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    Essential oils of plants and their combinations as an alternative adulticides against Anopheles gambiae (Diptera: Culicidae) populations

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    Sentinel2GlobalLULC: A Sentinel-2 RGB image tile dataset for global land use/cover mapping with deep learning

    To build Sentinel2GlobalLULC, we followed two main steps. First, we established a spatio-temporal consensus between 15 global LULC products for 29 LULC classes. Then, we extracted the maximum number of Sentinel-2 RGB images representing each class. Each image is a tile that has 224 × 224 pixels at 10 × 10 m spatial resolution and was built as a cloud-free composite from all the Sentinel-2 images acquired between June 2015 and October 2020. Both tasks were implemented using GEE, an efficient programming, processing and visualisation platform that allowed us to have free manipulation and access to all used LULC products and Sentinel-2 imagery, simultaneously.Finding spatio-temporal agreement across 15 global LULC productsTo establish the spatio-temporal consensus between different LULC products for each one of the 29 LULC classes, we followed four steps: (1)Identification of the LULC products to be used in the consensus, (2)Standardization and harmonization of the LULC legend that was subsequently used to annotate the image tiles, (3)Spatio-temporal aggregation across LULC products, and (4)Spatial reprojection and tile selection based on optimized spatial purity thresholds.Global LULC products selectionThe adopted purity measure for spatio-temporal agreement across the 15 global LULC products we selected from GEE (Table 2) aims to find areas of high consensus to maximize the annotation quality. Spatial and temporal consensus across such rich diversity of LULC products, in terms of spatial resolution, time coverage, satellite source, LULC classes and accuracy, was used as a source of robustness for our subsequent LULC annotation. Products outside GEE were not used due to computing limitations.Table 2 Main characteristics of the 15 global Land-Use and Land-Cover (LULC) products available in Google Earth Engine (GEE) that were combined to find consensus in the global distribution of 29 main LULC classes.Full size tableStandardization and Harmonization of LULC legendsLand cover (LC) data describes the main type of natural ecosystem that occupies an area; either by vegetation types such as shrublands, grasslands and forests, or by other biophysical classes such as permanent snow, bare land and water bodies. Land use (LU) includes the way in which humans modify or exploit an area, such as urban areas or agricultural fields.To build our 29 LULC classes nomenclature, we established a standardization and harmonization approach based on expert knowledge. During this process, we took into account both the needs of different practitioners in the global and regional LULC mapping field and the thematic resolution of the global LULC legends available in GEE. Our nomenclature consists of 23 LC and 6 LU distinct classes identified through specific consensus rules across 15 LULC products (see Table 4). A six-level (L0 to L5) hierarchical structure was adopted in the creation of these 29 LULC classes (Fig. 2). To facilitate the inter-operability of our 29 legends at the finest level L5 across all LULC products and with the widely used FAO’s hierarchical Land Cover Classification System (LCCS)1, we have established an LULC classification system where the 29 classes can be mapped directly to FAO’s LCCS as explained in the table of Supplementary File 1. The LC part in our dataset contains 20 terrestrial ecosystems and 3 aquatic ecosystems. The terrestrial systems are: Barren lands, Grasslands, Permanent snow, Moss and Lichen lands, Close shrublands, Open shrublands, in addition to 12 Forests classes that differed in their tree cover, phenology, and leaf type. The aquatic classes are: Marine water bodies, Continental water bodies, and Wetlands; furthermore, wetlands were divided into 3 classes: Marshlands, Mangroves and Swamps. The LU part is composed of urban areas and 5 coarse cropland types that differed in their irrigation regime and leaf type. In Table 3, you can find the semantic definition of each one of the 29 classes in Sentinel2GlobalLULC. We provided a table in Supplementary File 2, for a more detailed definition of each LULC class.Fig. 2Tree representation of the six-level (L0 to L5) hierarchical structure of the Land-Use and Land-Cover (LULC) classes contained in the Sentinel2GlobalLULC dataset. Outter circular leafs represent the final or most detailed 29 LULC classes (C1 to C29) of level L5. The followed path to define each class is represented through inner ellipses that contain the names of intermediate classes at different levels between the division of the Earth’s surface (square) into LU and LC (level L0) and the final class circle (level L5). All LULC classes belong to three levels at least, except the 12 forest classes that belong to L5 only.Full size imageTable 3 Semantic signification of each one of the 29 Land Use and Land Cover (LULC) classes contained in the Sentinel2GlobalLULC dataset according to the six-level (L0 to L5) hierarchical structure.Full size tableCombining products across time and spaceFor each one of the 29 LULC classes, we combined in space and time the global LULC information among the 15 GEE LULC products. This way, each image was annotated with a LULC class only if all combined products agreed in its corresponding tile (i.e., 100% of agreement in space and time). For each product and LULC type, we first set one or more criteria to create a global mask at the native resolution of the product in which each pixel was classified as 1 or 0 depending on whether it met the criteria for belonging to that LULC type or not, respectively (see first stage in Table 4). For certain LULC classes, some products did not provide any relevant information, so they were not used. For example (Table 4), in Grasslands (C3), Open Shrublands (C4) and Close Shrublands (C5), we combined 14 products, while in UrbanBlUpArea (C29) and Permanent Snow (C23) we only combined 10 and 7 products, respectively.Table 4 First stage of the rule set criteria used to find consensus across the 15 Land-Use and Land-Cover (LULC) products available in Google Earth Engine (GEE) for each of the 29 LULC classes contained in the Sentinel2GlobalLULC dataset.Full size tableThen (see second stage in Table 5), for each LULC type, we calculated the average of all the masks obtained from each product to create a final global probability map from all products with values ranging between 0 and 1. Value 1 meant that all products agreed to assign that pixel to a particular LULC class, while 0 meant that none of the products assigned it to that particular class (Fig. 3). These 0-to-1 values are interpreted as the spatio-temporal purity level of each pixel to belong to a particular LULC class and are provided as metadata with each image.Table 5 Second stage of the rule set criteria used to find consensus across the 15 Land-Use and Land-Cover (LULC) products available in Google Earth Engine (GEE) for each of the 29 LULC classes contained in the Sentinel2GlobalLULC dataset.Full size tableFig. 