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1. Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

   https://doi.org/10.1038/s43705-023-00326-5  

   Romanowicz, Karl J. ; Crump, Byron C. ; Kling, George W. ( November 2023 , ISME Communications)

   Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.

    

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2. Assessing dynamic vegetation model parameter uncertainty across Alaskan arctic tundra plant communities

   https://doi.org/10.1002/EAP.2499  

   Euskirchen, Eugénie S. ; Serbin, Shawn P. ; Carman, Tobey B. ; Fraterrigo, Jennifer M. ; Genet, Hélène ; Iversen, Colleen M. ; Salmon, Verity ; McGuire, A. David ( November 2021 , Ecological Applications)

   As the Arctic region moves into uncharted territory under a warming climate, it is important to refine the terrestrial biosphere models (TBMs) that help us understand and predict change. One fundamental uncertainty in TBMs relates to model parameters, configuration variables internal to the model whose value can be estimated from data. We incorporate a version of the Terrestrial Ecosystem Model (TEM) developed for arctic ecosystems into the Predictive Ecosystem Analyzer (PEcAn) framework. PEcAn treats model parameters as probability distributions, estimates parameters based on a synthesis of available field data, and then quantifies both model sensitivity and uncertainty to a given parameter or suite of parameters. We examined how variation in 21 parameters in the equation for gross primary production influenced model sensitivity and uncertainty in terms of two carbon fluxes (net primary productivity and heterotrophic respiration) and two carbon (C) pools (vegetation C and soil C). We set up different parameterizations of TEM across a range of tundra types (tussock tundra, heath tundra, wet sedge tundra, and shrub tundra) in northern Alaska, along a latitudinal transect extending from the coastal plain near Utqiaġvik to the southern foothills of the Brooks Range, to the Seward Peninsula. TEM was most sensitive to parameters related to the temperature regulation of photosynthesis. Model uncertainty was mostly due to parameters related to leaf area, temperature regulation of photosynthesis, and the stomatal responses to ambient light conditions. Our analysis also showed that sensitivity and uncertainty to a given parameter varied spatially. At some sites, model sensitivity and uncertainty tended to be connected to a wider range of parameters, underlining the importance of assessing tundra community processes across environmental gradients or geographic locations. Generally, across sites, the flux of net primary productivity (NPP) and pool of vegetation C had about equal uncertainty, while heterotrophic respiration had higher uncertainty than the pool of soil C. Our study illustrates the complexity inherent in evaluating parameter uncertainty across highly heterogeneous arctic tundra plant communities. It also provides a framework for iteratively testing how newly collected field data related to key parameters may result in more effective forecasting of Arctic change. 

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3. Methane, Microbes and Models in Amazonian Floodplains: State of the Art and Perspectives

   https://doi.org/http://dx.doi.org/10.5772/intechopen.90247  

   Barros, D.J. ; Bento, M.S. ; Ferreira, M.S. ; Carmo, J.B. ; Toppa, R.H. ; Neu, V. ; Varesche, M.B.A. ; Morais, P.B. ; and Navarrete, A.A. ( January 2019 , Changing Ecosystems and Their Services)

   Amazon floodplain ecosystems include open water and intermittent flood forest and agricultural systems with different water types. They are a significant natural source of methane (CH4) in the tropics. When soils are flooded and become anoxic, CH4 is produced by methanogenesis, while microbially mediated aerobic and anaerobic oxidation of CH4 serves as the primary biological sink of this greenhouse gas. Measurements of rates and controls on CH4 production and emission in the Amazon basin mainly come from studies on individual wetlands and floodplain lakes. Similarly, microbial communities in those Amazon floodplain habitats have been studied on individual lakes based on sequence-specific DNA analysis. Existing biogeochemical ecosystem models of CH4 from the Amazon floodplains focus on soil properties or involve factors such as pH, redox potentials, or substrates. None of these models incorporate appropriate seasonal inundation; neither the microbiota does it as a component. In this sense, our chapter will highlight how the important efforts already contributed to understand the CH4 emission and its connections with abiotic and biotic factors in Amazon floodplains, as well as emphasize the need of encouraging cooperation and exchange of experience between research teams by using different approaches and scientific methods." 

