dominant role in DNRA community composition. PCoA analysis(OTUs level) shows that the difference between the north and the south was the main factor leading to the structure of DNRA bacteria in wetland sediments. The abundance of DNRA bacteria was positively correlated with C/N, annual average precipitation and annual average temperature. in summary, this study reveals the community structure and diversity of DNRA bacteria in typical wetland sediments of China and their relationship with environmental factors.
To investigate the community structure of dissimilatory nitrate reduction to ammonium(DNRA) process in wetland sediments of China, high-throughput sequencing was carried out for the functional gene nrfA of DNRA bacteria. A total of 8 samples of surface sediments from typical wetlands in China were selected. After quality control, 60000 sequences were obtained for each sample, and 279 OTUs were obtained for community analysis at 90% sequence similarity. The abundance of DNRA bacteria ranged from(6.69±0.28)×10~7～(8.44±0.48)×10~8 copies·g~(-1). Results of diversity analysis(OTUs level) show that the diversity of wetland sediment samples in the south was higher than that in the north. The representative OTUs was classified into 8 phyla and 23 genera. The three highest richness genera were Anaeromyxobacter(24.71%), Anaerolinea(9.70%) and Dokdonella(7.94%), indicating their dominant role in DNRA community composition. PCoA analysis(OTUs level) shows that the difference between the north and the south was the main factor leading to the structure of DNRA bacteria in wetland sediments. The abundance of DNRA bacteria was positively correlated with C/N, annual average precipitation and annual average temperature. in summary, this study reveals the community structure and diversity of DNRA bacteria in typical wetland sediments of China and their relationship with environmental factors.
引文
An S,Gardner W.2002.Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link,versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay,Texas)[J].Marine Ecology Progress,237(1499):41-50
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Bonaglia S,Hylén A,Rattray J E,et al.2017.The fate of fixed nitrogen in marine sediments with low organic loading:an in situ study[J].Biogeosciences,14(2):1-31
Bradbury D C,Firestone M K.2007.Environmental control of microbial N transformations in redwood forests [R].In (eds Standiford R B,Giusti G A,Valachovic Y,et al.),Proceedings of the Redwood Region Forest Science Symposium:What Does the Future Hold?Gen.Tech.Rep.PSW-GTR-194.Pacific Southwest Research Station,Forest Service,U.S.Department of Agriculture,Albany,CA,USA,203-204
Chen Z,Wang C,Gschwendtner S,et al.2015.Relationships between denitrification gene expression,dissimilatory nitrate reduction to ammonium and nitrous oxide and dinitrogen production in montane grassland soils[J].Soil Biology and Biochemistry,87:67-77
Dunn R J K,Robertson D,Teasdale P R,et al.2013.Benthic metabolism and nitrogen dynamics in an urbanised tidal creek:Domination of DNRA over denitrification as a nitrate reduction pathway[J].Estuarine,Coastal and Shelf Science,131:271-281
Edgar R C.2010.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,26(19):2460
Em V D B,Van D U,Abbas B,et al.2015.Enrichment of DNRA bacteria in a continuous culture[J].Isme Journal Multidisciplinary Journal of Microbial Ecology,9(12):2749
Groffman P M,Boulware N J,Zipperer W C,et al.2002.Soil nitrogen cycle processes in urban riparian zones[J].Environmental Science & Technology,36(21):4547-4552
Jahangir M M R,Fenton O,Müller C,et al.2017.In situ,denitrification and DNRA rates in groundwater beneath an integrated constructed wetland[J].Water Research,111:254-264
Jetten M S,Lv N,Strous M,et al.2009.Biochemistry and molecular biology of anammox bacteria[J].Crit Rev Biochem Mol Biol,44(2/3):65-84
