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    Taking metagenomics under the wings

    AffiliationsSanger Institute, Wellcome Trust Genome Campus, Hinxton, UKPhysilia Ying Shi ChuaLaboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, DenmarkJacob Agerbo RasmussenCenter for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DenmarkJacob Agerbo RasmussenAuthorsPhysilia Ying Shi ChuaJacob Agerbo RasmussenCorresponding authorCorrespondence to
    Physilia Ying Shi Chua. More

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    A dataset of winter wheat aboveground biomass in China during 2007–2015 based on data assimilation

    We selected eleven major wheat production provinces of China for the study area, which comprise the largest winter wheat-sowing fraction: Henan, Shandong, Anhui, Jiangsu, Hebei, Hubei, Shanxi, Shaanxi, Sichuan, Xinjiang, and Gansu (Fig. 1). The wheat planting area is about 22 million ha in these provinces, accounting for more than 93% of the total wheat planting area. The total wheat production in these regions contributes more than 96% of the total wheat production in China, with more than 128 million tons in 201933.We developed a methodological framework for high-resolution AGB mapping. It mainly includes three parts: (1) Data acquisition and processing. (2) The WOFOST model parameterization and calibration. (3) Data assimilation (Fig. 1). Each part is explained in more detail below.Data acquisition and processingMeteorological dataChina Meteorological Forcing Dataset34,35 is used as weather driving data for the WOFOST model. The dataset is based on the internationally existing Princeton reanalysis data, Global Land Data Assimilation System data, Global Energy and Water Cycle Experiment-Surface Radiation Budget radiation data, and Tropical Rainfall Measuring Mission precipitation data. It is made by fusing the conventional meteorological observation data of the China Meteorological Administration. It includes seven elements: near-surface air temperature, air pressure, near-surface total humidity, wind speed, ground downward shortwave radiation, ground downward longwave radiation, and ground precipitation rate. The meteorological drive elements required for WOFOST are daily radiation, minimum temperature, maximum temperature, water vapor pressure, average wind speed, and precipitation. Details of these variables that participated in the WOFOST model can be referred to in Table S1.Soil characteristics measurements and phenology observationsSoil and phenology data were collected at 177 agricultural meteorological stations (AMS) from 2007 to 2015 (Fig. 1). Soil characteristics include soil moisture content at wilting points, field capacity, and saturation. To be consistent with the corresponding units in the crop model, the original data in weight water content was converted into volume water content through the corresponding soil bulk density measurements. Winter wheat phenology observations include the date of emergence (more than 50% of the wheat seedlings in the field show the first green leaves and reached about 2 cm), anthesis (the inner and outer glumes of the middle and upper florets of more than 50% of the wheat ears in the whole field are open, and the anthers loose powder), and maturity (more than 80% of the wheat grains turn yellow, the glumes and stems turn yellow, and only the upper first and second nodes are still slightly green). In most cases, the phenological stage “anthesis” is missing. The anthesis date was calculated by adding seven days to the observed heading date (when more than 50% of the wheat in the whole field exposes the tip of the ear from the sheath of the flag leaf).County-level yield statistics dataThe county-level yield data was collected from city statistical yearbooks of the study area from 2007 to 2015. Since most statistical yearbooks do not directly record per-unit yield data, the county-level yield was obtained by dividing the total yield and planting area. It is worth noting that all yields were calculated in units of metric kilograms per cultivated hectares (kg·ha−1).The winter wheat land cover dataWe used a winter wheat land cover product from a 1 km resolution dataset named ChinaCropArea1km36. This data was derived from GLASS leaf area index products and crop phenology from 2000 to 2015. This dataset is the base map of our data production.The MODIS LAI dataWe used the improved 8-days MODIS LAI products (i.e., 1 km) generated by Yuan et al.32 to assimilate the WOFOST model. The products applied the modified temporal-spatial filter and Savitzky-Golay filter to overcome the spatial-temporal discontinuity and inconsistence of raw MODIS LAI products, which makes them more applicable for the realm of land surface and climate modeling. The products can be accessed via the Land-Atmosphere Interaction Research Group website at Sun Yat-sen University (http://globalchange.bnu.edu.cn/research/lai).The WOFOST model parameterization and calibrationThe WOFOST model introductionThe WOFOST model was initially developed as a crop growth simulation model to evaluate the yield potential of various crops in tropical countries37. In this study, we chose the WOFOST model because the model reaches a trade-off of the complexity of the crop model and is suitable for large-scale simulations3. The WOFOST model is a typical crop growth model that explains crop growth based on underlying processes such as photosynthesis and respiration and their response to changing environmental conditions38. The WOFOST model estimates phenology, LAI, aboveground biomass, and storage organ biomass (i.e., grain yield) at a daily time step39 (Fig. 2).Fig. 2Schematic overview of the major processes implemented in WOFOST. The Astronomical module calculates day length, some variables relating to solar elevation, and the fraction of diffuse radiation.Full size imageZonal parameterizationWe first divided the study area covered by AMS into seamless Thiessen polygon zones. Each Thiessen polygon contains only a single AMS. These zones represent the whole areas where any location is closer to its associated AMS point than any other AMS point. Then, we assigned parameters to the entire zone based on the AMS data, including crop calendar (date of emergence) and soil water retention parameters (soil moisture content at wilting point, field capacity, and saturation). Besides, we also optimized two main crop parameters for controlling phenological development stages, namely TSUM1 (accumulated temperature required from emergence