Responses of Active Ammonia Oxidizers to Eutrophication and Oxygen Statuses in Taihu Freshwater Sediments

References

• Abeliovich A, Vonshak A. 1992. Anaerobic metabolism of nitrosomonas europaea. Arch Microbiol 158(4):267–270.
   Web of Science ®Google Scholar
• Auguet JC, Triadó-Margarit X, Nomokonova N, Camarero L, Casamayor EO. 2012. Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake. Isme J 6(9):1786–1797.
   PubMed Web of Science ®Google Scholar
• Berg P, Klemedtsson L, Rosswall T. 1982. Inhibitory effect of low partial pressures of acetylene on nitrification. Soil Biol Biochem 14(3):301–303.
   Web of Science ®Google Scholar
• Bollmann A, Bullerjahn GS, McKay RM. 2014. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior. PLoS One 9(5):e97068.
   PubMed Web of Science ®Google Scholar
• Bremner J, Jenkinson D. 1960. Determination of organic carbon in soil. J Soil Sci 11(2):394–402.
   Web of Science ®Google Scholar
• Cao H, Auguet JC, Gu JD. 2013. Global ecological pattern of ammonia-oxidizing archaea. PLoS One 8(2):e52853.
   PubMed Web of Science ®Google Scholar
• Chen X, Zhu Y, Xia Y, Shen J, He J. 2008. Ammonia-oxidizing archaea: important players in paddy rhizosphere soil. Environ Microbiol 10(8):1978–1987.
   PubMed Web of Science ®Google Scholar
• Chen X, Zhang LM, Shen JP, Xu ZH, He JZ. 2010. Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils. J Soils Sediments 10(8):1510–1516.
   Web of Science ®Google Scholar
• Chen GY, Qiu SL, Zhou YY. 2009a. Diversity and abundance of ammonia-oxidizing bacteria in eutrophic and oligotrophic basins of a shallow Chinese lake (Lake Donghu)). Res Microbiol 160(3):173–178.
   PubMed Web of Science ®Google Scholar
• Chen WM, Wang XF, Zhou WP. 2004. Observation methods of lake ecosystem. Beijing: Environmental Science Press. 301p.
   Google Scholar
• Chen Y, Wu L, Boden R, Hillebrand A, Kumaresan D, Moussard H, Baciu M, Lu Y, Colin Murrell J. 2009b. Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. Isme J 3(9):1093–1104.
   PubMed Web of Science ®Google Scholar
• De Bie MJM, Speksnijder AGCL, Kowalchuk GA, Schuurman T, Zwart G, Stephen JR, Diekmann OE, Laanbroek HJ. 2001. Shifts in the dominant populations of ammonia-oxidizing sz-subclass Proteobacteria along the eutrophic Schelde estuary. Aquat Microb Ecol 23:225–236.
   Web of Science ®Google Scholar
• Duan H, Ma R, Xu X, Kong F, Zhang S, Kong W, Hao J, Shang L. 2009. Two-decade reconstruction of algal blooms in China’s Lake Taihu. Environ Sci Technol. 43(10):3522–3528.
   PubMed Web of Science ®Google Scholar
• Fan FL, Yang QB, Li ZJ, Wei D, Cui X, Liang YC. 2011. Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community. Microb Ecol 62(4):982–990.
   PubMed Web of Science ®Google Scholar
• French E, Kozlowski JA, Mukherjee M, Bullerjahn G, Bollmann A. 2012. Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol 78(16):5773–5780.
   PubMed Web of Science ®Google Scholar
• Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, Martinelli LA, Seitzinger SP, Sutton MA. 2008. Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science. 320(5878):889–892.
   PubMed Web of Science ®Google Scholar
• Gieseke A, Purkhold U, Wagner M, Amann R, Schramm A. 2001. Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Appl Environ Microbiol 67(3):1351–1362.
   PubMed Web of Science ®Google Scholar
• Gleeson DB, Müller C, Banerjee S, Ma W, Siciliano SD, Murphy DV. 2010. Response of ammonia oxidizing archaea and bacteria to changing water filled pore space. Soil Biol Biochem 42(10):1888–1891.
   Web of Science ®Google Scholar
• Gruber N, Galloway JN. 2008. An Earth-system perspective of the global nitrogen cycle. Nature 451(7176):293–296.
   PubMed Web of Science ®Google Scholar
• Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW. 2011. Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA. 108(52):21206–21211.
   PubMed Web of Science ®Google Scholar
• Herrmann M, Saunders AM, Schramm A. 2008. Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. Appl. Environ Microbiol 74(10):3279–3283.
