Search Results (31)

The dynamics of methane (CH₄), nitrous oxide (N₂O) and carbon dioxide (CO₂) in groundwater have rarely been investigated. As dissolved gases they may be transported to distant sites and, hence, to the atmosphere. Crumps Cave (CC) is located on a perched aquifer in south-central Kentucky. Water was sampled at a waterfall within the cave located 15 m below the surface, at two adjacent surface wells 15 m and 50 m deep, providing samples from the epikarst and regional aquifer, respectively. Dissolved gases and geochemistry parameters were analyzed for seasonal changes across three years of weekly monitoring (2015–2017) using Kruskal–Wallis H tests and Bonferroni-corrected pairwise comparisons. Dissolved CO₂ concentrations are mainly controlled by percolation through the epikarst, influenced by soil respiration, and vary with rainfall and seasonal temperature fluctuations. CH₄ showed a site-dependent pattern: concentrations were significantly elevated in warm seasons at the shallow and deep wells, where anaerobic conditions and agriculturally derived organic matter promote methanogenesis; no seasonal variation was detected at the cave site, where oxic conditions limit CH₄ year-round. N₂O was significantly elevated in cold seasons at all three sites, driven by cold-season denitrification of agriculturally derived nitrates. N₂O did not differ between sites, indicating seasonal temperature-driven denitrification as the primary control rather than site hydrology, with cold-season denitrification of agriculturally derived nitrates from fertilizer application. Indirect gas emissions are characteristic of karst systems and may be transported or stored in aquifers through complex interactions of groundwater recharge, microbial activity, and seasonal land-use variability. Full article

For soil processes that are known to be temporally dynamic, such as soil respiration, methanogenesis, and nitrification–denitrification, it is challenging to capture temporal variations with field-portable greenhouse gas (GHG) analyzers to provide the most accurate estimates of season-long GHG emissions and global warming potentials (GWPs). The objective of this field study was to evaluate the effects of measurement frequency (i.e., weekly, every other week, and every third week), replication (i.e., three, four, or five), and their interaction on the consistency of season-long carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) emissions and GWP estimates across multiple ecosystems. Results are based on direct, in-field measurements with a field-portable gas analyzer. Field research was conducted throughout the 2024 growing season in a minimally grazed pasture, tallgrass prairie, soybean under conventional and conservation management practices, and cotton under conservation management in Arkansas, USA. Season-long CO₂ emissions and GWP from the tallgrass prairie were 1.1 times (12%) greater from the weekly and every-other-week (16.9 and 17.0 Mg ha⁻¹, respectively), which did not differ, than the every-third-week (14.2 and 14.2 Mg ha⁻¹, respectively) measurement frequencies. Season-long CH₄ emissions from the minimally grazed pasture and conservation-tilled soybean system were ≥7.5 times greater with four and five replications, which did not differ, than with three replications. Global warming potential in the conservation-tilled soybean (13.9 Mg ha⁻¹) and conservation-tilled cotton (21.1 Mg ha⁻¹) systems were ≥1.1 times (13%) greater with the every-third-week than with the weekly data set. Though this study was somewhat limited due the data sub-setting approach used, even using current, state-of-the-art, field-portable GHG analyzers, an appropriate in-field measurement frequency and number of spatial replications should be considered to reliably quantify whole-field, season-long GHG emissions and GWP estimates. Full article

Greenhouse gas generated from wastewater treatment plants has attracted much attention as it has the potential to be recovered and used as an energy source. In this study, a membrane biofilm reactor was designed to simultaneously enhance nitrate removal and reduce methane (CH₄) emissions during methane oxidation coupled with the denitrification process. The enrichment of CH₄-driven denitrification microbes with a relatively short hydraulic retention time (HRT) and its effects on the stable operation of the reactor were studied within 250 d. With an increasing HRT from 8 to 20 h, a removal rate of up to approximately 0.51 mg/L·h⁻¹ was achieved, which also kept the effluent NO₂⁻-N below 0.5 mg/L. Microbial community analysis showed that the diversity and uniformity of microorganism communities decreased with the addition of CH₄ as a carbon source, and the microbial structure changed significantly. Compared with that of seed sludge at the phylum level, the relative abundance of Proteobacteria increased significantly, Alphaproteobacteria and Sphingobacteriia continued to become enriched, and the abundance of Methylocystis increased significantly. Neither denitrifying anaerobic methane oxidation (DAMO) archaea nor bacteria were found in the sequencing analysis. Methylocystis was the dominant CH₄ oxidizing bacteria, in synergy with the co-occurrence of autotrophic and heterotrophic denitrifying bacteria, which likely join up in nitrogen removal. Unlike the systems described in most methane-driven denitrification studies, our system achieved nitrate removal without detectable DAMO microbes. Full article

