pmoA Gene Copy Numbers Research Articles

Effects of Fallow Season Water and Straw Management on Methane Emissions and Associated Microorganisms

The effects of fallow season water and straw management on methane (CH4) emissions during the fallow season and the subsequent rice-growing season are rarely reported, and the underlying microbial mechanisms remain unclear. A field experiment was conducted with four treatments: (1) fields flooded in both the fallow and rice seasons (FF), (2) fields drained in the fallow season and flooded in the rice season (DF), (3) FF with straw retention (FFS), and (4) DF with straw retention (DFS). The CH4 emissions in fields under different water and straw treatments were monitored using the static closed chamber method. Methanogenic and methanotrophic communities in these fields were examined using terminal restriction fragment length polymorphism (T-RFLP) analysis based on the mcrA gene and pmoA gene encoding methyl coenzyme M reductase and particulate methane monooxygenase, respectively. The results showed that CH4 emissions were significantly affected by water management, straw retention, season, and their interactions. Over 80% of CH4 emissions occurred during the rice season. Field drainage during the fallow season reduced CH4 emissions by 47.0% and 53.8% with and without straw during the rice season, respectively. Water management altered the abundance and composition of methanogens and methanotrophs, whereas the effects of straw retention were less pronounced. The quantitative polymerase chain reaction (qPCR) assay revealed that field drainage in the fallow season decreased the mcrA gene abundance by 30.0% and 23.2% with and without straw in rice season, respectively, and increased the pmoA gene abundance by 108.9% and 213.7% with and without straw in rice season, respectively. CH4 flux was significantly positively associated with mcrA gene copy number and the ratio of mcrA to pmoA gene copy number, whereas it was significantly negatively correlated with the pmoA gene copy number. Results indicated that fallow drainage greatly decreased CH4 emission not only during the fallow season but also during the subsequent rice season by altering the community composition of methanogens and methanotrophs. These findings provide scientific insight into the role of water and straw management in controlling CH4 emissions through microbial community dynamics.

Field study on the effect of vegetation on the performance of soil methanotrophy-based engineered systems – Column experiments

Current literature provides conflicting information on the role vegetation plays when considering methane (CH4) oxidation potential of engineered Biosystems, such as landfill biocovers (LBCs), bio-windows and methane biofilters. The primary objective of this study was to determine whether the impact of vegetation on biological CH4 oxidation was positive or negative and to explain the reasons for the observations using a variety of experiments. A total of eight flow-through columns (two alfalfa, two native grass, two canola and two bare-soil replicates) were set up outdoors to simulate field operation in cold climatic conditions. Each column was layered with 18 cm of topsoil and 32 cm of compost mixture (compost 30%: topsoil 70% v/v) as packing material and treated with CH4 fluxes ranging from 180 to 815 g CH4 m−2 d−1. The bare-soil columns exhibited the highest CH4 oxidation rate of 455 g CH4 m−2 d−1, while the maximum CH4 oxidation rates for the vegetated columns ranged between 147 and 171 g CH4 m−2 d−1 with the alfalfa column showing the lowest. Gas profiles of vegetated columns showed high concentrations of nitrogen (N2) and oxygen (O2) at all depths, possibly due to increased permeability created by the plant root systems. Quantitative Polymerase Chain Reaction (q-PCR) assessment showed that pmoA gene copy numbers, indicative of methanotrophic population levels, were higher in bare-soil columns than in vegetated columns. The Illumina based sequencing of 16S rRNA gene showed that Type I methanotrophs dominated both vegetated and bare-soil columns. Soil incubation experiments conducted to determine oxidation kinetic parameters also indicated greater methanotrophic activity in the bare-soil columns than in vegetated columns. The plant data collected at the end of the column experiments provided clear evidence of CH4 escape due to preferential pathways created by plant roots (reaching 38 cm, 31.5 cm and 26.5 cm by alfalfa, canola and native grass, respectively) that resulted in decreased CH4 oxidation in vegetated columns. The study results clearly demonstrate that vegetation decreases CH4 oxidation at high loading rates, notwithstanding the type of vegetation.

Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea)

Rhizoremediation, CH4 emission, and bacterial community dynamics were evaluated in diesel-contaminated soil cultivated with tall fescue via a pot experiment. At the beginning of the experiment, total petroleum hydrocarbons (TPHs) removal efficiency was 30.2% in tall fescue-cultivated soil, which was significantly higher than that of unplanted soil (19.4%). However, when compost was added as a soil amendment, TPHs removal efficiency increased to 39.2% in tall fescue-cultivated soil. Interestingly, potential CH4 emissions were more affected by the initial diesel concentration than by compost addition or tall fescue planting. Specifically, the potential CH4 emission was approximately 3.8 times higher in the treatment with the highest initial diesel concentration (T-WC38) than that of the treatment with the lowest initial diesel concentration (T-WC5). Functional gene analysis revealed that TPHs removal had a linear correlation with the alkB/16S gene ratio, whereas potential CH4 emission had a linear correlation with pmoA gene copy numbers. Initial diesel concentrations in soil also affected bacterial community structures and the genera Rhizobium, Halothiobacillus, and Geobacter were found to be positively linked to diesel-contaminated soil rhizoremediation. Therefore, this study provides useful insights into the development of strategies to enhance rhizoremediation efficiency and CH4 emission mitigation in diesel-contaminated soils.

Temporal shift in methanotrophic community and methane oxidation potential in forest soils of dry tropics: high-throughput metagenomic approach

Forest soil contributes to global methane (CH4) cycle as the natural sink for atmospheric CH4 by methane-oxidizing bacteria (MOB). In this study, high-throughput sequencing of pmoA gene amplicons based approach was used to investigate temporal variations in molecular diversity of MOB in soil of tropical dry forest. Quantitative PCR (qPCR) analysis revealed pmoA and 16S rRNA gene copy numbers (copies g−1 dws) ranging from 2.23 × 106 to 14.62 × 106 and from 0.92 × 109 to 14.99 × 109, respectively, in the year 2016. In 2017, the respective values varied from 1.96 × 106 to 13.62 × 106 and from 2.55 × 109 to 20.15 × 109, respectively. The sequence analysis revealed the existence of both type I and type II methanotrophs in soils. The average observed OTUs were about 800/sample, and Shannon diversity index ranged between 4.24 and 6.22 being highest in winter season. The rice paddy clusters (RPCs), Methylocystis, Methlylocystis-Methylosinus and JR2 and JR3, dominated the methanotrophic community with relative abundance of 32.7–50.2, 15.4–34.2, 0.45–15.8, 0.0–17.8 and 1.6–19.2%, respectively. Relatively, higher CH4 oxidation potential (MOP) (ng CH4 g−1 h−1 dws) was observed in winter (14.12) compared with rainy (2.10) and summer (3.72) coinciding with high methanotrophic diversity and abundance. Overall, the study suggests that tropical dry deciduous forest soils favour considerable range of methanotrophic diversity and abundance that positively correlates with MOP of soils across season.

Co‐incorporation of Chinese milk vetch (Astragalus sinicus L.) and rice (Oryza sativa L.) straw minimizes CH4 emissions by changing the methanogenic and methanotrophic communities in a paddy soil

