| 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. |
- Artaxo, Paulo, et al.
(författare)
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Tropical and Boreal Forest – Atmosphere Interactions : A Review
- 2022
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Ingår i: Tellus. Series B, Chemical and physical meteorology. - : Stockholm University Press. - 0280-6509 .- 1600-0889. ; 74:1, s. 24-163
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Forskningsöversikt (refereegranskat)abstract
- This review presents how the boreal and the tropical forests affect the atmosphere, its chemical composition, its function, and further how that affects the climate and, in return, the ecosystems through feedback processes. Observations from key tower sites standing out due to their long-term comprehensive observations: The Amazon Tall Tower Observatory in Central Amazonia, the Zotino Tall Tower Observatory in Siberia, and the Station to Measure Ecosystem-Atmosphere Relations at Hyytiäla in Finland. The review is complemented by short-term observations from networks and large experiments.The review discusses atmospheric chemistry observations, aerosol formation and processing, physiochemical aerosol, and cloud condensation nuclei properties and finds surprising similarities and important differences in the two ecosystems. The aerosol concentrations and chemistry are similar, particularly concerning the main chemical components, both dominated by an organic fraction, while the boreal ecosystem has generally higher concentrations of inorganics, due to higher influence of long-range transported air pollution. The emissions of biogenic volatile organic compounds are dominated by isoprene and monoterpene in the tropical and boreal regions, respectively, being the main precursors of the organic aerosol fraction.Observations and modeling studies show that climate change and deforestation affect the ecosystems such that the carbon and hydrological cycles in Amazonia are changing to carbon neutrality and affect precipitation downwind. In Africa, the tropical forests are so far maintaining their carbon sink.It is urgent to better understand the interaction between these major ecosystems, the atmosphere, and climate, which calls for more observation sites, providing long-term data on water, carbon, and other biogeochemical cycles. This is essential in finding a sustainable balance between forest preservation and reforestation versus a potential increase in food production and biofuels, which are critical in maintaining ecosystem services and global climate stability. Reducing global warming and deforestation is vital for tropical forests.
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| 3. |
- Chi, Jinshu
(författare)
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Adjustment of CO2 flux measurements due to the bias in the EC150 infrared gas analyzer
- 2019
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923 .- 1873-2240. ; 276
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Tidskriftsartikel (refereegranskat)abstract
- During the Regional Approaches to Climate Change (REACCH) program, eddy covariance monitoring over agricultural fields were used to estimate annual carbon and water budgets in the inland Pacific Northwest. Here, we assess the effect of a bias in the high-frequency CO2 concentration measurements using the Campbell Scientific EC150 infra-red gas analyzer on the CO2 fluxes and field-scale carbon balances. The bias stems from using a lower frequency temperature measurement to calculate the CO2 density, which misses higher frequency temperature fluctuations. To generate the bias adjustment, data were collected over four similar agricultural sites as part of the Long-Term Agroecosystem Research network for multiple months using the same four instrument sets used in the REACCH project. The difference between the high-frequency and low-frequency CO2 fluxes were regressed against the kinematic heat fluxes to generate a correction equation for each instrument set, which were applied to the historical REACCH data to determine the effect of the bias on the measured and gap-filled flux values. The re-calculated positive biases in the measured fluxes were 40 gC-CO(2)m(-2) yr(-1) to 126 gC-CO(2)m(-2) yr-1, indicating greater losses to the atmosphere than initially estimated. Once gap-filled, three out of fourteen site-years switched from weak carbon sinks to weak carbon sources. When the carbon exported via harvest was included in the budget calculation the bias correction still impacted the source/sink strength but did not change the sign of the carbon balance. Overall, the total net ecosystem exchange decreased between 300-470 gC-CO(2)m(-2) per site (29-46%) over the 4 crop-years from the bias adjustment process.
