Shifts in the Composition and Activities of Denitrifiers Dominate CO2 Stimulation of N2O Emissions

Arbuscular mycorrhizal fungi reduce soil N2O emissions by altering root traits and soil denitrifier community composition

Arbuscular mycorrhizal fungi (AMF) increase the ability of plants to obtain nitrogen (N) from the soil, and thus can affect emissions of nitrous oxide (N2O), a long-lived potent greenhouse gas. However, the mechanisms underlying the effects of AMF on N2O emissions are still poorly understood, particularly in agroecosystems with different forms of N fertilizer inputs. Utilizing a mesocosm experiment in field, we examined the effects of AMF on N2O emissions via their influence on maize root traits and denitrifying microorganisms under ammonia and nitrate fertilizer input using 15N isotope tracer. Here we show that the presence of AMF alone or both maize roots and AMF increased maize biomass and their 15N uptake, root length, root surface area, and root volume, but led to a reduction in N2O emissions under both N input forms. Random forest model showed that root length and surface area were the most important predictors of N2O emissions. Additionally, the presence of AMF reduced the (nirK + nirS)/nosZ ratio by increasing the relative abundance of nirS-Bradyrhizobium and Rubrivivax with ammonia input, but reducing nosZ-Azospirillum, Cupriavidus and Rhodopseudomonas under both fertilizer input. Further, N2O emissions were significantly and positively correlated with the nosZ-type Azospirillum, Cupriavidus and Rhodopseudomonas, but negatively correlated with the nirS-type Bradyrhizobium and Rubrivivax. These results indicate that AMF reduce N2O emissions by increasing root length to explore N nutrients and altering the community composition of denitrifiers, suggesting that effective management of N fertilizer forms interacting with the rhizosphere microbiome may help mitigate N2O emissions under future N input scenarios.

Warming-Induced Stimulation of Soil N2O Emissions Counteracted by Elevated CO2 from Nine-Year Agroecosystem Temperature and Free Air Carbon Dioxide Enrichment

Globally, agricultural soils account for approximately one-third of anthropogenic emissions of the potent greenhouse gas and stratospheric ozone-depleting substance nitrous oxide (N2O). Emissions of N2O from agricultural soils are affected by a number of global change factors, such as elevated air temperatures and elevated atmospheric carbon dioxide (CO2). Yet, a mechanistic understanding of how these climatic factors affect N2O emissions in agricultural soils remains largely unresolved. Here, we investigate the soil N2O emission pathway using a 15N tracing approach in a nine-year field experiment using a combined temperature and free air carbon dioxide enrichment (T-FACE). We show that the effect of CO2 enrichment completely counteracts warming-induced stimulation of both nitrification- and denitrification-derived N2O emissions. The elevated CO2 induced decrease in pH and labile organic nitrogen (N) masked the stimulation of organic carbon and N by warming. Unexpectedly, both elevated CO2 and warming had little effect on the abundances of the nitrifying and denitrifying genes. Overall, our study confirms the importance of multifactorial experiments to understand N2O emission pathways from agricultural soils under climate change. This better understanding is a prerequisite for more accurate models and the development of effective options to combat climate change.

Arbuscular mycorrhizal fungi alleviate erosional soil nitrogen loss by regulating nitrogen cycling genes and enzymes in experimental agro-ecosystems

Nutrient losses from agricultural ecosystems are increasingly threatening global environmental and human health. Although arbuscular mycorrhizal (AM) fungi have the potential to regulate soil nitrogen (N) loss by enhancing plant uptake and soil particle immobilization, the microbial mechanism behind such mycorrhizal effect is unknown. Herein, by conducting a simulated erosion experiment, we compared the effects of exogenous AM fungal inoculation (Funneliformis mosseae) on the gene abundances and enzyme activities of N-cycling processes, and associated such effect to N uptake and loss. The experiment was composed of combinations of two AM fungal treatments (control vs. AM fungal inoculation), two crops (maize vs. soybean) and two slopes of the plots (6° vs. 20°). The experimental plots subjected to natural rainfalls to simulate the erosion events. We showed that the effects of AM fungi were greater in the maize soils than in the soybean soils. In the maize soils, AM fungi increased the abundances of N-fixing (+81.1 %) and nitrifying genes (+200.7 %) and N cycling enzyme activity (+22.3 %). In the soybean soils, AM fungi increased the N-fixing gene abundance (+36.9 %) but decreased the abundance of nitrifying genes (-18.9 %). The abundance of N-fixing gene was positively correlated with N uptake but negatively correlated with N loss. Additionally, AM fungi enhanced the effects of mycorrhizal colonization and moisture but decreased the effects of nutrients on soil microbial metrics related to N-cycling processes. Therefore, AM fungal inoculation enhanced N uptake and reduced N loss by increasing N-fixing gene abundance, and that AM fungi should be preferably used for the low N environments or for the ecosystems highly limited by or competing for N.