Hefting M M,Bobbink R,Janssens M P.2006.Spatial variation in denitrification and N2O emission in relation to nitrate removal efficiency in a N-stressed riparian buffer zone[J].Ecosystems,9(4):550-563
Hefting M,Clément J C,Dowrick D,et al.2004.Water table elevation controls on soil nitrogen cycling in riparian wetlands along a European climatic gradient[J].Biogeochemistry,67(1):113-134
Kelly-Gerreyn B A,Trimmer M,Hydes D J.2001.A diagenetic model discriminating denitrification and dissimilatory nitrate reduction to ammonium in a temperate estuarine sediment[J].Marine Ecology Progress,220(1):33-46
Lu W W,Zhang H L,Shi W M.2013.Dissimilatory nitrate reduction to ammonium in an anaerobic agricultural soil as affected by glucose and free sulfide[J].European Journal of Soil Biology,58(58):98-104
Mohan S B,Cole J A.2007.Chapter 7-the dissimilatory reduction of nitrate to ammonia by anaerobic bacteria[J].Biology of the Nitrogen Cycle,93-106
Nizzoli D,Carraro E,Nigro V,et al.2010.Effect of organic enrichment and thermal regime on denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in hypolimnetic sediments of two lowland lakes[J].Water Research,44(9):0-2724
Ogilvie B G,Rutter M,Nedwell D B.1997.Selection by temperature of nitrate-reducing bacteria from estuarine sediments:species composition and competition for nitrate[J].FEMS Microbiology Ecology,23(1):11-22
Ribas D,Calderer M,Martí V,et al.2015.Effect of different seasonal conditions on the potential of wetland soils for groundwater denitrification[J].Desalination & Water Treatment,53(4):994-1000
Risgaard-Petersen N,Nielsen L P,Rysgaard S,et al.2003.Erratum:Application of the isotope pairing technique in sediments where anammox and denitrification co-exist[J].Limnology & Oceanography Methods,1(1):63-73
Roberts K L,Kessler A J,Grace M R,et al.2014.Increased rates of dissimilatory nitrate reduction to ammonium (DNRA) under oxic conditions in a periodically hypoxic estuary[J].Geochimica Et Cosmochimica Acta,133(6):313-324
Robertson T R,Tissue Z D T.2010.Precipitation magnitude and timing differentially affect species richness and plant density in the sotol grassland of the Chihuahuan Desert[J].Oecologia,162(1):185-197
Rooks C,Schmid M C,Mehsana W,et al.2012.The depth-specific significance and relative abundance of anaerobic ammonium-oxidizing bacteria in estuarine sediments (Medway Estuary,UK)[J].Fems Microbiology Ecology,80(1):19-29
Rütting T,Huygens D,Müller C,et al.2008.Functional role of DNRA and nitrite reduction in a pristine south Chilean Nothofagus forest[J].Biogeochemistry,90(3):243-258
Schloss P D,John Q.2009.A high-throughput DNA sequence aligner for microbial ecology studies[J].PLoS ONE,4(12):e8230
Wang S Y,Wang W,Liu L,et al.2018.Microbial nitrogen cycle hotspots in the plant-bed/ditch system of a constructed wetland with N2O mitigation[J].Environmental Science & Technology,52(11):6226-6236
Sher Y,Schneider K,Schwermer C U,et al.2008.Sulfide-induced nitrate reduction in the sludge of an anaerobic digester of a zero-discharge recirculating mariculture system[J].Water Research,42(16):4386-4392
Song B,Lisa J A,Tobias C R.2014.Linking DNRA community structure and activity in a shallow lagoonal estuarine system[J].Frontiers in Microbiology,5:460
Steenkamp D J,Peck H D.1981.Proton translocation associated with nitrite respiration in Desulfovibrio desulfuricans[J].The Journal of Biological Chemistry,256(11):5450-5458
Thomas S H,Wagner R D,Arakaki A K,et al.2008.The mosaic genome of anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria[J].PLOS ONE,3(5):2103
Tomaszek J A,Rokosz G R.2007.Rates of dissimilatory nitrate reduction to ammonium in two Polish reservoirs:impacts of temperature,organic matter content,and nitrate concentration[J].Environmental Technology,28(7):771-778
Wang W,Wang D,Yin C.2010.A field study on the hydrochemistry of land/inland water ecotones with reed domination[J].Clean-Soil Air Water,30(2/3):117-127
Wang W,Liu W,Wu D,et al.2018.Differentiation of nitrogen and microbial community in the littoral and limnetic sediments of a large shallow eutrophic lake (Chaohu Lake,China)[J].Journal of Soils and Sediments,1-12
