Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media




Abstract. Saukoly SA, Meitiniarti VI, Nugroho RA, Krave AS. 2024. Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media. Biodiversitas 25: 916-923. Nitrification is the process of ammonium oxidation to form nitrites and nitrates. Ammonium availability in the soil is one of the factors influencing the activity, abundance, and diversity of ammonia-oxidizing microorganisms (AOM). This study aimed to determine the effect of enriching a soil media with different ammonium concentrations on the abundance and diversity of AOM as well as the potential for nitrification. Soil as the media was prepared from an agricultural land receiving cow dung sewage. The media was then placed in the microcosms, and was added to a nitrification medium containing ammonium at three levels; 0 (control soil), 200 (low ammonium-enriched soil), and 500 mg L-1 (high ammonium-enriched soil). The microcosms were further incubated for 42 days at room temperature. The nitrification potential determination was based on the formation of nitrite from ammonium oxidation. The abundance of AOM and the potential nitrification were measured every 14-day interval, including day 0 as the initial condition. The AOM composition was analyzed based on the similarity level of the amoA gene sequence to the NCBI BLAST GenBank database. However, this analysis was only conducted for the control and high ammonium-enriched soil. This study indicated that ammonium enrichment increased the nitrification activity and the abundance of AOM, but it decreased the diversity of AOM communities. There were positive correlations between nitrification and nitrate potential, as well as between ammonium content and AOM abundance. Negative correlations appeared between pH and nitrification potential, nitrate concentrations, ammonium concentrations, and MPN. The diversity of ammonium-oxidizing archaea (AOA) in the control soil was higher than in the high ammonium-enriched soil. The enrichment with ammonium also changed the AOA composition. The Candidatus Nitrosocosmicus oleophilus strain of the MY3 chromosome was the most dominant archaea in the control and high ammonium-enriched soil. This implies that the high diversity of AOA in this soil may be beneficial for further use of the soil as a source for inocula in the development of nitrifiers-based biofertilizers.


Ahn JY, Kil DY, Kong, C, Kim BG. 2014. Comparison of oven drying methods for determination of moisture content in feed ingredients. Asian-Australas J Anim Sci 27 (11): 1615-1622. DOI: 10.5713/ajas.2014.14305.
Agustiyani D, Hartati I, Erni NF, Eodjijono. 2004. Effect of pH and organic substrate on growth and activities of ammonia-oxidizing bacteria. Biodiversitas 5 (2): 43-47. DOI: 10.13057/biodiv/d050201.
Azziz G, Trasante T, Monza J, Irisarri P. 2016. The effect of soil type, rice cultivar and water management on ammonia-oxidizing archaea and bacteria populations. Appl Soil Ecol 100:8–17. DOI: 10.1016/j.apsoil.2015.11.009.
Beeckman F, Hans M dan Tom B. 2018. Nitrification in agricultural soils: impact, actors and mitigation. Curr Opin Biotechnol 50: 166-173. DOI: 10.1016/j.copbio.2018.01.014.
Berg C, Vandieken V, Thamdrup B, Jurgens K. 2015. Significane of archaeal nitrification in hypoxic waters of the Baltic sea. ISME J 9: 1219-1332. DOI: 10.1038/ismej.2014.218.
Berg P, Rosswall T. 1985. Amonium oxidizer numbers, potential and actual oxidation rates in two Swedish arable soils. Biol Fert Soils 1:131-140. DOI: 10.1007/BF00301780.
Cavagnaro TR, Jackson LE, Hristova K, Scow KM. 2008. Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil. Appl Soil Ecol 40:13–18. DOI:
Chen C, Yinghao S,Yanchao Y. 2021. The operating characteristics of partial nitrification by controlling pH and alkalinity. Water 13 (3): 1-10. DOI: 10.3390/w13030286.
Chicano TM, Dietrich L, de Almeida NM, Akram M, Hartmann E, Leidreiter F, Leopoldus D, Mueller M, Sánchez R, Nuijten GHL, Reimann J, Seifert KA, Schlichting I, van Niftrik L, Jetten MSM, Dietl A, Kartal B, Parey K, Barends TRM. 2021. Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nat Microbiol 6 (9):1129-1139. DOI: 10.1038/s41564-021-00934-8.