Moderate precipitation reduction enhances nitrogen cycling and soil nitrous oxide emissions in a semi-arid grassland

The ongoing climate change is predicted to induce more weather extremes such as frequent drought and high-intensity precipitation events, causing more severe drying-rewetting cycles in soil. However, it remains largely unknown how these changes will affect soil nitrogen (N)-cycling microbes and the emissions of potent greenhouse gas nitrous oxide (N₂ O). Utilizing a field precipitation manipulation in a semi-arid grassland on the Loess Plateau, we examined how precipitation reduction (ca. -30%) influenced soil N₂ O and carbon dioxide (CO₂ ) emissions in field, and in a complementary lab-incubation with simulated drying-rewetting cycles. Results obtained showed that precipitation reduction stimulated plant root turnover and N-cycling processes, enhancing soil N₂ O and CO₂ emissions in field, particularly after each rainfall event. Also, high-resolution isotopic analyses revealed that field soil N₂ O emissions primarily originated from nitrification process. The incubation experiment further showed that in field soils under precipitation reduction, drying-rewetting stimulated N mineralization and ammonia-oxidizing bacteria in favor of genera Nitrosospira and Nitrosovibrio, increasing nitrification and N₂ O emissions. These findings suggest that moderate precipitation reduction, accompanied with changes in drying-rewetting cycles under future precipitation scenarios, may enhance N cycling processes and soil N₂ O emissions in semi-arid ecosystems, feeding positively back to the ongoing climate change.

Integrated rice-crayfish farming system does not mitigate the global warming potential during rice season

Integrated rice-crayfish farming system (RCS) has become increasingly popular in China. However, previous research has largely ignored the effect of trench around the paddy field on GHG emissions, which may cause inaccurate estimation of the global warming potential (GWP) from the system. This study compared the GWP between rice monoculture (RM) and RCS. The results indicated that the field of RCS had significantly lower CH₄ emissions compared with RM due to lower mcrA abundance and higher pmoA abundance, while there was no difference in N₂O emissions. In addition, the trench resulted in remarkably more CH₄ emissions due to higher mcrA abundance and lower pmoA abundance and less N₂O emissions than the field in RCS. In general, RCS seems not to mitigate GWP compared with RM due to more CH₄ emissions from the trench in the current mode. Furthermore, our results indicate that RCS can reduce GWP relative to RM only when the area ratio of the trench to the system is controlled to be lower than 13.9 %.

Arbuscular Mycorrhizal Fungi Shift Soil Bacterial Community Composition and Reduce Soil Ammonia Volatilization and Nitrous Oxide Emissions

Arbuscular mycorrhizal fungi (AMF) establish mutualistic relationships with the majority of terrestrial plants, increasing plant uptake of soil nitrogen (N) in exchange for photosynthates. And may influence soil ammonia (NH₃) volatilization and nitrous oxide (N₂O) emissions directly by improving plant N uptake, and/or indirectly by modifying soil bacterial community composition for the soil C availability increasing. However, the effects of AMF on soil NH₃ volatilization and N₂O emissions and their underlying mechanisms remain unclear. We carried out two independent experiments using contrasting methods, one with a compartmental box device (in 2016) and the other with growth pot experiment (in 2020) to examine functional relationships between AMF and soil NH₃ volatilization and N₂O emissions under varying N input. The presence of AMF significantly reduced soil NH₃ volatilization and N₂O emissions while enhancing plant biomass and plant N acquisition, and reducing soil NH₄⁺ and NO₃^-, even with high N input. The presence of AMF also significantly reduced the relative abundance within the bacterial orders Sphingomonadales and Rhizobiales. Sphingomonadales correlated significantly and positively with soil NH₃ volatilization in 2016 and N₂O emissions, whereas Rhizobiales correlated positively with soil N₂O emissions. High N input significantly increased soil NH₃ volatilization and N₂O emissions with increasing relative abundance of Sphingomonadales and Rhizobiales. These findings demonstrate the contribution of AMF in regulating NH₃ and N₂O emission by improving plant N uptake and altering soil bacterial communities. They also suggest that altering the rhizosphere microbiome might offer additional potential for restoration of N-enriched agroecosystems.

