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Aquatic ecosystems are major sources of greenhouse gases (GHGs). Robust measurements of natural GHG emissions are vital for evaluating regional to global carbon budgets and for assessing climate feedbacks of natural emissions to improve climate models. Diffusive and ebullitive (bubble) transport are two major pathways of gas release from surface waters. To capture the high temporal variability of these fluxes in a well-defined footprint, we designed and built an inexpensive device that includes an easily mobile diffusive flux chamber and a bubble counter all in one. In addition to automatically collecting gas samples for subsequent various analyses in the laboratory, this device also utilized a low-cost carbon dioxide (CO2) sensor (SenseAir, Sweden) and methane (CH4) sensor (Figaro, Japan) to measure GHG fluxes. Each of the devices was equipped with an XBee module to enable local radio communication (DigiMesh network) for time synchronization and data readout at a server controller station on the lakeshore. The software of this server controller was operated on a lowcost computer (Raspberry Pi), which has a 3G connection for remote control and monitor functions from anywhere in the world. This study shows the potential of a low-cost automatic sensor network system for studying GHG fluxes on lakes in remote locations. Funding Agencies|US National Science Foundation (NSF) (MacroSystems Biology, EF)National Science Foundation (NSF) [1241937]; US National Science Foundation (NSF) (Northern Ecosystems Research for Undergraduates program, NSF REU site EAR) [1063037]; Swedish Research Council (VR)Swedish Research Council [2012-00048, 2016-04829]; European Research Council (ERC)European Research Council (ERC) [725546]; VINNOVAVinnova [2015-03529]

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 understood1–7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8–10, 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., The recovery of viral populations from peatland soils across a permafrost thaw gradient provides insights into soil viral diversity, their hosts and the potential impacts on carbon cycling in this environment.

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 (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ13C-CH4 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.

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.

Recent warming in the Arctic, which has been amplified during the winter1–3, greatly enhances microbial decomposition of soil organic matter and subsequent release of carbon dioxide (CO2)4. However, the amount of CO2 released in winter is not known and has not been well represented by ecosystem models or empirically based estimates5,6. Here we synthesize regional in situ observations of CO2 flux from Arctic and boreal soils to assess current and future winter carbon losses from the northern permafrost domain. We estimate a contemporary loss of 1,662 TgC per year from the permafrost region during the winter season (October–April). This loss is greater than the average growing season carbon uptake for this region estimated from process models (−1,032 TgC per year). Extending model predictions to warmer conditions up to 2100 indicates that winter CO2 emissions will increase 17% under a moderate mitigation scenario—Representative Concentration Pathway 4.5—and 41% under business-as-usual emissions scenario—Representative Concentration Pathway 8.5. Our results provide a baseline for winter CO2 emissions from northern terrestrial regions and indicate that enhanced soil CO2 loss due to winter warming may offset growing season carbon uptake under future climatic conditions. Winter warming in the Arctic will increase the CO2 flux from soils. A pan-Arctic analysis shows a current loss of 1,662 TgC per year over the winter, exceeding estimated carbon uptake in the growing season; projections suggest a 17% increase under RCP 4.5 and a 41% increase under RCP 8.5 by 2100.

The spatial extent of northern peatlands remains highly uncertain in spite of rapidly developing satellite observation datasets. This is limiting progress in the understanding of fundamental biogeochemical processes, such as the global carbon (C) cycle and climate feedback effects on C fluxes. In this study, we evaluated the capabilities of two new satellite datasets that enable regional scale mapping of peatland extent at high spatial resolution, including Sentinel-1 synthetic aperture radar (SAR) and the Arctic digital elevation model (ArcticDEM). Terrain indices and temporal features derived from these datasets provided input to Random Forest models for delineating four main land cover classes (forest, open upland, water and peatland) in an area in northern Sweden consisting of both lowland and mountainous terrain. The contribution of ArcticDEM to the classification accuracy was assessed by comparing the results with those derived when a high quality LiDAR based DEM (LiDEM) was used as alternative model input. This study shows that multi-seasonal SAR alone can produce reasonable classification results in terms of overall accuracy (OA; 81.6%), but also that it has limitations. The inclusion of terrain indices improved classification performance substantially. OA increased to 87.5% and 90.9% when terrain indices derived from ArcticDEM and LiDEM were included, respectively. The largest increase in accuracy was achieved for the peatland class, which suggests that terrain indices do have the ability to capture the features in the geographic context that aid the discrimination of peatland from other land cover classes. The relatively small difference in classification accuracy between LiDEM and ArcticDEM is encouraging since the latter provides circumpolar coverage. Thus, the combination of Sentinel-1 time series and terrain indices derived from ArcticDEM presents opportunities for substantially improving regional estimates of peatland extent at high latitudes. Funding Agencies|Swedish Research Council VRSwedish Research Council [VR 2012-48]; IZOMET project [VR 2014-6584]; Swedish Research Council for Sustainable Development (Formas)Swedish Research Council Formas [2018-00570, 2018-01794]

