Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots

Aromatic compound 2-acetyl-1-pyrroline coordinates nitrogen assimilation and methane mitigation in fragrant rice

Rice paddy has been the main source of anthropogenic methane (CH4) emissions, with significant variations among rice varieties. 2-Acetyl-1-pyrroline (2-AP) is the key component of the pleasant aroma in fragrant rice. Here, we show that fragrant rice is metabolically active in nitrogen assimilation and exhibits high levels of 2-AP and that CH4 fluxes at the booting stage and cumulative emissions are 25.5% and 14.8% lower, respectively, in fragrant rice paddies compared with nonfragrant rice paddies. Three precursors involved in 2-AP synthesis-proline, glutamic acid, and ornithine-are identified as crucial nitrogen compounds that significantly promote CH4 oxidation in the rhizosphere. Augmenting 2-AP synthesis, either through foliar spraying or by utilizing CRISPR-Cas9 technology to generate knockout lines of BETAINE ALDEHYDE DEHYDROGENASE 2 gene, effectively enhances CH4 oxidation and reduces CH4 fluxes. Our findings reveal that the 2-AP metabolic pathway coordinates the carbon/nitrogen cycle to improve nitrogen assimilation along with high 2-AP levels and mitigate CH4 emissions in paddy ecosystems.

Methanogen-methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane

Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high-throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross-feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance-decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.

Ridge with no-tillage facilitates microbial N2 fixation associated with methane oxidation in rice soil

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.

Global warming potential assessment under reclaimed water and livestock wastewater irrigation coupled with co-application of inhibitors and biochar

The application of nitrification inhibitors (nitrapyrin) and urease inhibitors (N-(N-butyl) thiophosphoric triamide) under conventional water resources has been considered as an effective means to improve nitrogen utilization efficiency and mitigate soil greenhouse gas emissions. However, it is not known whether the inhibitors still have an inhibitory effect under unconventional water resources (reclaimed water and livestock wastewater) irrigation and whether their use in combination with biochar improves the mitigation effect. Therefore, unconventional water resources were used for irrigation, with groundwater (GW) control. Nitrapyrin and N-(N-butyl) thiophosphoric triamide were used alone or in combination with biochar in a pot experiment, and CO2, N2O, and CH4 emissions were measured. The results showed that irrigation of unconventional water resources exacerbated global warming potential (GWP). All exogenous substance treatments increased CO2 and CH4 emissions and suppressed N2O emissions, independent of the type of water, compared to no substances (NS). The inhibitors were ineffective in reducing the GWP whether or not in combination with biochar, and the combined application of inhibitors with biochar further increased the GWP. This study suggests that using inhibitors and biochar in combination to regulate the greenhouse effect under unconventional water resources irrigation should be done with caution.

Effects of integrated nutrient management and urea deep placement on rice yield, nitrogen use efficiency, farm profits and greenhouse gas emissions in saline soils of Bangladesh

Soil salinity is one of the major yield-limiting factors in the coastal ecosystems of Bangladesh. An efficient fertilizer management practice and selection of appropriate crop cultivars could play a crucial role in improving yield and promoting low-carbon agriculture across saline soils. A two-year multi-location field experiment was conducted during the Boro (dry) season (December-April) to investigate the effects of fertilizer management and rice cultivar selection on rice yield, economic viability, and global warming potential (GWP) in coastal saline soils of Bangladesh. The study included seven fertilizer treatments with varying nitrogen rates and sources, as well as two rice cultivars (BRRI dhan67 and BRRI dhan88). The results showed that integrated nutrient management-2 (INM-2) significantly (p < 0.05) increased rice yield and nitrogen use efficiency compared to other treatments for both BRRI dhan67 and BRRI dhan88. Similarly, INM-2 gave a higher return on fertilizer investment and marginal benefit-cost ratio than other treatments in both locations and under both cultivars. BRRI dhan67 significantly (p < 0.05) increased rice yield relative to BRRI dhan88 by 21 % and 52 % at the BRRI farm and Kaliganj in Satkhira, respectively. The cost-dominant analysis excluded BRRI dhan88 and all fertilizer treatments, except urea deep placement (UDP) and INM-2, from consideration in both locations. Consequently, INM-2 and UDP proved to be economically viable in both locations, with INM showing a higher marginal rate of return than UDP in BRRI dhan67. In terms of environmental sustainability, UDP significantly (p < 0.05) reduced GWP and yield-scaled emissions of CH4 by 31 % and 38 % without causing yield loss compared to INM-2. Similarly, BRRI dhan67 significantly (p < 0.05) reduced GWP and yield-scaled emissions of CH4 by 5 and 22 % compared to BRRI dhan88. These findings suggest that selecting salt-tolerant rice cultivars and implementing appropriate fertilizer management practices can enhance economic profitability, ensure food security, and mitigate the adverse effects of climate change in coastal saline soils.

Adding Corbicula fluminea altered the effect of plant species diversity on greenhouse gas emissions and nitrogen removal from constructed wetlands in the low-temperature season

Plant species diversity is crucial in greenhouse gas emissions and nitrogen removal from constructed wetlands (CWs). However, previous studies have overlooked the impact of benthos on cumulative greenhouse gas emissions during the low-temperature season in CWs. In this study, we established 66 vertical flow CWs with three levels of species richness (1, 2, and 4 species) and eleven species compositions. The Corbicula fluminea was added or not added at each diversity level and monitored greenhouse gas emissions and effluent nitrogen concentration. Our findings indicated that (1) in microcosms without C. fluminea, high species richness significantly increased effluent nitrogen concentrations (NO3--N, NH4+-N, and TIN), but plant species richness did not affect cumulative CH4, N2O, and CO2 emissions. The presence of Hemerocallis fulva significantly increased cumulative CO2 emissions, while the presence of Iris tectorum significantly increased effluent nitrogen (NO3--N and TIN) concentrations and cumulative N2O emissions; (2) in microcosms with C. fluminea, the lowest cumulative CH4 emissions occurred when there were two species, but plant species richness did not affect cumulative CO2 and N2O emissions. The presence of H. fulva significantly increased cumulative CH4 emissions, while the presence of Reineckea carnea significantly increased effluent nitrogen (NO3--N, NH4+- N, TIN) concentrations; (3) at the same diversity level, the addition of C. fluminea significantly increased cumulative CH4 and N2O emissions, as well as effluent nitrogen concentrations. These results demonstrate that C. fluminea alters the effect of plant species diversity on cumulative greenhouse gas emissions and nitrogen removal from CWs during the low-temperature season. We recommend using a two-species mixture to reduce greenhouse gas emissions. However, we caution against using plant compositions with H. fulva or I. tectorum for effective wastewater treatment and greenhouse gas reduction in CWs.