AbstractThe practice of co‐incorporating rice straw and leguminous green manure (such as Chinese milk vetch) into paddy soils has become increasingly popular in the last 10 years, although its effect on soil CH4 emissions and microbial community structure is poorly understood. In this study, data from a 2‐year pot experiment were used to reveal the effects of the co‐incorporation of rice straw and Chinese milk vetch on CH4 emissions and methanogenic and methanotrophic communities in paddy soil. Five treatments were chosen: CK (unamended control), CF (inorganic fertilizer), FM (inorganic fertilizer and Chinese milk vetch, 20 g 10 kg−1 dry soil, 4.5 t ha−1), FR (inorganic fertilizer and rice straw, 20 g 10 kg−1 dry soil, 4.5 t ha−1) and FMR (inorganic fertilizer and Chinese milk vetch and rice straw mixture, 5 + 15 g 10 kg−1 dry soil, 1.125 + 2.375 t ha−1). Overall, the soil CH4 emissions in the 2 years under all residue treatments (104.4–122.8 and 83.3–133.3 g CH4 m−2) were higher than those in CK (57.0 and 20.7 g CH4 m−2) and CF (71.8 and 21.9 g CH4 m−2) treatments. The FMR treatment decreased CH4 emissions when compared with FM and FR, especially in the second year. A higher abundance of methanogens (mcrA gene copies) was found under the plant residue‐treated soils (4.35 × 108 g−1 dry soil on average) and FM increased the abundance of methanotrophs (pmoA gene copies, 2.68 × 106 g−1 dry soil). Application of plant residues changed the methanogenic and methanotrophic community structures in comparison with CF (e.g., markedly increased the populations of Methanobacteriales and Methylomonas and suppressed Methanomicrobiales and Methylobacter populations). Methane emissions were significantly and positively related to the mcrA and pmoA gene copy numbers, as well as the mcrA/pmoA ratio. The partial least squares path model (PLS‐PM) indicated that the rice plant biomass (path coefficient = 0.64), the abundance of methanogens (path coefficient = 0.57) and the community structure of methanotrophs (path coefficient = −0.59) were determinants of CH4 emissions. Among the three residue‐treated soils, FMR showed the lowest CH4 emissions and was associated with a slight decrease in the mcrA/pmoA ratio and a significant increase in the Type I/Type II methanotrophs ratio. Thus, we recommend the co‐incorporation of Chinese milk vetch and rice straw as a sustainable fertilization pattern to improve the growth of rice and minimize CH4 emissions.Highlights Residue application improves rice productivity (except for FR), soil fertility and CH4 emissions. Co‐incorporation of MV and RS reduces CH4 emissions in comparison with pure MV or RS addition. Residue application changes the community structure of methanogens and methanotrophs. The methanogenic abundance and the methanotrophic community structure determine the CH4 emissions.

Methane and Nitrous Oxide Flux after Biochar Application in Subtropical Acidic Paddy Soils under Tobacco-Rice Rotation

Biochar amendment is a good means of mitigating methane (CH4) and nitrous oxide (N2O) emissions. However, the effects of biochar amendment on N2O and CH4 reduction in soil under rotation with different soil moisture contents is not well understood. To understand CH4 and N2O flux from soil with biochar amendment under water-unsaturated and water-saturated conditions, a field experiment was conducted in a tobacco-rice rotation field in subtropical China to investigate N2O and CH4 emissions following soil amendment with tobacco straw biochar at rates of 0, 10, 40 and 80 t·ha−1 (B0, B10, B40 and B80, respectively). N2O and CH4 emissions were monitored by a closed-chamber method in the water-unsaturated tobacco (UT) and water-saturated rice (SR) seasons during the 2015 planting season. The soil pH increased from 5.4 in the control to 6.1 in the soil amended with biochar at 80 t·ha−1 in the UT season. During both the UT and SR seasons, with biochar amendment at 40 and 80 t·ha−1, the soil bulk density (BD) decreased, while the soil organic matter (SOM) and available potassium (Av. K) contents increased. N2O flux was significantly greater in UT than in SR in the controls but decreased with the application of biochar during both the UT and SR seasons. The cumulative CH4 emission decreased with the rate of biochar application and the methanotroph pmoA gene copy number in soils and increased with the methanogenic archaea 16Sr DNA gene copy number in soils during the rice-cropping season. These results indicated that biochar amendment could decrease methanogenic archaea and increase of methanotroph pmoA gene, which are the mechanistic origin for CH4 reduction.