Arbuscular Mycorrhizae Shift Community Composition of N-Cycling Microbes and Suppress Soil N2O Emission

Mycorrhizae are ubiquitous symbiotic associations between arbuscular mycorrhizal fungi (AMF) and terrestrial plants, in which AMF receive photosynthates from and acquire soil nutrients for their host plants. Plant uptake of soil nitrogen (N) reduces N substrate for microbial processes that generate nitrous oxide (N₂O), a potent greenhouse gas. However, the underlying microbial mechanisms remain poorly understood, particularly in agroecosystems with high reactive N inputs. We examined how plant roots and AMF affect N₂O emissions, N₂O-producing (nirK and nirS) and N₂O-consuming (nosZ) microbes under normal and high N inputs in conventional (CONV) and organically managed (OM) soils. Here, we show that high N input increased soil N₂O emissions and the ratio of nirK to nirS microbes. Roots and AMF did not affect the (nirK + nirS)/nosZ ratio but significantly reduced N₂O emissions and the nirK/nirS ratio. They reduced the nirK/nirS ratio by reducing nirK-Rhodobacterales but increasing nirS-Rhodocyclales in the CONV soil while decreasing nirK-Burkholderiales but increasing nirS-Rhizobiales in the OM soil. Our results indicate that plant roots and AMF reduced N₂O emission directly by reducing soil N and indirectly through shifting the community composition of N₂O-producing microbes in N-enriched agroecosystems, suggesting that harnessing the rhizosphere microbiome through agricultural management might offer additional potential for N₂O emission mitigation.

Unexpected Parabolic Temperature Dependency of CH4 Emissions from Rice Paddies

Global warming is expected to affect methane (CH₄) emissions from rice paddies, one of the largest human-induced sources of this potent greenhouse gas. However, the large variability in warming impacts on CH₄ emissions makes it difficult to extrapolate the experimental results over large regions. Here, we show, through meta-analysis and multi-site warming experiments using the free air temperature increase facility, that warming stimulates CH₄ emissions most strongly at background air temperatures during the flooded stage of ∼26 °C, with smaller responses of CH₄ emissions to warming at lower and higher temperatures. This pattern can be explained by divergent warming responses of plant growth, methanogens, and methanotrophs. The effects of warming on rice biomass decreased with the background air temperature. Warming increased the abundance of methanogens more strongly at the medium air temperature site than the low and high air temperature sites. In contrast, the effects of warming on the abundance of methanotrophs were similar across the three temperature sites. We estimate that 1 °C warming will increase CH₄ emissions from paddies in China by 12.6%─substantially higher than the estimates obtained from leading ecosystem models. Our findings challenge model assumptions and suggest that the estimates of future paddy CH₄ emissions need to consider both plant and microbial responses to warming.

Effects of multiple global change factors on soil microbial richness, diversity and functional gene abundances: A meta-analysis

Soil microbial richness, diversity, and functional gene abundance are crucial factors affecting belowground ecosystem functions; however, there is still a lack of systematic understanding of their responses to global change. Here, we conducted a worldwide meta-analysis using 1071 observation data concerning the effects of global change factors (GCFs), including warming (W), increased precipitation (PPT+), decreased precipitation (PPT-), elevated CO₂ concentration (eCO₂), and nitrogen deposition (N), to evaluate their individual, combined, and interactive effects on soil microbial properties across different groups and ecosystems. Across the dataset, eCO₂ increased microbial richness and diversity by 40.5% and 4.6%, respectively; warming and N addition decreased the abundance of denitrification functional genes (nirS, nirK, and nozS); N addition had a greater impact on soil C-cycling functional genes than on N-cycling ones. Long-term precipitation change was conducive to the increase in soil microbial richness, and fungal richness change was more sensitive than bacterial richness, but the sensitivity of bacteria richness to N addition was positively correlated with experimental duration. Soil microbial richness, diversity, and functional gene abundances could be significantly affected by individual or multiple GCF changes, and their interactions are mainly additive. W×eCO₂ on microbial diversity, and N×PPT+ and W×N on N-cycling functional gene abundance showed synergistic interactions. Based on the limitations of the collected data and the findings, we suggest designing experiments with multiple GCFs and long experimental durations and incorporating the effects and interactions of multiple drivers into ecosystem models to accurately predict future soil microbial properties and functions under future global changes.

Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2 O emission

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N₂ O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N₂ O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N₂ O emission by 261%, whereas there was no clear relationship between changes in soil N₂ O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N₂ O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N₂ O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N₂ O emission.

Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N2 O emission

Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N₂ O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N₂ O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N₂ O emission by 261%, whereas there was no clear relationship between changes in soil N₂ O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N₂ O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N₂ O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N₂ O emission.

Arbuscular mycorrhizal fungi mitigate soil nitrogen and phosphorus losses: A meta-analysis

Nutrient loss from terrestrial ecosystems via leaching and gaseous emissions is increasingly threatening global environmental and human health. Although arbuscular mycorrhizal fungi (AMF) have been shown to regulate soil N and P losses, a comprehensive quantitative overview of their influences on the losses of these soil nutrients across global scales is currently lacking. This study used a meta-analysis of 322 observations from 36 studies to assess the effect of AMF inoculum on 11 variables related to the loss of soil N and P. We found that the presence of AMF significantly reduced soil N and P losses, with the most pronounced reduction occurring in soil NO₃^--N (-32%), followed by total P (-21%), available P (-16%) and N₂O (-10%). However, the mitigation effects of AMF on soil N and P loss were dependent on the identity of AMF inoculum, plant type and soil biotic and abiotic factors. Generally, the mitigation effects of AMF increased with increasing AMF root colonization rate, microbial diversity of inoculants, soil organic carbon (SOC) content and experimental duration as well as with decreasing soil sand contents and soil N and P availability. Overall, this meta-analysis highlights the importance of AMF inoculation in mitigating N and P nutrient loss and environmental pollution for terrestrial ecosystem sustainability.