The recent paper in Geosciences, “Understanding the Permafrost−Hydrate System and Associated Methane Releases in the East Siberian Arctic Shelf” by Shakhova, Semiletov, and Chuvilin, (henceforth “S2019”), contains a number of false statements about our 2016 paper, “Methane fluxes from the sea to the atmosphere across the Siberian shelf seas”, (henceforth “T2016”). S2019 use three paragraphs of section 5 of their paper to claim methodological errors and issues in T2016. Notably they claim that in T2016, we systematically removed data outliers including data with high methane concentrations; this claim is false. While we appreciate that flawed methodologies can be a problem in any area of science, in this case, the claims made in S2019 are simply false. In this comment, we detail the incorrect claims made in S2019 regarding T2016, and then discuss some additional problematic aspects of S2019.

Research infrastructures play a key role in launching a new generation of integrated long-term, geographically distributed observation programmes designed to monitor climate change, better understand its impacts on global ecosystems, and evaluate possible mitigation and adaptation strategies. The pan-European Integrated Carbon Observation System combines carbon and greenhouse gas (GHG; CO2, CH4, N2O, H2O) observations within the atmosphere, terrestrial ecosystems and oceans. High-precision measurements are obtained using standardised methodologies, are centrally processed and openly available in a traceable and verifiable fashion in combination with detailed metadata. The Integrated Carbon Observation System ecosystem station network aims to sample climate and land-cover variability across Europe. In addition to GHG flux measurements, a large set of complementary data (including management practices, vegetation and soil characteristics) is collected to support the interpretation, spatial upscaling and modelling of observed ecosystem carbon and GHG dynamics. The applied sampling design was developed and formulated in protocols by the scientific community, representing a trade-off between an ideal dataset and practical feasibility. The use of open-access, high-quality and multi-level data products by different user communities is crucial for the Integrated Carbon Observation System in order to achieve its scientific potential and societal value.

Chamber measurements of trace gas fluxes between the land surface and the atmosphere have been conducted for almost a century. Different chamber techniques, including static and dynamic, have been used with varying degrees of success in estimating greenhouse gases (CO2, CH4, N2O) fluxes. However, all of these have certain disadvantages which have either prevented them from providing an adequate estimate of greenhouse gas exchange or restricted them to be used under limited conditions. Generally, chamber methods are relatively low in cost and simple to operate. In combination with the appropriate sample allocations, chamber methods are adaptable for a wide variety of studies from local to global spatial scales, and they are particularly well suited for in situ and laboratory-based studies. Consequently, chamber measurements will play an important role in the portfolio of the Pan-European long-term research infrastructure Integrated Carbon Observation System. The respective working group of the Integrated Carbon Observation System Ecosystem Monitoring Station Assembly has decided to ascertain standards and quality checks for automated and manual chamber systems instead of defining one or several standard systems provided by commercial manufacturers in order to define minimum requirements for chamber measurements. The defined requirements and recommendations related to chamber measurements are described here.

The closed chamber technique is widely used to measure the exchange of methane (CH4) and carbon dioxide (CO2) from terrestrial ecosystems. There is, however, large uncertainty about which model should be used to calculate the gas flux from the measured gas concentrations. Due to experimental uncertainties the simple linear regression model (first-order polynomial) is often applied, even though theoretical considerations of the technique suggest the application of other, curvilinear models. High-resolution automatic chamber systems which sample gas concentrations several hundred times per flux measurement make it possible to resolve the curvilinear behavior and study the information imposed by the natural variability of the temporal concentration changes. We used more than 50 000 such flux measurements of CH4 and CO2 from five field sites located in peat-forming wetlands ranging from 56 to 78° N to quantify the typical differences between flux estimates of different models. In addition, we aimed to assess the curvilinearity of the concentration time series and test the general applicability of curvilinear models. Despite significant episodic differences between the calculated flux estimates, the overall differences are generally found to be smaller than the local flux variability on the plot scale. The curvilinear behavior of the gas concentrations within the chamber is strongly influenced by wind-driven chamber leakage, and less so by changing gas concentration gradients in the soil during chamber closure. Such physical processes affect both gas species equally, which makes it possible to isolate biochemical processes affecting the gases differently, such as photosynthesis limitation by chamber headspace CO2 concentrations under high levels of incoming solar radiation. We assess the possibility to exploit this effect for a partitioning of the net CO2 flux into photosynthesis and ecosystem respiration as an example of how high-resolution automatic chamber measurements could be used for purposes beyond the estimation of the net gas flux. This shows that while linear and curvilinear calculation schemes can provide similar net fluxes, only curvilinear models open additional possibilities for high-resolution automatic chamber measurements.