3Example of the process of building the final global probability map for one of the 29 Land-Use and Land-Cover (LULC) classes (e.g. C1: “Barren”) by means of spatio-temporal agreement of the 15 LULC products available in Google Earth Engine (GEE). The final map is normalized to values between 0 (white, i.e., areas with no presence of C1 in any product) and 1 (black spots, i.e., areas containing or compatible with the presence of C1 in all 15 products), whereas the shades of grey corresponds to the values in between (i.e., areas that did not contain or were not compatible with the presence of C1 in some of the products). This process is divided into two stages: the first stage (the blue part, see details in Table 4) and the second stage (the yellow part, see details in Table 5). LULC products available for several years are represented with superposed rectangles, while single year products are represented with single rectangles. GMP: global probability map, NA: Not Available.Full size imageAs an example of the first stage (see details in Table 4), to specify if a given pixel belongs to Dense Evergreen Needleleaf Forest, we evaluated its tree cover level using “ ≤ “ and “ ≥ “, while for bands containing the leaf type information, we used the equal operator “ = “. For the spatio-temporal combination of multiple criteria we have used the following operators: “AND”,“OR” and “ADD”. For example, we combined the tree cover percentage criteria with the leaf type criteria using “AND” to select forest pixels that met both conditions. To combine many years instances of the same product, we used “ADD”, except for product P13, where we used “AND” to identify permanent water areas only. Whenever we used the “ADD” operator, we normalized pixel values afterwards to bring it back to a probability interval between 0 and 1 using the division by the total number of combined years or criteria.In the second stage (see details in Table 5), we combined for each LULC class the 15 global probability maps previously derived from each product to create a final global probability map (Fig. 3). This combination was carried out using various operators such as “ADD”, “MULTIPLY” and “OR”, depending on the LULC type. When “ADD” was used, the final pixel values were normalized by dividing the final addition value of each pixel by the total number of added products. The “MULTIPLY” operator was mostly used at the end, to remove urban areas from non-urban LULC classes, or to remove water from non-water LULCs. The multiplication operator was also adopted to make sure that a certain criteria was respected in the final probability map. For instance, for the swamp class, we multiplied all pixels in the final stage by a water mask where saline water areas have a value of 0 in order to eliminate mangrove from swamp pixels and vice versa. Finally, we used “OR” operator between different water related products to take advantage of the fact that they complement each other in terms of spatial-temporal coverage and accuracy.In GEE, when two products are aggregated using “ADD”, “MULTIPLY” or any other operator, the output is aggregated at the spatial resolution of the product at the left of the operator. Hence, to maintain the finest spatial resolution in the final probability map, we multiplied everything by product P15 and placed it at the left of the final “MULTIPLY” operation (See Table 5). Hence, all the 29 final probability maps were generated at the P15 spatial resolution of 30 m/pixel (except the urban class C29 which maintained the 30 m/pixel resolution of product P14).Re-projection and Selection of purity thresholdSince our objective was finding pure Sentinel-2 image tiles of 224 × 224 10-m pixels representing each LULC class, we reprojected the 30 m/pixel probability maps to 2240 m/pixel using the spatial mean reducer in GEE. That is, each pixel value at 2240 m resolution was computed using the mean over all the 30m-pixel values contained within it. Hence, the resulting pixel values at 2240 m resolution represent the purity level that each Sentinel-2 image tile of 224 × 224 10-m pixels has. We illustrated the reprojection and selection processes in Fig. 4.Fig. 4Example of the workflow to obtain a Sentinel-2 image tile of 2240 × 2240 m for one of the 29 Land-Use and Land-Cover (LULC) classes (e.g. C1: “Barren”). The process starts with the reprojected final global probability map obtained from stage two (Table 5) and ends with its exportation to the repository of a Sentinel-2 image tile of 224 × 224 pixels. The white rectangle is the only one having a probability value of 1 (Recall that the purity threshold used for Barren was 1, i.e., 100%). The black pixels has a null probability value, while the probability values between 0 and 1 are represented in gray scale levels.Full size imageFor each one of the reprojected maps, we defined a pixel value threshold to decide whether a given 2240 × 2240 m tile was representative of each LULC class or not. Since training DL image classification models needs a large number of high quality (both in terms of image quality and annotation quality) image tiles to reach a good accuracy, when the spatial purity of 100% (full agreement across products in all the pixels of the 224 × 224 tile) resulted in a small number of agreement tiles for a particular class, the purity threshold was decreased for that class until the number of tiles was larger than 1000 or further decreased in less abundant classes to a minimum of 75% of purity. The found purity value is always provided as metadata for each image in the dataset, so the user can always restrict its analysis to those image tiles and classes at any desired purity level. Decreasing the purity threshold down to 75% for the less abundant classes (e.g swamp, mangrove, etc.) was a trade-off between maintaining a good data annotation quality and providing a sufficient number of tiles in each class. In Table 6, we present the number of agreement tiles found at different purity thresholds ranging from 75% to 100% for each LULC class. This spatial purity was not further decreased since machine learning image classification models are known to be robust when the target class is spatially dominant in each training image (it occupies more than 60% of the pixels in the scene)42. On the other hand, when the number of pure tiles for a LULC class was too large to be downloaded (i.e., greater than 14000), we applied a selection algorithm as described in the Supplementary File 3, to download a maximum of 14000 spatially representative images. For this, the world was divided into a one-degree squared cell grid. If a cell contained less than 50 image tiles, we selected them all. If it contained more than 50, we applied that automatic maximum geographic distance algorithm that selected images as far from each other as possible in a number proportional to the number of existing images in that cell. The map in Fig. 6 shows the global distribution of the selected 194877 image tiles contained in Sentinel2GlobalLULC and distributed in 29 LULC classes.Table 6 Summary of the varying number of found and eventually selected Sentinel-2 image tiles of 224 × 224 pixels depending on the different consensus level reached across the 15 Land-Use and Land-Cover (LULC) products available in Google Earth Engine (GEE) for each of the 29 LULC classes contained in the Sentinel2GlobalLULC dataset.Full size tableData extractionSentinel2GlobalLULC provides the user with two types of data: Sentinel-2 RGB images (jpeg and geotif versions) and CSV files with associated metadata. In the following subsections, we describe the process for associating metadata, including the Global Human Modification (GHM) index.Global human modification index extractionAs an additional metadata related to the level of human influence in each image, we calculated for each tile in GEE, the spatial mean of the global human modification index for terrestrial lands43, where 0 means no human modification and 1 means complete transformation. Since the original GHM product was mapped at 1 × 1 km resolution, we reprojected it to 2240 × 2240 m using the same reprojection procedure explained in (Re-projection and Selection of purity threshold).CSV files generationOnce the tiles were selected, for each LULC class we listed the image tiles in descendent order of purity. Metadata included: geographical coordinates of each tile centroid, tile purity value, name and ID of the LULC class, and average GHM index for that tile. Then, we used the geographical coordinates of each tile to identify its exact administrative address geolocation. To implement this reverse geo-referencing operation, we used a free request-unlimited python module called reverse_geocoder. This way, we assigned a country code, two levels of administrative departments, and the locality to each tile.For LULC classes that had more than 14000 pure tiles, we have released the coordinates before and after the distance-based selection in case the user wants to download more tiles or use our consensus coordinates for other purposes.Sentinel-2 RGB images exportationAfter extracting all these pieces of information and grouping them into CSV files, we went back to the geographic center coordinates of each tile and used them to extract the corresponding 224 × 224 Sentinel-2 RGB tiles using GEE. Each exported image was identical to the 2240 × 2240 m area covered by its Sentinel-2 tile.We chose “Sentinel-2 MSI (Multi-Spectral Instrument) product” since it is free and publicly available in GEE at the fine resolution of 10 × 10 m. We chose “Level-1C” (i.e., top-of-atmosphere reflectance) since it provides the longest data availability of Sentinel-2 images without any modification of the data. To build RGB images, we extracted the three bands B4, B3 and B2 that correspond