More stories

  • in

    Optical vegetation indices for monitoring terrestrial ecosystems globally

    Houborg, R., Fisher, J. B. & Skidmore, A. K. Advances in remote sensing of vegetation function and traits. Int. J. Appl. Earth Obs. Geoinf. 43, 1–6 (2015).
    Google Scholar 
    Bannari, A., Morin, D., Bonn, F. & Huete, A. A review of vegetation indices. Remote Sens. Rev. 13, 95–120 (1995).Article 

    Google Scholar 
    Gao, X., Huete, A. R., Ni, W. & Miura, T. Optical–biophysical relationships of vegetation spectra without background contamination. Remote Sens. Environ. 74, 609–620 (2000).Article 

    Google Scholar 
    Huete, A. R. A soil-adjusted vegetation index (SAVI). Remote Sens. Environ. 25, 295–309 (1988).Article 

    Google Scholar 
    Badgley, G., Field, C. B. & Berry, J. A. Canopy near-infrared reflectance and terrestrial photosynthesis. Sci. Adv. 3, e1602244 (2017).Article 

    Google Scholar 
    Gamon, J. A. et al. A remotely sensed pigment index reveals photosynthetic phenology in evergreen conifers. Proc. Natl Acad. Sci. USA 113, 13087–13092 (2016).Article 

    Google Scholar 
    Joiner, J. et al. Estimation of terrestrial global gross primary production (GPP) with satellite data-driven models and eddy covariance flux data. Remote Sens. 10, 1346 (2018).Article 

    Google Scholar 
    Piao, S. et al. Characteristics, drivers and feedbacks of global greening. Nat. Rev. Earth Environ. 1, 14–27 (2020).Article 

    Google Scholar 
    Tian, F. et al. Evaluating temporal consistency of long-term global NDVI datasets for trend analysis. Remote Sens. Environ. 163, 326–340 (2015).Article 

    Google Scholar 
    Fan, X. & Liu, Y. A global study of NDVI difference among moderate-resolution satellite sensors. ISPRS J. Photogramm. Remote Sens. 121, 177–191 (2016).Article 

    Google Scholar 
    AghaKouchak, A. et al. Remote sensing of drought: progress, challenges and opportunities. Rev. Geophys. 53, 452–480 (2015).Article 

    Google Scholar 
    Anyamba, A. & Tucker, in Remote Sensing of Drought: Innovative Monitoring Approaches Ch. 2 (eds Wardlow, B. D., Anderson, M. C. & Verdin, J. P.) (Taylor & Francis, 2012).Veraverbeke, S. et al. Hyperspectral remote sensing of fire: state-of-the-art and future perspectives. Remote Sens. Environ. 216, 105–121 (2018).Article 

    Google Scholar 
    Tucker, C. J. Red and photographic infrared linear combinations for monitoring vegetation. Remote Sens. Environ. 8, 127–150 (1979).Article 

    Google Scholar 
    Rouse, J. W., Haas, R. H., Schell, J. A. & Deering, D. W. Monitoring vegetation systems in the Great Plains with ERTS. NASA Spec. Publ. 351, 309 (1974).
    Google Scholar 
    Rouse, J. W., Haas, R. H., Schell, J. A., Deering, D. W. & Harlan, J. C. Monitoring the vernal advancement and retrogradation (green wave effect) of natural vegetation. NASA/GSFCT Type III Final Report, 371 (NASA, 1974).Gutman, G., Skakun, S. & Gitelson, A. Revisiting the use of red and near-infrared reflectances in vegetation studies and numerical climate models. Sci. Remote Sens. 4, 100025 (2021).Article 

    Google Scholar 
    Jackson, R. D. & Huete, A. R. Interpreting vegetation indices. Prev. Vet. Med. 11, 185–200 (1991).Article 

    Google Scholar 
    Richardson, A. J. & Wiegand, C. Distinguishing vegetation from soil background information. Photogramm. Eng. Remote Sens. 43, 1541–1552 (1977).
    Google Scholar 
    Baret, F., Guyot, G. & Major, D. in 12th Canadian Symposium on Remote Sensing Geoscience and Remote Sensing Symposium 1355–1358 (IEEE, 1989).Qi, J., Chehbouni, A., Huete, A. R., Kerr, Y. H. & Sorooshian, S. A modified soil adjusted vegetation index. Remote Sens. Environ. 48, 119–126 (1994).Article 

    Google Scholar 
    Chen, J. M. Evaluation of vegetation indices and a modified simple ratio for boreal applications. Can. J. Remote Sens. 22, 229–242 (1996).Article 

    Google Scholar 
    Brown, L., Chen, J. M., Leblanc, S. G. & Cihlar, J. A shortwave infrared modification to the simple ratio for LAI retrieval in boreal forests: an image and model analysis. Remote Sens. Environ. 71, 16–25 (2000).Article 

    Google Scholar 
    Pinty, B. & Verstraete, M. GEMI: a non-linear index to monitor global vegetation from satellites. Vegetatio 101, 15–20 (1992).Article 

    Google Scholar 
    Huete, A. et al. Overview of the radiometric and biophysical performance of the MODIS vegetation indices. Remote Sens. Environ. 83, 195–213 (2002).Article 

    Google Scholar 
    Kaufman, Y. J. & Tanre, D. Atmospherically resistant vegetation index (ARVI) for EOS-MODIS. IEEE Trans. Geosci. Remote Sens. 30, 261–270 (1992).Article 

    Google Scholar 
    Jiang, Z., Huete, A. R., Didan, K. & Miura, T. Development of a two-band enhanced vegetation index without a blue band. Remote Sens. Environ. 112, 3833–3845 (2008).Article 

    Google Scholar 
    Jin, H. & Eklundh, L. A physically based vegetation index for improved monitoring of plant phenology. Remote Sens. Environ. 152, 512–525 (2014).Article 

    Google Scholar 
    Yang, P., van der Tol, C., Campbell, P. K. & Middleton, E. M. Fluorescence Correction Vegetation Index (FCVI): A physically based reflectance index to separate physiological and non-physiological information in far-red sun-induced chlorophyll fluorescence. Remote Sens. Environ. 240, 111676 (2020).Article 

    Google Scholar 
    Badgley, G., Anderegg, L. D., Berry, J. A. & Field, C. B. Terrestrial gross primary production: Using NIRV to scale from site to globe. Glob. Change Biol. 25, 3731–3740 (2019).Article 

    Google Scholar 
    Camps-Valls, G. et al. A unified vegetation index for quantifying the terrestrial biosphere. Sci. Adv. 7, eabc7447 (2021).Article 

    Google Scholar 
    Roberts, D. A., Roth, K. L. & Perroy, R. L. in Hyperspectral Remote Sensing of Vegetation Ch. 14 (eds Thenkabail, P. S., Lyon, J. G. & Huete, A.) (CRC, 2016).Gitelson, A. A., Vina, A., Ciganda, V., Rundquist, D. C. & Arkebauer, T. J. Remote estimation of canopy chlorophyll content in crops. Geophys. Res. Lett. 32, L08403 (2005).Article 

    Google Scholar 
    Gitelson, A. & Merzlyak, M. N. Spectral reflectance changes associated with autumn senescence of Aesculus hippocastanum L. and Acer platanoides L. leaves. Spectral features and relation to chlorophyll estimation. J. Plant Physiol. 143, 286–292 (1994).Article 

    Google Scholar 
    Dash, J. & Curran, P. The MERIS terrestrial chlorophyll index. Int. J. Remote Sens. 25, 5403–5413 (2004).Article 

    Google Scholar 
    Penuelas, J., Baret, F. & Filella, I. Semi-empirical indices to assess carotenoids/chlorophyll a ratio from leaf spectral reflectance. Photosynthetica 31, 221–230 (1995).
    Google Scholar 
    Peñuelas, J., Gamon, J., Fredeen, A., Merino, J. & Field, C. Reflectance indices associated with physiological changes in nitrogen- and water-limited sunflower leaves. Remote Sens. Environ. 48, 135–146 (1994).Article 

    Google Scholar 
    Merzlyak, M. N., Gitelson, A. A., Chivkunova, O. B. & Rakitin, V. Y. Non-destructive optical detection of pigment changes during leaf senescence and fruit ripening. Physiol. Plant. 106, 135–141 (1999).Article 

    Google Scholar 
    Gitelson, A. A., Merzlyak, M. N. & Chivkunova, O. B. Optical properties and nondestructive estimation of anthocyanin content in plant leaves. Photochem. Photobiol. 74, 38–45 (2001).Article 

    Google Scholar 
    van den Berg, A. K. & Perkins, T. D. Nondestructive estimation of anthocyanin content in autumn sugar maple leaves. HortScience 40, 685–686 (2005).Article 

    Google Scholar 
    Gamon, J. & Surfus, J. Assessing leaf pigment content and activity with a reflectometer. New Phytol. 143, 105–117 (1999).Article 

    Google Scholar 
    Gao, B.-C. NDWI — a normalized difference water index for remote sensing of vegetation liquid water from space. Remote Sens. Environ. 58, 257–266 (1996).Article 

    Google Scholar 
    Xiao, X., Boles, S., Liu, J., Zhuang, D. & Liu, M. Characterization of forest types in Northeastern China, using multi-temporal SPOT-4 VEGETATION sensor data. Remote Sens. Environ. 82, 335–348 (2002).Article 

    Google Scholar 
    Xiao, X. et al. Satellite-based modeling of gross primary production in an evergreen needleleaf forest. Remote Sens. Environ. 89, 519–534 (2004).Article 

    Google Scholar 
    Yilmaz, M. T., Hunt, E. R. Jr & Jackson, T. J. Remote sensing of vegetation water content from equivalent water thickness using satellite imagery. Remote Sens. Environ. 112, 2514–2522 (2008).Article 

    Google Scholar 
    Cheng, Y.-B., Ustin, S. L., Riaño, D. & Vanderbilt, V. C. Water content estimation from hyperspectral images and MODIS indexes in Southeastern Arizona. Remote Sens. Environ. 112, 363–374 (2008).Article 

    Google Scholar 
    Serrano, L., Penuelas, J. & Ustin, S. L. Remote sensing of nitrogen and lignin in Mediterranean vegetation from AVIRIS data: decomposing biochemical from structural signals. Remote Sens. Environ. 81, 355–364 (2002).Article 

    Google Scholar 
    Filella, I. et al. PRI assessment of long-term changes in carotenoids/chlorophyll ratio and short-term changes in de-epoxidation state of the xanthophyll cycle. Int. J. Remote Sens. 30, 4443–4455 (2009).Article 

    Google Scholar 
    Gamon, J., Penuelas, J. & Field, C. A narrow-waveband spectral index that tracks diurnal changes in photosynthetic efficiency. Remote Sens. Environ. 41, 35–44 (1992).Article 

    Google Scholar 
    Cheng, R. et al. Decomposing reflectance spectra to track gross primary production in a subalpine evergreen forest. Biogeosciences 17, 4523–4544 (2020).Article 

    Google Scholar 
    Seyednasrollah, B. et al. Seasonal variation in the canopy color of temperate evergreen conifer forests. New Phytol. 229, 2586–2600 (2021).Article 

    Google Scholar 
    Merton, R. in Proceedings of the Seventh Annual JPL Airborne Earth Science Workshop 12–16 (NASA, 2004).Naidu, R. A., Perry, E. M., Pierce, F. J. & Mekuria, T. The potential of spectral reflectance technique for the detection of Grapevine leafroll-associated virus-3 in two red-berried wine grape cultivars. Comput. Electron. Agric. 66, 38–45 (2009).Article 

    Google Scholar 
    Chen, Y. et al. Generation and evaluation of LAI and FPAR products from Himawari-8 Advanced Himawari imager (AHI) data. Remote Sens. 11, 1517 (2019).Article 

    Google Scholar 
    Zhu, Z. et al. Global data sets of vegetation leaf area index (LAI)3g and fraction of photosynthetically active radiation (FPAR)3g derived from global inventory modeling and mapping studies (GIMMS) normalized difference vegetation index (NDVI3g) for the period 1981 to 2011. Remote Sens. 5, 927–948 (2013).Article 

    Google Scholar 
    Liu, Y., Liu, R. & Chen, J. M. Retrospective retrieval of long-term consistent global leaf area index (1981–2011) from combined AVHRR and MODIS data. J. Geophys. Res. 117, G04003 (2012).
    Google Scholar 
    Croft, H. et al. The global distribution of leaf chlorophyll content. Remote Sens. Environ. 236, 111479 (2020).Article 

    Google Scholar 
    Bayat, B. et al. Toward operational validation systems for global satellite-based terrestrial essential climate variables. Int. J. Appl. Earth Obs. Geoinf. 95, 102240 (2021).
    Google Scholar 
    Cui, Y., Song, L. & Fan, W. Generation of spatio-temporally continuous evapotranspiration and its components by coupling a two-source energy balance model and a deep neural network over the Heihe River Basin. J. Hydrol. 597, 126176 (2021).Article 

    Google Scholar 
    Ali, I., Greifeneder, F., Stamenkovic, J., Neumann, M. & Notarnicola, C. Review of machine learning approaches for biomass and soil moisture retrievals from remote sensing data. Remote Sens. 7, 16398–16421 (2015).Article 

    Google Scholar 
    Gitelson, A. A. et al. Remote estimation of leaf area index and green leaf biomass in maize canopies. Geophys. Res. Lett. 30, 1248 (2003).Article 

    Google Scholar 
    Huang, M. et al. Air temperature optima of vegetation productivity across global biomes. Nat. Ecol. Evol. 3, 772–779 (2019).Article 

    Google Scholar 
    Wang, S. et al. Recent global decline of CO2 fertilization effects on vegetation photosynthesis. Science 370, 1295–1300 (2020).Article 

    Google Scholar 
    Morton, D. C. et al. Amazon forests maintain consistent canopy structure and greenness during the dry season. Nature 506, 221–224 (2014).Article 

    Google Scholar 
    Jiang, Z. et al. Analysis of NDVI and scaled difference vegetation index retrievals of vegetation fraction. Remote Sens. Environ. 101, 366–378 (2006).Article 