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| 4. |
- Chi, Jinshu
(författare)
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Carbon and Water Budgets in Multiple Wheat-Based Cropping Systems in the Inland Pacific Northwest US: Comparison of CropSyst Simulations with Eddy Covariance Measurements
- 2017
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Accurate carbon and water flux simulations for croplands are greatly dependent on high quality representation of management practices and meteorological conditions, which are key drivers of the surface-atmosphere exchange processes. Fourteen site-years of carbon and water fluxes were simulated using the CropSyst model over four agricultural sites in the inland Pacific Northwest (iPNW) US from October 1, 2011 to September 30, 2015. Model performance for field-scale net ecosystem exchange of CO2 (NEE) and evapotranspiration (ET) was evaluated by comparing simulations with long-term eddy covariance measurements. The model captured the temporal variations of NEE and ET reasonably well with an overall r of 0.78 and 0.80, and a low RMSE of 1.82 g C m(-2) d(-1) and 0.84 mm d(-1) for NEE and ET, respectively. The model slightly underestimated NEE and ET by 0.51 g C m(-2) d(-1) and 0.09 mm d(-1), respectively. ET simulations showed better agreement with eddy covariance measurements than NEE. The model performed much better for the sites with detailed initial conditions (e.g., SOC content) and management practice information (e.g., tillage type). The CropSyst results showed that the winter wheat fields could be annual net carbon sinks or close to neutral with the net ecosystem carbon balance (NECB) ranging from 92 to -17 g C m(-2), while the spring crop fields were net carbon sources or neutral with an annual NECB of -327 to -3 g C m(-2). Simulations for the paired tillage sites showed that the no-till site resulted in lower CO2 emissions for the crop rotations of winter wheat-spring garbanzo, but had higher carbon loss into the atmosphere for spring canola compared to the conventional tillage site. Water budgets did not differ significantly between the two tillage systems. Winter wheat in the high-rainfall area had higher crop yields and water use efficiency but emitted larger amounts of CO2 into the atmosphere than in the low-rainfall area. Based on model evaluations in this study, CropSyst appears promising as a tool to simulate field-scale carbon and water budgets and assess the effects of different management practices and local meteorological conditions for the wheat-based cropping systems in this region.
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| 5. |
- Chi, Jinshu
(författare)
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Effects of Climatic Conditions and Management Practices on Agricultural Carbon and Water Budgets in the Inland Pacific Northwest USA
- 2017
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Ingår i: Journal of Geophysical Research: Biogeosciences. - 2169-8953 .- 2169-8961. ; 122, s. 3142-3160
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Tidskriftsartikel (refereegranskat)abstract
- Cropland is an important land cover influencing global carbon and water cycles. Variability of agricultural carbon and water fluxes depends on crop species, management practices, soil characteristics, and climatic conditions. In the context of climate change, it is critical to quantify the long-term effects of these environmental drivers and farming activities on carbon and water dynamics. Twenty site-years of carbon and water fluxes covering a large precipitation gradient and a variety of crop species and management practices were measured in the inland Pacific Northwest using the eddy covariance method. The rain-fed fields were net carbon sinks, while the irrigated site was close to carbon neutral during the winter wheat crop years. Sites growing spring crops were either carbon sinks, sources, or neutral, varying with crops, rainfall zones, and tillage practices. Fluxes were more sensitive to variability in precipitation than temperature: annual carbon and water fluxes increased with the increasing precipitation while only respiration increased with temperature in the high-rainfall area. Compared to a nearby rain-fed site, irrigation improved winter wheat production but resulted in large losses of carbon and water to the atmosphere. Compared to conventional tillage, no-till had significantly lower respiration but resulted in slightly lower yields and water use efficiency over 4 years. Under future climate change, it is expected that more carbon fixation by crops and evapotranspiration would occur in a warmer and wetter environment.