Welsh A,Chee-Sanford J C,Connor L M,et al.2014.Refined nrfA phylogeny improves PCR-based nrfA gene detection[J].Applied & Environmental Microbiology,80(7):2110-2119
Yang Y,Rao S,Hu H,et al.2004.Plant species richness of alpine grasslands in relation to environmental factors and biomass on the Tibetan Plateau[J].Chinese Biodiversity,12(1):200-205
张文河,穆桂金.2007.烧失法测定有机质和碳酸盐的精度控制[J].干旱区地理(汉文版),30(3):137-141
Zhou J M,Song Z Y,Yan D J,et al.2014.Performance of a haloalkaliphilic bioreactor under different,NO-3/ SO■ math Container Loading Mathjax,ratios[J].Bioresource Technology,153(1):216-222
Zhu G,Wang S,Wang Y,et al.2011.Anaerobic ammonia oxidation in a fertilized paddy soil[J].Isme Journal,5(12):1905-1912
Zhu G,Xia C,Wang S,et al.2015.Occurrence,activity and contribution of anammox in some freshwater extreme environments[J].Environmental Microbiology Reports,7(6):961-969
庄林杰,夏超,田晴,等.2017.高通量测序技术研究典型湖泊岸边陆向深层土壤中厌氧氨氧化细菌的群落结构[J].环境科学学报,37(1):261-271
鲍士旦.2000.土壤农化分析(第3版)[M].北京:中国农业出版社
Bonaglia S,Hylén A,Rattray J E,et al.2017.The fate of fixed nitrogen in marine sediments with low organic loading:an in situ study[J].Biogeosciences,14(2):1-31
Bradbury D C,Firestone M K.2007.Environmental control of microbial N transformations in redwood forests [R].In (eds Standiford R B,Giusti G A,Valachovic Y,et al.),Proceedings of the Redwood Region Forest Science Symposium:What Does the Future Hold?Gen.Tech.Rep.PSW-GTR-194.Pacific Southwest Research Station,Forest Service,U.S.Department of Agriculture,Albany,CA,USA,203-204
Chen Z,Wang C,Gschwendtner S,et al.2015.Relationships between denitrification gene expression,dissimilatory nitrate reduction to ammonium and nitrous oxide and dinitrogen production in montane grassland soils[J].Soil Biology and Biochemistry,87:67-77
Dunn R J K,Robertson D,Teasdale P R,et al.2013.Benthic metabolism and nitrogen dynamics in an urbanised tidal creek:Domination of DNRA over denitrification as a nitrate reduction pathway[J].Estuarine,Coastal and Shelf Science,131:271-281
Edgar R C.2010.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,26(19):2460
Em V D B,Van D U,Abbas B,et al.2015.Enrichment of DNRA bacteria in a continuous culture[J].Isme Journal Multidisciplinary Journal of Microbial Ecology,9(12):2749
Groffman P M,Boulware N J,Zipperer W C,et al.2002.Soil nitrogen cycle processes in urban riparian zones[J].Environmental Science & Technology,36(21):4547-4552
Jahangir M M R,Fenton O,Müller C,et al.2017.In situ,denitrification and DNRA rates in groundwater beneath an integrated constructed wetland[J].Water Research,111:254-264
Jetten M S,Lv N,Strous M,et al.2009.Biochemistry and molecular biology of anammox bacteria[J].Crit Rev Biochem Mol Biol,44(2/3):65-84
Hefting M M,Bobbink R,Janssens M P.2006.Spatial variation in denitrification and N2O emission in relation to nitrate removal efficiency in a N-stressed riparian buffer zone[J].Ecosystems,9(4):550-563
Hefting M,Clément J C,Dowrick D,et al.2004.Water table elevation controls on soil nitrogen cycling in riparian wetlands along a European climatic gradient[J].Biogeochemistry,67(1):113-134
Kelly-Gerreyn B A,Trimmer M,Hydes D J.2001.A diagenetic model discriminating denitrification and dissimilatory nitrate reduction to ammonium in a temperate estuarine sediment[J].Marine Ecology Progress,220(1):33-46
Lu W W,Zhang H L,Shi W M.2013.Dissimilatory nitrate reduction to ammonium in an anaerobic agricultural soil as affected by glucose and free sulfide[J].European Journal of Soil Biology,58(58):98-104
Mohan S B,Cole J A.2007.Chapter 7-the dissimilatory reduction of nitrate to ammonia by anaerobic bacteria[J].Biology of the Nitrogen Cycle,93-106
Nizzoli D,Carraro E,Nigro V,et al.2010.Effect of organic enrichment and thermal regime on denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in hypolimnetic sediments of two lowland lakes[J].Water Research,44(9):0-2724
