Manure amendment increased the abundance of methanogens and methanotrophs but suppressed the type I methanotrophs in rice paddies

The interplay of soil physicochemical properties, methanogenic diversity, and abundance governs methane production potential in paddy soil subjected to multi-decadal straw incorporation

Straw incorporation holds significant promise for enhancing soil fertility and mitigating air pollution stemming from straw burning. However, this practice concurrently elevates the production and emission of methane (CH4) from paddy ecosystems. Despite its environmental impact, the precise mechanisms behind the heightened CH4 production resulting from long-term straw incorporation remain elusive. In a 32-year field experiment featuring three fertilization treatments (CFS-chemical fertilizer with wheat straw, CF-chemical fertilizer, and CK-unamended), we investigated the impact of abiotic (soil physicochemical properties) and biotic (methanogenic abundance, diversity, and community composition) factors on CH4 production in paddy fields. Results revealed a significantly higher CH4 production potential under CFS treatment compared to CF and CK treatments. The partial least squares path model revealed that soil physicochemical properties (path coefficient = 0.61), methanogenic diversity (path coefficient = -0.43), and methanogenic abundance (path coefficient = 0.29) collectively determined CH4 production potential, explaining 77% of the variance. Enhanced soil organic carbon content and water content, resulting from straw incorporation, emerged as pivotal factors positively correlated with CH4 production potential. Under CFS treatment, lower Shannon index of methanogens, compared to CF and CK treatments, was attributed to increased Methanosarcina. Notably, the Shannon index and relative abundance of Methanosarcina exhibited negative and positive correlations with CH4 production potential, respectively. Methanogenic abundance, bolstered by straw incorporation, significantly amplified overall potential. This comprehensive analysis underscores the joint influence of abiotic and biotic factors in regulating CH4 production potential during multi-decadal straw incorporation.

Global Atlas of Methane Metabolism Marker Genes in Soil

Methane, a greenhouse gas, plays a pivotal role in the global carbon cycle, influencing the Earth's climate. Only a limited number of microorganisms control the flux of biologically produced methane in nature, including methane-oxidizing bacteria, anaerobic methanotrophic archaea, and methanogenic archaea. Although previous studies have revealed the spatial and temporal distribution characteristics of methane-metabolizing microorganisms in local regions by using the marker genes pmoA or mcrA, their biogeographical patterns and environmental drivers remain largely unknown at a global scale. Here, we used 3419 metagenomes generated from georeferenced soil samples to examine the global patterns of methane metabolism marker gene abundances in soil, which generally represent the global distribution of methane-metabolizing microorganisms. The resulting maps revealed notable latitudinal trends in the abundances of methane-metabolizing microorganisms across global soils, with higher abundances in the sub-Arctic, sub-Antarctic, and tropical rainforest regions than in temperate regions. The variations in global abundances of methane-metabolizing microorganisms were primarily governed by vegetation cover. Our high-resolution global maps of methane-metabolizing microorganisms will provide valuable information for the prediction of biogenic methane emissions under current and future climate scenarios.

Equal importance of humic acids and nitrate in driving anaerobic oxidation of methane in paddy soils

Methane (CH4) is both generated and consumed in paddy soils, where anaerobic oxidation of methane (AOM) serves as a crucial process for mitigating CH4 emissions. Although the participation of humic acids (HA) and nitrate in AOM has been recognized, their relative roles and significance in paddy soils remain insufficiently investigated. In this study, we explored the potential activity of AOM driven by HA and nitrate, as well as the composition of archaeal communities in paddy soils across different rice growth periods and fertilization treatments. AOM activity ranged from 0.81 to 1.33 and 1.26 to 2.38 nmol of 13CO2 g-1 (dry soil) day-1 with HA and nitrate, respectively. No significant differences (p < 0.05) were observed between the AOM activity driven by HA and nitrate across the three fertilization treatments. According to AOM activity, the annual consumption of CH4 was estimated at approximately 0.49 ± 0.06 and 0.83 ± 0.19 Tg for AOM processes driven by HA and nitrate in Chinese paddy soils. Nitrate-driven AOM activity exhibited a positive (p < 0.05) correlation with the abundance of the ANME-2d mcrA gene but a negative (p < 0.05) correlation with the content of dissolved organic carbon. Intriguingly, HA-driven AOM activity was only correlated positively with the nitrate-driven AOM activity. Soil water content, soil organic carbon, nitrate and nitrite contents were significantly correlated with the relative abundance of methanogenic and methanotrophic archaea. These results identified the potential importance of HA and nitrate in driving AOM processes within paddy soils, providing a comprehensive understanding of the complex microbial processes regulating greenhouse gas emissions from paddy soils.

Soil organic carbon regulates CH4 production through methanogenic evenness and available phosphorus under different straw managements

Methane (CH₄) is the main greenhouse gas emitted from rice paddy fields driven by methanogens, for which methanogenic abundance on CH₄ production has been intensively investigated. However, information is limited about the relationship between methanogenic diversity (e.g., richness and evenness) and CH₄ production. Three independent field experiments with different straw managements including returning method, burial depth, and burial amount were used to identify the effects of methanogenic diversity on CH₄ production, and its regulating factors from soil properties in a rice-wheat cropping system. The results showed that methanogenic evenness (dominance) can explain 23% of variations in CH₄ production potential. CH₄ production potential was positively related to methanogenic evenness (R² = 0.310, p < 0.001), which is driven by soil organic carbon (SOC), available phosphorus (AP), and nitrate (NO₃^-) through structure equation model (SEM). These findings indicate that methanogenic evenness has a critical role in evaluating the responses of CH₄ production to agricultural practices following changes in soil properties. The SEM also revealed that SOC concentration influenced CH₄ production potential indirectly via complementarity of methanogenic evenness (dominance) and available phosphorus (AP). Increasing SOC accumulation improved AP release and stimulated CH₄ production when SOC was at a low level, whereas decreased evenness and suppressed CH₄ production when SOC was at a high level. A nonlinear relationship was detected between SOC and CH₄ production potential, and CH₄ production potential decreased when SOC was ≥14.16 g kg^-1. Our results indicated that the higher SOC sequestration can not only mitigate CO₂ emissions directly but CH₄ emissions indirectly, highlighting the importance to enhance SOC sequestration using optimum agricultural practices in a rice-wheat cropping system.