to anthesis) and TSUM2 (accumulated temperature required from anthesis to maturity), by minimizing the cost function of the observational and simulated date corresponding to anthesis and maturity.Parameter calibration within a single zoneWe implemented the calibration of parameters within every single zone, as illustrated in Fig. 3. We calculated the average statistical yield of each county within every single zone from 2007 to 2015, then ranked the counties in descending order and divided them into three groups, namely high, medium, and low-level yield counties, by the 33% quantile and 67% quantile of the average statistical yield. The three counties corresponding to 17% quantile, 50% quantile, and 83% quantile would be used for subsequent calibration and represent the corresponding three yield level groups. We used the statistical yields (converted to dry matter mass based on the standard moisture content of 12.5%) of the three counties for multiple years and a harvest index for each province to convert the county-level yield to AGB for calibration. The harvest index of each province was mainly estimated from the AMS’s dynamic growth records on the biomass composition of the dominant winter wheat varieties of the province and a published literature40. Besides, we collected the maximum LAI observations on all agrometeorological stations in all years in the study area, according to its histogram. We found that the histogram follows a normal distribution with a mean of 6.5 and a standard deviation of 1.5. Finally, we calibrated three sets of parameters corresponding to three yield level groups in each single zone according to the three selected counties.Fig. 3Flow chart of parameter calibration within a single zone.Full size imageWe designed a three-step calibration strategy for a specific yield level group. Firstly, as winter wheat varieties did not change significantly according to information recorded by agrometeorological stations from 2007 to 2015, we assumed the crop parameters of winter wheat remain unchanged every three years to combine three years of observational data to calibrate the parameters of the WOFOST model better. We maximized a log-likelihood function based on the maximum LAI statistics and every three-year county-level yield and AGB data mentioned to optimize selected crop parameters (see Table S2 in the Supplement Materials).The log-likelihood function was constructed as follows:$$log;{{rm{L}}}_{{rm{LAI}}}=-frac{1}{2}left[dlogleft(2pi right)+logleft(left|{Sigma }_{{rm{LAI}}}right|right)+{rm{MD}}{left({{bf{x}}}_{{rm{LAI}}};{mu }_{{rm{LAI}}},{Sigma }_{{rm{LAI}}}right)}^{2}right]$$
    (1)
    $$log;{{rm{L}}}_{{rm{TWSO}}}=-frac{1}{2}left[dlog(2pi )+logleft(left|{{boldsymbol{Sigma }}}_{{rm{TWSO}}}right|right)+{rm{MD}}{left({{bf{x}}}_{{rm{TWSO}}};{{boldsymbol{mu }}}_{{rm{TWSO}}},{{boldsymbol{Sigma }}}_{{rm{TWSO}}}right)}^{2}right]$$
    (2)
    $$log;{{rm{L}}}_{{rm{AGB}}}=-frac{1}{2}left[dlog(2pi )+logleft(left|{{boldsymbol{Sigma }}}_{{rm{AGB}}}right|right)+{rm{MD}}{left({{bf{x}}}_{{rm{AGB}}};{{boldsymbol{mu }}}_{{rm{AGB}}},{{boldsymbol{Sigma }}}_{{rm{AGB}}}right)}^{2}right]$$
    (3)
    $$log;{rm{L}}=log;{L}_{{rm{LAI}}}+log;{L}_{{rm{TWSO}}}+log;{L}_{{rm{AGB}}}$$
    (4)
    Where log L is the natural logarithm of the likelihood function, d is the dimension, that is, the number of years of joint calibration, which is set to 3 in this study xLAI is the vector composed of the maximum value of the 3-year LAI simulated by WOFOST, μLAI and ΣLAI are the mean vector and error covariance matrix of maximum LAI based on observation statistics. The annual maximum LAI was assumed to be independent, and the mean and standard deviation for each year was set the same as the result of Fig. 3. Similarly, xTWSO and xAGB are the yield vector and AGB vector at maturity of 3 years simulated by WOFOST, and μTWSO, μAGB are their corresponding county-level statistic vector, ΣTWSO and ΣAGB are their corresponding error covariance matrix. In this study, we assumed that the annual yield or AGB was independent, and their corresponding standard deviation was 10% of their statistical value. |Σ| is the determinant of Σ. The expression ({rm{MD}}{({bf{x}};{boldsymbol{mu }},{boldsymbol{Sigma }})}^{2}={({bf{x}}-{boldsymbol{mu }})}^{{rm{T}}}{{boldsymbol{Sigma }}}^{-1}({bf{x}}-{boldsymbol{mu }})), where MD is the Mahalanobis distance between the point x and the mean vector μ.Secondly, we optimized the inter-annual irrigation. We optimized two parameters every year: the critical value of soil moisture (denoted as SMc) and the amount of irrigation (denoted as V). When the soil moisture simulated by WOFOST is lower than SMc, an irrigation event will be triggered, and the irrigation amount is V cm. In this study, we combined three-year data for calibration with six parameters for optimization. The optimization strategy is the same as the previous step by maximizing the log-likelihood function. Finally, we fixed the optimized irrigation parameters and repeated the first step to calibrate the selected crop parameters and obtain the final optimal parameters.Data assimilationConsidering that MODIS LAI is relatively low compared to the actual LAI of winter wheat41, we select a weak-constraint cost function based on the least square of normalized observational and simulated LAI as shown in Eq. (5), which is assimilating the trend information of MODIS LAI into the crop growth model.$$J={sum }_{{rm{t}}=1}^{{rm{n}}}{left(frac{{{rm{LAI}}}_{{rm{MODIS}}}^{{rm{t}}}-{{rm{LAI}}}_{{rm{MODIS}}}^{min}}{{{rm{LAI}}}_{{rm{MODIS}}}^{max}-{{rm{LAI}}}_{{rm{MODIS}}}^{min}}-frac{{{rm{LAI}}}_{{rm{WOFOS}}}^{{rm{t}}}-{{rm{LAI}}}_{{rm{WOFOS}}}^{min}}{{{rm{LAI}}}_{{rm{WOFOS}}}^{max}-{{rm{LAI}}}_{{rm{WOFOS}}}^{min}}right)}^{2}$$
    (5)
    Where ({{rm{LAI}}}_{{rm{MODIS}}}^{{rm{t}}}) and .. are MODIS LAI and WOFOST simulated LAI of time t. ({{rm{LAI}}}_{{rm{MODIS}}}^{max}) and ({{rm{LAI}}}_{{rm{WOFOS}}}^{max}) are maximum of MODIS LAI and WOFOST simulated LAI. ({{rm{LAI}}}_{{rm{MODIS}}}^{min}) and ({{rm{LAI}}}_{{rm{WOFOS}}}^{min}) are minimum of MODIS LAI and WOFOST simulated LAI. J is the value of the cost function.We reinitialize the day of emergence (IDEM), the life span of leaves growing at 35 °C (SPAN), and thermal time from emergence to anthesis (TSUM1) in the WOFOST model on each 1 km winter wheat pixel according to cost function between WOFOST LAI and MODIS LAI. Besides, we applied the Subplex algorithm from the NLOPT library (https://github.com/stevengj/nlopt) for parameter optimization. More