Effect of nitrogen application on greenhouse gas emissions and nitrogen uptake by plants in integrated rice-crayfish farming

Integrated rice-crayfish farming is an ecological rice farming mode. However, limited research has examined the comprehensive impacts of greenhouse gas (GHG) emissions, nitrogen (N) uptake, and N utilization in rice under this farming modality. Herein, a dual-factor experiment was performed from 2021 to 2022 to assess the comprehensive impacts of N application and rice farming mode on greenhouse gas (GHG) emissions, N uptake, N utilization, and rice yield in paddy fields. Under N application, the rice-crayfish co-culture exhibits a 2.3 % decrease in global warming potential (GWP) and a 17.3 % increase in greenhouse gas intensity relative to the rice monoculture. Moreover, the N uptake of rice within the rice-crayfish co-culture is 5.2 %-10.4 % higher than that in the rice monoculture. However, owing to low rice yield under the rice-crayfish co-culture, its N partial factor productivity decreases by 5.6 %-22.6 %, while N agronomic efficiency is reduced by 18.3 %-46.9 % compared with the rice monoculture. In addition, N application significantly inhibits CH4 emissions from paddy fields in the rice-crayfish co-culture mode. Compared with no N application, the CH4 emissions and GWP of N-applied treatment are decreased by 12.1 %-31.0 % and 6.0 %-15.8 %, respectively. Hence, N regulation might reduce GHG emissions in rice-aquatic animal co-culturing agriculture. Collectively, the results of this study suggest that switching from a rice monoculture to rice-crayfish co-culture can mitigate GHG emissions and promote rice N uptake; however, continuously improving the productivity of co-culturing agriculture is key to achieving high N utilization efficiency and low environmental impact.

Application of nitrogen-rich sunflower husks biochar promotes methane oxidation and increases abundance of Methylobacter in nitrogen-poor soil

The area of sunflower crops is steadily increasing. A beneficial way of managing sunflower waste biomass could be its use as a feedstock for biochar production. Biochar is currently being considered as an additive for improving soil parameters, including the ability to oxidise methane (CH4) - one of the key greenhouse gases (GHG). Despite the high production of sunflower husk, there is still insufficient information on the impact of sunflower husk biochar on the soil environment, especially on the methanotrophy process. To fill this knowledge gap, an experiment was designed to evaluate the effects of addition of sunflower husk biochar (produced at 450-550 °C) at a wide range of doses (1-100 Mg ha-1) to Haplic Luvisol. In the presented study, the CH4 oxidation potential of soil with and without sunflower husk biochar was investigated at 60 and 100% water holding capacity (WHC), and with the addition of 1% CH4 (v/v). The comprehensive study included GHG exchange (CH4 and CO2), physicochemical properties of soil (pH, soil organic carbon (SOC), dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), WHC), and the structure of soil microbial communities. That study showed that even low biochar doses (5 and 10 Mg ha-1) were sufficient to enhance pH, SOC, DOC and NO3--N content. Importantly, sunflower husk biochar was significant source of NO3--N, which soil concentration increased from 9.40 ± 0.09 mg NO3--N kg-1 for the control to even 19.40 ± 0.26 mg NO3--N kg-1 (for 100 Mg ha-1). Significant improvement of WHC (by 11.0-12.4%) was observed after biochar addition at doses of 60 Mg ha-1 and higher. At 60% WHC, application of biochar at a dose of 40 Mg ha-1 brought significant improvements in CH4 oxidation rate, which was 4.89 ± 0.37 mg CH4-C kg-1 d-1. Higher biochar doses were correlated with further improvement of CH4 oxidation rates, which at 100 Mg ha-1 was seventeen-fold higher (8.36 ± 0.84 mg CH4-C kg-1 d-1) than in the biochar-free control (0.48 ± 0.28 mg CH4-C kg-1 d-1). CO2 emissions were not proportional to biochar doses and only grew circa (ca.) twofold from 3.16 to 6.90 mg CO2-C kg-1 d-1 at 100 Mg ha-1. Above 60 Mg ha-1, the diversity of methanotrophic communities increased, with Methylobacter becoming the most abundant genus, which was as high as 7.45%. This is the first, such advanced and multifaceted study of the wide range of sunflower husk biochar doses on Haplic Luvisol. The positive correlation between soil conditions, methanotroph abundance and CH4 oxidation confirmed the multifaceted, positive effect of sunflower husk biochar on Haplic Luvisol. Sunflower husk biochar can be successfully used for Haplic Luvisol supplementation. This additive facilitates soil protection against degradation and has the potential to mitigate GHG emissions.

Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin

Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.

Subsurface fertilization boosts crop yields and lowers greenhouse gas emissions: A global meta-analysis

The subsurface application (SA) of nitrogenous fertilizers is a potential solution to mitigate climate change and improve food security. However, the impacts of SA technology on greenhouse gas (GHG) emissions and agronomic yield are usually evaluated separately and their results are inconsistent. To address this gap, we conducted a meta-analysis synthesizing 40 peer-reviewed studies on the effects of SA technology on GHG and ammonia (NH₃) emissions, nitrogen uptake (NU), crop yield, and soil residual NO₃-N in rice paddies and upland cropping system. Compared to the surface application of N, SA technology significantly increased rice yields by 32 % and crop yield in upland systems by 62 %. The largest SA-induced increases in crop yield were found at low N input rates (<100 kg Nha^-1) in rice paddies and medium N input rates (100-200 kg Nha^-1) in upland systems, suggesting that soil moisture is a key factor determining the efficiency of SA technology. SA treatments increased yields by more at reduced fertilizer rates (~30 % less N), a shallow depth (<10 cm), and with urea in both cropping systems than at the full (recommended) N rate, a deeper depth (10-20 cm), and with ammonical fertilizer. SA treatments significantly increased NU in rice paddies (34 %) and upland systems (18 %), and NO₃-N (40 %) in paddyland; however, NO₃-N decreased (28 %) in upland conditions. Ammonia mitigation was greater in paddyland than in upland conditions. SA technology decreased the carbon footprint (CF) in paddyland by 29 % and upland systems by 36 %, and overall by 33 %. Compared with broadcasting, SA significantly reduced CH₄ emissions by 16 %, N₂O emissions by 30 %, and global warming potential (GWP) by 10 % in paddy cultivation. Given SA increased grain yield and NU while reducing NH₃, CF, and GWP, this practice provides dual benefits - mitigating climate change and ensuring food security.

Eichhornia crassipes-rhizospheric biofilms contribute to nutrients removal and methane oxidization in wastewater stabilization ponds receiving simulative sewage treatment plants effluents

Wastewater stabilization ponds (WSPs) have been used in treating sewage treatment plants (STPs) effluents. However, little is known about the role of rhizospheric biofilms on methane release in WSPs with floating plants. In the present study, the nutrient removal, CH₄ fluxes, CH₄ oxidization potential and rhizospheric bacterial community were investigated in WSPs with Eichhornia crassipes under simulate STPs effluents for 31 days. At the end of the experiment, E. crassipes biomass was 5.60-8.81 times of initial weight and increased with increasing nutrients concentration. E. crassipes effectively reduced methane release and nutrients. Compared to control, E. crassipes reduced 52.30%-83.21% of CH₄ fluxes at water-atmosphere interface and had better inhibition effect on CH₄ fluxes in treatments with high nutrients. However, methane oxidization rates of E. crassipes roots were higher in low nutrients (0.83 ± 0.046 mg CH₄ (kg fresh plant)^-1 day^-1) than high nutrients (0.12 ± 0.04 mg CH₄ (kg fresh plant)^-1 day^-1). Structural equation modeling revealed that biomass of E. crassipes has negative effect on CH₄ fluxes (-0.453, p = 0.000). Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi and Actinobacteria were the predominant phyla in the rhizospheric biofilm of E. crassipes and contributed to nutrients removal. Aerobic methanotrophs and pomA abundances were higher in rhizospheric biofilm exposed to high nutrients than low nutrients and aerobic methanotrophs had close interactions with other microorganisms and participated in the carbon and nitrogen cycle, demonstrating that many bacteria harboring pmoA gene did not fully involve in methane oxidization. These data highlight plants E. crassipes have an important role in both reducing methane release and nutrients removal.

