References

1. Yu, X.; Zhang, C. Nitrogen cycling and environmental impacts in upland agricultural soils in North China: A review. J. Integr. Agric. 2017, 16, 2848–2862.
2. Martinez-Espinosa, R.M.; Cole, J.A.; Richardson, D.J.; Wartmough, N.J. Enzymology and ecology of the nitrogen cycle. Biochem. Soc. Trans. 2011, 39, 175–178.
3. Purwanto, P.; Yuwariah, Y.; Sumadi, S.; Simarmata, T. Nitrogenase Activity and IAA Production of Indigenous Diazotroph and Its Effect on Rice Seedling Growth. AGRIVITA J. Agric. Sci. 2017, 39, 31–37.
4. Rütting, T.; Aronsson, H.; Delin, S. Efficient use of nitrogen in agriculture. Nutr. Cycling Agroecosyst. 2018, 110, 1–5.
5. Gholami, A.; Biyari, A.; Gholipoor, M.; Rahmani, H.A. Growth Promotion of Maize (Zea mays L.) by Plant-Growth-Promoting Rhizobacteria under Field Conditions. Commun. Soil. Sci. Plant Anal. 2012, 43, 1263–1272.
6. Ibáñez, F.; Tonelli, M.L.; Muñoz, V.; Figueredo, M.S.; Fabra, A. Bacterial Endophytes of Plants: Diversity, Invasion Mechanisms and Effects on the Host. In Endophytes: Biology and Biotechnology. Sustainable Development and Biodiversity; Maheshwari, D.K., Ed.; Springer: Berlin/Heidelberg, Germany, 2017; Volume 15.
7. Zhu, L.; Zhao, Y.; Zhang, W.; Zhou, H.; Chen, X.; Li, Y.; Wei, D.; Wei, Z. Roles of bacterial community in the transformation of organic nitrogen toward enhanced bioavailability during composting with different waste. Bioresour. Technol. 2019, 285, 121326.
8. Garrido-Oter, R.; Nakano, R.T.; Dombrowski, N.; Ma, K.W.; McHardy, A.C.; Schulze-Lefert, P. Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Cell Host Microbe 2018, 24, 155–167.
9. Nardi, S.; Pizzeghello, D.; Schiavon, M.; Ertani, A. Plant biostimulants: Physiological responses induced by protein hydrolyzed-based products and humic substances in plant metabolizm. Sci. Agric. 2016, 73, 18–23.
10. Gao, C.; El-Sawah, A.M.; Ali, D.F.I.; Alhaj Hamoud, Y.; Shaghaleh, H.; Sheteiwy, M.S. The Integration of Bio and Organic Fertilizers Improve Plant Growth, Grain Yield, Quality and Metabolism of Hybrid Maize. Agronomy 2020, 10, 319.
11. Di Mola, I.; Ottaiano, L.; Cozzolino, E.; Senatore, M.; Giordano, M.; El-Nakhel, C.; Sacco, A.; Rouphael, Y.; Colla, G.; Mori, M. Plant-Based Biostimulants Influence the Agronomical, Physiological, and Qualitative Responses of Baby Rocket Leaves under Diverse Nitrogen Conditions. Plants 2019, 8, 522.
12. Drobek, M.; Frąc, M.; Cybulska, J. Plant Biostimulants: Importance of the Quality and Yield of Horticultural Crops and the Improvement of Plant Tolerance to Abiotic Stress—A Review. Agronomy 2019, 9, 335.
13. Chen, S.K.; Subler, S.; Edwards, C.A. Effects of agricultural biostimulants on soil microbial activity and nitrogen dynamics. Appl. Soil Ecol. 2002, 19, 249–259.
14. Sangiorgio, D.; Cellini, A.; Donati, I.; Pastore, C.; Onofrietti, C.; Spinelli, F. Facing Climate Change: Application of Microbial Biostimulants to Mitigate Stress in Horticultural Crops. Agronomy 2020, 10, 794.
15. De Luca, V.; De Barreda, D.G.; Lidón, A.; Lull, C. Effect of Nitrogen-fixing Microorganisms and Amino Acid-based Biostimulants on Perennial Ryegrass. ASHS 2020, 30, 280–291.
