Spatiotemporal distributions and environmental drivers of diversity and community structure of nosZ-type denitrifiers and anammox bacteria in sediments of the Bohai Sea and North Yellow Sea, China
|
摘要
Denitrification and anammox processes are major nitrogen removal processes in coastal ecosystems.However,the spatiotemporal dynamics and driving factors of the diversity and community structure of involved functional bacteria have not been well illustrated in coastal environments,especially in human-dominated ecosystems.In this study,we investigated the distributions of denitrifiers and anammox bacteria in the eutrophic Bohai Sea and the northern Yellow Sea of China in May and November of2012 by constructing clone libraries employing nosZ and 16 S rRNA gene biomarkers.The diversity of nosZ-denitrifier was much higher at the coastal sites compared with the central sites,but not significant among basins or seasons.Alphaproteobacteria were predominant and prevalent in the sediments,whereas Betaproteobacteria primarily occurred at the site near the Huanghe(Yellow)River estuary.Anammox bacteria Candidatus Scalindua was predominant in the sediments,and besides,Candidatus Brocadia and Candidatus Kuenenia were also detected at the site near the Huanghe River estuary that received strong riverine and anthropogenic impacts.Salinity was the most important in structuring communities of nosZdenitrifier and anammox bacteria.Additionally,anthropogenic perturbations(e.g.nitrogen overloading and consequent high primary productivity,and heavy metal discharges)contributed significantly to shaping community structures of denitrifier and anammox bacteria,suggesting that anthropogenic activities would influence and even change the ecological function of coastal ecosystems.
Denitrification and anammox processes are major nitrogen removal processes in coastal ecosystems.However,the spatiotemporal dynamics and driving factors of the diversity and community structure of involved functional bacteria have not been well illustrated in coastal environments,especially in human-dominated ecosystems.In this study,we investigated the distributions of denitrifiers and anammox bacteria in the eutrophic Bohai Sea and the northern Yellow Sea of China in May and November of2012 by constructing clone libraries employing nosZ and 16 S rRNA gene biomarkers.The diversity of nosZ-denitrifier was much higher at the coastal sites compared with the central sites,but not significant among basins or seasons.Alphaproteobacteria were predominant and prevalent in the sediments,whereas Betaproteobacteria primarily occurred at the site near the Huanghe(Yellow)River estuary.Anammox bacteria Candidatus Scalindua was predominant in the sediments,and besides,Candidatus Brocadia and Candidatus Kuenenia were also detected at the site near the Huanghe River estuary that received strong riverine and anthropogenic impacts.Salinity was the most important in structuring communities of nosZdenitrifier and anammox bacteria.Additionally,anthropogenic perturbations(e.g.nitrogen overloading and consequent high primary productivity,and heavy metal discharges)contributed significantly to shaping community structures of denitrifier and anammox bacteria,suggesting that anthropogenic activities would influence and even change the ecological function of coastal ecosystems.
Denitrification and anammox processes are major nitrogen removal processes in coastal ecosystems.However,the spatiotemporal dynamics and driving factors of the diversity and community structure of involved functional bacteria have not been well illustrated in coastal environments,especially in human-dominated ecosystems.In this study,we investigated the distributions of denitrifiers and anammox bacteria in the eutrophic Bohai Sea and the northern Yellow Sea of China in May and November of2012 by constructing clone libraries employing nosZ and 16 S rRNA gene biomarkers.The diversity of nosZ-denitrifier was much higher at the coastal sites compared with the central sites,but not significant among basins or seasons.Alphaproteobacteria were predominant and prevalent in the sediments,whereas Betaproteobacteria primarily occurred at the site near the Huanghe(Yellow)River estuary.Anammox bacteria Candidatus Scalindua was predominant in the sediments,and besides,Candidatus Brocadia and Candidatus Kuenenia were also detected at the site near the Huanghe River estuary that received strong riverine and anthropogenic impacts.Salinity was the most important in structuring communities of nosZdenitrifier and anammox bacteria.Additionally,anthropogenic perturbations(e.g.nitrogen overloading and consequent high primary productivity,and heavy metal discharges)contributed significantly to shaping community structures of denitrifier and anammox bacteria,suggesting that anthropogenic activities would influence and even change the ecological function of coastal ecosystems.
引文
Abascal F,Zardoya R,Posada D.2005.ProtTest:selection of best-fit models of protein evolution.Bioinformatics,21(9):2104-2 105,https://doi.org/10.1093/bioinformatics/bti263.
Amano T,Yo shinaga I,Okada K,Yamagishi T,Ueda S,Obuchi A,Sako Y,Suwa Y.2007.Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan.Microbes and Environments,22(3):232-242,https://doi.org/10.1264/j sme2.22.232.
Anderson D M,Glibert P M,Burkholder J M.2002.Harmful algal blooms and eutrophication:nutrient sources,composition,and consequences.Estuaries,25(4):704-726,https://doi.org/10.1007/bf02804901.
Babbin A R,Jayakumar A,Ward B B.2016.Organic matter loading modifies the microbial community responsible for nitrogen loss in estuarine sediments.Microbial Ecology,71(3):5 55-565,https://doi.org/10.1007/s00248-01 5-0693-5.
Babbin A R,Keil R G,Devol A H,Ward B B.2014.Organic matter stoichiometry,flux,and oxygen control nitrogen loss in the ocean.Science,344(6182):406-408,https://doi.org/10.1126/science.1248364.
Bale N J,Villanueva L,Fan H X,Stal L J,Hopmans E C,Schouten S,DamstéJ S S.2014.Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea.FEMS Microbiology Ecology,89(1):99-110,https://doi.org/10.1111/1574-6941.1233 8.
