mcrA Gene Research Articles

Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments

Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.

Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river

Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH4 cycle. This AOM process acts as a novel pathway for CH4 emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 105–2.47 × 107 copies g−1 (dry weight), and the activity of nitrate-driven AOM was 0.25–1.73 nmol CH4 g−1 (dry weight) d−1, which could potentially reduce 10.3% of CH4 emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH4+ and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH4 emissions from riverine ecosystems.

Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples

Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples-or in this case, chicken droppings.

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.

Different characteristics of soil CH4 emissions and methanogenic communities in paddy fields under gradually and abruptly elevated CO2 concentrations

Studying methanogenesis in paddy fields under future climate change scenarios is important for carbon sequestration and reduction in agroecosystems. Most studies have investigated the effects of elevated CO2 concentrations (e[CO2]) on CH4 emissions in paddy fields under a constant CO2 concentration ([CO2]). However, the increase in the [CO2] in the atmosphere is a gradual process rather than an abrupt increase, and the [CO2] in the atmosphere has remained high and relatively constant. In this research, we explored the differences in methanogenesis in paddy fields under gradually and abruptly e[CO2] using open-top chambers (OTCs). CH4 flux, soil physicochemical properties, enzyme activities, methane production potential (MPP), and methanogenic (mcrA gene) characteristics were analyzed under CK (ambient [CO2]), C1 (gradually e[CO2] by 200 μmol mol−1), and C2 (abruptly e[CO2] by 200 μmol mol−1) treatments. The results showed that the C1 and C2 treatments significantly promoted the cumulative amount of CH4 emissions (CAC) by 63.3% and 86.5%, respectively, and significantly increased the CAC/yield by 30.8% and 47.3%, respectively, compared with the CK treatment. In addition, the C1 and C2 treatments increased the DOC concentration, enzyme activities (urease, invertase, and catalase), MPP, and mcrA gene abundance in paddy soils. Notably, CAC/yield, shoot biomass, and soil seasonal average urease activity under the C2 treatment were increased by 12.6%, 12.2%, and 3.0%, respectively, compared with those in C1. The methanogenic activity of the C2 treatment was significantly increased by 24.1% and 24.4% during the tillering and grain-filling stages, respectively, and the methanogenic abundance of the C2 treatment was significantly increased by 53.9% and 72.2% during the tillering and elongation stages, respectively, compared with that of C1. Therefore, it is inappropriate to ignore the fact that [CO2] increases gradually and to only examine the effects of high e[CO2] on agroecosystems.

Wastewater treatment performance and gaseous emissions in MFC-CWs affected by influent C/N ratios

Constructed wetlands with microbial fuel cells (MFC-CWs) are widely acknowledged to be efficient in pollutant removal, and have been reported to be beneficial in reducing specific gaseous emissions. However, as a critical parameter that directly addresses, the behavior of carbon (C) and nitrogen (N), the impact of the influent C/N ratio on the comprehensive performance of MFC-CWs remains unknown. Herein, the impact of C/N ratios (i.e., 1, 5, 10, 15) on pollutants (COD, NH4+-N, NO3–-N, NO2–-N, TN and TP) removal, multiple gaseous (CO2, CH4, N2O and NH3) emissions and electricity generation of MFC-CWs were evaluated, and the internal mechanisms were explored. Increasing the C/N ratio enhanced COD removal, and the MFC-CWs achieved superior NH4+-N, TN, and TP removal efficiencies at C/N ratios of 5 and 10. The higher C/N ratio was generally accompanied by greater CO2, CH4, and NH3 fluxes. Nevertheless, the lowest global warming potential (GWP) was observed at C/N of 5 due to the lowest N2O flux having been obtained. The functional gene analysis results showed that the decrease in N2O flux was attributed to an increase in the nosZ/(nirS + nirK) ratio, and the CH4 flux was regulated by the abundance of pomA and mcrA genes. The highest power density (152.54 mA/m3) and current intensity (649.03 mW/m3) were also observed in MFC-CWs with a C/N ratio of 5, mainly due to the increase in electrogenic bacteria (e.g., Proteobacteria and Firmicutes). Consequently, the influent C/N ratio of 5 was optimal for treating wastewater and generating electricity efficiently, and also attenuating the corresponding GWP in MFC-CWs.