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    Urban blue–green space landscape ecological health assessment based on the integration of pattern, process, function and sustainability

    Study areaHarbin is located in the centre of Northeast Asia, between 44°04’–46° 40′ N and 125° 42′–130° 10′ E24,26. The site has a mid-temperate continental monsoon climate, with an average annual temperature of 3.6° C and an average annual precipitation is 569.1 mm. The main precipitation months being from June to September, accounting for about 60% of the annual precipitation, the main snow months are from November to January24,25. The overall topography is high in the east and low in the west, with mountains and hills predominating in the east and plains predominating in the west27. In this study, we identified the central district of Harbin, where urban construction activities are frequent and the population is dense, as the study area. According to the “Harbin City Urban Master Plan (2011–2020)” (revised draft in 2017), the specific scope includes Daoli District, Daowai District, Nangang District, Xiangfang District, Pingfang District, Songbei District’s administrative district, Hulan District, and Acheng District part of the area, with a total area of 4187 km2 (Fig. 2). The blue–green space in this study included woodland, grassland, cultivated land, wetland and water that permeate inside and outside the construction sites. They all have integrated functions such as ecology, supply, beautification, culture, and disaster prevention and avoidance, and have a decisive influence on the urban ecological environment.Figure 2Schematic of study area. The Figure is created using ArcGIS ver.10.2 (https://www.esri.com/).Full size imageData sourcesThe data used in this research included the following: land-cover date (30 m × 30 m) of two periods (2011, 2020) spported by the China Geographic National Conditions Data Cloud Platform (http://www.dsac.cn/), Meteorological datasets (1 km × 1 km) were obtained from the Resource and Environmental Science Data Center of the Chinese Academy of Sciences (http:∥www.resdc.cn/), including air temperature, precipitation, and surface runoff. ASTER GDFM elevation data (30 m × 30 m) came from the Geospatial Data Cloud (http:∥www.gscloud.cn), from which the slope was extracted. Soil data (1 km × 1 km) were from the World Soil Database (HWSD) China Soil Data Set (v1.1). The normalized difference vegetation index (NDVI) and modified normalized difference water index (MNDWI) data (30 m × 30 m) came from the National Comprehensive Earth Observation Data Sharing Platform (http://www.chinageoss.org/), ET datasets (30 m × 30 m) were drawn from the NASA-USGS (https://lpdaac.usgs.gov/). Social and economic data were mainly obtained through the Harbin statistical yearbook and the Harbin social and economic bulletin.Framework of urban blue–green space LEH assessmentUrban blue–green space is a politically defined man-land coupling region composed of ecological, economic, and social systems, which is greatly disturbed by human activities11. The essence of urban blue–green space LEH is that the landscape ecological function sustainably meets human needs28,29. The landscape ecological function reflects the value orientation of human beings to blue–green space, and to a large extent affects the blue–green landscape ecological pattern and process. The interaction between the blue–green landscape ecological pattern and process drives the overall dynamics of blue–green space. Meanwhile, presenting certain landscape ecological function characteristics, which provide ecological support for various human activities30,31,32. While the pattern and process of blue–green space both profoundly influence and are influenced by human activities33,34. This influence is long-term, the standard of LEH should not be fixed in real-time health, but should fully consider the sustainability of the health state.In summary, the landscape ecological pattern, process, function, and sustainability are not separate, but a complex of mutual integration, and organic unity. In this study, we constructed an integrated assessment framework of blue–green space LEH that included four units: pattern, process, service, and sustainability (Fig. 3). In the assessment framework, the LEH of urban blue–green space involves two dimensions: the first is the health status of the urban blue–green space itself, emphasizing the maintenance of the ecological conditions, thereby potentially satisfying a series of diversity goals. The other is that urban blue–green space, as a part of social and economic development, could sustainably provide the ability to meet (subject) needs and goals.Figure 3Key units, interactions of urban blue–green space LEH.Full size imageLandscape ecological patternThe landscape ecological pattern of urban blue–green space is a spatial mosaic combination of landscape elements at different levels or the same level. Affected by human activities interference31, the landscape ecological pattern shows the changing trend of landscape structure complexity, landscape type diversification, and landscape fragmentation. The assessment of urban landscape ecological pattern should be a comprehensive reflection of this changing trend1. Landscape pattern indexes are the most frequently applied which could reflect the structural composition and spatial configuration characteristics of the landscape4,35. This study took landscape ecology as the entry point and selected the landscape pattern indexes that can quantitatively reflect the change characteristics of landscape structural composition and spatial configuration under the disturbance. In this way, the landscape disturbance index (U), landscape connectivity index (CON), and landscape adaptability index (LAI) were used as the indexes for the assessment of landscape ecological pattern health.

    (1)

    Landscape disturbance index (U)

    There are two kinds of relationships between the landscape ecological pattern and the external disturbance: compatibility and conflict. As the landscape ecological pattern has accommodating characteristics, the disturbance beyond the accommodating capacity will degrade the landscape ecological pattern36,37. The landscape disturbance index (U) could characterize the degree of fragmentation, dispersion, and morphological changes in landscape pattern38. The index is a comprehensive index that can reflect the health of the landscape pattern by quantifying the ability of ecosystems to accommodate external disturbances. It consists of the landscape fragmentation index, the inverse of the fractional dimension, and the dominance index. They measure the response of the landscape pattern to external disturbance from the perspective of different landscape types, the same landscape type, and landscape diversity, respectively36,38, and their weights were determined by the entropy weight method. The formula is as follows:$$ U = alpha N_{{{Fi}}} + bD_{{{Fi}}} + cD_{{{Oi}}} $$
    (1)
    where NFi is the landscape fragmentation index, DFi is the inverse of the fractional dimension, DOi is the dominance index, and a, b, and c are the corresponding weights, which were 0.20, 0.5, and 0.3 in this study, respectively.