Bouvier T,Del Giorgio P A.2003.Factors influencing the detection of bacterial cells using fluorescence in situ hybridization(FISH):a quantitative review of published reports.FEMS Microbiology Ecology,44(1):3-15,https://doi.org/10.1016/S0168-6496(02)00461-0.
Brin L D,Giblin A E,Rich J J.2014.Environmental controls of anammox and denitrification in southern New England estuarine and shelf sediments.Limnology and Oceanography,59(3):851-860,https://doi.org/10.4319/lo.2014.59.3.0851.
Bürgi H R,Stadelmann P.2002.Alteration of phytoplankton structure in Lake Lucerne due to trophic conditions.Aquatic Ecosystem Health&Management,5(1):45-59,https://doi.org/10.1080/14634980260199954.
Camargo J A,Alonso A.2006.Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems:a global assessment.Environment International,32(6):831-849,https://doi.org/10.1016/j.envint.2006.05.002.
Codispoti L A.2007.An oceanic fixed nitrogen sink exceeding400 Tg Na~(-1)vs the concept of homeostasis in the fixednitrogen inventory.Biogeosciences,4(2):23 3-2 5 3,https://doi.org/10.51 94/bg-4-23 3-2007.
Crump B C,Armbrust E V,Baross J A.1999.Phylogenetic analysis of particle-attached and free-living bacterialcommunities in the Columbia River,its estuary,and the adjacent coastal ocean.Applied and Environmental Microbiology,65(7):3 192-3 204.
Dale O R,Tobias C R,Song B.2009.Biogeographical distribution of diverse anaerobic ammonium oxidizing(anammox)bacteria in Cape Fear River Estuary.Environmental Microbiology,11(5):1 194-1 207,https://doi.org/10.1111/j.1462-2920.2008.01850.x.
Dang H Y,Chen R P,Wang L,Guo L Z,Chen P P,Tang Z W,Tian F,Li S Z,Klotz M G.2010.Environmental factors shape sediment anammox bacterial communities in hypernutrified Jiaozhou Bay,China.Applied and En vironmen tal Microbiology,76(2 1):7 036-7 047,https://doi.org/10.1128/aem.01264-10.
Dang H Y,Zhou H X,Zhang Z N,Yu Z S,Hua E,Liu X S,Jiao N Z.201 3.Molecular detection of Candidatus Scalindua Pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea,China.PLoS One,8(4):e61 3 30.https://doi.org/10.1 371/journal.pone.00613 30.
El Hanafy A A E M,Anwar Y,Mohamed S A,Al-Gami S M S,Sabir J S M,AbuZinadah O A,A1 Mehdar H,Alfaidi A W,Ahmed M M M.2016.Isolation and identification of bacterial consortia responsible for degrading oil spills from the coastal area of Yanbu,Saudi Arabia.Biotechnology&Biotechnological Equipment,30(1):69-74,https://doi.org/10.1080/13102818.2015.1086282.
Feng B W,Li X R,Wang J H,Hu Z Y,Meng H,Xiang L Y,Quan Z X.2009.Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea.FEMS Microbiology Ecology,70(2):236-248,https://doi.org/10.1111/j.1 574-6941.2009.00772.x.
Fernandes S O,Michotey V D,Guasco S,Bonin P C,Bharathi P A L.2012.Denitrification prevails over anammox in tropical mangrove sediments(Goa,India).Marine Environmental Research,74:9-19,https://doi.org/10.1016/j.marenvres.2011.11.008.
Galloway J N,Townsend A R,Erisman J W,Bekunda M,Cai Z C,Freney J R,Martinelli L A,Seitzinger S P,Sutton M A.2008.Transformation of the nitrogen cycle:recent trends,questions,and potential solutions.Science,320(5 878):889-892,https://doi.org/10.1126/science.1136674.
Goecke F,Thiel V,Wiese J,Labes A,Imhoff J F.2013.Algae as an important environment for bacteria-Phylogenetic relationships among new bacterial species isolated from algae.Phycologia,52(1):14-24,https://doi.org/10.2216/12-24.1.
Gonzalez-Silva B M,Ronning A J,Andreassen I K,Bakke I,Cervantes F J,Ostgaard K,Vadstein O.2017.Changes in the microbial community of an anammox consortium during adaptation to marine conditions revealed by 454pyrosequencing.Applied Microbiology and Biotechnology,101(12):5 149-5 162,https://doi.org/10.1007/s00253-017-8160-5.
Hall T.2011.BioEdit:an important software for molecular biology.GERF Bulletin of Biosciences,2(1):60-6 1.
Hietanen S,Kuparinen J.2008.Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland,Baltic Sea.Hydrobiologia,596(1):67-77,https://doi.org/10.1007/s10750-007-905 8-5.
Hou L J,Zheng Y L,Liu M,Gong J,Zhang X L,Yin G Y,You L.2013.Anaerobic ammonium oxidation(anammox)bacterial diversity,abundance,and activity in marsh sediments of the Yangtze Estuary.Journal of Geophysical Research.Biogeosciences,118(3):1 237-1 246,https://doi.org/10.1002/jgrg.20108.
Hu L M,Shi X F,Bai Y Z,Qiao S Q,Li L,Yu Y G,Yang G,Ma D Y,Guo Z G.2016.Recent organic carbon sequestration in the shelf sediments of the Bohai Sea and Yellow Sea,China.Journal of Marine Systems,155:50-5 8,https://doi.org/10.1 0 1 6/j.jmarsy s.201 5.10.018.
Humbert S,Tarnawski S,Fromin N,Mallet M P,Aragno M,Zopfi J.2010.Molecular detection of anammox bacteria in terrestrial ecosystems:distribution and diversity.The ISME Journal,4(3):450-454,https://doi.org/10.1038/ismej.2009.125.