In permanently submerged coastal wetlands, interactions between biogeochemical processes and microbial communities strongly influence greenhouse gas (GHG) fluxes. To improve our understanding of how redox-driven processes shape GHG dynamics in these ecosystems, we investigated the relationships among iron (Fe) pools, microbial dynamics, and the potential GHG production in subaqueous soils from an interdunal wetland in San Vitale Park (Italy), permanently submerged and affected by seasonal oscillations of the saline water table. Two subaqueous soil columns (WAS-2 and WAS-4), collected from similar settings, were analyzed. Surface layers of WAS-4 showed higher salinity and carbonate content, whereas WAS-2 was characterized by overall higher Fe concentrations. Distinct vertical distributions of organic matter and sulfur (S) were shown along depth. Laboratory incubations revealed that nitrous oxide (N₂O) production was up to ten times higher in WAS-2 than in WAS-4, with peaks in the top 13–14 cm, consistent with more active nitrification-denitrification in surface layers. Methane (CH₄) and carbon dioxide (CO₂) fluxes decreased with depth, reflecting reduced availability of labile carbon. Methanomicrobiales dominated CH₄-producing layers, indicating hydrogenotrophic methanogenesis, while amoA-carrying Nitrosomonadales and Thaumarchaeota, occurred in shallow, organic-rich layers where ammonia supported nitrification and denitrification. Denitrifiers mainly belonged to α- and β-Proteobacteria, consistent with their direct contribution to N₂O peaks. Spearman’s correlations showed N₂O positively correlated to sulfur and labile carbon (C), supporting denitrification under moderately reducing conditions. CH₄ and CO₂ positively correlated with organic C (Corg), total nitrogen (TN), and reactive Fe forms, reflecting redox-mediated microbial respiration and methanogenesis. Trace elements (B, Cr, Cu, Ni) acted as micronutrients or inhibitors depending on concentration. Canonical correspondence analysis indicated depth-structured links among gas fluxes, soil chemistry (Corg, TN, S/C, CaCO₃, P), and microbial distributions: surface layers, rich in labile C and nutrients, supported active bacteria and archaea involved in decomposition, nitrification, and denitrification, whereas deeper layers hosted oligotrophic archaea adapted to inorganic substrates. Overall, Fe pools appeared to be associated with soil processes relevant to GHG dynamics, although the extent of their regulatory role remains uncertain due to potential alterations of redox-sensitive Fe fractions during sample handling. These results contribute to broader efforts to predict GHG emissions in submerged wetland soils by linking redox stratification, inorganic chemistry, and microbial functional groups. Full article

Piggery farming is the largest source of livestock manure in South Korea, yet greenhouse gas (GHG) data from piggery wastewater treatment systems remain limited. This study quantified methane (CH₄) and nitrous oxide (N₂O) fluxes from a full-scale treatment facility to develop stage-, seasonal-, and diurnal-specific emission factors. Continuous laser-based monitoring using a PVC air-pool chamber was applied across raw wastewater storage, an anoxic nitrogen-conversion reactor, and strongly aerated nitrification units. Mean CH₄ fluxes ranged from 1.1 to 15.6 mg s⁻¹ m⁻² peaking in summer, while N₂O fluxes ranged from 0.01 to 17,971 mg s⁻¹ m⁻², with maxima in fall. Emissions were dominated by two functional zones: aerated basins where vigorous mixing enhanced CH₄ stripping, and an upstream anoxic reactor where oxygen instability and nitrite accumulation produced extreme N₂O peaks. Derived emission factors were 0.11 kg CH₄ head⁻¹ yr⁻¹ and 45.2 kg N₂O head⁻¹ yr⁻¹, equivalent to 3.1 and 12,300 kg CO₂-eq head⁻¹ yr⁻¹. CH₄ variability was controlled mainly by treatment stage and temperature, whereas N₂O was governed by internal redox conditions. These results refine emission factors for inventories and underscore the need for improved aeration stability and denitrification control to reduce GHG emissions from piggery wastewater systems. Full article

