Land-use effects on microbial methane dynamics across European peatlands

Spatio-temporal variations in activity of aerobic methane oxidation and community structure of methanotrophs in sediment of Wuxijiang river

Methane is one of the potential greenhouse gases contributing to global climate change, with a global warming potential of about 25 times than that of carbon dioxide. Aerobic methane oxidation (methanotrophy) is the key process that counteracts emission of methane to atmosphere. In this study, methane oxidation capacity of different methane-oxidizing bacteria (methanotrophs) isolated from six different ecosystems was investigated. Methanotrophic consortium isolated from dumpsite proved to be most effective in oxidizing methane. Initially, methane oxidation rate was found to be 0.72 ± 0.036 mM/day; in course of the study consortium M5 showed an increase in methane oxidation rate up to 1.7 ± 0.016 mM/day. A maximum of 0.78 mol of CO2 production was found during methane oxidation in methanotrophs from dumpsite (M5). While varying temperatures, methane oxidation rate was in the range of 1.3–1.7 mM/day which has been found in the temperature range of 30–40 °C. Even at higher temperature (50 °C), 0.076 ± 0.14 mM of the methane was utilized per day. Methane oxidation was assessed by Michaelis–Menten kinetics. By varying the methane concentration, methane oxidation was studied and kinetic parameters such as V max and K m were derived using Lineweaver–Burk plot and found to be 1.497 mM/day and 2.23 mM, respectively. In methane mitigation approach, Methane soil sink is very essential because a balance between methane production by methanogens and consumption by methanotrophs plays an important role in methane emission reduction. Enhancing the methane soil sink will be a cost-effective method to cut down methane emission.

Peat contains high levels of phenols and lignin, which are resistant to decomposition. Drainage canals lower the groundwater table, promoting microbial degradation. This study investigated microbial decomposition in a secondary peat swamp forest by quantifying phenol-degrading bacterial colonies and measuring phenol concentrations in peat soil from Malikian Village, Mempawah Regency, West Kalimantan. Samples were collected from three plots at two depths, the aerobic layer and the anaerobic layer, with fifteen (15) samples from each depth. Bacterial colonies were counted via mineral salt medium (MSM) with up to five dilutions, whereas phenolic compounds were measured via the Folin–Ciocalteu method. Paired t-tests revealed highly significant differences in both phenol concentration (p-value < 0.001) and the number of phenol-degrading bacterial colonies (p-value < 0.003) between the aerobic layer and the anaerobic layers. These findings indicate that peat decomposition is more pronounced in the aerobic surface layer than in the permanently waterlogged layer. This observation is attributed to the greater number of phenol-degrading bacterial colonies and lower phenol concentration in the surface layer than in the deeper layer. Consequently, the aerobic conditions in the surface layer of the secondary peat swamp forest facilitate accelerated peat decomposition

Methane oxidation and response of Methylobacter/Methylosarcina methanotrophs in flooded rice soil amended with urea

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.

This study focuses on the influence of gas seepage on methane sources and sinks, aerobic and anaerobic oxidation of methane and the mediating microbial organisms in the Black Sea. We present data from two cruises that took place in 2001 and 2003. Seven stations (two from the shelf, four from the upper and lower slope, and one from the central basin) were compared with respect to methane concentration and isotope signature. The stations differed in methane concentration depending on the location on the slope. A strong change in the concentration and isotopic composition of methane was observed below the oxic/anoxic interface, coinciding with increased levels of archaeal biomarkers (archaeol and sn-2-hydroxy-archaeol). Concentration and isotopic composition of methane in the water column and sediments indicate that sediments from the shelf, slope, and deep basin are only minor sources of methane. The main methane sources are seeps located on the shelf and upper slope, but also in the deep basin. The comparison of two shelf stations with and without methane seepage showed a difference in methane concentrations, isotopic composition and oxidation rates, but the presence of similar methanotrophic microbial assemblages. Also two deep stations at a seep and outside of a seep area were compared, but here methane concentrations and oxidation rates were not different from each other. Anaerobic methane oxidizers (ANME-1 and ANME-2 group) were observed at both stations with slightly higher cell counts at the seep station.

Evaluation of the impact of dissolved oxygen concentration on biofilm microbial community in sequencing batch biofilm reactor

Beyond nitrogen: The importance of phosphorus for CH4 oxidation in soils and sediments

The effect of water onto the rate and selectivity of methane and ethane oxidation in the conditions of oxidative coupling of methane (OCM) is studied. The effect of water strongly depends on the OCM catalyst composition: whereas PbOX/Al2O3 undergoes an irreversible deactivation, no effect of water is observed on both reaction rate and OCM selectivity over La/MgO. Over NaWMn/SiO2 catalyst both rate of reaction and selectivity are enhanced by water addition to the feed at low conversions during methane oxidation. In the case of ethane oxidation, the rate of reaction is strongly affected by water addition, whereas selectivity to ethylene does not change at equal conversions. At increasing concentration of water in the feed gas its relative effect onto the methane oxidation substantially decreases, so the increasing concentration of water above ~8 vol% does not further enhance the rate of methane oxidation. The observed effects are explained by the participation of water in the active site turnover, namely in its re-oxidation by shifting the prevailing re-oxidation route from filling surface oxygen vacancies to oxidative dehydrogenation of surface hydroxy-groups.

Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved pmoA sequences showed a broad diversity of aerobic methane oxidizers including the type I methanotrophs Methylobacter (the dominant genus), Methylomicrobium, and Methylothermus, and the type II methanotroph Methylocystis. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of pmoA using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in methanotroph community composition.

Lacustrine ecosystems are regarded as one of the important natural sources of greenhouse gas methane. Aerobic methane oxidation, carried out by methane-oxidizing bacteria, is a key process regulating methane emission. And ammonium is believed to greatly influence aerobic methane oxidation activity. To date, disagreement exists in the threshold of ammonium effect. Moreover, knowledge about how aerobic methanotrophic community composition and functional gene transcription respond to ammonium is still lacking. In the present study, microcosms with freshwater lake sediment were constructed to explore the effect of ammonium level on aerobic methanotrophs. Methane oxidation potential, and the density, diversity and composition of pmoA gene and its transcripts were examined during 2-week incubation. A negative impact of ammonium on aerobic methane oxidation potential and a positive impact on pmoA gene density were observed only at a very high level of ammonium. However, pmoA gene transcription increased notably at all ammonium levels. The composition of functional pmoA gene and transcripts were also influenced by ammonium. But a great shift was only observed in pmoA transcripts at the highest ammonium level.

Semi-analytical model for methane transport and oxidation through CCL cover was developed. Influence of gas diffusion coefficient and methane oxidation rate on the transport of methane and oxygen through CCL cover was investigated. Methane diffusion coefficient has great influence on methane transport through CCL cover but has no obvious influence on oxygen concentration profile. When t = 0.1 day, methane concentration for the case with Dm = 3.81 × 10−6 m2/s is 8 times greater than the case with Dm = 3.81 × 10−7 m2/s at depth z = 0.1 m. Oxygen concentration at the same depth increases with the increase of oxygen diffusion coefficient. Methane oxidation rate has great influence on methane transport through CCL cover but has on effect on oxygen transport through CCL cover. When t = 1 day, concentration of methane at z = 0.1 m for the case with k = 9.12 × 10−5 s−1 is approximately 40 times greater than the case with k = 9.12 × 10−4 s−1. It is also indicated that time needed to reach steady-state increases with the decrease of methane oxidation rate.KeywordsLandfillMethane oxidationSemi-analytical model

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

Abstract. Estuaries are important natural sources of methane (CH4) to the atmosphere. These transitional aquatic systems connect freshwater, brackish and fully marine environments. The pronounced salinity gradient, characteristic of estuaries, impose particular challenges to microbes and influence the biogeochemical processes they mediate. Salinity changes can inhibit methanotrophic activity. Here we analysed methane dynamics and microbial communities in the estuary of the Scheldt River, which flows through northern France, western Belgium, and the southwestern Netherlands, and finally discharges into the North Sea. During a research cruise conducted in June 2022 from the river mouth to Antwerp, water samples were collected at ten stations along the estuarine salinity gradient. We investigated water column CH4 inventory and stable carbon isotope dynamics, together with methane oxidation rates. Elevated CH4 concentrations of up to 110 nM with associated δ¹³C -values of about −46 ‰ were found in the freshwater zone of the upper estuary (in the area of the city of Antwerp). Rather than a gradual decrease in CH4 towards the North Sea, we observed a second maximum of 180 nM in the marine zone, with a contrasting isotopic composition of -66 ‰ indicating distinct methanogenic pathways and/or substrates in the estuary. Methane oxidation rates showed no clear relationship with the salinity gradient. In contrast, the composition of the methanotrophic community shifted markedly along the estuary and the salinity gradient, with Methyloparacoccus and Crenothrix prevailing in the freshwater zone Methyloceanibacter and PLTB-vmat-59 dominating in the mixing and marine zones. Our results thus demonstrate that the salinity gradient is not the primary control on estuarine methane oxidation capacity but the community composition of the methane oxidizing bacteria (MOB). In sediments, the MOB community composition mirrored the patterns observed in the overlying water column, indicating that estuarine sediments represent both a key habitat and an important recruitment source sustaining methanotrophic communities in the water column. Despite an active microbial filter, methane oxidation accounted for only a minor fraction of the estuaries’ CH₄ budget. Most methane (about 98 %) was lost through advection and diffusive fluxes to the atmosphere, while a smaller fraction was exported to the North Sea, contributing to sustained methane supersaturation in coastal waters.

The production and oxidation of methane and diversity of culturable aerobic methanotrophic bacteria in the water column and upper sediments of the meromictic oligotrophic Lake Gek-Gel (Azerbaijan) were studied by radioisotope, molecular, and microbiological techniques. The rate of methane oxidation was low in the aerobic mixolimnion, increased in the chemocline, and peaked at the depth where oxygen was detected in the water column. Aerobic methanotrophic bacteria of type II belonging to the genus Methylocystis were identified in enrichment cultures obtained from the chemocline. Methane oxidation in the anaerobic water of the monimolimnion was much more intense than in the aerobic zone. However, below 29–30 m methane concentration increased and reached 68 μM at the bottom. The highest rate of methane oxidation under anaerobic conditions was revealed in the upper layer of bottom sediments. The rate of methane oxidation significantly exceeding that of methane production suggests a deep source of methane in this lake.