mcrA Gene Research Articles

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.

Emission mitigation of CH4 and N2O during semi-permeable membrane covered hyperthermophilic aerobic composting of livestock manure

Membrane-covered composting and hyperthermophilic composting technologies have been proven to be effective and have been widely applied as organic waste recycling strategies. However, attempts to combine the two technologies have not been reported. Thus, this study constructed a novel semi-permeable membrane covered hyperthermophilic composting (smHTC) and investigated its potential in CH4 and N2O mitigation. Results showed that smHTC reduced the average emission flux of CH4 and N2O in the thermophilic phase of composting by 79% and 45%, compared to conventional thermophilic composting (cTC). The abiotic mechanism of CH4 and N2O emission mitigation could be attributed to the double barrier of semi-permeable membrane and sub-membrane water layer, which made it difficult for CH4 and N2O to escape, resulting in less CH4 and N2O being released into environment. As for the biotic mechanism, smHTC could suppress the abundance of mcrA gene and methanogens participated in methanogenic process through the high-temperature, which also contribute to the reduction of CH4 emissions. smHTC also could reduce the abundance of denitrification-related functional genes and related microbial taxa, this also facilitated the N2O mitigation. Overall, this work demonstrated the advantages of smHTC in greenhouse gas mitigation and could be a promising recycling strategy for organic waste.

Winter drainage and film mulching cultivation mitigated CH4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil

AbstractWinter flooding of harvested rice fields is a typical cropping system in mountainous areas, which emits considerable amounts of CH4. Plastic film mulching cultivation is recognized as an important rice cultivation practice in paddy field for water-saving irrigation. However, the effects of these managements on CH4 emissions in paddy soil and the underlying microbial mechanism are unclear. A field experiment was carried out with the application of winter drainage followed by traditional rice cultivation (WD), winter drainage followed by plastic film mulching cultivation (MC), as well as winter flooding followed by traditional rice cultivation (WF) as control in hilly paddy fields. We investigated the CH4 emissions, functional (CH4 production rate, 13C isotope) and structural (abundance, structure) responses of soil methanogenic archaeal and fermenting bacterial communities during rice season. Shifting the fields from WF into WD and MC substantially mitigated CH4 emissions by 62.3% and 59.2%, respectively, paralleled with the enhancement of soil Eh and the reductions of soil DOC content. Compared with WF, WD and MC both significantly decreased CH4 production rates and the copy numbers of mcrA gene. Moreover, an increasing contribution of hydrogenotrophic methanogenesis (from 30.7% to 50.0%) to total CH4 production was observed during the conversion from WF to MC under an anaerobic incubation, paralleled with the decreased acetate content and increased δ13C values of acetate-methyl and total acetate. The communities of methanogenic archaea and fermenting bacteria strongly responded to the shift from WF to WD, while MC only showed significant effects on the methanogenic archaeal communities. Compared with WF, WD and MC significantly increased the relative abundance of Methanothrix, Methanosarcina and Methanocella, while those of Methanoregula, Massilia and Geobacter were decreased. The co-occurrence networks showed that WD and MC induced the loss of mixed methanogenic fermentation modules, indicating the decrease in functional biodiversity and redundancy of fermenting bacterial and methanogenic archaeal communities.The findings suggest that WD and MC approach mitigate CH4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil, which represent the effective management strategies considering the water availability and CH4 mitigation in paddy-field agriculture.

Arsenic Methylation Efficiency Changes During Paddy Soil Drying and Its Key Influencing Factors Analysis