Ogilvie B G,Rutter M,Nedwell D B.1997.Selection by temperature of nitrate-reducing bacteria from estuarine sediments:species composition and competition for nitrate[J].FEMS Microbiology Ecology,23(1):11-22
Ribas D,Calderer M,Martí V,et al.2015.Effect of different seasonal conditions on the potential of wetland soils for groundwater denitrification[J].Desalination & Water Treatment,53(4):994-1000
Risgaard-Petersen N,Nielsen L P,Rysgaard S,et al.2003.Erratum:Application of the isotope pairing technique in sediments where anammox and denitrification co-exist[J].Limnology & Oceanography Methods,1(1):63-73
Roberts K L,Kessler A J,Grace M R,et al.2014.Increased rates of dissimilatory nitrate reduction to ammonium (DNRA) under oxic conditions in a periodically hypoxic estuary[J].Geochimica Et Cosmochimica Acta,133(6):313-324
Robertson T R,Tissue Z D T.2010.Precipitation magnitude and timing differentially affect species richness and plant density in the sotol grassland of the Chihuahuan Desert[J].Oecologia,162(1):185-197
Rooks C,Schmid M C,Mehsana W,et al.2012.The depth-specific significance and relative abundance of anaerobic ammonium-oxidizing bacteria in estuarine sediments (Medway Estuary,UK)[J].Fems Microbiology Ecology,80(1):19-29
Rütting T,Huygens D,Müller C,et al.2008.Functional role of DNRA and nitrite reduction in a pristine south Chilean Nothofagus forest[J].Biogeochemistry,90(3):243-258
Schloss P D,John Q.2009.A high-throughput DNA sequence aligner for microbial ecology studies[J].PLoS ONE,4(12):e8230
Wang S Y,Wang W,Liu L,et al.2018.Microbial nitrogen cycle hotspots in the plant-bed/ditch system of a constructed wetland with N2O mitigation[J].Environmental Science & Technology,52(11):6226-6236
Sher Y,Schneider K,Schwermer C U,et al.2008.Sulfide-induced nitrate reduction in the sludge of an anaerobic digester of a zero-discharge recirculating mariculture system[J].Water Research,42(16):4386-4392
Song B,Lisa J A,Tobias C R.2014.Linking DNRA community structure and activity in a shallow lagoonal estuarine system[J].Frontiers in Microbiology,5:460
Steenkamp D J,Peck H D.1981.Proton translocation associated with nitrite respiration in Desulfovibrio desulfuricans[J].The Journal of Biological Chemistry,256(11):5450-5458
Thomas S H,Wagner R D,Arakaki A K,et al.2008.The mosaic genome of anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria[J].PLOS ONE,3(5):2103
Tomaszek J A,Rokosz G R.2007.Rates of dissimilatory nitrate reduction to ammonium in two Polish reservoirs:impacts of temperature,organic matter content,and nitrate concentration[J].Environmental Technology,28(7):771-778
Wang W,Wang D,Yin C.2010.A field study on the hydrochemistry of land/inland water ecotones with reed domination[J].Clean-Soil Air Water,30(2/3):117-127
Wang W,Liu W,Wu D,et al.2018.Differentiation of nitrogen and microbial community in the littoral and limnetic sediments of a large shallow eutrophic lake (Chaohu Lake,China)[J].Journal of Soils and Sediments,1-12
Welsh A,Chee-Sanford J C,Connor L M,et al.2014.Refined nrfA phylogeny improves PCR-based nrfA gene detection[J].Applied & Environmental Microbiology,80(7):2110-2119
Yang Y,Rao S,Hu H,et al.2004.Plant species richness of alpine grasslands in relation to environmental factors and biomass on the Tibetan Plateau[J].Chinese Biodiversity,12(1):200-205
张文河,穆桂金.2007.烧失法测定有机质和碳酸盐的精度控制[J].干旱区地理(汉文版),30(3):137-141
Zhou J M,Song Z Y,Yan D J,et al.2014.Performance of a haloalkaliphilic bioreactor under different,NO-3/ SO■ math Container Loading Mathjax,ratios[J].Bioresource Technology,153(1):216-222
Zhu G,Wang S,Wang Y,et al.2011.Anaerobic ammonia oxidation in a fertilized paddy soil[J].Isme Journal,5(12):1905-1912
Zhu G,Xia C,Wang S,et al.2015.Occurrence,activity and contribution of anammox in some freshwater extreme environments[J].Environmental Microbiology Reports,7(6):961-969
庄林杰,夏超,田晴,等.2017.高通量测序技术研究典型湖泊岸边陆向深层土壤中厌氧氨氧化细菌的群落结构[J].环境科学学报,37(1):261-271