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

Methane and nitrous oxide emissions in the rice-shrimp rotation system of the Vietnamese Mekong Delta

Rice-shrimp rotation systems are one of the widespread farming practices in the Vietnamese Mekong Delta coastal areas. However, greenhouse gas (GHG) emissions in the system have remained unclear. This study aimed to examine methane (CH4) and nitrous oxide (N2O) emissions from the system, including (i) land-based versus high-density polyethylene-lined (HDPE) nursery ponds and (ii) conventional versus improved grow-out ponds inoculated with effective microorganisms (EM) bioproducts. The results showed that CH4 flux in land-based and HDPE-lined nursery ponds were 1.04 and 0.25 mgCH4 m-2 h-1, respectively, while the N2O flux was 8.37 and 6.62 μgN2O m-2 h-1, respectively. Global warming potential (GWP) from land-based nursery ponds (18.3 g CO2eq m-2) was approximately 3 folds higher than that of the HDPE-lined nursery pond (6.1 g CO2eq m-2). Similarly, the mean CH4 and N2O fluxes were 15.84 mg CH4 m-2 h-1 and 7.17 μg N2O m-2 h-1 for the conventional ponds, and 10.51 mg CH4 m-2 h-1 and 7.72 μg N2O m-2 h-1 for the improved grow-out ponds. Conventional practices (2388 g CO2eq m-2) had a higher 1.5-fold GWP compared to the improved grow-out pond (1635 g CO2eq m-2). The continuation of the land-based nursery pond and conventional aquacultural farming practices increase CH4 emission and GWP, while applying HDPE-lined nursery ponds combined with improved grow-out ponds could be a promising approach for reducing GHG emissions in rice-shrimp rotation systems. This study recommends further works in the rice-shrimp rotation systems, including (i) an examination of the effects of remaining rice stubbles in the platform on the availability of TOC levels and GHG emissions and (ii) ameliorating dissolved oxygen (DO) concentration on the effectiveness of GHG emission reduction.

Global net climate effects of anthropogenic reactive nitrogen

Anthropogenic activities have substantially enhanced the loadings of reactive nitrogen (Nr) in the Earth system since pre-industrial times1,2, contributing to widespread eutrophication and air pollution3-6. Increased Nr can also influence global climate through a variety of effects on atmospheric and land processes but the cumulative net climate effect is yet to be unravelled. Here we show that anthropogenic Nr causes a net negative direct radiative forcing of -0.34 [-0.20, -0.50] W m-2 in the year 2019 relative to the year 1850. This net cooling effect is the result of increased aerosol loading, reduced methane lifetime and increased terrestrial carbon sequestration associated with increases in anthropogenic Nr, which are not offset by the warming effects of enhanced atmospheric nitrous oxide and ozone. Future predictions using three representative scenarios show that this cooling effect may be weakened primarily as a result of reduced aerosol loading and increased lifetime of methane, whereas in particular N2O-induced warming will probably continue to increase under all scenarios. Our results indicate that future reductions in anthropogenic Nr to achieve environmental protection goals need to be accompanied by enhanced efforts to reduce anthropogenic greenhouse gas emissions to achieve climate change mitigation in line with the Paris Agreement.

Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration

Anoxic microsites are potentially important but unresolved contributors to soil organic carbon (C) storage. How anoxic microsites vary with soil management and the degree to which anoxic microsites contribute to soil C stabilization remain unknown. Sampling from four long-term agricultural experiments in the central United States, we examined how anoxic microsites varied with management (e.g., cultivation, tillage, and manure amendments) and whether anoxic microsites determine soil C concentration in surface (0-15 cm) soils. We used a novel approach to track anaerobe habitat space and, hence, anoxic microsites using DNA copies of anaerobic functional genes over a confined volume of soil. No-till practices inconsistently increased anoxic microsite extent compared to conventionally tilled soils, and within one site organic matter amendments increased anaerobe abundance in no-till soils. Across all long-term tillage trials, uncultivated soils had ∼2-4 times more copies of anaerobic functional genes than their cropland counterparts. Finally, anaerobe abundance was positively correlated to soil C concentration. Even when accounting for other soil C protection mechanisms, anaerobe abundance, our proxy for anoxic microsites, explained 41% of the variance and 5% of the unique variance in soil C concentration in cropland soils, making anoxic microsites the strongest management-responsive predictor of soil C concentration. Our results suggest that careful management of anoxic microsites may be a promising strategy to increase soil C storage within agricultural soils.