    Google Scholar 
    Haboudane, D., Miller, J. R., Pattey, E., Zarco-Tejada, P. J. & Strachan, I. B. Hyperspectral vegetation indices and novel algorithms for predicting green LAI of crop canopies: modeling and validation in the context of precision agriculture. Remote Sens. Environ. 90, 337–352 (2004).Article 

    Google Scholar 
    Wu, C., Wang, L., Niu, Z., Gao, S. & Wu, M. Nondestructive estimation of canopy chlorophyll content using Hyperion and Landsat/TM images. Int. J. Remote Sens. 31, 2159–2167 (2010).Article 

    Google Scholar 
    Wang, R. & Gamon, J. A. Remote sensing of terrestrial plant biodiversity. Remote Sens. Environ. 231, 111218 (2019).Article 

    Google Scholar 
    Ustin, S. L. & Gamon, J. A. Remote sensing of plant functional types. New Phytol. 186, 795–816 (2010).Article 

    Google Scholar 
    Hilker, T. et al. Vegetation dynamics and rainfall sensitivity of the Amazon. Proc. Natl Acad. Sci. USA 111, 16041–16046 (2014).Article 

    Google Scholar 
    Zhang, Y., Commane, R., Zhou, S., Williams, A. P. & Gentine, P. Light limitation regulates the response of autumn terrestrial carbon uptake to warming. Nat. Clim. Change 10, 739–743 (2020).Article 

    Google Scholar 
    Weber, M. et al. Exploring the use of DSCOVR/EPIC satellite observations to monitor vegetation phenology. Remote Sens. 12, 2384 (2020).Article 

    Google Scholar 
    Ganguly, S., Friedl, M. A., Tan, B., Zhang, X. & Verma, M. Land surface phenology from MODIS: characterization of the Collection 5 global land cover dynamics product. Remote Sens. Environ. 114, 1805–1816 (2010).Article 

    Google Scholar 
    Gray, J., Sulla-Menashe, D. & Friedl, M. A. User Guide to Collection 6 MODIS Land Cover Dynamics Product (MCD12Q2) (NASA, 2019).Wang, S., Zhang, Y., Ju, W., Qiu, B. & Zhang, Z. Tracking the seasonal and inter-annual variations of global gross primary production during last four decades using satellite near-infrared reflectance data. Sci. Total Environ. 755, 142569 (2021).Article 

    Google Scholar 
    Tian, F. et al. Calibrating vegetation phenology from Sentinel-2 using eddy covariance, PhenoCam, and PEP725 networks across Europe. Remote Sens. Environ. 260, 112456 (2021).Article 

    Google Scholar 
    Yin, G., Verger, A., Filella, I., Descals, A. & Peñuelas, J. Divergent estimates of forest photosynthetic phenology using structural and physiological vegetation indices. Geophys. Res. Lett. 47, e2020GL089167 (2020).Article 

    Google Scholar 
    Qin, Y. et al. Carbon loss from forest degradation exceeds that from deforestation in the Brazilian Amazon. Nat. Clim. Change 11, 442–448 (2021).Article 

    Google Scholar 
    Samanta, A. et al. Amazon forests did not green-up during the 2005 drought. Geophys. Res. Lett. 37, L05401 (2010).Article 

    Google Scholar 
    Shi, Y., Huang, W., Luo, J., Huang, L. & Zhou, X. Detection and discrimination of pests and diseases in winter wheat based on spectral indices and kernel discriminant analysis. Comput. Electron. Agric. 141, 171–180 (2017).Article 

    Google Scholar 
    Zhang, Z., Liu, M., Liu, X. & Zhou, G. A new vegetation index based on multitemporal Sentinel-2 images for discriminating heavy metal stress levels in rice. Sensors 18, 2172 (2018).Article 

    Google Scholar 
    Yengoh, G. T., Dent, D., Olsson, L., Tengberg, A. E. & Tucker III, C. J. Use of the Normalized Difference Vegetation Index (NDVI) to Assess Land Degradation at Multiple Scales: Current Status, Future Trends, and Practical Considerations (Springer, 2015).Potter, C. S. et al. Terrestrial ecosystem production: a process model based on global satellite and surface data. Glob. Biogeochem. Cycles 7, 811–841 (1993).Article 

    Google Scholar 
    Running, S. W. et al. A continuous satellite-derived measure of global terrestrial primary production. Bioscience 54, 547–560 (2004).Article 

    Google Scholar 
    Yuan, W. et al. Deriving a light use efficiency model from eddy covariance flux data for predicting daily gross primary production across biomes. Agric. For. Meteorol. 143, 189–207 (2007).Article 

    Google Scholar 
    Chen, M. et al. Quantification of terrestrial ecosystem carbon dynamics in the conterminous United States combining a process-based biogeochemical model and MODIS and AmeriFlux data. Biogeosciences 8, 2665–2688 (2011).Article 

    Google Scholar 
    Xiao, J. et al. A continuous measure of gross primary production for the conterminous United States derived from MODIS and AmeriFlux data. Remote Sens. Environ. 114, 576–591 (2010).Article 

    Google Scholar 
    Jiang, C., Guan, K., Wu, G., Peng, B. & Wang, S. A daily, 250 m, and real-time gross primary productivity product (2000–present) covering the contiguous United States. Earth Syst. Sci. Data Discuss. 2020, 1–28 (2020).
    Google Scholar 
    Schubert, P. et al. Modeling GPP in the Nordic forest landscape with MODIS time series data — comparison with the MODIS GPP product. Remote Sens. Environ. 126, 136–147 (2012).Article 

    Google Scholar 
    Zeng, Y. et al. A practical approach for estimating the escape ratio of near-infrared solar-induced chlorophyll fluorescence. Remote Sens. Environ. 232, 111209 (2019).Article 

    Google Scholar 
    Baldocchi, D. D. et al. Outgoing near infrared radiation from vegetation scales with canopy photosynthesis across a spectrum of function, structure, physiological capacity and weather. J. Geophys. Res. 125, e2019JG005534 (2020).
    Google Scholar 
    Dechant, B. et al. Canopy structure explains the relationship between photosynthesis and sun-induced chlorophyll fluorescence in crops. Remote Sens. Environ. 241, 111733 (2020).Article 

    Google Scholar 
    Rahman, A. F., Gamon, J. A., Fuentes, D. A., Roberts, D. A. & Prentiss, D. Modeling spatially distributed ecosystem flux of boreal forest using hyperspectral indices from AVIRIS imagery. J. Geophys. Res. Atmos. 106, 33579–33591 (2001).Article 

    Google Scholar 
    Zhu, Z. et al. Comment on “Recent global decline of CO2 fertilization effects on vegetation photosynthesis”. Science 373, eabg5673 (2021).Article 

    Google Scholar 
    Doughty, R. et al. Small anomalies in dry-season greenness and chlorophyll fluorescence for Amazon moist tropical forests during El Niño and La Niña. Remote Sens. Environ. 253, 112196 (2021).Article 

    Google Scholar 
    Huang, N. et al. Spatial and temporal variations in global soil respiration and their relationships with climate and land cover. Sci. Adv. 6, eabb8508 (2020).Article 

    Google Scholar 
    Huang, N., He, J.-S. & Niu, Z. Estimating the spatial pattern of soil respiration in Tibetan alpine grasslands using Landsat TM images and MODIS data. Ecol. Indic. 26, 117–125 (2013).Article 

    Google Scholar 
    Neale, C. M., Gonzalez-Dugo, M. P., Serrano-Perez, A., Campos, I. & Mateos, L. Cotton canopy reflectance under variable solar zenith angles: implications of use in evapotranspiration models. Hydrol. Process. 35, e14162 (2021).Article 

    Google Scholar 
    Chen, J. M. & Liu, J. Evolution of evapotranspiration models using thermal and shortwave remote sensing data. Remote Sens. Environ. 237, 111594 (2020).Article 

    Google Scholar 
    Glenn, E. P., Huete, A. R., Nagler, P. L. & Nelson, S. G. Relationship between remotely-sensed vegetation indices, canopy attributes and plant physiological processes: what vegetation indices can and cannot tell us about the landscape. Sensors 8, 2136–2160 (2008).Article 

    Google Scholar 
    Cui, Y., Jia, L. & Fan, W. Estimation of actual evapotranspiration and its components in an irrigated area by integrating the Shuttleworth-Wallace and surface temperature-vegetation index schemes using the particle swarm optimization algorithm. Agric. For. Meteorol. 307, 108488 (2021).Article 

    Google Scholar 
    Glenn, E. P., Neale, C. M., Hunsaker, D. J. & Nagler, P. L. Vegetation index-based crop coefficients to estimate evapotranspiration by remote sensing in agricultural and natural ecosystems. Hydrol. Process. 25, 4050–4062 (2011).Article 

    Google Scholar 
    French, A. N. et al. Satellite-based NDVI crop coefficients and evapotranspiration with eddy covariance validation for multiple durum wheat fields in the US Southwest. Agric. Water Manag. 239, 106266 (2020).Article 

    Google Scholar 
    Lotsch, A., Friedl, M. A., Anderson, B. T. & Tucker, C. J. Coupled vegetation-precipitation variability observed from satellite and climate records. Geophys. Res. Lett. 30, 1774 (2003).Article 

    Google Scholar 
    Nezlin, N. P., Kostianoy, A. G. & Li, B.-L. Inter-annual variability and interaction of remote-sensed vegetation index and atmospheric precipitation in the Aral Sea region. J. Arid Environ. 62, 677–700 (2005).Article 

    Google Scholar 
    Notaro, M., Liu, Z. & Williams, J. W. Observed vegetation–climate feedbacks in the United States. J. Clim. 19, 763–786 (2006).Article 

    Google Scholar 
    Fensholt, R. & Proud, S. R. Evaluation of earth observation based global long term vegetation trends — Comparing GIMMS and MODIS global NDVI time series. Remote Sens. Environ. 119, 131–147 (2012).Article 

    Google Scholar 
    Trishchenko, A. P., Cihlar, J. & Li, Z. Effects of spectral response function on surface reflectance and NDVI measured with moderate resolution satellite sensors. Remote Sens. Environ. 81, 1–18 (2002).Article 

    Google Scholar 
    Ustin, S. L. & Middleton, E. M. Current and near-term advances in Earth observation for ecological applications. Ecol. Process. 10, 1 (2021).Article 

    Google Scholar 
    Wang, D. et al. Impact of sensor degradation on the MODIS NDVI time series. Remote Sens. Environ. 119, 55–61 (2012).Article 

    Google Scholar 
    Zhang, Y., Song, C., Band, L. E., Sun, G. & Li, J. Reanalysis of global terrestrial vegetation trends from MODIS products: browning or greening? Remote Sens. Environ. 191, 145–155 (2017).Article 

    Google Scholar 
    Bhatt, R. et al. A consistent AVHRR visible calibration record based on multiple methods applicable for the NOAA degrading orbits. Part I: Methodology. J. Atmos. Ocean. Technol. 33, 2499–2515 (2016).Article 

    Google Scholar 
    Frankenberg, C., Yin, Y., Byrne, B., He, L. & Gentine, P. Comment on “Recent global decline of CO2 fertilization effects on vegetation photosynthesis”. Science 373, eabg2947 (2021).Article 

    Google Scholar 
    Los, S. O. Estimation of the ratio of sensor degradation between NOAA AVHRR channels 1 and 2 from monthly NDVI composites. IEEE Trans. Geosci. Remote Sens. 36, 206–213 (1998).Article 

    Google Scholar 
    Jiang, C. et al. Inconsistencies of interannual variability and trends in long-term satellite leaf area index products. Glob. Change Biol. 23, 4133–4146 (2017).Article 

    Google Scholar 
    de Beurs, K. M. & Henebry, G. M. Trend analysis of the Pathfinder AVHRR Land (PAL) NDVI data for the deserts of Central Asia. IEEE Geosci. Remote Sens. Lett. 1, 282–286 (2004).Article 

    Google Scholar 
    Wang, Z. et al. Large discrepancies of global greening: indication of multi-source remote sensing data. Global Ecol. Conserv. 34, e02016 (2022).Article 

    Google Scholar 
    Miura, T., Huete, A. R. & Yoshioka, H. Evaluation of sensor calibration uncertainties on vegetation indices for MODIS. IEEE Trans Geosci. Remote Sens. 38, 1399–1409 (2000).Article 

    Google Scholar 
    Lyapustin, A. et al. Scientific impact of MODIS C5 calibration degradation and C6+ improvements. Atmos. Meas. Tech. 7, 4353–4365 (2014).Article 

    Google Scholar 
    Buchhorn, M., Raynolds, M. K. & Walker, D. A. Influence of BRDF on NDVI and biomass estimations of Alaska Arctic tundra. Environ. Res. Lett. 11, 125002 (2016).Article 

    Google Scholar 
    Fensholt, R., Sandholt, I., Proud, S. R., Stisen, S. & Rasmussen, M. O. Assessment of MODIS sun-sensor geometry variations effect on observed NDVI using MSG SEVIRI geostationary data. Int. J. Remote Sens. 31, 6163–6187 (2010).Article 

    Google Scholar 
    Saleska, S. R. et al. Dry-season greening of Amazon forests. Nature 531, E4–E5 (2016).Article 

    Google Scholar 
    Lyapustin, A. I. et al. Multi-angle implementation of atmospheric correction for MODIS (MAIAC): 3. Atmospheric correction. Remote Sens. Environ. 127, 385–393 (2012).Article 

    Google Scholar 
    Norris, J. R. & Walker, J. J. Solar and sensor geometry, not vegetation response, drive satellite NDVI phenology in widespread ecosystems of the western United States. Remote Sens. Environ. 249, 112013 (2020).Article 

    Google Scholar 
    Roy, D. P. et al. A general method to normalize Landsat reflectance data to nadir BRDF adjusted reflectance. Remote Sens. Environ. 176, 255–271 (2016).Article 

    Google Scholar 
    Schaaf, C. B. et al. First operational BRDF, albedo nadir reflectance products from MODIS. Remote Sens. Environ. 83, 135–148 (2002).Article 