Heavy metals accumulate in forest soils worldwide, yet their effects on greenhouse gas dynamics remain poorly understood. Mycorrhizal fungi lie at the heart of this issue. These symbiotic organisms regulate carbon and nutrient flow between trees and soil, positioning them to influence fluxes of CO₂, N₂O, and CH₄. However, research on mycorrhizal ecology, metal toxicology, and greenhouse gas biogeochemistry has proceeded largely in isolation. This review bridges these fields through a conceptual framework built on three contamination scenarios and four mechanistic pathways. Our confidence in these mechanisms varies by gas: well-established for CO₂, developing for N₂O, and mostly inferential for CH₄. Critical gaps remain. Studies measuring mycorrhizal communities, metal availability, and gas emissions simultaneously are rare. Comparisons between ectomycorrhizal and arbuscular mycorrhizal systems are virtually absent. This framework establishes a basis for understanding how metal-contaminated forests regulate greenhouse gas exchange and identifies priority areas for future investigation. Full article

Straw returning is a critical practice with profound strategic importance for sustainable agricultural development. However, within a comprehensive soil health evaluation framework, research analyzing the impact of tobacco straw returning on soil ecosystem health from the perspectives of microbial taxa and functional genes remains insufficient. To investigate the effects of tobacco straw returning on virulence factor genes (VFGs), methane-cycling genes (MCGs), nitrogen-cycling genes (NCGs), carbohydrate-active enzyme genes (CAZyGs), antibiotic resistance genes (ARGs), and their host microorganisms in soil, this study collected soil samples from a long-term tobacco-rice rotation field with continuous tobacco straw incorporation in Shaowu City, Fujian Province. Metagenomic high-throughput sequencing was performed on the samples. The results demonstrated that long-term tobacco straw returning influenced the diversity of soil VFGs, MCGs, NCGs, CAZyGs, ARGs, and their host microorganisms, with richness significantly increasing compared to the CK treatment (p < 0.05). In the microbially mediated methane cycle, long-term tobacco straw returning resulted in a significant decrease in the abundance of the key methanogenesis gene mttB and the methanogenic archaeon Methanosarcina, along with a reduced mtaB/pmoA functional gene abundance ratio compared to CK. This suggests enhanced CH₄ oxidation in the tobacco-rice rotation field under straw returning. Notably, the abundance of plant pathogens increased significantly under tobacco straw returning. Furthermore, a significantly higher norB/nosZ functional gene abundance ratio was observed, indicating a reduced capacity of soil microorganisms to convert N₂O in the tobacco-rice rotation field under straw amendment. Based on the observation that the full-rate tobacco straw returning treatment (JT2) resulted in the lowest abundances of functional genes prkC, stkP, mttB, and the highest abundances of nirK, norB, malZ, and bglX, it can be concluded that shifts in soil physicochemical properties and energy substrates drove a transition in microbial metabolic strategies. This transition is characterized by a decreased pathogenic potential of soil bacteria, alongside an enhanced potential for microbial denitrification and cellulose degradation. Non-parametric analysis of matrix correlations revealed that soil organic carbon, dissolved organic carbon, alkaline-hydrolyzable nitrogen, available phosphorus, and available potassium were significantly correlated with the composition of soil functional groups (p < 0.05). In conclusion, long-term tobacco straw returning may increase the risk of soil-borne diseases in tobacco-rice rotation systems while potentially elevating N₂O and reducing CH₄ greenhouse gas emission rates. Analysis of functional gene abundance changes identified the full-rate tobacco straw returning treatment as the most effective among all treatments. Full article