    (2)

    Landscape connectivity index (CON)

    The most direct result of landscape ecological pattern degradation caused by external disturbance is that the flow of energy, material, and information among ecological patches is reduced or even blocked, ultimately the stability of the landscape pattern is decreased. The connectivity could characterize the ability of landscape ecological pattern to mitigate risk transmission, which is significant for the dynamic stability of landscape ecological pattern39,40. The landscape connectivity index (CON) could measure the connectivity between ecosystem components through the aggregation or dispersion trend of patches41. The better the connectivity, the stronger the stability of landscape ecological pattern. The formula is as follows:$$ CON = frac{{100sumlimits_{s = 1}^{q} {sumlimits_{h ne l}^{p} {C_{{{shl}}} } } }}{{sumlimits_{s = 1}^{s} {left[ {q_{{s}} (q_{{s}} – 1)/2} right]} }} $$
    (2)
    where qs is the number of plaques of patch type s, Cshl is the link between patch h and patch l in s within the delimited distance.

    (3)

    Landscape Restorability Index (LRI)

    The ability to recover to its original structure when subjected to disturbances is an important criterion for the landscape ecological pattern42. Research confirmed that the restorability of the landscape ecological pattern is closely related to the structure, function, diversity, and uniformity of distribution. The landscape restorability index (LRI) combines the above landscape information and could indicate the restorability of the landscape ecological pattern in response to disturbance43. The index consists of the patch density, Shannon diversity index, and the landscape evenness, the patch density is the number of patches per square kilometer. The Shannon diversity index reflects the change in the proportion of landscape types. The landscape evenness index shows the distribution evenness of patches in terms of area. The larger the LRI index, the more complex and evenly distributed the structure is, and the more recovery ability of the landscape pattern against disturbance is. The formula is as follows:$$ LRI = PD times SHDI times SHEI $$
    (3)
    where PD is the patch density, SHDI is the Shannon diversity index, and SHEI is the landscape evenness index.Landscape ecological processThe landscape ecological process of urban blue–green space is extremely complex for it involves multiple factors such as natural ecology, economy, and culture. Landscape ecological process assessment is the measure of the self-organized capacity and the efficiency of ecological processes within and among patches44. A blue–green space with a healthy landscape ecological process should have the ability to adapt to conventional land use under human management and maintain physiological integrity while maintaining the balance of ecological components. Specifically, the landscape ecological process could quickly restore its balance after severe disturbances, with strong organization, suitability, recoverability, and low sensitivity45,46. A single model hardly to gets good research on landscape ecological process under the urban scale. The comprehensive application of multidisciplinary methods is effective means to solve the problem. Regarding this, we selected ecological indexes and models from four aspects: organization, suitability, restoration, and sensitivity to assess the landscape ecological process of urban blue–green space.

    (1)

    Organization index (O)

    The organization of the landscape ecological process is the maintenance ability of stable and orderly material cycling and energy flow within and between landscapes47. The normalized vegetation index (NDVI) and the modified normalized difference water index (MNDWI) could reflect the efficiency and order of ecological processes. Such as accumulation of organic matter, fixation of solar energy, nutrient cycling, regeneration, and metabolism13. The indexes are the external performance of the internal dynamics and organizational capabilities of the ecological process. In recent years, it has been widely used in the assessment of related to landscape ecological process. The formulas are as follows:$$ NDVI = frac{NIR – R}{{NIR + R}} $$$$ MNDWI = frac{p(green) – p(MIR)}{{p(green) + p(MIR)}} $$
    (4)
    where (NDVI) is the normalized vegetation index, (MNDWI) is the modified water body index, (NIR) is the reflectance value in the near-infrared band, (R) is the reflectance value in the visible channel, (p(green)) and (p(MIR)) are the normalized values in the green and mid-infrared bands.

    (2)

    Suitability index (Q)

    The suitability of the landscape ecological process is a measurement of the self-regulating ability of the landscape ecosystem. That is, to effectively maintain the ecological process in a state of being protected from disturbance during the occasional changes caused by the external environment2. The water conservation amount index (Q) can measure the operating capacity of ecosystems to maintain ecological balance, water conservation, climate regulation, and other ecological processes by integrating the water balance of rainfall, surface runoff, and evaporation41. It could reflect the suitability of landscape ecological process to regional environment and developmental conditions. The formula is as follows:$$ Q = R – J – ET $$
    (5)
    where Q is the water conservation amount, R is the annual rainfall, J is the surface runoff, ET is the evapotranspiration.

    (3)

    Recoverability index (ECO)

    The recoverability of the landscape ecological process refers to the ability of an ecosystem to return to its original operating state after being subjected to external impacts. Land-use types play an essential role in landscape ecological recoverability48. The ecological recoverability index (ECO) uses the resilience coefficients of land-use types to reflect the level of ecosystem resilience38. Based on previous studies, the resilience coefficient of land-use types was assigned (Table 1).

    (4)

    Sensitivity index(A)

