23 research outputs found

    Host-linked soil viral ecology along a permafrost thaw gradient

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    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 understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, 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

    Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production

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    The mechanisms, pathways, and rates of CO2 and CH4 production are central to understanding carbon cycling and greenhouse gas flux in wetlands. Thawing permafrost regions are of particular interest because they are disproportionally affected by climate warming and store large reservoirs of organic C that may be readily converted to CO2 and CH4 upon thaw. This conversion is accomplished by a community of microorganisms interacting in complex ways to transform large organic compounds into fatty acids and ultimately CO2 and CH4. While the central role of microbes in this process is well-known, geochemical rate models rarely integrate microbiological information. Herein, we expanded the geochemical rate model of Neumann et al., (2016, Biogeochemistry 127: 57-87) to incorporate a Bayesian probability analysis and applied the result to quantifying rates of CO2, CH4, and acetate production in closed-system incubations of peat collected from three habitats along a permafrost thaw gradient. The goals of this analysis were twofold. First, we integrated microbial community analyses with geochemical rate modeling by using microbial data to inform the best model choice among equally mathematically feasible model variants. Second, based on model results, we described changes in organic carbon transformation among habitats to understand the changing pathways of greenhouse gas production along the permafrost thaw gradient. We found that acetoclasty, hydrogenotrophy, CO2 production, and homoacetogenesis were the important reactions in this system, with little evidence for anaerobic CH4 oxidation. There was a distinct transition in the reactions across the thaw gradient. The collapsed palsa stage presents an initial disequilibrium where the abrupt (physically and temporally) change in elevation introduces freshly fixed carbon into anoxic conditions then fermentation products build up over time as the system transitions through the acid phase and electron acceptors are depleted. In the bog, fermentation slows, while methanogenesis increases. In the fully thawed fen, most of the terminal electron acceptors are depleted and the system becomes increasingly methanogenic. This suggests that as permafrost regions thaw and dry palsas transition into wet fens, CH4 emissions will rise, increasing the warming potential of these systems and accelerating climate warming feedbacks

    Latitude, Elevation, and Mean Annual Temperature Predict Peat Organic Matter Chemistry at a Global Scale

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    Peatlands contain a significant fraction of global soil carbon, but how these reservoirs will respond to the changing climate is still relatively unknown. A global picture of the variations in peat organic matter chemistry will aid our ability to gauge peatland soil response to climate. The goal of this research is to test the hypotheses that (a) peat carbohydrate content, an indicator of soil organic matter reactivity, will increase with latitude and decrease with mean annual temperatures, (b) while peat aromatic content, an indicator of recalcitrance, will vary inversely, and (c) elevation will have a similar effect to latitude. We used Fourier Transform Infrared Spectroscopy to examine variations in the organic matter functional groups of 1034 peat samples collected from 10 to 20, 30ā€“40, and 60ā€“70 cm depths at 165 individual sites across a latitudinal gradient of 79Ā°Nā€“65Ā°S and from elevations of 0ā€“4,773 m. Carbohydrate contents of high latitude peat were significantly greater than peat originating near the equator, while aromatic content showed the opposite trend. For peat from similar latitudes but different elevations, the carbohydrate content was greater and aromatic content was lower at higher elevations. Higher carbohydrate content at higher latitudes indicates a greater potential for mineralization, whereas the chemical composition of low latitude peat is consistent with their apparent relative stability in the face of warmer temperatures. The combination of low carbohydrates and high aromatics at warmer locations near the equator suggests the mineralization of high latitude peat until reaching recalcitrance under a new temperature regime.EstaciĆ³n Experimental Agropecuaria BarilocheFil: Verbeke, Brittany A. Florida State University. Department of Earth, Ocean, and Atmospheric Science; Estados UnidosFil: Lamit, Louis J. Syracuse University. Department of Biology, Department of Environmental and Forest Biology; Estados UnidosFil: Lilleskov, Erik A. USDA Forest Service; Estados UnidosFil: Hodgkins, Suzanne B. Florida State University. Department of Chemistry and Biochemistry; Estados UnidosFil: Basiliko, Nathan. Laurentian University. Department of Biology and the Vale Living with Lakes Centre; CanadaFil: Kane, Evan S. USDA Forest Service; Estados UnidosFil: Andersen, Roxane. University of the Highlands and Islands. Environmental Research Institute; Reino UnidoFil: Artz, Rebekka R. E. Ecological Sciences, James Hutton Institute; Reino UnidoFil: Benavides, Juan Carlos. Pontificia Universidad Javeriana. Departmento de EcologĆ­a y Territorio; ColombiaFil: Enriquez, Andrea Soledad. Instituto Nacional de Tecnologia Agropecuaria (INTA). EstaciĆ³n Experimental Agropecuaria Bariloche. Ɓrea de Recursos Naturales; ArgentinaFil: Enriquez, Andrea Soledad. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; ArgentinaFil: Chanton, Jeffrey P. Florida State University. Department of Earth, Ocean, and Atmospheric Science; Estados Unido