    Google Scholar 
    Didan, K., Munoz, A. B., Solano, R. & Huete, A. MODIS Vegetation Index User’s Guide (MOD13 Series) (Univ. Arizona, 2015).Wang, Z., Schaaf, C. B., Sun, Q., Shuai, Y. & Román, M. O. Capturing rapid land surface dynamics with Collection V006 MODIS BRDF/NBAR/Albedo (MCD43) products. Remote Sens. Environ. 207, 50–64 (2018).Article 

    Google Scholar 
    Saleska, S. R., Didan, K., Huete, A. R. & Da Rocha, H. R. Amazon forests green-up during 2005 drought. Science 318, 612 (2007).Article 

    Google Scholar 
    Vargas, M., Miura, T., Shabanov, N. & Kato, A. An initial assessment of Suomi NPP VIIRS vegetation index EDR. J. Geophys. Res. Atmos. 118, 12,301–12,316 (2013).Article 

    Google Scholar 
    Kobayashi, H. & Dye, D. G. Atmospheric conditions for monitoring the long-term vegetation dynamics in the Amazon using normalized difference vegetation index. Remote Sens. Environ. 97, 519–525 (2005).Article 

    Google Scholar 
    Jiang, C. & Fang, H. GSV: a general model for hyperspectral soil reflectance simulation. Int. J. Appl. Earth Obs. Geoinf. 83, 101932 (2019).
    Google Scholar 
    Verrelst, J., Schaepman, M. E., Malenovský, Z. & Clevers, J. G. Effects of woody elements on simulated canopy reflectance: Implications for forest chlorophyll content retrieval. Remote Sens. Environ. 114, 647–656 (2010).Article 

    Google Scholar 
    Huete, A. & Tucker, C. Investigation of soil influences in AVHRR red and near-infrared vegetation index imagery. Int. J. Remote Sens. 12, 1223–1242 (1991).Article 

    Google Scholar 
    Farrar, T., Nicholson, S. & Lare, A. The influence of soil type on the relationships between NDVI, rainfall, and soil moisture in semiarid Botswana. II. NDVI response to soil oisture. Remote Sens. Environ. 50, 121–133 (1994).Article 

    Google Scholar 
    Huete, A. & Warrick, A. Assessment of vegetation and soil water regimes in partial canopies with optical remotely sensed data. Remote Sens. Environ. 32, 155–167 (1990).Article 

    Google Scholar 
    Wang, C. et al. A snow-free vegetation index for improved monitoring of vegetation spring green-up date in deciduous ecosystems. Remote Sens. Environ. 196, 1–12 (2017).Article 

    Google Scholar 
    Myers-Smith, I. H. et al. Complexity revealed in the greening of the Arctic. Nat. Clim. Change 10, 106–117 (2020).Article 

    Google Scholar 
    Shen, M. et al. No evidence of continuously advanced green-up dates in the Tibetan Plateau over the last decade. Proc. Natl Acad. Sci. 110, E2329 (2013).
    Google Scholar 
    Hao, D. et al. Modeling anisotropic reflectance over composite sloping terrain. IEEE Trans. Geosci. Remote Sens. 56, 3903–3923 (2018).Article 

    Google Scholar 
    Matsushita, B., Yang, W., Chen, J., Onda, Y. & Qiu, G. Sensitivity of the enhanced vegetation index (EVI) and normalized difference vegetation index (NDVI) to topographic effects: a case study in high-density cypress forest. Sensors 7, 2636–2651 (2007).Article 

    Google Scholar 
    Wen, J. et al. Characterizing land surface anisotropic reflectance over rugged terrain: a review of concepts and recent developments. Remote Sens. 10, 370 (2018).Article 

    Google Scholar 
    Friedl, M. A., Davis, F. W., Michaelsen, J. & Moritz, M. Scaling and uncertainty in the relationship between the NDVI and land surface biophysical variables: an analysis using a scene simulation model and data from FIFE. Remote Sens. Environ. 54, 233–246 (1995).Article 

    Google Scholar 
    Tan, B. et al. The impact of gridding artifacts on the local spatial properties of MODIS data: implications for validation, compositing, and band-to-band registration across resolutions. Remote Sens. Environ. 105, 98–114 (2006).Article 

    Google Scholar 
    Wolfe, R. E. et al. Achieving sub-pixel geolocation accuracy in support of MODIS land science. Remote Sens. Environ. 83, 31–49 (2002).Article 

    Google Scholar 
    Ferreira, M. P. et al. Retrieving structural and chemical properties of individual tree crowns in a highly diverse tropical forest with 3D radiative transfer modeling and imaging spectroscopy. Remote Sens. Environ. 211, 276–291 (2018).Article 

    Google Scholar 
    Huete, A. R. et al. Amazon rainforests green-up with sunlight in dry season. Geophys. Res. Lett. 33, L06405 (2006).Article 

    Google Scholar 
    Herrmann, S. M. & Tappan, G. G. Vegetation impoverishment despite greening: a case study from central Senegal. J. Arid Environ. 90, 55–66 (2013).Article 

    Google Scholar 
    Wang, X. et al. No consistent evidence for advancing or delaying trends in spring phenology on the Tibetan Plateau. J. Geophys. Res. Biogeosci. 122, 3288–3305 (2017).Article 

    Google Scholar 
    Donnelly, A., Yu, R. & Liu, L. Comparing in situ spring phenology and satellite-derived start of season at rural and urban sites in Ireland. Int. J. Remote Sens. 42, 7821–7841 (2021).Article 

    Google Scholar 
    Templ, B. et al. Pan European Phenological database (PEP725): a single point of access for European data. Int. J. Biometeorol. 62, 1109–1113 (2018).Article 

    Google Scholar 
    Fu, Y. H. et al. Declining global warming effects on the phenology of spring leaf unfolding. Nature 526, 104–107 (2015).Article 

    Google Scholar 
    Chen, X. & Yang, Y. Observed earlier start of the growing season from middle to high latitudes across the Northern Hemisphere snow-covered landmass for the period 2001–2014. Environ. Res. Lett. 15, 034042 (2020).Article 

    Google Scholar 
    Alatorre, L. C. et al. Temporal changes of NDVI for qualitative environmental assessment of mangroves: shrimp farming impact on the health decline of the arid mangroves in the Gulf of California (1990–2010). J. Arid Environ. 125, 98–109 (2016).Article 

    Google Scholar 
    Jacquemoud, S. & Baret, F. PROSPECT: a model of leaf optical properties spectra. Remote Sens. Environ. 34, 75–91 (1990).Article 

    Google Scholar 
    Wu, S. et al. Quantifying leaf optical properties with spectral invariants theory. Remote Sens. Environ. 253, 112131 (2021).Article 

    Google Scholar 
    Wang, Z. et al. Mapping foliar functional traits and their uncertainties across three years in a grassland experiment. Remote Sens. Environ. 221, 405–416 (2019).Article 

    Google Scholar 
    Van Leeuwen, W. & Huete, A. Effects of standing litter on the biophysical interpretation of plant canopies with spectral indices. Remote Sens. Environ. 55, 123–138 (1996).Article 

    Google Scholar 
    Dechant, B. et al. NIRvP: a robust structural proxy for sun-induced chlorophyll fluorescence and photosynthesis across scales. Remote Sens. Environ. 268, 112763 (2022).Article 

    Google Scholar 
    Zeng, Y. et al. Estimating near-infrared reflectance of vegetation from hyperspectral data. Remote Sens. Environ. 267, 112723 (2021).Article 

    Google Scholar 
    Claverie, M. et al. The Harmonized Landsat and Sentinel-2 surface reflectance data set. Remote Sens. Environ. 219, 145–161 (2018).Article 

    Google Scholar 
    Hantson, S. & Chuvieco, E. Evaluation of different topographic correction methods for Landsat imagery. Int. J. Appl. Earth Obs. Geoinf. 13, 691–700 (2011).
    Google Scholar 
    Zhang, H. K. et al. Characterization of Sentinel-2A and Landsat-8 top of atmosphere, surface, and nadir BRDF adjusted reflectance and NDVI differences. Remote Sens. Environ. 215, 482–494 (2018).Article 

    Google Scholar 
    Gao, F., Masek, J., Schwaller, M. & Hall, F. On the blending of the Landsat and MODIS surface reflectance: predicting daily Landsat surface reflectance. IEEE Trans. Geosci. Remote Sens. 44, 2207–2218 (2006).Article 

    Google Scholar 
    Zhu, X. et al. A flexible spatiotemporal method for fusing satellite images with different resolutions. Remote Sens. Environ. 172, 165–177 (2016).Article 

    Google Scholar 
    Luo, Y., Guan, K. & Peng, J. STAIR: A generic and fully-automated method to fuse multiple sources of optical satellite data to generate a high-resolution, daily and cloud-/gap-free surface reflectance product. Remote Sens. Environ. 214, 87–99 (2018).Article 

    Google Scholar 
    Houborg, R. & McCabe, M. F. Daily retrieval of NDVI and LAI at 3 m resolution via the fusion of CubeSat, Landsat, and MODIS data. Remote Sens. 10, 890 (2018).Article 

    Google Scholar 
    Kimm, H. et al. Deriving high-spatiotemporal-resolution leaf area index for agroecosystems in the US Corn Belt using Planet Labs CubeSat and STAIR fusion data. Remote Sens. Environ. 239, 111615 (2020).Article 

    Google Scholar 
    Kong, J. et al. Evaluation of four image fusion NDVI products against in-situ spectral-measurements over a heterogeneous rice paddy landscape. Agric. For. Meteorol. 297, 108255 (2021).Article 

    Google Scholar 
    Köhler, P. et al. Global retrievals of solar-induced chlorophyll fluorescence with TROPOMI: first results and intersensor comparison to OCO-2. Geophys. Res. Lett. 45, 10,456–10,463 (2018).Article 

    Google Scholar 
    Sun, Y. et al. OCO-2 advances photosynthesis observation from space via solar-induced chlorophyll fluorescence. Science 358, eaam5747 (2017).Article 

    Google Scholar 
    Joiner, J., Yoshida, Y., Vasilkov, A. & Middleton, E. First observations of global and seasonal terrestrial chlorophyll fluorescence from space. Biogeosciences 8, 637–651 (2011).Article 

    Google Scholar 
    Frankenberg, C. et al. New global observations of the terrestrial carbon cycle from GOSAT: patterns of plant fluorescence with gross primary productivity. Geophys. Res. Lett. 38, L17706 (2011).Article 

    Google Scholar 
    Qiu, B., Ge, J., Guo, W., Pitman, A. J. & Mu, M. Responses of Australian dryland vegetation to the 2019 heat wave at a subdaily scale. Geophys. Res. Lett. 47, e2019GL086569 (2020).
    Google Scholar 
    Magney, T. S. et al. Mechanistic evidence for tracking the seasonality of photosynthesis with solar-induced fluorescence. Proc. Natl Acad. Sci. USA 116, 11640–11645 (2019).Article 

    Google Scholar 
    Guanter, L. et al. Potential of the TROPOspheric Monitoring Instrument (TROPOMI) onboard the Sentinel-5 Precursor for the monitoring of terrestrial chlorophyll fluorescence. Atmos. Meas. Tech. 8, 1337–1352 (2015).Article 

    Google Scholar 
    Knyazikhin, Y. et al. Hyperspectral remote sensing of foliar nitrogen content. Proc. Natl Acad. Sci. USA 110, E185–E192 (2013).
    Google Scholar 
    Li, X. & Xiao, J. A global, 0.05-degree product of solar-induced chlorophyll fluorescence derived from OCO-2, MODIS, and reanalysis data. Remote Sens. 11, 517 (2019).Article 

    Google Scholar 
    Zeng, Y. et al. Combining near-infrared radiance of vegetation and fluorescence spectroscopy to detect effects of abiotic changes and stresses. Remote Sens. Environ. 270, 112856 (2022).Article 

    Google Scholar 
    Shi, J. et al. Microwave vegetation indices for short vegetation covers from satellite passive microwave sensor AMSR-E. Remote Sens. Environ. 112, 4285–4300 (2008).Article 

    Google Scholar 
    Talebiesfandarani, S. et al. Microwave vegetation index from multi-angular observations and its application in vegetation properties retrieval: theoretical modelling. Remote Sens. 11, 730 (2019).Article 

    Google Scholar 
    Wigneron, J.-P. et al. SMOS-IC data record of soil moisture and L-VOD: historical development, applications and perspectives. Remote Sens. Environ. 254, 112238 (2021).Article 

    Google Scholar 
    Zhang, Y., Zhou, S., Gentine, P. & Xiao, X. Can vegetation optical depth reflect changes in leaf water potential during soil moisture dry-down events? Remote Sens. Environ. 234, 111451 (2019).Article 

    Google Scholar 
    Frappart, F. et al. Global monitoring of the vegetation dynamics from the vegetation optical depth (VOD): a review. Remote Sens. 12, 2915 (2020).Article 

    Google Scholar 
    Xiao, J., Fisher, J. B., Hashimoto, H., Ichii, K. & Parazoo, N. C. Emerging satellite observations for diurnal cycling of ecosystem processes. Nat. Plants 7, 877–887 (2021).Article 

    Google Scholar 
    Hashimoto, H. et al. New generation geostationary satellite observations support seasonality in greenness of the Amazon evergreen forests. Nat. Commun. 12, 684 (2021).Article 

    Google Scholar 
    Somkuti, P. et al. Solar-induced chlorophyll fluorescence from the Geostationary Carbon Cycle Observatory (GeoCarb): An extensive simulation study. Remote Sens. Environ. 263, 112565 (2021).Article 

    Google Scholar 
    Gorelick, N. et al. Google Earth Engine: planetary-scale geospatial analysis for everyone. Remote Sens. Environ. 202, 18–27 (2017).Article 

    Google Scholar 
    Richardson, A. D., Braswell, B. H., Hollinger, D. Y., Jenkins, J. P. & Ollinger, S. V. Near-surface remote sensing of spatial and temporal variation in canopy phenology. Ecol. Appl. 19, 1417–1428 (2009).Article 