The straight head disease of rice is one of the main problems limiting rice production. Arsenic (As) methylation in paddy soils is considered to be highly related to the occurrence of the straight head disease. As a typical field practice, rice fields are usually drained during the late tillering stage and the mid-late grain filling stage. Nevertheless, the key influencing factors on the As methylation efficiency during paddy soil drying remain unclear. In this study, an indoor cultivation experiment was set up to simulate the drying process of paddy soil. Two As-contaminated soils collected from Xingren (XR) in Guizhou province and Nandan (ND) in Guangxi province were used as test soils. Each soil was treated with the addition of rice straw (RS) and without rice straw (CK). With the drying of paddy soil (0, 24, 36, 48, and 60 h), the changes in soil Eh, pH, total organic carbon (TOC), and As chemical species in the porewater were determined. The abundance of the As methylation functional gene (arsM), sulfate-reducing bacteria (harboring dsrA, As methylation-related microorganism), and methanogens (harboring mcrA, As demethylation-related microorganism), as well as the diversity of arsM-harboring microorganisms, were also observed. The results showed that during the process of drying paddy soil, soil Eh changed from -300--200 mV under complete flooding to -150--50 mV after drying; however, the change in soil pH was not obvious. The concentrations of inorganic As (iAs) and dimethylarsenic (DMAs) in porewater significantly increased (P<0.05) with the drying process. Additionally, the concentration of DMAs in the RS treatment was prominently higher than that in CK. Compared with XR soil, the concentration of DMAs in ND soil was higher. As a function of soil drying time, the As methylation efficiency of XR soil (XR-CK and XR-RS) slightly increased but was not significant (P>0.05), whereas the As methylation efficiency of ND soil (ND-CK and ND-RS) increased significantly (P<0.05). After the drying time reached 60 h, the As methylation efficiency of ND-CK and ND-RS increased by 61.8% and 23.2%, respectively, compared with those at the early stage of drying (0 hours). The copy numbers of the arsM and dsrA genes greatly increased with the extension of drying time, whereas an opposite trend was observed for the copy number of the mcrA gene. Furthermore, the addition of straw obviously increased the gene abundance of whole bacteria and arsM-, dsrA-, and mcrA-harboring bacteria. Based on the multi-factor analysis of variance and the redundancy analysis, it was found that the test soil type, straw addition, drying time, and their interaction had a critical influence on the changes in As species, As methylation efficiency, and the gene abundance in soils. TOC, Eh, and the functional genes associated with As methylation were positively linked with the methylated As content in soil porewater but negatively correlated with that of iAs. According to the sequence of the arsM-harboring microbe, it was clearly demonstrated that a community shift of As-methylating microbe occurred with the soil drying. Here, the following conclusions were derived:① the drying process did not lower the As methylation efficiency in paddy soil. On the contrary, in this study, the As methylation efficiency, especially that for ND soil, remarkably improved. The addition of straw notably promoted the As methylation efficiency and the content of DMAs in porewater. ② An increasing tendency was observed for the abundance of microbes related to As methylation, whereas a reverse trend was indicated for microbes related to As demethylation. The community shift of arsM-harboring microbes might be the crucial reason for the improved As methylation efficiency during the soil drying. These observations contribute to a better understanding of the As methylation process during paddy soil drying and will shed light on the future mitigation of rice straight head disease in paddy soils.

Discrepant impact of polyethylene microplastics on methane emissions from different paddy soils

Microplastics (MPs) can affect soil organic carbon (C) cycling in paddy soil by changing microbial function and soil properties. In this study, a laboratory incubation experiment was applied to explore the effect of polyethylene (PE) MP on methane (CH4) and carbon dioxide (CO2) emissions from paddy soils after rice straw addition. Moreover, the microbial functional genes encoding CH4 oxidation and production and organic C degradation were measured. MP addition significantly (p < 0.05) affected the release of CH4, but this effect varied with soil type. The amendment of PE MPs significantly (p < 0.05) reduced CH4 emission by 16.9 % for the acidic soil (pH = 5.0) and 16.1 % for the alkaline soil (pH = 8.2), which was probably due to these plastic particles inhibiting CH4 production by reducing the abundance of the mcrA gene or stimulating CH4 oxidation with the increasing number of pmoA gene copies, respectively. For the neutral soils, the presence of PE MPs did not significantly (p > 0.05) alter CH4 emissions and their associated microbial functional genes. Across the experimental paddy soils, the response of CH4 emissions to MPs was negatively and positively correlated with those of soil ammonium (NH4+) content and mcrA gene abundance, respectively, suggesting that the change in these variables may control the release of CH4 in the presence of MPs. In addition, PE MPs had a negligible effect on soil CO2 emissions and the abundances of all functional genes encoding starch, hemicellulose, and lignin degradation. Our results demonstrated that the presence of MPs affects the release of CH4, probably by regulating NH4+ substrates and methanogens, and this emerging environmental factor should be considered when estimating CH4 emissions from paddy fields.

Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change

Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.