Long-term positioning tests can systematically reveal the evolution characteristics of soil fertility and crop productivity, and reflect the spatiotemporal changes in soil quality and their driving factors. While soil microorganisms mediating nutrient cycling are crucial for maintaining crop productivity and the long-term resilience of agricultural ecosystems, how prolonged use of different fertilization strategies affects their functional capacity remains insufficiently understood. In this study, we applied metagenomic sequencing to investigate how three fertilization treatments, namely (i) N0 receiving only phosphorus (P) and potassium (K) fertilizers, (ii) N250 receiving conventional urea + P and K, and (iii) F250 receiving humic acid urea + P and K, influence soil microbial communities, functional genes related to C and N cycling, and associated soil properties in a long-term field experiment. The F250 treatment significantly increased average annual yields of wheat and maize to 7166.21 kg hm⁻² and 8309.96 kg hm⁻², respectively. These values were 148.66% and 73.47% higher than those under N0, and 8.22% and 11.64% higher than those under N250. Compared with N0, both N250 and F250 signally augmented soil nitrate, ammonium, total nitrogen (TN), and soil organic carbon (SOC), altered microbial community composition, and enhanced the relative abundance of genes engaged in C fixation and methane oxidation. Both treatments also promoted denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Relative to N250, F250 specifically enriched the beneficial bacterial genus Pedobacter, further increased the abundance of the C fixation gene pccA, and markedly upregulated the DNRA gene nrfA. Soil TN and SOC were identified as the key environmental factors regulating microbial community structure and the functional potential of C and N cycling pathways. Collectively, our findings provide a mechanistic understanding of how long-term application of humic acid urea enhances crop productivity by modulating the genetic potential of soil microorganisms in biogeochemical cycles, offering a biological foundation for optimizing fertilization strategies in sustainable agriculture. Full article

A novel species of the genus Methylocystis is proposed based on polyphasic evidence from strain SC2^T, isolated from the heavily polluted Saale River near Wichmar, Germany. Digital DNA–DNA hybridization and phylogenomic analyses demonstrate that strain SC2^T represents a distinct species within the genus, clearly separated from its closest relatives, namely Methylocystis suflitae NLS-7^T, Methylocystis rosea SV97^T, Methylocystis silviterrae FS^T, and Methylocystis hirsuta CSC1^T. As is typical of the family Methylocystaceae, cells possess intracytoplasmic membranes arranged parallel to the cytoplasmic membrane, and the dominant fatty acids are C18:1ω8c and C18:1ω7c. The strain grows aerobically on methane as the primary carbon and energy source and expresses both low- and high-affinity particulate methane monooxygenase (pMMO), but lacks the soluble form. The species epithet reflects the strain’s ability to utilize hydrogen as an alternative energy source. A further feature is its use of asparagine as an osmoprotectant, enhancing salt tolerance. Genomic analysis reveals complete pathways for nitrogen fixation, denitrification, and hydrogen oxidation. These genetic and physiological characteristics support the designation of a novel species, for which the name Methylocystis hydrogenophila sp. nov. is proposed. The type strain is SC2^T (=DSM 114506 = NCIMB 15437). Full article

As an important agricultural ecosystem, greenhouse gas (GHG) emissions and arsenic (As) mobilization in rice paddy fields have gained significant attention on climate change and food safety. There is a certain correlation between the GHG and As migration in rice paddy fields. The oxidation of methane in paddy fields can provide electrons for the reduction and release of arsenate. Nitrate in rice paddy soil can promote the fixation of As by oxidizing Fe (II) to form iron oxide–As complexes or directly oxidize As (III) to As (V) to reduce the toxicity of As. However, incomplete denitrification of nitrate can lead to the emission of N₂O. This review systematically expounds the research advances, influencing factors and simultaneous mitigation measures of GHG emissions and As mobilization in rice paddy fields. It focuses on discussing the influence mechanisms of soil physical and chemical properties, water management measures, fertilization methods, and the addition of soil conditioner on As migration and GHG emission, and it looks forward to future research directions. It aims to provide a theoretical basis and practical guidance for reducing the risk of As contamination in rice fields, reducing GHG emission, and achieving sustainable development of rice production. Full article

