Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH4) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH4 formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH4 budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant in situ and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.

Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland

Permafrost thaw is a major potential feedback source to climate change as it can drive the increased release of greenhouse gases carbon dioxide (CO₂ ) and methane (CH₄ ). This carbon release from the decomposition of thawing soil organic material can be mitigated by increased net primary productivity (NPP) caused by warming, increasing atmospheric CO₂ , and plant community transition. However, the net effect on C storage also depends on how these plant community changes alter plant litter quantity, quality, and decomposition rates. Predicting decomposition rates based on litter quality remains challenging, but a promising new way forward is to incorporate measures of the energetic favorability to soil microbes of plant biomass decomposition. We asked how the variation in one such measure, the nominal oxidation state of carbon (NOSC), interacts with changing quantities of plant material inputs to influence the net C balance of a thawing permafrost peatland. We found: (1) Plant productivity (NPP) increased post-thaw, but instead of contributing to increased standing biomass, it increased plant biomass turnover via increased litter inputs to soil; (2) Plant litter thermodynamic favorability (NOSC) and decomposition rate both increased post-thaw, despite limited changes in bulk C:N ratios; (3) these increases caused the higher NPP to cycle more rapidly through both plants and soil, contributing to higher CO₂ and CH₄  fluxes from decomposition. Thus, the increased C-storage expected from higher productivity was limited and the high global warming potential of CH₄ contributed a net positive warming effect. Although post-thaw peatlands are currently C sinks due to high NPP offsetting high CO₂ release, this status is very sensitive to the plant community's litter input rate and quality. Integration of novel bioavailability metrics based on litter chemistry, including NOSC, into studies of ecosystem dynamics, is needed to improve the understanding of controls on arctic C stocks under continued ecosystem transition.

Permafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970 to 2014

Permafrost thaw increases active layer thickness, changes landscape hydrology and influences vegetation species composition. These changes alter belowground microbial and geochemical processes, affecting production, consumption and net emission rates of climate forcing trace gases. Net carbon dioxide (CO₂) and methane (CH₄) fluxes determine the radiative forcing contribution from these climate-sensitive ecosystems. Permafrost peatlands may be a mosaic of dry frozen hummocks, semi-thawed or perched sphagnum dominated areas, wet permafrost-free sedge dominated sites and open water ponds. We revisited estimates of climate forcing made for 1970 and 2000 for Stordalen Mire in northern Sweden and found the trend of increasing forcing continued into 2014. The Mire continued to transition from dry permafrost to sedge and open water areas, increasing by 100% and 35%, respectively, over the 45-year period, causing the net radiative forcing of Stordalen Mire to shift from negative to positive. This trend is driven by transitioning vegetation community composition, improved estimates of annual CO₂ and CH₄ exchange and a 22% increase in the IPCC's 100-year global warming potential (GWP_100) value for CH₄. These results indicate that discontinuous permafrost ecosystems, while still remaining a net overall sink of C, can become a positive feedback to climate change on decadal timescales. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes

Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH₄) from sediments. Ebullitive CH₄ flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH₄ flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH₄ emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH₄ emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH₄-cycling microorganisms and syntrophs, were predictive of porewater CH₄ concentrations. Results suggest that deeper lake regions, which currently emit less CH₄ than shallower edges, could add substantially to CH₄ emissions in a warmer Arctic and that CH₄ emission predictions may be improved by accounting for spatial variations in sediment microbiota.

Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.

Bimodal diel pattern in peatland ecosystem respiration rebuts uniform temperature response

Accurate projections of climate change impacts on the vast carbon stores of northern peatlands require detailed knowledge of ecosystem respiration (ER) and its heterotrophic (Rh) and autotrophic (Ra) components. Currently, however, standard flux measurement techniques, i.e. eddy covariance and manual chambers, generate empirical ER data during only night- or daytime, respectively, which are extrapolated to the daily scale based on the paradigm that assumes a uniform diel temperature response. Here, using continuous autochamber measurements, we demonstrate a distinct bimodal pattern in diel peatland ER which contrasts the unimodal pattern inherent to the classical assumption. This feature results from divergent temperature dependencies of day- and nighttime ER due to varying contributions from Rh and Ra. We further find that disregarding these bimodal dynamics causes significant bias in ER estimates across multiple temporal scales. This calls for improved process-based understanding of ER to advance our ability to simulate peatland carbon cycle-climate feedbacks.

Predicting the fate of carbon in peatlands relies on assumptions of behaviour in response to temperature. Here, the authors show that the temperature dependency of respiratory carbon losses shift strongly over day-night cycles, an overlooked facet causing bias in peatland carbon cycle simulations.

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.

