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The results of Spearman’s correlation analysis and Mantel’s test. A Spearman’s rank correlation analysis of individual gene abundance with soil properties, vegetation characteristics, and N2O emissions showed above in A. The blue and red colors show, respectively, positive and negative relationships between two variables. The deeper the color and the larger the square, the stronger correlation relationships. Significant correlations are indicated by *P < 0.05, **P < 0.01, ***P < 0.001. Functional microbial composition (based on OTU) was related to each environmental factor and N2O emissions by partial Mantel tests using Bray–Curtis distance shown in an interaction network in the bottom of A. Edge color corresponds to the Mantel’s R statistic for the corresponding distance correlations. The nodes’ size of environmental factor is proportional to the number of connections with significant correlation to microbial communities through partial Mantel tests. Insignificant correlations (P > 0.05) are not shown in mantel test. B Relative variable importance in multiple linear regression. GM, grazing meadow; FM, fencing meadow; FRM, fencing + reseeding meadow; UM, undisturbed meadow; SM, soil moisture; SOC, soil organic C; TN. total N; TP, total P; DOC, dissolved organic C; DON, dissolved organic N; AP, soil available P; C/N, the ratio of SOC and TN; AGB, aboveground biomass; BGB, belowground biomass
Source publication
Purpose
Knowledge of soil N cycling and the associated functional microbial groups of N2O production under different management measures could provide clues for the restoration of degraded meadows in alpine ecosystems.
Materials and methods
We investigated soil N2O emissions, the genes related to N2O production and reduction (AOA-amoA, AOB-amoA, n...
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Citations
... Even though Clade I nosZ has lower diversity, some of the existing primer sets for Clade I may not be suitable for high throughput analyses (Ma et al., 2019). Recently a new primer set was developed to target a broader range of Clade I sequences found in soils (Zhang L. et al., 2021). Due to the clear phylogenetic separation between Clades (Figures 2, 6) a truly universal nosZ primer set covering both clades would be impossible to design. ...
Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments.
... Our study not only revealed changes in the relative abundance of these dominant phyla but also found that Acidobacteriota has a high explanatory rate in the desert steppe. Zhang et al. (2021) and Li et al. (2022) pointed out that fencing could increase the relative abundance of Acidobacteria in the soil and was positively correlated with SOC, TN, AK, and AP. ...
One of the goals of grazing management in the desert steppe is to improve its ecosystem. However, relatively little is known about soil microbe communities in the desert steppe ecosystem under grazing management. In this study, we investigated the diversity and aboveground biomass of Caragana korshinskii Kom. shrub communities in long-term fencing and grazing areas, combined with an analysis of soil physical-chemical properties and genomics, with the aim of understanding how fence management affects plant-soil-microbial inter-relationships in the desert steppe, China. The results showed that fence management (exclosure) increased plant diversity and aboveground biomass in C. korshinskii shrub area and effectively enhanced soil organic carbon (233.94%), available nitrogen (87.77%), and available phosphorus (53.67%) contents. As well, the Shannon indices of soil bacteria and fungi were greater in the fenced plot. Plant-soil changes profoundly affected the alpha- and beta-diversity of soil bacteria. Fence management also altered the soil microbial community structure, significantly increasing the relative abundances of Acidobacteriota (5.31%–8.99%), Chloroflexi (3.99%–5.58%), and Glomeromycota (1.37%–3.28%). The soil bacterial-fungal co-occurrence networks under fence management had higher complexity and connectivity. Based on functional predictions, fence management significantly increased the relative abundance of bacteria with nitrification and nitrate reduction functions and decreased the relative abundance of bacteria with nitrate and nitrite respiration functions. The relative abundances of ecologically functional fungi with arbuscular mycorrhizal fungi, ectomycorrhizal fungi, and saprotrophs also significantly increased under fence management. In addition, the differential functional groups of bacteria and fungi were closely related to plant-soil changes. The results of this study have significant positive implications for the ecological restoration and reconstruction of dry desert steppe and similar areas.
... Soil N cycling and transforming processes in terrestrial ecosystems are predominantly regulated by soil microorganisms, with their functional genes and their extracellular enzymes playing a central role in these processes [26][27][28][29]. Soil N 2 O is produced from microbial activities, involving archaea, bacteria, and fungi, engaged in the conversion of inorganic N through a series of processes. ...