   PubMed Web of Science ®Google Scholar
• Herrmann M, Saunders AM, Schramm A. 2009. Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sediments. Appl Environ Microbiol 75(10):3127–3136.
   PubMed Web of Science ®Google Scholar
• Herrmann M, Scheibe A, Avrahami S, Kusel K. 2011. Ammonium availability affects the ratio of ammonia-oxidizing bacteria to ammonia-oxidizing archaea in simulated creek ecosystems. Appl Environ Microbiol 77(5):1896–1899.
   PubMed Web of Science ®Google Scholar
• He JZ, Hu HW, Zhang LM. 2012. Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biol Biochem 55(6):146–154.
   Google Scholar
• He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di H. 2007. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9(9):2364–2374.
   PubMed Web of Science ®Google Scholar
• Hou J, Song CL, Cao XY, Zhou YY. 2013. Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu). Water Research 47(7):2285–2296.
   PubMed Web of Science ®Google Scholar
• Hu HW, Zhang LM, Yuan CL, Zheng Y, Wang JT, Chen DL. 2015. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors. Front Microbiol. 4938.
   Google Scholar
• Huang LQ, Dong HL, Wang S, Huang Q, Jiang H. 2014. Diversity and abundance of ammonia-oxidizing archaea and bacteria in diverse Chinese paddy soils. Geomicrobiol J. 31(1):12–22.
   Web of Science ®Google Scholar
• Huo S, Ma C, Xi B, Su J, Zan F, Ji D, He Z. 2013. Establishing eutrophication assessment standards for four lake regions, China. J Environ Sci. 25(10):2014–2022.
   Web of Science ®Google Scholar
• Jia ZJ, Conrad R. 2009. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11(7):1658–1671.
   PubMed Web of Science ®Google Scholar
• Kalvelage T, Jensen MM, Contreras S, Contreras NP, Lam P, Günter M, LaRoche J, Lavik G, Kuypers MMM. 2011. Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones. PLoS One 6(12):e29299.
   PubMed Web of Science ®Google Scholar
• Koops HP, Purkhold U, Pommerening-Röser A, Timmermann G, Wagner M. 2006. The lithoautotrophic ammonia-oxidizing bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The Prokaryotes. 3rd ed. New York: Springer. P 778–811.
   Google Scholar
• Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW. 2011. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci USA 108(38):15892–15897.
   PubMed Web of Science ®Google Scholar
• Lehtovirta-Morley LE, Verhamme DT, Nicol GW, Prosser JI. 2013. Effect of nitrification inhibitors on the growth and activity of Nitrosotalea devanaterra in culture and soil. Soil Biol Biochem 62129–133.
   Web of Science ®Google Scholar
• Li H, Weng BS, Huang FY, Su JQ, Yang XR. 2015. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China. Appl Microbiol Biotechnol 99(14):6113–6123.
   PubMed Web of Science ®Google Scholar
• Limpiyakorn T, Fürhacker M, Haberl R, Chodanon T, Srithep P, Sonthiphand P. 2013. amoA-encoding archaea in wastewater treatment plants: a review. Appl Microbiol Biotechnol 97(4):1425–1439.
   PubMed Web of Science ®Google Scholar
• Lipschultz F, Wofsy SC, Ward BB, Codispoti LA, Friedrich G, Elkins JW. 1990. Bacterial transformations of inorganic nitrogen in the oxygen-deficient waters of the Eastern Tropical South Pacific Ocean. Deep Sea Res A 37(10):1513–1541.
   Web of Science ®Google Scholar
• Liu S, Shen L, Lou L, Tian G, Zheng P, Hu B. 2013. Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China. Appl Environ Microbiol 79(13):4065–4071.
   PubMed Web of Science ®Google Scholar
• Lu SM, Liu XG, Ma ZJ, Liu QG, Wu ZF, Zeng XL, Shi X, Gu ZJ. 2016. Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond. Front Microbiol 6: 1539.
   PubMed Web of Science ®Google Scholar
• Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461(7266):976–979.
   PubMed Web of Science ®Google Scholar
• Matthew RB, Alireza T, Dmitri S. 2013. Mathematical modeling of competition for ammonium among bacteria, archaea and cyanobacteria within cyanobacterial mats: can ammonia-oxidizers force nitrogen fixation? Ocean Sci J. 48(3):269–277.
   Web of Science ®Google Scholar
• Mosier AC, Francis CA. 2008. Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 10(11):3002–3016.