    Table 1 Resilience coefficients of different land use types.Full size tableThe sensitivity index (A) could be used to indicate landscape ecological process formation, change, and vulnerability to disturbance31. We started from the physical effects of blue–green space on sand production, water confluence, and sediment transport, introduced the Soil Erosion Modulus to characterize the sensitivity of landscape ecological processes to disturbance. The index effectively combines landscape ecology, erosion mechanics, soil science, and sediment dynamics49. The formula is as follows:$$ begin{gathered} A = R_{{i}} cdot K cdot LS cdot C cdot P hfill \ L = (l/22.1)^{m} hfill \ S = left{ begin{gathered} 10.8sin theta + 0.03,theta < 5^{ circ } hfill \ 16.8sin theta - 0.50,5^{ circ } le theta < 10^{ circ } hfill \ 21.9sin theta - 0.96,theta ge 10^{ circ } hfill \ end{gathered} right. hfill \ C = left{ begin{gathered} 1,c = 0 hfill \ 0.6508 - 0.3436lg c,0 < c le 78.3% hfill \ 0,c > 78.3% hfill \ end{gathered} right. hfill \ end{gathered} $$
    (6)
    where A is the soil erosion modulus. Ri is the rainfall erosion factor, K is the soil erosion factor, L and S are slope the length factor and the slope factor respectively, C is the vegetation coverage and management factor, P is the soil and water conservation factor, l is the slope length value, m is the slope length index, and θ the is slope value.Landscape ecological functionThe landscape ecological function determines the ability of ecological service50,51,52, the ecological service of urban blue–green space depends on the human value orientation48. It includes four categories: supply, support, regulation, and culture. Based on Maslow’s Hierarchy of Needs and Alderfer’s ERG theory, scholars have summarized the three major needs of human beings for urban blue–green space. Namely, securing the living environment to meet the survival needs, improving social relationships to meet the interaction needs, and cultivating cultural cultivation to meet the development needs53. Specifically corresponding to the landscape ecological function of urban blue–green space, supply is not the main function, only plays a subsidiary role, support is the basic guarantee, regulation is the basic need for urban environmental construction, and culture is an important element of high-quality social life. Ecosystem service value (ESV) can realize the measurement of ecological service function by calculating the specific value of life support products and services produced by the ecosystem54,55,56. Considering the human value orientation of the urban blue–green space landscape ecological function, the weights were given by consulting 16 experts, with supply, regulation, support, and culture weights of 0.2, 0.3, 0.3, 0.2, respectively. The formula is as follows:$$ ESV = sumlimits_{k = 1}^{n} {S_{k} times V_{k}^{{}} } $$
    (7)
    where Sk is the area of landscape type k, Vk is the value coefficient of the ecosystem service function of landscape type k .Landscape ecological sustainabilityWu (2013) proposed a research framework for landscape sustainability based on a summary of related studies, stating that landscape ecological sustainability is the ability to provide ecosystem services in a long-term and stable manner34. The framework emphasized that landscape sustainability should focus on the analysis of ecosystem service trade-offs effect34,57. In the process of dynamic change of urban blue–green space ecosystem, there are complex trade-offs among various ecosystem services. This is important for promoting the optimal overall benefits of various ecosystem services and achieving sustainable development of urban ecology58. In addition, as a special type of human-centered ecosystem developed by humans based on nature, human well-being is also very important for the landscape ecological sustainability of urban blue–green space. For this reason, we introduced ecosystem service trade-offs (EST) and ecological construction input (IEC) as assessment indexes of landscape ecological sustainability.

    (1)

    Ecosystem service trade-offs (EST)

    This study applied the root mean square deviation of ecological services to quantify ecosystem service trade-offs (EST). The index could effectively measure the average difference in standard deviation between individual ecosystem services and the average ecosystem services. It is a simple and effective way to evaluate the trade-offs among ecosystem services. The formula is as follows:$$ EST = sqrt {frac{1}{n – 1}sumnolimits_{i = 1}^{n} {(ES_{std} – overline{ES}_{std} } } )^{2} $$
    (8)
    where ESstd is the normalized ecosystem services, n is the number of ecosystem services , and (overline{ES}_{std}) is the mean value of normalized ecosystem services.

    (2)

    Ecological construction input (ECI)

    Human well-being is a premise for the landscape ecological sustainability of urban blue–green spaces, it is closely related to government investment in ecological construction planning34. From the perspective of economics, this study assessed the human well-being obtained by urban blue–green space with the ratio of urban ecological construction investment to GDP, that is, the ecological construction input (ECI). The formula is as follows:$$ ECI = EI/G $$
    (9)
    where EI is the amount of ecological construction investment, and G is the gross regional product.Evaluation methodThe index weight determines its relative importance in the index system, and the selection of the weight calculation method in the decision-making of multi-attribute problems has an important impact on the assessment results21. Traditional weighting methods can be divided into two categories, subjective weighting method and objective weighting method21,38. The subjective weighting method is represented by the analytic hierarchy process (AHP), Delphi method, and so on. It has the advantage of simplicity, but the disadvantage is too subjective and randomness because it was completely dependent on the knowledge and experience of decision makers. The objective weighting method is represented by the entropy weighting method (EWM), principal component analysis, variation coefficient method, and so on. And it has been widely recognized for reflecting the variability of assessment results18, but the values of indexes have significant influence and the calculation results are not stable. Considering the limitations of the single weighting method, the weights of each assessment index in this study were determined by the combination of subjective weight and objective weight. Among them, the subjective weighting selected the AHP, and the objective weighting selected the EWM (Table 2). The formula is as follows:$$ w_{{j}} = alpha w_{{j}}^{{{AHP}}} + (1 – alpha )w_{{j}}^{{{EWM}}} $$
    (10)
    $$ w_{{j}}^{{{EWM}}} = d_{{j}} /sumlimits_{i = 1}^{m} {d_{{j}} } $$
    (11)
    $$ d_{{j}} = 1 – e_{{j}} $$
    (12)
    $$ e_{{j}} = – ksumlimits_{i = 1}^{n} {f_{{{ij}}} ln (f_{{{ij}}} )} ,;k = 1/ln (n) $$
    (13)
    $$ f_{{{ij}}} = X^{prime}_{{{ij}}} /sumlimits_{i = 1}^{n} {X^{prime}_{{{ij}}} } $$
    (14)
    where (W_{{j}}^{{}}) is the combined weight. (W_{{j}}^{{_{AHP} }}) is the weight of the j-th index of the AHP, (W_{{j}}^{{{EWM}}}) is the weight of the j-th index of the EWM, dj is the information entropy of the j-th index, ej is the entropy value of the j-th index, (f_{{{ij}}}) is the proportion of the index value of the j-th sample under the i-th indexm, (X^{prime}_{{{ij}}}) is the standardized value of the i-th sample of the j-th index, m is the number of index, n is the number of samples, and (alpha) was taken as 0.5.Table 2 Weight of assessment index.Full size tableSince the dimensions of indexes are different, it is necessary to unify the dimensions of the index to avoid the errors caused by direct calculation to make the evaluation results inaccurate. The range standardization was used to normalize the index data and bound its value in the interval [0, 1], the range standardization can be expressed as follows15,23:$$ {text{Positive indicator}}left( + right):A_{{{ij}}} = (X_{{{ij}}} – X_{{{jmin}}} )/(X_{{{jmax}}} – X_{{{jmin}}} ) $$
    (15)
    $$ {text{Negative indicator}}left( – right):A_{{{ij}}} = (X_{{{jmax}}} – X_{ij} )/(X_{{{jmax}}} – X_{{{jmin}}} ) $$
    (16)
    Additionally, we divided the LEH index into five levels from high to low using an equal-interval approach as follows40: [1–0.8) healthy, [0.8–0.6) sub-healthy, [0.6–0.4) moderately healthy, [0.4–0.2) unhealthy, [0.2–0] pathological, corresponding level I–V. And the level transfer of LEH in different periods was divided into three types: improvement type, degradation type, and stabilization type. For example, III-II means that the transfer from level III to level II is the improvement type.Spatial autocorrelation analysisSpatial autocorrelation analysis is one of the basic methods in theoretical geography. It could deeply investigate the spatial correlation characteristics of data, including global spatial autocorrelation and local spatial autocorrelation23. The global spatial autocorrelation uses global Moran’s I to evaluate the degree of their spatial agglomeration or differentiation of an attribute value in the study area. The local spatial autocorrelation is a decomposed form of the global spatial autocorrelation18,21, including four types: HH(High-High), LL(Low-Low), HL(High-Low), LH(Low–High). In this study, spatial autocorrelation analysis was applied to study the spatial correlation characteristics of blue–green space LEH. The calculation formulas are as follows:$$ I = frac{{Nsumlimits_{i} {sumlimits_{v} {W_{iv} (Y_{i} – overline{Y} )(Y_{v} – overline{Y} )} } }}{{(sumlimits_{i} {sumlimits_{v} {W_{iv} } } )sumlimits_{i} {(Y_{i} – overline{Y} )} }} $$
    (17)
    $$ I_{i} = frac{{Y_{i} – overline{Y} }}{{S_{x}^{2} }}sumlimits_{v} {left[ {W_{iv} (Y_{i} – overline{Y} )} right]} $$
    (18)
    where N is the number of space units, (W_{iv}) is the spatial weight, (Y_{i} ,Y_{v}) are the variable attribute values of the area (i,v), (overline{Y}) is the variable mean, (S_{x}^{2}) is the variance, (I) is the global Moran’s I index, and (I_{i}) is the local Moran’s I index. More