High-yielding nitrate transporter cultivars also mitigate methane and nitrous oxide emissions in paddy

Development of high yield rice varieties is critical to ensuring global food security. However, the emission of greenhouse gases (GHG) such as Methane (CH₄) and Nitrous oxide (N₂O) from paddy fields threatens environmental sustainability. In this study, we selected overexpressed high-affinity nitrate transporters (NRT2.3 along with their partner protein NAR2.1) cultivars, which are effective nitrogen use efficient transgenic lines pOsNAR2.1: OsNAR2.1 (Ox2) and p35S:OsNRT2.3b (O8). We used high (270 kg N/ha) and low (90 kg N/ha) nitrogen (N) fertilizers in paddy fields to evaluate morphophysiological traits, including GHG emission. We found that Ox2 and O8 reduced CH₄ emissions by 40% and 60%, respectively, compared to their wild type (WT). During growth stages, there was no consistent N₂O discharge pattern between WT and transgenics (Ox2, O8) in low and high N application. However, total cumulative N₂O in a cropping season reduced in O8 and increased in Ox2 cultivars, compared to WT. Root aerenchyma formation reduced by 30-60% in transgenic lines. Methanogens like mcrA in low and high N were also reduced by up to 50% from rhizosphere of Ox2 and O8. However, the nitrifying bacterial population such as nosZ reduced in both transgenics significantly, but nirK and nirS did not show a consistent variation. The high yield of transgenic rice with limited aerenchyma mitigates the discharge of CH₄ and N₂O by reducing root exudates that provide substrates for GHG. Our results improve understanding for breeders to serve the purpose of sustainable development.

The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis

Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH₄) and nitrous oxide (N₂O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH₄ at the global scale. We also address the effects of N enrichment on N₂O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH₄ oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH₄⁺ enrichment, inhibits CH₄ oxidation, resulting in higher CH₄ emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N₂O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.

Trends and research features on greenhouse gas emissions from rice production: review based on bibliometric analysis

Greenhouse gas from rice production has become a great concern and the focus of a lot of research in recent years. The main aim of the study was to explore the research trend of GHG emissions from rice production by exploring the research hotspots and providing suggestions for future research directions over the period 1991 to 2020. A bibliometric analysis was conducted using the Scopus database, and the sample included 2535 articles. The methodology was based on descriptive analysis, co-occurrence analysis, factorial analysis, word dynamic over time, and the author's keyword analysis over time. The results indicate a remarkable increase in the number of articles published on this topic, mainly in the journals of "Agriculture," "Ecosystems," and "Environment." The main authors were Conrad R. and Wassmann R. Relating to the number of published articles, very few were contributed by African countries, whereas China, Japan, and India were the main contributors. The co-occurrence analysis showed that rice, methane, and nitrous oxide are the core keywords of the network. The multiple factorial analysis pointed out that greenhouse gas emissions from rice production depend on the farming practices, the environmental factors, and the plant growth as well. The evolutionary path showed that the current author's keywords are more related to global warming potential, climate change, and biochar. The findings of this review can help researchers and scholars by providing a better overview of development trends that have emerged over the past 30 years and suggestions for the future direction in this field.

Prospecting the significance of methane-utilizing bacteria in agriculture

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.

A global meta-analysis of crop yield and agricultural greenhouse gas emissions under nitrogen fertilizer application

Nitrogen fertilization (NF) is one of the common practices to increase crop production worldwide over the past several decades. Nevertheless, unreasonable NF results in massive greenhouse gas (GHG) emissions, leading to climate change and global warming. Many studies have already reported the impact of NF on crop yield, global warming potential (GWP) and greenhouse gas intensity (GHGI), but the studies were limited to only some parameters. In this study, a total of 174 studies from 16 countries were collected and then a regression analysis was conducted to obtain the appropriate N fertilization rates that enhance crop yield while reducing GWP and GHGI. After that, a meta-analysis was performed to evaluate the effects of NF on crop yield, GHGI, GWP and GHG emissions and identify NF management strategies that benefit crop yield and maintain GWP. The results showed that the suitable N fertilization rate was 180, 150, 130 and 200 kg ha^-1 for wheat, maize, rice and vegetables or industrial crops, respectively. Overall, NF resulted in positive effect size in crop yield (0.56) and negative effect size in GHGI (-0.14) compared to NNF. GWP showed positive effect size (0.37) due to an increase in N₂O emissions (0.91) relative to NNF, which is higher than the increase of CH₄ emissions (0.01) and CO₂ emissions (0.22). It was recommended that split and banded application of urea or urea plus manure is employed for cereals (especially wheat) in the arid and semi-arid regions with medium-textured and neutral or alkaline soil.

Will climate warming of terrestrial ecosystem contribute to increase soil greenhouse gas fluxes in plot experiment? A global meta-analysis

One of the main manifestations of global climate change is its profound impact on the emission of greenhouse gases from terrestrial soil. Numerous field warming experiments have explored the effects of different temperature rise intensities and durations on soil greenhouse gas fluxes in the growing season of different terrestrial ecosystems. However, the results were inconsistent due to the variations in vegetation, soil, and climatic conditions in different ecosystems. In the present work, we carried meta-analysis to synthesize 99 datasets from 52 field warming experiments in growing seasons of terrestrial ecosystems to evaluate the response of soil greenhouse gas fluxes to global warming. The results showed that warming greatly stimulated soil CO₂ in temperate forest and farmland by 12.64% and 25.57%, respectively, significantly increased soil N₂O emissions in grassland (27.23%), farmland (44.33%), and shrubland (223.36%), and increased soil CH₄ uptake by 57.81% in grasslands. However, no significant impact on the greenhouse gas fluxes in other ecosystems was observed. Generally, short-and medium-term (≤ 3 years) warming can promote soil greenhouse gas fluxes. Also, low temperature and low-medium temperature (≤ 2 °C) significantly promoted N₂O emission and CH₄ absorption, and medium temperature (2-4 °C) considerably assisted CO₂ flux, but high temperature (> 4 °C) had no significant effect on greenhouse gas flux. Our results demonstrated that soil greenhouse gas fluxes in terrestrial ecosystems during the growing season do not increase linearly with the increasing climate warming, and it is still uncertain whether there is acclimatization to long-term climate warming.