Shipborne eddy covariance observations of methane fluxes constrain Arctic sea emissions

We demonstrate direct eddy covariance (EC) observations of methane (CH4) fluxes between the sea and atmosphere from an icebreaker in the eastern Arctic Ocean. EC-derived CH4 emissions averaged 4.58, 1.74, and 0.14 mg m-2 day-1 in the Laptev, East Siberian, and Chukchi seas, respectively, corresponding to annual sea-wide fluxes of 0.83, 0.62, and 0.03 Tg year-1. These EC results answer concerns that previous diffusive emission estimates, which excluded bubbling, may underestimate total emissions. We assert that bubbling dominates sea-air CH4 fluxes in only small constrained areas: A ~100-m2 area of the East Siberian Sea showed sea-air CH4 fluxes exceeding 600 mg m-2 day-1; in a similarly sized area of the Laptev Sea, peak CH4 fluxes were ~170 mg m-2 day-1. Calculating additional emissions below the noise level of our EC system suggests total ESAS CH4 emissions of 3.02 Tg year-1, closely matching an earlier diffusive emission estimate of 2.9 Tg year-1.

Partitioning of the net CO2 exchange using an automated chamber system reveals plant phenology as key control of production and respiration fluxes in a boreal peatland

The net ecosystem CO₂ exchange (NEE) drives the carbon (C) sink-source strength of northern peatlands. Since NEE represents a balance between various production and respiration fluxes, accurate predictions of its response to global changes require an in depth understanding of these underlying processes. Currently, however, detailed information of the temporal dynamics as well as the separate biotic and abiotic controls of the NEE component fluxes is lacking in peatland ecosystems. In this study, we address this knowledge gap by using an automated chamber system established across natural and trenching/vegetation removal plots to partition NEE into its production (i.e., gross and net primary production; GPP and NPP) and respiration (i.e., ecosystem, heterotrophic and autotrophic respiration; ER, Rh and Ra) fluxes in a boreal peatland in northern Sweden. Our results showed that daily NEE patterns were driven by GPP while variations in ER were governed by Ra rather than Rh. Moreover, we observed pronounced seasonal shifts in the Ra/Rh and above/belowground NPP ratios throughout the main phenological phases. Generalized linear model analysis revealed that the greenness index derived from digital images (as a proxy for plant phenology) was the strongest control of NEE, GPP and NPP while explaining considerable fractions also in the variations of ER and Ra. In addition, our data exposed greater temperature sensitivity of NPP compared to Rh resulting in enhanced C sequestration with increasing temperature. Overall, our study suggests that the temporal patterns in NEE and its component fluxes are tightly coupled to vegetation dynamics in boreal peatlands and thus challenges previous studies that commonly identify abiotic factors as key drivers. These findings further emphasize the need for integrating detailed information on plant phenology into process-based models to improve predictions of global change impacts on the peatland C cycle.

Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups, India

Fossil microbiotas are rare in the early rock record, limiting the type of ecological information extractable from ancient microbialites. In the absence of body fossils, emphasis may instead be given to microbially derived features, such as microbialite growth patterns, microbial mat morphologies, and the presence of fossilized gas bubbles in lithified mats. The metabolic affinity of micro-organisms associated with phosphatization may reveal important clues to the nature and accretion of apatite-rich microbialites. Stromatolites from the 1.6 Ga Chitrakoot Formation (Semri Group, Vindhyan Supergroup) in central India contain abundant fossilized bubbles interspersed within fine-grained in situ-precipitated apatite mats with average δ¹³ C_org indicative of carbon fixation by the Calvin cycle. In addition, the mats hold a synsedimentary fossil biota characteristic of cyanobacterial and rhodophyte morphotypes. Phosphatic oncoid cone-like stromatolites from the Paleoproterozoic Aravalli Supergroup (Jhamarkotra Formation) comprise abundant mineralized bubbles enmeshed within tufted filamentous mat fabrics. Construction of these tufts is considered to be the result of filamentous bacteria gliding within microbial mats, and as fossilized bubbles within pristine mat laminae can be used as a proxy for oxygenic phototrophy, this provides a strong indication for cyanobacterial activity in the Aravalli mounds. We suggest that the activity of oxygenic phototrophs may have been significant for the formation of apatite in both Vindhyan and Aravalli stromatolites, mainly by concentrating phosphate and creating steep diurnal redox gradients within mat pore spaces, promoting apatite precipitation. The presence in the Indian stromatolites of alternating apatite-carbonate lamina may result from local variations in pH and oxygen levels caused by photosynthesis-respiration in the mats. Altogether, this study presents new insights into the ecology of ancient phosphatic stromatolites and warrants further exploration into the role of oxygen-producing biotas in the formation of Paleoproterozoic shallow-basin phosphorites.