Interaction mechanism between chlorinated polyfluoroalkyl ether potassium sulfonate (F-53B) and chromium on different types of soil surfaces

The coexistence of per- and polyfluoroalkyl substances (PFASs) and heavy metals have been found in soils. However, the interaction between the combined pollutants in soils remains unclear. In this study, the adsorption processes of single and combined Cr(VI) and chlorinated polyfluoroalkyl ether potassium sulfonate (F-53 B) in red, yellow and black soils were simulated. When compared with the single F-53 B and Cr(VI), the adsorption amount of the combined F-53 B and Cr(VI) on soils changed with the types of soils. The interactions between F-53 B and Cr(VI) in soils affected their adsorption behavior. The adsorption of the combined F-53 B and Cr(VI) best fit second-order kinetics and the Freundlich equation. Moreover, aluminum and iron oxides are highly correlated with adsorption of F-53 B and Cr(VI). Both F-53 B and Cr(VI) can form complexes with aluminum and iron oxides through electrostatic interactions, but PFOS could be bridged with iron oxides to form an inner sphere complex and with aluminum oxides to form an outer sphere complex. The coexistence of F-53 B and Cr(VI) could change the fluorescent group of dissolved organic matter (DOM) in soils due to the complexation between F-53 B and DOM. In addition, F-53 B increased the acid-soluble portion of Cr and decreased its residual form, which promoted the environmental risk of Cr in soils.

Temporal variation of the coupling relationship between methanogens and biogeochemical process in soil-microbes-rice system

Microbial community were most resilient option for methane associated mitigation strategies. Biogas slurry provides plant nutrition and affects microbial community. However, little is known about the changes of the functional guilds (methanogen and methanotroph) in the geochemical context after addition biogas slurry. For this purpose, a pot experiment was conducted. Six treatment groups were included in this study, four with biogas slurry: water ratio (1:4, T02; 2:3, T04; 3:2, T06; 4:1, T08), one with a chemical fertilizer (F), and a control (CK). The effective tiller and biomass significantly increased by 1.9 times and 2.1 times in T02 relative to CK. The relative abundance of Bacteroidetes in the biogas slurry treatments was 31.5%, while that in CK was 11.4%. The dominant methanogens in CK, F and treatments were different at heading and mature stages. CK and F were hydrogenotrophs with relative abundance of 0.09% and 0.06%, and the treatment group was acetotrophs with mean value of 1.21% at heading stage. Compared with CK, the number of methanotrophs in the treatments at heading stage increased by 4.1 times, while that at mature increased by 10.3 times. The methanogenic community in the treatments may be shaped by the amount of biogas slurry applied rather than by biogeochemical processes at heading stage. Nevertheless, there may be existed synergistic interaction in the soil-microbes-rice system at mature stage. These findings may provide a better understanding of regulating soil respiration in agricultural land.

Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils

The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH₄ ) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance and community composition of M. oxyfera-like bacteria were investigated in paddy fields under three long-term (32 years) fertilization treatments, i.e. unfertilized control (CK), chemical fertilization (NPK) and straw incorporation with chemical fertilization (SNPK). Relative to the CK, both NPK and SNPK treatments significantly (p < 0.05) increased the potential n-damo activity (88%-110%) and the abundance (52%-105%) of M. oxyfera-like bacteria. The variation of soil organic carbon (OrgC) content and inorganic nitrogen content caused by the input of chemical fertilizers and straw returning were identified as the key factors affecting the potential n-damo activity and the abundance of M. oxyfera-like bacteria. However, the community composition and diversity of M. oxyfera-like bacteria did not change significantly by the input of fertilizers. Overall, our results provide the first evidence that long-term fertilization greatly stimulates the n-damo process, indicating its active role in controlling CH₄ emissions from paddy fields.

Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary

Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH₄⁺ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.

Methane mitigation is associated with reduced abundance of methanogenic and methanotrophic communities in paddy soils continuously sub-irrigated with treated wastewater

Herein, we examined emissions of CH₄ and the community structures of methanogenic archaea and methanotrophic bacteria in paddy soils subjected to a novel irrigation system, namely continuous sub-irrigation with treated wastewater (TWW). This system has recently been developed by our group to effectively reuse TWW for the cultivation of protein-rich rice. The results showed that, despite not using mineral fertilisers, the wastewater reuse system produced a rice yield comparable to that of a conventional cultivation practice and reduced CH₄ emissions from paddy fields by 80%. Continuous sub-irrigation with TWW significantly inhibited the growth of methanogens in the lower soil layer during the reproductive stage of rice plants, which was strongly consistent with the effective CH₄ mitigation, resulting in a vast reduction in the abundance of methanotrophs in the upper soil layer. The compositions of the examined microbial communities were not particularly affected by the studied cultivation practices. Overall, this study demonstrated that continuous sub-irrigation with TWW was an effective method to produce high rice yield and simultaneously reduce CH₄ emissions from paddy fields, and it also highlighted the potential underlying microbial mechanisms of the greenhouse gas mitigation.