Mitigating greenhouse gas emissions from irrigated rice cultivation through improved fertilizer and water management

Greenhouse gas (GHG) emissions from agriculture sector play an important role for global warming and climate change. Thus, it is necessary to find out GHG emissions mitigation strategies from rice cultivation. The efficient management of nitrogen fertilizer using urea deep placement (UDP) and the use of the water-saving alternate wetting and drying (AWD) irrigation could mitigate greenhouse gas (GHG) emissions and reduce environmental pollution. However, there is a dearth of studies on the impacts of UDP and the integrated plant nutrient system (IPNS) which combines poultry manure and prilled urea (PU) with different irrigation regimes on GHG emissions, nitrogen use efficiency (NUE) and rice yields. We conducted field experiments during the dry seasons of 2018, 2019, and 2020 to compare the effects of four fertilizer treatments including control (no N), PU, UDP, and IPNS in combination with two irrigation systems- (AWD and continuous flooding, CF) on GHG emissions, NUE and rice yield. Fertilizer treatments had significant (p < 0.05) interaction effects with irrigation regimes on methane (CH₄) and nitrous oxide (N₂O) emissions. PU reduced CH₄ and N₂O emissions by 6% and 20% compared to IPNS treatment, respectively under AWD irrigation, but produced similar emissions under CF irrigation. Similarly, UDP reduced cumulative CH₄ emissions by 9% and 15% under AWD irrigation, and 9% and 11% under CF condition compared to PU and IPNS treatments, respectively. Across the year and fertilizer treatments, AWD irrigation significantly (p < 0.05) reduced cumulative CH₄ emissions and GHG intensity by 28%, and 26%, respectively without significant yield loss compared to CF condition. Although AWD irrigation increased cumulative N₂O emissions by 73%, it reduced the total global warming potential by 27% compared to CF irrigation. The CH₄ emission factor for AWD was lower (1.67 kg ha^-1 day^-1) compared to CF (2.33 kg ha^-1 day^-1). Across the irrigation regimes, UDP increased rice yield by 21% and N recovery efficiency by 58% compared to PU. These results suggest that both UDP and AWD irrigation might be considered as a carbon-friendly technology.

Changes in Soil Chemical Properties Due to Long-Term Compost Fertilization Regulate Methane Turnover Related Gene Abundances in Rice Paddy

Maintaining rice yield, soil function, and fertility are essential components of long-term compost fertilization. However, paddy fields are major sources of anthropogenic methane emissions. The aim of the study is to evaluate the changes in soil chemical properties and their concurrent impact on the abundance of methanogenesis (mcrA) and methane oxidation (pmoA) related genes among compost (Com), NPK+Compost (NPKCom), and unfertilized (NF) fallow paddy fields under long-term compost fertilization. Results showed that compost and NPK+Compost fertilization altered the soil chemical properties of paddy fields with a significant increase in the functional gene abundance potentially associated with Methanobacteriaceae for mcrA (1.23 × 106 to 3.84 × 106 copy number g−1 dry soil) and methane oxidizing bacteria such as Methylomonas and Methylobacter for pmoA (1.65 × 106 to 4.3 × 106 copy number g−1 dry soil). Ordination plots visualized these changes, where treatments clustered distinctly indicating that Com and NPKCom treatments were characterized by paddy soils with elevated OM, TN, K and P content and higher abundances of methanogenesis and methane oxidation related genes. The study showed that long-term compost fertilization resulted in paddy fields with high nutrient content and high gene abundance, attributed to methanogens and methane oxidizing bacteria that responded well with compost fertilization. These results indicated the potential of these fallow paddy fields for methane emission and methane oxidation and that they are ‘primed’, potentially influencing subsequent paddy field responses to long-term compost application.

Plant Growth-Promoting Rhizobacteria With ACC Deaminase Activity Enhance Maternal Lateral Root and Seedling Growth in Switchgrass

Switchgrass, a C4 plant with high potential as a bioenergy source, is unsteady in yield under sub-optimal conditions. Bacteria containing 1-aminocyclopropane-1-carboxylate synthase (ACC) deaminase can promote plant growth. We isolated bacteria containing ACC deaminase activity from switchgrass rhizosphere using an orthogonal matrix experimental design with four factors (bacterial liquid concentration, bacterial liquid treatment time, nitrogen content, and NaCl) to quantitatively investigate the effects and pairwise interactions on the seedling growth. Pseudomonas sp. Y1, isolated from the switchgrass cv. Blackwell rhizomes was selected. We optimized the inoculation bacterial concentration, treatment time, NaCl, and nitrogen concentration for the seedling growth. The optimal bacterial concentration, treatment time, NaCl, and nitrogen content was 0.5-1.25 OD at 600 nm, 3 h, 60-125 mM and 158 mg L-1, respectively. Pseudomonas sp. Y1 significantly increased the total root length, root surface, shoot length, and fresh and dry weight through an effective proliferation of the number of first-order lateral roots and root tips. This indicated that Pseudomonas sp. Y1 has a higher potential to be used as a plant growth-promoting rhizobacteria bacteria.

Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils

Grassland soils serve as a biological sink and source of the potent greenhouse gases (GHG) methane (CH4) and nitrous oxide (N2O). The underlying mechanisms responsible for those GHG emissions, specifically, the relationships between methane- and ammonia-oxidizing microorganisms in grazed grassland soils are still poorly understood. Here, we characterized the effects of grazing on in situ GHG emissions and elucidated the putative relations between the active microbes involving in methane oxidation and nitrification activity in grassland soils. Grazing significantly decreases CH4 uptake while it increases N2O emissions basing on 14-month in situ measurement. DNA-based stable isotope probing (SIP) incubation experiment shows that grazing decreases both methane oxidation and nitrification processes and decreases the diversity of active methanotrophs and nitrifiers, and subsequently weakens the putative competition between active methanotrophs and nitrifiers in grassland soils. These results constitute a major advance in our understanding of putative relationships between methane- and ammonia-oxidizing microorganisms and subsequent effects on nitrification and methane oxidation, which contribute to a better prediction and modeling of future balance of GHG emissions and active microbial communities in grazed grassland ecosystems.

The Effect of Multi-Years Reclaimed Water Irrigation on Dryland Carbon Sequestration in the North China Plain

Reclaimed water is an alternative water source which could alleviate the shortage of water resources in agricultural systems. Many researchers have studied the effect of reclaimed water on soil environment, crop yield, etc. However, carbon sequestration in reclaimed water irrigated agricultural systems is less studied. This study investigates methane uptake and photosynthesis in reclaimed water irrigation systems contributing to carbon sequestration estimation and analyzes the important factors impacting them. The results show that CH4 uptake is related to soil water-filled pore space (WFPS) with a quadratic and it has the highest uptake when WFPS is between 40 and 50%. Long-term reclaimed water irrigation could significantly decrease (p < 0.05) CH4 uptake and macroaggregate stability in the topsoil. However, reclaimed water had no significant impact on photosynthesis in comparison. The type of fertilizer is an important factor which impacts CH4 emission from soil; urea had a lower CH4 uptake and a higher CO2 emission than slow-released fertilizer. Overall, reclaimed water irrigation could effectively decrease soil carbon sequestration. A soil wetted proportion level of 40–50% was recommended in this study for favorable methane oxidation. Slow-released fertilizer in reclaimed water irrigated agriculture could better control soil carbon emission and soil carbon absorption.