Sediment methane dynamics along the Elbe River

Methane (CH4) is an important atmospheric trace gas mostly released from wet anoxic soils and sediments. While many studies have focused on relatively homogenous environments like rice fields and lake sediments, the changing contribution of heterogeneous sediments e.g. along the longitudinal profile of a rivers has not been covered very frequently. Here we investigated sediment samples from 11 locations of the Elbe River. Sediments were incubated to measure methanogenic/methanotrophic potentials and contribution of individual methanogenic pathways using isotope analysis of δ13C. Additionally, we determined the diversity of the methanogenic communities (analysis of T-RFLP targeting the mcr-A gene in the sediment samples), while abundances of archaea, methanogens and methanotrophs were determined by qPCR. The CH4 production was detected in six samples (out of 11 examined) and ranged from 0.12 to 644.72 nmol gDW−1 d−1. Methanotrophy was found in all examined sediment samples and ranged from 654 to 10,875 nmol gDW−1 d−1. Abundance of methanogens and methanotrophs (Mcr-A and pmo-A gene copy numbers) was not significantly different and quite stable around 106 to 107 copies gDW−1. The group specific qPCR showed high fluctuations, while the highest counts were reported for Methanomicrobiales and Methanosarcinales (105 to 108 copies per gram dry sediment), followed by Methanobacteriales (103 to 105 copies per gram dry sediment). A significant proportion of unidentified methanogens was found in almost every locality. Isotope analysis of δ13C showed that (CH4) is produced mainly by hydrogenotrophic methanogens. We see no trend in the studied parameters along the Elbe River. The molecular data showed no spatial characteristics, while we found hotspots of the measured CH4 processes (CH4 production and oxidation) due to other local driving factors (e.g. carbon content). Thus, out results indicate that the observed variability of the CH4 production and oxidation rates is only indirectly linked to the presence or quantities of different microbial guilds.

Moderate grazing increases the abundance of soil methane-oxidizing bacteria and CH4 uptake rate in a typical steppe of Inner Mongolia, China.

Microbial oxidation is the only biological sink of atmospheric methane (CH4). It is essential to understand the variation of CH4 fluxes among different grassland use types for developing low-emission management system. Here, we measured the CH4 flux and the soil methane-oxidizing bacteria abundance in a typical steppe under grazing, mowing and fencing management in central Inner Mongolia, with the aims to determine the effects of these grassland use types on CH4 flux, and to test the hypothesis that pmoA functional gene abundance regulates CH4 fluxes. The measurements were conducted on the experimental grassland that had experienced four grassland use treatments over five years. The treatments were whole growing season grazing from May to September (T1), spring and summer grazing (twice in May and July)(T2), autumn mowing (T3) and enclosure (T0). We measured CH4 flux using static chamber method, and quantified the abundance of pmoA functional genes using molecular techniques. Moreover, we measured plant biomass and soil physicochemical properties. The results showed that moderate grazing significantly enhanced CH4 uptake rate and the methane-oxidizing bacteria abundance (i.e., the pmoA gene copy number per gram of dry soil). The pmoA gene copy number ranged from 6.9×104 to 3.9×105 per gram of dry soil in growing season. The CH4 uptake rate was (68.21±3.01) μg·m-2·h-1 under T1, which was 22.1%, 37.5% and 30.9% higher than that under T2, T3 or T0 , respectively. The CH4 uptake rate was positively correlated with abundance of CH4 oxidizing bacteria and soil sand content, but negatively correlated with soil silt content, soil moisture, NH4+-N and NO3--N content, and plant biomass. These results suggested that the steppe ecosystem is a CH4 sink under all land-use types in central Inner Mongolia, and that moderate grazing would enhance methane-oxidizing bacteria abundance and CH4 uptake by improving soil sand content, reducing soil mineral nitrogen content and plant production in the typical steppe ecosystem. These results were of significance for the development of low-emission grassland management system.