Jones C M,Hallin S.2010.Ecological and evolutionary factors underlying global and local assembly of denitrifier communities.The ISME Journal,4(5):633-641,https://doi.org/10.103 8/ismej.2009.1 52.
Kartal B,Rattray J,Van Niftrik L A,Van De Vossenberg J,Schmid M C,Webb R I,Schouten S,Fuerst J A,DamstéJ S,Jetten M S M,Strous M.2007.Candidatus“Anammoxoglobus propionicus”a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria.Systematic and Applied Microbiology,30(1):39-49,https://doi.org/10.1016/j.sy apm.2006.03.004.
Kartal B,Van Niftrik L,Rattray J,Van De Vo ssenberg J L C M,Schmid M C,Sinninghe DamstéJ,Jetten M S M,Strous M.2008.Candidatus ‘Brocadia fulgida':an autofiuore sc ent anaerobic ammonium oxidizing bacterium.FEMS Microbiology Ecology,63(1):46-55,https://doi.org/10.1111/j.1 574-6941.2007.00408.x.
LabbéN,Parent S,Villemur R.2004.Nitratireductor aquibiodomus gen.nov.,sp.nov.,a novel a-proteobacterium from the marine denitrification system of the Montreal Biodome(Canada).International Journal of Systematic and Evolutionary Microbiology,54(1):269-273,https://doi.org/10.109 9/ij s.0.02793-0.
Lai Q L,Yu Z W,Wang J N,Zhong H Z,Sun F Q,Wang L P,Wang B J,Shao Z Z.2011a.Nitratireductor pacficus sp.nov.,isolated from a pyrene-degrading consortium.International Journal of Systematic and Evolutionary Microbiology,61(6):1386-1 391,https://doi.org/10.1099/ij s.0.024356-0.
Lai Q L,Yu Z W,Yuan J,Sun F Q,Shao Z Z.2011b.Nitratireductor indicus sp.nov.,isolated from deep-sea water.International Journal of Systematic and Evolutionary Microbiology,61(2):295-298,https://doi.org/10.1099/ij s.0.022962-0.
Li M,Cao H L,Hong Y G,Gu J D.2011a.Seasonal dynamics of anammox bacteria in estuarial sediment of the Mai PoNature Reserve revealed by analyzing the 16S rRNA and hydrazine oxidoreductase(hzo)genes.Microbes and Environments,26(1):15-22,https://doi.org/10.1264/jsme2.ME10131.
Li M,Ford T,Li X Y,Gu J D.2011b.Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing(anammox)bacteria.Environmental Science&Technology,45(8):3 547-3 553,https://doi.org/10.1021/es103826w.
Li M,Hong Y G,Klotz M G,Gu J D.2010.A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments.Applied Microbiology and Biotechnology,86(2):781-790,https://doi.org/10.1007/s00253-009-2361-5.
Lipsewers Y A,Hopmans E C,Meysman F J R,DamstéJ S S,Villanueva L.2016.Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake Grevelingen.Frontiers in Microbiology,7:1661,https://doi.org/10.3389/fmicb.2016.01661.
Liu J W,Fu B B,Yang H M,Zhao M X,He B Y,Zhang X H.201 5.Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary:the potential impact of hypoxia and nutrients.Frontiers in Microbiology,6:64,https://doi.org/10.3 3 89/fmicb.201 5.00064.
Liu X D,Tiquia S M,Holguin G,Wu L Y,Nold S C,Devol A H,Luo K,Palumbo A V,Tiedje J M,Zhou J Z.2003.Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico.Applied and Environmental Microbiology,69(6):3 549-3 560,https://doi.org/10.1128/aem.69.6.3549-3560.2003.
Magalhaes C M,Wiebe W J,Joye S B,Bordalo A A.2005.Inorganic nitrogen dynamics in intertidal rocky biofilms and sediments of the Douro River estuary(Portugal).Estuaries,28(4):592-606,https://doi.org/10.1007/BF02696070.
Magalhaes C,Bano N,Wiebe W J,Bordalo A A,Hollibaugh J T.2008.Dynamics of nitrous oxide reductase genes(nosZ)in intertidal rocky biofilms and sediments of the Douro River Estuary(Portugal),and their relation to N-biogeochemistry.Microbial Ecology,55(2):259-269,https://doi.org/10.1007/s00248-007-9273-7.
Malovanyy A,Plaza E,Trela J,Malovanyy M.2015.Ammonium removal by partial nitritation and anammox processes from wastewater with increased salinity.Environmental Technology,36(5):595-604,https://doi.or g/10.1080/09593330.2014.953601.
Mills H J,Hunter E,Humphrys M,Kerkhof L,McGuinness L,Huettel M,Kostka J E.2008.Characterization of nitrifying,denitrifying,and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico.Applied and Environmental Microbiology,74(14):4 440-4 453,https://doi.org/10.1128/aem.02692-07.
Pan G C,Qiu S Y,Liu X,Hu X K.2015.Estimating the economic damages from the Penglai 19-3 oil spill to the Yantai fisheries in the Bohai Sea of northeast China.Marine Policy,62:18-24,https://doi.org/10.1016/j.marpol.2015.08.007.
Piao Z,Zhang W W,Ma S,Li Y M,Yin S X.2012.Succession of denitrifying community compo sition in coastal wetland soils along a salinity gradient.Pedosphere,22(3):367-374.
Posada D,Crandall K A.1998.MODELTEST:testing the model of DNA substitution.Bioinformatics,14(9):817-81 8,https://doi.org/10.1093/bioinformatic s/14.9.817.
Qiao S Q,Shi X F,Wang G Q,Zhou L,Hu B Q,Hu L M,Yang G,Liu Y G,Yao Z Q,Liu S F.2017.Sediment accumulation and budget in the Bohai Sea,Yellow Sea and East China Sea.Marine Geology,390:270-281,https://doi.org/10.1 0 1 6/j.margeo.2017.06.004.