    Google Scholar 
    Daughtry, C. S. Discriminating crop residues from soil by shortwave infrared reflectance. Agron. J. 93, 125–131 (2001).Article 

    Google Scholar  More

  • in

    Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships

    Flemming, H. C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bulgarelli, D., Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu Rev. Plant Biol. 64, 807–838 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Venturelli, O. S. et al. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol. Syst. Biol. 14, e8157 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Foster, K. R. & Bell, T. Competition, not cooperation, dominates interactions among culturable microbial species. Curr. Biol. 22, 1845–1850 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Helfrich, E. J. N. et al. Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. Nat. Microbiol. 3, 909–919 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Coyte, K. Z. & Rakoff-Nahoum, S. Understanding competition and cooperation within the mammalian gut microbiome. Curr. Biol. 29, 538–544 (2019).Article 
    CAS 

    Google Scholar 
    Turner, T. R. et al. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J. 7, 2248–2258 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Müller, D. B., Vogel, C., Bai, Y. & Vorholt, J. A. The plant microbiota: systems-level insights and perspectives. Annu. Rev. Genet. 50, 211–234 (2016).PubMed 
    Article 
    CAS 

    Google Scholar 
    Lugtenberg, B. & Kamilova, F. Plant-growth-promoting Rhizobacteria. Annu. Rev. Microbiol. 63, 541–556 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Innerebner, G., Knief, C. & Vorholt, J. A. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77, 3202–3210 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Shekhawat, K. et al. Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci. EMBO Rep. 22, e51049 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bodenhausen, N., Bortfeld-Miller, M., Ackermann, M. & Vorholt, J. A. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet. 10, e1004283 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Reisberg, E. E., Hildebrandt, U., Riederer, M. & Hentschel, U. Distinct phyllosphere bacterial communities on Arabidopsis wax mutant leaves. PLoS ONE 8, e78613 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kniskern, J. M., Traw, M. B. & Bergelson, J. Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol. Plant Microbe Interact. 20, 1512–1522 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Pfeilmeier, S. et al. The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves. Nat. Microbiol. 6, 852–864 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chen, T. et al. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hassani, M. A., Duran, P. & Hacquard, S. Microbial interactions within the plant holobiont. Microbiome 6, 58 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lidicker, W. Z. Clarification of interactions in ecological systems. Bioscience 29, 475–477 (1979).Article 

    Google Scholar 
    Schlechter, R. O., Miebach, M. & Remus-Emsermann, M. N. P. Driving factors of epiphytic bacterial communities: a review. J. Adv. Res. 19, 57–65 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Grosskopf, T. & Soyer, O. S. Synthetic microbial communities. Curr. Opin. Microbiol. 18, 72–77 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Blair, P. M. et al. Exploration of the biosynthetic potential of the Populus microbiome. mSystems 3, e00045-00018 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Suda, W., Nagasaki, A. & Shishido, M. Powdery mildew-infection changes bacterial community composition in the phyllosphere. Microbes Environ. 24, 217–223 (2009).PubMed 
    Article 

    Google Scholar 
    Manching, H. C., Balint-Kurti, P. J. & Stapleton, A. E. Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization. Front. Plant Sci. 5, 403 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Agler, M. T. et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, 100235 (2016).Article 
    CAS 

    Google Scholar 
    Layeghifard, M., Hwang, D. M. & Guttman, D. S. Disentangling interactions in the microbiome: a network perspective. Trends Microbiol. 25, 217–228 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Carr, A., Diener, C., Baliga, N. S. & Gibbons, S. M. Use and abuse of correlation analyses in microbial ecology. ISME J. 13, 2647–2655 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vorholt, J. A., Vogel, C., Carlström, C. I. & Müller, D. B. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22, 142–155 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Knief, C., Frances, L. & Vorholt, J. A. Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb. Ecol. 60, 440–452 (2010).PubMed 
    Article 

    Google Scholar 
    Fan, J., Crooks, C. & Lamb, C. High-throughput quantitative luminescence assay of the growth in planta of Pseudomonas syringae chromosomally tagged with Photorhabdus luminescens luxCDABE. Plant J. 53, 393–399 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vogel, C. M., Potthoff, D. M., Schäfer, M., Barandun, N. & Vorholt, J. A. Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen. Nat. Microbiol. 6, 1537–1548 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Chen, I.-M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, 751–763 (2020).Article 
    CAS 

    Google Scholar 
    Ortiz, A., Vega, N. M., Ratzke, C. & Gore, J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. ISME J. 15, 2131–2145 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Goberna, M. & Verdú, M. Predicting microbial traits with phylogenies. ISME J. 10, 959–967 (2016).PubMed 
    Article 

    Google Scholar 
    Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33, 475–505 (2002).Article 

    Google Scholar 
    Cahill, J. F., Kembel, S. W., Lamb, E. G. & Keddy, P. A. Does phylogenetic relatedness influence the strength of competition among vascular plants? Perspect. Plant Ecol. 10, 41–50 (2008).Article 

    Google Scholar 
    Maherali, H. & Klironomos, J. N. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316, 1746–1748 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Duncan, R. P. & Williams, P. A. Ecology – Darwin’s naturalization hypothesis challenged. Nature 417, 608–609 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    Slingsby, J. A. & Verboom, G. A. Phylogenetic relatedness limits co-occurrence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa. Am. Nat. 168, 14–27 (2006).PubMed 
    Article 

    Google Scholar 
    Mayfield, M. M. & Levine, J. M. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol. Lett. 13, 1085–1093 (2010).PubMed 
    Article 

    Google Scholar 
    Teixeira, P. J. P. L., Colaianni, N. R., Fitzpatrick, C. R. & Dangl, J. L. Beyond pathogens: microbiota interactions with the plant immune system. Curr. Opin. Microbiol. 49, 7–17 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Maier, B. A. et al. A general non-self response as part of plant immunity. Nat. Plants 7, 696–705 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 0109 (2017).Article 

    Google Scholar 
    Kehe, J. et al. Positive interactions are common among culturable bacteria. Sci. Adv. 7, eabi7159 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lindow, S. E. & Brandl, M. T. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Remus-Emsermann, M. N. P. et al. Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization. Environ. Microbiol. 16, 2329–2340 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Billick, I. & Case, T. J. Higher-order interactions in ecological communities – what are they and how can they be detected. Ecology 75, 1529–1543 (1994).Article 

    Google Scholar 
    Grilli, J., Barabas, G., Michalska-Smith, M. J. & Allesina, S. Higher-order interactions stabilize dynamics in competitive network models. Nature 548, 210–213 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Levine, J. M., Bascompte, J., Adler, P. B. & Allesina, S. Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546, 56–64 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sundarraman, D. et al. Higher-order interactions dampen pairwise competition in the zebrafish gut microbiome. mBio 11, e01667-20 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Morris, C. in Encyclopedia for Life Sciences (National Publishing Group, 2002).Raaijmakers, J. M. & Mazzola, M. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu. Rev. Phytopathol. 50, 403–424 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Iversen, O. J. & Grov, A. Studies on lysostaphin – separation and characterization of 3 enzymes. Eur. J. Biochem. 38, 293–300 (1973).CAS 
    PubMed 
    Article 

    Google Scholar 
    Recsei, P. A., Gruss, A. D. & Novick, R. P. Cloning, sequence, and expression of the lysostaphin gene from Staphylococcus simulans. Proc. Natl Acad. Sci. USA 84, 1127–1131 (1987).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kessler, E., Safrin, M., Abrams, W. R., Rosenbloom, J. & Ohman, D. E. Inhibitors and specificity of Pseudomonas aeruginosa LasA. J. Biol. Chem. 272, 9884–9889 (1997).CAS 
    PubMed 
    Article 

    Google Scholar 
    Trayer, H. R. & Buckley, C. E. Molecular properties of lysostaphin, a bacteriolytic agent specific for Staphylococcus aureus. J. Biol. Chem. 245, 4842–4846 (1970).CAS 
    PubMed 
    Article 

    Google Scholar 
    Heymer, B. & Schmidt, W. C. Purification and characterization of a Streptomyces albus endo-N-acetylmuramidase lytic for group A and other beta hemolytic streptococci. Microbios 12, 51–66 (1975).CAS 
    PubMed 

    Google Scholar 
    Vollmer, W., Joris, B., Charlier, P. & Foster, S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol. Rev. 32, 259–286 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    Peyraud, R. et al. Demonstration of the ethylmalonyl-CoA pathway by using C-13 metabolomics. Proc. Natl Acad. Sci. USA 106, 4846–4851 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schlesier, B., Breton, F. & Mock, H. P. A hydroponic culture system for growing Arabidopsis thaliana plantlets under sterile conditions. Plant Mol. Biol. Rep. 21, 449–456 (2003).CAS 
    Article 

    Google Scholar 
    Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).Article 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Integrated Development Environment for R (R Studio, 2020).R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Oksanen, J. et al. vegan: Community Ecology Package. R package v. 2.5-7 (2020).Armenteros, J. J. A. et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).Article 
    CAS 

    Google Scholar 
    Gasteiger, E. et al. in The Proteomics Protocols Handbook 571–607 (ed Walker, J. M.) (Humana Press, 2005).Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bushnell, B. BBMap short read aligner, and other bioinformatic tools (SourceForge, version 38.87); https://sourceforge.net/projects/bbmapDeatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165–188 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Visible-NIR hyperspectral classification of grass based on multivariate smooth mapping and extreme active learning approach