Methane emissions and microbial communities under differing flooding conditions and seasons in littoral wetlands of urban lake

Wetlands are the largest natural sources of methane (CH4) emissions worldwide. Littoral wetlands of urban lakes represent an ecotone between aquatic and terrestrial ecosystems and are strongly influenced by water levels, environmental conditions, and anthropogenic activities. Despite these littoral zones being potential "hotspots" of CH4 emissions, the status of CH4 emissions therein and the role of physicochemical properties and microbial communities regulating these emissions remain unclear. This study compared the CH4 fluxes, physicochemical properties, and CH4-cycling microbial communities (methanogens and methanotrophs) of three zones (a non-flooded supralittoral zone, a semi-flooded eulittoral zone, and a flooded infralittoral zone) in the littoral wetlands of Lake Pipa, Jiangsu Province, China, for two seasons (summer and winter). The eulittoral zone was a CH4 source (median: 11.49 and 0.02 mg m-2 h-1 in summer and winter, respectively), whereas the supralittoral zone acted as a CH4 sink (median: -0.78 and -0.09 mg m-2 h-1 in summer and winter, respectively). The infralittoral zone shifted from CH4 sink to source between the summer (median: -10.65 mg m-2 h-1) and winter (median: 0.11 mg m-2 h-1). The analysis of the functional genes of methanogenesis (mcrA) and methanotrophy (pmoA) and path analysis showed that CH4 fluxes were strongly regulated by biotic factors (abundance of the mcrA gene and alpha diversity of CH4-cycling microbial communities) and abiotic factors (ammonia nitrogen, moisture, and soil organic carbon). In particular, biotic factors had a major influence on the variation in the CH4 flux, whereas abiotic factors had a minor influence. Our findings provide novel insights into the spatial and seasonal variations in CH4-cycling microbial communities and identify the key factors influencing CH4 fluxes in littoral wetlands. These results are important for managing nutrient inputs and regulating the hydrological regimes of urban lakes.

Urea fertilization increased CO2 and CH4 emissions by enhancing C-cycling genes in semi-arid grasslands

Global climate change is predicted to increase exogenous N input into terrestrial ecosystems, leading to significant changes in soil C-cycling. However, it remains largely unknown how these changes affect soil C-cycling, especially in semi-arid grasslands, which are one of the most vulnerable ecosystems. Here, based on a 3-year field study involving N additions (0, 25, 50, and 100 kg ha-1 yr-1 of urea) in a semi-arid grassland on the Loess Plateau, we investigated the impact of urea fertilization on plant characteristics, soil properties, CO2 and CH4 emissions, and microbial C cycling genes. The compositions of genes involved in C cycling, including C fixation, degradation, methanogenesis, and methane oxidation, were determined using metagenomics analysis. We found that N enrichment increased both above- and belowground biomasses and soil organic C content, but this positive effect was weakened when excessive N was input (N100). N enrichment also altered the C-cycling processes by modifying C-cycle-related genes, specifically stimulating the Calvin cycle C-fixation process, which led to an increase in the relative abundance of cbbS, prkB, and cbbL genes. However, it had no significant effect on the Reductive citrate cycle and 3-hydroxypropionate bi-cycle. N enrichment led to higher soil CO2 and CH4 emissions compared to treatments without added N. This increase showed significant correlations with C degradation genes (bglA, per, and lpo), methanogenesis genes (mch, ftr, and mcr), methane oxidation genes (pmoA, pmoB, and pmoC), and the abundance of microbial taxa harboring these genes. Microbial C-cycling genes were primarily influenced by N-induced changes in soil properties. Specifically, reduced soil pH largely explained the alterations in methane metabolism, while elevated available N levels were mainly responsible for the shift in C fixation and C degradation genes. Our results suggest that soil N enrichment enhances microbial C-cycling processes and soil CO2 and CH4 emissions in semi-arid ecosystems, which contributes to more accurate predictions of ecosystem C-cycling under future climate change.

Temporal dynamics of soil dissolved organic carbon in temperate forest managed by prescribed burning in Northeast China

Dissolved organic carbon (DOC) is an important function of soil organic carbon and sensitive to environmental disturbance. Few studies have explored the variations in soil DOC dynamics and effects on soil physicochemical properties following prescribed burnings. In this study, Pinus koraiensis plantation forests in Northeast China were selected and subjected to prescribed burning in early November 2018. Soil DOC and different soil physicochemical and biological properties in the 0-10 cm and 10-20 cm soil layers were sampled six times within two years after a prescribed burning. In this study, some soil physicochemical (SOC, TN, and ST) and microbial biomass properties (MBC) recovered within two years after a prescribed burning. Compared to the unburned control stands, the post-fire soil DOC concentrations in the upper and lower soil layers increased by 16% and 12%, respectively. Soil DOC concentrations varied with sampling time, and peaked one year after the prescribed burning. Our results showed that soil chemical properties (NH4+-N and pH) rather than biological properties (microbial biomass) were the main driving factors for changes in post-fire soil DOC concentrations. Current study provides an important reference for post-fire and seasonal soil C cycling in plantation forests of Northeast China.

Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift

Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.

Enhanced CO2 uptake is marginally offset by altered fluxes of non-CO2 greenhouse gases in global forests and grasslands under N deposition

Despite the increasing impact of atmospheric nitrogen (N) deposition on terrestrial greenhouse gas (GHG) budget, through driving both the net atmospheric CO2 exchange and the emission or uptake of non-CO2 GHGs (CH4 and N2 O), few studies have assessed the climatic impact of forests and grasslands under N deposition globally based on different bottom-up approaches. Here, we quantify the effects of N deposition on biomass C increment, soil organic C (SOC), CH4 and N2 O fluxes and, ultimately, the net ecosystem GHG balance of forests and grasslands using a global comprehensive dataset. We showed that N addition significantly increased plant C uptake (net primary production) in forests and grasslands, to a larger extent for the aboveground C (aboveground net primary production), whereas it only caused a small or insignificant enhancement of SOC pool in both upland systems. Nitrogen addition had no significant effect on soil heterotrophic respiration (RH ) in both forests and grasslands, while a significant N-induced increase in soil CO2 fluxes (RS , soil respiration) was observed in grasslands. Nitrogen addition significantly stimulated soil N2 O fluxes in forests (76%), to a larger extent in grasslands (87%), but showed a consistent trend to decrease soil uptake of CH4 , suggesting a declined sink capacity of forests and grasslands for atmospheric CH4 under N enrichment. Overall, the net GHG balance estimated by the net ecosystem production-based method (forest, 1.28 Pg CO2 -eq year-1 vs. grassland, 0.58 Pg CO2 -eq year-1 ) was greater than those estimated using the SOC-based method (forest, 0.32 Pg CO2 -eq year-1 vs. grassland, 0.18 Pg CO2 -eq year-1 ) caused by N addition. Our findings revealed that the enhanced soil C sequestration by N addition in global forests and grasslands could be only marginally offset (1.5%-4.8%) by the combined effects of its stimulation of N2 O emissions together with the reduced soil uptake of CH4 .

Effects of nitrogen addition on greenhouse gas fluxes during continuous freeze-thaw cycles in a cold temperate forest

Both nitrogen (N) deposition and soil freeze-thaw cycles (FTCs) induce pulses of greenhouse gas (GHG) emissions in cold temperate zones due to changes in soil carbon (C) and nitrogen (N) turnover. However, the combined effects of N addition and FTCs on GHG fluxes have received little research attention, particularly in boreal forests. We conducted a laboratory incubation experiment using intact soil cores from Rhododendron dauricum-Larix dahurica plots to investigate the GHG flux response to these combined effects. We separated the soil samples into seven groups (no, low, medium, and high sodium nitrate addition and low, medium, and high ammonium chloride addition) and exposed each group to continuous FTC conditions. The N2O and CO2 emissions were eventually stimulated by the FTCs, while CH4 uptake was inhibited by FTCs but responded differently under different N addition treatments. All the treatments had substantially increased N2O emissions compared to the control. However, the soil respiration rate significantly increased only with medium sodium nitrate addition, and high levels of N addition (regardless of form) inhibited CH4 uptake. These findings demonstrate that FTCs and N addition (in various forms and levels) have considerable effects on GHG emissions in temperate forest ecosystems. Moreover, dissolved organic carbon (DOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and inorganic nitrogen in soil are potential factors that drive GHG emissions and are necessary considerations in predicting future feedback effects of GHG emissions on climate change.

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.

How Can Litter Modify the Fluxes of CO2 and CH4 from Forest Soils? A Mini-Review

Forests contribute strongly to global carbon (C) sequestration and the exchange of greenhouse gases (GHG) between the soil and the atmosphere. Whilst the microbial activity of forest soils is a major determinant of net GHG exchange, this may be modified by the presence of litter through a range of mechanisms. Litter may act as a physical barrier modifying gas exchange, water movement/retention and temperature/irradiance fluctuations; provide a source of nutrients for microbes; enhance any priming effects, and facilitate macro-aggregate formation. Moreover, any effects are influenced by litter quality and regulated by tree species, climatic conditions (rainfall, temperature), and forest management (clear-cutting, fertilization, extensive deforestation). Based on climate change projections, the importance of the litter layer is likely to increase due to an litter increase and changes in quality. Future studies will therefore have to take into account the effects of litter on soil CO2 and CH4 fluxes for various types of forests globally, including the impact of climate change, insect infestation, and shifts in tree species composition, as well as a better understanding of its role in monoterpene production, which requires the integration of microbiological studies conducted on soils in different climatic zones.