Real-time quantification of mcrA, pmoA for methanogen, methanotroph estimations during composting

The biological mechanism of a lower carbon/nitrogen ratio increases methane emissions during vegetable waste composting

The initial carbon/nitrogen (C/N) ratio is one of the most important factors impacting composting processes, such as methane (CH4) emissions. However, the effects of the C/N ratio on CH4 emissions and the associated biological mechanisms during vegetable waste composting are largely unknown. In this study, a lab-scale experiment was conducted to investigate the effects of different C/N ratios on CH4 emissions and the mechanisms associated with methane-metabolizing microorganisms (methanogens and methanotrophs) during capsicum straw composting. The initial C/N ratios were set to 18, 30 and 50 to simulate the low (L), medium (M) and high (H) C/N ratios, respectively. The results showed that CH4 emissions were mainly concentrated in the thermophilic phase and that the cumulative CH4 emissions were significantly greater in the L treatment than in the M and H treatments by 10.8 and 15.4 times, respectively. During the methanogenic process, the relative abundance of the dominant genus Methanoculleus (47.59 % ∼ 76.92 %) was higher than in the L treatment than in the M and H treatments at the thermophilic and maturation stages, and the Chao1 index and the mcrA gene abundance followed the order of L > M > H at each composting stage. During the methanotrophic process, the dominant genus unclassified_d_bacteria (51.3 % ∼ 91.87 %), Chao1 index, pmoA gene abundance and CO2 emissions were in the order of L > M > H at each composting stage. This pattern suggests that a lower C/N ratio simultaneously enhanced CH4 production and oxidation. A structural equation model further revealed that the methanogenic community, which was driven directly by the relative contents of hemicellulose and cellulose in the substrates, as indicated by the C/N ratio, made greater contributions to CH4 emissions than did the methanotrophic community. In conclusion, a lower C/N ratio increased CH4 emissions mainly by regulating the population and composition of methanogen community.

The archaeal and bacterial community structure in composted cow manures is defined by the original populations: a shotgun metagenomic approach

Introduction

Organic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.

Methods

Cow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.

Results

The bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes. Most of these archaeal and bacterial groups showed considerable variation after composting and between the cow manures. However, the differences in the relative abundance of their genes were much smaller compared to those of the archaeal or bacterial groups.

Discussion

It was found that composting of different cow manures did not result in similar bacterial or archaeal communities, and the changes that were found after 74 days were defined by the original populations. However, more research is necessary to determine if other composting conditions will give the same results.

Micro-positive pressure significantly decreases greenhouse gas emissions by regulating archaeal community during industrial-scale dairy manure composting

In this study, the effects of micro-positive pressure formed by covering with a semipermeable membrane in the heating phase of dairy manure composting on greenhouse gas emissions and the mechanism of reducing methane emissions by the archaeal community were investigated. A large-scale experiment was conducted with semipermeable membrane-covered composting (SMC), forced aeration composting (FAC), and traditional static composting (TSC) groups. The results showed that the oxygen concentration and methanogen abundance were key factors in regulating methane emissions. In the heating phase of SMC, the micro-positive pressure could enhance the O2 utilization rate and heating rate, resulting in Methanobrevibacter and Methanobacterium greatly decreasing, and the abundance of mcrA decreased by 90.03%, while that of pmoA did not increase. Compared with FAC and TSC, the cumulative methane emissions in SMC decreased by 51.75% and 96.04%, respectively. Therefore, the micro-positive pressure could effectively reduce greenhouse gas emissions by inhibiting the growth of methanogens.

Semi-permeable membrane-covered high-temperature aerobic composting: A review

Semi-permeable membrane-covered high-temperature aerobic composting (SMHC) is a suitable technology for the safe treatment and disposal of organic solid waste as well as for improving the quality of the final compost. This paper presents a comprehensive summary of the impact of semi-permeable membranes centered on expanded polytetrafluoroethylene (e-PTFE) on compost physicochemical properties, carbon and nitrogen transformations, greenhouse gas emission reduction, microbial community succession, antibiotic removal, and antibiotic resistance genes migration. It is worth noting that the semi-permeable membrane can form a micro-positive pressure environment under the membrane, promote the uniform distribution of air in the heap, reduce the proportion of anaerobic area in the heap, improve the decomposition rate of organic matter, accelerate the decomposition of compost and improve the quality of compost. In addition, this paper presents several recommendations for future research areas in the SMHC. This investigation aims to guide for implementation of semi-permeable membranes in high-temperature aerobic fermentation processes by systematically compiling the latest research progress on SMHC.