Linking methane emissions to methanogenic and methanotrophic communities under different fertilization strategies in rice paddies

Rice paddies are a significant source of atmospheric methane (CH4) threatening global warming. Methane fluxes from rice soils are mediated by both methanogens and methanotrophs, while subject to fertilization regimes. A field experiment was conducted to investigate the response of CH4 emissions, with a close link to methanogenic and methanotrophic communities, to different fertilization strategies over two consecutive rice growing seasons in a paddy field. Four fertilized treatments were established consisting of chemical phosphorous (P) and potassium (K) fertilizer (PK), chemical nitrogen (N) PK fertilizer (NPK), chemical NPK combined with organic manure (NPKM), and organic manure alone (M). Results showed that, relative to chemical PK treatment without N fertilizer input, the application of chemical NPK fertilizer, manure, and their combination significantly increased seasonal mean CH4 emissions by 67.4, 20.4 and 101.2%, respectively. Methane fluxes were significantly and positively (r2 = 0.75) related to mcrA gene copy numbers and the ratio of mcrA/pmoA, while negatively (r2 = 0.40) related to pmoA gene copy numbers, which was mainly regulated by the dynamics of water irrigation regime. The abundance of mcrA and pmoA had trade-off relationship over the rice growing season. In comparison with PK fertilization, N fertilized treatments did not alter the seasonal trend of CH4 fluxes, but enhanced the source strength of CH4 emissions through increased mcrA abundances rather than reduced pmoA-dominated methanotrophic CH4 oxidation in rice paddies. In contrast, N fertilization showed no effect on pmoA abundance and associated methanotrophic community in rice paddies. Results highlight that, given the fertilizer-driven balance between methanogenic and methanotrophic communities, fertilization options with either chemical or organic N input stimulated CH4 emissions mainly through improving soil C substrate and methanogenic activities, especially under the combination of chemical and organic N fertilization in rice paddies.

Methane oxidation in industrial biogas plants—Insights in a novel methanotrophic environment evidenced by pmoA gene analyses and stable isotope labelling studies

A broad methanotrophic community consisting of 16 different operational taxonomic units (OTUs) was detected by particulate methane monooxygenase A (pmoA) gene analyses of reactor sludge samples obtained from an industrial biogas plant. Using a cloning-sequencing approach, 75% of the OTUs were affiliated to the group of type I methanotrophs (γ-Proteobacteria) and 25% to type II methanotrophs (α-Proteobacteria) with a distinct predominance of the genus Methylobacter. By database matching, half of the total OTUs may constitute entirely novel species. For evaluation of process conditions that support growth of methanotrophic bacteria, qPCR analyses of pmoA gene copy numbers were performed during a sampling period of 70 days at varying reactor feeding scenarios. During the investigation period, methanotrophic cell counts estimated by qPCR fluctuated between 3.4 × 104 and 2 × 105 cells/mL with no distinct correlation to the organic loading rate, the amount of CH4, O2 and NH4-N. Methanotrophic activity was proofed even at low O2 levels (1%) by using stable carbon isotope labelling experiments of CH4 in batch experiments inoculated with reactor sludge. Supplementation of 13C labelled CH4 in the headspace of the reaction vials unambiguously confirmed the formation of 13C labelled CO2. Thus, industrial biogas reactors can be considered as a further methanotrophic habitat that exhibits a unique methanotrophic community which is specifically adapted to high CH4 and low O2 concentrations. To the best of our knowledge, our study is the first accurate detection and quantification of methanotrophic bacteria in industrial biogas reactors.

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

Paddy soil accounts for 10% of global atmospheric methane (CH4) emissions. Many types of fertilizers may enhance CH4 emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH4 and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha−1. Paddy CH4, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH4 emissions were significantly higher in OT (145.31 kg ha−1) than MT (84.62 kg ha−1), CT (77.88 kg ha−1) or ctrl (32.19 kg ha−1). Soil organic acids were also increased by organic fertilization. CH4 effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH4 production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH4 emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha−1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.