Decreased CH4 emissions associated with methanogenic and methanotrophic communities and their interactions following Fe(III) fertiliser application in rice paddies

Rice paddies are important sources of atmospheric methane (CH4), where CH4 fluxes are determined by the balance of production and oxidation. While the application of Fe(III) fertilizer is a proven effective strategy for mitigating CH4 emissions from rice paddies, little is known about the role of methanogen and methanotroph communities and their interactions. In this study, we measured the CH4 flux in a rice paddy field experiment, where the responses of methanogenic and methanotrophic activities to Fe(III) fertiliser applied at medium (Fe-M) and high (Fe-H) levels were examined using real-time quantitative PCR coupled with co-occurrence network analysis after Illumina MiSeq sequencing of the mcrA and pmoA genes. Relative to the control without Fe(III) fertiliser application, in the Fe-M and Fe-H treatments, seasonal CH4 emissions were significantly decreased by 65% and 62%, respectively. Fe(III) fertilisation significantly decreased the copy numbers and potential activity of methanogens, and had an opposite effect on methanotrophs. We found Methanothrix was the predominant genus more adaptive to grow in Fe-rich environments. Fe(III) fertilisation caused a shift in the methanotrophic community towards a predominance of Type II methanotrophs. Soil total Fe concentration, soil electrical conductivity, and different valences of iron were key factors in the composition of methanogenic and methanotrophic communities. Fe(III) fertilisation led to a less complex community taxonomic structure mostly attributed to fewer nodes and edges in both the co-occurrence and mutual exclusion networks of methanogen and methanotrophs. Our findings suggest that adding Fe(III) fertiliser in rice paddies could mitigate CH4 emissions by regulating both methanogens and methanotrophs.

Combining Geobacter spp. Dominated Biofilms and Anaerobic Digestion Effluents─The Effect of Effluent Composition and Electrode Potential on Biofilm Activity and Stability.

The combination of anaerobic digestion (AD) and microbial electrochemical technologies (METs) offers different opportunities to increase the efficiency and sustainability of AD processes. However, methanogenic archaea and/or particles may partially hinder combining MET and AD processes. Furthermore, it is unclear if the applied anode potential affects the activity and efficiency of electroactive microorganisms in AD-MET combinations as it is described for more controlled experimental conditions. In this study, we confirm that 6-week-old Geobacter spp. dominated biofilms are by far more active and stable in AD-effluents than 3-week-old Geobacter spp. dominated biofilms. Furthermore, we show that the biofilms are twice as active at -0.2 V compared to 0.4 V, even under challenging conditions occurring in AD-MET systems. Paired-end amplicon sequencing at the DNA level using 16S-rRNA and mcrA gene shows that hydrogenotrophic methanogens incorporate into biofilms immersed in AD-effluent without any negative effect on biofilm stability and electrochemical activity.

Conductive Materials on Biocathodes Altered the Electron-Transfer Paths and Modulated γ-HCH Dechlorination and CH4 Production in Microbial Electrochemical Systems.

Adding conductive materials to the cathode of a microbial electrochemical system (MES) can alter the route of interspecies electron transfer and the kinetics of reduction reactions. We tested reductive dechlorination of γ-hexachlorocyclohexane (γ-HCH), along with CH4 production, in MES systems whose cathodes were coated with conductive magnetite nanoparticles (NaFe), biochar (BC), magnetic biochar (FeBC), or anti-conductive silica biochar (SiBC). Coating with NaFe enriched electroactive microorganisms, boosted electro-bioreduction, and accelerated γ-HCH dechlorination and CH4 production. In contrast, BC only accelerated dechlorination, while FeBC only accelerated methanogenesis, because of their assemblies of functional taxa that selectively transferred electrons to those electron sinks. SiBC, which decreased electro-bioreduction, yielded the highest CH4 production and increased methanogens and the mcrA gene. This study provides a strategy to selectively control the distribution of electrons between reductive dechlorination and methanogenesis by adding conductive or anti-conductive materials to the MES's cathode. If the goal is to maximize dechlorination and minimize methane generation, then BC is the optimal conductive material. If the goal is to accelerate electro-bioreduction, then the best addition is NaFe. If the goal is to increase the rate of methanogenesis, adding anti-conductive SiBC is the best.