... While most N-fixation occurs within the root nodules of legumes via symbiotic bacteria, free-living N fixation serves as a potential source for biological N inputs in non-leguminous crops [27,33]. Regarding mineralization, the N-cycling enzymes in soil microbes regulate inorganic N availability via mineralization and hydrolysis [29,36]. Key enzymes (and marker genes) involved in N mineralization include protease (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF) [37]. ...
... While most N-fixation occurs within the root nodules of legumes symbiotic bacteria, free-living N fixation serves as a potential source for biological N puts in non-leguminous crops [27,33]. Regarding mineralization, the N-cycling enzym in soil microbes regulate inorganic N availability via mineralization and hydroly [29,36]. Key enzymes (and marker genes) involved in N mineralization include prote (npr and sub), chitinase (chiA), urease (ureC), and arginase (rocF) [37]. ...
Microbial-driven processes, including nitrification and denitrification closely related to soil nitrous oxide (N2O) production, are orchestrated by a network of enzymes and genes such as amoA genes from ammonia-oxidizing bacteria (AOB) and archaea (AOA), narG (nitrate reductase), nirS and nirK (nitrite reductase), and nosZ (N2O reductase). However, how climatic factors and agricultural practices could influence these genes and processes and, consequently, soil N2O emissions remain unclear. In this comprehensive review, we quantitatively assessed the effects of these factors on nitrogen processes and soil N2O emissions using mega-analysis (i.e., meta-meta-analysis). The results showed that global warming increased soil nitrification and denitrification rates, leading to an overall increase in soil N2O emissions by 159.7%. Elevated CO2 stimulated both nirK and nirS with a substantial increase in soil N2O emission by 40.6%. Nitrogen fertilization amplified NH4+-N and NO3−-N contents, promoting AOB, nirS, and nirK, and caused a 153.2% increase in soil N2O emission. The application of biochar enhanced AOA, nirS, and nosZ, ultimately reducing soil N2O emission by 15.8%. Exposure to microplastics mostly stimulated the denitrification process and increased soil N2O emissions by 140.4%. These findings provide valuable insights into the mechanistic underpinnings of nitrogen processes and the microbial regulation of soil N2O emissions.
... The objectives of our study were (1) to investigate the effect of grazing exclusion on the product stoichiometry and gas emissions of soil biological processes, (2) understand the associated changes in the production of soil biological processes and the functional microbial community structure in relation to N loss processes, and (3) identify the N 2 O and N 2 production pathways in QTP grass meadows. Considering the result of previous studies which showed that increased grazing meadow has higher N 2 O emission (Yin et al., 2020;Zhang et al., 2021) and more microbial taxa coexistence (Eldridge et al., 2017;Wu et al., 2022), we hypothesize that (1) N 2 O emissions and the N 2 O/(N 2 O + N 2 ) ratio are stimulated by free grazing, (2) the microbial diversity under free grazing is higher than that under grazing exclusion, and (3) the proportion of denitrification-derived N 2 O is increased by grazing exclusion. ...
... denitrification pathway under "hot moments" in the alpine meadow on the QTP (Table S2 and Fig. S2). Some studies on the QTP demonstrated that grazing exclusion reduced N 2 O emissions owing to zero excreta deposition (Yin et al., 2020;Zhang et al., 2021), whereas others showed opposite results (Hu et al., 2010;Wolf et al., 2010). These discrepancies are likely due to the heterogeneity of soil N 2 O emission caused by excreta deposition. ...