In response to increasingly stringent emission regulations, low-carbon fuels have received significant attention as sustainable energy sources for internal combustion engines. This study investigates four representative low-carbon fuels, methane, methanol, hydrogen, and ammonia, by systematically summarizing their combustion characteristics and emission profiles, along with a review of existing after-treatment technologies tailored to each fuel type. For methane engines, unburned hydrocarbon (UHC) produced during low-temperature combustion exhibits poor oxidation reactivity, necessitating integration of oxidation strategies such as diesel oxidation catalyst (DOC), particulate oxidation catalyst (POC), ozone-assisted oxidation, and zoned catalyst coatings to improve purification efficiency. Methanol combustion under low-temperature conditions tends to produce formaldehyde and other UHCs. Due to the lack of dedicated after-treatment systems, pollutant control currently relies on general-purpose catalysts such as three-way catalyst (TWC), DOC, and POC. Although hydrogen combustion is carbon-free, its high combustion temperature often leads to elevated nitrogen oxide (NO_x) emissions, requiring a combination of optimized hydrogen supply strategies and selective catalytic reduction (SCR)-based denitrification systems. Similarly, while ammonia offers carbon-free combustion and benefits from easier storage and transportation, its practical application is hindered by several challenges, including low ignitability, high toxicity, and notable NO_x emissions compared to conventional fuels. Current exhaust treatment for ammonia-fueled engines primarily depends on SCR, selective catalytic reduction-coated diesel particulate filter (SDPF). Emerging NO_x purification technologies, such as integrated NO_x reduction via hydrogen or ammonia fuel utilization, still face challenges of stability and narrow effective temperatures. Full article

The Okinawa Trough (OT) has been a focus of scientific research for many years due to the presence of vibrant hydrothermal and cold seep activity within its narrow basin. However, the spatial distribution and environmental drivers of microbial communities in OT sediments remain poorly understood. The present study aims to address this knowledge gap by investigating microbial diversity and abundance at ten different sampling sites in a transitional zone between hydrothermal vents and cold seeps in the OT. The microbial community at two sampling sites (G08 and G09) in close proximity to hydrothermal vents showed a high degree of similarity. However, lower bacterial and archaeal abundances were found in these sites. The archaeal groups, classified as Hydrothermarchaeota and Thermoplasmata, showed a comparatively higher relative abundance at these sites. In addition, ammonia-oxidizing archaea (AOA), from the family Nitrosopumilaceae, were found to have a higher relative abundance in the OT surface sediments at sampling sites G03, G04, G05, G06, and G07. This result suggests that ammonia oxidation may be actively occurring in these areas. Furthermore, Methylomirabilaceae, which are responsible for methane oxidation coupled with nitrite reduction, dominated three sampling sites (G07, G08, and G09), implying that N-DAMO may play an important role in mitigating methane emissions. Using the FAPROTAX database, we found that predicted prokaryotic microbial functional groups involved in methyl-reducing methanogenesis and hydrogenotrophic methanogenesis were most abundant at sites G08 and G09. At sampling sites G01 and G02, functional groups such as hydrocarbon degradation, methanotrophy, methanol oxidation, denitrification, sulfate respiration, and sulfur oxidation were more abundant. Nitrogen content is the most important environmental factor determining the bacterial and archaeal communities in the OT surface sediments. These results expand our knowledge of the spatial distribution of microbial communities in the transitional zone between hydrothermal vents and cold seeps in the OT. Full article

