High-affinity Methanotrophs Research Articles

Depth-dependent patterns of activity and abundance of atmospheric methane-oxidizing bacteria in semiarid grassland on the Loess Plateau of China

High-affinity methanotrophs in upland soils are responsible for the well-known biological sink of atmospheric methane. However, the vertical distribution pattern of their abundance and activity remains largely unknown. Here, we collected soil samples in 2 cm intervals from the surface to a depth of 40 cm in a typical semiarid steppe in the Loess Plateau of China. We found a bell-shaped distribution of the atmospheric methane-oxidizing potential (atmMOP) along the soil depth, and its peak appeared in the 10–20 cm soil layers. The abundance of methanotrophs (dominated by the upland soil cluster gamma, USCγ) showed a similar vertical distribution pattern and was well correlated with the atmMOP (P < 0.01). Pearson correlation analysis and the structural equation model showed that pH and inorganic nitrogen concentration were the main environmental factors that affecting atmMOP and USCγ abundance.

Diversity and Composition of Methanotroph Communities in Caves.

ABSTRACTMethane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations, suggesting these microorganisms contribute to CH4 flux in subterranean ecosystems.IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.

Atmospheric methane oxidation is affected by grassland type and grazing and negatively correlated to total soil respiration in arid and semiarid grasslands in Inner Mongolia

Methane (CH4) is an important trace greenhouse gas and atmospheric CH4 uptake by high-affinity methanotrophs in grassland soil accounts for an important proportion of the terrestrial CH4 sink. However, our understanding of the comprehensive effects of grassland type and grazing treatment on active soil methanotrophs and atmospheric CH4 uptake is still under debate. This study investigates the impact of grazing on CH4 oxidation rate and active atmospheric CH4 oxidizing methanotroph communities in two arid and semiarid grassland ecosystems (meadow and desert) by detecting transcripts of methane monooxygenase (pmoA) genes. Atmospheric CH4 oxidation rates differed according to grassland type and grazing treatment. The highest activity was found in desert grasslands with moderate grazing and the lowest activity in meadow grasslands with exclosures. The differences in activities were linked with changes in abundance, composition and co-occurrence network patterns of active methanotrophs and CO2 production rate. Redundancy, correlation and random forest analyses indicated that pmoA transcripts, available phosphorus (AP), NO3−-N, and CO2 production rate were the most important factors predicting active methanotroph community composition and atmospheric CH4 oxidation activity in these grassland ecosystems. A glucose amendment incubation experiment showed that addition of glucose increased heterotrophic microbial respiration and inhibited atmospheric CH4 oxidation. This study provides evidence that CO2 production rate is an important factor associated with atmospheric CH4 oxidation activity in arid and semiarid grassland ecosystems and suggests that interactions between methanotrophs and other heterotrophs influence methanotroph activity in grassland ecosystems.

Reduced net methane emissions due to microbial methane oxidation in a warmer Arctic

Methane emissions from organic-rich soils in the Arctic have been extensively studied due to their potential to increase the atmospheric methane burden as permafrost thaws1–3. However, this methane source might have been overestimated without considering high-affinity methanotrophs (HAMs; methane-oxidizing bacteria) recently identified in Arctic mineral soils4–7. Herein we find that integrating the dynamics of HAMs and methanogens into a biogeochemistry model8–10 that includes permafrost soil organic carbon dynamics3 leads to the upland methane sink doubling (~5.5 Tg CH4 yr−1) north of 50 °N in simulations from 2000–2016. The increase is equivalent to at least half of the difference in net methane emissions estimated between process-based models and observation-based inversions11,12, and the revised estimates better match site-level and regional observations5,7,13–15. The new model projects doubled wetland methane emissions between 2017–2100 due to more accessible permafrost carbon16–18. However, most of the increase in wetland emissions is offset by a concordant increase in the upland sink, leading to only an 18% increase in net methane emission (from 29 to 35 Tg CH4 yr−1). The projected net methane emissions may decrease further due to different physiological responses between HAMs and methanogens in response to increasing temperature19,20. Models overestimate Arctic methane emissions compared to observations. Incorporating microbial dynamics into biogeochemistry models helps reconcile this discrepancy; high-affinity methanotrophs are an important part of the Arctic methane budget and double previous estimates of methane sinks.

Unexpected role of canonical aerobic methanotrophs in upland agricultural soils

Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13CCH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13CCO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.

Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy.

ABSTRACTAerated soils form the second largest sink for atmospheric CH4. A near-complete genome of uncultured upland soil cluster Gammaproteobacteria that oxidize CH4 at <2.5 ppmv was obtained from incubated Antarctic mineral cryosols. This first genome of high-affinity methanotrophs can help resolve the mysteries about their phylogenetic affiliation and metabolic potential.

