1. INTRODUCTION
Soil microorganisms, which are critical to many of the biological, chemical, physical processes, are the most abundant and diverse group of organisms in soils on earth. It is estimated that one gram of soil contains of about 104–106 distinct genomes (Torsvik and Goksoyr 1978, Gans et al. 2005, Wu et al. 2008). Soil microorganisms play important roles in terrestrial ecosystems, and greatly affect soil ecosystem functions. Because soil microbiome regulates biogeochemical cycling of macronutrients and micronutrients such as carbon, nitrogen, copper, and iron, as well as other elements vital for the growth of plants and animal life, they greatly affect climate change, plant and soil health. Anthropogenic activities especially agricultural practices greatly affect the soil microbial diversity, community structure, and nitrogen (N) functional genes (Bevivino et al. 2014, Goss-Souza et al. 2019). We are in the processes for understanding and predicting the human impact on soil microbiomes and their ecosystem functions, providing fundamental evidence for climate change and soil health, and presenting a magnificent challenge and most important opportunity towards the most challenging problems facing our planet.
Soil microbes exert strong influence over the soil N cycle, playing critical roles in both nitrification and denitrification (Le Roux et al. 2013). The nitrification and denitrification processes which are the key processes of N cycling are regulated by a variety of N functional genes (Levy-Booth et al. 2014, Ouyang et al. 2018). In the process of nitrification, autotrophic microorganisms, both archaea and bacteria play roles in the process. Two genes in archaea and bacteria respectively related to ammonia oxidation to nitrite: ammonia oxidizing (amo ) genes from archaea AOA amo A and from bacteria AOBam oA, are the rate-limiting factor in nitrification, therefore are critical for the assessment of nitrification potential and communities (Szukics et al. 2012). The nitrite oxidized from ammonia is further oxidized to nitrate (NO3-) through nitrite oxidoreductase genes (nrx A and nrx B) of nitrite oxidizers, such as nitrite-oxidizing bacteria (NOB), to finish the nitrification process (Daims et al. 2016). Heterotrophic denitrification is a serial reduction process of reducing NO3- to N2 gas through serial intermediate products. First, NO3- is reduced nitrite (NO2- ) regulated by nitrate reductase (nar ); second, NO2- to nitric oxide (NO) by nitrite reductase (nir ); third, NO to nitrous oxide (N2O) through nitric oxide reductase (nor ); and finally, N2O to N2 gas regulated by nitrous oxide reductase (nos ), respectively. The incomplete oxidation of NH4+ by AOB forms intermediate product NH2OH, which could be converted to N2O through hydroxylamine oxidation (HAO) process. Autotrophic nitrifier is also involved in the N2O emission, which is the pathway of nitrification by oxidizing ammonia (NH3) to NO2-, followed by the reduction of NO2- to nitric oxide (NO) and further to N2O. N2O can be emitted as a byproduct of ammonia oxidation as an intermediate product of heterotrophic denitrification. Soil chemical, physical, and microbial characteristics closely affect the N cycling processes thus determine the N2O emission in soil ecosystems. Soil moisture such as Water Filled Pore Space (WFPS) plays important roles in the mitigation of N2O emission. With the decreasing soil oxygen (O2) concentration, soil N2O concentration increased exponentially in well-structured agricultural soil (Song et al. 2019). Four orders of magnitude higher N2O was measured in the wettest soil (100% WFPS) compared with the dry soil (40% WFPS) in tested peat, clay and loamy sand soils (Pihlatie et al. 2004). Denitrification-derived N2O emission could be triggered with application of organic matter with high contents of labile C, however, substantially lower N2O/(N2O + N2) production ratio and hence N2O emission was generated in soils with low NO3 contents (Senbayram et al. 2012).
Soil microbiome also plays important roles in soil functioning and maintaining soil health, including the capability of soil microbiome to control diseases caused by soilborne pathogens. Relationship between microbial community structure and the occurrence of soilborne disease is not completely understood, but crop management practices have been widely reported influencing ecological processes that affect microbial communities involved in the suppression of soilborne disease development and incidence (Vanbruggen 1995, Burton et al. 2010, Chellemi et al. 2012). Through the proper manipulation of the microbial community structure, the population of antagonistic microorganisms can be altered thus decrease the amounts of soilborne pathogens (Vanbruggen 1995, Chellemi et al. 2012).
Agricultural practices have been widely reported in altering soil microbial diversity and community (Wu et al. 2008, Bevivino et al. 2014, de Graaff et al. 2019), especially in the conversion from forest to agriculture (Upchurch et al. 2008, Rodrigues et al. 2013, Goss-Souza et al. 2019, Lammel et al. 2021). The consequence of shifting in microbial diversity and community greatly affect the ecosystem functions. Nitrification and denitrification in regulating soil microbiomes for N2O emission and NO3-leaching are critical processes for climate change effects on the environment and human welfare. The agricultural practices change N cycling of nitrification and denitrification may also affect the soil microbiome and N forms, thus potentially affect soilborne diseases. Human activities and inputs greatly affect soil chemical and biochemical composition as well as bacterial community. A more stable soil chemical and biological composition was observed in soils subjected to low human inputs than in those with high human input, which is likely to be one of main drivers of biodiversity changes (Bevivino et al., 2014). We focused on the vegetation types and soil disturbance intensity levels, especially the transition from forest to crop soils, on soil microbiomes in regulating microbial diversity, community structure, and N cycling and their potential on microbial-mediated nitrous oxide (N2O) emission for global warming, nitrate (NO3-) leaching for groundwater pollution, as well as microbial community in the mitigation of soilborne diseases for soil health. Agricultural practices altering soil bacterial community and functional genes involved in N cycling processes were explored, in order to understand their effects on fundamental knowledge in maintaining healthy soils, sustaining plant productivity, and enhancing water and air quality.