    Study areaGrassland herbage samples are from Shaerqin base, institute of grassland research of CAAS (Chinese Academy of Agricultural Sciences). We obtained the permission of the institution to take HSI of the grassland sample. Our work did not cause damage to grassland. Researcher Weihong Yan of the institute provided us with relevant information about grassland. The land use type in the study area is mainly grassland, which is composed of forage species, most of which are representative species of typical grassland. We take this area as an example to conduct research on grass classification. By enriching the relevant recognition technology, it can also be used as a reference for the pastures of other grasslands. The grass species Grass1 for the experiment is shown in Table 1. The official introduction of plant materials is detailed in the flora of China15.Table 1 Samples information for Grass1 dataset.Full size tableThe field hyperspectral platformWe assemble a system for collecting HSI in the field: HyperSpec©PTU-D48E HSI instrument, high-precision scanning PTZ, tripod, data analysis software Hyperspec, etc. The light source is natural light. The imaging instrument is in line scanning mode. Table 2 shows the technical parameters.Table 2 Technical parameters of hyperspectral instrument.Full size tableData collectionIn July 2021, the data was collected during the lush grass growth period. Collect data from 11:00 a.m. to 2:00 p.m. every day. At this time, it is sunny, cloudless and the wind force does not exceed level 2. So as to ensure the consistency of the acquisition time line and avoid the influence of different degrees of light on the reflectivity as far as possible. The measuring points are arranged facing the sun and the opposite direction of the shadow. We collect data from different angles of the grassland, which is based on the growth of various types of forages, and selects relatively concentrated places within the study area. Each shot is a single category of grass. The image resolution is 1166 × 1004 pixels (Fig. 1). The imaging spectrometer is fixed with scanning head when shooting. Data acquisition and transmission are executed on Hyperspec software. Then save it as a BIL file. The ENVI5.3 software was used to extract the forage spectrum to establish the dataset Grass1. Well balanced regions with a clear image, uniform spectral distribution are selected for further segmentation. The average value of spectral reflectance of grass pixels was taken as the reflectance spectrum of a single type of grass.Figure 1True color map of grass samples.Full size imageMethodologyIn Fig. 2, we present the framework of visible-NIR hyperspectral classification of grass based on multivariate smooth mapping and extreme active learning (MSM–EAL). Specifically, we first introduce the proposed MSM algorithm for global enhanced spectral reconstruction, which utilizes smooth manifold projection technology to alleviate the problems of difficult feature selection and redundant data. Then, the EAL framework is proposed to address the matter of hyperspectral labeled samples and spectral classification. In the following, each step of this method will be presented in detail.Figure 2Proposed MSM–EAL framework for grass HSI classification.Full size imageThe proposed MSM algorithmIn the process of field HSI acquisition, on the one hand, the surface distribution of grass is uneven and the plant height is different, causing certain scattering effect and coverage spectrum change. On the other hand, HSI is easy to be disturbed by external natural factors such as light, wind and shadow, resulting in a certain degree of distortion. Multiplicative scatter correction (MSC) is a scattering correction effect, which helps to eliminate the scattering effect caused by the above reasons and enhance the spectral variability. The moving window smooth spectral matrix (Nirmaf) belongs to the smooth effect, which improve the signal-to-noise ratio of the spectrum and reduce the influence of random noise16,17. Preprocessing methods are different and related to each other. We design an enhanced preprocessing multivariate smooth (MS) method that fusing MSC and smooth Nirmaf to target grass spectral signal features. In the follow-up, a model will be established to verify the validity of MS.Most of the high-dimensional spatial data have the characteristics of being embedded in a manifold body, so the manifold learning isometric feature mapping (Isomap) based on spectral theory is adopted. Isomap preserves the global geometric features of the initial data and extracts features by reconstructing the underlying smooth manifold of HSI. It is nonlinear dimensionality reduction based on linear and multidimensional scaling transformation18. Isomap has been applied in image and HSI classification19,20, but there is no report on visible-NIR hyperspectral classification of grass.In view of the above, we proposed the multivariate smooth mapping (MSM) spectral reconstruction algorithm, which can be represented as follows:$$ MSM_{z} { } = { }frac{{left( {P_{j} – b_{j} } right)left( {2n + 1} right) + n_{j} cdot mathop sum nolimits_{j = – n}^{n} C_{j} P_{k + j} }}{{n_{j} left( {2n + 1} right)}} + V_{Z} F_{Z}^{frac{1}{2}} { } $$
    (1)
    where Pj, bj, and Cj represent the raw reflectance value of spectrum j, baseline shift amount, and weight factor, respectively, k and nj represent the polynomial degree and offset, respectively. MSMz is the feature cube reconstructed to Z dimension from the spectrum calculated by 2n + 1 moving window width, V eigenvector matrix and F eigenvalue matrix.In Isomap equidistant mapping, the shortest path of edge Pi Pj needs to be solved, and the representation matrix is:$$ D_{G} = [d_{G}^{2} (P_{i} ,P_{j} )]_{i,j = 1}^{n} $$
    (2)
    where d (Pi, Pj) is the weight of the edge Pi Pj calculated from the neighborhood graph G and its side Pi Pj.The proposed EAL frameworkLabeling hyperspectral samples is expensive in terms of time and cost, at the same time, the lower spatial resolution and more bands increase the difficulty of labeling. Active learning (AL) provides an efficient labeling strategy, which only needs to label a relatively small number of samples to learn a more accurate model21. The pool-based AL selects the most informative samples according to the query strategy for limited labeling through iteration, so as to facilitate model improvement. Commonly used query strategies are uncertainty criteria, such as least confidence22, the bayesian active learning disagreement (BALD), the entropy sampling23, etc.Due to there is still an over-fitting problem, different strategies such as hybrid prediction and regularization need to be used for non-recursive datasets24. The research25 proposed that extreme gradient boosting algorithm (XGBoost) based on gradient boosting. As a classification method, XGBoost has been successfully applied in Kaggle competition and other fields. Its most important feature for visible-NIR hyperspectral classification is that can easily and directly classify according to features, and the physical interpretation of features can help understand the electronic nature behind spectral classification. XGBoost is a machine learning algorithm based tree structure that integrates multiple weak classifiers to achieve flexible and high-precision classification. It is an upgraded version of gradient boosting decision tree. The optimization process of XGBoost entailed: (1) Expanding the objective function to the second order, and finds a new objective function for the new base model to improve the calculation accuracy. (2) L2 regularization term is added to the loss function to prevent over-fitting. (3) Using blocks storage structure realize automatic parallel computing26,27. The algorithm steps are as follows:The objective function:$$ Lleft( Phi right) = mathop sum limits_{i} lleft( {y^{i} ,widehat{{y^{i} }}} right) + mathop sum limits_{k} Omega left( {f_{k} } right) $$
    (3)
    In formula (3), the first and second terms are the loss function term and the regularization term, respectively. Where,$$ Omega left( {f_{k} } right) =upgamma {text{T}} + frac{1}{2}lambda left| w right|^{2} $$
    (4)
    γ and λ are regularization parameters which are used to adjust complexity of the tree.Next, second derivative Taylor expansion of the objective function. Where (g_{i}) and (h_{i}) are the first derivative and second derivative, respectively.$$ L^{left( t right)} = mathop sum limits_{i = 1}^{n} lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }} + f_{t} left( {x_{i} } right)} right) + Omega left( {f_{t} } right) $$
    (5)
    $$ g_{i} = partial_{{hat{y}_{i} (t – 1)}} lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }}} right) $$
    (6)
    $$ h_{i} = partial_{{widehat{{y_{i} }}(t – 1)}}^{2} lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }}} right) $$
    (7)
    $$ {text{L}}^{left( t right)} approx mathop sum limits_{i = 1}^{n} left[ {lleft( {y_{i} ,widehat{{y_{i}^{t – 1} }}} right) + g_{i} f_{i} left( {x_{i} } right) + frac{1}{2}h_{i} f_{t}^{2} left( {x_{i} } right)} right] + Omega left( {f_{t} } right) $$
    (8)
    Final objective function:$$ {hat{text{L}}}^{ i} left( q right) = – frac{1}{2}mathop sum limits_{j = 1}^{T} frac{{(mathop sum nolimits_{{i in I_{j} }} g_{i} )^{2} }}{{mathop sum nolimits_{{i in I_{j} }} h_{i} + lambda }} + gamma T $$
    (9)
    Equation (9) can be used as the fraction of tree cotyledons, and the tree structure is directly proportional to the fraction. If the result after splitting is less than the maximum value of the given parameter, the cotyledon depth stops growing24,28.AL solves the problems of limited number and high cost of grass hyperspectral labeling samples. The default model of traditional AL is logistic regression, which is mostly studied on the ideal public dataset. However, the actual data has more uncertain noise, which still poses a certain challenge to AL. Consequently, we propose the extreme active learning (EAL) framework to minimize the classification cost of visible-NIR hyperspectral. The framework replaces the logistic regression model with XGBoost. Taking advantage of AL, XGBoost can improve performance with less training marker samples. By jointing of XGBoost and AL, EAL provides significantly better results than AL in field Grassl dataset recognition. Additionally, based on the characteristics of XGBoost, EAL more intuitively enhances the physical essence behind spectral classification than AL. Algorithm 1 summarizes the workflow of EAL framework.Random forest (RF) and decision tree (DT) were used to compare with EAL. RF and DT are frequently used in the field of grassland remote sensing9,29. Furthermore, RF, DT and XGBoost have the same point is that are learning algorithms based on tree structure. DT determines the direction by judging the conditions of the decision node12. RF is an integrated learning of multiple decision trees30. More

  • in

    Regional asymmetry in the response of global vegetation growth to springtime compound climate events

    Illustration of the compound event indicesBuilding on earlier studies24,25, we develop two univariate indices to model concurrent climate conditions, i.e., a CWD index that varies from compound cold-wet conditions to CWD conditions, and a CCD index that varies from compound warm-wet conditions to CCD conditions (see “Methods”). The two indices incorporate the dependence between temperature and precipitation and are a measure of how warm/cold and dry a point is relative to the distribution of climate conditions at a given location. We illustrate the two indices on two grid points that have strong but opposite temperature-precipitation correlation. In the case where temperature and precipitation are strongly negatively correlated, the CWD index is well aligned with the primary axis of the bivariate distribution (Fig. 1a). In the case where temperature and precipitation are strongly positively correlated, the same holds for the CCD index (Fig. 1d). As illustrated for several concurrent hot-dry and cold-dry events that occurred around the globe, the two indices well capture these events (Supplementary Figs. 1 and 2).Fig. 1: The relationship between precipitation and temperature and compound indices.a Scatter plot of summer precipitation and temperature anomalies (z-score) with corresponding CWD index in color (see “Methods”). The location is at 97.25°W and 33.75°N from 1901 to 2018. b The same as a but for spring at 84.75°E and 66.75°N. c Same distribution as in a but colored based on the CCD index. d Same distribution as in b but colored based on the CCD index.Full size imageNotably, in the case where precipitation and temperature are strongly positively correlated, the CWD index indicates the relative anomalies of bivariate joint distribution, and some counterintuitive situations might occur relative to the univariate marginals (Fig. 1b). For instance, points might be labeled as strong CWD events (CWD index > 1.5) even though temperature is anomalously cold (temperature anomalies < 0, red dots in lower left quadrant of Fig. 1b). The CCD index exhibits similar behavior (Fig. 1c). This indicates an interesting property of the compound indices to identify strong compound conditions relative to bivariate distribution that are not necessarily extreme from a univariate perspective3,24,26,27.Widespread direct and lagged impacts of springtime compound climate conditionsTo evaluate the lagged summer vegetation responses to spring compound climate conditions, we compute partial correlation between CWD (CCD) spring and subsequent summer vegetation variation by controlling for the influence of summer compound climate conditions on these correlations (see “Methods”). Results show widespread negative associations between CWD spring and subsequent summer vegetation in the mid-latitudes (50°N).a–c The average standardized anomalies (z-score) of GPP during CWD spring but subsequent non-CWD summer (a), non-CWD spring but subsequent CWD summer (b), and consecutive CWD spring and summer (c) for areas in Fig. 2a where summer vegetation responds positively (r ≥ 0.22) to spring CWD climate conditions. d–f The same as a–c, but for soil moisture. g–i The same as a–c, but for runoff. The bar plots with dash lines (without dash line) indicate the average anomalies of multiple observation-based (model-based) products, and the circles indicate the average anomalies of each product. GLASS, LUE, NIRv, Flux-CRU, and Flux-ERA5 are observation-based GPP products, while model simulations are taken from TRENDYv6. GLEAM is observation-based soil moisture. GRUN represents observation-based runoff. GLDAS-VIC, GLDAS-Noah, GLDAS-Catchment, and FLDAS indicate assimilatory soil moisture and runoff that incorporate satellite- and ground-based observational products.Full size imageFig. 4: The responses of vegetation productivity and hydrological variables to CWD events in mid-latitudes (23.5–50°N/S).a–c The average standardized anomalies (z-score) of GPP during CWD spring but subsequent non-CWD summer (a), non-CWD spring but subsequent CWD summer (b), and consecutive CWD spring and summer (c) for areas in Fig. 2a where summer vegetation responds negatively (r ≤ −0.22) to spring CWD climate conditions. d–f The same as a–c, but for soil moisture. g–i The same as a–c, but for runoff. The bar plots with dash lines (without dash line) indicate the average anomalies of multiple observation-based (model-based) products, and the circles indicate the average anomalies of each product. For details on data see Fig. 3.Full size imageFig. 5: The effects of CCD events on vegetation productivity and hydrological variables in mid-to-high latitudes.a–c The average standardized anomalies (z-score) of GPP during CCD spring but subsequent non-CCD summer (a), non-CCD spring but subsequent CCD summer (b), and consecutive CCD spring and summer (c) for areas in Fig. 2b where summer vegetation responds negatively (r ≤ −0.22) to spring CCD climate conditions. d–f The same as a–c, but for soil moisture. g–i The same as a–c, but for runoff. The bar plots with dash lines (without dash line) indicate the average anomalies of multiple observation-based (model-based) products, and the circles indicate the average anomalies of each product. For details on data see Fig. 3.Full size imageCWD events increase vegetation productivity in high latitudesWe first analyze the direct responses of productivity to springtime and summertime CWD events across high latitudes ( >50°N, Fig. 3). Productivity increases during CWD spring and summer (Fig. 3a–c), which is consistent with vegetation responses (Supplementary Fig. 8a–c). Despite elevated spring greenness, spring water overall shows positive anomalies during CWD spring (Fig. 3d, f, g, i). This result indicates that spring greenness during CWD conditions is not associated with dry spring across high latitudes, which is further confirmed by similar anomalies in springtime TWS (Supplementary Fig. 8d, f). In contrast, severe water reduction is found in CWD summer (Fig. 3e, f, h, i). This suggests that despite the beneficial effects of CWD events on productivity in summer, they are associated with summer water deficit.Next, to analyze the lagged effects of springtime CWD events, we investigate the productivity anomalies in summer under three cases, namely CWD spring but non-CWD summer, non-CWD spring but CWD summer, and consecutive CWD spring and summer. Our results indicate that springtime CWD events have positive lagged effects on summer productivity across high latitudes (Fig. 3). Specifically, we find that during non-CWD summer (that is not favorable for summer vegetation growth) preceded by CWD spring, positive anomalies are still found in summer productivity (Fig. 3a). In contrast, during CWD summer (preceded by non-CWD spring), some models and observation-based products exhibit a reduction in summer productivity (Fig. 3b). We further find that summer productivity highly increases during consecutive events (Fig. 3c). Vegetation anomalies show similar behaviors (Supplementary Fig. 8a–c). Regarding the lagged responses of hydrological variables, CWD springs followed by non-CWD summers do not lead to water dryness, despite increased vegetation greenness (Fig. 3d, g). The magnitude of summer water deficit is similar for both cases that include CWD summer (Fig. 3e, f, h, i) and is consistent with summer TWS anomalies (Supplementary Fig. 8e, f). These results imply that in high latitudes, summer water reductions characterized by TWS, soil moisture, and runoff are not associated with increased spring greenness but are primarily caused by summer precipitation deficit.The productivity responses to compound climate conditions may be stronger than that to individual events through the synergistic effects of temperature and precipitation28. To investigate this, we compute the average anomalies in GPP and soil moisture associated with univariate events across the focus areas, which are then compared with the effects of CWD and CCD events in high latitudes (see “Methods”). Warm events can not only directly increase productivity but also show positive lagged effects (Supplementary Fig. 9a, b). In contrast, dry events reduce productivity (Supplementary Fig. 9e, f). This indicates that the direct and lagged positive effects of CWD events across high latitudes are mainly dominated by the warm component, while dry conditions have negative effects. Therefore, the warm-induced increase in productivity slightly exceeds that associated with CWD events (Supplementary Fig. 9b). Soil moisture under warm springs shows positive anomalies (Supplementary Fig. 9c, d), while they slightly decline during dry spring (Supplementary Fig. 9g, h). This suggests that the positive anomalies in soil water during CWD spring are driven by the warm component.CWD events reduce vegetation productivity in mid-latitudesHere, we first investigate the direct effects of springtime and summertime CWD events across mid-latitudes (23.5–50°N/S). Springtime productivity exhibits little changes during CWD spring (Fig. 4a, c), despite dry spring (Fig. 4d, f, g, i). When considering the direct effects of CWD events in summer, the results are similar, whereas the negative magnitude of productivity in summer is larger than that in spring (Fig. 4b, c). This difference suggests CWD conditions in summer show more adverse effects on productivity than that in spring in mid-latitudes. The anomalies in vegetation and TWS are consistent (Supplementary Fig. 10).Next, the lagged effects of springtime CWD events in mid-latitudes are assessed. In cases with CWD spring but non-CWD summer, summer productivity exhibits slight anomalies (Fig. 4a), with slightly decreased summer water (Fig. 4d, g). Summer productivity and water show much higher reductions in case with consecutive events (Fig. 4c, f, i) than for the case with only CWD summer (Fig. 4b, e, h). These results are supported by the responses of vegetation indices and TWS (Supplementary Fig. 10), revealing that springtime CWD events in mid-latitudes have negative lagged effects on summer productivity and water availability.The direct and lagged effects of individual events are finally compared with that of CWD events in mid-latitudes. Dry conditions in spring and summer directly decrease productivity and cause soil water dryness (Supplementary Fig. 11a–d). Moreover, dry spring depletes soil moisture earlier, which, in turn, causes dry summer and reduction in productivity during non-dry summer (Supplementary Fig. 11a, c). This indicates that dry springs have negative lagged effects on summer productivity. In contrast, productivity and soil water show positive anomalies during warm springs, while they show negative anomalies in summer (Supplementary Fig. 11e–h). These results suggest that the direct and lagged negative effects of CWD springs are dominated by the dry component in mid-latitudes, while the warm component mitigates the negative effects of the dry component in spring. Accordingly, the decline in productivity due to dry conditions thus exceeds that triggered by CWD events (Supplementary Fig. 11b).Decreased vegetation productivity due to the negative synergistic effects of CCD eventsHere, we first investigate the direct effects of CCD events across mid-to-high latitudes. Productivity reductions are found during springtime and summertime CCD events (Fig. 5a–c) concurrent with water reductions (Fig. 5). Vegetation and TWS show similar behaviors during CCD spring and summer (Supplementary Fig. 12). These results reveal that CCD events in spring and summer can impose direct adverse impacts on productivity and soil water across mid-to-high latitudes. The productivity reductions in spring and summer are similar in magnitude (Fig. 5a, b), indicating that CCD events between spring and summer can cause similar damage to productivity.We then analyze the lagged effects of springtime CCD events. Our results indicate that springtime CCD events show negative lagged effects on summer productivity and cause summer water reductions in mid-to-high latitudes (Fig. 5). Specifically, we find that in cases with CCD spring but non-CCD summer, summer productivity and water exhibit strongly negative anomalies (Fig. 5a, d, g). Moreover, summer anomalies are higher during consecutive events (Fig. 5c, f, i) than the cases including only CCD summer (Fig. 5b, e, h). Vegetation indices and TWS show similar responses (Supplementary Fig. 12). Our results further indicate that CCD spring has more severe negative lagged effects on productivity than CWD spring. That is, we find that in comparison to cases with preceding CWD spring and consecutive CWD events, summer productivity shows higher reduction in cases with preceding CCD spring and consecutive CCD events (Fig. 4a, c versus Fig. 5a, c). Moreover, in cases with CCD spring but non-CCD summer (Fig. 5a, d, g), summer anomalies are close to those in scenarios with non-CCD spring but CCD summer (Fig. 5b, e, h). The vegetation and TWS anomalies further confirm this situation (Supplementary Fig. 12a, b, d, e). These results suggest that the lagged effects of CCD spring can be of similar magnitude as their direct adverse effects.We finally compare the direct and lagged effects of individual events with that of CCD events in mid-to-high latitudes. Cold conditions in spring and summer directly reduce productivity but show weak effects on soil moisture (Supplementary Fig. 13a–d), and cold spring shows negative lagged effects on summer productivity (Supplementary Fig. 13a). Dry events show direct and lagged negative effects on productivity and soil moisture (Supplementary Fig. 13e–h). These results imply that the negative lagged effects of CCD springs are dominated by both cold and dry components. The effects of CCD events on productivity mostly exceeds the individual dry or cold impacts (Supplementary Fig. 13a, b, e, f). More