Long-term isotopic model study for ecofriendly rice (Oryza sativa L.) authentication: Updating a case study in South Korea

To overcome the lack of consumer trust in ecofriendly products due to low reliability of ecofriendly certification and decreasing areas certified for growing ecofriendly agricultural products, alternative approaches for reliable certification are required. Isotopic-chemometric analysis has potential for determining organic authenticity, but previous studies have struggled to differentiate the authenticities of different rice types. The present study examined 5-year variations in δ¹³C and δ¹⁵N in ecofriendly and conventional rice sold at retail markets in South Korea, while assessing the feasibility of discriminant models for authentication of organic rice. Supporting vector machine analysis showed 4.4-14.6% better overall predictability of rice types than discriminant analysis and was effective in discriminating organic or conventional rice from pesticide-free rice, potentially enabling high-throughput screening to authenticate organic rice at marketplaces. Our findings provide reliable information for authenticating ecofriendly rice, with a potential to improve consumer safety and thus the confidence in organic products.

Paddy-upland rotation with Chinese milk vetch incorporation reduced the global warming potential and greenhouse gas emissions intensity of double rice cropping system

It is a common practice to maintain soil fertility based on the paddy-upland rotation with green manure in the subtropical region of China. However, rare studies are known about greenhouse gas (GHG) emissions from the paddy-upland rotation with green manure incorporation. Therefore, we conducted a field experiment of two years to compared with the effect of two kinds of green manure (CV: Chinese milk vetch and OR: Oilseed rape), and two kinds of cropping system (DR: double rice system and PR: paddy-upland rotation) on greenhouse gases emissions. We have found that the annual accumulation of CH₄ of Chinese milk vetch-rice-sweet potato || soybean was significantly reduced by 32.95%∼63.22% compared with other treatments, mainly because Chinese milk vetch reduced the abundance of methanogens by reducing soil C/N ratio. Meanwhile increasing soil permeability resulting from paddy-upland rotation also reduced soil CH₄ emission. However, The annual accumulation of N₂O of Chinese milk vetch-rice-sweet potato || soybean was increased by 17.39%∼870.11% compared with other treatments, mainly attributed to paddy-upland rotation decreased soil pH and nosZ abundance and increased nirK and nirS, thus enhancing N₂O emission, meanwhile the Chinese milk vetch incorporation and its interaction with the paddy-upland rotation has greatly enhanced the contents of NO₃^--N and abundance of ammonia-oxidizing archaea (AOA). The area-scaled global warming potential (GWP) and the biomass-scaled greenhouse gas emissions intensity (GHGI) of Chinese milk vetch-rice-sweet potato || soybean was reduced by 19.01%∼50.69% and 5.38%∼35.77% respectively. Thereby, the Chinese milk vetch-rice-sweet potato || soybean cropping system was suitable for agricultural sustainable development.

Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum

The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.

Water-washed hydrochar in rice paddy soil reduces N2O and CH4 emissions: A whole growth period investigation

Hydrochar (HC), an environment-friendly material, enhances soil carbon sequestration and mitigate greenhouse gases (GHGs) emissions in croplands. In this study, the water-washed HC (WW-HC) was applied to paddy soil to investigate effects on nitrous oxide (N₂O) and methane (CH₄) emissions during rice growth period. Four treatments, namely control (without N fertilizer and WW-HC), N fertilizer (WW-HC00), N fertilizer with 0.5 wt% WW-HC (WW-HC05) and N fertilizer with 1.5 wt% WW-HC (WW-HC15), were established. Results showed the WW-HC addition reduced N₂O and CH₄ emissions, global warming potential (GWP) and greenhouse gas intensity (GHGI) during the growing season. Moreover, the WW-HC application reduced N₂O cumulative emission (P < 0.05) (by 28.6% and 23.8% for WW-HC05 and WW-HC15, respectively). It was mainly due to the reduced ratio of (nirK + nirS) to nosZ under WW-HC15 (P < 0.05). Compared with WW-HC00, the WW-HC05 reduced CH₄ cumulative emissions by 14.8%, while the WW-HC15 increased by 9.7%. This might be ascribed to the significantly reduced expression of the methanogenic mcrA gene and ratio of mcrA to pmoA by WW-HC (P < 0.05). The WW-HC05 amendment decreased GWP and GHGI by 18.6% and 32.5%, respectively. Furthermore, the WW-HC application greatly improved nitrogen use efficiency by 116-145% compared with the control. Our study indicates the WW-HC application is a promising GHGs mitigation practice in paddy fields.

Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest

Forest soils play an important role in controlling global warming by reducing atmospheric methane (CH₄) concentrations. However, little attention has been paid to how nitrogen (N) deposition may alter microorganism communities that are related to the CH₄ cycle or CH₄ oxidation in subtropical forest soils. We investigated the effects of N addition (0, 30, 60, or 90 kg N ha⁻¹ yr⁻¹) on soil CH₄ flux and methanotroph and methanogen abundance, diversity, and community structure in a Moso bamboo (Phyllostachys edulis) forest in subtropical China. N addition significantly increased methanogen abundance but reduced both methanotroph and methanogen diversity. Methanotroph and methanogen community structures under the N deposition treatments were significantly different from those of the control. In N deposition treatments, the relative abundance of Methanoculleus was significantly lower than that in the control. Soil pH was the key factor regulating the changes in methanotroph and methanogen diversity and community structure. The CH₄ emission rate increased with N addition and was negatively correlated with both methanotroph and methanogen diversity but positively correlated with methanogen abundance. Overall, our results suggested that N deposition can suppress CH₄ uptake by altering methanotroph and methanogen abundance, diversity, and community structure in subtropical Moso bamboo forest soils.

Response of a methane-driven interaction network to stressor intensification

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.

Eco-friendly yield-scaled global warming potential assists to determine the right rate of nitrogen in rice system: A systematic literature review

Rice paddies are one of the largest greenhouse gases (GHGs) facilitators that are predominantly regulated by nitrogen (N) fertilization. Optimization of N uses based on the yield has been tried a long since, however, the improvement of the state-of-the-art technologies and the stiffness of global warming need to readjust N rate. Albeit, few individual studies started to, herein attempted as a systematic review to generalize the optimal N rate that minimizes global warming potential (GWP) concurrently provides sufficient yield in the rice system. To satisfy mounted food demand with inadequate land & less environmental impact, GHGs emissions are increasingly evaluated as yield-scaled basis. This systematic review (20 published studies consisting of 21 study sites and 190 observations) aimed to test the hypothesis that the lowest yield-scaled GWP would provide the minimum GWP of CH₄ and N₂O emissions from rice system at near optimal yields. Results revealed that there was a strong polynomial quadratic relationship between CH₄ emissions and N rate and strong positive correlation between N₂O emissions and N rate. Compared to control the low N dose emitted less (23%) CH₄ whereas high N dose emitted higher (63%) CH₄ emission. The highest N₂O emission observed at moderated N level. In total GWP, about 96% and 4%, GHG was emitted as CH₄ and N₂O, respectively. The mean GWP of CH₄ and N₂O emissions from rice was 5758 kg CO₂ eq ha^-1. The least yield-scaled GWP (0.7565 (kg CO₂ eq. ha^-1)) was recorded at 190 kg N ha^-1 that provided the near utmost yield. This dose could be a suitable dose in midseason drainage managed rice systems especially in tropical and subtropical climatic conditions. This yield-scaled GWP supports the concept of win-win for food security and environmental aspects through balancing between viable rice productivity and maintaining convincing greenhouse gases.

