| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Berchet, Antoine, et al.
(författare)
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The Community Inversion Framework v1.0 : A unified system for atmospheric inversion studies
- 2021
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 14:8, s. 5331-5354
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric inversion approaches are expected to play a critical role in future observation-based monitoring systems for surface fluxes of greenhouse gases (GHGs), pollutants and other trace gases. In the past decade, the research community has developed various inversion software, mainly using variational or ensemble Bayesian optimization methods, with various assumptions on uncertainty structures and prior information and with various atmospheric chemistry-Transport models. Each of them can assimilate some or all of the available observation streams for its domain area of interest: flask samples, in situ measurements or satellite observations. Although referenced in peer-reviewed publications and usually accessible across the research community, most systems are not at the level of transparency, flexibility and accessibility needed to provide the scientific community and policy makers with a comprehensive and robust view of the uncertainties associated with the inverse estimation of GHG and reactive species fluxes. Furthermore, their development, usually carried out by individual research institutes, may in the future not keep pace with the increasing scientific needs and technical possibilities. We present here the Community Inversion Framework (CIF) to help rationalize development efforts and leverage the strengths of individual inversion systems into a comprehensive framework. The CIF is primarily a programming protocol to allow various inversion bricks to be exchanged among researchers. In practice, the ensemble of bricks makes a flexible, transparent and open-source Python-based tool to estimate the fluxes of various GHGs and reactive species both at the global and regional scales. It will allow for running different atmospheric transport models, different observation streams and different data assimilation approaches. This adaptability will allow for a comprehensive assessment of uncertainty in a fully consistent framework. We present here the main structure and functionalities of the system, and we demonstrate how it operates in a simple academic case.
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| 3. |
- Saunois, Marielle, et al.
(författare)
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The Global Methane Budget 2000–2017
- 2020
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3516 .- 1866-3508. ; 12:3, s. 1561-1623
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Tidskriftsartikel (refereegranskat)abstract
- Understanding and quantifying the global methane (CH4) budget is important for assessing realistic pathways to mitigate climate change. Atmospheric emissions and concentrations of CH4 continue to increase, making CH4 the second most important human-influenced greenhouse gas in terms of climate forcing, after carbon dioxide (CO2). The relative importance of CH4 compared to CO2 depends on its shorter atmospheric lifetime, stronger warming potential, and variations in atmospheric growth rate over the past decade, the causes of which are still debated. Two major challenges in reducing uncertainties in the atmospheric growth rate arise from the variety of geographically overlapping CH4 sources and from the destruction of CH4 by short-lived hydroxyl radicals (OH). To address these challenges, we have established a consortium of multidisciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate new research aimed at improving and regularly updating the global methane budget. Following Saunois et al. (2016), we present here the second version of the living review paper dedicated to the decadal methane budget, integrating results of top-down studies (atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up estimates (including process-based models for estimating land surface emissions and atmospheric chemistry, inventories of anthropogenic emissions, and data-driven extrapolations).For the 2008–2017 decade, global methane emissions are estimated by atmospheric inversions (a top-down approach) to be 576 Tg CH4 yr−1 (range 550–594, corresponding to the minimum and maximum estimates of the model ensemble). Of this total, 359 Tg CH4 yr−1 or ∼ 60 % is attributed to anthropogenic sources, that is emissions caused by direct human activity (i.e. anthropogenic emissions; range 336–376 Tg CH4 yr−1 or 50 %–65 %). The mean annual total emission for the new decade (2008–2017) is 29 Tg CH4 yr−1 larger than our estimate for the previous decade (2000–2009), and 24 Tg CH4 yr−1 larger than the one reported in the previous budget for 2003–2012 (Saunois et al., 2016). Since 2012, global CH4 emissions have been tracking the warmest scenarios assessed by the Intergovernmental Panel on Climate Change. Bottom-up methods suggest almost 30 % larger global emissions (737 Tg CH4 yr−1, range 594–881) than top-down inversion methods. Indeed, bottom-up estimates for natural sources such as natural wetlands, other inland water systems, and geological sources are higher than top-down estimates. The atmospheric constraints on the top-down budget suggest that at least some of these bottom-up emissions are overestimated. The latitudinal distribution of atmospheric observation-based emissions indicates a predominance of tropical emissions (∼ 65 % of the global budget, < 30∘ N) compared to mid-latitudes (∼ 30 %, 30–60∘ N) and high northern latitudes (∼ 4 %, 60–90∘ N). The most important source of uncertainty in the methane budget is attributable to natural emissions, especially those from wetlands and other inland waters.Some of our global source estimates are smaller than those in previously published budgets (Saunois et al., 2016; Kirschke et al., 2013). In particular wetland emissions are about 35 Tg CH4 yr−1 lower due to improved partition wetlands and other inland waters. Emissions from geological sources and wild animals are also found to be smaller by 7 Tg CH4 yr−1 by 8 Tg CH4 yr−1, respectively. However, the overall discrepancy between bottom-up and top-down estimates has been reduced by only 5 % compared to Saunois et al. (2016), due to a higher estimate of emissions from inland waters, highlighting the need for more detailed research on emissions factors. Priorities for improving the methane budget include (i) a global, high-resolution map of water-saturated soils and inundated areas emitting methane based on a robust classification of different types of emitting habitats; (ii) further development of process-based models for inland-water emissions; (iii) intensification of methane observations at local scales (e.g., FLUXNET-CH4 measurements) and urban-scale monitoring to constrain bottom-up land surface models, and at regional scales (surface networks and satellites) to constrain atmospheric inversions; (iv) improvements of transport models and the representation of photochemical sinks in top-down inversions; and (v) development of a 3D variational inversion system using isotopic and/or co-emitted species such as ethane to improve source partitioning.The data presented here can be downloaded from https://doi.org/10.18160/GCP-CH4-2019 (Saunois et al., 2020) and from the Global Carbon Project.
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| 4. |
- Zhang (张臻), Zhen, et al.
(författare)
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Anthropogenic emission is the main contributor to the rise of atmospheric methane during 1993–2017
- 2022
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Ingår i: National Science Review. - : Oxford University Press (OUP). - 2095-5138 .- 2053-714X. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric methane (CH4) concentrations have shown a puzzling resumption in growth since 2007 following a period of stabilization from 2000 to 2006. Multiple hypotheses have been proposed to explain the temporal variations in CH4 growth, and attribute the rise of atmospheric CH4 either to increases in emissions from fossil fuel activities, agriculture and natural wetlands, or to a decrease in the atmospheric chemical sink. Here, we use a comprehensive ensemble of CH4 source estimates and isotopic δ13C-CH4 source signature data to show that the resumption of CH4 growth is most likely due to increased anthropogenic emissions. Our emission scenarios that have the fewest biases with respect to isotopic composition suggest that the agriculture, landfill and waste sectors were responsible for 53 ± 13% of the renewed growth over the period 2007–2017 compared to 2000–2006; industrial fossil fuel sources explained an additional 34 ± 24%, and wetland sources contributed the least at 13 ± 9%. The hypothesis that a large increase in emissions from natural wetlands drove the decrease in atmospheric δ13C-CH4 values cannot be reconciled with current process-based wetland CH4 models. This finding suggests the need for increased wetland measurements to better understand the contemporary and future role of wetlands in the rise of atmospheric methane and climate feedback. Our findings highlight the predominant role of anthropogenic activities in driving the growth of atmospheric CH4 concentrations.
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