A Floresta Nacional do Tapajós (FLONA Tapajós) possui 600 mil hectares de floresta protegida, e está situada a 50 km ao sul da cidade de Santarém, Pará, Brasil, uma cidade portuária de 250 mil habitantes, localizada na confluência dos rios Tapajós e Amazonas. Há abundância de terras agrícolas na região, que oferecem muitas oportunidades para estudar mudanças no uso da terra, e um tipo de uso da terra, a colheita seletiva de madeira, é particularmente importante para a economia de Santarém. A deposição úmida e seca pode ser uma importante fonte de nutrientes para as plantas, e isto é especialmente verdade quando os solos são pobres, o que é o caso na região do planalto Santarém-Belterra, a área de estudo da presente investigação. Nesta região, a deposição de nutrientes atmosférico natural é reforçada pela frequente queima de biomassa que libera uma grande parte dos nutrientes da biomassa acima do solo para a atmosfera. Os objetivos deste estudo foram: 1) Estimar a deposição úmida total via precipitação direta e através da copa, incluindo a deposição seca; 2) Verificar potenciais fontes de nutrientes encontrados na deposição úmida total e deposição seca; e, 3) Verificar possíveis efeitos da cobertura vegetal no teor de nutrientes na precipitação e precipitação interna. Este estudo foi realizado na FLONA Tapajós no km 67 da rodovia Santarém - Cuiabá, ao sul da cidade de Santarém. A área de estudo consistiu de uma parcela de 100 x 100 m dividida em transectos de 10 x 10 m que foi localizada próximo de uma torre meteorológica de 65 m que com medidas de vários parâmetros climáticos, como precipitação, velocidade e direção do vento, radiação solar incidente e temperatura e umidade do ar, entre outros. Coletores de precipitação direta (PD) e de precipitação interna (PI) consistiram de frascos de 2 L de polietileno com um funil de diâmetro de 115 mm. As amostras foram coletadas semanalmente durante abril de 2003 a março de 2006. O volume da amostra foi medido individualmente para cada coletor (25 coletores para a precipitação interna e 4 para a precipitação direta). As conclusões que podem ser tiradas a partir deste estudo são: 1) A estação seca apresenta a maior variação no fluxo de íons; 2) A sazonalidade exerce uma forte influência sobre a concentração de cátions básicos; 3) A deposição seca é um das mais importantes caminhos para a entrada de nutrientes na FLONA Tapajós; 4) Há uma entrada significativa de macronutrientes, Cl e Na da agricultura de grãos intensivo nas proximidades; 5) Deposição seca é o processo mais importante para o enriquecimento de água que atinge o chão da floresta; 6) A análise de componentes principais facilita a interpretação e caracterização de águas pluviais e, neste estudo, mostra a influência de fontes antropogênicas como a agricultura, queima de biomassa, e poeira. The Tapajós National Forest (FLONA Tapajós) has 600,000 hectares of protected forest, and is situated 50 km south of the city of Santarém, Pará, Brazil, a port city of 250,000 inhabitants that is located at the confluence of the Tapajós and Amazon Rivers. There is a lot of farmland in the region, which offers many opportunities to study changes in land use. Selective wood harvesting is one type of land use that is particularly important to the economy of Santarém. Wet and dry deposition of organic material can be an important source of nutrients for plants, and this is especially true when the soil is poor, which is the case in Santarém-Belterra plateau region, the study area of this research. In this region, the natural atmospheric deposition of nutrients is often enhanced by the burning of biomass, which releases a large part of the above-ground biomass nutrients into the atmosphere. The objectives of this study were: 1 - estimate the total wet deposition via direct precipitation and through the canopy, including dry deposition; 2 - verify potential sources of nutrients found in the total wet deposition and dry deposition; and 3 - investigate the effects of coverage vegetation on nutrient content in precipitation and throughfall. The study was conducted in FLONA Tapajós at km 67 of Santarém- Cuiabá Highway, south of the city of Santarém. The study area consisted of a portion of 100 x 100 m transects divided into 10 x 10 m plots. The area was located next to a meteorological tower 65 m tall that measures various climate parameters such as rainfall, wind speed and direction, solar radiation, temperature and humidity, among others. Direct precipitation (PD) and internal precipitation (IP) collectors consisted of 2 L polyethylene bottles with a 115 mm diameter funnel. Samples were collected weekly from April 2003 to March 2006. The volume of the sample was measured individually for each collector (25 traps for internal precipitation and 4 for direct precipitation). The conclusions that can be drawn from this study are: 1 - the dry season has the highest variation in ion flux; 2 - seasonality has a strong influence on the concentration of basic cations; 3 - dry deposition is one of the most important ways that nutrients are acquired in FLONA Tapajos; 4 - there is a significant inflow of nutrients Cl and Na due to intensive grain farming nearby; 5 - dry deposition is the most important process for the enrichment of water that reaches the forest floor; 6 - principal component analysis facilitates the interpretation and characterization of rainwater and in this study shows the influence of anthropogenic sources such as agriculture, biomass burning, and dust.