  • in

    Changes in plant biodiversity facets of rocky outcrops and their surrounding rangelands across precipitation and soil gradients

    Larson, D. W., Matthes, U. & Kelly, P. E. Cliff Ecology (Cambridge University Press, 2000).Book 

    Google Scholar 
    Cooper, A. Plant species coexistence in cliff habitats. J. Biogeogr. 24, 483–494 (1997).Article 

    Google Scholar 
    Davis, P. H. Cliff vegetation in the eastern Mediterranean. J. Ecol. 39, 63–93 (1951).Article 

    Google Scholar 
    Snogerup, S. Evolutionary and plant geographical aspects of chasmophytic communities. In Plant life of South-West Asia (eds Davis, P. H. et al.) 157–170 (Bot. Soc. Edinb, 1971).
    Google Scholar 
    Baskin, J. M. & Baskin, C. C. Endemism in rock outcrop plant communities of unglaciated eastern United States: An evaluation of the roles of the edaphic, genetic and light factors. J. Biogeogr. 15, 829–840 (1988).Article 

    Google Scholar 
    Medina, B. M. O. & Fernandes, G. W. The potential of natural regeneration of rocky outcrop vegetation on rupestrian field soils in Serra do Cipo, Brazil. Braz. J. Bot. 30, 665–678 (2007).Article 

    Google Scholar 
    Alves, R. J. V., Cardin, L. & Kropf, M. S. Angiosperm disjunction “Campos Rupestres-Restingas”: Are-evaluation. Acta Bot. Bras. 2, 675–685 (2007).Article 

    Google Scholar 
    Harley, R. M. Introduction. In Flora of the Pico das Almas, Chapada Diamantina, Bahia, Brazil (eds Stannard, B. L., Harvey, Y. B. & Harley, R. M) 1–42 (Royal Botanic Gardens, 1995).Hubbell, S. P. Neutral theory in ecology and the evolution of ecological equivalence. Ecology 87, 1387–1398 (2006).PubMed 
    Article 

    Google Scholar 
    Conceição, A. A., Pirani, J. R. & Meirelles, S. T. Floristics, structure and soil of insular vegetation in four quartzite-sandstone outcrops of “Chapada Diamantina”, Northeast Brazil. Rev. Bras. Bot. 30, 641–656 (2007).Article 

    Google Scholar 
    Le Stradic, S., Buisson, E. & Wilson, F. G. Vegetation composition and structure of some Neotropical mountain grasslands in Brazil. J Mt Sci 12:864–77. An. Acad. Bras. Ciênc. 87(4), 2097–2110 (2015).Article 
    CAS 

    Google Scholar 
    Nunes, J. A. et al. Soil–vegetation relationships on a banded ironstone ‘island’, Carajás Plateau, Brazilian Eastern Amazonia. An. Acad. Bras. Cienc. 87(4), 2097–2110 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Silva, W. A. Gradiente vegetacional e pedológico em complexo rupestre de quartzito no Quadrilátero Ferrífero, Minas Gerais, Brasil. MSc Thesis. (Universidade Federal de Viçosa, 2013).Vincent, R. C. & Meguro, M. Influence of soil properties on the abundance of plant species in ferruginous rocky soils vegetation, southeastern Brazil. Braz. J. Bot. 31, 377–388 (2008).Article 

    Google Scholar 
    Porembski, S. Tropical inselbergs: Habitat types, adaptive strategies and diversity patterns. Rev. Bras. de Bot. 30, 579–586 (2007).Article 

    Google Scholar 
    De Paula, L. F. A., Forzza, R. C., Neri, A. V., Bueno, M. L. & Porembski, S. Sugar Loaf Land in south-eastern Brazil: A center of diversity for mat-forming bromeliads on inselbergs. Bot. J. Linn. Soc. 181, 459–476 (2016).Article 

    Google Scholar 
    Rezende, M. G., Elias, R. C. L., Salimena, F. R. G. & Neto, L. M. Flora vascular da Serra da Pedra Branca, Caldas, Minas Gerais e relações florísticas com áreas de altitude da Região Sudeste do Brasil. Biota Neotrop. 13, 201–224 (2013).Article 

    Google Scholar 
    Sarthou, C., Villiers, J. F. & Ponge, J. F. Shrub vegetation on tropical granitic inselbergs in French Guiana. J. Veg. Sci. 14, 645–652 (2003).Article 

    Google Scholar 
    Tinti, B. V. et al. Plant diversity on granite/gneiss rock outcrop at Pedra do Pato, Serra do Brigadeiro State Park, Brazil. Check List 11, 1780 (2015).Article 

    Google Scholar 
    Barbara, T., Martinelli, G., Fay, M. F., Mayo, S. J. & Lexer, C. Population differentiation and species cohesion in two closely related plants adapted to neotropical high-altitude “inselbergs”, Alcantarea imperialis and Alcantarea geniculata (Bromeliaceae). Mol. Ecol. 16, 1981–1992 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Boisselier-Dubayle, M. C., Leblois, R., Samadi, S., Lambourdière, J. & Sarthou, C. Genetic structure of the xerophilous bromeliad Pitcairnia geyskesii on inselbergs in French Guiana—A test of the forest refuge hypothesis. Ecography 33, 175–184 (2010).Article 

    Google Scholar 
    Domingues, R. et al. Genetic variability of an endangered Bromeliaceae species (Pitcairnia albiflos) from the Brazilian Atlantic rainforest. Genet. Mol. Res. 10, 2482–2491 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hmeljevski, K. V. et al. Conservation assessment of an extremely restricted bromeliad highlights the need for population-based conservation on granitic inselbergs of the Brazilian Atlantic Forest. Flora Morpho. Distribut. Funct. Ecolo. Plants. 209, 250–259 (2014).Article 

    Google Scholar 
    Palma-Silva, C. et al. Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs. Mol. Ecol. 20, 3185–3201 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gomes, P. & Alves, M. Floristic diversity of two crystalline rocky outcrops in the Brazilian northeast semi-arid region. Rev. Bras. Bot. 33(4), 661–676 (2010).Article 

    Google Scholar 
    Nunes, J. A., Villa, P. M., Neri, A. V., Silva, W. A. & Schaefer, C. E. G. R. Seasonality drives herbaceous community beta diversity in lithologically different rocky outcrops in Brazil. Plant. Ecol. Evol. 153(2), 208–218 (2020).Article 

    Google Scholar 
    Speziale, K. L. & Ezcurra, C. The role of outcrops in the diversity of Patagonian vegetation: Relicts of glacial palaeofloras?. Flora Morphol. Distrib. Funct. Ecol. Plant. 207, 141–149 (2012).
    Google Scholar 
    Speziale, K. L., Ruggiero, A. & Ezcurra, C. Plant species richness–environment relationships across the Subantarctic-Patagonian transition zone. J. Biogeogr. 37, 449–464 (2010).Article 

    Google Scholar 
    Yates, C. J. et al. High species diversity and turnover in granite inselberg floras highlight the need for a conservation strategy protecting many outcrops. Ecol. Evol. 9, 7660–7675 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gaston, K. J. Geographic range limits: Achieving synthesis. Proc. R. Soc. B Biol. Sci. 276, 1395–1406 (2009).Article 

    Google Scholar 
    McGann, T. D. How insular are ecological ‘islands’? An example from the granitic outcrops of the New England Batholith of Australia. Proc. R. Soc. Queensland. 110, 1–13 (2002).
    Google Scholar 
    Parmentier, I., Stévart, T. & Hardy, O. J. The inselberg flora of Atlantic Central Africa. I. Determinants of species assemblages. J. Biogeogr. 32, 685–696 (2005).Article 

    Google Scholar 
    Changwe, K. & Balkwill, K. Floristics of the Dunbar Valley serpentinite site, Songimvelo Game Reserve, South Africa. Bot. J. Linn. Soc. 143, 271–285 (2003).Article 

    Google Scholar 
    Clarke, P. J. Habitat islands in fire-prone vegetation: Do landscape features influence community composition?. J. Biogeogr. 29, 677–684 (2002).Article 

    Google Scholar 
    De Bello, F., Leps, J. & Sebastia, M. T. Variations in species and functional plant diversity along climatic and grazing gradients. Ecography 29(6), 801–810 (2006).Article 

    Google Scholar 
    Porembski, S., Martinelli, G., Ohlemüller, R. & Barthlott, W. Diversity and ecology of saxicolous vegetation mats on inselbergs in the Brazilian Atlantic rainforest. Divers. Distrib. 4, 107–119 (1998).Article 

    Google Scholar 
    Porembski, S., Szarzynski, J., Mund, J. P. & Barthlott, W. Biodiversity and vegetation of small-sized inselbergs in a West African rain forest (Taï, Ivory Coast). J. Biogeogr. 23, 47–55 (1996).Article 

    Google Scholar 
    Rahmanian, S. et al. Effects of livestock grazing on soil, plant functional diversity, and ecological traits vary between regions with different climates in northeastern Iran. Ecol. Evol. 9, 8225–8237 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Speziale, K. L. & Ezcurra, C. Patterns of alien plant invasions in northwestern Patagonia, Argentina. J. Arid Environ. 75, 890–897 (2011).ADS 
    Article 

    Google Scholar 
    Qian, H., Chen, S. H. & Zhang, J. L. Disentangling environmental and spatial effects on phylogenetic structure of angiosperm tree communities in China. Sci. Rep. 7, 5864 (2017).ADS 
    Article 
    CAS 

    Google Scholar 
    Farzam, M. & Ejtehadi, H. Effects of drought and canopy facilitation on plant diversity and abundance in a semiarid mountainous rangeland. J. Plant. Ecol. 10(4), 626–633 (2016).
    Google Scholar 
    Heino, J. & Tolonen, K. T. Ecological drivers of multiple facets of beta diversity in a lentic macroinvertebrate metacommunity. Limnol. Oceanogr. 62, 2431–2444. https://doi.org/10.1002/lno.10577 (2017).ADS 
    Article 

    Google Scholar 
    Miranda, J. D., Armas, C., Padilla, F. M. & Pugnaire, F. I. Climatic change and rainfall patterns: Effects on semi-arid plant communities of the Iberian Southeast. J. Arid. Environ. 75, 1302–1309 (2011).ADS 
    Article 

    Google Scholar 
    Pashirzad, M., Ejtehadi, H., Vaezi, J. & Shefferson, R. P. Multiple processes at different spatial scales determine beta diversity patterns in a mountainous semi-arid rangeland of Khorassan-Kopet Dagh floristic province, NE Iran. Plant. Ecol. 220(9), 829–844 (2019).Article 

    Google Scholar 
    Victorero, L., Robert, K., Robinson, L. F., Taylor, M. L. & Huvenne, V. A. I. Species replacement dominates megabenthos beta diversity in a remote seamount setting. Sci. Rep. 8, 4152 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Deil, U. Rock communities in tropical Arabia. Flora et Vegetation Mundi 9, 175–187 (1991).
    Google Scholar 
    Dimopoulos, P., Sýkora, K. V., Mucina, L. & Georgiadis, T. The high-rank syntaxa of the rock-cliff and scree vegetation of the mainland Greece and Crete. Folia Geobot. 32, 313–334 (1997).Article 