16. Berg, S.; Dennis, P.G.; Paungfoo-Lonhienne, C.; Anderson, J.; Robinson, N.; Brackin, R.; Royle, A.; DiBella, L.; Schmidt, S. Effects of commercial microbial biostimulants on soil and root microbial communities and sugarcane yield. Biol. Fertil. Soils 2020, 56, 565–580.
17. Chen, S.K.; Edwards, C.A.; Subler, S. The influence of two agricultural biostimulants on nitrogen transformations, microbial activity, and plant growth in soil microcosms. Soil Biol. Biochem. 2003, 35, 9–19.
18. Pylak, M.; Oszust, K.; Frąc, M. Review report on the role of bioproducts, biopreparations, biostimulants and microbial inoculants in organic production of fruit. Rev. Environ. Sci. Biotechnol. 2019, 18, 597–616.
19. Puri, A.; Padda, K.P.; Chanway, C.P. Nitrogen-fixation by endophytic bacteria in agricultural crops: Recent advances. In Nitrogen in Agriculture—Updates; Khan, A., Fahad, S., Eds.; InTech: Rijeka, Croatia, 2018; pp. 73–94. Available online: (accessed on 11 March 2021).
20. Boliyevich, M.S.; Asrorovna, S.G.; Ugli, B.D.K. Biological Nitrogen. AJMR 2020, 9, 66–68.
21. Wang, J.; Li, Q.; Shen, C.; Yang, F.; Wang, J.; Ge, Y. Significant dose effects of fertilizers on soil diazotrophic diversity, community composition, and assembly processes ina long-term paddy field fertilization experiment. Land Degrad. Dev. 2020, 1–10.
22. Vu HT, L.; Yukphan, P.; Charoenyingcharoen, P.; Malimas, S.; Nguyen, L.K.; Muramatsu, Y.; Yamada, Y. Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam. Ann. Microbiol. 2019, 69, 1155–1163.
23. Papik, J.; Folkmanova, M.; Polivkova-Majorova, M.; Suman, J.; Uhlik, O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol. Adv. 2020, 44, 107614.
24. Latef, A.A.H.A.; Alhmad, M.F.A.; Kordrostami, M.; Abo–Baker, A.B.A.E.; Zakir, A. Inoculation with Azospirillum lipoferum or Azotobacter chroococcum Reinforces Maize Growth by Improving Physiological Activities under Saline Conditions. J. Plant Growth Regul. 2020, 39, 1293–1306.
25. Batista, M.B.; Dixon, R. Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit. Biochem. Soc. Trans. 2019, 47, 603–614.
26. Kargapolova, K.Y.; Burygin, G.L.; Tkachenko, O.V.; Evseeva, N.V.; Pukhalskiy, Y.V.; Belimov, A.A. Effectiveness of inoculation of in vitro-grown potato microplants with rhizosphere bacteria of the genus Azospirillum. Plant Cell Tissue Organ Cult. 2020, 141, 351–359.
27. Soumare, A.; Diedhiou, A.G.; Thuita, M.; Hafidi, M.; Ouhdouch, Y.; Gopalakrishnan, S.; Kouisni, L. Exploiting Biological Nitrogen Fixation: A Route Towards a Sustainable Agriculture. Plants 2020, 9, 1011.
28. Aasfar, A.; Bargaz, A.; Yaakoubi, K.; Hilali, A.; Bennis, I.; Zeroual, Y.; Meftah Kadmiri, I.M. Nitrogen Fixing Azotobacter Species as Potential Soil Biological Enhancers for Crop Nutrition and Yield Stability. Front. Microbiol. 2021, 12, 628379.
29. Baldani, J.I.; Baldani, V.D.L. History on the biological nitrogen fixation research in graminaceous plants: Special emphasis on the Brazilian experience. An. Acad. Bras. Ciênc. 2005, 77, 549–579.
30. Torres-Cruz, T.J.; Howell, A.J.; Reibold, R.H.; McHugh, T.A.; Eickhoff, M.A.; Reed, S.C. Species-specific nitrogenase activity in lichen-dominated biological soil crusts from the Colorado Plateau, USA. Plant Soil 2018, 429, 113–125.