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    Bacterial matrix metalloproteases and serine proteases contribute to the extra-host inactivation of enteroviruses in lake water

    Virus propagation and enumerationEchovirus-11 (E11, Gregory strain, ATCC VR737) and Coxsackievirus-A9 (CVA9, environmental strain from sewage, kindly provided by the Finnish National Institute for Health and Welfare) stocks were produced by infecting sub-confluent monolayers of BGMK cells as described previously [7]. Viruses were released from infected cells by freezing and thawing the culture flasks three times. To eliminate cell debris, the suspensions were centrifuged at 3000 × g for 5 min. Each stock solution was stored at −20 °C until use. Infectious virus concentrations were enumerated by a most probable number (MPN) infectivity assay as described in the Supplementary Information. The assay limit of detection (LoD), defined as the concentration corresponding to one positive cytopathic effect in the lowest dilution of the MPN assay under the experimental conditions used, corresponding to 2 MPN/mL.Inactivation of enteroviruses by bacterial consortia from lake waterTo study the inactivation of CVA9 and E11 by a bacterial consortium from lake water, four surface water samples were collected from Lake Geneva (Ecublens, Switzerland) during the summer 2021. Each sampling event was conducted on warm and sunny days, to minimize biological variation. Immediately after sampling, large particles of the sample were removed by filtering 500 mL of water on a 8 μm nitrocellulose filter membrane (Merck Millipore, Cork, Ireland). The sample was then filtered through a 0.8 μm nitrocellulose filter membrane (Merck Millipore) to remove large microorganisms such as protists. The resulting water sample corresponds to the bacterial fraction used to study virus inactivation.For inactivation experiments, each virus was spiked into individual 1 mL aliquots of fractionated lake water to a final concentration of 106 MPN/mL, and samples were incubated for 48 h at 30 °C without shaking. Duplicate experiments were conducted for each virus and each lake water sample. Experiments to control for thermal inactivation were conducted using the same procedure but by replacing the fractionated lake water with sterile milliQ water. Viral infectivity at times 0 h and 48 h was determined by MPN as described above. Virus decay was calculated as log10 (C/C0), where C is the residual titer after 48 h of incubation, and C0 is the initial titer. The experimental LoD was approximately 5-log10.These same experiments were conducted for three new water samples in the presence of four protease inhibitors with the following final concentrations: E64—10 μM (E3132, Sigma–Aldrich, Saint-Louis, MO, USA), GM6001—4 μM (CC1010, Sigma–Aldrich), Chymostatin—100 μM (C7268, Sigma–Aldrich), and PMSF—100 μM (P7626, Sigma–Aldrich). Each inhibitor was added to 1 mL of fractionated lake water, vortexed for 30 seconds, and incubated at room temperature for 15 min, before adding the two viral strains under the same conditions as described above.Bacterial isolation, cultivation, and storageBacteria were isolated from two water samples from Lake Geneva’s Ecublens beach, taken in November 2019 (Fall, 89 isolates) and May 2020 (Spring, 47 isolates). Bacteria recovery was performed on R2A agar plate (BD Difco, Franklin Lakes, NJ, USA) as described previously [15]. Briefly, successive dilutions from 10−1 to 10−5 were carried out in sterile water for each sample. For each dilution, a volume of 1 mL was deposited on three separate R2A plates, before being incubated at 22, 30, and 37 °C. After 5 days of incubation, each colony was picked and enriched on a new R2A plate. To ensure purity, each isolate was successively plated five times on R2A plate and incubated at the same temperature as the initial isolation. Each purified isolate was cryopreserved in R2A / 20% glycerol at −80 °C. The isolates were named based on the water body (Lake (L)), isolation temperature, and the isolation order (L-T°C-number).Bacterial identificationThe identification of each isolate was performed by 16 S rRNA gene sequencing using the pair of primers 27 F (5’- AGA GTT TGA TCM TGG CTC AG- 3’, Microsynth AG, Balgach, Switzerland) / 786 R (5’- CTA CCA GGG TAT CTA ATC – 3’, Microsynth AG), following a methodology previously described [15]. The thermocycling conditions and the purification of PCR products are described in the Supplementary Information. The complete list of isolated bacteria and associated accession numbers is given in Supplementary Table 1.Phylogenetic inference and metadata visualizationThe consensus from 16 S rRNA gene sequences of the 136 isolates was aligned using the MUSCLE algorithm [16]. The phylogenetic analysis of 566 bp aligned sequences from the V2-V4 16 S rRNA gene regions (Positions: 152–717) was performed using Molecular Evolutionary Genetics Analysis X software [17]. Phylogeny was inferred by maximum likelihood, with 1000 bootstrap iterations to test the robustness of the nodes. The resulting tree was uploaded and formatted using iTOL [18].Virus incubation with bacterial isolatesFor the preparation of the bacteria before co-incubation, each one was first cultured on R2A agar for 48 h at their initial isolation temperature. Overnight suspensions of each bacterial isolate were grown in R2A broth at room temperature under constant agitation (180 rpm). For co-incubation experiments, 200 μL of each bacterial suspension were mixed with 100 μL of a 105 MPN/mL stock of E11 or CVA9. Then, each condition was supplemented with 600 μL of R2A broth. Incubation was carried out for 96 h at room temperature, without shaking. At the end of the co-incubation, each tube was centrifuged for 15 min at 9000 × g (4 °C) to eliminate bacteria, and the residual infectious viral titer was enumerated by MPN assay as described above [7]. Each co-incubation experiment was carried out in triplicate. Control experiments were performed under the same conditions but using sterile R2A. Virus decay was quantified as log10 (Cexp/Cctrl), where Cexp is the residual titer after a co-incubation for 96 h, and Cctrl is the titer after incubation of the virus in sterile R2A for 96 h. The experimental LoD was 3-log10.Protease activity measurement using casein and gelatin agar platesCasein agar was prepared as follows: 20 g of skim milk (BD Difco), supplemented with 1 g glucose were reconstituted with 200 mL of distilled water. Likewise, a 10% bacteriological agar solution was prepared in a final volume of 200 mL. Finally, a solution consisting of 0.8% NaCl, 0.02% KCl, 0.144% Na2HPO4, and 0.024% KH2PO4 was reconstituted in 600 mL of water. All solutions were autoclaved for 15 min at 110 °C. The solutions were mixed, and 25 mL were poured into each