Long-term effects of soluble and insoluble ferric irons on anaerobic oxidation of methane in paddy soil

Iron-dependent anaerobic oxidation of methane (Fe-AOM) is an important process to reduce methane emissions into the atmosphere. It is well known that iron bioavailability largely influences microbial iron reduction, but the long-term effects of different ferric irons on soil Fe-AOM remain unknown. In this work, paddy soil in the ferruginous zone was collected and inoculated with insoluble ferrihydrite and soluble EDTA-Fe(III) for 420 days. Stable isotope experiments, activity inhibition tests, and molecular biological techniques were performed to reveal the activity, microbial community, and possible mechanism of paddy soil Fe-AOM. The results showed that ferrihydrite was a better electron acceptor for long-term Fe-AOM cultivation. Although EDTA-Fe(III) is highly bioavailable and could stimulate Fe-AOM activity for a short time, it restricted the activity increase in the long term. The abundances of archaea, iron-reducing bacteria (IRB), and gene mcrA largely increased after cultivation, indicating the important roles of mcrA-carrying archaea and IRB. Remarkably, archaeal communities were similar, but bacteria were totally different with different ferric irons. The results of the microbial community and activity inhibition suggested that Fe-AOM was performed likely by the cooperation between archaea (Methanomassiliicoccaceae or pGrfC26) and IRB in the cultures.

Effects of influent organic load on TMAH (tetramethylammonium hydroxide) wastewater treatment by anaerobic process

Tetramethylammonium hydroxide (TMAH) is a corrosive alkaline and neuronal toxic compound, which is widely used in the thin-film transistor liquid crystal display industry. In this study the performance of the anaerobic sequencing batch reactors (SBR) for treating synthetic TMAH wastewater under different organic influent loads was evaluated thoroughly over a 208 day period. The results indicated that when the influent organic load was below 376.4 mg TOC/(L·day), total organic carbon (TOC) removal was enhanced with influent organic load increasing. And the maximum TOC removal efficiency and CH4 production reached 92.5% and 589 mL/L reactor of one cycle, respectively. Further raising the load suppressed the TMAH degradation and microbiological activity. Only 6.0% organic nitrogen converted to ammonium and TOC removal efficiency declined to 13.5% at the influent organic load of 1130.5 mg TOC/ (L·day), with anaerobic sludge settling performance decline. And the biogas production of one cycle dropped to 60 mL/L reactor. It was also found that reducing influent organic load could not restore the system. Microbial diversity and richness also varied in response to the influent organic load. Illumina MiSeq sequencing analysis indicated Caldisericum, norank_f_KD1–131, norank_f_Bacteroidetes_vadinHA17, and Treponema were enriched at the influent load of 376.4 mg TOC/(L·day). RT-qPCR results confirmed that high influent organic load suppressed the expression of the ureC gene and mcrA gene, and then inhibited ammonification and methanogenesis.

Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions.

