Production of nitrate spikes in a model of ammonium biodegradation

Alfreider A, Krössbacher M, Psenner R (1997) Groundwater samples do not reflect bacterial densities and activity in subsurface systems. Water Res 31(4):832–840

Bailey RT, Gates TK, Romero EC (2015) Assessing the effectiveness of land and water management practices on nonpoint source nitrate levels in an alluvial stream–aquifer system. J Contam Hydrol 179:102–115

Barber SA (1995) Soil nutrient bioavailability: a mechanistic approach. Wiley, New York

Blackburne R, Vadivelu VM, Yuan Z, Keller J (2007) Determination of growth rate and yield of nitrifying bacteria by measuring carbon dioxide uptake rate. Water Environ Res: A Res Publ Water Environ Federation 79(12):2437–2445

Broholm MM, Jones I, Torstensson D, Arvin E (1998) Groundwater contamination from a coal carbonization plant. Geol Soc, Lond, Eng Geology Special Publ 14(1):159–165

Capuno RE Jr (2007) Mathematical modeling for nitrogen removal via a nitritation: anaerobic ammonium oxidation-coupled biofilm in a hollow fiber membrane bioreactor and a rotating biological contactor. Master’s thesis, Virginia Polytechnic Institute and State University

Charoanwoodtipong T, Limpiyakorn T, Suwannasilp BB (2015) Kinetics of ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria enriched at high and low ammonia concentrations. In: Proceedings of the 3rd International Conference on Biological, Chemical and Environmental Sciences, pp 1–5

Cribbin LB, Winstanley HF, Mitchell SL, Fowler A, Sander GC (2014) Reaction front formation in contaminant plumes. J Contam Hydrol 171:12–21

Davison R (1998) Natural attenuation and risk assessment of groundwater contaminated with ammonium and phenolics. PhD thesis, University of Bradford

Fowler A (2011) Mathematical geoscience, vol 36. Springer Science & Business Media, Berlin

Fowler A (2014) Starvation kinetics of oscillating microbial populations. Math Proc R Ir Acad 114(2):173–189

Fowler A, Winstanley HF, McGuinness MJ, Cribbin LB (2014) Oscillations in soil bacterial redox reactions. J Theor Biol 342:33–38

Gleeson T, Befus KM, Jasechko S, Luijendijk E, Cardenas MB (2015) The global volume and distribution of modern groundwater. Nature Geoscience, Advance on(November):1–15

Hanaki K, Wantawin C, Ohgaki S (1990) Nitrification at low levels of dissolved oxygen with and without organic loading in a suspended-growth reactor. Water Res 24(3):297–302

Helder W, De Vries R (1983) Estuarine nitrite maxima and nitrifying bacteria (ems-dollard estuary). Neth J Sea Res 17(1):1–18

Huisman J, Weissing FJ (1999) Biodiversity of plankton by species oscillations and chaos. Nature 402 (6760):407–410

Johnsson H, Bergstrom L, Jansson P-E, Paustian K (1987) Simulated nitrogen dynamics and losses in a layered agricultural soil. Agric Ecosyst Environ 18(4):333–356

Kartal B, Tan NCG, Van Biezen ED, Kampschreur MJ, Van Loosdrecht MCM, Jetten MSM (2010) Effect of nitric oxide on anammox bacteria. Appl Environ Microbiol 76(18):6304–6306

Kindred JS, Celia MA (1989) Contaminant transport and biodegradation: 2. Conceptual model and test simulations. Water Resour Res 25(6):1149–1159

Kinzelbach W, Schäfer W, Herzer J (1991) Numerical modeling of natural and enhanced denitrification processes in aquifers. Water Resour Res 27(6):1123–1135

Kogure K, Koike I (1987) Particle counter detrmination of bacterial biomass in seawater. Appl Environ Microbiol 53(2):274–277

Koops HP, Pommerening-Rȯser A (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37(1):1–9

Kopell N, Howard L (1973) Plane wave solutions to reaction-diffusion equations. Stud Appl Math 52 (4):291–328

Kreft JU, Picioreanu C, Wimpenny JW, van Loosdrecht MC (2001) Individual-based modelling of biofilms. Microbiology (Reading, England) 147(Pt 11):2897–912

Laanbroek HJ, Bodelier PLE, Gerards S (1994) Oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter hamburgensis grown in mixed continuous cultures at different oxygen concentrations. Arch Microbiol 161(2):156–162

Langergraber G, Rousseau DPL, Garci̇a J, Mena J (2009) CWM1: A general model to describe biokinetic processes in subsurface flow constructed wetlands. Water Sci Technol 59(9):1687–1697

Maggi F, Gu C, Riley W, Hornberger G, Venterea R, Xu T, Spycher N, Steefel C, Miller N, Oldenburg C (2008) A mechanistic treatment of the dominant soil nitrogen cycling processes: model development, testing, and application. J Geophys Res Biogeosci 113(G2)

McGuinness MJ, Cribbin LB, Winstanley HF, Fowler A (2014) Modelling spatial oscillations in soil borehole bacteria. J Theor Biol 363:74–79

Mekala C, Gaonkar O, Nambi IM (2017) Understanding nitrogen and carbon biogeotransformations and transport dynamics in saturated soil columns. Geoderma 285:185–194

Michaelis L, Menten ML (1913) Die kinetik der invertinwirkung. Biochem z 49(333-369):352

Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3(1):371–394

Morrissey P, Johnston P, Gill L (2015) The impact of on-site wastewater from high density cluster developments on groundwater quality. J Contam Hydrol 182:36–50

Mulder A, van de Graaf AA, Robertson L, Kuenen J (1995) Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor. FEMS Microbiol Ecol 16(3):177–183

Munz G, Lubello C, Oleszkiewicz JA (2011) Factors affecting the growth rates of ammonium and nitrite oxidizing bacteria. Chemosphere 83(5):720–725

Nowka B, Daims H, Spieck E (2015) Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Appl Environ Microbiol 81(2):745–753

Oshiki M, Shimokawa M, Fujii N, Satoh H, Okabe S (2011) Physiological characteristics of the anaerobic ammonium-oxidizing bacterium ‘Candidatus Brocadia sinica’. Microbiology 157(6):1706–1713

Ranjbar F, Jalali M (2013) Measuring and modeling ammonium adsorption by calcareous soils. Environ Monit Assess 185(4):3191–3199

Salem S, Moussa MS, van Loosdrecht MCM (2006) Determination of the decay rate of nitrifying bacteria. Biotechnol Bioeng 94(2):252–62

Sander R (2015) Compilation of henry’s law constants (version 4.0) for water as solvent. Atmos Chem Phys 15(8)

Scaglione D, Caffaz S, Bettazzi E, Lubello C (2009) Experimental determination of Anammox decay coefficient. J Chem Technol Biotechnol 84(8):1250–1254

Schiesser WE (1991) The numerical method of lines. Academic Press, Cambridge

Schmidt I, Bock E (1997) Anaerobic ammonia oxidation with nitrogen dioxide by Nitrosomonas eutropha. Arch Microbiol 167(2-3):106–111

Schmidt I, Bock E (1998) Anaerobic ammonia oxidation by cell-free extracts of Nitrosomonas eutropha. Anton Leeuw Int J Gen Mol Microbiol 73(3):271–278

Schmidt I, Bock E, Jetten MS (2001a) Ammonia oxidation by nitrosomonas eutropha with no2 as oxidant is not inhibited by acetylene. Microbiology 147(8):2247–2253

Schmidt I, Sliekers AO, Schmid MC, Cirpus I, Strous M, Bock E, Kuenen JG, Jetten MSM (2001b) Aerobic and anaerobic ammonia oxidizing bacteria competitors or natural partners?. FEMS Microbiol Ecol 39(3):175–181

Schmidt I, Zart D, Bock E (2001c) Effects of gaseous NO2 on cells of nitrosomonas eutropha previously incapable of using ammonia as an energy source. Antonie Van Leeuwenhoek 79(1):39–47

Sliekers AO, Haaijer SCM, Stafsnes MH, Kuenen JG, Jetten MSM (2005) Competition and coexistence of aerobic ammonium- and nitrite-oxidizing bacteria at low oxygen concentrations. Appl Microbiol Biotechnol 68 (6):808–817

Smits THM, Hu̇ttmann A, Lerner DN, Holliger C (2009) Detection and quantification of bacteria involved in aerobic and anaerobic ammonium oxidation in an ammonium-contaminated aquifer. Bioremediation J 13 (1):41–51

Strohm TO, Griffin B, Zumft WG, Schink B (2007) Growth yields in bacterial denitrification and nitrate ammonification. Appl Environ Microbiol 73(5):1420–1424

Strous M, Heijnen J, Kuenen JG, Jetten MSM (1998) The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms. Appl Micorbial biotechnol 50:589–596

Van der Heijden R, Heijnen J, Hellinga C, Romein B, Luyben K (1994) Linear constraint relations in biochemical reaction systems: i. Classification of the calculability and the balanceability of conversion rates. Biotech Bioeng 43(1):3–10

Verhagen FJ, Laanbroek HJ (1991) Competition for ammonium between nitrifying and heterotrophic bacteria in dual energy-limited chemostats. Appl Environ Microbiol 57(11):3255–3263

Verhagen FJM, Duyts H, Laanbroek HJ (1992) Competition for ammonium between nitrifying and heterotrophic bacteria in continuously perculated soil columns. Appl Environ Microbiol 58(11):3303–3311

Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95(12):6578–6583

Widdowson MA, Molz FJ, Benefield LD (1988) A numerical transport model for oxygen-and nitrate-based respiration linked to substrate and nutrient availability in porous media. Water Resour Res 24(9):1553–1565

Wiesmann U (1994) Biological nitrogen removal from wastewater. In: Biotechnics/wastewater. Springer, pp 113–154

Wrage N, Velthof GL, Van Beusichem ML, Oenema O (2001) Role of nitrifier denitrification in the production of nitrous oxide. Soil Biol Biochem 33(12-13):1723–1732

Yu XF, Zhang YX, Zou YC, Zhao HM, Lu XG, Wang GP (2011) Adsorption and desorption of ammonium in wetland soils subject to freeze-thaw cycles. Pedosphere 21(2):251–258

Zart D, Bock E (1998) High rate of aerobic nitrification and denitrification by Nitrosomonas eutropha grown in a fermentor with complete biomass retention in the presence of gaseous NO2 or NO. Arch Microbiol 169(4):282–286

Zart D, Schmidt I, Bock E (2000) Significance of gaseous no for ammonia oxidation by nitrosomonas eutropha. Antonie Van Leeuwenhoek 77(1):49–55