to Red, Green and Blue channels, respectively. More bands available in Sentinel-2 or even in Sentinel-1 images can be incorporated in the future to our dataset. However, computational limitations (i.e., the size of the dataset would be impractical) did not allowed us to handle it as a first goal. In addition, the spatial resolution of the images would be heterogeneous across bands.To minimize the inherent noise due to atmospheric conditions (e.g. clouds, aerosols, smoke, etc.) that could affect the satellite RGB images, every image was built as a temporal aggregation of all images gathered by Sentinel-2 satellites between June 2015 and October 2020. During this aggregation, only the highest quality images in the corresponding image collection were considered, as we firstly discarded all image instances where the cloud probability exceeded 20% according to the metadata provided in their corresponding Sentinel-2 collection. Then, we calculated the 25th-percentile value between all remaining images for each reflectance band (R, G, and B), and built the final image with the obtained 25-percentile values in each pixel for its RGB bands. The 25th-percentile choice was adopted giving its suitability in atmospheric noise reduction44,45,46,47,48.Usually, Sentinel-2 MSI product includes true colour images in JPEG2000 format, except for the “Level-1C” collection used here. The three original bands (B4, B3, and B2) required a saturation mapping of their reflectance values into 0–255 RGB digital values. Thus, we mapped the saturation reflectance of 3558 into 255 to obtain true RGB channels with digital values between 0 and 255. The choice of these mapping numbers was taken from the Sentinel-2 true colour image recommendations section of Sentinel user guidelines. Finally, after exporting the selected tiles for each LULC class as “.tif” images, we converted them into “.jpeg” format using a lossless conversion algorithm.Technical implementationTo implement all our methodology steps, we first created a javascript in GEE for each LULC class. Each script is a multi-task javascript where we implemented a switch command to control which task we want to execute (between the spatio-temporal aggregation task, the spatial reprojection and tiles selection task, or the data exportation task). In each one of these scripts, we selected from GEE LULC datasets repository the 15 LULC products used to build the consensus of that LULC class. Each script was responsible of elaborating the spatio-temporal combination of the selected products and generating the final consensus map for that LULC class as described in the subsection “Combining products across time and space”. Then, it exports the final global probability map as an asset into GEE server storage to make its reprojection faster. In the same script, once the consensus map exportation was done, we imported it from the GEE assets storage and reprojected it to 2240 × 2240 m resolution; then, we exported the new reprojected map into GEE assets storage again to make its analysis and processing faster. Afterwards, we imported the reprojected map into the same script and applied different processing tasks. During this processing phase, many purity threshold values were evaluated. Then, we elaborated in this same script the pure tiles identification and their center coordinates exportation into a CSV file. A distinct GEE script was developed to import, reproject and export the global GHM map. The resulted GHM map was saved as an asset too, then imported and used in each one of the 29 LULC multi-task scripts.A python script was developed separately to read the exported CSV files for each LULC class and apply the reverse geo-referencing on their pure tiles coordinates then add the found geolocalization data (country code, locality…etc) to the original CSV files as new columns. Then, another python script was implemented to read the new resulted CSV files with all their added columns (reverse geo-referencing data, GHM data) and use the center coordinates of each pure tile in that class to export first its corresponding Sentinel-2 satellite geotiff image within GEE through the python API. Finally, after downloading all the selected geotiff images from our Google drive, we created another python script to convert these geotiff images into JPEG format. More

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    Addressing the dichotomy of fishing and climate in fishery management with the FishClim model

    DataSea Surface temperature (1850–2019)Sea Surface Temperature (SST, °C) from 1850 to 2019 originated from the COBE SST2 1° × 1° gridded dataset74, https://psl.noaa.gov/data/gridded/data.cobe2.html. SST data were interpolated on a 0.25° latitude × 0.25° longitude grid on a monthly scale from 1850 to 2019.BathymetryBathymetry (m) came from GEBCO Bathymetric Compilation Group 2019 (The GEBCO_2019 Grid—a continuous terrain model of the global oceans and land). Data are provided by the British Oceanographic Data Centre, National Oceanography Centre, NERC, UK. doi:10/c33m. (https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/836f016a-33be-6ddc-e053-6c86abc0788e/). These data were interpolated on a 0.25° latitude × 0.25° longitude grid.Biological dataDaily mass concentration of chlorophyll-a in seawater (mg/m3) originated from the Glob Colour project (http://www.globcolour.info/). The product merges together all the daily data from satellites (MODIS, SeaWIFS, VIIRS) available from September 1997 to December 2019, on a 4 km resolution spatial grid. These data were interpolated on a daily scale on a 0.25° latitude × 0.25° longitude grid. These data were only used to map the average maximum standardised SSB (mdSSB) around the North Sea (Fig. 1a). When long-term changes in mdSSB were examined, we used modelled chlorophyll data (see section “Climate projections” below).Cod recrutment at age 1, Spawning Stock Biomass (SSB) and fishing effort F for 1963–2019 originated from ICES35.We used a plankton index of larval cod survival, which was an update of the index proposed by Beaugrand and colleagues33. Based on data from the Continuous Plankton Recorder (CPR)75, the index is based on the simultaneous consideration of six key biological parameters important for the diet and growth of cod larvae and juveniles in the North Sea:76,77 (i) Total calanoid copepod biomass as a quantitative indicator of food for larval cod, (ii) mean size of calanoid copepods as a qualitative indicator of food, (iii-iv) the abundance of the two dominant congeneric species Calanus finmarchicus and C. helgolandicus, (v) the genus Pseudocalanus and (vi) the taxonomic group euphausiids. A standardised Principal Component Analysis (PCA) is performed on the six plankton indicators for each month from March to September for the period 1958–2017 (table 60 years × 7 months-6 indicators). The plankton index is simply the first principal component of the PCA33.Climate projectionsClimate projections for SST and mass concentration of chlorophyll in seawater (kg m−3) originated from the Coupled Model Intercomparison Project Phase 6 (CMIP6)5 and were provided by the Earth System Grid Federation (ESGF). We used the projections known as Shared Socioeconomic Pathways (SSP) 245 and 585 corresponding respectively to a medium and a high radiative forcing by 2100 (2.5 W m−2 and 8.5 W m−2)78. The daily simulations of four different models (i.e. CNRM-ESM2-1, GFDL-ESM4, IPSL-CM6A-LR, and UKESM1-0-LL) covering the time period 1850–2014 (historical simulation) and 2015–2100 (future projections for the two SSPs scenarios) were used. All the data were interpolated on a 0.25° by 0.25° regular grid. Key references (i.e. DOI and dataset version) are provided in Supplementary Text 1. Long-term changes in modelled SSB were based on these data (including modelled daily chlorophyll data).The FishClim modelLet Kt be the maximum standardised Spawning Stock Biomass (mdSSB hereafter) that can be reached by a fish stock at time t for a given environmental regime φt. Xt+1, standardised SSB (dSSB hereafter) at time t+1 was calculated from dSSB at time t as follows:$${X}_{t+1}={X}_{t}+r{X}_{t}left(1-frac{{X}_{t}}{{K}_{t}}right)-alpha {X}_{t}$$
    (1)