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 δ13Corg 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.

Wetlands are the largest natural source of atmospheric methane. Here, we assess controls on methane flux using a database of approximately 19 000 instantaneous measurements from 71 wetland sites located across subtropical, temperate, and northern high latitude regions. Our analyses confirm general controls on wetland methane emissions from soil temperature, water table, and vegetation, but also show that these relationships are modified depending on wetland type (bog, fen, or swamp), region (subarctic to temperate), and disturbance. Fen methane flux was more sensitive to vegetation and less sensitive to temperature than bog or swamp fluxes. The optimal water table for methane flux was consistently below the peat surface in bogs, close to the peat surface in poor fens, and above the peat surface in rich fens. However, the largest flux in bogs occurred when dry 30-day averaged antecedent conditions were followed by wet conditions, while in fens and swamps, the largest flux occurred when both 30-day averaged antecedent and current conditions were wet. Drained wetlands exhibited distinct characteristics, e.g. the absence of large flux following wet and warm conditions, suggesting that the same functional relationships between methane flux and environmental conditions cannot be used across pristine and disturbed wetlands. Together, our results suggest that water table and temperature are dominant controls on methane flux in pristine bogs and swamps, while other processes, such as vascular transport in pristine fens, have the potential to partially override the effect of these controls in other wetland types. Because wetland types vary in methane emissions and have distinct controls, these ecosystems need to be considered separately to yield reliable estimates of global wetland methane release.