Petri dish. Gelatin agar was composed of 0.4% peptone, 0.1% yeast extract, 1.5% gelatin and 1.5% bacteriological agar. The mixture was autoclaved 15 min at 120 °C, and 25 mL of medium was poured into each Petri dish.For each isolate, an overnight suspension was performed in R2A broth at room temperature, before spotting 15 μL of each suspension at the center of both gelatin and casein agar plates. Each plate was incubated at 22, 30, or 37 °C for 72 h, depending on the initial isolation temperature of the bacteria. Casein-degrading activity (cas), which is exerted by many different protease classes, and gelatin-degrading activity (gel), which is mostly caused by MMPs, were revealed by a hydrolysis halo around the producing bacteria. Hydrolysis diameters were measured in millimeters (mm) to report the extent of the proteolytic effect of each strain on both substrates.Protease activity quantification in cell-free supernatantUsing the same bacterial suspensions as for bacterial/virus co-incubation, 200 μL of each suspension was inoculated into 600 μL of R2A broth and incubated without shaking for 96 h at room temperature. Each culture was centrifuged for 15 min at 9000 × g at 4 °C. The resulting cell-free supernatants (CFS) were stored at −20 °C until use. For each CFS, protease activity was measured using the Protease Activity Assay Kit (ab112152, Abcam, Cambridge, UK), which measures general protease activity (pgen) except MMPs, and the MMP Activity Assay Kit (ab112146, Abcam), which selectively measures MMP activity (mmp). Briefly, for the Protease Activity Assay kit, 50 μL of the substrate was added into each well of a dark-bottom plate containing 50 μL of each CFS. Standard trypsin provided by the kit was used as a positive control. For the MMP Activity Assay kit, 50 μL of each CFS was incubated with 50 μL of 2 mM APMA for 3 h at 37 °C, prior to the activity test. Collagenase I (C0130, Sigma–Aldrich) was used as a positive control. R2A broth was used as a negative control for each assay. Protease activity was measured at time 0 and after 60 min, using a Synergy MX fluorescence reader (BioTek). The excitation and emission wavelengths were set to 485 and 530 nm, respectively. The emitted fluorescence, generated by proteolytic cleavage of the substrate of each kit, was calculated as follows: ∆RFU = RFU (60 min) − RFU (0 min). Proteolytic activity was calculated in mmol/min/μL based on the emitted fluorescence measured for trypsin and collagenase I at known proteolytic activities.Data analysisStatistical analyses to compare inactivation data were performed by one-way t-test or one-way ANOVA with Dunnett’s post-hoc test in GraphPad Prism v.9. An alpha value of 0.05 was used as a threshold for statistical significance. For each dataset we confirmed that data were normally distributed.To analyze a potential correlation between protease activity and viral decay, the decay values for each virus strain was related to the four protease activity tests of this study using a scatterplot combined with a Kernel density estimation. The analyses were performed with R v.3.6.1 using the SmoothScatter function of the R Base package.A Left-Censored Tobit model (CTM) with mixed effects was chosen to investigate interactions between protease activity and the decay measured for each virus strain. Briefly, the CTM with mixed effect was chosen for three reasons: (1) The protocol used to measure viral decay had a limit of quantification of −3-log10, and 152 measurement points reached the detection limit, requiring the use of this value as the left-censored value of the model; (2) The two virus strains used in the study showed distinct responses after exposure to environmental bacteria, preventing the use of a multiple linear regression model; (3) Among biological replicates of co-incubation experiments, inactivation variability was observed, suggesting the concomitant action of random biological effects (e.g., production of other compounds than proteases by bacteria, or differences in protease production rate between replicates for each bacterial isolate). The resulting statistical model was then formulated as follows:$$log left( {frac{{C_{{{{{{mathrm{exp}}}}}}}}}{{C_{{{{{{mathrm{ctrl}}}}}}}}}} right) = ; beta _0 + beta _1;{rm I}_{{{{{{{{mathrm{virus}}}}}}}}_i = 2} + beta _2sqrt {left[ {pgen} right]_i} + beta _3sqrt {left[ {mmp} right]_i} + beta _4sqrt {left[ {cas} right]_i} \ + beta _5sqrt {left[ {gel} right]_i} + beta _6I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2}sqrt {left[ {pgen} right]_i} + beta _7I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2}sqrt {left[ {mmp} right]_i} \ + beta _8I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2}sqrt {left[ {cas} right]_i} + beta _9I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2}sqrt {left[ {gel} right]_i} + alpha _{{{{{{{{mathrm{id}}}}}}}}_i} + varepsilon _i$$$${{{mbox{where}}}}; log left( {frac{{C_{{{{{{mathrm{exp}}}}}}}}}{{C_{{{{{{mathrm{ctrl}}}}}}}}}} right) = left{ {begin{array}{*{20}{c}} { – 3} & {{{{{{{{mathrm{if}}}}}}}};{{{{{{{mathrm{log}}}}}}}}left( {frac{{C_{{{{{{mathrm{exp}}}}}}}}}{{C_{{{{{{mathrm{ctrl}}}}}}}}}} right) le – 3} \ {{{{{{{{mathrm{log}}}}}}}}left( {frac{{C_{{{{{{mathrm{exp}}}}}}}}}{{C_{{{{{{mathrm{ctrl}}}}}}}}}} right)} & {{{{{{{{mathrm{otherwise}}}}}}}}} end{array}} right.$$$$alpha _{{{{{{{{mathrm{id}}}}}}}}_i}sim {{{{{{{mathrm{i}}}}}}}}.{{{{{{{mathrm{i}}}}}}}}.;{{{{{{{mathrm{d}}}}}}}}.;{rm N}left( {0,;sigma _{{{{{{{{mathrm{id}}}}}}}}}^2} right)$$$${{{{{{{mathrm{for}}}}}}}};i in left{ {1,2, ldots } right}$$for which β0 defines the model intercept, (beta _1{rm I}_{{{{{{{{mathrm{virus}}}}}}}}_i = 2}) corresponds to the main effect of the virus factor on the viral decay, (beta _2,;beta _3,;beta _4,;{{{{{{{mathrm{and}}}}}}}};beta _5) corresponds to the main effects of the different protease activity measurements on viral decay, (beta _6I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2},;beta _7I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2},;beta _8I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2},{{{{{{{mathrm{and}}}}}}}};beta _9I_{{{{{{{{mathrm{virus}}}}}}}}_i = 2}) corresponds to the interaction effects between each of these variables and the viral decay, (alpha _{{{{{{{{mathrm{id}}}}}}}}_i}) corresponds to the mixed effect of the model and (varepsilon _i) corresponds to the error term of the model. The selection of the model is further detailed in the Supplementary Information (Supplementary Material and Figs. S1 and S2).The full dataset included in the correlation analysis and the CTM is provided in Supplementary Table 2. A description of the variables used is given in the Supplementary Information. The dataset was analyzed using the censReg package in R [19]. The R code is given in the Supplementary Information. More