    Google Scholar 
    Hein, P., Kürschner, H. & Parolly, G. Phytosociological studies on high mountain plant communities of the Taurus Mountains (Turkey) 2. Rock communities. Phytocoenologia 28, 465–563 (1998).Article 

    Google Scholar 
    Nowak, A., Nowak, S., Nobis, M. & Nobis, A. Vegetation of rock clefts and ledges in the Pamir Alai Mts, Tajikistan (Middle Asia). Cent. Eur. J. Biol. 9, 444–460 (2014).
    Google Scholar 
    Urbis, A. & Blazyca, B. Rock vascular plant species of the Kraków-Częstochowa, Uplands. Thaiszia J. Bot. 21, 207–214 (2011).
    Google Scholar 
    Wiser, S. K., Peet, R. K. & White, P. S. High-elevation rock outcrop vegetation of the Southern Appalachian Mountains. J. Veg. Sci. 7, 703–722 (1996).Article 

    Google Scholar 
    Cadotte, M. W. Experimental evidence that evolutionarily diverse assemblages result in higher productivity. PNAS 110(22), 8996–9000 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Swenson, G.N. Functional and Phylogenetic Ecology in R (Use R!) Kindle Edition (2014).Cadotte, M. W. & Davies, P. R. Why phylogenies do not always predict ecological differences. Ecol. Monogr. 87(4), 535–551 (2016).Article 

    Google Scholar 
    De Bello, F., LepŠ, J. A. N. & Sebastià, M. T. Predictive value of plant traits to grazing along a climatic gradient in the Mediterranean. J. Appl. Ecol. 42(5), 824–833 (2005).Article 

    Google Scholar 
    Funk, J. et al. Revisiting the Holy Grail: Using plant functional traits to understand ecologica processes. Biol. Rev. 92(2), 1156–1173 (2017).PubMed 
    Article 

    Google Scholar 
    Lavorel, S. & Garnier, É. Predicting changes in community composition and ecosystem functioning from plant traits: Revisiting the Holy Grail. Funct. Ecol. 16(5), 545–556 (2002).Article 

    Google Scholar 
    Violle, C. et al. Let the concept of trait be functional!. Oikos 116, 882–892 (2007).Article 

    Google Scholar 
    Zheng, S., Li, W., Lan, Z., Ren, H. & Wang, K. Functional trait responses to grazing are mediated by soil moisture and plant functional group identity. Sci. Rep. 5, 18163 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gillison, A. N. Plant functional types and traits at the community, ecosystem and world level. In Vegetation Ecology (eds van der Maarel, E. & Franklin, J.) 347–386 (Wiley, 2013).Chapter 

    Google Scholar 
    Loreau, M. Biodiversity and ecosystem functioning: Recent theoretical advances. Oikos 91, 3–17 (2000).Article 

    Google Scholar 
    Akhani, H., Djamali, M., Ghorbanalizadeh, A. & Ramezani, E. Plant biodiversity of Hyrcanian relict forests, N Iran: An overview of the flora, vegetation, paleoecology and conservation. Pak. J. Bot. 42, 231–258 (2010).
    Google Scholar 
    Hamzehee, B. et al. Phytosociological survey of remnant Alnus glutinosa ssp. barbata communities in the lowland Caspian forests of northern Iran. Pytocoenologia. 38, 117–132 (2008).Article 

    Google Scholar 
    Moradi, H. et al. Elevational gradient and vegetation-environmental relationships in the central Hyrcanian forests of northern Iran. Nord. J. Bot. 34, 1–14 (2016).Article 

    Google Scholar 
    Naqinezhad, A., Esmailpoor, A. & Jafari, N. A new record of Pyrola minor (Pyrolaceae) for the flora of Iran as well as a description of its surrounding habitats. Taxon. Biosyst. 22, 71–80 (2015).
    Google Scholar 
    Naqinezhad, A., Zare-Maivan, H. & Gholizadeh, H. A floristic survey of the Hyrcanian forests in Northern Iran, using two lowland-mountain transects. J. For. Res. 26, 187–199 (2015).CAS 
    Article 

    Google Scholar 
    Sagheb-Talebi, K., Sajedi, T. & Pourhashemi, M. Forests of Iran (Springer Sci, 2014).Book 

    Google Scholar 
    Siadati, S. et al. Botanical diversity of Hyrcanian forests; a case study of a transect in the Kheyrud protected lowland mountain forests in northern Iran. Phytotaxa 7, 1–18 (2010).Article 

    Google Scholar 
    Akhani, H. & Ziegler, H. Photosynthetic pathways and habitats of grasses in Golestan National Park (NE Iran), with an emphasis on the C 4-grass dominated rock communities. Phytocoenologia 32, 455–501 (2002).Article 

    Google Scholar 
    Akhani, H., Mahdavi, P., Noroozi, J. & Zarrinpour, V. Vegetation patterns of the Irano-Turanian steppe along a 3,000 m altitudinal gradient in the Alborz Mountains of Northern Iran. Folia Geobot. 48, 229–255 (2013).Article 

    Google Scholar 
    Klein, J. C. The altitudinal vegetation Alborez The Central (Iran) between the Iranian-Turanian and Euro-Siberian regions (French) (Institut Français de Recherche en Iran, 2001).
    Google Scholar 
    Noroozi, J. Case study: High Mountain Regions in Iran 255–260. of Chapter 7 (Endemism in mainland regions-case studies). In Endemism in Vascular plants. Plant. Veg. (ed Hobohm, C.) 9. (Springer, 2014).Noroozi, J., Akhani, H. & Willner, W. Phytosociological and ecological study of the high alpine vegetation of Tuchal Mountains (Central Alborz, Iran). Phytocoenologia 40, 293–321 (2010).Article 

    Google Scholar 
    Do Carmo, F. F. & Jacobi, C. M. Diversity and plant trait-soil relationships among rock outcrops in the Brazilian Atlantic rainforest. Plant Soil. 403, 7–20 (2015).Article 
    CAS 

    Google Scholar 
    Cavender-Bares, J., Kozak, K. H., Fine, P. V. A. & Kembel, S. The merging of community ecology and phylogenetic biology. Ecol Lett. 12, 693–715 (2009).PubMed 
    Article 

    Google Scholar 
    Heydari, M., Poorbabaei, H., Esmailzadeh, O., Salehi, A. & EshaghiRad, J. Indicator plant species in monitoring forest soil conditions using logistic regression model in Zagros Oak (Quercus brantii var. persica) forest ecosystems. Ilam city. J. Plant Res. 27(5), 811–828 (2014).
    Google Scholar 
    Speziale, K. L. & Ezcurra, C. Rock outcrops as potential biodiversity refugia under climate change in North Patagonia. Plant Ecol. Diver. 8, 353–361 (2014).Article 

    Google Scholar 
    Rahmanian, S. et al. Effects of livestock grazing on plant species diversity vary along a climatic gradient in northeastern Iran. Appl. Veg. Sci. 23, 551–561 (2020).Article 

    Google Scholar 
    Huston, M. A. Biological Diversity: The Coexistence of Species in Changing Landscape (Cambridge University, 1994).
    Google Scholar 
    Mason, N. W., Mouillot, D. & Lee, W. G. Functional richness, functional evenness and functional divergence: The primary components of functional diversity. Oikos 111, 112–118 (2005).Article 

    Google Scholar 
    Stubbs, W. J. & Wilson, J. B. Evidence for limiting similarity in a sand dune community. J. Ecol. 92, 557567 (2004).Article 

    Google Scholar 
    Stanisci, A. et al. Functional composition and diversity of leaf traits in subalpine versus alpine vegetation in the Apennines. Ann. Bot. Comp. plants. 12, plaa004 (2020).CAS 

    Google Scholar 
    Chesson, P. et al. Resource pulses, species interactions, and diversity maintenance in arid and semi-arid environments. Oecologia 141, 236–253 (2004).ADS 
    PubMed 
    Article 

    Google Scholar 
    Rosbakh, S. et al. Contrasting effects of extreme drought and snowmelt patterns on mountain plants along an elevation gradient. Front. Plant Sci. 8, 1478 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Korner, C. Alpine Treelines: Functional Ecology of the Global High Elevation tree Limits (Springer Sci. & Business Media, 2012).Book 

    Google Scholar 
    Reich, P. B. et al. Generality of leaf trait relationships: A test across six biomes. Ecology 80, 1955–1969 (1999).Article 

    Google Scholar 
    Westoby, M., Falster, D. S., Moles, A. T., Vesk, P. A. & Wright, I. J. Plant ecological strategies: Some leading dimensions of variation between species. Ann. Rev. Ecol. Syst. 33, 125–159 (2002).Article 

    Google Scholar 
    Hautier, Y., Niklaus, P. A. & Hector, A. Competition for light causes plant biodiversity loss after eutrophication. Science 324, 636–638 (2009).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    De Bello, F. D. et al. Hierarchical effects of environmental filters on the functional structure of plant communities: A case study in the French Alps. Ecography 36, 393–402 (2013).Article 

    Google Scholar 
    Korner, C., Neumayer, M., Menendez-Riedl, S. P. & Smeets-Scheel, A. Functional morphology of mountain plants. Flora 182, 353–383 (1989).Article 

    Google Scholar 
    Rosbakh, S., Römermann, C. & Poschlod, P. Specific leaf area correlates with temperature new evidence of trait variation at the population, species and community levels. Alp. Bot. 125, 79–86 (2015).Article 

    Google Scholar 
    Ordonez, J. C. et al. Global study of relationships between leaf traits, climate and soil measures of nutrient fertility. Glob. Ecol. Biogeogr. 18, 137–149 (2009).Article 

    Google Scholar 
    Li, W. et al. Community-weighted mean traits but not functional diversity determine the changes in soil properties during wetland drying on the Tibetan Plateau. Solid Earth. 8, 137–147 (2017).ADS 
    Article 

    Google Scholar 
    Bardgett, R. D., Mommer, L. & De Vries, F. T. Going underground: Root traits as drivers of ecosystem processes. Trends Ecol. Evol. 29, 692–699 (2014).PubMed 
    Article 

    Google Scholar 
    Lane, D. R., Coffin, D. P. & Lauenroth, W. K. Effects of soil texture and precipitation on above-ground net primary productivity and vegetation structure across the Central Grassland region of the United States. J. Veg. Sci. 9, 239–250 (1998).Article 

    Google Scholar 
    Noy-Meir, I. Multivariate analysis of the semi-arid vegetation of southern Australia. II. Vegetation catenae an environmental gradients. Aust. J. Bot. 22, 40–115 (1973).
    Google Scholar 
    Moura, M. R., Villalobos, F., Costa, G. C. & Garcia, P. C. A. Disentangling the role of climate, topography and vegetation in species richness gradients. PLoS ONE 11(3), 0152468 (2016).Article 
    CAS 

    Google Scholar 
    Neri, A. V. et al. Soil and altitude drives diversity and functioning of Brazilian Páramos (Campo de Altitude). J. plant. Ecol. 10(5), 771–779 (2016).
    Google Scholar 
    Benites, V. M., Schaefer, C. E. G. R., Simas, F. N. B., Santos, H. G. & Mendonca, B. A. F. Soils associated to rock outcrops in the Brazilian mountain ranges Mantiqueira and Espinhaço. Rev. Bras. Bot. 30, 569–577 (2007).Article 

    Google Scholar 
    Flynn, D. F. B. et al. Loss of functional diversity under land use intensification across multiple taxa. Ecol. Lett. 12, 22–33 (2009).PubMed 
    Article 

    Google Scholar 
    Zuo, X. A. et al. Testing associations of plant functional diversity with along a restoration gradient of sandy grassland. Front. Plant. Sci. 7, 1–11 (2016).ADS 
    Article 

    Google Scholar 
    Myers-Smith, I. H. et al. Shrub expansion in tundra ecosystems: Dynamics, impacts and research priorities. Environ. Res. Lett. 6, 045509 (2011).ADS 
    Article 

    Google Scholar 
    Vankoughnett, M. R. & Grogan, P. Nitrogen isotope tracer acquisition in low and tall birch tundra plant communities: A 2-year test of the snow–shrub hypothesis. Biogeochemistry 118, 291–306 (2014).CAS 
    Article 

    Google Scholar 
    Pescador, D. S., de Bello, F., Valladares, F. & Escudero, A. Plant trait variation along an altitudinal gradient in Mediterranean high mountain grasslands: Controlling the species turnover effect. PLoS ONE 10, e0118876 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Pescador, D. S., Sierra-Almeida, A., Torres, P. J. & Escudero, A. Summer freezing resistance: A critical filter for plant community assemblies in Mediterranean high mountains. Front. Plant. Sci. 7, 194 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Heydarnejad, S. & Ranjbar, A. Investigation of the effect of salinity stress on growth characteristic and ion accumulation in plants. J. Desert Ecos. Eng. 3(4), 1–10 (2013).
    Google Scholar 
    Perez-Harguindeguy, N. et al. New handbook for standardized measurement of plant functional traits worldwide. Aust. J. Bot. 61, 167–234 (2013).Article 

    Google Scholar 
    Cornelissen, J. H. C. et al. A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Aust. J. Bot. 51, 335–380 (2003).Article 

    Google Scholar 
    Raunkiaer, C. The Life Forms of Plants and Statistical Plant Geography (Oxford University Press, 1934).
    Google Scholar 
    Gee, G. W. & Bauder, J. W. Particle size analysis. In Methods of Soil Analysis. Part 1, 2nd ed. (ed Klute, A.) Agronomy Monographs, Vol. 9, 383–409 (Am. Soc. Agr., 1986).Bremner, J. M. In Nitrogen-Total Methods of Soil Analysis. (eds Sparks, D. L.) Soil Sci Soc Am J. 1085–1122 (Am Soc Agr. Inc, 1996).Walkley, A. & Black, I. A. An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Sci. 37, 29–38 (1934).ADS 
    CAS 
    Article 