Wetlands are natural sources of methane (CH4) emissions, providing the largest contribution to the atmospheric CH4 pool. Changes in the ecohydrological environment of coastal salt marshes, especially the surface inundation level, cause instability in the CH4 emission levels of coastal ecosystems. Although soil methane-associated microorganisms play key roles in both CH4 generation and metabolism, how other microorganisms regulate methane emission and their responses to inundation has not been investigated. Here, we studied the responses of prokaryotic, fungal and cercozoan communities following 5 years of inundation treatments in a wetland experimental site, and molecular ecological networks analysis (MENs) was constructed to characterize the interdomain relationship. The result showed that the degree of inundation significantly altered the CH4 emissions, and the abundance of the pmoA gene for methanotrophs shifted more significantly than the mcrA gene for methanogens, and they both showed significant positive correlations to methane flux. Additionally, we found inundation significantly altered the diversity of the prokaryotic and fungal communities, as well as the composition of key species in interactions within prokaryotic, fungal, and cercozoan communities. Mantel tests indicated that the structure of the three communities showed significant correlations to methane emissions (p < 0.05), suggesting that all three microbial communities directly or indirectly contributed to the methane emissions of this ecosystem. Correspondingly, the interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan OTUs were all keystone taxa. Methane-associated OTUs were more likely to interact in pairs and correlated negatively with the fungal and cercozoan communities. In addition, the modules significantly positively correlated with methane flux were affected by environmental stress (i.e., pH) and soil nutrients (i.e., total nitrogen, total phosphorus and organic matter), suggesting that these factors tend to positively regulate methane flux by regulating microbial relationships under inundation. Our findings demonstrated that the inundation altered microbial communities in coastal wetlands, and the fungal and cercozoan communities played vital roles in regulating methane emission through microbial interactions with the methane-associated community.

Incorporating the Soil Gas Gradient Method and Functional Genes to Assess the Natural Source Zone Depletion at a Petroleum-Hydrocarbon-Contaminated Site of a Purification Plant in Northwest China.

An increasing number of studies have demonstrated that natural source zone depletion (NSZD) in the vadose zone accounts for the majority (90%~99%) of the natural attenuation of light non-aqueous phase liquid (LNAPL). Until now, 0.05 to 12 kg/a.m2 NSZD rates at tens of petroleum LNAPL source zones have been determined in the middle or late evolution stage of LNAPL release, in which limited volatile organic compounds (VOCs) and methane (CH4) were detected. NSZD rates are normally estimated by the gradient method, yet the associated functional microbial activity remains poorly investigated. Herein, the NSZD at an LNAPL-releasing site was studied using both soil gas gradient methods quantifying the O2, CO2, CH4, and VOCs concentrations and molecular biology methods quantifying the abundance of the pmoA and mcrA genes. The results showed that the methanogenesis rates were around 4 to 40 kg/a.m2. The values were greater than the rates calculated by the sum of CH4 escaping (0.3~1.2 kg/a.m2) and O2 consuming (3~13 kg/a.m2) or CO2 generating rates (2~4 kg/a.m2), suggesting that the generated CH4 was oxidized but not thoroughly to CO2. The functional gene quantification also supported the indication of this process. Therefore, the NSZD rates at the site roughly equaled the methanogenesis rates (4~40 kg/a.m2), which were greater than most of the previously studied sites with a 90th percentile value of 4 kg/a.m2. The study extended the current knowledge of the NSZD and has significant implications for LNAPL remediation management.

In situ probing methanogenesis in anaerobic wastewater treatment using front-face excitation-emission matrix (FF-EEM) fluorescence

Global warming and the energy crisis give rise to increasing demand for renewable energy production and resource recovery. Anaerobic methanogenesis, which transforms organic matter to methane, is the pivotal step in most resource-sustainable applications in wastewater treatment, while its evaluation and monitoring are still challenging. This study proposed a novel approach for probing methanogenesis in anaerobic wastewater treatment by in situ determining coenzyme F420 using front-face excitation-emission matrix (FF-EEM) fluorescence spectroscopy. The results indicated that the proposed method was simpler and more accurate than the conventional F420 measurement. The parallel factor analysis (PARAFAC) and the internal standard correction were used to address the fluorescence overlap and the inner-filter issues, respectively. The F420 fluorescence determined by the FF-EEM correlated well with the methane yield rate (R2 = 0.882) and the mcrA gene (R2 = 0.847), and it could be associated with the methanogenic activity of the anaerobic sludge. This study demonstrated that the FF-EEM-based method was promising in evaluating methanogenesis in anaerobic process, and could assist in the optimization of bioresource recycling in wastewater treatment.

Interactions among heavy metals and methane-metabolizing microorganisms and their effects on methane emissions in Dajiuhu peatland.

