| 1. |
- Emerson, Joanne B., et al.
(författare)
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Host-linked soil viral ecology along a permafrost thaw gradient
- 2018
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 3:8, s. 870-880
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Tidskriftsartikel (refereegranskat)abstract
- Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood(1-7). The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans(8-10), remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.
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| 2. |
- Benjamin, Bolduc, et al.
(författare)
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The IsoGenie database : an interdisciplinary data management solution for ecosystems biology and environmental research
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Kuhn, McKenzie A., et al.
(författare)
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Controls on Stable Methane Isotope Values in Northern Peatlands and Potential Shifts in Values Under Permafrost Thaw Scenarios
- 2024
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Ingår i: Journal of Geophysical Research - Biogeosciences. - : American Geophysical Union (AGU). - 2169-8953 .- 2169-8961. ; 129:7
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Tidskriftsartikel (refereegranskat)abstract
- Northern peatlands are a globally significant source of methane (CH4), and emissions are projected to increase due to warming and permafrost loss. Understanding the microbial mechanisms behind patterns in CH4 production in peatlands will be key to predicting annual emissions changes, with stable carbon isotopes (δ13C-CH4) being a powerful tool for characterizing these drivers. Given that δ13C-CH4 is used in top-down atmospheric inversion models to partition sources, our ability to model CH4 production pathways and associated δ13C-CH4 values is critical. We sought to characterize the role of environmental conditions, including hydrologic and vegetation patterns associated with permafrost thaw, on δ13C-CH4 values from high-latitude peatlands. We measured porewater and emitted CH4 stable isotopes, pH, and vegetation composition from five boreal-Arctic peatlands. Porewater δ13C-CH4 was strongly associated with peatland type, with δ13C enriched values obtained from more minerotrophic fens (−61.2 ± 9.1‰) compared to permafrost-free bogs (−74.1 ± 9.4‰) and raised permafrost bogs (−81.6 ± 11.5‰). Variation in porewater δ13C-CH4 was best explained by sedge cover, CH4 concentration, and the interactive effect of peatland type and pH (r2 = 0.50, p < 0.001). Emitted δ13C-CH4 varied greatly but was positively correlated with porewater δ13C-CH4. We calculated a mixed atmospheric δ13C-CH4 value for northern peatlands of −65.3 ± 7‰ and show that this value is more sensitive to landscape drying than wetting under permafrost thaw scenarios. Our results suggest northern peatland δ13C-CH4 values are likely to shift in the future which has important implications for source partitioning in atmospheric inversion models.
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| 4. |
- Mondav, Rhiannon, 1972-, et al.
(författare)
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Discovery of a novel methanogen prevalent in thawing permafrost
- 2014
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus ‘Methanoflorens stordalenmirensis’ gen. nov. sp. nov., belonging to the uncultivated lineage ‘Rice Cluster II’ (Candidatus ‘Methanoflorentaceae’ fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, ‘Methanoflorentaceae’ are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus ‘M. stordalenmirensis’ appears to be a key mediator of methane-based positive feedback to climate warming.
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| 5. |
- Wilson, Rachel M., et al.
(författare)
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Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland
- 2022
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 820
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Tidskriftsartikel (refereegranskat)abstract
- Peatlands are climate critical carbon (C) reservoirs that could become a C source under continued warming. A strong relationship between plant tissue chemistry and the soil organic matter (SOM) that fuels C gas emissions is inferred, but rarely examined at the molecular level. Here we compared Fourier transform infrared (FT-IR) spectroscopy measurements of solid phase functionalities in plants and SOM to ultra-high-resolution mass spectrometric analyses of plant and SOM water extracts across a palsa-bog-fen thaw and moisture gradient in an Arctic peatland. From these analyses we calculated the C oxidation state (NOSC), a measure which can be used to assess organic matter quality. Palsa plant extracts had the highest NOSC, indicating high quality, whereas extracts of Sphagnum, which dominated the bog, had the lowest NOSC. The percentage of plant compounds that are less bioavailable and accumulate in the peat, increases from palsa (25%) to fen (41%) to bog (47%), reflecting the pattern of percent Sphagnum cover. The pattern of NOSC in the plant extracts was consistent with the high number of consumed compounds in the palsa and low number of consumed compounds in the bog. However, in the FT-IR analysis of the solid phase bog peat, carbohydrate content was high implying high quality SOM. We explain this discrepancy as the result of low solubilization of bog SOM facilitated by the low pH in the bog which makes the solid phase carbohydrates less available to microbial decomposition. Plant-associated condensed aromatics, tannins, and lignin-like compounds declined in the unsaturated palsa peat indicating decomposition, but lignin-like compounds accumulated in the bog and fen peat where decomposition was presumably inhibited by the anaerobic conditions. A molecular-level comparison of the aboveground C sources and peat SOM demonstrates that climate-associated vegetation shifts in peatlands are important controls on the mechanisms underlying changing C gas emissions.
