Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System

Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils

Denitrifying nitrous oxide (N₂O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N₂O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N₂O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N₂O production (nirS and nirK) to the gene responsible for N₂O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N₂O-generating bacteria in BF and a higher abundance of N₂O-reducing bacteria in FF. High accumulation of N₂O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N₂O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N₂O and thus less N₂O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N₂O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N₂O accumulation. This knowledge would help to develop a strategy for mitigating N₂O emissions in agricultural soils by regulating the phenotypes of N₂O metabolism.

Effects of rumen undegradable protein sources on nitrous oxide, methane and ammonia emission from the manure of feedlot-finished cattle

The effects of sources of rumen undegradable protein (RUP) in diets on methane (CH₄), nitrous oxide (N₂O) and ammonia (NH₃) emissions from the manure of feedlot-finished cattle were evaluated. We hypothesized that the use of different RUP sources in diets would reduce N loss via urine and contribute to reduced N₂O, CH₄ and NH₃ emissions to the environment. Nellore cattle received different diets (18 animals/treatment), including soybean meal (SM, RDP source), by-pass soybean meal (BSM, RUP source) and corn gluten meal (CGM, RUP source). The protein source did not affect the N and C concentration in urine, C concentration in feces, and N balance (P > 0.05). The RUP sources resulted in a higher N₂O emission than the RDP source (P = 0.030), while BSM resulted in a higher N₂O emission than CGM (P = 0.038) (SM = 633, BSM = 2521, and CGM = 1153 g ha⁻² N–N₂O); however, there were no differences in CH₄ and NH₃ emission (P > 0.05). In conclusion, the use of RUP in diets did not affect N excretion of beef cattle or CH₄ and NH₃ emission from manure, but increased N₂O emission from the manure.

Decreased Methane Emissions Associated with Methanogenic and Methanotrophic Communities in a Pig Manure Windrow Composting System under Calcium Superphosphate Amendment

With the rapid growth of livestock breeding, manure composting has evolved to be an important source of atmospheric methane (CH4) which accelerates global warming. Calcium superphosphate (CaSSP), as a commonly used fertilizer, was proposed to be effective in reducing CH4 emissions from manure composting, but the intrinsic biological mechanism remains unknown. Methanogens and methanotrophs both play a key role in mediating CH4 fluxes, therefore we hypothesized that the CaSSP-mediated reduction in CH4 emissions was attributed to the shift of methanogens and methanotrophs, which was regulated by physicochemical parameter changes. To test this hypothesis, a 60-day pig manure windrow composting experiment was conducted to investigate the response of CH4 emissions to CaSSP amendment, with a close linkage to methanogenic and methanotrophic communities. Results showed that CaSSP amendment significantly reduced CH4 emissions by 49.5% compared with the control over the whole composting period. The decreased mcrA gene (encodes the α-subunit of methyl-coenzyme M reductase) abundance in response to CaSSP amendment suggested that the CH4 emissions were reduced primarily due to the suppressed microbial CH4 production. Illumina MiSeq sequencing analysis showed that the overall distribution pattern of methanogenic and methanotrophic communities were significantly affected by CaSSP amendment. Particularly, the relative abundance of Methanosarcina that is known to be a dominant group for CH4 production, significantly decreased by up to 25.3% accompanied with CaSSP addition. Only Type I methanotrophs was detected in our study and Methylocaldum was the dominant methanotrophs in this composting system; in detail, CaSSP amendment increased the relative abundance of OTUs belong to Methylocaldum and Methylobacter. Moreover, the increased SO42- concentration and decreased pH acted as two key factors influencing the methanogenic and methanotrophic composition, with the former has a negative effect on methanogenesis growth and can later promote CH4 oxidation at a low level. This study deepens our understanding of the interaction between abiotic factors, function microbiota and greenhouse gas (GHG) emissions, as well as provides implication for practically reducing composting GHG emissions.

Multivariate and Multiscale Approaches for Interpreting the Mechanisms of Nitrous Oxide Emission during Pig Manure-Wheat Straw Aerobic Composting

Nitrous oxide (N₂O) emission during composting causes nitrogen loss and air pollution. The interpretation of N₂O emission mechanisms will help to customize composting strategies that mitigate climate change. At pile and particle scales, this study characterized N₂O emission-related variables (gases, ions, and microbes) and their correlations during pig manure-wheat straw aerobic composting. Pile-scale results showed that N₂O emission mainly occurred in mesophilic, thermophilic, and cooling phases; the nitrification by ammonia-oxidizing bacteria ( AOB) and nitrite-oxidizing bacteria ( NOB) coexisted with the denitrification by denitrificans ( DEN); the major NOB and DEN were Nitrobacter ( NOB_Nba) and Thiobacillus denitrificans ( DEN_Tb), respectively. The mechanisms of nitrification, nitrifier denitrification, and anaerobic denitrification in composting particles were initially visualized by confocal laser scanning microscopy: Betaproteobacteria ( AOB_ Beta) sporadically distributed on the outer area of the particles, NOB_Nba internally attached to AOB_ Beta, and Nitrosomonas europea/ Nitrosomonas eutropha ( AOB_eu) and DEN_Tb concentrated in the interior. Correlation analysis of the variables showed that the distribution area of AOB_eu was proportional to N₂O emission ( R² = 0.84); AOB not only participated in nitrification but also nitrifier denitrification, and N₂O formation was mainly from nitrifier denitrification by AOB_eu during the mesophilic-thermophilic phase and from denitrification by AOB_eu and DEN during the cooling phase.

Engineered and Environmental Controls of Microbial Denitrification in Established Bioretention Cells

Bioretention cells (BRCs) are effective tools for treating urban stormwater, but nitrogen removal by these systems is highly variable. Improvements in nitrogen removal are hampered by a lack of data directly quantifying the abundance or activity of denitrifying microorganisms in BRCs and how they are controlled by original BRC design characteristics. We analyzed denitrifiers in twenty-three BRCs of different designs across three mid-Atlantic states (MD, VA, and NC) by quantifying two bacterial denitrification genes ( nirK and nosZ) and potential enzymatic denitrification rates within the soil medium. Overall, we found that BRC design factors, rather than local environmental variables, had the greatest effects on variation in denitrifier abundance and activity. Specifically, denitrifying populations and denitrification potential increased with organic carbon and inorganic nitrogen concentrations in the soil media and decreased in BRCs planted with grass compared to other types of vegetation. Furthermore, the top layers of BRCs consistently contained greater concentrations and activity of denitrifying bacteria than bottom layers, despite longer periods of saturation and the presence of permanently saturated zones designed to promote denitrification at lower depths. These findings suggest that there is still considerable potential for design improvements when constructing BRCs that could increase denitrification and mitigate nitrogen export to receiving waters.

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA-based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.