A Bacterial Consortium Interacts With Different Varieties of Maize, Promotes the Plant Growth, and Reduces the Application of Chemical Fertilizer Under Field Conditions

The success of beneficial bacteria in improving the crop growth and yield depends on an adequate plant-bacteria interaction. In this work, the capability of Azospirillium brasilense Sp7, Pseudomonas putida KT2440, Acinetobacter sp. EMM02, and Sphingomonas sp. OF178A to interact with six maize varieties was evaluated by both single-bacterium application and consortium application. The bacterial consortium efficiently colonized the rhizosphere of the autochthonous yellow and H48 hybrid varieties. Bacterial colonization by the consortium was higher than under single-bacterium colonization. The two maize varieties assayed under greenhouse conditions showed increased plant growth compared to the control. The effect of consortium inoculation plus 50% fertilization was compared with the 100% nitrogen fertilization under field conditions using the autochthonous yellow maize. Inoculation with the consortium plus 50% urea produced a similar grain yield compared to 100% urea fertilization. However, a biomass decrease was observed in plants inoculated with the consortium plus 50% urea compared to the other treatments. Furthermore, the safety of these bacteria was evaluated in a rat model after oral administration. Animals did not present any negative effects, after bacterial administration. In conclusion, the bacterial consortium offers a safety alternative that can reduce chemical fertilization by half while producing the same crop yield obtained with 100% fertilization. Decreased chemical fertilization could avoid contamination and reduce the cost in agricultural practices.

Belowground changes to community structure alter methane-cycling dynamics in Amazonia

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH₄) emission. To better understand the drivers of this change, we measured soil CH₄ flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH₄ (mean: 3454.6 ± 9482.3 μg CH₄ m^-2 d^-1), consistent with previous reports, while forest soils on average emit CH₄ at modest rates (mean: 9.8 ± 120.5 μg CH₄ m^-2 d^-1), but often act as CH₄ sinks. We report that secondary forest soils tend to consume CH₄ (mean: -10.2 ± 35.7 μg CH₄ m^-2 d^-1), demonstrating that pasture CH₄ emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH₄ directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH₄. Each land use type had a unique subset of taxa associated with CH₄ flux, suggesting that land use change alters CH₄ cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH₄ dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.

Global nitrogen input on wetland ecosystem: The driving mechanism of soil labile carbon and nitrogen on greenhouse gas emissions

Greenhouse gas emissions from wetlands are significantly promoted by global nitrogen input for changing the rate of soil carbon and nitrogen cycling, and are substantially affected by soil labile carbon and nitrogen conversely. However, the driving mechanism by which soil labile carbon and nitrogen affect greenhouse gas emissions from wetland ecosystems under global nitrogen input is not well understood. Working out the driving factor of nitrogen input on greenhouse gas emissions from wetlands is critical to reducing global warming from nitrogen input. Thus, we synthesized 72 published studies (2144 paired observations) of greenhouse gas fluxes and soil labile compounds of carbon and nitrogen (ammonium, nitrate, dissolved organic carbon, soil microbial biomass nitrogen and carbon), to understand the effects of labile carbon and nitrogen on greenhouse gas emissions under global nitrogen input. Across the data set, nitrogen input significantly promoted carbon dioxide, methane and nitrous oxide emissions from wetlands. In particular, at lower nitrogen rates (<100 kg ha^-1·yr^-1) and with added ammonium compounds, freshwater wetland significantly promoted carbon dioxide and methane emissions. Peatland was the largest nitrous oxide source under these conditions. This meta-analysis also revealed that nitrogen input stimulated dissolved organic carbon, ammonium, nitrate, microbial biomass carbon and microbial biomass nitrogen accumulation in the wetland ecosystem. The variation-partitioning analysis and structural equation model were used to analyze the relationship between the greenhouse gas and labile carbon and nitrogen further. These results revealed that dissolved organic carbon (DOC) is the primary factor driving greenhouse gas emission from wetlands under global nitrogen input, whereas microbial biomass carbon (MBC) more directly affects greenhouse gas emission than other labile carbon and nitrogen.

Effects of nitrogen addition on soil methane uptake in global forest biomes

Nitrogen (N) deposition has been conventionally thought to decrease forest soil methane (CH₄) uptake, while the biome specific and dose dependent effect is poorly understood. Based on a meta-analysis of 63 N addition trials from 7 boreal forests, 8 temperate forests, 13 subtropical and 4 tropical forests, we evaluated the effects of N addition on soil CH₄ uptake fluxes across global forest biomes. When combining all N addition levels, soil CH₄ uptake was insignificantly decreased by 7% in boreal forests, while N addition significantly decreased soil CH₄ uptake by 39% in temperate forests and by 21% in subtropical and tropical forests, respectively. Meta-regression analyses, however, indicated a shift from a positive to a negative effect on soil CH₄ uptake with increasing N additions both in boreal forests (threshold = 48 kg N ha^-1 yr^-1) and temperate forests (threshold = 27 kg N ha^-1 yr^-1), while no such shift was found in subtropical and tropical forests. Considering that current N deposition to most boreal and temperate forests is below the abovementioned thresholds, N deposition likely exerts a positive to neutral effect on soil CH₄ uptake in both forest biomes. Our results provide new insights on the biome specific and dose dependent effect of N addition on soil CH₄ sink in global forests and suggest that the current understanding that N deposition decreases forest soil CH₄ uptake is flawed by high levels of experimental N addition.

Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH₄ )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH₄ oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.

The response of methanotrophs to additions of either ammonium, nitrate or urea in alpine swamp meadow soil as revealed by stable isotope probing

Different forms of nitrogen (N) are deposited on the Qinghai-Tibetan plateau (QTP), while their differential effects on soil methanotrophs and their activity remain elusive. We constructed microcosms amended with different N fertilizers (ammonia, nitrate and urea) using the soils sampled from a swamp meadow on the QTP. The responses of active methanotrophs to different forms of nitrogen were determined by stable isotope probing with 5% 13C-methane. At the early stage of incubation, all N fertilizers, especially urea, suppressed methane oxidation compared with the control. The methane oxidation rate increased during the incubation, suggesting an adaptation and stimulation of some methanotrophs to elevated methane. At the onset of the incubation, the type II methanotrophs Methylocystis were most abundant, but decreased during the incubation and were replaced by the type Ia methanotrophs Methylomonas. Ammonia and urea had similar effects on the methanotroph communities, both characterized by an elevation in the proportion of Methylobacter and more diverse methanotroph communities. Nitrate had less effect on the methanotroph community. Our results uncovered the active methanotrophs responding to different nitrogen forms, and suggested that urea-N might have large effects on methanotroph diversity and activity in swamp meadow soils on the QTP.