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| 6. |
- Woodcroft, Ben J., et al.
(författare)
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Genome-centric view of carbon processing in thawing permafrost
- 2018
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 560:7716, s. 49-
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Tidskriftsartikel (refereegranskat)abstract
- As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.
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| 7. |
- Hodgkins, Suzanne B., et al.
(författare)
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Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production
- 2014
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:16, s. 5819-5824
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Tidskriftsartikel (refereegranskat)abstract
- Carbon release due to permafrost thaw represents a potentially major positive climate change feedback. The magnitude of carbon loss and the proportion lost as methane (CH4) vs. carbon dioxide (CO2) depend on factors including temperature, mobilization of previously frozen carbon, hydrology, and changes in organic matter chemistry associated with environmental responses to thaw. While the first three of these effects are relatively well understood, the effect of organic matter chemistry remains largely un-studied. To address this gap, we examined the biogeochemistry of peat and dissolved organic matter (DOM) along a similar to 40-y permafrost thaw progression from recently- to fully thawed sites in Stordalen Mire (68.35 degrees N, 19.05 degrees E), a thawing peat plateau in northern Sweden. Thaw-induced subsidence and the resulting inundation along this progression led to succession in vegetation types accompanied by an evolution in organic matter chemistry. Peat C/N ratios decreased whereas humification rates increased, and DOM shifted toward lower molecular weight compounds with lower aromaticity, lower organic oxygen content, and more abundant microbially produced compounds. Corresponding changes in decomposition along this gradient included increasing CH4 and CO2 production potentials, higher relative CH4/CO2 ratios, and a shift in CH4 production pathway from CO2 reduction to acetate cleavage. These results imply that subsidence and thermokarst-associated increases in organic matter lability cause shifts in biogeochemical processes toward faster decomposition with an increasing proportion of carbon released as CH4. This impact of permafrost thaw on organic matter chemistry could intensify the predicted climate feedbacks of increasing temperatures, permafrost carbon mobilization, and hydrologic changes.
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| 8. |
- Hodgkins, Suzanne B., et al.
(författare)
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Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland
- 2016
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037 .- 1872-9533. ; 187, s. 123-140
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Tidskriftsartikel (refereegranskat)abstract
- The fate of carbon stored in permafrost-zone peatlands represents a significant uncertainty in global climate modeling. Given that the breakdown of dissolved organic matter (DOM) is often a major pathway for decomposition in peatlands, knowledge of DOM reactivity under different permafrost regimes is critical for determining future climate feedbacks. To explore the effects of permafrost thaw and resultant plant succession on DOM reactivity, we used a combination of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), UV/Vis absorbance, and excitation-emission matrix spectroscopy (EEMS) to examine the DOM elemental composition and optical properties of 27 pore water samples gathered from various sites along a permafrost thaw sequence in Stordalen Mire, a thawing subarctic peatland in northern Sweden. The presence of dense Sphagnum moss, a feature that is dominant in the intermediate thaw stages, appeared to be the main driver of variation in DOM elemental composition and optical properties at Stordalen. Specifically, DOM from sites with Sphagnum had greater aromaticity, higher average molecular weights, and greater O/C, consistent with a higher abundance of phenolic compounds that likely inhibit decomposition. These compounds are released by Sphagnum and may accumulate due to inhibition of phenol oxidase activity by the acidic pH at these sites. In contrast, sites without Sphagnum, specifically fully-thawed rich fens, had more saturated, more reduced compounds, which were high in N and S. Optical properties at rich fens indicated the presence of microbially-derived DOM, consistent with the higher decomposition rates previously measured at these sites. These results indicate that Sphagnum acts as an inhibitor of rapid decomposition and CH4 release in thawing subarctic peatlands, consistent with lower rates of CO2 and CH4 production previously observed at these sites. However, this inhibitory effect may disappear if Sphagnum-dominated bogs transition to more waterlogged rich fens that contain very little to no living Sphagnum. Release of this inhibition allows for higher levels of microbial activity and potentially greater CH4 release, as has been observed in these fen sites.