The intrinsic methane mitigation potential and associated microbes add product value to compost

Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h-1 g dw compost-1 and 25.19 ± 6.75 pmol h-1 g dw compost-1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.

Application of thifluzamide alters microbial network structure and affects methane cycle genes in rice-paddy soil

Thifluzamide is an effective agent for controlling rice sheath blight and has a long half-life in soil. However, the effects of thifluzamide on the abundance of microbes harboring methane-cycle genes and soil microbial community assembly patterns are not well known. Thus, we conducted a three-month indoor mesocosm experiment to ascertain the effects of thifluzamide (0.05, 0.5, and 5 mg kg^-1 soil; 0.05 mg kg^-1 soil being recommended) on bacterial and archaeal community structure and on the abundance of methanogen genes using two typical paddy soils: sandy soil from Hangzhou (HZ) and loam sandy soil from Jiansanjiang (JSJ). The effects of thifluzamide on soil microorganisms were related to soil type. In JSJ loam sandy soil, thifluzamide significantly increased bacterial α diversity after 7-30 d and archaeal α diversity at 30 and 60 d. In HZ sandy soil, however, α diversity did not change significantly. Network analysis showed that thifluzamide-treated soils possessed more complex networks with more total nodes and links, a higher average degree of connectivity, and more keystone species. Thifluzamide application increased the number of keystone species associated with methane production in both types of paddy soil. A relatively greater number of modules were significantly negatively correlated with mcrA abundance in the HZ T10 network, but more modules were positively correlated with mcrA abundance in the JSJ T100 network. The half-life of thifluzamide varied for the different doses, i.e., from 152.0 to 419.6 d. The results reveal that methane-cycle genes, soil microbiome assembly, and interactions among microbial species all change in response to thifluzamide stress.

Hyperthermophilic composting significantly decreases methane emissions: Insights into the microbial mechanism

Methane (CH₄) emissions from thermophilic composting (TC) are a substantial contributor to climate change. Hyperthermophilic composting (HTC) can influence CH₄-related microbial communities at temperatures up to 80 °C, and thus impact the CH₄ emissions during composting. This work investigated CH₄ emissions in sludge-derived HTC, and explored microbial community succession with quantitative PCR and high-throughput sequencing. Results demonstrated that HTC decreased CH₄ emissions by 52.5% compared with TC. In HTC, the CH₄ production potential and CH₄ oxidation potential were nearly 40% and 64.1% lower than that of TC, respectively. There was a reduction in the quantity of mcrA (3.7 × 10⁸ to 0 g^-1 TS) in HTC, which was more significant than the reduction in pmoA (2.0 × 10⁵ to 2.1 × 10⁴ g^-1 TS), and thus lead to reduce CH₄ emissions. It was found that the abundance of most methanogens and methanotrophs was inhibited in the hyperthermal environment, with a decline in Methanosarcina, Methanosaeta and Methanobrevibacter potentially being responsible for reducing the CH₄ emissions in HTC. This work provides important insight into mitigating CH₄ emissions in composting.

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.

Exploring the mechanisms of organic matter degradation and methane emission during sewage sludge composting with added vesuvianite: Insights into the prediction of microbial metabolic function and enzymatic activity

Effect mechanisms of organic matter (OM) degradation and methane (CH₄) emission during sewage sludge (SS) composting with added vesuvianite (V) were studied by high-throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). Results show that the addition of V accelerated the OM degradation and decreased the cumulative CH₄ emissions by 33.6% relative to the control. In addition, V significantly decreased the mcrA gene abundance and the methanogen community richness at the genus level. PICRUSt also indicated that V strengthens the microbial metabolic function and enzymatic activity related to OM degradation, and reduced the enzymatic activity related to CH₄ production. Methanogens community variation analysis proved the ratio of carbon and nitrogen and moisture content are the significant variables affecting CH₄ emissions. Thus, optimizing the ratio of carbon and nitrogen and moisture content will decrease CH₄ emission during SS composting.