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| 6. |
- Chi, Jinshu
(författare)
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Estimating Biomass and Yield Using METRIC Evapotranspiration and Simple Growth Algorithms
- 2019
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Ingår i: Agronomy Journal. - : Wiley. - 0002-1962 .- 1435-0645. ; 111, s. 536-544
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Tidskriftsartikel (refereegranskat)abstract
- Crop models are used to assess crop yield under prescribed scenarios and at scales varying from point to field to region and beyond. The use of models to evaluate the performance of agricultural systems, as they exist in the real world, can be challenging and plagued with constraints. This is due to the difficulty in characterizing the spatial variability across the landscape of crops, soils, weather, management, miscellaneous stress factors, and the initial state of the system. We propose the use of actual evapotranspiration (ETa) estimated from remote sensing images and simple crop growth-transpiration algorithms as an alternative to the use of standalone crop models for real-world yield assessment. In this study, we combined ETa estimates from METRIC (Mapping Evapotranspiration at High Resolution with Internalized Calibration) with simple crop growth algorithms extracted from the CropSyst model to estimate biomass production and yield at high resolution (30 by 30 m). We tested this approach in four dryland agriculture sites in eastern Washington State with contrasting annual precipitation. All sites were equipped with an eddy covariance flux tower for ground ETa estimation. The proposed approach was able to provide good estimates of ETa, seasonal change of aboveground biomass and yields at all sites when compared with observations for a 3-year period, collectively including five different annual crops. Because estimations are made at high resolution, they can be scaled up to field or regional scales. Advantages and limitations of the proposed approach are discussed.
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| 7. |
- Chi, Jinshu, et al.
(författare)
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Forest floor fluxes drive differences in the carbon balance of contrasting boreal forest stands
- 2021
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923 .- 1873-2240. ; 306
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Tidskriftsartikel (refereegranskat)abstract
- The forest floor provides an important interface of soil-atmosphere CO2 exchanges but their controls and contributions to the ecosystem-scale carbon budget are uncertain due to measurement limitations. In this study, we deployed eddy covariance systems below- and above-canopy to measure the spatially integrated net forest floor CO2 exchange (NFFE) and the entire net ecosystem CO2 exchange (NEE) at two mature contrasting stands located in close vicinity in boreal Sweden. We first developed an improved cospectra model to correct below-canopy flux data. Our empirical below-canopy cospectra models revealed a greater contribution of large- and small-scale eddies in the trunk space compared to their distribution in the above-canopy turbulence cospectra. We found that applying the above-canopy cospectra model did not affect the below-canopy annual CO2 fluxes at the sparse pine forest but significantly underestimated fluxes at the dense mixed spruce-pine stand. At the mixed spruce-pine stand, forest floor respiration (Rff) was higher and photosynthesis (GPPff) was lower, leading to a 1.4 times stronger net CO2 source compared to the pine stand. We further found that drought enhanced Rff more than GPPff, leading to increased NFFE. Averaged across the six site-years, forest floor fluxes contributed 82% to ecosystem-scale respiration (Reco) and 12% to gross primary production (GPP). Since the annual GPP was similar between both stands, the considerable difference in their annual NEE was due to contrasting Reco, the latter being primarily driven by the variations in NFFE. This implies that NFFE acted as the driver for the differences in NEE between these two contrasting stands. This study therefore highlights the important role of forest floor CO2 fluxes in regulating the boreal forest carbon balance. It further calls for extended efforts in acquiring high spatiotemporal resolution data of forest floor fluxes to improve predictions of global change impacts on the forest carbon cycle.
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| 8. |
- Chi, Jinshu, et al.
(författare)
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Increasing contribution of peatlands to boreal evapotranspiration in a warming climate
- 2020
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 10, s. 555-560
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Tidskriftsartikel (refereegranskat)abstract
- Climate warming increases evapotranspiration (ET) more in boreal peatlands than in forests. Observations show that peatland ET can exceed forest ET by up to 30%, indicating a stronger warming response in peatlands. Earth system models do not fully account for peatlands and hence may underestimate future boreal ET.The response of evapotranspiration (ET) to warming is of critical importance to the water and carbon cycle of the boreal biome, a mosaic of land cover types dominated by forests and peatlands. The effect of warming-induced vapour pressure deficit (VPD) increases on boreal ET remains poorly understood because peatlands are not specifically represented as plant functional types in Earth system models. Here we show that peatland ET increases more than forest ET with increasing VPD using observations from 95 eddy covariance tower sites. At high VPD of more than 2 kPa, peatland ET exceeds forest ET by up to 30%. Future (2091-2100) mid-growing season peatland ET is estimated to exceed forest ET by over 20% in about one-third of the boreal biome for RCP4.5 and about two-thirds for RCP8.5. Peatland-specific ET responses to VPD should therefore be included in Earth system models to avoid biases in water and carbon cycle projections.