31. Wolińska, A.; Kuźniar, A.; Zielenkiewicz, U.; Banach, A.; Izak, D.; Stępniewska, Z.; Błaszczyk, M. Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes. Microb. Ecol. 2017, 73, 162–176.
32. Czaban, J.; Wróblewska, B. The Effect of Bentonite on the Survival of Azotobacter chroococcum in Sandy Soil in a Long-Term Plot Experiment. Pol. J. Environ. Stud. 2017, 26, 1–8.
33. Zheng, Y.; Liang, J.; Zhao, D.L.; Meng, C.; Xu, Z.C.; Xie, Z.H.; Zhang, C.S. The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils. Microorganisms 2020, 8, 207.
34. Tian, J.; Wei, K.; Condron, L.M.; Chen, Z.; Xu, Z.; Feng, J.; Chen, L. Effects of elevated nitrogen and precipitation on soil organic nitrogen fractions and nitrogen-mineralizing enzymes in semi-arid steppe and abandoned cropland. Plant Soil 2017, 417, 217–229.
35. Fujii, K.; Yamada, T.; Hayakawa, C.; Nakanishi, A.; Funakawa, S. Decoupling of protein depolymerization and ammonification in nitrogen mineralization of acidic forest soils. Appl. Soil Ecol. 2020, 153, 103572.
36. Wang, C.; Wang, N.; Zhu, J.; Liu, Y.; Xu, X.; Niu, S.; He, N. Soil Gross N ammonification and nitrification from tropi cal to tempera te forests in ekstern China. Funct. Ecol. 2018, 32, 83–94.
37. Mariano, E.; Jones, D.L.; Hill, P.W.; Trivelina, P.C.O. Mineralisation and sorption of dissolved organic nitrogen compounds in litter and soil from sugarcane fields. Soil Biol. Biochem. 2016, 103, 522–532.
38. Ye, J.; An, N.; Chen, H.; Ying, Z.; Zhang, S.; Zhao, J. Performance and mechanism of carbon dioxide fixation by a newly isolated chemoautotrophic strain Paracoccus denitrificans PJ-1. Chemosphere 2020, 252, 126473.
39. Li, Y.; Chapman, S.J.; Nicol, G.W.; Yao, H. Nitrification and nitrifiers in acidic soils. Soil Biol. Biochem. 2018, 116, 290–301.
40. Meinhardt, K.A.; Stopnisek, N.; Pannu, M.W.; Strand, S.E.; Fransen, S.C.; Casciotti, K.L.; Stahl, D.A. Ammonia-oxidizing bacteria are the primary N2O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil. Environ. Microbiol. 2018, 20, 2195–2206.
41. Jin, P.; Ren, B.; Wang, X.C.; Jin, X.; Shi, X. Mechanism of microbial metabolic responses and ecological system conversion under different nitrogen conditions in sewers. Water Res. 2020, 186, 116320.
42. Liu, W.; Nasry, A.A.N.B.; Zhao, J.; Laoyongxay, H.; Dai, W.; Zhao, Q. Start-up of the Simultaneous Nitrification, Anammox, and Denitrification (SNAD) Reactor and Efficacy of a Small Amount of Organic Carbon. Water Air Soil Pollut. 2019, 230, 256.
43. Wang, C.; Liu, Y.; Lv, W.; Xia, S.; Han, J.; Wang, Z.; Yu, X. Enhancement of nitrogen removal by supplementing fluidized-carriers into the aerobic tank in a full-scale A2/O system. Sci. Total Environ. 2019, 660, 817–825.
44. Wang, H.; He, X.; Nakhla, G.; Zhu, J.; Su, Y.K. Performance and bacterial community structure of a novel inverse fluidized bed bioreactor (IFBBR) treating synthetic municipal wastewater. Sci. Total Environ. 2020, 718, 137288.
45. Williams, S.T.; Sharpe, M.E.; Holt, J.G. (Eds.) Bergey’s Manual of Determinative Bacteriology, 8th ed.; Williams & Wilkins Company: Baltimore, ML, USA, 1989; pp. 1808–1834.
46. Bergey, D.H.; Holt, J.G. (Eds.) Bergey’s Manual of Determinative Bacteriology, 9th ed.; Williams & Wilkins Company: Baltimore, ML, USA, 1994; pp. 447–455.