Effect of gradual increase of atmospheric CO2 concentration on nitrate-dependent anaerobic methane oxidation in paddy soils

Nitrate-dependent anaerobic oxidation of methane (AOM) is a new pathway to reduce methane emissions from paddy ecosystems. The elevated atmospheric CO2 concentration can affect methane emissions from paddy ecosystems, but its impact on the process of nitrate-dependent AOM is poorly known. Based on the automatic CO2 control platform with open top chambers and the 13CH4 stable isotope experiments, the responses of the activity of nitrate-dependent AOM, abundance and community composition of Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea to the gradual increase of CO2 concentration were investigated in paddy fields. We set up two CO2 concentration treatments, including an ambient CO2 and a gradual increase of CO2(increase of 40 μL·L-1 per year above ambient CO2 concentration until 160 μL·L-1). The results showed the nitrate-dependent AOM rate of 0.7-11.3 nmol CO2·g-1·d-1 in the studied paddy fields, and quantitative PCR showed the abundance of M. nitroreducens-like archaeal mcrA genes of 2.2×106-8.5×106 copies·g-1. Compared to the ambient CO2 treatment, the slow elevated CO2 treatment enhanced the nitrate-dependent AOM rate and stimulated the abundance of M. nitroreducens-like archaea, particularly in 5-10 cm soil layer. The gradual increased CO2 concentration treatment did not change the community composition of M. nitroreducens-like archaea, but significantly decreased their diversity. The soil organic carbon content was an important factor influencing the nitrate-dependent AOM process. Overall, our results showed that the gradual increase of CO2 concentration could promote the nitrate-dependent AOM, suggesting its positive role in mitigating methane emissions from paddy ecosystems under future climate change.

Anaerobic Digestion in the Presence of Antimicrobials—Characteristics of Its Parameters and the Structure of Methanogens

Antibiotics are widely used in human and veterinary medicine, and they are accumulated in various types of waste, including sewage sludge (SS) and cattle slurry (CS), processed by anaerobic digestion (AD). Anaerobic treatment is a method enabling the stabilization of these substrates before transferring to the environment. The presence of contaminants, such as antimicrobials, in organic substrates processed by AD is not regulated by law. The accumulation of antimicrobials in SS and CS is a crucial issue because it may reduce the effectiveness of their stabilization. This study aimed to evaluate the long-term impact of growing concentrations of a mixture of antibiotics on the AD of SS and CS. Methane (CH4) yield, which is the main indicator of the efficiency of AD, was determined. Antibiotic exposure significantly decreased CH4 production only in SS (by 5–8% relative to control; p &lt; 0.05). The copy numbers of the mcrA gene, a functional marker of methanogenesis, were not reliable indicators of CH4 yields in either substrate. During long-term AD, the average concentrations of the mcrA gene were determined at 108 in 1 g of SS digestate and from 108 to 109 in 1 g of CS digestate samples. At the end of long-term AD, methanogens belonging to the family Methanosarcinaceae were more prevalent than methanogens of the family Methanosaetaceae both in SS and CS samples (107 and 108–109 gene copies in 1 g of digestate, respectively).

Acetoclastic methanogenesis pathway stability despite the high microbial taxonomic variability in the transition from acidogenesis to methanogenesis during food waste anaerobic digestion

Anaerobic digestion (AD) is a microbial-mediated biogeochemical process that includes hydrolysis, acidogenesis, acetogenesis and methanogenesis. AD instability usually occurs in the transition from the acidogenesis phase (AP) to the methanogenesis phase (MP) due to over acidification. However, the underlying microbial mechanism of this transition has not been well characterized. In the present study, the transition of bacterial and methanogenic community composition, methanogenesis functional gene expression and metabolic pathways from AP to MP during food waste (FW) AD were investigated in a bioreactor using metagenomics and reverse transcription PCR technology. AP and MP were identified by changes in methane production, gas accumulation, pH and volatile fatty acids (VFAs). Concomitant with the changes in these physiochemical parameters, the bacterial and methanogenic community composition showed succession patterns. The bacterial composition transformed from acidogenic bacteria (Propionispira and Bacteroides) to hydrolytic bacteria (Smithella, Syntrophus and Syntrophorhabdus), and the methanogen composition transformed from the domination of acetoclastic methanogens (Methanosaeta) to the codomination of hydrogenotrophic methanogens (Methanoculleus, Methanolinea and Methanobacterium) and acetoclastic methanogens (Methanosaeta). The expression level of the methanogenesis functional gene mcrA significantly (p < 0.05) increased in response to the increasing methane production. In contrast, acetoclastic methanogenesis as the main methanogenesis metabolic pathway remained stable. These results showed that FWAD key physiochemical parameters drive the variation in microbial community composition and functional genes expression but not the methanogenesis metabolic pathway. The finding suggests that FWAD process may be better predicted by methanogenic functional characteristics than by microbial community composition.