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    Unravelling seasonal trends in coastal marine heatwave metrics across global biogeographical realms

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    Modern aridity in the Altai-Sayan mountain range derived from multiple millennial proxies

    1500-year stable carbon and oxygen isotopes in larch tree-ring celluloseThe δ13Ccell (Fig. 1a, Fig. S2) and δ18Ocell (Fig. 1b, Fig. S3) records span 516–2016 CE, at annual resolution. The δ13Ccell timeseries shows mostly increasing trends during the first millennium of the Common Era (516–1120 CE), and similarly at the end of the last millennium (1720–2016 CE). The maximum δ13Ccell value occurs in 2016 CE (−19.6‰; + 3.2σ), while the minimum occurs in 686 CE (−24.7‰, −3.6σ) relative to the average for the period 516–2016 CE (−22.04‰) (Table S2, Fig. S2). The standard error (SE) for the whole analysed period is 0.02.Figure 1Annually resolved δ13Ccell (a) and δ18O cell (b) in Siberian larch tree-ring cellulose chronologies for the period from 516 to 2016 CE. Chronologies are smoothed by a 101-year Hamming window to highlight a centennial scale. The dotted and dashed lines indicate the number of trees analysed.Full size imageThe δ18Ocell timeseries (Fig. 1b, Fig. S3) showed two positive and one negative extreme over the past 1500 years, with the minimum value (19.9‰; −6.3σ), occurring in 536 CE, and maximum values (31.9‰; + 3.8σ and 32.2‰; + 4.4σ), occurring in 1266 and 2008 CE, respectively (Table S2, Fig. S3). The SE for the whole analysed period is 0.03. The δ18Ocell data has higher standard deviation (SD) (1.15) than δ13Ccell (0.75).Less than 1% of values in the δ18Ocell record are classified as extreme, with the standard deviation ≥  ± 3σ. The δ13Ccell and δ18Ocell records are significantly correlated (r = 0.1, p = 0.0001, n = 1500).Local climate signals preserved in δ13Ccell and δ18Ocell recordsWe used weather observations from the local Mugur-Aksy weather station (50°N, 90°E, 1850 m asl) (Table S1) to derive quantitative paleoclimatic reconstructions from our δ13Ccell and δ18Ocell timeseries. A multiple linear regression analysis revealed significant correlations between δ13Ccell and July precipitation (r = −0.58; p  More

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    Enhanced spring warming in a Mediterranean mountain by atmospheric circulation

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