Impact of Electron Acceptor Availability on Methane-Influenced Microorganisms in an Enrichment Culture Obtained From a Stratified Lake

Methanotrophs are of major importance in limiting methane emissions from lakes. They are known to preferably inhabit the oxycline of stratified water columns, often assumed due to an intolerance to atmospheric oxygen concentrations, but little is known on the response of methanotrophs to different oxygen concentrations as well as their preference for different electron acceptors. In this study, we enriched a methanotroph of the Methylobacter genus from the oxycline and the anoxic water column of a stratified lake, which was also present in the oxic water column in the winter. We tested the response of this Methylobacter-dominated enrichment culture to different electron acceptors, i.e., oxygen, nitrate, sulfate, and humic substances, and found that, in contrast to earlier results with water column incubations, oxygen was the preferred electron acceptor, leading to methane oxidation rates of 45–72 pmol cell⁻¹ day⁻¹. Despite the general assumption of methanotrophs preferring microaerobic conditions, methane oxidation was most efficient under high oxygen concentrations (>600 μM). Low (<30 μM) oxygen concentrations still supported methane oxidation, but no methane oxidation was observed with trace oxygen concentrations (<9 μM) or under anoxic conditions. Remarkably, the presence of nitrate stimulated methane oxidation rates under oxic conditions, raising the methane oxidation rates by 50% when compared to oxic incubations with ammonium. Under anoxic conditions, no net methane consumption was observed; however, methanotroph abundances were two to three times higher in incubations with nitrate and sulfate compared to anoxic incubations with ammonium as the nitrogen source. Metagenomic sequencing revealed the absence of a complete denitrification pathway in the dominant methanotroph Methylobacter, but the most abundant methylotroph Methylotenera seemed capable of denitrification, which can possibly play a role in the enhanced methane oxidation rates under nitrate-rich conditions.

Microbiomes inhabiting rice roots and rhizosphere

Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.

Ammonium Impacts Methane Oxidation and Methanotrophic Community in Freshwater Sediment

Lacustrine ecosystems are regarded as one of the important natural sources of greenhouse gas methane. Aerobic methane oxidation, carried out by methane-oxidizing bacteria, is a key process regulating methane emission. And ammonium is believed to greatly influence aerobic methane oxidation activity. To date, disagreement exists in the threshold of ammonium effect. Moreover, knowledge about how aerobic methanotrophic community composition and functional gene transcription respond to ammonium is still lacking. In the present study, microcosms with freshwater lake sediment were constructed to explore the effect of ammonium level on aerobic methanotrophs. Methane oxidation potential, and the density, diversity and composition of pmoA gene and its transcripts were examined during 2-week incubation. A negative impact of ammonium on aerobic methane oxidation potential and a positive impact on pmoA gene density were observed only at a very high level of ammonium. However, pmoA gene transcription increased notably at all ammonium levels. The composition of functional pmoA gene and transcripts were also influenced by ammonium. But a great shift was only observed in pmoA transcripts at the highest ammonium level.

A Gaseous Milieu: Extending the Boundaries of the Rhizosphere

Plant root activities shape microbial community functioning in the soil, making the rhizosphere the epicenter of soil biogeochemical processes. With this opinion article, we argue to rethink the rhizosphere boundaries: as gases can diffuse several centimeters away from the roots into the soil, the portion of soil influenced by root activities is larger than the strictly root-adhering soil. Indeed, gases are key drivers of biogeochemical processes due to their roles as energy sources or communication molecules, which has the potential to modify microbial community structure and functioning. In order to get a more holistic perspective on this key environment, we advocate for interdisciplinarity in rhizosphere research by combining knowledge of soluble compounds with gas dynamics.

Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields

Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.

Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota

BACKGROUND

Soils are a key component of agricultural productivity, and soil microbiota determine the availability of many essential plant nutrients. Agricultural domestication of soils, that is, the conversion of previously uncultivated soils to a cultivated state, is frequently accompanied by intensive monoculture, especially in the developing world. However, there is limited understanding of how continuous cultivation alters the structure of prokaryotic soil microbiota after soil domestication, including to what extent crop plants impact soil microbiota composition, and how changes in microbiota composition arising from cultivation affect crop performance.

RESULTS

We show here that continuous monoculture (> 8 growing seasons) of the major food crop rice under flooded conditions is associated with a pronounced shift in soil bacterial and archaeal microbiota structure towards a more consistent composition, thereby domesticating microbiota of previously uncultivated sites. Aside from the potential effects of agricultural cultivation practices, we provide evidence that rice plants themselves are important drivers of the domestication process, acting through selective enrichment of specific taxa, including methanogenic archaea, in their rhizosphere that differ from those of native plants growing in the same environment. Furthermore, we find that microbiota from soils domesticated by rice cultivation contribute to plant-soil feedback, by imparting a negative effect on rice seedling vigor.

CONCLUSIONS

Soil domestication through continuous monoculture cultivation of rice results in compositional changes in the soil microbiota, which are in part driven by the rice plants. The consequences include a negative impact on plant performance and increases in greenhouse gas emitting microbes.

Biochar can mitigate methane emissions by improving methanotrophs for prolonged period in fertilized paddy soils

Biochar application to fertilized paddy soils has been recommended as an effective countermeasure to mitigate methane (CH₄) emissions, but its mechanism and effective duration has not yet been adequately elucidated. A laboratory incubation experiment was performed to gain insight into the combined effects of fresh and six-year aged biochar on potential methane oxidation (PMO) in paddy soils with ammonium or nitrate-amendment. Results showed that both ammonium and nitrate were essential for CH₄ oxidation though high ammonium (4 mM) inhibited PMO as compared to low ammonium (1 mM and 2 mM), and that nitrate was better in promoting PMO than ammonium. Moreover, ammonium-amendment promoted type I pmoA, and nitrate-amendment enhanced type II pmoA abundance. Both fresh and aged biochar increased PMO as well as nitrification by enhancing the total, type I and type II methanotrophs as compared to the control. Increased soil PMO with mineral N input in both six-year aged biochar and fresh biochar amendment, indicating that biochar mitigated CH₄ by promoting PMO for prolonged period in fertilized paddy soils.

Effect of N dose on soil GHG emissions from a drip-fertigated olive (Olea europaea L.) orchard

Agronomic practices may mitigate greenhouse gas emissions (GHG) from crops. Appropriate nitrogen (N) and irrigation management provide the potential to reduce nitrous oxide (N₂O) and methane (CH₄) emissions. However, there is little information about the combination of both practices on the GHG emissions from olive orchards. This four-year study was conducted to qualitatively compare the effect of N doses applied through two drip irrigation strategies on N₂O and CH₄ emissions in a super-intensive (1010 trees ha^-1) olive orchard. The design (randomised blocks) was asymmetric: 0, 50 and 100 kg N ha^-1 yr^-1 were tested with full irrigation (FI; 2013 to 2016), but only 0 and 50 kg N ha^-1 yr^-1 were tested with regulated deficit irrigation (RDI; 2014 to 2016). The study shows that the soil acted as a main sink of N₂O and CH₄, regardless of the soil water content. Methane oxidation increased with N dose in the FI strategy (significant in 2013 and 2015). Overall, there was a tendency of yield to increase with the N dose without increasing emissions and without depending of the irrigation strategy. However, these results were not significant. Further confirmation of this tendency is necessary; particularly comparing FI + N100 (most promising treatment in terms of profitability) with the RDI + N100 (not available in this study) water-saving strategy.