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| 9. |
- Chi, Jinshu, et al.
(författare)
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The biophysical climate mitigation potential of boreal peatlands during the growing season
- 2020
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Peatlands and forests cover large areas of the boreal biome and are critical for global climate regulation. They also regulate regional climate through heat and water vapour exchange with the atmosphere. Understanding how land-atmosphere interactions in peatlands differ from forests may therefore be crucial for modelling boreal climate system dynamics and for assessing climate benefits of peatland conservation and restoration. To assess the biophysical impacts of peatlands and forests on peak growing season air temperature and humidity, we analysed surface energy fluxes and albedo from 35 peatlands and 37 evergreen needleleaf forests-the dominant boreal forest type-and simulated air temperature and vapour pressure deficit (VPD) over hypothetical homogeneous peatland and forest landscapes. We ran an evapotranspiration model using land surface parameters derived from energy flux observations and coupled an analytical solution for the surface energy balance to an atmospheric boundary layer (ABL) model. We found that peatlands, compared to forests, are characterized by higher growing season albedo, lower aerodynamic conductance, and higher surface conductance for an equivalent VPD. This combination of peatland surface properties results in a similar to 20% decrease in afternoon ABL height, a cooling (from 1.7 to 2.5 degrees C) in afternoon air temperatures, and a decrease in afternoon VPD (from 0.4 to 0.7 kPa) for peatland landscapes compared to forest landscapes. These biophysical climate impacts of peatlands are most pronounced at lower latitudes (similar to 45 degrees N) and decrease toward the northern limit of the boreal biome (similar to 70 degrees N). Thus, boreal peatlands have the potential to mitigate the effect of regional climate warming during the growing season. The biophysical climate mitigation potential of peatlands needs to be accounted for when projecting the future climate of the boreal biome, when assessing the climate benefits of conserving pristine boreal peatlands, and when restoring peatlands that have experienced peatland drainage and mining.
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| 10. |
- Chi, Jinshu, et al.
(författare)
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The carbon balance of a managed boreal landscape measured from a tall tower in northern Sweden
- 2019
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923 .- 1873-2240. ; 274, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Boreal forests exchange large amounts of carbon dioxide (CO2) with the atmosphere. A managed boreal landscape usually comprises various potential CO2 sinks and sources across forest stands of varying age classes, clear-cut areas, mires, and lakes. Due to this heterogeneity and complexity, large uncertainties exist regarding the net CO2 balance at the landscape scale. In this study, we present the first estimate of the net CO2 exchange over a managed boreal landscape (∼68 km2) in northern Sweden, based on tall tower eddy covariance measurements. Our results suggest that from March 1, 2016 to February 28, 2018, the heterogeneous landscape was a net CO2 sink with a 2-year mean uptake of −87 ± 6 g C m−2 yr−1. Due to an earlier and warmer spring and sunnier autumn, the landscape was a stronger CO2 sink during the first year (−122 ± 8 g C m−2) compared to the second year (−52 ± 9 g C m−2). Footprint analysis shows that 87% of the CO2 flux measurements originated from forests, whereas mires, clear-cuts, lakes, and grassland contributed 11%, 1%, 0.7%, and 0.2%, respectively. Altogether, the CO2 sink strength of the heterogeneous landscape was up to 38% lower compared to the sink strength of a mature stand surrounding the tower. Overall, this study suggests that the managed boreal landscape acted as a CO2 sink and advocates tall tower eddy covariance measurements to improve regional carbon budget estimates.
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