Environmental and physical controls on northern terrestrial methane emissions across permafrost zones

Methane (CH4 ) emissions from the northern high-latitude region represent potentially significant biogeochemical feedbacks to the climate system. We compiled a database of growing-season CH4 emissions from terrestrial ecosystems located across permafrost zones, including 303 sites described in 65 studies. Data on environmental and physical variables, including permafrost conditions, were used to assess controls on CH4 emissions. Water table position, soil temperature, and vegetation composition strongly influenced emissions and had interacting effects. Sites with a dense sedge cover had higher emissions than other sites at comparable water table positions, and this was an effect that was more pronounced at low soil temperatures. Sensitivity analysis suggested that CH4 emissions from ecosystems where the water table on average is at or above the soil surface (wet tundra, fen underlain by permafrost, and littoral ecosystems) are more sensitive to variability in soil temperature than drier ecosystems (palsa dry tundra, bog, and fen), whereas the latter ecosystems conversely are relatively more sensitive to changes of the water table position. Sites with near-surface permafrost had lower CH4 fluxes than sites without permafrost at comparable water table positions, a difference that was explained by lower soil temperatures. Neither the active layer depth nor the organic soil layer depth was related to CH4 emissions. Permafrost thaw in lowland regions is often associated with increased soil moisture, higher soil temperatures, and increased sedge cover. In our database, lowland thermokarst sites generally had higher emissions than adjacent sites with intact permafrost, but emissions from thermokarst sites were not statistically higher than emissions from permafrost-free sites with comparable environmental conditions. Overall, these results suggest that future changes to terrestrial high-latitude CH4 emissions will be more proximately related to changes in moisture, soil temperature, and vegetation composition than to increased availability of organic matter following permafrost thaw.

Emission of methane from plants

It has been proposed that plants are capable of producing methane by a novel and unidentified biochemical pathway. Emission of methane with an apparently biological origin was recorded from both whole plants and detached leaves. This was the first report of methanogenesis in an aerobic setting, and was estimated to account for 10-45 per cent of the global methane source. Here, we show that plants do not contain a known biochemical pathway to synthesize methane. However, under high UV stress conditions, there may be spontaneous breakdown of plant material, which releases methane. In addition, plants take up and transpire water containing dissolved methane, leading to the observation that methane is released. Together with a new analysis of global methane levels from satellite retrievals, we conclude that plants are not a major source of the global methane production.

Consumption of tropospheric levels of methyl bromide by C(1) compound-utilizing bacteria and comparison to saturation kinetics

Pure cultures of methylotrophs and methanotrophs are known to oxidize methyl bromide (MeBr); however, their ability to oxidize tropospheric concentrations (parts per trillion by volume [pptv]) has not been tested. Methylotrophs and methanotrophs were able to consume MeBr provided at levels that mimicked the tropospheric mixing ratio of MeBr (12 pptv) at equilibrium with surface waters ( approximately 2 pM). Kinetic investigations using picomolar concentrations of MeBr in a continuously stirred tank reactor (CSTR) were performed using strain IMB-1 and Leisingeria methylohalidivorans strain MB2(T) - terrestrial and marine methylotrophs capable of halorespiration. First-order uptake of MeBr with no indication of threshold was observed for both strains. Strain MB2(T) displayed saturation kinetics in batch experiments using micromolar MeBr concentrations, with an apparent K(s) of 2.4 microM MeBr and a V(max) of 1.6 nmol h(-1) (10(6) cells)(-1). Apparent first-order degradation rate constants measured with the CSTR were consistent with kinetic parameters determined in batch experiments, which used 35- to 1 x 10(7)-fold-higher MeBr concentrations. Ruegeria algicola (a phylogenetic relative of strain MB2(T)), the common heterotrophs Escherichia coli and Bacillus pumilus, and a toluene oxidizer, Pseudomonas mendocina KR1, were also tested. These bacteria showed no significant consumption of 12 pptv MeBr; thus, the ability to consume ambient mixing ratios of MeBr was limited to C(1) compound-oxidizing bacteria in this study. Aerobic C(1) bacteria may provide model organisms for the biological oxidation of tropospheric MeBr in soils and waters.

Sensitivity of boreal forest carbon balance to soil thaw

We used eddy covariance; gas-exchange chambers; radiocarbon analysis; wood, moss, and soil inventories; and laboratory incubations to measure the carbon balance of a 120-year-old black spruce forest in Manitoba, Canada. The site lost 0.3 +/- 0.5 metric ton of carbon per hectare per year (ton C ha-1 year-1) from 1994 to 1997, with a gain of 0.6 +/- 0.2 ton C ha-1 year-1 in moss and wood offset by a loss of 0.8 +/- 0.5 ton C ha-1 year-1 from the soil. The soil remained frozen most of the year, and the decomposition of organic matter in the soil increased 10-fold upon thawing. The stability of the soil carbon pool ( approximately 150 tons C ha-1) appears sensitive to the depth and duration of thaw, and climatic changes that promote thaw are likely to cause a net efflux of carbon dioxide from the site.