The global methane (CH4) budget is becoming an increasingly important component for managing realistic pathways to mitigate climate change. This relevance, due to a shorter atmospheric lifetime and a stronger warming potential than carbon dioxide, is challenged by the still unexplained changes of atmospheric CH4 over the past decade. Emissions and concentrations of CH4 are continuing to increase, making CH4 the second most important human-induced greenhouse gas after carbon dioxide. Two major difficulties in reducing uncertainties come from the large variety of diffusive CH4 sources that overlap geographically, and from the destruction of CH4 by the very short-lived hydroxyl radical (OH). To address these difficulties, we have established a consortium of multi-disciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate research on the methane cycle, and producing regular (similar to biennial) updates of the global methane budget. This consortium includes atmospheric physicists and chemists, biogeochemists of surface and marine emissions, and socio-economists who study anthropogenic emissions. Following Kirschke et al. (2013), we propose here the first version of a living review paper that integrates results of top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models, inventories and data-driven approaches (including process-based models for estimating land surface emissions and atmospheric chemistry, and inventories for anthropogenic emissions, data-driven extrapolations). For the 2003-2012 decade, global methane emissions are estimated by top-down inversions at 558 TgCH(4) yr(-1), range 540-568. About 60% of global emissions are anthropogenic (range 50-65 %). Since 2010, the bottom-up global emission inventories have been closer to methane emissions in the most carbon-intensive Representative Concentrations Pathway (RCP8.5) and higher than all other RCP scenarios. Bottom-up approaches suggest larger global emissions (736 TgCH(4) yr(-1), range 596-884) mostly because of larger natural emissions from individual sources such as inland waters, natural wetlands and geological sources. Considering the atmospheric constraints on the top-down budget, it is likely that some of the individual emissions reported by the bottom-up approaches are overestimated, leading to too large global emissions. Latitudinal data from top-down emissions indicate a predominance of tropical emissions (similar to 64% of the global budget, amp;lt;30 degrees N) as compared to mid (similar to 32 %, 30-60 degrees N) and high northern latitudes (similar to 4 %, 60-90 degrees N). Top-down inversions consistently infer lower emissions in China (similar to 58 TgCH(4) yr(-1), range 51-72, -14 %) and higher emissions in Africa (86 TgCH(4) yr(-1), range 73-108, + 19 %) than bottom-up values used as prior estimates. Overall, uncertainties for anthropogenic emissions appear smaller than those from natural sources, and the uncertainties on source categories appear larger for top-down inversions than for bottom-up inventories and models. The most important source of uncertainty on the methane budget is attributable to emissions from wetland and other inland waters. We show that the wetland extent could contribute 30-40% on the estimated range for wetland emissions. Other priorities for improving the methane budget include the following: (i) the development of process-based models for inland-water emissions, (ii) the intensification of methane observations at local scale (flux measurements) to constrain bottom-up land surface models, and at regional scale (surface networks and satellites) to constrain top-down inversions, (iii) improvements in the estimation of atmospheric loss by OH, and (iv) improvements of the transport models integrated in top-down inversions. The data presented here can be downloaded from the Carbon Dioxide Information Analysis Center (http://doi.org/10.3334/CDIAC/GLOBAL_METHANE_BUDGET_2016_V1.1) and the Global Carbon Project. Funding Agencies|Swiss National Science Foundation; NASA [NNX14AF93G, NNX14AO73G]; National Environmental Science Program - Earth Systems and Climate Change Hub; European Commission [283576, 633080]; ESA Climate Change Initiative Greenhouse Gases Phase 2 project; US Department of Energy, BER [DE-AC02-05CH11231]; FAO member countries; Environment Research and Technology Development Fund of the Ministry of the Environment, Japan [2-1502]; ERC [322998]; NERC [NE/J00748X/1]; Swedish Research Council VR; Research Council of Norway [244074]; NSF [1243232, 1243220]; National Science and Engineering Research Council of Canada (NSERC); Chinas QianRen Program; CSIRO Australia; Australian Bureau of Meteorology; Australian Institute of Marine Science; Australian Antarctic Division; NOAA USA; Meteorological Service of Canada; National Aeronautic and Space Administration (NASA) [NAG5-12669, NNX07AE89G, NNX11AF17G, NNX07AE87G, NNX07AF09G, NNX11AF15G, NNX11AF16G]; Department of Energy and Climate Change (DECC, UK) [GA01081]; Commonwealth Scientific and Industrial Research Organization (CSIRO Australia); Bureau of Meteorology (Australia); Joint DECC/Defra Met Office Hadley Centre Climate Programme [GA01101]

© 2016 Elsevier Ltd. Methane is a potent greenhouse gas, and there are concerns that its natural emissions from the Arctic could act as a substantial positive feedback to anthropogenic global warming. Determining the sources of methane emissions and the biogeochemical processes controlling them is important for understanding present and future Arctic contributions to atmospheric methane budgets. Here we apply measurements of multiply-substituted isotopologues, or clumped isotopes, of methane as a new tool to identify the origins of ebullitive fluxes in Alaska, Sweden and the Arctic Ocean. When methane forms in isotopic equilibrium, clumped isotope measurements indicate the formation temperature. In some microbial methane, however, non-equilibrium isotope effects, probably related to the kinetics of methanogenesis, lead to low clumped isotope values. We identify four categories of emissions in the studied samples: thermogenic methane, deep subsurface or marine microbial methane formed in isotopic equilibrium, freshwater microbial methane with non-equilibrium clumped isotope values, and mixtures of deep and shallow methane (i.e., combinations of the first three end members). Mixing between deep and shallow methane sources produces a non-linear variation in clumped isotope values with mixing proportion that provides new constraints for the formation environment of the mixing end-members. Analyses of microbial methane emitted from lakes, as well as a methanol-consuming methanogen pure culture, support the hypothesis that non-equilibrium clumped isotope values are controlled, in part, by kinetic isotope effects induced during enzymatic reactions involved in methanogenesis. Our results indicate that these kinetic isotope effects vary widely in microbial methane produced in Arctic lake sediments, with non-equilibrium δ18values spanning a range of more than 5‰.