   PubMed Web of Science ®Google Scholar
• Park BJ, Park SJ, Yoon DN, Schouten S, Sinninghe Damsté JS, Rhee SK. 2010. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl Environ Microbiol 76(22):7575–7287.
   PubMed Web of Science ®Google Scholar
• Park HD, Noguera DR. 2007. Characterization of two ammonia-oxidizing bacteria isolated from reactors operated with low dissolved oxygen concentrations. J Appl Microbiol 102(5):1401–1417.
   PubMed Web of Science ®Google Scholar
• Pauer JJ, Auer MT. 2000. Nitrification in the water column and sediment of a hypereutrophic lake and adjoining river system. Water Research 34(4):1247–1254.
   Web of Science ®Google Scholar
• Pelve EA, Lindås AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R. 2011. Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus. Mol Microbiol. 82(3):555–566.
   PubMed Web of Science ®Google Scholar
• Pett-Ridge J, Petersen DG, Nuccio E, Firestone MK. 2013. Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil. FEMS Microbiol Ecol. 85(1):179–194.
   PubMed Web of Science ®Google Scholar
• Prosser JI, Nicol GW. 2012. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20(11):523–531.
   PubMed Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541.
   PubMed Web of Science ®Google Scholar
• Smith MW, Zeigler AL, Allen AE, Herfort L, Simon HM. 2013. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front Microbiol 4120.
   PubMed Web of Science ®Google Scholar
• Sun RB, Guo XS, Wang DZ, Chu HY. 2015. Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle. Appl Soil Ecol 95171–178.
   Web of Science ®Google Scholar
• Sun W, Xia C, Xu M, Guo J, Wang A, Sun G. 2013. Distribution and abundance of archaeal and bacterial ammonia oxidizers in the sediments of the Dongjiang river, a drinking water supply for Hong Kong. Microbes Environ 28(4):457–465.
   PubMed Web of Science ®Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599.
   PubMed Web of Science ®Google Scholar
• Taylor AE, Bottomley PJ. 2006. Nitrite production by Nitrosomonas europaea and Nitrosospira sp. AV in soils at different solution concentrations of ammonium. Soil Biol Biochem 38(4):828–836.
   Web of Science ®Google Scholar
• Taylor AE, Giguere AT, Zoebelein CM, Myrold DD, Bottomley PJ. 2016. Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria. Isme J 11(4):896–813.
   PubMed Web of Science ®Google Scholar
• Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C. 2011. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil . Proc Natl Acad Sci USA 108(20):8420–8425.
   PubMed Web of Science ®Google Scholar
• Wagner M, Rath G, Amann R, Koops H-P, Schleifer KH. 1995. In situ identification of ammonia-oxidizing bacteria. Syst Appl Microbiol 18(2):251–264.
   Web of Science ®Google Scholar
• Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PSG, Chan PP, Gollabgir A, et al. 2010. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107(19):8818–8823.,
   PubMed Web of Science ®Google Scholar
• Wang SM, Dou HS. 1998. Lakes of China. Beijing: Science Press. 261p.
   Google Scholar
• Wang XL, Han C, Zhang JB, Huang QR, Deng H, Deng YC, Zhong WH. 2015. Long-term fertilization effects on active ammonia oxidizers in an acidic upland soil in China. Soil Biol Biochem 8428–37.
   Web of Science ®Google Scholar
• Wells GF, Park HD, Yeung CH, Eggleston B, Francis CA, Criddle CS. 2009. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ Microbiol 11(9):2310–2328.
   PubMed Web of Science ®Google Scholar
• Wu YC, Xiang Y, Wang JJ, Zhong JC, He JZ, Wu QL. 2010. Heterogeneity of archaeal and bacterial ammonia-oxidizing communities in Lake Taihu, China. Environ Microbiol Rep 2(4):569–576.
   PubMed Web of Science ®Google Scholar
• Wu YC, Ke XB, Hernández M, Wang BZ, Dumont MG, Jia ZJ, Conrad R. 2013. Autotrophic growth of bacterial and archaeal ammonia oxidizers in freshwater sediment microcosms incubated at different temperatures. Appl Environ Microbiol 79(9):3076–3084.
   PubMed Web of Science ®Google Scholar
• Wuchter C, Abbas B, Coolen MJL, Herfort L, Bleijswijk JV, Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Damsté JSS 2006. Archaeal nitrification in the ocean. Proc Natl Acad Sci USA 103:12317–12322.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Chen LJ, Dai TJ, Sun RH, Wen DH. 2015. Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms. Appl Microbiol Biotechnol 99(15):6481–6491.
   PubMed Web of Science ®Google Scholar