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.