47. Chen, R.; Takemura, Y.; Liu, Y.; Ji, J. Using Partial Nitrification and Anammox To Remove Nitrogen from Low-Strength Wastewater by Co-immobilizing Biofilm inside a Moving Bed Bioreactor. ACS Sustain. Chem. Eng. 2019, 7, 1353–1361.
48. Purkhold, U.; Pommerening-Röser, A.; Juretschko, S.; Schmid, M.C.; Koops, H.P.; Wagner, M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amaA sequence analysis: Implications for molecular diversity surveys. Appl. Environ. Microbiol. 2000, 66, 5368–5382.
49. Cai, M.; Ng, S.K.; Lim, C.K.; Lu, H.; Jia, Y. Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification. Front. Microbiol. 2018, 9, 280.
50. Ginawi, A.; Yan, Y. The Function of Ammonia Oxidizers Community in the Environment. PSM Microbiol. 2019, 4, 20–36. Available online: (accessed on 26 March 2021).
51. Duddleston, K.N.; Bottomley, P.J.; Porter, A.J.; Arp, D.J. New Insights into Methyl Bromide Cooxidation by Nitrosomonas europaea Obtained by Experimenting with Moderately Low Density Cell Suspensions. Appl. Environ. Microbiol. 2000, 66, 2726–2731.
52. Barker, L.K.; Giska, J.R.; Radniecki, T.S.; Semprini, L. Effects of short- and long-term exposure of silver nanoparticles and silver ions to Nitrosomonas europaea biofilms and planktonic cells. Chemosphere 2018, 206, 606–614.
53. Soman, C.; Li, D.; Wander, M.M.; Kent, A.D. Long-term fertilizer and crop-rotation treatments differentially affect soil bacterial community structure. Plant Soil 2017, 413, 145–159.
54. Jeong, D.; Cho, K.; Lee, C.H.; Lee, S.; Bae, H. Effects of salinity on nitrification efficiency and bacterial community structure in a nitrifying osmotic membrane bioreaktor. Process Biochem. 2018, 73, 132–141.
55. Bennett, K.; Sadler, N.C.; Wright, A.T.; Hyman, M.R. Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea. Appl. Environ. Microbiol. 2016, 82, 2270–2279.
56. Wright, C.L.; Schatteman, A.; Crombie, A.T.; Murrell, J.C.; Lehtovirta-Morley, L.E. Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes. Appl. Environ. Microbiol. 2020, 86, 1–14.
57. Ginawi, A.; Yan, Y. Molecular Techniques Applied to Investigations of Abundance of the Ammonia Oxidizing Bacteria and Ammonia Oxidizing Archaea Microorganisms in the Environment. IOSR J. Environ. Sci. Toxicol. Food Technol. 2019, 13, 19–24.
58. Ren, Y.; Ngo, H.H.; Guo, W.; Wang, D.; Peng, L.; Ni, B.J. New perspectives on microbial communities and biological nitrogen removal processes in wastewater treatment systems. Bioresour. Technol. 2020, 297, 122491.
59. Cole, J.A. Biodegradation of inorganic nitrogen compounds. In Biochemistry of Microbial Degradation; Ratledge, C., Ed.; Springer: Dordrecht, Germany, 1994; pp. 487–512.
60. Liu, H.; Ding, Y.; Zhang, Q.; Liu, X.; Xu, J.; Li, Y.; Di, H. Heterotrophic nitrification and denitrification are the main sources of nitrous oxide in two paddy soils. Plant Soil 2019, 445, 39–53.
61. Duan, P.; Shen, H.; Jiang, X.; Yan, X.; Xiong, Z. The contributions of hydroxylamine and nitrite to NO and N2O production in alkaline and acidic vegetable soils. J. Soils Sediments 2020, 20, 2903–2911.
62. Ushiki, N.; Jinno, M.; Fujitani, H.; Suenaga, T.; Terada, A.; Tsuneda, S. Nitrite oxidation kinetics of two Nitrospira strains: The quest for competition and ecological niche differentiation. J. Biosci. Bioeng. 2017, 123, 581–589.