Methane emissions from lakes are widely thought to be highly irregular and difficult to quantify with anything other than numerous distributed measurement stations and long-term sampling campaigns. In spite of this, a large majority of the study sites north of 50 degrees N have been measured over surprisingly short time periods of only one to a few days. Using long-term data from three intensively studied small subarctic lakes, we recommend that measurements of diffusive methane flux and ebullition should be made over at least 11 and 39days scattered throughout the ice-free season using depth-stratified sampling at 3 and 11 or more locations, respectively. We further show that low temporal and spatial resolutions are unlikely to cause overestimates. Therefore, we argue that most sites measured previously are likely underestimated in terms of emission potential. Avoiding these biases seen in much of the contemporary data is crucial to further constrain large-scale methane emissions from northern lakes and ponds. Funding Agencies|Swedish Research Council [2007-4547]; Nordic Center of Excellence DEFROST under Nordic Top-Level Research Initiative

Land-use change in the Amazon basin has occurred at an accelerated pace during the last decade, and it is important that the effects induced by these changes on soil properties are better understood. This study investigated the chemical, physical, and biological properties of soil in a field under cultivation of soy and rice, and at an adjacent primary rain forest. Increases in soil bulk density, exchangeable cations and pH were observed in the soy field soil. In the primary forest, soil microbial biomass and basal respiration rates were higher, and the microbial community was metabolically more efficient. The sum of basal respiration across the A, AB and BA horizons on a mass per area basis ranged from 7.31 to 10.05 Mg CO2-C ha-1yr-1, thus yielding estimates for total soil respiration between 9.6 and 15.5 Mg CO2-C ha-1yr-1across sites and seasons. These estimates are in good agreement with literature values for Amazonian ecosystems. The estimates of heterotrophic respiration made in this study help to further constrain the estimates of autotrophic soil respiration and will be useful for monitoring the effects of future land-use in Amazonian ecosystems. As mudanças no uso da terra na bacia Amazônica têm ocorridas num ritmo acelerado durante a última década, e é importante que os efeitos dessas mudanças nos recursos edáficos sejam explicados. Este trabalho teve como objetivo investigar as propriedades físicas, químicas, e biológicas de um solo sob cultivo de soja e arroz, e um solo de floresta primária adjacente. O solo do campo de soja teve aumentos na densidade, cátions trocáveis, e pH. Na floresta primária a biomassa microbiana e a respiração do solo foram maiores, e a comunidade microbiana demonstrou maior eficiência metabólica. A soma da respiração basal nos três horizontes estudados variou entre 7,31 a 10,05 Mg CO2-C ha-1ano-1, assim dando estimativas de 9,6 a 15,5 Mg CO2-C ha-1ano-1para a respiração total do solo somada para sítios e épocas de amostragem, valores que estão de acordo com dados reportados na literatura para ecossistemas amazônicos. As estimativas da respiração heterotrófica nesse estudo ajudarão a estreitar as estimativas de respiração autotrófica e serão importantes na determinação dos efeitos de futuras mudanças no uso da terra e no clima em sistemas amazônicos.

Forests are generally considered to be net sinks of atmospheric methane (CH 4 ) because of oxidation by methanotrophic bacteria in well-aerated forests soils. However, emissions from wet forest soils, and sometimes canopy fluxes, are often neglected when quantifying the CH 4 budget of a forest. We used a modified Bowen ratio method and combined eddy covariance and gradient methods to estimate net CH 4 exchange at a boreal forest site in central Sweden. Results indicate that the site is a net source of CH 4 . This is in contrast to soil, branch and leaf chamber measurements of uptake of CH 4 . Wetter soils within the footprint of the canopy are thought to be responsible for the discrepancy. We found no evidence for canopy emissions per se. However, the diel pattern of the CH 4 exchange with minimum emissions at daytime correlated well with gross primary production, which supports an uptake in the canopy. More distant source areas could also contribute to the diel pattern; their contribution might be greater at night during stable boundary layer conditions. Keywords: micrometeorology, Bowen ratio, eddy covariance, footprint, wet soil (Published: 6 July 20105) Citation: Tellus B 2015, 67 , 26688, http://dx.doi.org/10.3402/tellusb.v67.26688