Redfield A C.195 8.The biological control of chemical factors in the environment.American Scientist,46(3):205-22 1.
Rink B,Seeberger S,Martens T,Duerselen C D,Simon M,Brinkhoff T.2007.Effects of phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities.Aquatic Microbial Ecology,48(1):47-60,http s://doi.org/1 0.3 3 54/ame048047.
Scala D J,Kerkhof L J.1998.Nitrous oxide reductase(nosZ)gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments.FEMS Microbiology Letters,162(1):6 1-68.
Scala D J,Kerkhof L J.1999.Diversity of nitrous oxide reductase(nosZ)genes in continental shelf sediments.Applied and Environmental Microbiology,65(4):1 681-1 687.
Scala D J,Kerkhof L J.2000.Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis.Applied and Environmental Microbiology,66(5):1 980-1 986,https://doi.org/10.1128/aem.66.5.1980-1986.2000.
Schloss P D,Handelsman J.2005.Introducing DOTUR,a computer program for defining operational taxonomic units and estimating species richness.Applied and Environmental Microbiology 71(3):1501-1 506,https://doi.org/10.112 8/aem.71.3.1501-1506.2005.
Schmid M C,Risgaard-Petersen N,Van De Vossenberg J,Kuypers M M M,Lavik G,Petersen J,Hulth S,Thamdrup B,Canfield D,Dalsgaard T,Rysgaard S,Sejr M K,Strous M,Den Camp H J M O,Jetten M S M.2007.Anaerobic ammonium-oxidizing bacteria in marine environments:widespread occurrence but low diversity.Environmental Microbiology,9(6):1 476-1 484,https://doi.org/10.1111/j.1462-2920.2007.01266.x.
Schmid M,Walsh K,Webb R,Rijpstra W I,Van De PasSchoonen K,Verbruggen M J,Hill T,Moffett B,Fuerst J,Schouten S,Sinninghe DamstéJ S,Harris J,Shaw P,Jetten M,Strous M.2003.Candidatus"Scalindua brodae",sp.nov.,Candidatus"Scalindua wagneri",sp.nov.,two new species of anaerobic ammonium oxidizingbacteria.Systematic and Applied Microbiology,26(4):529-538,https://doi.org/10.1078/072320203770865837.Shao M F,Zhang T,Fang H H P.2010.Sulfur-driven
autotrophic denitrification:diversity,biochemistry,and engineering applications.Applied Microbiology and Biotechnology,88(5):1 027-1 042,https://doi.org/10.1007/s00253-010-2847-1.
Shehzad A,Liu J W,Yu M,Qismat S,Liu J L,Zhang X H.2016.Diversity,community composition and abundance of anammox bacteria in sediments of the north marginal seas of China.Microbes and Environments,31(2):111-120,https://doi.org/10.1264/j sme2.ME15140.
SOA(State Oceanic Administration People's Republic of China).2016.Chinese Marine Environment Quality Bulletin,20 1 5.http://www.nmdis.org.cn/g ongbao/huanjing/201604/t20160414_33875.html.(in Chinese)
Sonthiphand P,Hall M W,Neufeld J D.2014.Biogeography of anaerobic ammonia-oxidizing(anammox)bacteria.Fron tiers in Microbiology,5:399,https://doi.org/1 0.33 89/fmicb.2014.003 99.
Stamatakis A.2014.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics,30(9):1 312-1 313,https://doi.org/1 0.1 0 93/bioinfo rmatic s/btu033.
Throback I N,Enwall K,Jarvis A,Hallin S.2004.Reassessing PCR primers targeting nirS,nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE.FEMS Microbiology Ecology,49(3):401-417,https://doi.org/10.1016/j.femsec.2004.04.011.
Van De Vossenberg J,Woebken D,Maalcke W J,Wessels H J C T,Dutilh B E,Kartal B,Janssen-Megens E M,Roeselers G,Yan J,Speth D,Gloerich J,Geerts W,Van Der Biezen E,Pluk W,Francoijs K J,Russ L,Lam P,Malfatti S A,Tringe S G,Haaijer S C M,Op Den Camp H J M,Stunnenberg H G,Amann R,Kuypers M M M,Jetten M S M.2013.The metagenome of the marine anammox bacterium'Candida tus Scalindua profunda'illustrates the versatility of this globally important nitrogen cycle bacterium.Environmental Microbiology,15(5):1 275-1 289,https://doi.org/10.1111/j.1462-2920.2012.02774.x.
Wang H T,Su J Q,Zheng T L,Yang X R.2014.Impacts of vegetation,tidal process,and depth on the activities,abundances,and community compositions of denitrifiers in mangrove sediment.Applied Microbiology and Biotechnology,98(22):9 375-9 387,https://doi.org/10.1007/s00253-014-6017-8.
Wang X L,Cui Z G,Guo Q,Han X R,Wang J T.2009.Distribution of nutrients and eutrophication assessment in the Bohai Sea of China.Chinese Journal of Oceanology and Limnology,27(1):177-183,https://doi.org/10.1007/s00343-009-0177-x.
Ward B B.2013.How nitrogen is lost.Science,341(6144):352-3 5 3,https://doi.org/10.1126/science.12403 14.
Wei H,Sun J,Moll A,Zhao L.2004.Phytoplankton dynamics in the Bohai Sea—observations and modelling.Journal of Marine Systems,44(3-4):233-251,https://doi.org/10.1016/j.jmarsys.2003.09.012.
Wei H,Tian T,Zhou F,Zhao L.2002.Numerical study on the water exchange of the Bohai Sea:simulation of the halflife time by dispersion model.Journal of Ocean University of Qingdao,32(4):519-525.(in Chinese with English abstract)
Woebken D,Lam P,Kuypers M M M,Naqvi S W A,Kartal B,Strous M,Jetten M S M,Fuchs B M,Amann R.2008.A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones.Environmental Microbiology,10(11):3 106-3 119,https://doi.org/10.1111/j.1462-2920.2008.01640.x.