Peatlands play a crucial role in mediating the emissions of methane through active biogeochemical cycling of accumulated carbon driven by methane-metabolizing microorganisms; meanwhile, they serve as vital archives of atmospheric heavy metal deposition. Despite many edaphic factors confirmed as determinants to modulate the structure of methanotrophic and methanogenic communities, recognition of interactions among them is limited. In this study, peat soils were collected from Dajiuhu peatland to assess the presence of heavy metals, and methanotrophs and methanogens were investigated via high-throughput sequencing for functional genes mcrA and pmoA. Further analyses of the correlations between methane-related functional groups were conducted. The results demonstrated that both methane-metabolizing microorganisms and heavy metals have prominent vertical heterogeneity upward and downward along the depth of 20cm. Pb, Cd, and Hg strongly correlated with methanotrophs and methanogens across all seasons and depths, serving as forceful factors in structural variations of methanogenic and methanotrophic communities. Particularly, Pb, Cd, and Hg were identified as excessive elements in Dajiuhu peatland. Furthermore, seasonal variations of networks among methane-related functional groups and environmental factors significantly affected the changes of methane fluxes across different seasons. Concretely, the complicated interactions were detrimental to methane emissions in the Dajiuhu peatland, leading to the minimum methane emissions in winter. Our study identified the key heavy metals affecting the composition of methane-metabolizing microorganisms and linkages between seasonal variations of methane emissions and interaction among heavy metals and methane-metabolizing microorganisms, which provided much new reference and theoretical basis for integrated management of natural peatlands.

Long-term non-phosphorus application increased paddy methane emission by promoting organic acid and methanogen abundance in Tai Lake region, China

Rice paddy is a significant source of atmospheric methane (CH4), a major global warming source. CH4 emission from paddy fields is greatly influenced by phosphorus (P) management, especially the long-term non-P application on CH4 emission is largely unexplored. In the present study, long-term non-P application (NK) and P application (NPK) treatments of two paddy fields in Suzhou (from 1980) and Yixing (from 2009), Tai Lake region was done. The effect of P application on CH4 emissions and related microorganisms (i.e., methanogens and methanotrophs) from 2019 to 2020 was analyzed. Results revealed that long-term NK treatment didn't alter the seasonal trend of CH4 flux, but significantly promoted CH4 emissions at the tillering stage. The non-P application for >12 years caused the cumulative CH4 emissions of NK treatment in the whole rice season significantly increased by 41.9–221 % in two fields compared to NPK treatment in 2019 and 2020. NK treatment increased the abundance and diversity of methanogens, while reducing the abundance and diversity of methanotrophs. Community composition of soil pmoA gene differed in two experiment sites. Correlation analysis revealed that the CH4 emission was significant and positively related to soil mcrA gene and C/P while negatively related to soil pmoA gene and P. Structure equation model analysis show the low soil available P content was the dominant driving factor for the high CH4 emission under long-term non-P application through its direct impact on soil mcrA and pmoA genes. The increased soil organic acid content was another driver which was positively related to soil mcrA gene and negatively to soil pmoA gene. Our findings demonstrate the important role of soil P in regulating CH4 emissions from paddy fields in the Tai Lake region, China, and suitable P application is necessary for ensuring the yield while reducing CH4 emission.

Metagenomics analysis of ecosystem integrating methane and sulfide generation in urban sewer systems

Simultaneous generation of methane and sulfide is a major concern affecting sewer system operations, and the methanogenic archaea and sulfate-reducing bacteria may increase methane and sulfide production via their symbiotic activities. However, interactions between methane and sulfide metabolism are unclear. In this study, 18 high-quality draft genomes from sewer biofilms were obtained via genome-resolved metagenomics (Binning). The assembled bins 1, 5, 10, 12 and 15 contained abundant ackA, mcrA, mtsA, mtsB and serA genes were involved in methane generation, sulfide consumption via methane metabolism and sulfide metabolism to promote methane generation. Because of the independent and single functionality of these bins, they formed a bio-symbiotic system to promote methane and sulfide generation. Interestingly, for bins 2, 3, 8 and 9, the functions of methane generation, sulfide generation and sulfide consumption via methane metabolism occurred simultaneously. The community affiliations of the assembled bins were also unusual. For instance, bin 9 (Ignavibacteria bacterium) was derived from the Ignavibacteriae supercluster that was not been detected in sewer biofilms, but participated in both methane generation and sulfide consumption. Therefore, these bins formed another biological system with multiple functional aggregates. Two types of ecosystems integrating methane and sulfide generation in sewers were proposed. Our results improve the understanding of toxic gas emissions in sewers and provide a theoretical foundation for studies on gas suppression.

Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics.

Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10cm depth interval and in summer in the 10-20cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.

Methane and nitrous oxide production and their driving factors in Phragmites riparian wetlands of Dianchi Lake, China

The eutrophic lake Dianchi, china, is a hotspot for methane (CH4) and nitrous oxide (N2O) emissions. However, the potential factors driving CH4 and N2O production in the riparian wetlands of Dianchi Lake remain unclear. In the current study, the potential CH4 and N2O production was evaluated using incubation experiments. The abundance and community structure of the methanogenic communities and denitrifying bacteria were measured using quantitative polymerase chain reaction and Illumina MiSeq sequencing. The results indicated that the potential CH4 and N2O production differed significantly among the riparian wetlands of Dianchi Lake, with rates of 0.26–17.65 μg/g.d and 0.09–1.30 ng/g.h, respectively. The soil mcrA, nirS and nosZ gene copies differed significantly among the riparian wetlands, whereas the soil narG and nirk genes did not. Soil methanogenic archaea in the riparian wetlands were dominated by the order Bathyarchaeia (2.36–45.97 %). Forty-one potential denitrifying bacterial genera were detected in soils from the riparian wetlands, among which the majority belonged to the Proteobacteria (31 genera; 1.54–37.78 %). The variation in CH4 production was mediated through soil AP, water NO3−-N and soil mcrA abundance, while water NH4+-N, soil TN and soil NH4+-N were the main factors regulating N2O production in the riparian wetlands of Dianchi Lake. Our study highlighted the important implication of pollution abatement to greenhouse gas emission reduction in the riparian wetland.

Role of polyamide microplastic in altering microbial consortium and carbon and nitrogen cycles in a simulated agricultural soil microcosm

Microplastics (MPs) are persistent organic pollutants globally, with a continuous increase in MP wastes near and away from the regions of human activities. Studies to date aimed to explore the impact of MPs on ecosystems, but the area of research could not go beyond environmental pollution caused by MPs. To address the menace of MPs, scientists need to pay enough attention to the biogeochemical cycles, microbial communities, and functional microorganisms. Hence, this study aimed to evaluate the impact of adding 0.3% (mass ratio) [low-concentration (LC) group] and 1% [high-concentration (HC) group] of polyamide (PA) MP to the soil microenvironment with regard to the aforementioned parameters. PA MP decreased the soil microbial diversity (Shannon and Simpson indices, P < 0.05). At the phylum level, PA MP increased the abundance of Acidobacteria, Firmicutes, and Crenarchaeota (P < 0.05); at the genus level, it enhanced that of Geobacter, Thiobacillus, Pseudomonas, and Bradyrhizobium (P < 0.01) while decreased that of Bacillus, Flavisolibacter, Geothrix, and Pseudarthrobacter (P < 0.05). PA MP affected the carbon (C) cycle. PA MP accelerated the soil C fixation by enhancing the abundance of the genes accA and pccA. The LC PA MP accelerated organic C degradation and methane metabolism by changing the abundance of mnp, chiA, mcrA, pmoA, and mmoX genes, while the HC PA MP inhibited them with increasing the experimental time. Regarding the effects of PA on the nitrogen (N) cycle, the PA MP promoted N assimilation and ammonification by increasing the abundance of the genes gdh and ureC, the impact of PA MP on N fixation and denitrification depended on its concentration and treating time.This study showed that PA MP impacted the microbial consortium, it also affected the C and N cycles and its effect depended on its concentration and the treating time.