The contribution of denitrifying anaerobic methane oxidation (DAMO) as a methane sink across different habitats, especially those affected by anthropogenic activities, remains unclear. Mining and industrial and domestic use of metals/metal-containing compounds can all cause metal contamination in freshwater ecosystems. Precipitation of metal ions often limits their toxicity to local microorganisms, yet microbial activity may also cause the redissolution of various precipitates. In contrast to most other studies that apply soluble metal compounds, this study investigated the responses of enriched DAMO culture to model insoluble copper compounds, malachite and covellite, in simulated sedimentary environments. Copper ≤ 0.22 µm from covellite appeared to cause immediate inhibition in 10 h. Long-term tests (54 days) showed that apparent methane consumption was less impacted by various levels of malachite and covellite than soluble copper. However, the medium-/high-level malachite and covellite caused a 46.6–77.4% decline in denitrification and also induced significant death of the representative DAMO microorganisms. Some enriched species, such as Methylobacter tundripaludum, may have conducted DAMO or they may have oxidized methane aerobically using oxygen released by DAMO bacteria. Quantitative polymerase chain reaction analysis suggests that Candidatus Methanoperedens spp. were less affected by covellite as compared to malachite while Candidatus Methylomirabilis spp. responded similarly to the two compounds. Under the stress induced by copper, DAMO archaea, Planctomycetes spp. or Phenylobacterium spp. synthesized PHA/PHB-like compounds, rendering incomplete methane oxidation. Overall, the findings suggest that while DAMO activity may persist in ecosystems previously exposed to copper pollution, long-term methane abatement capability may be impaired due to a shift of the microbial community or the inhibition of representative DAMO microorganisms. Full article

Large-scale and multi-sample datasets have revealed that microbial diversity and geographic distribution patterns are distinct across various habitats, particularly between hydrothermal vent and cold seep ecosystems. To date, our understanding of the effects of spatial and geochemical gradients on marine microbial communities remains limited. Here, we report the microbial diversity and metabolic versatility of a remote seafloor sediment ecosystem at different sites (GC-2, -4, -5, -6, -8) in the Mid-Okinawa Trough (Mid-OT) using high-throughput metagenomic sequencing technology. Desulfobacteraceae (3.1%) were detected in a high abundance at GC-2 with intense methane concentrations (353 μL/L), which showed a clear correlation with cold seeping. Whereas Candidatus Brocadiaceae (1.7%), Rhodobacteraceae (0.9%), and Rhodospirillaceae (0.7%), which are commonly involved in denitrification and sulfur oxidation, were enriched at GC-8. Concurrently investigating the potential of deep-sea microbial metabolism, we gained insights into the adaptive capabilities and metabolic mechanisms of microorganisms within seafloor environments. Utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the analysis of functional modules revealed a significant enrichment (71–74%) of genes associated with metabolic pathways. These results expand our knowledge of the relationship between microbial biodiversity and metabolic versatility in deep-sea extreme environments. Full article

Anaerobic digestion (AD) produces useful biogas and waste streams with high levels of dissolved methane (CH₄) and ammonium (NH₄⁺), among other nutrients. Membrane biofilm reactors (MBfRs), which support dissolved methane oxidation in the same reactor as simultaneous nitrification and denitrification (ME-SND), are a potential bubble-less treatment method. Here, we demonstrate ME-SND taking place in single-stage, AD digestate liquid-fed MBfRs, where oxygen (O₂) and supplemental CH₄ were delivered via pressurized membranes. The effects of two O₂ pressures, leading to different O₂ fluxes, on CH₄ and N removal were examined. MBfRs achieved up to 98% and 67% CH₄ and N removal efficiencies, respectively. The maximum N removal rates ranged from 57 to 94 mg N L⁻¹ d⁻¹, with higher overall rates observed in reactors with lower O₂ pressures. The higher-O₂-flux condition showed NO₂⁻ as a partial nitrification endpoint, with a lower total N removal rate due to low N₂ gas production compared to lower-O₂-pressure reactors, which favored complete nitrification and denitrification. Membrane biofilm 16S rRNA amplicon sequencing showed an abundance of aerobic methanotrophs (especially Methylobacter, Methylomonas, and Methylotenera) and enrichment of nitrifiers (especially Nitrosomonas and Nitrospira) and anammox bacteria (especially Ca. Annamoxoglobus and Ca. Brocadia) in high-O₂ and low-O₂ reactors, respectively. Supplementation of the influent with nitrite supported evidence that anammox bacteria in the low-O₂ condition were nitrite-limited. This work highlights coupling of aerobic methanotrophy and nitrogen removal in AD digestate-fed reactors, demonstrating the potential application of ME-SND in MBfRs for the treatment of AD’s residual liquids and wastewater. Sensor-based tuning of membrane O₂ pressure holds promise for the optimization of bubble-less treatment of excess CH₄ and NH₄⁺ in wastewater. Full article