Wyman M,Hodgson S,Bird C.2013.Denitrifying Alphaproteobacteria from the Arabian Sea that express nosZ,the gene encoding nitrous oxide reductase,in oxic and suboxic waters.Applied and Environmental Microbiology;79(8):2 670-2 681,https://doi.org/10.1128/aem.03705-12.
Xu L L,Wu D X,Lin X P,Ma C.2009.The study of the Yellow Sea Warm Current and its seasonal variability.Journal of Hydrodynamics,21(2):159-165,https://doi.org/10.1016/S1001-6058(08)60133-X.
Yang A J,Zhang X L,AgoguéH,Dupuy C,Gong J.2015.Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers,denitrifiers,and anammox bacteria in sediments of estuarine tidal flats.Annals of Microbiology,65(2):879-890,https://doi.org/10.1007/s1321 3-014-0929-5.
Yu T T,Li M,Niu M Y,Fan X B,Liang W Y,Wang F P.2018.Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea.Applied Microbiology and Biotechnology,102(1):447-45 9,https://doi.org/10.1007/s0025 3-017-8594-9.
Zhang X L,Agogue H,Dupuy C,Gong J.2014.Relative abundance of ammonia oxidizers,denitrifiers,and anammox bacteria in sediments of hyper-nutrified estuarine tidal flats and in relation to environmental conditions.Clean-Soil Air Water,42(6):815-823,https://doi.org/10.1002/clen.201 30001 3.
Zhang X L,Zhang Q Q,Yang A J,Hou L J,Zheng Y L,Zhai W D,Gong J.2018.Incorporation of microbial functional traits in biogeochemistry models provides better estimations of benthic denitrification and anammox rates in coastal oceans.Journal of Geophysical Research.Biogeosciences,123(10):3 331-3 352,https://doi.org/10.1029/2018JG004682.
Zumft W G.1997.Cell biology and molecular basis of denitrification.Microbiology and Molecular Biology Reviews,61(4):533-616.
Amano T,Yo shinaga I,Okada K,Yamagishi T,Ueda S,Obuchi A,Sako Y,Suwa Y.2007.Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan.Microbes and Environments,22(3):232-242,https://doi.org/10.1264/j sme2.22.232.
Anderson D M,Glibert P M,Burkholder J M.2002.Harmful algal blooms and eutrophication:nutrient sources,composition,and consequences.Estuaries,25(4):704-726,https://doi.org/10.1007/bf02804901.
Babbin A R,Jayakumar A,Ward B B.2016.Organic matter loading modifies the microbial community responsible for nitrogen loss in estuarine sediments.Microbial Ecology,71(3):5 55-565,https://doi.org/10.1007/s00248-01 5-0693-5.
Babbin A R,Keil R G,Devol A H,Ward B B.2014.Organic matter stoichiometry,flux,and oxygen control nitrogen loss in the ocean.Science,344(6182):406-408,https://doi.org/10.1126/science.1248364.
Bale N J,Villanueva L,Fan H X,Stal L J,Hopmans E C,Schouten S,DamstéJ S S.2014.Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea.FEMS Microbiology Ecology,89(1):99-110,https://doi.org/10.1111/1574-6941.1233 8.
Bouvier T,Del Giorgio P A.2003.Factors influencing the detection of bacterial cells using fluorescence in situ hybridization(FISH):a quantitative review of published reports.FEMS Microbiology Ecology,44(1):3-15,https://doi.org/10.1016/S0168-6496(02)00461-0.
Brin L D,Giblin A E,Rich J J.2014.Environmental controls of anammox and denitrification in southern New England estuarine and shelf sediments.Limnology and Oceanography,59(3):851-860,https://doi.org/10.4319/lo.2014.59.3.0851.
Bürgi H R,Stadelmann P.2002.Alteration of phytoplankton structure in Lake Lucerne due to trophic conditions.Aquatic Ecosystem Health&Management,5(1):45-59,https://doi.org/10.1080/14634980260199954.
Camargo J A,Alonso A.2006.Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems:a global assessment.Environment International,32(6):831-849,https://doi.org/10.1016/j.envint.2006.05.002.
Codispoti L A.2007.An oceanic fixed nitrogen sink exceeding400 Tg Na~(-1)vs the concept of homeostasis in the fixednitrogen inventory.Biogeosciences,4(2):23 3-2 5 3,https://doi.org/10.51 94/bg-4-23 3-2007.
Crump B C,Armbrust E V,Baross J A.1999.Phylogenetic analysis of particle-attached and free-living bacterialcommunities in the Columbia River,its estuary,and the adjacent coastal ocean.Applied and Environmental Microbiology,65(7):3 192-3 204.
Dale O R,Tobias C R,Song B.2009.Biogeographical distribution of diverse anaerobic ammonium oxidizing(anammox)bacteria in Cape Fear River Estuary.Environmental Microbiology,11(5):1 194-1 207,https://doi.org/10.1111/j.1462-2920.2008.01850.x.
Dang H Y,Chen R P,Wang L,Guo L Z,Chen P P,Tang Z W,Tian F,Li S Z,Klotz M G.2010.Environmental factors shape sediment anammox bacterial communities in hypernutrified Jiaozhou Bay,China.Applied and En vironmen tal Microbiology,76(2 1):7 036-7 047,https://doi.org/10.1128/aem.01264-10.
Dang H Y,Zhou H X,Zhang Z N,Yu Z S,Hua E,Liu X S,Jiao N Z.201 3.Molecular detection of Candidatus Scalindua Pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea,China.PLoS One,8(4):e61 3 30.https://doi.org/10.1 371/journal.pone.00613 30.