    α is the fishing intensity that varies between 0 (i.e. no fishing) and 1 (i.e. 100% of SSB fished in a year). It is important to note that α (see Eq. (10)) should not be mistaken with ICES fishing effort F79 (calculated from SSB). The second term of Eq. (1) is the intrinsic growth rate of the fish stock that is a function of both Kt and the population growth rate r (r was fixed to 0.5 in most analyses, but see Fig. 3d however where r varied from 0.25 to 0.75). The population growth rate r is highly influenced by the life history traits of a species80 but also by environmental variability54,55,81. Here, the population growth rate was assumed to be constant in space and time and the influence of environmental variability occurred exclusively through its effects on Kt. We made this choice to not multiply the sources of complexity and errors (i.e. population growth rate is very difficult to assess and varies with age80). The third term reflects the part of dSSB that is lost by fishing. Note that natural mortality is not explicitly integrated in Eq. (1) because this process is difficult to assess with confidence at the scale of our study. Here, we assumed that the second term of Eq. (1) implicitly considered this process; when K increases, it is likely that natural mortality diminishes, especially at age 134. We tested this assumption below. Most of the time when fishing occurs, Xt {y}_{{{{rm{opt}}}}}$$
    (3)
    Here yopt= 5.4 °C and t1 and t2 were fixed to 5.7 °C and 4 °C, respectively, so that the thermal niche was close to that assessed by Beaugrand and colleagues31 (Supplementary Fig. 2). This Supplementary Figure compares the thermal response curve we chose in the present study with the data analysed in Beaugrand and colleagues31. The figure shows that the response curve (red curve) is close to the histogram showing the number of geographical cells with a cod occurrence as a function of temperature varying between −2 °C (frozen seawater) and 20 °C.Because t1  > t2, the niche was slightly negative asymmetrical (Supplementary Fig. 1). U1(y) was the first component of mdSSB along the thermal gradient y. c was the maximum value of mdSSB; c was fixed to 1 so that mdSSB varied between 0 and 184,85. y was the value of SST. Slight variations in the different parameters of the niche did not alter either the spatial patterns in the distribution of mdSSB nor the correlations with recruitment.To model the bathymetric niche of cod, we used a trapezoidal function. Changes in mdSSB, U2, along bathymetry, were assessed using four points (θ1, θ2, θ3, θ4):$$begin{array}{cc}{{U}}_2({{z}})=0 & {{{{{{{rm{When}}}}}}; z}}le {{{{rm{theta }}}}}_{1}end{array}$$
    (4)
    $$begin{array}{cc}{{U}}_2({{z}})=frac{z-{theta }_{1}}{{theta }_{2}-{theta }_{1}}c & {{{{{rm{When}}}}}},{{{{rm{theta }}}}}_{1} < {{z}}le {{{{rm{theta }}}}}_{2}end{array}$$ (5) $$begin{array}{cc}{{U}}_2({{z}})={{c}} & {{{rm{When}}}},{{{{rm{theta }}}}}_{2} < {{z}} < {{{{rm{theta }}}}}_{3}end{array}$$ (6) $${{U}}_2begin{array}{cc}(z)=frac{{theta }_{4}-z}{{theta }_{4}-{theta }_{3}}c & {{{rm{When}}}},{{{{rm{theta }}}}}_{3}le {{z}} < {{{{rm{theta }}}}}_{4}end{array}$$ (7) $$begin{array}{cc}{{{rm{U}}}}_2({{z}})=0 & {{{rm{When}}}}; {{{rm{z}}}}ge {{{theta }}}_{4}end{array}$$ (8) With θ2 ≥ θ1, θ3 ≥ θ2 and θ4≥ θ3 and y the bathymetry; θ1 = 0, θ2 = 10−4, θ3 = 200 and θ4 = 600 m (Supplementary Fig. 1). These parameters were retrieved from the litterature86,87. Here also c, the maximum abundance reached by the target species was fixed to 1 and U2 varied between 0 and 1. Trapezoidal niches have been used frequently to model the spatial distribution of fish and marine mammals88,89.The trophic niche was modelled by a rectangular function on a daily basis. To the best of our knowledge, no information on the trophic niche is available. We modelled the trophic niche by fixing U3 to 1 when chlorophyll-a concentration was higher than 0.05 mg m−3 during a minimum period of 15 days and 0 otherwise (Supplementary Fig. 1). This minimum of chlorophyll was implemented as a proxy for suitable food, which has been shown to be important in the North Atlantic for cod recruitment and distribution6,33.There exists two ways to combine the different ecological dimensions of a niche: (i) use an additive or (ii) a multiplicative model82,90. We used a multiplicative model because when one dimension is associated to a nil abundance, the resulting abundance combining all dimensions is also nil in contrast to an additive model; therefore only one unsuitable environmental value may explain a nil abundance. All dimensions were associated to abundance values that varied between 0 and 190.Therefore, maximum dSSB, K, for a given environmental regime E was given by multiplying the three niches (thermal, bathymetric and trophic):$$K=mathop{prod }limits_{i=1}^{p}{U}_{i}$$ (9) where p = 3, the three dimensions of the niche.AnalysesMapping of maximum standardised SSBmdSSB is close to the “dynamic B0” approach; B0 is the SSB in the absence of fishing (generally expressed in tonnes)51 whereas mdSSB is the SSB in the absence of fishing standardised between 0 and 1 and assessed from the knowledge of the niche of the species. We first assessed mdSSB in the North-east Atlantic (around UK) at a spatial resolution of 0.25° latitude × 0.25° longitude on a daily basis from 1850 to 2019. For this analysis, FishClim was run on monthly COBE SST (1850–2019), mean bathymetry and a climatology of daily mass concentration of chlorophyll-a in seawater from the Glob Colour project (see Data section). We then calculated an annual average based on the main seasonal productive period around UK, i.e. from March to October90. Finally, we averaged all years to examine spatial patterns in mean mdSSB (Fig. 1a).Temporal changes in maximum standardised SSBWe assessed average long-term changes in mdSSB in the North Sea (51°N–62°N and 3°W–9.5°E); the annual average was calculated from March to October because this is a period of high production90 . We compared long-term changes in mdSSB with cod recruitment at age 1, a plankton index of larval cod survival based on the period March to October33, and ICES-based SSB35 for 1963-2019 (Fig. 1b–d).Correlation analyses with modelled maximum standardised SSBPearson correlations between long-term changes in mdSSB (average for the North Sea, 51°N–62°N and 3°W–9.5°E) and cod recruitment at age 1 in decimal logarithm35, a plankton index of larval cod survival in the North Sea33, and observed ICES SSB in decimal logarithm35 for the period 1963–2019 were calculated (Fig. 1b–d). The same analysis was performed between assessed fishing intensity α from our FishClim model and fishing effort F35 in the North Sea (Fig. 1e). The probability of significance of the coefficients of correlation was adjusted to correct for temporal autocorrelation91.Assessment of fishing intensity from ICES spawning stock biomassUsing North Sea ICES SSB, we applied Eq. (1) to assess fishing intensity α:$$alpha =1+rleft(1-frac{{X}_{t}}{{K}_{t}}right)-frac{{X}_{t+1}}{{X}_{t}}$$ (10) With Xt+1 and Xt the ICES dSSB (in decimal logarithm). Standardisation of ICES SSB, necessary for this analysis, was complicated because many different kinds of standardisation were achievable so long as X remained strictly above 0 (i.e. full cod extirpation, not observed so far35) and strictly below min(K) (i.e. all black curves always below all points of the blue curve were possible, Supplementary Fig. 3). Indeed, ICES SSB includes exploitation and environmental fluctuations whereas K (i.e. mdSSB) integrates only environmental forcing; the difference is mainly caused by the negative influence of fishing. We chose the black curve (ICES SSB) that maximised the correlation between α (fishing intensity in the FishClim model) and F (ICES fishing effort)35.Reconstruction of long-term changes in ICES spawning stock biomassThe estimation of α allowed us to reconstruct long-term changes in cod (ICES) dSSB and to examine the respective influence of fishing and CIEC by means of Eq. (1) (“Methods”) using four hypothetical scenarios (Fig. 1f). First, we fixed fishing intensity and considered exclusively environmental variations through its influence on dSSB. (i–ii) We assessed long-term changes in dSSB from long-term variation in observed mdSSB (called Kt in Eq. (1)) with a constant level of exploitation fixed to (i) minimum (upper blue curve, i.e. the lowest fishing intensity observed in 1963–2019) or (ii) maximum (lower blue curve, i.e. the highest fishing intensity observed in 1963–2019).Second, we fixed the environmental influence on dSSB and considered variations in fishing intensity. We estimated long-term changes in dSSB from long-term variation in estimated α with a constant mdSSB fixed to (iii) minimum (lower red curve, i.e. the lowest mdSSB observed in 1963–2019) or (iv) maximum (upper red curve, i.e. the highest mdSSB observed in 1963–2019). It