Exploring the mechanisms of decreased methane during pig manure and wheat straw aerobic composting covered with a semi-permeable membrane

It is very important to reduce methane production and emission during aerobic composting. In this study, the effects of covering with a semi-permeable membrane during pig manure and wheat straw composting were investigated. Two laboratory-scale composting reactors were used: the membrane covered treatment (treatment A) and the control treatment (treatment B). Composting in treatment A effectively improved the oxygen utilization rate and decreased methane emissions by 22.42% relative to the control treatment. Quantification of functional genes and Pearson rank correlations showed that the mcrA and mcrA/pmoA gene abundances were significantly positively correlated with temperature and negatively correlated with the interstitial oxygen concentration, and that the pmoA gene abundance was positively correlated with the carbon: nitrogen ratio and moisture content. Therefore, increasing the aeration rate and optimizing the carbon: nitrogen ratio and moisture content will decrease methane emissions. Together, the results demonstrate that coverage membrane could be a novel strategy for reducing methane emissions during composting.

Particle-scale visualization of the evolution of methanogens and methanotrophs and its correlation with CH4 emissions during manure aerobic composting

Methane (CH₄) emissions are a major environmental concern in composting facilities. Therefore, this study initially visualized the dynamic distribution and quantity of methanogens and methanotrophs in composting particles during manure aerobic composting using fluorescence in situ hybridization-confocal laser scanning microscopy (FISH-CLSM) and quantified their correlation with CH₄ emissions. The visualization results showed that methanogens existed inside the particles, while methanotrophs clustered in the outer layer; a facultative anaerobic zone existed in between. The quantification results of integral optical density of methanogens and methanotrophs per unit particle area (U_gen and U_oxi, respectively) indicated that, in the cooling phase, CH₄ generation and oxidation could still be high and could strike a balance if the initial organic matter content of composting materials is high, while both could be extremely low if the content is low. A strong linearity between U_gen obtained by FISH-CLSM and methyl-coenzyme M reductase copy number obtained by quantitative polymerase chain reaction analysis (R² = 0.88) was observed, which justified the effectiveness of the FISH-CLSM method and demonstrated that macro-scale CH₄ emissions were essentially an accumulation of particle-scale CH₄ emissions. CH₄ emissions were equal to 3.3297 × 10⁷U_gen - 3.1814 × 10⁶U_oxi - 3902.9900 (R² = 0.98). Overall, the results showed that methanogens exerted more influence on CH₄ emissions than methanotrophs. Combining these results with CH₄-generation and -oxidation kinetics may help illustrate CH₄-emission mechanisms, improve particle-scale CH₄-emission models, and thereby provide theoretical guidance for operation optimization and emission reduction in composting processes.

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

Manure composting is a significant source of atmospheric methane (CH₄) and nitrous oxide (N₂O) that are two potent greenhouse gases. The CH₄ and N₂O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH₄ and N₂O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH₄ and N₂O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH₄-related functional genes (mcrA and pmoA genes) and N₂O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH₄ and N₂O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH₄⁺ together as the best predictors for CH₄ fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N₂O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH₄ and N₂O fluxes to elevated atmospheric CO₂ concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.

Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

Provided that infectious prions (PrP(Sc)) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gas emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P<0.05) headspace concentrations of CH4 primarily during the early stages of the first cycle and N2O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP(Sc).

Changes in biochemical and microbiological parameters during the period of rapid composting of dairy manure with rice chaff

Various parameters were measured during the period of composting of dairy manure and rice chaff in different ratios (dairy manure/rice chaff=V/V, pile 1: 75/25; pile 2: 80/20; pile 3: 85/15) to evaluate their suitability as indicators for the composting process. The temperature in pile 1 increased rapidly and remained above 60 °C for 30 days, while the temperature in pile 3 increased slowly relative to the other two piles. Furthermore, the degradation of organic substrates, as indicated by the reduction of C/N ratio, was rapid in pile 1 (below 20% 28 days after beginning of the composting). The major fluctuations of various water-soluble fractions in all piles were observed during the first 3 weeks, and the results in general showed that the highest microbial populations and enzymatic activities also appeared in this phase. Various parameters indicated that the rapid composting method was a feasible one for treating agricultural wastes.