Effect of rice panicle size on paddy field CH4 emissions

Developing large rice (Oryza sativa L.) panicles has been widely regarded as an effective approach to increasing rice yield. However, it is unclear whether panicle size affects CH4 emissions from rice fields, especially during the reproductive stage. Here, we conducted two experiments (rice variety and mutant) to examine the effects of rice panicle size on CH4 emissions. The variety experiment under field conditions at two sites showed that rice yield was significantly and positively correlated with the spikelet number. Mean CH4 emissions during the reproductive stage were significantly and negatively correlated with spikelet number. The rice mutant experiment under pot and field conditions using a wild-type rice variety (WT) and its mutant (Mutant) demonstrated that CH4 emissions were significantly lower in the former with large panicles than in the later with small panicles, during the reproductive and grain filling stages (P < 0.01), whereas the rice yields showed an opposite. Root exudates and soil dissolved organic C concentration were significantly lower under the WT than under the Mutant. Soil CH4 production potential and mcrA gene copy number of the soil under Mutant were significantly higher than those of the soil under WT. There was no significant difference in soil CH4 oxidation potential and pmoA gene copy number between soils of these two rice varieties. Our results suggest that developing large panicles would benefit rice production for high yield with low CH4 emission.

Spatio-temporal Variation of Sediment Methanotrophic Microorganisms in a Large Eutrophic Lake.

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the methane emission from lake ecosystems to the atmosphere. However, the distribution of methanotrophic community in shallow and eutrophic lake and its influential factors remain essentially unclear. The present study investigated sediment methanotrophic microorganisms at different sites in eutrophic freshwater Dianchi Lake (China) in two different seasons. The abundance, diversity, and structure of sediment methanotrophic community showed a profound spatial and seasonal variation. The pmoA gene copy number in lake sediments ranged from 8.71 ± 0.49 × 10(4) to 2.09 ± 0.03 × 10(7) copies per gram of dry sediment. Sediment methanotrophic communities were composed of Methylococcus and Methylobacter (type I methanotrophs) and Methylosinus (type II methanotrophs), while type I MOB usually outnumbered type II MOB. Moreover, ammonia nitrogen was found to be a potential determinant of methanotrophic community structure in Dianchi Lake.

The influence of nitrogen fertiliser rate and crop rotation on soil methane flux in rain-fed potato fields in Wuchuan County, China

As one of the important greenhouse gases, the characteristics and principles of methane exchange characteristics in cultivated lands have become hot topics in current climate change research. This study examines the influences of nitrogen fertilisation, temperature and soil water content on methane exchange characteristic and methane exchange functional gene-pmoA gene abundance based on experimental observations of methane exchange fluxes using the static chamber–gas chromatographic method and measurements of methanotroph gene copy numbers in three growing periods by real-time PCR in rain-fed potato fields. The results indicate that the rain-fed potato fields were a CH4 sink with an average annual methane absorption (negative emission) of 940.8±103.2gCH4-C/ha/year. The cumulative methane absorption first exhibited flat and subsequently increasing trend with the increase of nitrogen fertilisation from 0~135kgN·ha−1. Methane cumulative absorption significantly increased with the increase of temperature when temperatures were below 19.6°C. Methane oxidation capacity (methanotroph pmoA gene copy numbers) showed an increasing and subsequently decreasing trend with the increase of soil moisture. Crop rotation was observed to increase the methane absorption in rain-fed potato fields and nearly one time higher than that under continuous cropping. A mechanism concept model of the methane exchange in rain-fed potato fields was advanced in this paper.

Inhibitory effects of sulfur compounds on methane oxidation by a methane-oxidizing consortium