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4. Response of CO 2 and CH 4 emissions from Arctic tundra soils to a multifactorial manipulation of water table, temperature and thaw depth

   https://doi.org/10.1088/2752-664X/ad089d  

   Best, K. ; Zona, D. ; Briant, E. ; Lai, Chun-Ta ; Lipson, D. A. ; McEwing, K. R. ; Davidson, S. J. ; Oechel, W. C. ( November 2023 , Environmental Research: Ecology)

   Significant uncertainties persist concerning how Arctic soil tundra carbon emission responds to environmental changes. In this study, 24 cores were sampled from drier (high centre polygons and rims) and wetter (low centre polygons and troughs) permafrost tundra ecosystems. We examined how soil CO₂and CH₄fluxes responded to laboratory-based manipulations of soil temperature (and associated thaw depth) and water table depth, representing current and projected conditions in the Arctic. Similar soil CO₂respiration rates occurred in both the drier and the wetter sites, suggesting that a significant proportion of soil CO₂emission occurs via anaerobic respiration under water-saturated conditions in these Arctic tundra ecosystems. In the absence of vegetation, soil CO₂respiration rates decreased sharply within the first 7 weeks of the experiment, while CH₄emissions remained stable for the entire 26 weeks of the experiment. These patterns suggest that soil CO₂emission is more related to plant input than CH₄production and emission. The stable and substantial CH₄emission observed over the entire course of the experiment suggests that temperature limitations, rather than labile carbon limitations, play a predominant role in CH₄production in deeper soil layers. This is likely due to the presence of a substantial source of labile carbon in these carbon-rich soils. The small soil temperature difference (a median difference of 1 °C) and a more substantial thaw depth difference (a median difference of 6 cm) between the high and low temperature treatments resulted in a non-significant difference between soil CO₂and CH₄emissions. Although hydrology continued to be the primary factor influencing CH₄emissions, these emissions remained low in the drier ecosystem, even with a water table at the surface. This result suggests the potential absence of a methanogenic microbial community in high-centre polygon and rim ecosystems. Overall, our results suggest that the temperature increases reported for these Arctic regions are not responsible for increases in carbon losses. Instead, it is the changes in hydrology that exert significant control over soil CO₂and CH₄emissions.

    

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5. The Controls of Iron and Oxygen on Hydroxyl Radical (•OH) Production in Soils

   https://doi.org/10.3390/soilsystems3010001  

   Trusiak, Adrianna ; Treibergs, Lija ; Kling, George ; Cory, Rose ( March 2019 , Soil Systems)

   Hydroxyl radical (•OH) is produced in soils from oxidation of reduced iron (Fe(II)) by dissolved oxygen (O2) and can oxidize dissolved organic carbon (DOC) to carbon dioxide (CO2). Understanding the role of •OH on CO2 production in soils requires knowing whether Fe(II) production or O2 supply to soils limits •OH production. To test the relative importance of Fe(II) production versus O2 supply, we measured changes in Fe(II) and O2 and in situ •OH production during simulated precipitation events and during common, waterlogged conditions in mesocosms from two landscape ages and the two dominant vegetation types of the Arctic. The balance of Fe(II) production and consumption controlled •OH production during precipitation events that supplied O2 to the soils. During static, waterlogged conditions, •OH production was controlled by O2 supply because Fe(II) production was higher than its consumption (oxidation) by O2. An average precipitation event (4 mm) resulted in 200 µmol •OH m−2 per day produced compared to 60 µmol •OH m−2 per day produced during waterlogged conditions. These findings suggest that the oxidation of DOC to CO2 by •OH in arctic soils, a process potentially as important as microbial respiration of DOC in arctic surface waters, will depend on the patterns and amounts of rainfall that oxygenate the soil. 

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