Soil methanotroph abundance and community composition are not influenced by substrate availability in laboratory incubations

Variations in the rates of atmospheric CH4 uptake in upland soils can arise from both abiotic and biotic factors. Among the less-studied biotic factors is the degree to which methanotroph activity and community composition interact with supply of CH4 to the soil. Here, we investigated whether the abundance of high affinity methanotrophs in a range of soils representing different land use types is substrate (CH4) dependent. Field replicates of three soils sampled from deciduous forest, spruce forest and agricultural sites were incubated in columns flushed continuously for 24 days with air at one of four CH4 concentrations: <1 ppm (starvation), 1.8 (ambient), 30 (low elevated) and 60 (high elevated) ppm. In all soils, CH4 oxidation rates increased linearly with CH4 supply. For all levels of CH4 supply, CH4 oxidation rates were the highest in deciduous forest soil followed by spruce forest and agricultural soils. Terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that the agricultural soil had a distinct methanotrophic community compared to the two forest soils. In particular, the T-RFs (Terminal restriction fragments) associated with USCα and Type II methanotrophs (Methylocystis sp, Methylosinus sp.) were the most abundant in forest soils while Type 1a associated T-RFs dominated in agricultural soil. The agricultural and forest soils also differed in their fractionation of stable isotopes, 13C and 2H, during CH4 oxidation. Altering CH4 concentration in the inlet air did not change methanotroph abundance, as evidenced by three different assays, two qPCR and T-RFLP, that recorded no changes in the number of pmoA genes and/or the relative abundance of T-RFs. Altogether, it is proposed that intrinsic differences in CH4 oxidation rates between soils, particularly between temperate agricultural and forest soils, are driven by methanotroph community structure. The population size of methanotrophs in upland soils did not respond to CH4 availability and is most probably regulated by other factors, such as the availability of nitrogen, cross-feeding or other carbon sources.

Varying atmospheric methane concentrations affect soil methane oxidation rates and methanotroph populations in pasture, an adjacent pine forest, and a landfill

We describe experiments to better understand how CH4 oxidation rates by different methanotroph communities respond to changing CH4 concentrations. We used a novel system of automatically monitored chambers to investigate the response of CH4 oxidation rates in a New Zealand pasture and adjacent pine forest soil exposed to varying atmospheric CH4 concentrations.Type II methanotrophs that dominate CH4 oxidation in the forest soil became progressively saturated as CH4 concentrations rose from ambient (1.8ppmv) to 570ppmv, as shown by a decrease in uptake efficiency from 20% to 2% removal. By contrast, CH4 oxidation in the pasture soil where Type I methanotrophs dominate increased in proportion to the increase in CH4 inlet concentration, oxidising about 2% of the inlet CH4 flux throughout. Modelling based on Michaelis-Menten kinetics revealed that low-affinity (Type I) methanotrophs were solely responsible for CH4 oxidation in pasture soils, whereas high affinity (Type II) methanotrophs only contributed about 10% of the CH4 oxidation in the forest soil. Increased aeration status using a soil–perlite (1:1) mixture doubled CH4 oxidation rates at both ambient (1.8ppmv) and 40ppmv atmospheric CH4. A similar volcanic soil previously exposed for 8 y to high CH4 fluxes from a landfill had removal efficiencies consistently above 95% for atmospheric CH4 concentrations up to 7500ppmv when the CH4 oxidation rate was7000μg CH4 kg−1soil h−1.

Spatial Patterns of Soil Development, Methane Oxidation, and Methanotrophic Diversity along a Receding Glacier Forefield, Southeast Greenland

Increasing global annual temperature leads to massive loss of ice cover worldwide. Consequently, glaciers retreat and ice-covered areas become exposed. We report on a study from the Mittivakkat Gletscher forefield in Southeast Greenland with special focus on methanotrophy in relation to exposure time to the atmosphere. The Mittivakkat Gletscher has receded since the end of the Little Ice Age (LIA; about AD 1850) and has left behind a series of deposits of decreasing age concurrently with its recession. Soil samples from this chronosequence were examined in order to elucidate main soil variables, as well as the activity and community structure of methanotrophs, a group of microorganisms involved in regulation of atmospheric methane. Soil variables revealed poor soil development, and incubation experiments showed methane consumption rates of 2.14 nmol CH4 day−1 gsoil −1 at 22 °C and 1.24 nmol CH4 day−1 gsoil −1 at 10 °C in the LIA terminal moraine. Methane consumption was not detected in younger samples, despite the presence of high-affinity methanotrophs in all samples. This was indicated by successful amplification of partial pmoA genes, which code for a subunit of a key enzyme involved in methane oxidation. In addition, the results of the diversity study show that the diversity of the methanotrophic community at the younger, recently deglaciated site P5 is poorer than the diversity of the community retrieved from the LIA moraine. We put forward the hypothesis that aerobic methanotrophs were at very low abundance and diversity during glaciation probably due to anoxia at the ice-sediment interface and that colonization after deglaciation is not completed yet. More detailed studies are required to explain the causes of discrepancy between activity and presence of high-affinity methanotrophs and its relation to the transit from ice-covered probably anoxic to ice-free oxic conditions.