Claros J, Jimenez E, Aguado D, Ferrer J, Seco A, Serralta J. 2013. Effect of pH and HNO2 concentration on the activity of ammonia-oxidizing bacteria in a partial nitritation reactor. Water Sci Technol 67 (11): 2587-2594. DOI: 10.2166/wst.2013.132.
Dalu G, Belayneh B, Kaiwen P, Si Shen, Jian Z, Xianjun J, Zijie Y, Jianjun J, Hongyan L. 2021. Response of nitrification and nitrifying microorganisms to different nitrogen sources in the acid ultisols of jinyun mountain. J Soil Sci Plant Nutr 67 (5): 576-584. DOI: 10.1080/00380768.2021.1963639.
Duan P, Wu Z, Zhang Q, Fan C, Xiong Z. 2018. Thermodynamic responses of ammonia-oxidizing archaea and bacteria explain N2O production from greenhouse vegetable soils. Soil Biol Chem 120: 37–47. DOI: 10.1016/j.soilbio.2018.01.027.
Gao SJ, Chang DN, Zou CQ, Cao WD, Gao JS, Huang J, Bai JS, Zeng NH, Rees RM, Thorup-Kristensen K.2018. Archaea are the predominant and responsive ammonia oxidizing prokaryotes in a red paddy soil receiving green manures. J Soil Biol 88: 27–35. DOI: 10.1016/j.ejsobi.2018.05.008.
Graham BMB, Judith L, McWirter, Matthew HD. 2003. Uncertainty in most probable number calculations for microbiological assays. J AOAC Int 86 (5): 1085-1088.
Hazard C, James I P, Graeme WN. 2021. Use and abuse of potential rates in soil microbiology. J Soil Biol Biochem 157: 1-6. DOI: 10.1016/j.soilbio.2021.108242.
He H, Zhen Y, Mi T, Fu L, Yu Z. 2018. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in sediments from adjacent waters of rushan bay, china. Front Microbiol 9 (116): 1-14. DOI: 10.3389/fmicb.2018.00116.
Hink L, Cecile GR, Graeme WN, James IP. 2018. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J 12: 1084–1093. DOI: 10.1038/s41396-017-0025-5.
Jung MY, Kim JG, Damsté JSS, Rijpstra WIC, Madsen EL, Kim SJ. 2016. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment. Environ Microbiol Rep 8 (6): 983–992. DOI: 10.1111/1758-2229.12477.
Jung MY, Park SJ, Min D, Kim JS, Rijpstra WIC, Damsté JSS. 2011. Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil. Appl Environ Microbiol 77: 8635–8647. DOI: 10.1128/AEM.05787-11.
Kessel MAV, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lücker S. 2015. Complete nitrification by a single microorganism. Nature 528 (7583): 555-559. DOI: 10.1038/nature16459.
Kjeldahl, J. 1883. A New method for the determination of nitrogen in organic matter. J Anal Chemist 22: 366-382. DOI: 10.1007/BF0133815.
Kusuma AP, Rini NH, Harry SD. 2014. DSS untuk Menganalisis pH Kesuburan Tanah Menggunakan Metode Single Linkage. J EECCIS 8 (1): 61-66.
Konneke M, Schubert DM, Brown PC, Hugler M, Standfest S, Schwander T, Schada von Borzyskowski L, Erb TJ, Stahl DA, Berg IA. 2014. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc Natl Acad Sci USA 111(22): 8239-44. DOI: 10.1073/pnas.1402028111.
Leghari SJ, Niaz AW, Ghulam ML , Abdul HL, Bhabhan GM, Khalid HT. 2016. Role of nitrogen for plant growth and development: a review. Adv Environ Biol 10 (9): 1-6.
Lehtovirta ML E, Verhamme DT, Nicol GW, Prosser JI. 2013. Effect of nitrification inhibitors on the growth and activity of Nitrosotalea devanaterra in culture and soil. J Soil Biol Biochem 62:129–133. DOI: 10.1016/j.soilbio.2013.01.020.
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C. 2006. Archaea predominate among ammonia-oxidising prokaryotes in soils. Nature 442 (7104): 806–809. DOI: 10.1038/nature04983.