Grazing exclusion has been implemented worldwide as a nature-based solution for restoring degraded grassland ecosystems that arise from overgrazing. However, the effect of grazing exclusion on soil nitrogen cycle processes, subsequent greenhouse gas emissions and underlying mechanisms remain unclear. Here, we investigated the effect of four-year grazing exclusion on plant communities, soil properties, and soil nitrogen cycle-related functional gene abundance in an alpine meadow on the Qinghai–Tibet Plateau. Using an automated continuous-flow incubation system, we performed an incubation experiment and measured soil-borne N2O, N2, and CO2 fluxes to three successive “hot moment” events (precipitation, N deposition, and oxic-to-anoxic transition) between grazing-excluded and grazing soil. Higher soil N contents (total nitrogen, NH4+, NO3−) and extracellular enzyme activities (β-1,4-glucosidase, β-1,4-N-acetyl-glucosaminidase, cellobiohydrolase) are observed under grazing exclusion. The aboveground and litter biomass of plant community was significantly increased by grazing exclusion, but grazing exclusion decreased the average number of plant species and microbial diversity. The N2O+N2 fluxes observed under grazing exclusion were higher than those observed under free grazing. The N2 emissions and N2O/(N2O+N2) ratios observed under grazing exclusion were higher than those observed under free grazing in oxic conditions. Instead, higher N2O fluxes and lower denitrification functional gene abundances (nirS, nirK, nosZ, and nirK+nirS) under anoxia were found under grazing exclusion than under free grazing. The N2O site-preference value indicates that under grazing exclusion, bacterial denitrification contributes more to higher N2O production compared with under free grazing (81.6% vs. 59.9%). We conclude that grazing exclusion could improve soil fertility and plant biomass, nevertheless it may lower plant and microbial diversity and increase potential N2O emission risk via the alteration of the denitrification end-product ratio. This indicates that not all grassland management options result in a mutually beneficial situation among wider environmental goals such as greenhouse gas mitigation, biodiversity, and social welfare.
... Nitrous oxide is an intermediate product of nitrification and denitrification processes catalyzed by several enzymes encoded by multiple N 2 O-related functional genes (Kool et al., 2011). Grazing has been shown to altered N 2 O emissions and N 2 O-related functional gene abundances in grassland ecosystems (Zhang et al., 2021;Zhong et al., 2017). However, a global analysis of the impact of grazing on N 2 O emissions, N 2 O-related gene abundances and corresponding soil nitrogen (N) cycling processes in grasslands has not been reported. ...
... Lastly, grazing can lead to soil compaction and reduce air permeability (Chroňáková et al., 2009;Saggar et al., 2004). Studies on grazing effects on N 2 O emissions have reported inconsistent results, with some reporting an increase (Hyde et al., 2006;Luo et al., 2008;Zhang et al., 2021), a reduction (Wolf et al., 2010;Liu et al., 2010;Yan et al., 2016), or no effect on N 2 O emission (Groffman et al., 1993;Li et al., 2012). A meta-analysis based on 23 studies reported that N 2 O emissions decreased with heavy grazing compared to non-grazing, which was associated with a decrease in soil moisture and substrate availability (Tang et al., 2019). ...
... To assess the impact of grazing on the response variables, we employed a mixed-effects model using the statistical package metafor version 2.4.0 (Viechtbauer, 2010) and metaforest (Van Lissa, 2020) in R version 4.0.3. As some studies contributed more than one effect size, we treated "study" and "observation" as random factors to account for within-paper non-independence in observations (Tang et al., 2023;Zhang et al., 2021). We considered the effect of grazing significant if the 95% confidence interval (CIs) of the response variables did not overlap with 0. The mixed-effects model was further used to evaluate the residual heterogeneity of the mean effect size (InRR * ) for N 2 O emission, functional gene abundances, and potential nitrification and denitrification rates, all of which showed a significant residual heterogeneity (p < 0.0001). ...
... Moreover, there is little information regarding how the duration of grazing prohibition influences nirS-and nirK denitrfying bacterical communities and and its drivering factors (Pan et al., 2016). Furthermore, environmental characteristics in salt marsh soil different from other systems, such as high salinity, lower redox potential, and the occurrence of periodic tidal inundation (Zhang et al., 2021;Li et al., 2022), so abundance and composition of nirS-and nirK denitrfying bacterical communities are likely influenced by elevations. ...
Introduction
Grazing prohibition is an effective management practice to restore salt marsh functioning. However, the effects of grazing exclusion on denitrifying microbial communities and their controlling factors in salt marshes remain unclear.
Methods
In this study, we surveyed soil physicochemical properties and above- and below-ground biomass and using quantitative polymerase chain reaction and Illumina MiSeq high-throughput sequencing technology to determine the relative abundance, composition, and diversity of nitrite reductase nirS - and nirK -type denitrifying bacterial communities associated with grazing prohibition treatments and elevations.