Unravelling how biochar and dung amendments determine the functional structure and community assembly related to methane metabolisms in grassland soils

Biochar and dung amendments have been extensively employed in soil remediation and fertilization of grasslands, which are the largest terrestrial sinks for methane. However, how these exogenous amendments regulate methane metabolisms at the molecular and community levels remains elusive. In this study, we investigated the functional genes and community assemblies of methanogens and methanotrophs using Geochip 5.0 and high-throughput sequencing to reveal the impacts of biochar and dung on soil methanogenesis and methane oxidation. The interactions between methane metabolic genes and other biogeochemical genes were also examined. According to Geochip microarrays, methanogenic gene mcrA decreased and increased with dung or biochar amendment, respectively; The methanotrophic gene pmoA showed a reverse but not significant tendency. Undominated processes contributed 65.51% to replace homogeneous selections as primary driving forces of methanogen assembly after dung amendment; the contribution of dispersal limitation increased to 46.13% in methanotroph assembly after biochar amendment. The diversity and association of co-occurrence networks for carbon–nitrogen cycling genes decreased after exogenous amendments. These results indicated that biochar and dung amendments prominently regulated the functional genes and community assembly involved in methane metabolisms. The co-existence patterns of methane metabolic genes and other related geochemical genes were also shaped by these amendments. This study provides the scientific reference for the development of grassland management in the context of global warming.Graphical

Reduction of greenhouse gas (GHG) emission in the vegetation-activated sludge process (V-ASP) involving decontaminated plants for decentralized wastewater treatment

Wastewater treatment plant (WWTP) is one of the important sources for anthropogenic greenhouse gases (GHGs) emission. The objective of this study was to evaluate vegetation-activated sludge process (V-ASP) that simultaneously achieved the improvement of decentralized wastewater treatment performance and reduction of GHGs emission, in contrast to conventional ASP. With the same organic and nitrogen loading rates and operational modes, V-ASP achieved a decreasing of 19.79% for total GHGs emission in comparison to ASP. From the microbial community analysis on activated sludge microbes and plant roots, V-ASP had a much lower abundance of Chloroflexi, and a comparable abundance of denitrifiers, in contrast to conventional ASP, which likely correlated with the differences of CH4 production and emission. Specifically, it was noted that the relatively higher abundance of mcrA and nirS genes in the V-ASP would take a certain responsible for reducing CH4 and N2O emission, respectively. The V-ASP also demonstrated the increased enzymatic activities, such as ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO), which could help to reduce GHGs emission flux. It was proved that V-ASP process, compared to the traditional ASP process, was an effective decentralized wastewater treatment technique for reducing GHGs emission.

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea.

The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann-Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfate-reducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

Anaerobic Digestion of Chicken Manure in the Presence of Magnetite, Granular Activated Carbon, and Biochar: Operation of Anaerobic Reactors and Microbial Community Structure

The influence of magnetite nanoparticles, granular activated carbon (GAC), and biochar, as well as their combinations on the anaerobic digestion of chicken manure and the structure of microbial communities was studied. The addition of magnetite, GAC, and biochar increased the rate of methane production and the total methane yield. It has been observed that these additives stimulated anaerobic microorganisms to reduce the concentration of accumulated volatile organic acids. Various bacterial species within the classes Bacteroidia and Clostridia were found at higher levels in the anaerobic reactors but in different proportions depending on the experiment. Members of the genera Methanosarcina, Methanobacterium, Methanothrix, and Methanoculleus were mainly detected within the archaeal communities in the anaerobic reactors. Compared to the 16S rRNA gene-based study, the mcrA gene approach allowed a higher level of Methanosarcina in the system with GAC + magnetite to be detected. Based on our findings, the combined use of granular activated carbon and magnetite at appropriate dosages will improve biomethane production.

Evaluation of the synergistic effects of biochar and biogas residue on CO2 and CH4 emission, functional genes, and enzyme activity during straw composting

This study examined the effects of biochar, biogas residue, and their combined amendments on CO2 and CH4 emission, enzyme activity, and related functional genes during rice straw composting. Results showed that the biogas residue increased CO2 and CH4 emissions by 13.07 % and 74.65 %, while biochar had more obvious inhibition. Biogas residue addition enhanced functional gene abundance more than biochar. Biogas residue raised the methanogens mcrA gene by 2.5 times. Biochar improved the Acetyl-CoA synthase and β-glucosidase activities related to carbon fixation and decreased coenzyme activities related to methanogens. Biochar and biogas residue combined amendments enhanced the acsB gene abundance for CO2 assimilation process and decreased methyl-coenzyme M reductase α subunit activity. Pearson correlation analysis indicated that organic matter was the significant variable affecting CO2 and CH4 emissions (P < 0.01). These results indicated biochar played significant roles in carbon loss and greenhouse emissions caused by biogas residue incorporation during composting.