El Hanafy A A E M,Anwar Y,Mohamed S A,Al-Gami S M S,Sabir J S M,AbuZinadah O A,A1 Mehdar H,Alfaidi A W,Ahmed M M M.2016.Isolation and identification of bacterial consortia responsible for degrading oil spills from the coastal area of Yanbu,Saudi Arabia.Biotechnology&Biotechnological Equipment,30(1):69-74,https://doi.org/10.1080/13102818.2015.1086282.
Feng B W,Li X R,Wang J H,Hu Z Y,Meng H,Xiang L Y,Quan Z X.2009.Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea.FEMS Microbiology Ecology,70(2):236-248,https://doi.org/10.1111/j.1 574-6941.2009.00772.x.
Fernandes S O,Michotey V D,Guasco S,Bonin P C,Bharathi P A L.2012.Denitrification prevails over anammox in tropical mangrove sediments(Goa,India).Marine Environmental Research,74:9-19,https://doi.org/10.1016/j.marenvres.2011.11.008.
Galloway J N,Townsend A R,Erisman J W,Bekunda M,Cai Z C,Freney J R,Martinelli L A,Seitzinger S P,Sutton M A.2008.Transformation of the nitrogen cycle:recent trends,questions,and potential solutions.Science,320(5 878):889-892,https://doi.org/10.1126/science.1136674.
Goecke F,Thiel V,Wiese J,Labes A,Imhoff J F.2013.Algae as an important environment for bacteria-Phylogenetic relationships among new bacterial species isolated from algae.Phycologia,52(1):14-24,https://doi.org/10.2216/12-24.1.
Gonzalez-Silva B M,Ronning A J,Andreassen I K,Bakke I,Cervantes F J,Ostgaard K,Vadstein O.2017.Changes in the microbial community of an anammox consortium during adaptation to marine conditions revealed by 454pyrosequencing.Applied Microbiology and Biotechnology,101(12):5 149-5 162,https://doi.org/10.1007/s00253-017-8160-5.
Hall T.2011.BioEdit:an important software for molecular biology.GERF Bulletin of Biosciences,2(1):60-6 1.
Hietanen S,Kuparinen J.2008.Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland,Baltic Sea.Hydrobiologia,596(1):67-77,https://doi.org/10.1007/s10750-007-905 8-5.
Hou L J,Zheng Y L,Liu M,Gong J,Zhang X L,Yin G Y,You L.2013.Anaerobic ammonium oxidation(anammox)bacterial diversity,abundance,and activity in marsh sediments of the Yangtze Estuary.Journal of Geophysical Research.Biogeosciences,118(3):1 237-1 246,https://doi.org/10.1002/jgrg.20108.
Hu L M,Shi X F,Bai Y Z,Qiao S Q,Li L,Yu Y G,Yang G,Ma D Y,Guo Z G.2016.Recent organic carbon sequestration in the shelf sediments of the Bohai Sea and Yellow Sea,China.Journal of Marine Systems,155:50-5 8,https://doi.org/10.1 0 1 6/j.jmarsy s.201 5.10.018.
Humbert S,Tarnawski S,Fromin N,Mallet M P,Aragno M,Zopfi J.2010.Molecular detection of anammox bacteria in terrestrial ecosystems:distribution and diversity.The ISME Journal,4(3):450-454,https://doi.org/10.1038/ismej.2009.125.
Jones C M,Hallin S.2010.Ecological and evolutionary factors underlying global and local assembly of denitrifier communities.The ISME Journal,4(5):633-641,https://doi.org/10.103 8/ismej.2009.1 52.
Kartal B,Rattray J,Van Niftrik L A,Van De Vossenberg J,Schmid M C,Webb R I,Schouten S,Fuerst J A,DamstéJ S,Jetten M S M,Strous M.2007.Candidatus“Anammoxoglobus propionicus”a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria.Systematic and Applied Microbiology,30(1):39-49,https://doi.org/10.1016/j.sy apm.2006.03.004.
Kartal B,Van Niftrik L,Rattray J,Van De Vo ssenberg J L C M,Schmid M C,Sinninghe DamstéJ,Jetten M S M,Strous M.2008.Candidatus ‘Brocadia fulgida':an autofiuore sc ent anaerobic ammonium oxidizing bacterium.FEMS Microbiology Ecology,63(1):46-55,https://doi.org/10.1111/j.1 574-6941.2007.00408.x.
LabbéN,Parent S,Villemur R.2004.Nitratireductor aquibiodomus gen.nov.,sp.nov.,a novel a-proteobacterium from the marine denitrification system of the Montreal Biodome(Canada).International Journal of Systematic and Evolutionary Microbiology,54(1):269-273,https://doi.org/10.109 9/ij s.0.02793-0.
Lai Q L,Yu Z W,Wang J N,Zhong H Z,Sun F Q,Wang L P,Wang B J,Shao Z Z.2011a.Nitratireductor pacficus sp.nov.,isolated from a pyrene-degrading consortium.International Journal of Systematic and Evolutionary Microbiology,61(6):1386-1 391,https://doi.org/10.1099/ij s.0.024356-0.
Lai Q L,Yu Z W,Yuan J,Sun F Q,Shao Z Z.2011b.Nitratireductor indicus sp.nov.,isolated from deep-sea water.International Journal of Systematic and Evolutionary Microbiology,61(2):295-298,https://doi.org/10.1099/ij s.0.022962-0.
Li M,Cao H L,Hong Y G,Gu J D.2011a.Seasonal dynamics of anammox bacteria in estuarial sediment of the Mai PoNature Reserve revealed by analyzing the 16S rRNA and hydrazine oxidoreductase(hzo)genes.Microbes and Environments,26(1):15-22,https://doi.org/10.1264/jsme2.ME10131.