was possible to compare long-term changes in reconstructed (ICES) dSSB (thick black curve in Fig. 1f) with these four hypothetical scenarios (Fig. 1f); note that these comparisons were not affected by the choice we made earlier on the standardisation of (ICES) SSB.Quantification of the respective influence of fishing and climate/environment on spawning stock biomassUsing the previous curves, we examined the respective influence of fishing and CIEC on reconstructed (ICES) dSSB (Fig. 2). First, the influence of fishing was investigated by estimating the residuals between reconstructed (ICES) dSSB based on long-term changes in mdSSB (i.e. Kt in Eq. (1)) and α (thick black curves in Fig. 1f) and modelled dSSB based on fluctuating fishing intensity α and invariant K (average of the two red curves in Fig. 1f). This calculation led to the red curve in Fig. 2b. Next, we performed the opposite procedure to examine the influence of CIEC on dSSB (i.e. invariant fishing intensity α based on the two blue curves in Fig. 1f). This calculation led to the blue curve in Fig. 2b.A cluster analysis, based on a matrix years × three time series with (i) long-term changes in reconstructed standardised (ICES) SSBs, (ii) fishing and (iii) CIEC, was performed to identify key periods (vertical dashed lines in Fig. 2). We standardised each variable between 0 and 1 and used an Euclidean distance to assess the year (1963–2019) × year (1963–2019) square matrix so that each variable contributed equally to each association coefficient. We used an agglomerative hierarchical clustering technique using average linkage, which was a good compromise between the two extreme single and complete clustering techniques92. In this paper, we were only interested in the timing between the different time periods (i.e. the groups of years) revealed by the cluster analysis (Fig. 2).We also calculated an index of fishing influence (ε, expressed in percentage) by means of two indicators γ and δ, which were slightly different to the ones we used above. The first one, γ, was modelled dSSB with fluctuating fishing intensity and a constant mdSSB based on the best suitable environment observed during 1963–2019 (only the upper red curve in Fig. 1f; fishing influence). The second one, δ, was modelled dSSB based on fluctuating environment and fishing intensity (black curve in Fig. 1f) on modelled dSSB based on a fluctuating environment but a constant fishing intensity fixed to the lowest value of the time series (only the upper blue curve in Fig. 1f; environmental influence). The index of fishing influence (ε, expressed in percentage) was calculated as follows:$$varepsilon =frac{100gamma }{gamma +delta }$$ (11) For each period of 1963–2019 identified by the cluster analysis, we quantified the influence of fishing (and therefore the environment) using a Jackknife procedure93,94. The resampling procedure recalculated ε by removing each time 1 year of the time period, which allowed us to provide a range of values (i.e. minimum and maximum) in addition to the average value (bar{varepsilon }) calculated for each interval, including the whole period (Fig. 2c).Long-term changes in modelled spawning stock biomass (1850–2019, 2020–2100 and 2020-2300)We modelled mdSSB (Kt in Eq. (1)) using outputs from four Earth System models (ESMs) based on two scenarios of SST/Chlorophyll changes (i.e. SSP245 and SSP585) for the period 1850–2100 (and for one scenario and one ESM until 2300; Fig. 3).For the period 1850–2019, we used daily SST/Chlorophyll changes from the four ESMs to estimate potential changes in mdSSB (thin dashed black curves in Fig. 3a). An average of mdSSB was also calculated (thick green curve in Fig. 3a).For the period 2020–2100, we showed all potential changes in mdSSB based on the four ESMs and both scenarios SSP245 (thin dashed blue curves in Fig. 3a) and SSP585 (thin dashed red curves). An average of mdSSB was also calculated for scenarios SSP245 (thick continuous blue curve) and SSP585 (thick continuous red curve). In addition, we assessed dSSB based on a constant standardised catch fixed to the average of 2008–2019, the last period identified by the cluster analysis (G5, i.e. (alpha X) = 0.03 in Eq. (1)), and the average values of all ESMs for SSP245 (thick dashed blue curve in Fig. 3a) and SSP585 (thick dashed red curve). This analysis was performed to show how a constant catch might alter long-term changes in mdSSB. When Xt (Eq. (1)) reached 0.1, the stock was considered as fully extirpated.Understanding how fishing and climate/environment interact now and in the futureWe modelled dSSB as a function of fishing intensity α and CIEC to show how fishing and the environment interact (Fig. 3b, c). We calculated dSSB for fishing intensity between α = 0 and α = 0.5 every step Ɵ = 0.001 and for mdSSB between K = 0 and K = 1 every step Ɵ = 0.001 to represent values of dSSB as a function of fishing and CIEC. We then superimposed reconstructed ICES dSSB (1963–2019) on the diagram for three periods: 1963–1985 (high SSB), 1986–1999 (pronounced reduction in SSB), and 2000–2019 (low SSB). Maximum standardised SSB for 2020–2100 (or 2300 exclusively for Scenario SSP 585 of IPSL ESM) assessed from four ESMs and scenarios SSP245 and SSP585 were also superimposed. Fishing intensity is unpredictable for 2020–2100 and so we arbitrarily fixed it constant between 0.08 and 0.17 in increments of 0.1 for display purposes, starting by ESMs based on scenario SSP 245 followed by scenario SSP 585 (Fig. 3b). When Xt (Eq. (1)) reached 0.1, the stock was considered as fully extirpated.We calculated an index of sensitivity of dSSB as a function of fishing intensity and CIEC. To do so, we first calculated sensitivity of dSSB to fishing intensity α. Index ζi was calculated at point i from dSSB X and fishing intensity α at i−1 and i+1 (see also Eq. (1)):$$begin{array}{cc}{zeta }_{i}=frac{left|{X}_{i+1}-{X}_{i-1}right|}{left|{alpha }_{i+1}-{alpha }_{i-1}right|} & {{{rm{with}}}},{{{rm{min }}}}(alpha )+{{uptheta }}le ile {{{rm{max }}}}(alpha )-{{uptheta }}end{array}$$ (12) With min(α) = 0, max(α) = 0.5 and Ɵ = 0.001.Similarly, we calculated sensitivity of dSSB to K. Index ηj was calculated at point j from dSSB X and mdSSB K at j−1 and j+1 (see also Eq. (1)):$$begin{array}{cc}{eta }_{j}=frac{left|{X}_{j+1}-{X}_{j-1}right|}{left|{K}_{j+1}-{K}_{j-1}right|} & {{{rm{with}}}},{{{rm{min }}}}left(Kright)+{{{rm{theta }}}}le {{j}}le {{{rm{max }}}}({{{rm{K}}}})-{{uptheta }}end{array}$$ (13) With min(K) = 0, max(K) = 1 and Ɵ = 0.001.Then, we summed the two indices to assess the joint sensitivity of dSSB to fishing intensity Z and mdSSB H:$${{{{bf{I}}}}}_{{{i}},{{j}}}={{{bf{Z}}}}({{{{rm{zeta }}}}}_{{{i}}})+{{{bf{H}}}}({eta }_{{{j}}})$$ (14) Matrix I was subsequently standardised between 0 and 1:$${{{{boldsymbol{I}}}}}^{{{{boldsymbol{* }}}}}=frac{{{{boldsymbol{I}}}}-min ({{{boldsymbol{I}}}})}{max left({{{boldsymbol{I}}}}right)-min ({{{boldsymbol{I}}}})}$$ (15) With I* the matrix of sensitivity of dSSB to fishing intensity and mdSSB standardised between 0 and 1 (Fig. 3c).Number of years needed for recovery after stock collapseWe investigated how the number of years needed for a stock to recover after stock collapse (i.e. dSSB=0.05 in Eq. (1); i.e. 10% of mdSSB) varied as a function of mdSSB (between 0 and 1 by increment of 0.001); this was only influenced by the environmental regime φt and population growth rate r. For this analysis, we fixed a target dSSB of 0.4 (vertical dashed green vertical line in Fig. 3d) and three different values of r: 0.25, 0.5 and 0.75. We simulated a hypothetical moratorium with a fishing intensity α = 0 in Eq. (1).Here, stock collapse was defined as dSSB ≤ 0.1 × mdSSB, i.e. when the dSSB reached less than 10% of the unfished biomass mdSSB. This threshold corresponds to values usually defined in the literature; e.g. Pinsky and colleagues95 defined a collapse when landings are below 10% the average of the five highest landings recorded for more than 2 years, Worm and colleagues69 defined stock collapse when the biomass becomes lower than 10% of the unfished biomass, Andersen96 when it is lower than 20% and Thorpe and De Oliveira67 when it is lower than 10–20%.Potential consequences of fisheries management and climate-induced environmental changesWe examined how fishing and CIEC may affect cod stocks and their exploitation around UK with a focus in the North Sea (Figs. 4, 5). For these analyses, we averaged long-term changes in modelled dSSB corresponding to each scenario (all thin dashed blue and thin red curves in Fig. 3a