    Methanotrophy across a natural permafrost thaw environment

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    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 (USCĪ±) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater Ī“C-CH 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

    Discovery of a novel methanogen prevalent in thawing permafrost

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    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 ā€˜Methanoflorens stordalenmirensisā€™ gen. nov. sp. nov., belonging to the uncultivated lineage ā€˜Rice Cluster IIā€™ (Candidatus ā€˜Methanoflorentaceaeā€™ 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, ā€˜Methanoflorentaceaeā€™ 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 ā€˜M. stordalenmirensisā€™ appears to be a key mediator of methane-based positive feedback to climate warming

    Carbon accumulation, flux, and fate in Stordalen Mire, a permafrost peatland in transition

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    Author Posting. Ā© American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 36(1), (2022): e2021GB007113, https://doi.org/10.1029/2021GB007113.Stordalen Mire is a peatland in the discontinuous permafrost zone in arctic Sweden that exhibits a habitat gradient from permafrost palsa, to Sphagnum bog underlain by permafrost, to Eriophorum-dominated fully thawed fen. We used three independent approaches to evaluate the annual, multi-decadal, and millennial apparent carbon accumulation rates (aCAR) across this gradient: seven years of direct semi-continuous measurement of CO2 and CH4 exchange, and 21 core profiles for 210Pb and 14C peat dating. Year-round chamber measurements indicated net carbon balance of āˆ’13 Ā± 8, āˆ’49 Ā± 15, and āˆ’91 Ā± 43 g C māˆ’2 yāˆ’1 for the years 2012ā€“2018 in palsa, bog, and fen, respectively. Methane emission offset 2%, 7%, and 17% of the CO2 uptake rate across this gradient. Recent aCAR indicates higher C accumulation rates in surface peats in the palsa and bog compared to current CO2 fluxes, but these assessments are more similar in the fen. aCAR increased from low millennial-scale levels (17ā€“29 g C māˆ’2 yāˆ’1) to moderate aCAR of the past century (72ā€“81 g C māˆ’2 yāˆ’1) to higher recent aCAR of 90ā€“147 g C māˆ’2 yāˆ’1. Recent permafrost collapse, greater inundation and vegetation response has made the landscape a stronger CO2 sink, but this CO2 sink is increasingly offset by rising CH4 emissions, dominated by modern carbon as determined by 14C. The higher CH4 emissions result in higher net CO2-equivalent emissions, indicating that radiative forcing of this mire and similar permafrost ecosystems will exert a warming influence on future climate.We would like to acknowledge the following funding in support of this project: Swedish Research Council (VetenskapsrĆ„det, VR) grants (NT 2007-4547 and NT 2013-5562 to P. Crill), U.S. Department of Energy grants (DE-SC0004632 and DE-SC0010580 to V. Rich and S. Saleska), and U.S. National Science Foundation MacroSystems Biology grant (NSF EF #1241037, PI Varner). This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under the Genomic Science program. We also acknowledge funding from the National Science Foundation for the EMERGE Biology Integration Institute, NSF Award #2022070.2022-07-0
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