Forest management practices can alter soil conditions, affecting the consumption and production processes that control soil methane (CH4) exchange. We studied the short-term effects of thinning, clear-cutting and stump harvesting on the CH4 exchange between soil and atmosphere at a boreal forest site in central Sweden, using an undisturbed plot as the control. Chambers in combination with a highprecision laser gas analyser were used for continuous measurements. Both the undisturbed plot and the thinned plot were net sinks of CH4, whereas the clear-cut plot and the stump harvested plot were net CH4 sources. The CH4 uptake at the thinned plot was reduced in comparison to the undisturbed plot. The shift from sink to source at the clear-cut and stump harvested plots was probably due to a rise in the water table and an increase in soil moisture, leading to lower gas diffusivity and more reduced conditions, which favour CH4 production by archea. Reduced evapotranspiration after harvesting leads to wetter soils, decreased CH4 consumption and increased CH4 production, and should be accounted for in the CH4 budget of managed forests.

Permafrost contains about 50% of the global soil carbon1. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions2, 3. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown3 and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ13C signature (10–15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden4, 5 as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus ‘Methanoflorens stordalenmirensis’6 is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models3, 7. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change. funded by US Department of Energy Office of Biological and Environmental Research (award DE-SC0004632) IsoGenie

A system was developed for collecting from the ambient atmosphere the methyl halides CH3Cl and CH3Br in quantities sufficient for chlorine and bromine isotope analysis. The construction and operation of the novel cryogenic collection system (cryosampler) and sample purification system developed for this task are described. This study demonstrates the capability of the cryosampler by quantifying the CH3Cl and CH3Br collected from atmospheric samples and the nonfractionating bromine isotope fingerprint of CH3Br from synthetic air samples of controlled composition. An optimized cryosampler operation time of 4 h at a flow rate of 15 L min−1 is applied to yield the nearly 40 ng required for subsequent δ81Br-CH3Br analyses. The sample purification system is designed around a packed column gas chromatography–quadropole–mass spectrometry (GCqMS) system with three additional cryotraps and backflushing capacity. The system's suitability was tested by observing both the mass recovery and the lack of Δ81Br isotope fractionation induced during sample purification under varying flow rates and loading scenarios. To demonstrate that the entire system samples and dependably delivers CH3Br to the isotope analysis system without inducing isotope fractionation, diluted synthetic air mixtures prepared from standard gases were processed through the entire system, yielding a Δ81Br-CH3Br of +0.03‰ ± 0.10‰ relative to their starting composition. Finally, the combined cryosampler–purification and analysis system was applied to demonstrate the first-ever δ81Br-CH3Br in the ambient atmosphere with two samples collected in the autumn of 2011, yielding −0.08‰ ± 0.43‰ and +1.75‰ ± 0.13‰ versus standard mean ocean bromide for samples collected at a suburban Stockholm, Sweden, site.

The aim of this study was to reconstruct diatom production in the subarctic northern tip of the Baltic Sea, Bothnian Bay, based on down-core analysis of Si isotopes in biogenic silica (BSi). Dating of the sediment showed that the samples covered the period 1820 to 2000. The sediment core record can be divided into two periods, an unperturbed period from 1820 to 1950 and a second period affected by human activities (from 1950 to 2000). This has been observed elsewhere in the Baltic Sea. The shift in the sediment core record after 1950 is likely caused by large scale damming of rivers. Diatom production was inferred from the Si isotope composition which ranged between δ30Si −0.18‰ and +0.58‰ in BSi, and assuming fractionation patterns due to the Raleigh distillation, the production was shown to be correlated with air and water temperature, which in turn were correlated with the mixed layer (ML) depth. The sedimentary record showed that the deeper ML depth observed in colder years resulted in less production of diatoms. Pelagic investigations in the 1990's have clearly shown that diatom production in the Baltic Sea is controlled by the ML depth. Especially after cold winters and deep water mixing, diatom production was limited and dissolved silicate (DSi) concentrations were not depleted in the water column after the spring bloom. Our method corroborates these findings and offers a new method to estimate diatom production over much longer periods of time in diatom dominated aquatic systems, i.e. a large part of the world's ocean and coastal seas.