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| 9. |
- Hodgkins, Suzanne B., et al.
(författare)
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Soil incubations reproduce field methane dynamics in a subarctic wetland
- 2015
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 126:1-2, s. 241-249
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge in peatland carbon cycle modeling is the estimation of subsurface methane (CH4) and carbon dioxide (CO2) production and consumption rates and pathways. The most common methods for modeling these processes are soil incubations and stable isotope modeling, both of which may involve departures from field conditions. To explore the impacts of these departures, we measured CH4/CO2 concentration ratios and C-13 fractionation factors (alpha(C), indicating CH4 production pathways) in field pore water from a thawing subarctic peatland, and compared these values to those observed in incubations of corresponding peat samples. Incubation CH4/CO2 production ratios were significantly and positively correlated with observed field CH4/CO2 concentration ratios, though observed field ratios were similar to 20 % of those in incubations due to CH4's lower solubility in pore water. After correcting the field ratios for CH4 loss with an isotope mass balance model, the incubation CH4/CO2 ratios and alpha(C) were both significantly positively correlated with field ratios and alpha(C) (respectively), both with slopes indistinguishable from 1. Although CH4/CO2 ratios and alpha(C) were slightly higher in the incubations, these shifts were consistent along the thaw progression, indicating that ex situ incubations can replicate trends in in situ CH4 production.
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| 10. |
- Li, Zhen, et al.
(författare)
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Soil incubation methods lead to large differences in inferred methane production temperature sensitivity
- 2024
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Ingår i: Environmental Research Letters. - 1748-9326. ; 19:4
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Tidskriftsartikel (refereegranskat)abstract
- Quantifying the temperature sensitivity of methane (CH4) production is crucial for predicting how wetland ecosystems will respond to climate warming. Typically, the temperature sensitivity (often quantified as a Q10 value) is derived from laboratory incubation studies and then used in biogeochemical models. However, studies report wide variation in incubation-inferred Q10 values, with a large portion of this variation remaining unexplained. Here we applied observations in a thawing permafrost peatland (Stordalen Mire) and a well-tested process-rich model (ecosys) to interpret incubation observations and investigate controls on inferred CH4 production temperature sensitivity. We developed a field-storage-incubation modeling approach to mimic the full incubation sequence, including field sampling at a particular time in the growing season, refrigerated storage, and laboratory incubation, followed by model evaluation. We found that CH4 production rates during incubation are regulated by substrate availability and active microbial biomass of key microbial functional groups, which are affected by soil storage duration and temperature. Seasonal variation in substrate availability and active microbial biomass of key microbial functional groups led to strong time-of-sampling impacts on CH4 production. CH4 production is higher with less perturbation post-sampling, i.e. shorter storage duration and lower storage temperature. We found a wide range of inferred Q10 values (1.2–3.5), which we attribute to incubation temperatures, incubation duration, storage duration, and sampling time. We also show that Q10 values of CH4 production are controlled by interacting biological, biochemical, and physical processes, which cause the inferred Q10 values to differ substantially from those of the component processes. Terrestrial ecosystem models that use a constant Q10 value to represent temperature responses may therefore predict biased soil carbon cycling under future climate scenarios.
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| 11. |
- Mondav, Rhiannon, 1972-, et al.
(författare)
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Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient
- 2017
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 19:8, s. 3201-3218
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Tidskriftsartikel (refereegranskat)abstract
- Biogenic production and release of methane (CH4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.
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| 12. |
- Singleton, Caitlin M., et al.
(författare)
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Methanotrophy across a natural permafrost thaw environment
- 2018
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12:10, s. 2544-2558
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Tidskriftsartikel (refereegranskat)abstract
- The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCa) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater delta C-13-CH 4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.
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