Tree species affect atmospheric CH 4 oxidation without altering community composition of soil methanotrophs

Plant species exert strong effects on ecosystem functions and one of the emerging, and difficult to test hypotheses, is that plants alter soil functions through changing the community structure of soil microorganisms. We tested the hypothesis for atmospheric CH 4 oxidation by using soil samples from a Siberian afforestation experiment and exposing them to 13C–CH 4. We determined the activity of the soil methanotrophs under different tree species at three levels of initial CH 4 concentration (30, 200 and 1000 ppm) thus distinguishing the activities of low- and high-affinity methanotrophs. Half of the samples were incubated with 13C-enriched CH 4 (99.9%) and half with 12C–CH 4. This allowed an estimation of the amount of 13C incorporated into individual PLFAs and determination of PLFAs of methanotrophs involved in CH 4 oxidation at the different CH 4 concentrations. Tree species strongly altered the activity of atmospheric CH 4 oxidation without appearing to change the composition of high-affinity methanotrophs as evidenced by PLFA 13C labeling. The low diversity of atmospheric CH 4 oxidizers, presumably belonging to the UCSα group, may explain the lack of tree species effects on the composition of soil methanotrophs. We submit that the observed tree species effects on atmospheric CH 4 oxidation indicate an effect on biomass or cell-specific activities rather than by a community change and this may be related to the impact of the tree species on soil N cycling.

Substantial high‐affinity methanotroph populations in Andisols effect high rates of atmospheric methane oxidation

Methanotrophic bacteria in soils derived from volcanic ash (Andisols) were characterized via time series (13) C-phospholipid fatty acid (PLFA) labelling. Three Andisols were incubated under 2 ppmv (13) CH4 for up to 18 weeks, thus enabling high-affinity methanotrophs to be selectively characterized and quantified. PLFA profiles from all soils were broadly similar, but the magnitude of the high-affinity methanotrophic populations determined through (13) C-PLFA-stable isotope probing displayed sizeable differences. Substantial incorporation of (13) C indicated very large high-affinity methanotrophic populations in two of the soils. Such high values are far in excess (10×) of those observed for a range of mineral soils incubated under similar conditions (Bull et al., 2000; Maxfield et al., 2006; 2008a, b). Two of the three Andisols studied also displayed high but variable CH4 oxidation rates ranging from 0.03 to 1.58 nmol CH4 g(-1) d.wt. h(-1) . These findings suggest that Andisols, a previously unstudied soil class with respect to high-affinity methanotrophic bacteria, may oxidize significant amounts of atmospheric methane despite their low areal coverage globally.

Environmental and chemical factors regulating methane oxidation in a New Zealand forest soil

Tropospheric methane (CH4) is oxidised by soil microbes called methanotrophs. We examined them in soil samples from a pristine Nothofagus forest located in New Zealand. Laboratory incubations indicated the presence of high-affinity methanotrophs that displayed Michaelis–Menton kinetics (Km = 8.4 µL/L where Km is the substrate concentration at half the maximal rate). When the soil was dried from its field capacity water content of 0.34 to 0.16 m3/m3, CH4 oxidation rate increased nearly 7-fold. The methanotrophs were thus metabolically poised for very high activity, but substrate availability was commonly limiting. When water content was held constant, CH4 oxidation rate nearly doubled as temperature increased from 5 to 12°C, a range found in the forest. By contrast, CH4 oxidation rate did not change much from 12 to 30°C, and it was zero at 35°C. When water content and temperature were held constant, the optimal soil pH for CH4 oxidation was 4.4, as found in the forest. Soil disturbance by nitrogen (N) and non-N salt amendment decreased CH4 oxidation rate, but this depended on the amendment species and concentration. The methanotrophs were adapted to native conditions and exhibited a great sensitivity to disturbance.

Notches and edges as reference flaws in ultrasonic testing

Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13CCH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13CCO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.