Kinetic and enzymatic inhibition experiments were performed to investigate the effects of methanethiol (MT) and hydrogen sulfide (H2S) on methane oxidation by a methane-oxidizing consortium. In the coexistence of MT and H2S, the oxidation of methane was delayed until MT and H2S were completely degraded. MT and H2S could be degraded, both with and without methane. The kinetic analysis revealed that the methane-oxidizing consortium showed a maximum methane oxidation rate (Vmax) of 3.7 mmol g-dry cell weight (DCW)(-1) h(-1) and a saturation constant (Km) of 184.1 μM. MT and H2S show competitive inhibition on methane oxidation, with inhibition values (Ki) of 1504.8 and 359.8 μM, respectively. MT was primary removed by particulate methane monooxygenases (pMMO) of the consortium, while H2S was degraded by the other microorganisms or enzymes in the consortium. DNA and mRNA transcript levels of the pmoA gene expressions were decreased to ∼10(6) and 10(3)pmoA gene copy number g-DCW(-1) after MT and H2S degradation, respectively; however, both the amount of the DNA and mRNA transcript recovered their initial levels of ∼10(7) and 10(5)pmoA gene copy number g-DCW(-1) after methane oxidation, respectively. The gene expression results indicate that the pmoA gene could be rapidly reproducible after methane oxidation. This study provides comprehensive information of kinetic interactions between methane and sulfur compounds.

Effects of granular activated carbon on methane removal performance and methanotrophic community of a lab-scale bioreactor

Two identical lab-scale bioreactor systems were operated to examine the effects of granular activated carbon (GAC) on methane removal performance and methanotrophic community. Both bioreactor systems removed methane completely at a CH4 loading rate of 71.2 g-CH4·d−1 for 17 days. However, the methane removal efficiency declined to 88% in the bioreactor without GAC, while the bioreactor amended with GAC showed greater methane removal efficiency of 97% at a CH4 loading rate of 107.5 g-CH4·d−1. Although quantitative real-time PCR showed that methanotrophic populations were similar levels of 5–10 × 108 pmoA gene copy number·VSS−1 in both systems, GAC addition changed the methanotrophic community composition of the bioreactor systems. Microarray assay revealed that GAC enhanced the type I methanotrophic genera including Methylobacter, Methylomicrobium, and Methylomonas of the system, which suggests that GAC probably provided a favorable environment for type I methanotrophs. These results indicated that GAC is a promising support material in bioreactor systems for CH4 mitigation.

Tobermolite effects on methane removal activity and microbial community of a lab-scale soil biocover

Three identical lab-scale biocovers were packed with an engineered soil (BC 1), tobermolite only (BC 2), and a mixture of the soil and tobermolite (BC 3), and were operated at an inlet load of 338-400g-CH4m(-2)d(-1) and a space velocity of 0.12h(-1). The methane removal capacity was 293±47g-CH4m(-2)d(-1) in steady state in the BC 3, which was significantly higher than those in the BC 1 and BC 2 (106±24 and 114±48g-CH4m(-2)d(-1), respectively). Quantitative PCR indicated that bacterial and methanotrophic densities (6.62-6.78×10(7) 16S rDNA gene copy numberg-dry sample(-1) and 1.37-2.23×10(7) pmoA gene copy numberg-dry sample(-1) in the BC 1 and BC 3, respectively) were significantly higher than those in the BC 2. Ribosomal tag pyrosequencing showed that methanotrophs comprised approximately 60% of the bacterial community in the BC 2 and BC 3, while they only comprised 43% in the BC 1. The engineered soil favored the growth of total bacteria including methanotrophs, while the presence of tobermolite enhanced the relative abundance of methanotrophs, resulting in an improved habitat for methanotrophs as well as greater methane mitigation performance in the mixture. Moreover, a batch experiment indicated that the soil and tobermolite mixture could display a stable methane oxidation level over wide temperature (20-40°C, at least 38μmolg-dry sample(-1)h(-1)) and pH (5-8, at least 61μmolg-dry sample(-1)h(-1)) ranges. In conclusion, the soil and tobermolite mixture is promising for methane mitigation.