for SSP245 and 585, respectively). In these analyses, the stock was considered fully extirpated when Xt (Eq. (1)) reached 0.1.Year of cod extirpation for 2020–2100 We estimated year of cod extirpation from 2020 to 2100 in each geographical cell based on (i) a constant fishing intensity (α = 0.04) in time and space, and (ii) an adjusted fishing intensity using the concept of Mean Sustainable Yield (MSY). The choice of α = 0.04 did not alter our conclusions; a lower or a higher value delayed or speed cod extirpation in a predictable way, respectively. In fisheries, MSY is defined as the maximum catch (abundance or biomass) that can be removed from a population over an indefinite period with dX/dt = 0, with X for dSSB and t for time. Despite some criticisms about MSY66, the concept remains a key paradigm in fisheries management35,63. We used this concept to show that controlling fishing intensity delayed cod extirpation. From Eq. (1), we calculated fishing intensity, called αMSYt, so that X remained above XMSYt at all time t:$${alpha }_{{{{{rm{MSY}}}}t}}=rleft(1-frac{{X}_{{{{{rm{MSY}}}}t}}}{{K}_{t}}right)$$ (16) In this analysis, we fixed XMSY t = Kt/2. We assessed ({alpha }_{{{{{rm{MSY}}}}t}}) from Eq. (16) and then estimated dSSB from ({alpha }_{{{{{rm{MSY}}}}t}}) and Kt (based on averaged SSP245 and SSP585) by means of Eq. (1). Although results were displayed at the scale of the north-east Atlantic (around UK), we calculated the difference in year of cod extirpation between scenarios of warming (SSP245 and SSP585) and between scenarios of cod management (constant versus adjusted—MSY— fishing intensity). Differences were presented by means of histograms (Fig. 4). From each histogram, we calculated the median of the differences in year of cod extirpation E97. Pooled standardised catch by 2100 (2020–2100) In term of fishing exploitation, we assessed pooled standardised catch (i.e. pooled dSSB) in 2100 (2020–2100), again for two scenarios of CIEC (SSP245 and 585) and two scenarios of cod management (constant versus adjusted—MSY—fishing intensity; Fig. 5). We then calculated the percentage of reduction in pooled standardised catch caused by fishing or the intensity of warming. Finally, we assessed the median of the percentage of reduction in pooled standardised catch for the North Sea area (51°N–62°N and 3°W–9.5°E). The goal of this analysis was to demonstrate that controlling fishing intensity optimises cod exploitation. Statistics and reproducibilityAll statistical analyses can be reproduced from the equations provided in the text, the cited references or the data available in Supplementary Data.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

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    Phosphate limitation intensifies negative effects of ocean acidification on globally important nitrogen fixing cyanobacterium

    Laboratory experimentsCulturingThe marine cyanobacterium Trichodesmium erythraeum IMS101 was obtained from the National Center for Marine Algae and Microbiota (Maine, USA) and was grown in Aquil-tricho medium prepared with 0.22 µm-filtered and microwave-sterilized oligotrophic South China Sea surface water6. The medium was enriched with various concentrations of chelexed and filter-sterilized NaH2PO4 as where indicated, and filter-sterilized vitamins and trace metals buffered with 20 µM EDTA6. The cultures were unialgal, and although they were not axenic, sterile trace metal clean techniques were applied for culturing and experimental manipulations. T. erythraeum was pre-adapted to low P condition by semi-continuously culturing at 0.5 μM PO43− and at two pCO2 levels (400 and 750 µatm) for more than one year. To start the chemostat culture, three replicates per treatment were grown in 1-L Nalgene® magnetic culture vessels (Nalgene Nunc International, Rochester, NY, USA), in which the cultures were continuously mixed by bubbling with humidified and 0.22 µm-filtered CO2–air mixtures and stirring using a suspended magnetic stir bar. The reservoirs contained Aquil-tricho medium with 1.2 μM NaH2PO4, which was delivered to the culture vessels using a peristaltic pump (Masterflex® L/S®, USA) at the dilution rate of 0.2 d−1. In all experiments, cultures were grown at ;27 °C and ~80 μmol photons m−2 s−1 (14 h:10 h light–dark cycle) in an AL-41L4 algae chamber (Percival). The concentration of Chlorophyll a (Chla) was monitored daily in the middle of the photoperiod as an indicator of biomass. When the Chla concentration remained constant for more than one generation, the system was considered to have reached steady-state, and was maintained for at least another four generations prior to sampling for further analysis.Carbonate chemistry manipulationpCO2/pH of seawater media in the culture vessels and in the reservoir was controlled by continuously bubbling with humidified and 0.22 µm-filtered CO2-air mixtures generated by CO2 mixers (Ruihua Instrument & Equipment Ltd.). During the experimental period, the pHT (pH on the total scale) of media was monitored daily using a spectrophotometric method46. The dissolved inorganic carbon (DIC) of media was analyzed by acidification and subsequent quantification of released CO2 with a CO2 analyzer (LI 7000, Apollo SciTech). Calculations of alkalinity and pCO2 were made using the CO2Sys program47, based on measurements of pHT and DIC, and the carbonate chemistry of the experiments are shown in Supplementary Table 1.Chla concentration and cell density and sizeChla concentration was measured daily following Hong et al.6. Briefly, T. erythraeum was filtered onto 3 μm polycarbonate membrane filters (Millipore), followed by heating at 65 °C for 6 min in 90% (vol/vol) methanol. After extraction the filter was removed and cell debris were spun down via centrifugation (5 min at 20,000×g) before spectrophotometric analysis. Cell density and the average cell length and width were determined at regular intervals when the chemostat cultures reached steady-state using ImageJ software. Photographs of Trichodesmium were taken using a camera (Canon DS126281, Japan) connected with an inverted microscope (Olympus CKX41, Japan). Total number and length of filaments in 1 mL of culture were measured, and the cell number of ~20 filaments was counted. The average length of cells was obtained by dividing the total length of the 20 filaments by their total cell number. The cell density of the culture was then calculated by dividing the total length of filaments in 1 mL culture by the average cell length. The average cell width was determined by measuring the width of around 1000 cells in each treatment.Elemental compositionTo determine particulate organic C (POC) and N (PON), at the end of the chemostat culturing T. erythraeum cells were collected on pre-combusted 25 mm GF/F filters (Whatman) and stored at −80 °C. Prior to analysis, the filters were dried overnight at 60 °C, treated with fuming HCl for 6 h to remove all inorganic carbon, and dried overnight again at 60 °C. After being packed in tin cups, the samples were subsequently analyzed on a PerkinElmer Series II CHNS/O Analyzer 2400.Particulate organic P (POP) was measured following Solorzano et al.48. Cells were filtered on pre-combusted 25 mm GF/F filters and rinsed twice with 2 mL of 0.17 M Na2SO4. The filters were then placed in combusted glass bottles with the addition of 2 mL of 0.017 M MgSO4, and subsequently evaporated to dryness at 95 °C and baked at 450 °C for 2 h. After cooling, 5 mL of 0.2 M HCl was added to each bottle. The bottle was then tightly capped and heated at 80 °C for 30 min, after which 5 mL Milli-Q H2O was added. Dissolved phosphate from the digested POP sample was measured colorimetrically following the standard phosphomolybdenum blue method.C uptake and N2 fixation ratesRates of short-term C uptake were determined at the end of the chemostat culturing. 