Polycyclic aromatic hydrocarbons stimulate acidogenesis, acetogenesis and methanogenesis during anaerobic co-digestion of waste activated sludge and food waste

Polycyclic aromatic hydrocarbons (PAHs) have been reported to influence acetic acid production during anaerobic treatment. However, investigations of the impacts of PAHs on the anaerobic co-digestion of waste activated sludge and food waste are limited. Therefore, the effects of PAHs on anaerobic co-digestion were explored in this study. Four kinds of PAHs all exhibited positive contributions to methane production, especially phenanthrene. Mechanism exploration revealed that acidogenesis, acetogenesis, and methanogenesis were improved in the presence of phenanthrene, and acetotrophic methanogenesis had the greatest improvement with 69.4%. Dominant bacteria and archaea related to acetic acid and methane accumulation were changed by phenanthrene. Moreover, extracellular polymeric substances, coenzyme F420, and McrA gene copy number were promoted by phenanthrene, which was beneficial for the generation of acetic acid and methane. Overall, this study provides new insights into the role of organic pollutants in the anaerobic co-digestion of solid wastes.

System performance and functional analysis for the methanogenic bioreactor of a two-phase anaerobic digestion system: The effect of influent sulfate

In this study, a lab-scale bioreactor was built to investigate the influence of sulfate on the overall performance, microbial community, and metabolic pathways in the methanogenic bioreactor of a two-phase anaerobic digestion system. The results demonstrated that by gradually cultivating the sludge of the methanogenic bioreactor, a chemical oxygen demand (COD) degradation efficiency of over 65% was achieved for sulfate contents from 10,000 mg/L to 30,000 mg/L. The sulfate reduction performance could only be maintained at a high level for influent COD/sulfate ratios no less than 1.88. In addition, the methane production rate (MPR) decreased from 0.92 L/L/d to 0.28 L/L/d, and the proportion of methane in biogas dropped from 51% to 33% when the influent sulfate exceeded 30,000 mg/L. High-throughput sequencing coupled with PICRUSt2 revealed that the dissimilatory sulfate process could be enhanced by sulfate within 30,000 mg/L. While an amount of greater than 5000 mg/L sulfate remarkably inhibited the assimilatory sulfate reduction process, and this inhibition was induced by the down-regulation of the cysNC, cysC, cysI and cysJ genes. For the methanogenic process, sulfate contents within 30,000 mg/L had no obvious impact on all of the acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis processes, but serious suppression was observed for sulfate amounts greater than 30,000 mg/L. This inhibition primarily originated from the decrease in mcrA, mcrB, and mcrG genes that regulate the conversion of methylcoenzyme M to methane, the last step of all three methanogenesis pathways.

Soil-tree-atmosphere CH4 flux dynamics of boreal birch and spruce trees during spring leaf-out

AimsStudies on tree CH4 exchange in boreal forests regarding seasonality and role of tree canopies are rare. We aimed to quantify the contribution of boreal trees to the forest CH4 budget during spring leaf-out and to reveal the role of microbes in the CH4 exchange.MethodsMethane fluxes of downy birch and Norway spruce (Betula pubescens and Picea abies) growing on fen and upland sites were measured together with soil CH4 flux, environmental variables and microbial abundances involved in the CH4 cycle. Tree CH4 fluxes were studied from three stem heights and from shoots.ResultsThe trees emitted CH4 with higher stem emissions detected from birch and higher shoot emissions from spruce. The stem CH4 emissions from birches at the fen were high (mean 45 µg m−2 h−1), decreasing with stem height. Their dynamics followed soil temperature, suggesting the emitted CH4 originated from methanogenic activity, manifested in high mcrA gene copy numbers, in the peat soil. Methanogens were below the quantification limit in the tree tissues. Upscaled tree CH4 emissions accounted for 22% of the total CH4 emissions at the fen.ConclusionsThe variation in stem CH4 flux between the trees and habitats is high, and the emissions from high-emitting birches increase as the spring proceeds. The lack of detection of methanogens or methanotrophs in the aboveground plant tissues suggests that these microbes did not have a significant role in the observed tree-derived fluxes. The stem-emitted CH4 from birches at the fen is presumably produced microbially in the soil.

​Quantification and Microbial Diversity Analysis of Ruminal Methanogenic Populations in Indian Gir Native Cattle

Background: Methane emission from the ruminants is receiving global attention due to its global warming potential. It imposes the development of cost-effective and easily adoptable energy to reduce methane emissions from ruminants. Apart from this, the information available on the methanogenic microflora and their populations in the Indian native cattle is also very limited. In this study, the normal methanogenic microflora of Indian native Gir cattle was studied using molecular methods and compared with cross breed cattles. Methods: The rumen fluid was collected and DNA isolation was carried out from Gir, Gir cross and Kangayam crossbred cattle. The partial 16S rRNA and mcrA gene amplification were carried out by PCR and further subjected to sequence analysis. Further, Methanogenic population in the ruminal fluid were analyzed by SYBR Green-based real-time PCR. Result: This study provides a basic understanding of the normal methanogenic microfloral diversity and their population in the Gir native cattle of Indian origin compared with cross breed cattle.

Suppression of methanogenesis in paddy soil increases dimethylarsenate accumulation and the incidence of straighthead disease in rice

Some soil microbes can methylate arsenic (As) and produce dimethylarsenate (DMA) as a main product. Excessive accumulation of DMA by rice plants can cause the straighthead disease, a physiological disorder leading to substantial yield losses. DMA can also be demethylated in soil, but the mechanism and the microbes involved are not well understood. We investigated the dynamics of methylated As species, including monomethylarsenate (MMA), DMA and dimethyl-monothioarsenate (DMMTA), in three paddy soils that produced the straighthead disease. The soils were incubated under flooded conditions with or without the addition of 2-bromoethanesulfonate (BES), a specific inhibitor of methanogenesis. DMA and DMMTA concentrations in porewater increased initially as soil redox potential decreased, and then decreased rapidly coinciding with the production of methane. BES addition largely suppressed methanogenesis and the disappearance of DMA and DMMTA, but not of MMA. BES addition suppressed the transcript levels of archaeal 16S rRNA and, particularly, mcrA gene encoding methyl-coenzyme reductase subunit A. Among the core genera of archaea, the absolute abundances of Methanomassiliicoccus and Methanosarcina were decreased significantly by BES in the three soils. In a pot experiment with two soils, BES addition significantly increased DMA accumulation in rice husks and the incidence of the straighthead disease in rice. The results suggest that DMA and DMMTA demethylation in paddy soil is coupled to methanogenesis with Methanomassiliicoccus and Methanosarcina likely playing an important role.

Effect of microbial community structures and metabolite profile on greenhouse gas emissions in rice varieties

Rice paddy fields are major sources of atmospheric methane (CH4) and nitrous oxide (N2O). Rice variety is an important factor affecting CH4 and N2O emissions. However, the interactive effects of rice metabolites and microorganisms on CH4 and N2O emissions in paddy fields are not clearly understood. In this study, a high greenhouse gas-emitting cultivar (YL 6) and a low greenhouse gas-emitting cultivar (YY 1540) were used as experimental materials. Metabolomics was used to examine the roots, root exudates, and bulk soil metabolites. High-throughput sequencing was used to determine the microbial community composition. YY 1540 had more secondary metabolites (flavonoids and isoflavonoids) in root exudates than YL 6. It was enriched with the uncultured members of the families Gemmatimonadanceae and Rhizobiales_Incertae_Sedis in bulk soil, and genera Burkholderia-Caballeronia-Paraburkholderia, Magnetospirillum, Aeromonas, and Anaeromyxobacter in roots, contributing to increased expression of pmoA and nosZ genes and reducing CH4 and N2O emissions. YL 6 roots and root exudates contained higher contents of carbohydrates [e.g., 6-O- acetylarbutin and 2-(3- hydroxyphenyl) ethanol 1′-glucoside] than those of YY 1540. They were enriched with genera RBG-16-58-14 in bulk soil and Exiguobacterium, and uncultured member of the Kineosporiaceae family in roots, which contributed to increased expression of mcrA, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nirS, and nirK genes and greenhouse gas emissions. In general, these results established a link between metabolites, microorganisms, microbial functional genes, and greenhouse gas emissions. The metabolites of root exudates and roots regulated CH4 and N2O emissions by influencing the microbial community composition in bulk soil and roots.