Li M, Gu JD. 2013. Community structure and transcript responses of anammox bacteria, AOA, and AOB in mangrove sediment microcosms amended with ammonium and nitrite. Appl Microbiol Biotechnol 97 (22): 9859–9874. DOI: 10.1007/s00253-012-4683-y.
Liu R, Hayden H, Suter H, He J, Chen D. 2015. The effect of nitrification inhibitors in reducing nitrification and the ammonia oxidizer population in three contrasting soils. J Soil Sediment 15:1113–1118. DOI: 10.1007/s11368-015-1086-6
Lu L, Wenyan H, Jinbo Z, Yucheng W Baozhan W, Xiangui L, Jianguo Z, Zucong C dan Zhongjun J. 2012. Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea. ISME J 6: 1978-1984. DOI: 10.1038/ismej.2012.45.
Liu L, Mengfan L, Yiming J, Weitie L, Jianfei L. 2019. Physiological and genomic analysis of Candidatus Nitrosocosmicus agrestis, an ammonia tolerant ammonia-oxidizing archaeon from vegetable soil. DOI: 10.1101/2019.12.11.872556.
Maia LB dan Jose? J GM. 2014. How Biology Handles Nitrite. Chem Rev 114: 5273?5357. DOI: 10.1021/cr400518y.
Mawaddah A, Roto, Adhitasari S. 2016. Pengaruh Penambahan urea terhadap peningkatan pencemaran nitrit dan nitrat dalam tanah. JML 23 (3): 360-364. DOI: 10.22146/jml .22473.
Msimbira LA and Smith DL. 2020. The Roles of Plant Growth Promoting Microbes in Enhancing Plant Tolerance to Acidity and Alkalinity Stresses. Front Sustain Food Syst 4 (106): 1-14. DOI: 10.3389/fsufs.2020.00106.
Musiani F, Broll V, Evangelisti E, Ciurli S. 2020. The model structure of the copper-dependent ammonia monooxygenase. J Biol Inorg Chem 25 (7): 995–1007. DOI: 10.1007/s00775-020-01820-0.
Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF, Gebreyesus B, Lebauer D, Scow KM. 2004. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidising bacteria in soil. Appl Environ Microb 70 (2): 1008–1016. DOI: 10.1128/AEM.70.2.1008-1016.2004.
Qu Z, Mingjiang L, Quanjiu W, Yan S, Yichen W, Jian L. 2022. Effects of Ionized Water Addition on Soil Nitrification Activity and Nitrifier Community Structure. Agronom 12 (6): 1-14. DOI: 10.3390/agronomy12061399.
Pjavac P, C Cleme S, Lianna P, Craig WH, Maartje AHJ Van K, Anne D, Michaela S, Mike SM Jetten, Sebastian L, Michael W, Daims H. 2017. amoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment. Front Microbiol 8: 1508. DOI: 10.3389/fmicb.2017.01508.
Rotthauwe JH, Witzel KR, Liesack W. 1997. The ammonia monooxygenase structural gene amoA as a functional marker: molecular ?ne-scale analysis of natural ammonia oxidizing populations. Appl Environ Microb 63 (12): 4704–4712. DOI: 10.1128/aem.63.12.4704-4712.1997.
Rowe R, Todd R, Waide J. 1976. Microtechnique for most-probable-number analysis. Appl Environ Microbiol 33 (3): 675-680. DOI: 10.1128/aem.33.3.675-680.1977.
Sauder LA, Mad A, Katja E, Jasmin S, Per H Nielsen, Michael W, Josh DN. 2017. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME J 11:1142–1157. DOI: 10.1038/ismej.2016.192.
Shen JP, Zhang LM, Di HJ, He JZ. 2012. A review of ammonia-oxidizing bacteria and archaea in Chinese soils. Front Microbiol 3 (239): 1-7. DOI: 10.3389/fmicb.2012.00296.
Siliakus MF, van der Oost J, Kengen SWM. 2017. Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extrophil 21(4): 651-670. DOI: 10.1007/s00792-017-0939-x.
Song H, Che Z, Cao W, Huang T, Wang J, Dong Z. 2016. Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen. Environ Sci Pollut Res 23: 11964–11974. DOI: 10.1007/s11356-016-6396-8.