100 µM NaH14CO3 (PerkinElmer) was added to 50 mL of cultures in the middle of the photoperiod, which was then incubated for 20 min under the growth conditions. After incubation, the samples were collected onto 3 μm polycarbonate membrane filters (Millipore), which were then washed with 0.22 µm-filtered oligotrophic seawater and placed on the bottom of scintillation vials. The filters were acidified to remove inorganic C by adding 500 µL of 2% HCl. The radioactivity was determined using a Tri-Carb 2800TR Liquid Scintillation Analyzer (PerkinElmer). Rates of N2 fixation (nitrogenase activity) were measured in the middle of the photoperiod for 2 h by the acetylene reduction assay49, using a ratio of 4:1 to convert ethylene production to N2 fixation.Soluble reactive phosphate (SRP) analysisWhen the chemostat cultures reached a steady-state, SRP concentrations in the culture vessels were measured at regular intervals, using the classic phosphomolybdenum blue (PMB) method with an additional step to enrich PMB on an Oasis HLB cartridge50. Briefly, 100 mL of GF/F filtered medium sample was fortified with 2 mL of ascorbic acid (100 g L−1) and 2 mL of mixed reagent (MR, the mixture of 100 mL of 130 g L−1 ammonium molybdate tetrahydrate, 100 mL of 3.5 g L−1 potassium antimony tartrate, and 300 mL of 1:1 diluted H2SO4), and then mixed completely. After standing at room temperature for 5 min, the solution was loaded onto a preconditioned Oasis HLB cartridge (3 cm3/60 mg, P/N: WAT094226, Waters Corp.) via a peristaltic pump, and then 1 mL eluent solution (0.2 M NaOH) was added to elute the sample into a cuvette, to which 0.06 mL of MR and 0.03 mL of ascorbic acid solution was added to fully develop PMB. Finally, the absorbance of PMB was measured at 700 nm using a spectrophotometer.Alkaline phosphatase (AP) activityAP activities were measured in the middle of the photoperiod using p-nitrophenylphosphate (pNPP) as a substrate51. Briefly, 5 mL of culture was incubated with 250 μL of 10 mM pNPP, 675 μL of Tris-glycine buffer (50 mM, pH 8.5) and 67.5 μL of 1 mM MgCl2 for 2 h under growth conditions. The absorbance of formed p-nitrophenol (pNP) was measured at 410 nm using a spectrophotometer.PolyP analysisAt the end of the chemostat culturing, T. erythraeum cells were filtered in the middle of the photoperiod onto 3 μm polycarbonate membrane filters (Millipore), flash frozen in liquid nitrogen, and stored at −80 °C until analysis. PolyP was quantified fluorometrically following Martin and Van Mooy22 and Martin et al.23. Briefly, samples were re-suspended in 1 mL Tris buffer (pH 7.0), sonicated for 30 s, immersed in boiling water for 5 min, sonicated for another 30 s, and then digested by 10 U DNase (Takara), RNase (2.5 U RNase A + 100 U RNase T1) (Invitrogen) and 20 μl of 20 mg mL−1 proteinase K at 37 °C for 30 min. After centrifugation for 5 min at 14,000×g, the supernatant was diluted with Tris buffer according to the range of standards curve, stained with 60 μL of 100 μM 4, 6-diamidino-2-phenylindole (DAPI) per 500 μL of samples, incubated for 7 min and then vortexed. The samples were then loaded onto a black 96-well plate and the absorption of fluorescence at an excitation wavelength of 415 nm and emission wavelength of 550 nm was measured using a PerkinElmer EnSpire® Multimode Plate Reader. PolyP standard (sodium phosphate glass Type 45) was purchased from Sigma-Aldrich. This method gives a relative measure of polyP concentration23 that is expressed as femto-equivalents of the standard per cell (feq cell−1).Cellular ATP measurementCellular ATP contents were determined when the chemostat cultures reached a steady state. T. erythraeum cells were collected in the middle of the photoperiod using an ATP Assay Kit (Beyotime Biotechnology, Shanghai, China) according to the manufacturer’s instructions. Briefly, the sample was lysed and centrifuged, and the supernatant (100 μL) was mixed with ATP detection working reagent (100 μL) and loaded onto a black 96-well plate. The luminescence was measured using a PerkinElmer EnSpire® Multimode Plate Reader.Intracellular metabolites measurementsNAD(H), NADP(H), and Glu were measured at the end of the chemostat culturing, using the liquid chromatography-tandem quadrupole mass spectrometry (LC–MS/MS) method modified from Luo et al.52. Briefly, T. erythraeum cells were gently filtered at the middle of photoperiod onto 3 μm polycarbonate membrane filters (Millipore), rapidly suspended in −80 °C precooled methanol-water (60%, v/v) mixture. After being kept in −80 °C freezer for 30 min, the sample was sonicated for 30 s, centrifuged at 12,000×g and 4 °C for 5 min, and the supernatant was filtered through a 0.2 μm filter (Jinteng®, China) and stored at −80 °C for further LC–MS/MS analysis.A 2.0 × 50 mm Phenomenex® Gemini 5u C18 110 Å column (particle size 5.2 µm, Phenomenex, USA) was used for the analysis. The mobile phases consisted of two solvents: mobile phase A (10 mM tributylamine aqueous solution, pH 4.95 with 15 mM acetic acid) and mobile phase B (100% methanol), which were delivered using an Agilent 1290 UPLC binary pump (Agilent Technologies, Palo Alto, CA, USA) at a flow rate of 200 µL min−1, with a linear gradient program implemented as follows: hold isocratic at 0% B (0–2 min); linear gradient from 0% to 85% B (2–28 min); hold isocratic at 0% B (28–34 min). The effluent from the LC column was delivered to an Agilent 6490 triple-quadrupole mass spectrometer, equipped with an electrospray ionization source operating in negative-ion mode. NAD, NADH, NADP, NADPH, and Glu were monitored in the multiple reaction monitoring modes with the transition events at m/z 662.3  > 540, 664.3  > 79, 742  > 620, 744  > 79, and 147  > 84, respectively.RNA extraction, library preparation, and sequencingAt the end of the chemostat culturing, T. erythraeum was collected in the middle of the photoperiod by filtering onto 3 μm polycarbonate membrane filters (Millipore), flash frozen in liquid nitrogen and stored at −80 °C until extraction. Total RNA was extracted using TRIzol® Reagent (Invitrogen) combined with a physical cell disruption approach by glass beads according to the manufacturer’s instructions. Genomic DNA was removed thoroughly by treating it with RNAase-free DNase I (Takara, Japan). Ribosomal RNA was removed from a total amount of 3 µg RNA using Ribo-Zero rRNA Removal kit (Illumina, USA). Subsequently, cDNA libraries were generated according to the manufacturer’s protocol of NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA). The quality of the library was assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Libraries were sequenced on an Illumina Hiseq 2500 platform, yielding 136-bp paired-end reads.RNA-Seq bioinformaticsClean reads were obtained from raw data by removing reads containing adapter, ploy-N and low-quality read. Qualified sequences were mapped to the Trichodesmium erythraeum IMS101 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_008312.1) by using Bowtie2-2.2.353. Differential expression analysis for high/low pCO2 with P limitation was performed using the DESeq2 R package54. The resulting p-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted p-value  More

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    Javanese Homo erectus on the move in SE Asia circa 1.8 Ma

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    Rebooting GDP: new ways to measure economic growth gain momentum

    The numbers are heading in the wrong direction. If the world continues on its current track, it will fall well short of achieving almost all of the 17 Sustainable Development Goals (SDGs) that the United Nations set to protect the environment and end poverty and inequality by 2030.The projected grade for:Eliminating hunger: F.Ensuring healthy lives for all: F.Protecting and sustainably using ocean resources: F.The trends were there before 2020, but then problems increased with the COVID-19 pandemic, war in Ukraine and the worsening effects of climate change. The world is in “a new uncertainty complex”, says economist Pedro Conceição, lead author of the United Nations Human Development Report.One measure of this is the drastic change in the Human Development Index (HDI), which combines educational outcomes, income and life expectancy into a single composite indicator. After 2019, the index has fallen for two successive years for the first time since its creation in 1990. “I don’t think this is a one-off, or a blip. I think this could be a new reality,” Conceição says.UN secretary-general António Guterres is worried. “We need an urgent rescue effort for the SDGs,” he wrote in the foreword to the latest progress report, published in July. Over the past year, Guterres and the heads of big UN agencies, such as the Statistics Division and the UN Development Programme, have been assessing what’s gone wrong and what needs to be done. They’re converging on the idea that it’s time to stop using gross domestic product (GDP) as the world’s main measure of prosperity, and to complement it with a dashboard of indicators, possibly ones linked to the SDGs. If this happens, it would be the biggest shift in how economies are measured since nations first started using GDP in 1953, almost 70 years ago1.