Li M,Ford T,Li X Y,Gu J D.2011b.Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing(anammox)bacteria.Environmental Science&Technology,45(8):3 547-3 553,https://doi.org/10.1021/es103826w.
Li M,Hong Y G,Klotz M G,Gu J D.2010.A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments.Applied Microbiology and Biotechnology,86(2):781-790,https://doi.org/10.1007/s00253-009-2361-5.
Lipsewers Y A,Hopmans E C,Meysman F J R,DamstéJ S S,Villanueva L.2016.Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake Grevelingen.Frontiers in Microbiology,7:1661,https://doi.org/10.3389/fmicb.2016.01661.
Liu J W,Fu B B,Yang H M,Zhao M X,He B Y,Zhang X H.201 5.Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary:the potential impact of hypoxia and nutrients.Frontiers in Microbiology,6:64,https://doi.org/10.3 3 89/fmicb.201 5.00064.
Liu X D,Tiquia S M,Holguin G,Wu L Y,Nold S C,Devol A H,Luo K,Palumbo A V,Tiedje J M,Zhou J Z.2003.Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico.Applied and Environmental Microbiology,69(6):3 549-3 560,https://doi.org/10.1128/aem.69.6.3549-3560.2003.
Magalhaes C M,Wiebe W J,Joye S B,Bordalo A A.2005.Inorganic nitrogen dynamics in intertidal rocky biofilms and sediments of the Douro River estuary(Portugal).Estuaries,28(4):592-606,https://doi.org/10.1007/BF02696070.
Magalhaes C,Bano N,Wiebe W J,Bordalo A A,Hollibaugh J T.2008.Dynamics of nitrous oxide reductase genes(nosZ)in intertidal rocky biofilms and sediments of the Douro River Estuary(Portugal),and their relation to N-biogeochemistry.Microbial Ecology,55(2):259-269,https://doi.org/10.1007/s00248-007-9273-7.
Malovanyy A,Plaza E,Trela J,Malovanyy M.2015.Ammonium removal by partial nitritation and anammox processes from wastewater with increased salinity.Environmental Technology,36(5):595-604,https://doi.or g/10.1080/09593330.2014.953601.
Mills H J,Hunter E,Humphrys M,Kerkhof L,McGuinness L,Huettel M,Kostka J E.2008.Characterization of nitrifying,denitrifying,and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico.Applied and Environmental Microbiology,74(14):4 440-4 453,https://doi.org/10.1128/aem.02692-07.
Pan G C,Qiu S Y,Liu X,Hu X K.2015.Estimating the economic damages from the Penglai 19-3 oil spill to the Yantai fisheries in the Bohai Sea of northeast China.Marine Policy,62:18-24,https://doi.org/10.1016/j.marpol.2015.08.007.
Piao Z,Zhang W W,Ma S,Li Y M,Yin S X.2012.Succession of denitrifying community compo sition in coastal wetland soils along a salinity gradient.Pedosphere,22(3):367-374.
Posada D,Crandall K A.1998.MODELTEST:testing the model of DNA substitution.Bioinformatics,14(9):817-81 8,https://doi.org/10.1093/bioinformatic s/14.9.817.
Qiao S Q,Shi X F,Wang G Q,Zhou L,Hu B Q,Hu L M,Yang G,Liu Y G,Yao Z Q,Liu S F.2017.Sediment accumulation and budget in the Bohai Sea,Yellow Sea and East China Sea.Marine Geology,390:270-281,https://doi.org/10.1 0 1 6/j.margeo.2017.06.004.
Redfield A C.195 8.The biological control of chemical factors in the environment.American Scientist,46(3):205-22 1.
Rink B,Seeberger S,Martens T,Duerselen C D,Simon M,Brinkhoff T.2007.Effects of phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities.Aquatic Microbial Ecology,48(1):47-60,http s://doi.org/1 0.3 3 54/ame048047.
Scala D J,Kerkhof L J.1998.Nitrous oxide reductase(nosZ)gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments.FEMS Microbiology Letters,162(1):6 1-68.
Scala D J,Kerkhof L J.1999.Diversity of nitrous oxide reductase(nosZ)genes in continental shelf sediments.Applied and Environmental Microbiology,65(4):1 681-1 687.
Scala D J,Kerkhof L J.2000.Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis.Applied and Environmental Microbiology,66(5):1 980-1 986,https://doi.org/10.1128/aem.66.5.1980-1986.2000.
Schloss P D,Handelsman J.2005.Introducing DOTUR,a computer program for defining operational taxonomic units and estimating species richness.Applied and Environmental Microbiology 71(3):1501-1 506,https://doi.org/10.112 8/aem.71.3.1501-1506.2005.
Schmid M C,Risgaard-Petersen N,Van De Vossenberg J,Kuypers M M M,Lavik G,Petersen J,Hulth S,Thamdrup B,Canfield D,Dalsgaard T,Rysgaard S,Sejr M K,Strous M,Den Camp H J M O,Jetten M S M.2007.Anaerobic ammonium-oxidizing bacteria in marine environments:widespread occurrence but low diversity.Environmental Microbiology,9(6):1 476-1 484,https://doi.org/10.1111/j.1462-2920.2007.01266.x.
Schmid M,Walsh K,Webb R,Rijpstra W I,Van De PasSchoonen K,Verbruggen M J,Hill T,Moffett B,Fuerst J,Schouten S,Sinninghe DamstéJ S,Harris J,Shaw P,Jetten M,Strous M.2003.Candidatus"Scalindua brodae",sp.nov.,Candidatus"Scalindua wagneri",sp.nov.,two new species of anaerobic ammonium oxidizingbacteria.Systematic and Applied Microbiology,26(4):529-538,https://doi.org/10.1078/072320203770865837.Shao M F,Zhang T,Fang H H P.2010.Sulfur-driven
autotrophic denitrification:diversity,biochemistry,and engineering applications.Applied Microbiology and Biotechnology,88(5):1 027-1 042,https://doi.org/10.1007/s00253-010-2847-1.