Stein LY, Klotz MG. The nitrogen cycle. 2016. Curr Biol 26 (3): 94-98. DOI: 10.1016/j.cub.2015.12.021.
Sterngren AE, Hallin S, Bengtson P. 2015. Archaeal ammonia oxidizers dominate in numbers, but bacteria drive gross nitrification in n-amended grassland soil. Front Microbiol 6 (1350): 1-8. DOI: 10.3389/fmicb.2015.01350.
Stopnisek, N, Gubry RC, Höfferle S, Nicol GW, Mandic MI, Prosser JI. 2010. Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by amonium amendment. Appl Environ Microbiol 76 (22): 7626–7634. DOI: 10.1128/AEM.00595-10.
Tago K, Takashi O, Yumi S, Yoshitomo K,Tomoyuki H, Atsushi N, Masahito H. 2015. Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil. Microbes environ 30 (1): 21-28. DOI: 10.1264/jsme2.ME14137.
Tsiknia M, Paranychianakis NV, Varouchakis EA, Nikolaidis NP. 2015. Environmental drivers of the distribution of nitrogen functional genes at a watershed scale. FEMS Microbiol Ecol 91(6): 1-11. DOI: 10.1093/femsec/fiv052.
Tzanakakisa VA, Antonios A, Nikolaos PN, Nikolaos VP. 2018. Ammonia oxidizing archaea do not respond to ammonium or urea supply in T an alkaline soil. Appl Soil Ecol 132: 194-198. DOI: 10.1016/j.apsoil.2018.08.002.
Verhamme, DT, Prosser JI, Nicol GW. 2011. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5 (6): 1067–1071. DOI: 10.1038/ismej.2010.191.
Wang X, Han C, Zhang J, Huang Q, Deng H, Deng Y, Zhong W. Long-term fertilization effects on active ammonia oxidizers in an acidic upland soil in China. J Soil Biol Biochem 84: 28–37. DOI: 10.1016/j.soilbio.2015.02.013.
Weatherburn, M.W. 1967. Phenol Hipochlorite Reaction for Determination of Ammonia. Anal Chemist 39: 971-974. DOI: 10.1021/ac60252a045.
White CJ, Nicolai L. 2016. Is there a pathway for N2O production from hydroxylamine oxidoreductase in ammonia-oxidizing bacteria?. Proc Natl Acad Sci USA 113 (51): 14474–14476. DOI: 10.1073/pnas.1617953114.
Wuchter C, Abbas B, Coolen MJL, Herfort L, Bleijswijk J, van Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Damste JSS. 2006. Archaeal nitrification in the ocean. Pro Natl Acad Sci USA 103: 12317–12322. DOI: 10.1073/pnas.0600756103.
Xu A, Li L, Xie J, Gopalakrishnan S, Zhang R, Luo Z, Cai L, Liu C, Wang L, Anwar S, Jiang Y. 2022. Changes in ammonia-oxidizing archaea and bacterial communities and soil nitrogen dynamics in response to long-term nitrogen fertilization. Int J Environ Res Public Health19 (5):1-18. DOI: 10.3390/ijerph19052732.
Yao H, Campbell CD, Chapman SJ, Freitag TE, Nicol GW, et al. 2013. Multi-factorial drivers of ammonia oxidizer communities: Evidence from a national soil survey. Environ Microbiol 15: 2545–2556. DOI: 10.1111/1462-2920.12141.
Yaying L, Ruijiao X, Weijin W, Huaiying Y. 2018. The relative contribution of nitrifiers to autotrophic nitrification across a pH-gradient in a vegetable cropped soil. J Soils Sediments 5: 1-11. DOI: 10.1007/s11368-018-2109-x.
Zhang J, Sun W, Zhong W, Cai Z. 2014. The substrate is an important factor in controlling the significance of heterotrophic nitrification in acidic forest soils. J Soil Biol Biochem 76: 143-148. DOI: 10.1016/j.soilbio.2014.05.0.
Zhang XM, Wei HW, Chen QS, Han XG. 2014. The counteractive effects of nitrogen addition and watering on soil bacterial communities in a steppe ecosystem. J Soil Biol Biochem 72: 26-34. DOI: 10.1016/j.soilbio.2014.01.0.

Most read articles by the same author(s)