Importance of rice root oxidation potential as a regulator of CH4 production under waterlogged conditions

One of the most important characteristics of a rice cultivar controlling methane (CH4) production can be the root oxidation potential because a cultivar with a high oxygen (O2)-releasing capacity can create an oxidized root area in the rhizosphere and this can oxidize CH4 during rice cultivation. The root oxidation potential of six Korean rice cultivars grown in a minirhizotron was measured by digital image analysis of the oxidized root areas and compared with the conventional method (root oxidase activity by using α-napthylamine as a substrate). In addition, pmoA gene copy numbers of the rhizosphere of the cultivars, indicating soil methanotrophic bacterial population and measured by qPCR assays, were compared. Oxidized root area and pmoA gene copy numbers differed significantly among cultivars (P < 0.05), but not the root oxidase activity. Oxidized root area was significantly and negatively correlated with rhizospheric dissolved CH4-C and mean CH4 emission rate by plants and significantly and positively correlated with the rhizospheric dissolved carbon dioxide (CO2)-C and pmoA gene copy number as well as with some of selected plant growth parameters such as root biomass and root volume. The Dongjin cultivar had a high root oxidation potential, while Nampyeong, Chuchung, and Samkwang had a low root oxidation potential under a flooded paddy soil environment. In addition, the characterization of oxidized root area by digital image analysis rather than the α-napthylamine oxidation method was more effective in differentiating root oxidation potential among different lowland rice cultivars.

Effect of trichloroethylene and tetrachloroethylene on methane oxidation and community structure of methanotrophic consortium

The methane oxidation rate and community structure of a methanotrophic consortium were analyzed to determine the effects of trichloroethylene (TCE) and tetrachloroethylene (PCE) on methane oxidation. The maximum methane oxidation rate (Vmax ) of the consortium was 326.8 μmol·g-dry biomass−1·h−1, and it had a half-saturation constant (Km ) of 143.8 μM. The addition of TCE or PCE resulted in decreased methane oxidation rates, which were decreased from 101.73 to 5.47–24.64 μmol·g-dry biomass−1·h−1 with an increase in the TCE-to-methane ratio, and to 61.95–67.43 μmol·g-dry biomass−1·h−1 with an increase in the PCE-to-methane ratio. TCE and PCE were non-competitive inhibitors for methane oxidation, and their inhibition constants (Ki ) were 33.4 and 132.0 μM, respectively. When the methanotrophic community was analyzed based on pmoA using quantitative real-time PCR (qRT-PCR), the pmoA gene copy numbers were shown to decrease from 7.3 ± 0.7 × 108 to 2.1–5.0 × 107 pmoA gene copy number · g-dry biomass−1 with an increase in the TCE-to-methane ratio and to 2.5–7.0 × 107 pmoA gene copy number · g-dry biomass−1 with an increase in the PCE-to-methane ratio. Community analysis by microarray demonstrated that Methylocystis (type II methanotrophs) were the most abundant in the methanotrophic community composition in the presence of TCE. These results suggest that toxic effects caused by TCE and PCE change not only methane oxidation rates but also the community structure of the methanotrophic consortium.

Comparison of Methanotrophic Activity at Top and Bottom Layers in Up-flow Biofilters

The methane oxidation characteristics at the top and bottom layers in up-flow biofilters were investigated. Two biofilters were packed with perlite and tobermolite (biofilter A: respectively top and bottom; biofilter B: respectively bottom and top) and then compared. The methane oxidation rate was analyzed with the packed bed of the biofilter layers. The bacterial population in the biofilter was characterized using quantitative real-time PCR. For the methane oxidation rate of the biofilter A column, the perlite top part () gave a relatively higher value than the tobermolite bottom part (). For the methane oxidation rate of the biofilter B column, the tobermolite top part () provided a relatively higher value than the perlite bottom part (). The pmoA gene copy numbers, responsible for methanotrophs, in the top layer of biofilter A (1.27E+13 pmoA gene copy number/mg-VSS) was higher than in the bottom layer (3.33E+13 pmoA gene copy number/mg-VSS). However, the population of methanotrophs in biofilter B was not significantly different between the top and bottom layers. These results suggest that although the methane oxidation rates of perlite and tobermolite in the top parts of biofilter A and B were high, methanotroph populations were higher in the bottom parts of both biofilters, with a rapid decline in methane concentrations within the biofilters.