63. Giguere, A.T.; Taylor, A.E.; Myrold, D.D. Nitrite-oxidizing activity responds to nitrite accumulation in soil. FEMS Microbiol. Ecol. 2018, 94, 1–9.
64. Daims, H.; Lücker, S.; Wagner, M. A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria. Trends Microbiol. 2016, 24, 699–712.
65. Huang, X.; Zhao, J.; Su, J.; Jia, Z.; Shi, X.; Wright, A.L. Neutrophilic bacteria are responsible for autotrophic ammonia oxidation in an acidic forest soil. Soil Biol. Biochem. 2018, 119, 83–89.
66. Ho, A.; Di Lonardo, D.P.; Bodelier, P.L.E. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol. Ecol. 2017, 93, 1–14.
67. Hu, B.; Wang, T.; Ye, J.; Zhao, J.; Yang, L.; Wu, P. Effects of carbon sources and operation modes on the performances of aerobic denitrification process and its microbial community shifts. J. Environ. Manag. 2019, 239, 299–305.
68. Forsmark, B.; Nordin, A.; Maaroufi, N.I.; Lundmark, T. Low and High Nitrogen Deposition Rates in Northern Coniferous Forests Have Different Impacts on Aboveground Litter Production, Soil Respiration, and Soil Carbon Stocks. Ecosystems 2020.
69. Gayon, U.; Dupetit, G. Sur la fermentation des nitrates en nitrites. C. R. Acad. Sci. 1882, 95, 664–666.
70. Guo, B.; Zheng, X.; Yu, J.; Ding, H.; Pan, B.; Lu, S. Dissolved organic carbon enhances both soil N2O production and uptake. Glob. Ecol. Conserv. 2020, 24.
71. Liu, C.W.; Sung, Y.; Chen, B.C.; Lai, H.Y. Effects of Nitrogen Fertilizers on the Growth and Nitrate Content of Lettuce (Lactuca sativa L.). Int. J. Environ. Res. Public Health 2014, 11, 4427–4440.
72. Jacoby, R.; Peukert, M.; Succurro, A.; Koprivova, A.; Kopriva, S. The Role of Soil Microorganisms in Plant Mineral Nutrition-Current Knowledge and Future Directions. Front. Plant Sci. 2017, 19.
73. Dey, S.; Awata, T.; Mitsushita, J.; Zhang, D.; Kasai, T.; Matsuura, N.; Katayama, A. Promotion of biological nitrogen fixation activity of an anaerobic consortium using humin as an extracellular electron mediator. Sci. Rep. 2021, 11.
74. Tiso, M.; Schechter, A.N. Nitrate Reduction to Nitrite, Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions. PLoS ONE 2015.
75. Maintinguer, S.I.; Sakamoto, I.K.; Adorno, M.A.T.; Varesche, M.B.A. Evaluation of the microbial diversity of denitrifying bacteria in batch reactor. Braz. J. Chem. Eng. 2013, 30.
76. Beristain-Cardoso, R.; Sierra-Alvarez, R.; Rowlette, P.; Razo-Flores, E. Sulfide oxidation under chemolithoautotrophic denitrifying conditions. Biotechnol. Bioeng. 2006, 95, 11481157.
77. Sparacino-Watkins, C.; Stolz, J.F.; Basu, P. Nitrate and periplasmic nitrate reductases. Chem. Soc. Rev. 2014, 43, 676–706.
78. Ona-Nguema, G.; Guerbois, D.; Pallud, C.; Brest, J.; Abdelmoula, M.; Morin, G. Biogenic Fe(II-III) Hydroxycarbonate Green Rust Enhances Nitrate Removal and Decreases Ammonium Selectivity during Heterotrophic Denitrification. Minerals 2020, 10, 818.
79. Olaya-Abril, A.; Hidalgo-Carrillo, J.; Luque-Almagro, V.M.; Fuentes-Almagro, C.; Urbano, F.J.; Moreno-Vivián, C.; Richardson, D.J.; Roldán, M.D. Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222. Front. Microbiol. 2018, 9.
80. Natywa, M.; Selwet, M.; Maciejewski, T. Effect of some agrotechnical factors on the number and activity soil microorganisms. Fragm. Agron. 2014, 31, 56–63.