Results
The abundance of nirS -type denitrifiers increased with grazing prohibition time, whereas the abundance of nirK -type denitrifiers remained unaltered. Moreover, nirS -type denitrifiers were more abundant and diverse than nirK -type denitrifiers in all treatments. Grazing prohibition significantly altered the operational taxonomic unit richness, abundance-based coverage estimator, and Chao1 indices of the nirS -type denitrifying bacterial communities, whereas it only minimally affected the structure of the nirK -type denitrifying bacterial community.
Discussion
The results imply that the nirS community, rather than nirK , should be the first candidate for use as an indicator in the process of salt marsh restoration after grazing prohibition. Substances of concern, total nitrogen, and salinity were the key environmental factors affecting the abundance and community composition of nirS and nirK denitrifiers. The findings of this study provide novel insights into the influence of the length of grazing prohibition and elevation on nirS - and nirK -type denitrifying bacterial community composition in salt marshes.
... However, long-term grazing also leads to higher N mineralization and N 2 O emissions (McNaughton et al. 1997) due to the activities of heterotrophs, nitrifiers, and denitrifiers (Patra et al. 2005), leading to more soil N losses than in the earlier stages. Long-term intensive grazing reduces the biological nitrogen fixation capacity (Zhang et al. 2021b). So, soil C/N ultimately increased following long-term grazing (Fig. 6). ...
Globally, livestock grazing is an important management factor infuencing soil degradation, soil health and carbon (C) stocks of grassland ecosystems. However, the efects of grassland types, grazing intensity and grazing duration on C stocks are unclear across large geographic scales. To provide a more comprehensive assessment of how grazing drives ecosystem C stocks in grasslands, we compiled and analyzed data from 306 studies featuring four grassland types across China: desert steppes, typical steppes, meadow steppes and alpine steppes. Light grazing was the best management practice for desert steppes (<2 sheep ha−1) and typical steppes (3 to 4 sheep ha−1), whereas medium grazing pressure was optimal for meadow steppes (5 to 6 sheep ha−1) and alpine steppes (7 to 8 sheep ha−1
) lead�ing to the highest ecosystem C stocks under grazing. Plant biomass (desert steppes) and soil C stocks (meadow steppes) increased under light or medium grazing, confrming the ‘intermediate disturbance hypothesis’. Heavy grazing
decreased all C stocks regardless of grassland ecosystem types, approximately 1.4 Mg ha−1 per year for the whole ecosystem. The regrowth and regeneration of grasslands in response to grazing intensity (i.e., grazing optimization) depended on grassland types and grazing duration. In conclusion, grassland grazing is a double-edged sword. On the one hand, proper management (light or medium grazing) can maintain and even increase C stocks above- and belowground, and increase the harvested livestock products from grasslands. On the other hand, human-induced
overgrazing can lead to rapid degradation of vegetation and soils, resulting in signifcant carbon loss and requiring long-term recovery. Grazing regimes (i.e., intensity and duration applied) must consider specifc grassland characteris�tics to ensure stable productivity rates and optimal impacts on ecosystem C stocks.
... The mechanisms involved in N conversion in agricultural ecosystems could be clarified by related functional genes. Considering close associations between specific functional genes and ecosystem functions (Sun and Badgley 2019;Zhang et al. 2021), the copy numbers of N functional genes can be employed to estimate the strength of distinct N-transformation pathways (Zhong et al. 2018). Additionally, due to the sensitivity of microbes to environmental fluctuations, the microbial taxa harboring functional genes involved in the microbial N cycling can be dramatically changed by environmental variations. ...
Purpose
Water and nutrient availability are critical factors that affect soil biological processes in agroecological systems, which are regulated by extracellular ecoenzymatic activity; however, the response of these enzymes to water and nutrient levels is poorly understood.
Methods
A 4-year field experiment with three levels of irrigation (high, 400 mm; medium, 300 mm; and low, 200 mm) and two levels of fertilization (high, 600 kg/ha P2O5 + 300 kg/ha urea; and low, 300 kg/ha P2O5 + 150 kg/ha urea) was conducted to investigate the microbial metabolic status in an arid agroecological system in China using the model of extracellular enzymatic stoichiometry.