Influence of Flooding, Salinization, and Soil Properties on Degradation of Chlorantraniliprole in California Rice Field Soils

Chlorantraniliprole (3-bromo-N-[4-chloro-2-methyl-6-(methylcarbamoyl)phenyl]-1-(3-chloro-2-pyridine-2-yl)-1H-pyrazole-5-carboxamide; CAP) was granted supplemental registration for use in rice cultivation in California through December, 2018. Previous work investigated the partitioning of CAP in California rice field soils; however, its degradation in soils under conditions relevant to California rice culture has not been investigated. The degradation of CAP in soils from two California rice fields was examined under aerobic and anaerobic conditions with varying salinity via microcosm experiments. Results indicate that soil properties governing bioavailability may have a greater influence on degradation than flooding practices or field salinization over a typical growing season. Differences between native and autoclaved soils (t_1/2 = 59.0-100.2 and 78.5-171.7 days) suggest that biological processes were primarily responsible for CAP degradation; however, future work should be done to confirm specific biotic processes as well as to elucidate abiotic processes, such as degradation via manganese oxides and formation of nonextractable residues, which may contribute to its dissipation.

Microbial mechanism underlying high and stable methane oxidation rates during mudflat reclamation with long-term rice cultivation: Illumina high-throughput sequencing-based data analysis

This study aimed to determine the methane oxidation rates (MOR), pmoA gene abundance and diversity, and microbial community composition using Illumina high-throughput sequencing. Mudflats located within Yancheng City, divided into different plots with 0-, 11-, and 20-year successive rice planting histories, were selected and sampled. The study found that the relative MOR (normalized with the 16S rRNA gene) increased dramatically after 11-year cultivation and remained stable in 20-year treatment, indicating that long-term rice cultivation in mudflats promoted MOR. The sequencing data analysis revealed that high MOR was related to the synergistic growth of methane-producing archaea (MPA) and aerobic and facultative methane-consuming bacteria (MCB) mainly belonging to Proteobacteria. Redundancy and correlation analyses showed that Methylophilaceae and Methylococcaceae affiliated within β- and γ-Proteobacterial methanotrophs were closely related to the relative MOR. Methane-oxidizing archaea (MOA) coupled to sulfate and nitrite reductions contributed more to the high and stable MOR compared with Proteobacterial MCB. Chloroflexi and Geobacter were the potential hydrogen donors for hydrogenotrophic MPA. The results showed that long-term rice cultivation in mudflats promoted the relative MOR. The unknown MOA coupled to sulfate and nitrite reductions, besides the necessary hydrogenotrophic MPA and their hydrogen donors (Chloroflexi and Geobacter) collectively contributed to methane cycling.

Effects of nitrogen loading on emission of carbon gases from estuarine tidal marshes with varying salinity

Estuarine tidal marshes sequester significant quantities of carbon and are suffering from anthropogenic nitrogen (N) enhancement. However, the effects of this N loading on carbon gas emissions from freshwater-oligohaline tidal marshes are unknown. In this paper, we report on our evaluation of the effects of a N gradient (0, 24, 48 and 96 g NH₄NO₃-N m^-2 y^-1) on the methane (CH₄) and carbon dioxide (CO₂) emissions from freshwater and oligohaline tidal marshes in the Min River estuary, southeast China. On an annual scale, the oligohaline marsh has significantly higher CO₂ emissions, while it has slightly lower CH₄ emissions relative to freshwater marsh. The addition of N increased CH₄ emission from the freshwater marsh and decreased CH₄ emission from the oligohaline marsh, although there was no statistically significant difference in CH₄ emission between either of the two marshes and the control. The addition of 96 g NH₄NO₃-N m^-2 y^-1 significantly increased CO₂ emission from the freshwater marsh, while it did not significantly influence CO₂ emission from the oligohaline marsh. CH₄ and CO₂ emission levels were positively correlated with soil temperature under all conditions. The CH₄ flux resulting from both the control and the addition of N was negatively correlated with porewater SO₄^2- and Cl^- concentrations and soil EC in the oligohaline marsh. Overall, N addition significantly increased carbon gas emissions under freshwater conditions while slightly inhibiting carbon gas emissions from the oligohaline marsh. Our findings suggested that even under low salinity conditions, the effects of N loading on CH₄ and CO₂ emissions from freshwater and oligohaline tidal marshes can vary. We propose that the addition of N to estuarine tidal marshes has a significant effect on the carbon cycle and promotes soil carbon loss, phenomena which may be influenced by salinity.

Soil nitrogen determines greenhouse gas emissions from northern peatlands under concurrent warming and vegetation shifting

Boreal peatlands store an enormous pool of soil carbon that is dependent upon - and vulnerable to changes in - climate, as well as plant community composition. However, how nutrient availability affects the effects of climate and vegetation change on ecosystem processes in these nutrient-poor ecosystems remains unclear. Here we show that although warming promoted higher CH4 emissions, the concurrent addition of N counteracted most (79%) of this effect. The regulation effects of the vegetation functional group, associated with the substrate quality, suggest that CH4 emissions from peatlands under future warming will be less than expected with predicted shrub expansion. In contrast, N2O flux will be enhanced under future warming with predicted shrub expansion. Our study suggests that changes in greenhouse gas emissions in response to future warming and shifts in plant community composition depend on N availability, which reveals the complex interactions that occur when N is not a limiting nutrient.

Unimodal Response of Soil Methane Consumption to Increasing Nitrogen Additions

Nitrogen (N) status has a great impact on methane (CH₄) consumption by soils. Modeling studies predicting soil CH₄ consumption assume a linear relationship between CH₄ uptake and N addition rate. Here, we present evidence that a nonlinear relationship may better characterize changes in soil CH₄ uptake with increasing N additions. By conducting a field experiment with eight N-input levels in a Tibetan alpine steppe, we observed a unimodal relationship; CH₄ uptake increased at low to medium N levels but declined at high N levels. Environmental and microbial properties jointly determined this response pattern. The generality of the unimodal trend was further validated by two independent analyses: (i) we examined soil CH₄ uptake across at least five N-input levels in upland ecosystems across China. A unimodal CH₄ uptake-N addition rate relationship was observed in 3 out of 4 cases; and (ii) we performed a meta-analysis to explore the N-induced changes in soil CH₄ uptake with increasing N additions across global upland ecosystems. Results showed that the changes in CH₄ uptake exhibited a quadratic correlation with N addition rate. Overall, we suggest that the unimodal relationship should be considered in biogeochemistry models for accurately predicting soil CH₄ consumption under global N enrichment.

Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland)

Methanotrophic bacteria are able to use methane (CH₄) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH₄ oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH₄ oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.