Climate warming promotes deterministic assembly of arbuscular mycorrhizal fungal communities

Arbuscular mycorrhizal fungi (AMF) significantly contribute to plant resource acquisition and play important roles in mediating plant interactions and soil carbon (C) dynamics. However, it remains unclear how AMF communities respond to climate change. We assessed impacts of warming and precipitation alterations (30% increase or decrease) on soil AMF communities, and examined major ecological processes shaping the AMF community assemblage in a Tibetan alpine meadow. Our results showed that warming significantly increased root biomass, and available nitrogen (N) and phosphorus (P) in soil. While precipitation alterations increased AMF abundances, they did not significantly affect the composition or diversity of AMF communities. In contrast, warming altered the composition of AMF communities and reduced their Shannon-Wiener index and Pielou's evenness. In particular, warming shifted the AMF community composition in favor of Diversisporaceae over Glomeraceae, likely through its impact on soil N and P availability. In addition, AMF communities were phylogenetically random in the unwarmed control but clustered in warming plots, implying more deterministic community assembly under climate warming. Warming enhancement of root growth, N and P availability likely reduced plant C-allocation to AMF, imposing stronger environmental filtering on AMF communities. We further proposed a conceptual framework that integrates biological and geochemical processes into a mechanistic understanding of warming and precipitation changes' effects on AMF. Taken together, these results suggest that soil AMF communities may be more sensitive to warming than expected, highlighting the need to monitor their community structure and associated functional consequences on plant communities and soil C dynamics under the future warmer climate.

Fungi Dominated the Incorporation of 13C-CO2 into Microbial Biomass in Tomato Rhizosphere Soil under Different CO2 Concentrations

An elevated CO₂ (eCO₂) fumigation experiment was carried out to study the influence of various CO₂ concentrations on microorganisms involved in the incorporation of root-derived C in greenhouse soil systems. In this study, 400 and 800 µmol·mol⁻¹ CO₂ fumigation treatments were conducted during tomato planting. Phospholipid fatty acid (PLFA) profiling based on the stable isotope probing (SIP) technique was applied to trace active microorganisms. The absolute total abundance of ¹³C-PLFAs was much higher under eCO₂ treatment. Most of the ¹³C-CO₂ was incorporated into the ¹³C-PLFAs 18:2ω6,9 (fungi), 16:0 (general PLFA), 18:1ω9c (Gram-negative bacteria, G⁻) and i17:0 (Gram-positive bacteria, G⁺) via rhizodeposition from tomato under ambient CO₂ (aCO₂) and eCO₂ treatments, suggesting similar responses of active microorganisms to different CO₂ treatments. However, the fungi (characterized by the ¹³C-PLFA 18:2ω6,9) played a much more dominant role in the incorporation of root-derived C under eCO₂. Actinomycetes, marked by the ¹³C-PLFA 10-Me-18:0, occurred only on labeling day 15 under the eCO₂ treatment, indicating that the actinomycetes fed on both soil organic carbon and fresh rhizodeposition. It was indicated that eCO₂ significantly affected microbial biomass and microbial community structures involved in the incorporation of ¹³C-CO₂ via tomato root secretions, as supported by Adonis analysis and the Mantel test.

Warming and elevated ozone induce tradeoffs between fine roots and mycorrhizal fungi and stimulate organic carbon decomposition

Climate warming and elevated ozone (eO₃) are important climate change components that can affect plant growth and plant-microbe interactions. However, the resulting impact on soil carbon (C) dynamics, as well as the underlying mechanisms, remains unclear. Here, we show that warming, eO₃, and their combination induce tradeoffs between roots and their symbiotic arbuscular mycorrhizal fungi (AMF) and stimulate organic C decomposition in a nontilled soybean agroecosystem. While warming and eO₃ reduced root biomass, tissue density, and AMF colonization, they increased specific root length and promoted decomposition of both native and newly added organic C. Also, they shifted AMF community composition in favor of the genus Paraglomus with high nutrient-absorbing hyphal surface over the genus Glomus prone to protection of soil organic C. Our findings provide deep insights into plant-microbial interactive responses to warming and eO₃ and how these responses may modulate soil organic C dynamics under future climate change scenarios.