    Get the Sustainable Development Goals back on track
    Guterres’s is the latest in a crescendo of voices calling for GDP to be dropped as the world’s primary go-to indicator, and for a dashboard of metrics instead. In 2008, then French president Nicolas Sarkozy endorsed such a call from a team of economists, including Nobel laureates Amartya Sen and Joseph Stiglitz.And in August, the White House announced a 15-year plan to develop a new summary statistic that would show how changes to natural assets — the natural wealth on which economies depend — affect GDP. The idea, according to the project’s main architect, economist Eli Fenichel at the White House Office of Science and Technology Policy, is to help society to determine whether today’s consumption is being accomplished without compromising the future opportunities that nature provides. “GDP only gives a partial and — for many common uses — an incomplete, picture of economic progress,” Fenichel says.The fact that Guterres has made this a priority, amid so many major crises, is a sign that “going beyond GDP has been picked up at the highest level”, says Stefan Schweinfest, the director of the UN Statistics Division, based in New York City.Grappling with growth GDP is a measure of economic activity that has ended up becoming the world’s main index for economic progress. By a commonly used definition, it is the numerical sum of countries’ consumer and government spending and their business investments, adding the value of exports minus imports. When governments and businesses talk, as they regularly do, about boosting ‘economic growth’, what they mean is boosting GDP.But GDP is more than a growth target. It is also the benchmark for how countries measure themselves against each other (see ‘Growth gaps’). The United States is the world’s largest economy, as measured by GDP. China, currently second, is on a path to overtake it.

    Source: World Bank

    GDP also matters greatly to politicians. When India leapfrogged the United Kingdom to become the world’s fifth largest economy earlier this year, it made headline news. Last month, China reportedly delayed publication of its latest (and less-than-flattering) quarterly GDP figures so they would not appear during the Communist party’s national congress, at which Xi Jinping took a third term as president.“GDP is without question the superstar of indicators,” says Rutger Hoekstra, a researcher who studies sustainability metrics at Leiden University in the Netherlands and author of Replacing GDP by 2030.The problem with using GDP as a proxy for prosperity, says Hoekstra, is that it doesn’t reflect equally important indicators that have been heading in the opposite direction. Global GDP has increased exponentially since the Industrial Revolution, but this has coincided with high levels of income and wealth inequality, according to data compiled by the economist Thomas Piketty at the World Inequality Lab in Paris2. This is not a coincidence. Back in the 1950s, when countries pivoted economies to maximizing GDP, they knew it would mean “making the labourer produce more than he is allowed to consume”, as Pakistan’s then chief economist Mahbub ul Haq graphically put it3. “It is well to recognize that economic growth is a brutal, sordid process.”What is more, to boost GDP, nations need to indulge in environmentally damaging behaviour. In his 2021 report, entitled Our Common Agenda, Guterres writes: “Absurdly, GDP rises when there is overfishing, cutting of forests or burning of fossil fuels. We are destroying nature, but we count it as an increase in wealth.”This tension is apparent when it comes to the SDGs. GDP growth is associated with several SDG targets; in fact SDG 8 is about boosting growth. But GDP growth “can also come at the expense of progress towards other goals”, such as climate and biodiversity action, says environmental economist Pushpam Kumar, who directs a UN Environment Programme (UNEP) project, called the Inclusive Wealth Report, to measure sustainability and inequality. The latest report will be published next month.The one-number problemThe present effort by Guterres and his colleagues is not the first time policymakers have tried to improve on GDP. In 1990, a group of economists led by ul Haq and Sen designed the HDI. They were motivated in part by frustration that their countries’ often impressive growth rates masked more-dismal quality-of-life data, such as life expectancy or education.More recently, environment ministers have found that GDP-boosting priorities have got in the way of their SDG efforts. Carlos Manuel Rodríguez, the former environment minister of Costa Rica, says he urged his finance and economics colleagues to take account of the impact of economic development on water, soils, forests and fish. But they were concerned about possible reductions in GDP calculations, says Rodríguez, now chief executive of the Global Environment Facility, based in Washington DC. Costa Rica didn’t want to be the first country to implement such a change only to possibly see itself slide down the growth rankings as a result.

    Industrial production, such as the work at this automobile plant in Japan, goes into GDP calculations.Credit: Akio Kon/Bloomberg via Getty

    China’s environmental policymakers were confronted with a similar response when, in 2006, they tried to implement a plan called Green GDP4. Local authorities were asked to measure the economic cost of pollution and environmental damage, and offset that against their economic growth targets. “They panicked and the project was shelved,” says Vic Li, a political economist at the Education University of Hong Kong, who has studied the episode. “Reducing GDP would have affected their performance reviews, which needed GDP to always increase,” he says.It’s been a similar story in Italy. In 2019, then research minister Lorenzo Fioramonti helped to establish an agency, Well-being Italy, attached to the prime minister’s office. It was intended to test economic policy decisions against sustainability targets. “It was an uphill battle because the various economic ministries did not see this as a priority,” says Fioramonti, now an economist at the University of Surrey in Guildford, UK.Revising the rulesSo, can the latest attempt to complement GDP succeed? Economists and national statisticians who help to determine GDP’s rules say it will be a struggle.Guterres and his colleagues are proposing to include 10–20 indicators alongside GDP. But that’s a tough sell because countries see a lot of value (not to mention ease of use) in relying on one number. And GDP’s great success is that countries produce their own figures, according to internationally agreed rules, which allow for cross-comparison over time. “It’s not a metric compiled by Washington DC, Beijing or London,” says Schweinfest.At the same time, GDP is not something that can just be turned on or off. In each country, tracking the data that goes into calculating GDP is an industrial-scale operation involving government data as well as surveys of households and businesses.
    Are there limits to economic growth? It’s time to call time on a 50-year argument
    China, Costa Rica and Italy’s experiences suggest that an environment-adjusted GDP might be accepted only if every country signs up to the concept at the same time. In theory, this could happen at the point when GDP’s rules — known as the System of National Accounts — are being reviewed, an event that takes place roughly once every 15 years.The next revision to the rules is under way and is due to be completed in 2025. The final decision will be made by the UN Statistical Commission, a group of chief statisticians from different nations, together with the European Commission, the International Monetary Fund, the World Bank and the Organisation for Economic Co-operation and Development (OECD), the network of the world’s wealthy countries.Because the UN oversees this process, Guterres has some influence over the questions that the review is asking. As part of their research, national statisticians are exploring how to measure well-being and sustainability, along with improving the way the digital economy is valued. Economists Diane Coyle and Annabel Manley, both at the University of Cambridge, say that technology and data companies, which make up seven out of the global top ten firms by stock-market capitalization, are probably undervalued in national accounts5.However, according to Peter van de Ven, a former OECD statistician who is the lead editor of the GDP revision effort, some aspects of digital-economy valuation, along with putting a value on the environment, are unlikely to make it into a revised GDP formula, and will instead be part of the report’s supplementary data tables. One of the reasons, he says, is that national statisticians have not agreed on a valuation methodology for the environment. Nor is there agreement on how to value digital services such as when people use search engines or social-media accounts that (like the environment) are not bought and sold for money.Yet other economists, including Fenichel, say that there are well-established methods that economists use to value both digital and environmental goods and services. One way involves asking people what they would be willing to pay to keep or use something that might otherwise be free, such as a forest or an Internet search engine. Another method involves asking what people would be willing to accept in exchange for losing something otherwise free. Management scientists Erik Brynjolfsson and Avinash Collis, both at the Massachusetts Institute of Technology in Cambridge, did an experiment6 in which they computed the value of social media by paying people to give up using it.The value of natureEconomist Gretchen Daily at Stanford University in California says it’s not true that valuing the environment would make economies look smaller. It all depends on what you value. Daily is among the principal investigators of a project called Gross Ecosystem Product (GEP) that has been trialled across China and is now set to be replicated in other countries. GEP adds together the value of different kinds of ecosystem goods and services, such as agricultural products, water, carbon sequestration and recreational sites. The researchers found7 that in the Chinese province of Qinghai, the region’s total GEP exceeded its GDP.Although past efforts to avoid using GDP have stalled, this time could be different. It’s likely, as van de Ven says, that national statisticians will not add nature (or indeed the value of social media and Internet search) to the GDP formula. But the pressure for change is greater than at any time in the past.GDP is like a technical standard, such as the voltage of household electricity or driving on the left, says Coyle. “So if you want to switch to the right, you need to align people on the same approach. Everyone needs to agree.” More

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