Shehzad A,Liu J W,Yu M,Qismat S,Liu J L,Zhang X H.2016.Diversity,community composition and abundance of anammox bacteria in sediments of the north marginal seas of China.Microbes and Environments,31(2):111-120,https://doi.org/10.1264/j sme2.ME15140.
SOA(State Oceanic Administration People's Republic of China).2016.Chinese Marine Environment Quality Bulletin,20 1 5.http://www.nmdis.org.cn/g ongbao/huanjing/201604/t20160414_33875.html.(in Chinese)
Sonthiphand P,Hall M W,Neufeld J D.2014.Biogeography of anaerobic ammonia-oxidizing(anammox)bacteria.Fron tiers in Microbiology,5:399,https://doi.org/1 0.33 89/fmicb.2014.003 99.
Stamatakis A.2014.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics,30(9):1 312-1 313,https://doi.org/1 0.1 0 93/bioinfo rmatic s/btu033.
Throback I N,Enwall K,Jarvis A,Hallin S.2004.Reassessing PCR primers targeting nirS,nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE.FEMS Microbiology Ecology,49(3):401-417,https://doi.org/10.1016/j.femsec.2004.04.011.
Van De Vossenberg J,Woebken D,Maalcke W J,Wessels H J C T,Dutilh B E,Kartal B,Janssen-Megens E M,Roeselers G,Yan J,Speth D,Gloerich J,Geerts W,Van Der Biezen E,Pluk W,Francoijs K J,Russ L,Lam P,Malfatti S A,Tringe S G,Haaijer S C M,Op Den Camp H J M,Stunnenberg H G,Amann R,Kuypers M M M,Jetten M S M.2013.The metagenome of the marine anammox bacterium'Candida tus Scalindua profunda'illustrates the versatility of this globally important nitrogen cycle bacterium.Environmental Microbiology,15(5):1 275-1 289,https://doi.org/10.1111/j.1462-2920.2012.02774.x.
Wang H T,Su J Q,Zheng T L,Yang X R.2014.Impacts of vegetation,tidal process,and depth on the activities,abundances,and community compositions of denitrifiers in mangrove sediment.Applied Microbiology and Biotechnology,98(22):9 375-9 387,https://doi.org/10.1007/s00253-014-6017-8.
Wang X L,Cui Z G,Guo Q,Han X R,Wang J T.2009.Distribution of nutrients and eutrophication assessment in the Bohai Sea of China.Chinese Journal of Oceanology and Limnology,27(1):177-183,https://doi.org/10.1007/s00343-009-0177-x.
Ward B B.2013.How nitrogen is lost.Science,341(6144):352-3 5 3,https://doi.org/10.1126/science.12403 14.
Wei H,Sun J,Moll A,Zhao L.2004.Phytoplankton dynamics in the Bohai Sea—observations and modelling.Journal of Marine Systems,44(3-4):233-251,https://doi.org/10.1016/j.jmarsys.2003.09.012.
Wei H,Tian T,Zhou F,Zhao L.2002.Numerical study on the water exchange of the Bohai Sea:simulation of the halflife time by dispersion model.Journal of Ocean University of Qingdao,32(4):519-525.(in Chinese with English abstract)
Woebken D,Lam P,Kuypers M M M,Naqvi S W A,Kartal B,Strous M,Jetten M S M,Fuchs B M,Amann R.2008.A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones.Environmental Microbiology,10(11):3 106-3 119,https://doi.org/10.1111/j.1462-2920.2008.01640.x.
Wyman M,Hodgson S,Bird C.2013.Denitrifying Alphaproteobacteria from the Arabian Sea that express nosZ,the gene encoding nitrous oxide reductase,in oxic and suboxic waters.Applied and Environmental Microbiology;79(8):2 670-2 681,https://doi.org/10.1128/aem.03705-12.
Xu L L,Wu D X,Lin X P,Ma C.2009.The study of the Yellow Sea Warm Current and its seasonal variability.Journal of Hydrodynamics,21(2):159-165,https://doi.org/10.1016/S1001-6058(08)60133-X.
Yang A J,Zhang X L,AgoguéH,Dupuy C,Gong J.2015.Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers,denitrifiers,and anammox bacteria in sediments of estuarine tidal flats.Annals of Microbiology,65(2):879-890,https://doi.org/10.1007/s1321 3-014-0929-5.
Yu T T,Li M,Niu M Y,Fan X B,Liang W Y,Wang F P.2018.Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea.Applied Microbiology and Biotechnology,102(1):447-45 9,https://doi.org/10.1007/s0025 3-017-8594-9.
Zhang X L,Agogue H,Dupuy C,Gong J.2014.Relative abundance of ammonia oxidizers,denitrifiers,and anammox bacteria in sediments of hyper-nutrified estuarine tidal flats and in relation to environmental conditions.Clean-Soil Air Water,42(6):815-823,https://doi.org/10.1002/clen.201 30001 3.
Zhang X L,Zhang Q Q,Yang A J,Hou L J,Zheng Y L,Zhai W D,Gong J.2018.Incorporation of microbial functional traits in biogeochemistry models provides better estimations of benthic denitrification and anammox rates in coastal oceans.Journal of Geophysical Research.Biogeosciences,123(10):3 331-3 352,https://doi.org/10.1029/2018JG004682.
Zumft W G.1997.Cell biology and molecular basis of denitrification.Microbiology and Molecular Biology Reviews,61(4):533-616.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |