Methanotroph populations and CH4 oxidation potentials in high-Arctic peat are altered by herbivory induced vegetation change

Thermal acclimation of methanotrophs from the genus Methylobacter

Methanotrophs oxidize most of the methane (CH₄) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH₄ oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH₄ oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH₄ is consumed to support growth at different CH₄ concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH₄ uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96^T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH₄ oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96^T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH₄ consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH₄ uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH₄ emissions.

Muskoxen homogenise soil microbial communities and affect the abundance of methanogens and methanotrophs

Grazing herbivores may affect soil microbial communities indirectly by impacting soil structure and vegetation composition. In high arctic environments, this impact is poorly elucidated, while having potentially wide-reaching effects on the ecosystem. This study examines how a key arctic herbivore, the muskox Ovibos moschatus, affects the soil microbial community in a high arctic fen. Environmental DNA was extracted from soil samples taken from grazed control plots and from muskox exclosures established 5 years prior. We sequenced amplicons of the 16S rRNA gene to provide insight into the microbial communities. We found that in the grazed control plots, microbial communities exhibited high evenness and displayed highly similar overall diversity. In plots where muskoxen had been excluded, microbial diversity was significantly reduced, and had more uneven intra-sample populations and overall lower ecological richness and evenness. We observed that the composition of microbial communities in grazed soils were significantly affected by the presence of muskoxen, as seen by elevated relative abundances of Bacteroides and Firmicutes, two major phyla found in muskox faeces. Furthermore, an increase in relative abundance of bacteria involved in degradation of recalcitrant carbohydrates and cycling of nitrogen was observed in grazed soil. Ungrazed soils displayed increased abundances of bacteria potentially involved in anaerobic oxidation of methane, whereas some methanogens were more abundant in grazed soils. This corroborates a previous finding that methane emissions are higher in arctic fens under muskox grazing. Our results show that the presence of large herbivores stimulates soil microbial diversity and has a homogenizing influence on the inter-species dynamics in soil microbial communities. The findings of this study, thus, improve our understanding of the effect of herbivore grazing on arctic ecosystems and the derived methane cycling.

Biochar as soil amendment: Syngas recycling system is essential to create positive carbon credit

Biochar utilization is accepted as the most cost-effective practice to mitigate global warming via increase in soil C stock. However, its utilization effect on greenhouse gas (GHG) fluxes was evaluated only within land application without considering industrial processes. To evaluate the net effect of biochar utilization on global warming within whole system boundary, swine manure-saw dust mixture was pyrolyzed under four different temperatures, and GHG fluxes were characterized under with/without syngas recycling systems. To determine GHG fluxes from biochar amended soil, 40 Mg ha^-1 of biochar was mixed with soil and incubated under flooded and dried soil conditions. Finally, the effect of biochar utilization was generalized using net global warming potential (GWP) from industrial process to land application. Under without syngas recycling system, huge amounts of GHGs were emitted during pyrolysis, and GHG fluxes highly increased with increasing pyrolysis temperature, due to direct and indirect GHG emissions from feedstock combustion and electricity, respectively. However, syngas recycling system removed most of GHGs, except for direct N₂O and indirect GHG emissions from electricity. Biochar application was very effective to mitigate GHG emissions within soil system boundary, and biochar produced at higher pyrolysis temperature showed higher effectivity in decreasing GHG fluxes. Within the whole system boundary from pyrolysis to soil application, without the installation of syngas recycling system, fresh manure application was more effective than biochar to reduce GHG emissions, regardless of soil water conditions. However, with the installation of syngas recycling system, biochar application was much more effective than fresh manure to decrease GHG fluxes. Biochar produced at higher temperature had higher effectivity to mitigate global warming impacts. In conclusion, to functionally mitigate global warming in soils, biochar should be produced in pyrolysis reactors equipped with syngas recycling system under higher temperature.

Effects of experimental fire in combination with climate warming on greenhouse gas fluxes in Arctic tundra soils

The frequency and severity of fire is increasing in Arctic tundra regions with climate change. Here we investigated effects of experimental low-intensity fire and shrub cutting, in combination with warming, on soil biogeochemical cycles and post-fire greenhouse gas (GHG) emissions in a dry heath tundra, West Greenland. We performed in vitro incubation experiments based on soil samples collected for up to two years after the fire. We observed tendency for increased soil nitrate (14-fold) and significant increases in soil ammonium and phosphate (four-fold and five-fold, respectively) two years after the fire, but no effects of shrub cutting on these compounds. Thus, changes appear to be largely due to fire effects rather than indirect effects by vegetation destruction. Two years after fire, nitrous oxide (N₂O) and carbon dioxide (CO₂) production was significantly increased (three-fold and 32% higher, respectively), in burned than unburned soils, while methane (CH₄) uptake remained unchanged. This stimulated N₂O and CO₂ production by the fire, however, was only apparent under conditions when soil was at maximum water holding capacity, suggesting that fire effects can be masked under dry conditions in this tundra ecosystem. There were positive effects by modest 2.5 °C warming on CO₂ production in control but not in burned soils, suggesting that fire may decrease the temperature response in soil respiration. Methane uptake was neither altered by the modest warming in shrub-cut nor in burned soils after two years, suggesting that the removal of vegetation may play a key role in controlling future temperature response of CH₄ oxidation. Altogether, our results show that post-fire tundra soils have the potential to enhance soil GHG emissions (e.g. N₂O and CO₂) especially during episodes with wet soil conditions. On the other hand, the lack of warming responses in post-fire soil respiration may weaken this positive feedback to climate change.

The Influence of Above-Ground Herbivory on the Response of Arctic Soil Methanotrophs to Increasing CH4 Concentrations and Temperatures

Rising temperatures in the Arctic affect soil microorganisms, herbivores, and peatland vegetation, thus directly and indirectly influencing microbial CH₄ production. It is not currently known how methanotrophs in Arctic peat respond to combined changes in temperature, CH₄ concentration, and vegetation. We studied methanotroph responses to temperature and CH₄ concentration in peat exposed to herbivory and protected by exclosures. The methanotroph activity was assessed by CH₄ oxidation rate measurements using peat soil microcosms and a pure culture of Methylobacter tundripaludum SV96, qPCR, and sequencing of pmoA transcripts. Elevated CH₄ concentrations led to higher CH₄ oxidation rates both in grazed and exclosed peat soils, but the strongest response was observed in grazed peat soils. Furthermore, the relative transcriptional activities of different methanotroph community members were affected by the CH₄ concentrations. While transcriptional responses to low CH₄ concentrations were more prevalent in grazed peat soils, responses to high CH₄ concentrations were more prevalent in exclosed peat soils. We observed no significant methanotroph responses to increasing temperatures. We conclude that methanotroph communities in these peat soils respond to changes in the CH₄ concentration depending on their previous exposure to grazing. This “conditioning” influences which strains will thrive and, therefore, determines the function of the methanotroph community.

Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using ¹³ C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H₄ MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.

Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming

Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH₄ and CO₂ production rates (Tveit et al., 2015). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1 - 30 °C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomics-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.