Nitrogen Deposition Reduces the Diversity and Abundance of cbbL Gene-Containing CO2-Fixing Microorganisms in the Soil of the Stipa baicalensis Steppe

Abstract

CO2 fixation by autotrophic microbes has a significant effect on the carbon cycle in temperate grasslands. Nitrogen (N) deposition in soil has been steadily increasing for decades, which has consequences for soil microorganisms. However, the impact of this deposition on the diversity and abundance of CO2-fixing soil microorganisms remains unclear in temperate grasslands. In the present study, the cbbL gene, a key gene in the Calvin–Benson–Bassham cycle that encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, was used to study CO2-fixing microbes under different rates of N addition (0, 15, 30, 50, 100, and 150 kg N ha–1 yr–1) in a 9-year field experiment in a temperate grassland. The results showed that N addition led to significant reductions in cbbL gene abundance and genetic diversity and altered cbbL gene community composition. High N addition enhanced the relative abundances of Acidiferrobacterales and Rhizobiales but reduced those of Burkholderiales and Rhodobacterales. Structural equation modeling further revealed that N addition primarily reduced cbbL genetic diversity by increasing the soil NO3-N content and decreasing the soil pH. N addition indirectly reduced cbbL gene abundance, possibly by increasing the soil N/phosphorus (P) ratio and decreasing the soil pH. These findings suggest that N addition increases the soil available N and causes soil acidification, which may inhibit growth of CO2-fixing microbes to some extent.

Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics

“…Our results, therefore, point to the potential effects of N deposition on soil carbon stocks and CO 2 fluxes via affecting the soil microbiome (Averill et al, 2018;Z. Li et al, 2021;Qin et al, 2021). Our results are in agreement with Zhang et al (2022), who reported increasing abundances of C fixation and methane metabolism genes under N addition in a subtropical forest.…”

“…We conclude that the indirect effects of N deposition through soil acidification on functional gene diversity and composition are stronger than its direct effects. Such indirect effects have been previously reported for a group of genes involved in C cycling (Qin et al ., 2021).…”

“…Soil autotrophic bacteria have an important role in ecosystem C fixation (Ge et al ., 2013), while methane‐oxidizing bacteria play a substantial role in methane metabolism, especially oxidation of CH 4 , which affects the CO 2 fluxes from soils (Ho et al ., 2013). Our results, therefore, point to the potential effects of N deposition on soil carbon stocks and CO 2 fluxes via affecting the soil microbiome (Averill et al ., 2018; Z. Li et al ., 2021; Qin et al ., 2021). Our results are in agreement with Zhang et al .…”

“…For instance, N deposition affects CO 2 ‐fixing soil microorganisms and genes involved in the Calvin–Benson–Bassham cycle (e.g. cbbL ) by increasing soil NO 3 –N content and N : P ratios and reducing soil pH (Qin et al ., 2021). It can also reduce the relative abundance of cellulose‐ and chitin‐degrading genes but increase the abundance of denitrification genes such as narG and norB (Tian et al ., 2019).…”

The responses to long-term nitrogen addition of soil bacterial, fungal, and archaeal communities in a desert ecosystem

“…The microbial β-diversity index was 1 http://ccb.jhu.edu/software/FLASH/ 2 http://qiime.org/scripts/split_libraries_fastq.html 3 http://www.drive5.com/uparse/ 4 http://www.arb-silva.de/ 5 http://qiime.org/scripts/assign_taxonomy.html 6 https://unite.ut.ee/ calculated using the QIIME software (version 1.9.1), and pairwise differences were further compared based on the Wilcoxon rank sum test. A LEfSe analysis (LDA score ≥ 2.0) was used to determine the significant differences in microbial community from the phylum to the genus levels using the LEfSe software (version 1.0; Qin et al, 2021). The soil properties as explanatory variables and the dominant microbial phyla as species variables were used to perform a redundancy analysis (RDA) with the vegan packages in the R software (version 2.15.3).…”