The amount of methane (CH(4)) emitted from northern lakes to the atmosphere is uncertain but is expected to increase as a result of arctic warming. A majority of CH4 is thought to be released through ebullition (bubbling), a pathway with extreme spatial variability that limits the accuracy of measurements. We assessed ebullition during early and late winter by quantifying bubbles trapped in the ice cover of two lakes in a landscape with degrading permafrost in arctic Sweden using random transect sampling and a digital image processing technique. Bubbles covered up to similar to 8% of the lake area and were largely dominated by point source emissions with spatial variabilities of up to 1056%. Bubble occurrence differed significantly between early and late season ice, between the two lakes and among different zones within each lake (p < 0.001). Using a common method, we calculated winter fluxes of up to 129 +/- 486 mg CH(4) m(-2) d(-1). These calculations are, on average, two times higher than estimates from North Siberian and Alaskan lakes and four times higher than emissions measured from the same lakes during summer. Therefore, the calculations are likely overestimates and point to the likelihood that estimating CH(4) fluxes from ice bubble distributions may be more difficult than believed. This study also shows that bubbles quantified using few transects will most likely be unsuitable in making large-scale flux estimates. At least 19 transects covering similar to 1% of the lake area were required to examine ebullition with high precision in our studied lakes. authorCount :5

Hydrocarbons such as CH4 are known to be formed through the Fischer-Tropsch or Sabatier type reactions in hydrothermal systems usually at temperatures above 100°C. Weathering of olivine is sometimes suggested to account for abiotic formation of CH4 through its redox lowering and water splitting properties. Knowledge about the CH4 and H2 formation processes at low temperatures is important for the research about the origin and cause of early Earth and Martian CH4 and for CO2 sequestration. We have conducted a series of low temperature, long-term weathering experiments in which we have tested the CH4 and H2 formation potential of forsteritic olivine. The results show low temperature CH4 production that is probably influenced by chromite and magnetite as catalysts. Extensive analyses of a potential CH4 source trapped in the crystal structure of the olivine showed no signs of incorporated CH4. Also, the available sources of organic carbon were not enough to support the total amount of CH4 detected in our experiments. There was also a linear relationship between silica release into solution and the net CH4 accumulation into the incubation bottle headspaces suggesting that CH4 formation under these conditions could be a qualitative indicator of olivine dissolution. It is likely that minerals such as magnetite, chromite and other metal-rich minerals found on the olivine surface catalyze the formation of CH4, because of the low temperature of the system. This may expand the range of environments plausible for abiotic CH4 formation both on Earth and on other terrestrial bodies.

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. Refereed/Peer-reviewed

A model of the daily carbon balance of a black spruce/feathermoss boreal forest ecosystem was developed and results compared to preliminary data from the 1994 BOREAS field campaign in northern Manitoba, Canada. The model, driven by daily weather conditions, simulated daily soil climate status (temperature and moisture profiles), spruce photosynthesis and respiration, moss photosynthesis and respiration, and litter decomposition. Model agreement with preliminary field data was good for net ecosystem exchange (NEE), capturing both the asymmetrical seasonality and short-term variability. During the growing season simulated daily NEE ranged from -4 g C m(exp -2) d(exp -1) (carbon uptake by ecosystem) to + 2 g C m(exp -2) d(exp -1) (carbon flux to atmosphere), with fluctuations from day to day. In the early winter simulated NEE values were + 0.5 g C m(exp -2) d(exp -1), dropping to + 0.2 g C m(exp -2) d(exp -1) in mid-winter. Simulated soil respiration during the growing season (+ 1 to + 5 g C m(exp -2) d(exp -1)) was dominated by metabolic respiration of the live moss, with litter decomposition usually contributing less than 30% and live spruce root respiration less than 10% of the total. Both spruce and moss net primary productivity (NPP) rates were higher in early summer than late summer. Simulated annual NEE for 1994 was -51 g C m(exp -2) y(exp -1), with 83% going into tree growth and 17% into the soil carbon accumulation. Moss NPP (58 g C m(exp -2) d(exp -1)) was considered to be litter (i.e. soil carbon input; no net increase in live moss biomass). Ecosystem respiration during the snow-covered season (84 g Cm(exp -2)) was 58% of the growing season net carbon uptake. A simulation of the same site for 1968-1989 showed about 10-20% year-to-year variability in heterotrophic respiration (mean of + 113 g C m-2 y@1). Moss NPP ranged from 19 to 114 g C m(exp -2) y(exp -1); spruce NPP from 81 to 150 g C nt-2 y,@l; spruce growth (NPP minus litterfall) from 34 to 103 g C m(exp -2) y(exp -1); NEE ranged from +37 to -142 g C m(exp -2) y(exp -1). Values for these carbon balance terms in 1994 were slightly smaller than the 1969 - 89 means. Higher ecosystem productivity years (more negative NEE) generally had early springs and relatively wet summers; lower productivity years had late springs and relatively dry summers.