Results
Higher C-acquisition enzyme activity and lower N-acquisition enzyme activity were observed during the crop growth stage, suggesting promoted C limitation and alleviated N limitation for microbes by the combination of medium irrigation and low fertilization. Increased microbial C limitation surged the abundance of amoA-AOA and amoA-AOB genes involved in nitrification and strengthened this process. Decreased microbial N limitation hindered the denitrification potential by reducing the abundance of the involved nirK, nirS, nosZ, and narG genes. Increased microbial C limitation was due to the elevated soil water content, which further promoted the activity of C-acquiring enzymes and facilitated microbial decomposition of organic matter. The decreased microbial N limitation was largely related to the increased soil N availability.
Conclusions
These findings suggest that a combination of medium irrigation and low fertilization is effective for organic matter decomposition, by promoting microbial C metabolism and reducing the risk of N loss via alleviation of microbial N limitation. Our results emphasize the roles of stoichiometry-regulated microbial metabolism in soil nutrient transformation and have implications for agricultural practices in arid fertigation agroecosystems.
Soil bacteria play pivotal roles in agroecosystem functioning. However, the immense diversity of soil bacterial communities masks the effects of some species, such as bacterial biomarkers, on soil nutrient cycling and crop growth. We analyzed biological and chemical soil parameters of five fertilization treatments (CK, LN, CN, HN, LNM: 0, 150, 200, 250 kg N hm–2, 150 kg N hm–2 + 15,000 kg hm–2 sheep manure). The random forest models were used to select bacterial biomarkers and assess the contributions of bacterial biomarkers and overall bacteria to wheat yield. Moreover, we used a partial least squares path modeling to explore the relationship between fertilization, bacterial biomarkers, carbon (C) and nitrogen (N) cycling functions, soil nutrients, and wheat yield. The results showed that bacterial biomarkers are better predictors of wheat yield than overall bacteria, explaining 52.54% and 16.00% of the variation in yield, respectively. Bacterial biomarkers affected wheat production by increasing soil organic carbon, and available nitrogen content. The LNM treatment significantly improved the relative abundance of beneficial biomarkers, such as Sphingomonadales, Xanthomonadaceae, Lysobacter, and Streptomyces, compared to the LN treatment. In addition, the LNM treatment promoted chitinlysis, cellulolysis, xylanolysis, aromatic hydrocarbon degradation, and aerobic ammonia oxidation, relative to the other inorganic N treatments (LN, CN, and HN). Our results emphasize the role of bacterial biomarkers in wheat yield formation, providing new insights into maintaining agricultural productivity by taking advantage of soil bacterial biomarkers.
nirK-Denitrifying bacteria are closely related to N2O emissions and they have been studied widely in agro-ecosystems. However, the mechanisms associated with maintenance of the diversity of nirK bacterial communities in agro-ecosystems are unclear. In particular, the ecological roles of “generalists” and “specialists” in nirK bacterial communities under different soil organic carbon (SOC) levels have not been characterized. In this study, we divided 102 soil samples (0–20 and 20–40 cm) from 62 apple orchards in China's main apple producing areas (Shaanxi and Shandong provinces) into four groups according to the SOC content and soil depth, i.e., high organic carbon soils in the 0–20 cm depth, low organic carbon soils in the 0–20 cm depth, high organic carbon soils in the 20–40 cm depth, and low organic carbon soils in the 20–40 cm depth. In the nirK bacterial community, 4187 operational taxonomic units (OTUs) (∼51.32 %) were classified as specialists and 1781 OTUs (∼21.83 %) as generalists. The α-diversity of generalists was higher in the high SOC soils than the low SOC soils, which was consistent with the α-diversity of the whole nirK bacterial community. However, the observed number of specialist species was lower in high SOC soils than low SOC soils. Analysis based on the Spearman's correlation coefficients also showed that the α-diversity and relative abundances of generalists and specialists responded differently to environmental factors. Both deterministic and stochastic processes contributed to the assembly of generalists and specialists. Among the deterministic processes, variable selection was important for the assembly of the generalist community, whereas homogeneous selection was important for the assembly of the specialist community. The niche breadth of generalists was higher than that of specialists, whereas the niche overlap of specialists was higher than that of generalists. The niche breadth of generalists was higher in high SOC soils than low SOC soils. In both networks, generalists had higher degrees than specialists, although the number of generalists was much lower than that of specialists. Our findings demonstrate the contributions of generalists and specialists to the changes in the diversity of the nirK bacterial community at different SOC levels as well as providing new insights into the mechanisms responsible for maintaining the diversity of the nirK bacterial community.