    Google Scholar 
    Nelson, D. W. & Sommers, L. Total carbon, organic carbon, and organic matter 1. Methods of soil analysis. Part 2. Chemical and microbi‐ological properties, (methodsofsoilan2), 539–579 (1982).Miller, R. H. & Keeney, D. R. Methods of soil analysis, 2nd ed. In Part 2. Chemical and Microbiological Properties (eds Page, A. L. et al.) 1–129 (ASA, SSSA, 1982).
    Google Scholar 
    Food and Agriculture Organization-FAO. Management of gypsiferous soils. Soil Bulletin, 62, (FAO, 1990).Chao, A. et al. Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol. Monogr. 84, 45–67 (2014).Article 

    Google Scholar 
    Shipley, B., Vile, D. & Garnier, É. from plant traits to plant communities: A statistica mechanistic approach to biodiversity. Science 314(5800), 812–814 (2006).ADS 
    MathSciNet 
    CAS 
    PubMed 
    MATH 
    Article 

    Google Scholar 
    Zhu, J., Jiang, L. & Zhang, Y. Relationships between functional diversity and aboveground biomass production in the Northern Tibetan alpine grasslands. Sci. Rep. 6, 34105 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Laliberte, E. & Legendre, P. A distance-based framework for measuring functional diversity from multiple traits. Ecology 91(1), 299–305 (2010).PubMed 
    Article 

    Google Scholar 
    Wheeler, D. & Tiefelsdorf, M. Multicollinearity and correlation among local regression coefficients in geographically weighted regression. J. Geogr. Syst. 7, 161–187 (2005).Article 

    Google Scholar 
    Fox, J. & Weisberg, S. A review of: an R companion to applied regression, second edition. J. Biopharm. Stat. 22, 418–419 (2011).
    Google Scholar 
    Brien, R. M. A caution regarding rules of thumb for variance inflation factors. Qual. Quant. 41, 673–690 (2007).Article 

    Google Scholar 
    Dray, S., Legendre, P. & Blanchet, F. G. packfor: forward selection with permutation (Canoco p. 46). (2011) http://R-Forge.R-project.org/projects/sedar (Accessed 7 Nov 2016).Blanchet, F. G., Legendre, P. & Borcard, D. Forward selection of explanatory variables. Ecology 89, 2623–2632 (2008).PubMed 
    Article 

    Google Scholar 
    Oksanen, J. et al. vegan: Community Ecology Package (2017).Wickham, H. et al. Ggplot2: Elegant Graphics for Data Analysis 2nd edn. (Springer International Publishing, 2016).MATH 
    Book 

    Google Scholar  More

  • in

    A bottom-up view of antimicrobial resistance transmission in developing countries

    Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).CAS 
    Article 

    Google Scholar 
    Nelson, R. E. et al. National estimates of healthcare costs associated with multidrug-resistant bacterial infections among hospitalized patients in the United States. Clin. Infect. Dis. 72, S17–S26 (2021).PubMed 
    Article 

    Google Scholar 
    Ludden, C. et al. One Health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock. mBio 10, e02693-18 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gouliouris, T. et al. Genomic surveillance of Enterococcus faecium reveals limited sharing of strains and resistance genes between livestock and humans in the United Kingdom. mBio 9, e01780-18 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Labar, A. S. et al. Regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. PLoS ONE 7, e38142 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lamikanra, A. et al. Rapid evolution of fluoroquinolone-resistant Escherichia coli in Nigeria is temporally associated with fluoroquinolone use. BMC Infect. Dis. 11, 312 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kunhikannan, S. et al. Environmental hotspots for antibiotic resistance genes. MicrobiologyOpen 10, e1197 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Sulis, G., Sayood, S. & Gandra, S. Antimicrobial resistance in low- and middle-income countries: current status and future directions. Expert Rev. Anti Infect. Ther. 20, 147–160 (2022).CAS 
    PubMed 
    Article 

    Google Scholar 
    Okeke, I. N. & Nwoko, E. in Urban Crisis and Management in Africa: A Festschrift (eds Albert, I. O. & Mabogunje, A.) 125–148 (Pan-African Univ. Press, 2019).Doron, A. & Jeffrey, R. Waste of a Nation: Garbage and Growth in India (Harvard Univ. Press, 2018).Nadimpalli, M. L. et al. Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission. Nat. Microbiol. 5, 787–795 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Okeke, I. & Lamikanra, A. A study of the effect of the urban/rural divide on the incidence of antibiotic resistance in Escherichia coli. Biomed. Lett. 55, 91–97 (1997).
    Google Scholar 
    Aijuka, M., Charimba, G., Hugo, C. J. & Buys, E. M. Characterization of bacterial pathogens in rural and urban irrigation water. J. Water Health 13, 103–117 (2015).PubMed 
    Article 

    Google Scholar 
    Hendriksen, R. S. et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat. Commun. 10, 1124 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Mahmud, Z. H. et al. Presence of virulence factors and antibiotic resistance among Escherichia coli strains isolated from human pit sludge. J. Infect. Dev. Ctries 13, 195–203 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Beukes, L. S., King, T. L. B. & Schmidt, S. Assessment of pit latrines in a peri-urban community in KwaZulu-Natal (South Africa) as a source of antibiotic resistant E. coli strains. Int. J. Hyg. Environ. Health 220, 1279–1284 (2017).PubMed 
    Article 

    Google Scholar 
    Zhang, H., Gao, Y. & Chang, W. Comparison of extended-spectrum β-lactamase-producing Escherichia coli isolates from drinking well water and pit latrine wastewater in a rural area of China. Biomed. Res. Int. 2016, 4343564 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    Nji, E. et al. High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings. Sci. Rep. 11, 3372 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ramblière, L., Guillemot, D., Delarocque-Astagneau, E. & Huynh, B. T. Impact of mass and systematic antibiotic administration on antibiotic resistance in low- and middle-income countries? A systematic review. Int. J. Antimicrob. Agents 58, 106396 (2021).PubMed 
    Article 
    CAS 

    Google Scholar 
    Hlashwayo, D. F. et al. A systematic review and meta-analysis reveal that Campylobacter spp. and antibiotic resistance are widespread in humans in sub-Saharan Africa. PLoS ONE 16, e0245951 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Van Boeckel, T. P. et al. Global trends in antimicrobial resistance in animals in low- and middle-income countries. Science 365, eaaw1944 (2019).PubMed 
    Article 
    CAS 

    Google Scholar 
    Argudín, M. A. et al. Genotypes, exotoxin gene content, and antimicrobial resistance of Staphylococcus aureus strains recovered from foods and food handlers. Appl. Environ. Microbiol. 78, 2930–2935 (2012).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Sivagami, K., Vignesh, V. J., Srinivasan, R., Divyapriya, G. & Nambi, I. M. Antibiotic usage, residues and resistance genes from food animals to human and environment: an Indian scenario. J. Environ. Chem. Eng. 8, 102221 (2020).CAS 
    Article 

    Google Scholar 
    Wall, B. A. et al. Drivers, Dynamics and Epidemiology of Antimicrobial Resistance in Animal Production (FAO, 2016).Hassani, A. & Khan, G. Human–animal interaction and the emergence of SARS-CoV-2. JMIR Public Health Surveill. 6, e22117 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Madoshi, B. P. et al. Characterisation of commensal Escherichia coli isolated from apparently healthy cattle and their attendants in Tanzania. PLoS ONE 11, e0168160 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Guetiya Wadoum, R. E. et al. Abusive use of antibiotics in poultry farming in Cameroon and the public health implications. Br. Poult. Sci. 57, 483–493 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rousham, E. K., Unicomb, L. & Islam, M. A. Human, animal and environmental contributors to antibiotic resistance in low-resource settings: integrating behavioural, epidemiological and One Health approaches. Proc. Biol. Sci. 285, 20180332 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    Jibril, A. H., Okeke, I. N., Dalsgaard, A. & Olsen, J. E. Association between antimicrobial usage and resistance in Salmonella from poultry farms in Nigeria. BMC Vet. Res. 17, 234 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Tiseo, K., Huber, L., Gilbert, M., Robinson, T. P. & Van Boeckel, T. P. Global trends in antimicrobial use in food animals from 2017 to 2030. Antibiotics 9, 918 (2020).PubMed Central 
    Article 

    Google Scholar 
    Schar, D., Sommanustweechai, A., Laxminarayan, R. & Tangcharoensathien, V. Surveillance of antimicrobial consumption in animal production sectors of low- and middle-income countries: optimizing use and addressing antimicrobial resistance. PLoS Med. 15, e1002521 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Liu, Y. Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161–168 (2016).PubMed 
    Article 
    CAS 

    Google Scholar 
    Sun, J., Zhang, H., Liu, Y. H. & Feng, Y. Towards understanding MCR-like colistin resistance. Trends Microbiol. 26, 794–808 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wang, C. et al. Identification of novel mobile colistin resistance gene mcr-10. Emerg. Microbes Infect. 9, 508–516 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    He, T. et al. Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nat. Microbiol. 4, 1450–1456 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sun, C. et al. Plasmid-mediated tigecycline-resistant gene tet(X4) in Escherichia coli from food-producing animals, China, 2008–2018. Emerg. Microbes Infect. 8, 1524–1527 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Lowder, B. V. et al. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc. Natl Acad. Sci. USA 106, 19545–19550 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bachiri, T. et al. First report of the plasmid-mediated colistin resistance gene mcr-1 in Escherichia coli ST405 isolated from wildlife in Bejaia, Algeria. Microb. Drug Resist. 24, 890–895 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Roberts, M. C. et al. The human clone ST22 SCCmec IV methicillin-resistant Staphylococcus aureus isolated from swine herds and wild primates in Nepal: is man the common source? FEMS Microbiol. Ecol. 94, fiy052 (2018).PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Aliyu, A. B., Saleha, A. A., Jalila, A. & Zunita, Z. Risk factors and spatial distribution of extended spectrum β-lactamase-producing-Escherichia coli at retail poultry meat markets in Malaysia: a cross-sectional study. BMC Public Health 16, 699 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Alam, M. U. et al. Human exposure to antimicrobial resistance from poultry production: assessing hygiene and waste-disposal practices in Bangladesh. Int. J. Hyg. Environ. Health 222, 1068–1076 (2019).PubMed 
    Article 

    Google Scholar 
    Donado-Godoy, P. et al. Prevalence, risk factors, and antimicrobial resistance profiles of Salmonella from commercial broiler farms in two important poultry-producing regions of Colombia. J. Food Prot. 75, 874–883 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Moser, K. A. et al. The role of mobile genetic elements in the spread of antimicrobial-resistant Escherichia coli from chickens to humans in small-scale production poultry operations in rural Ecuador. Am. J. Epidemiol. 187, 558–567 (2018).PubMed 
    Article 

    Google Scholar 
    Songe, M. M., Hang’ombe, B. M., Knight-Jones, T. J. D. & Grace, D. Antimicrobial resistant enteropathogenic Escherichia coli and Salmonella spp. in houseflies infesting fish in food markets in Zambia. Int. J. Environ. Res. Public Health 14, (2017).Alves, T. S., Lara, G. H. B., Maluta, R. P., Ribeiro, M. G. & Leite, D. S. Carrier flies of multidrug-resistant Escherichia coli as potential dissemination agent in dairy farm environment. Sci. Total Environ. 633, 1345–1351 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Allen, H. K. et al. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hasan, B. et al. Antimicrobial drug–resistant Escherichia coli in wild birds and free-range poultry, Bangladesh. Emerg. Infect. Dis. 18, 2055–2058 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Blanco, G. Supplementary feeding as a source of multiresistant Salmonella in endangered Egyptian vultures. Transbound. Emerg. Dis. 65, 806–816 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Matias, C. A. R. et al. Frequency of zoonotic bacteria among illegally traded wild birds in Rio de Janeiro. Braz. J. Microbiol. 47, 882–888 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brealey, J. C., Leitão, H. G., Hofstede, T., Kalthoff, D. C. & Guschanski, K. The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans. Curr. Biol. 31, 4650–4658.e6 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Liu, C. M. et al. Escherichia coli ST131-H22 as a foodborne uropathogen. mBio 9, e00470-18 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Randad, P. R. et al. Transmission of antimicrobial-resistant Staphylococcus aureus clonal complex 9 between pigs and humans, United States. Emerg. Infect. Dis. 27, 740–748 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jørgensen, S. L. et al. Diversity and population overlap between avian and human Escherichia coli belonging to sequence type 95. mSphere 4, e00333-18 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ludden, C. et al. A One Health study of the genetic relatedness of Klebsiella pneumoniae and their mobile elements in the east of England. Clin. Infect. Dis. 70, 219–226 (2020).PubMed 
    Article 

    Google Scholar 
    Thorpe, H. et al. One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment. Preprint at bioRxiv https://doi.org/10.1101/2021.08.05.455249 (2021).Ingham, A. C. et al. Dynamics of the human nasal microbiota and Staphylococcus aureus cc398 carriage in pig truck drivers across one workweek. Appl. Environ. Microbiol. 87, e0122521 (2021).PubMed 
    Article 

    Google Scholar 
    Hickman, R. A. et al. Exploring the antibiotic resistance burden in livestock, livestock handlers and their non-livestock handling contacts: a One Health perspective. Front. Microbiol. 12, 65161 (2021).Article 

    Google Scholar 
    Okeke, I. N. African biomedical scientists and the promises of ‘big science’. Can J. Afr. Stud. https://doi.org/10.1080/00083968.2016.1266677 (2017).Nadimpalli, M. L. & Pickering, A. J. A call for global monitoring of WASH in wet markets. Lancet Planet. Health 4, e439–e440 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Grace, D. & Little, P. Informal trade in livestock and livestock products. Rev. Sci. Tech. 39, 183–192 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Caudell, M. A. et al. Towards a bottom-up understanding of antimicrobial use and resistance on the farm: a knowledge, attitudes, and practices survey across livestock systems in five African countries. PLoS ONE 15, e0220274 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Adekanye, U. O. et al. Knowledge, attitudes and practices of veterinarians towards antimicrobial resistance and stewardship in Nigeria. Antibiotics 9, 453 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Mangesho, P. E. et al. ‘We are doctors’: drivers of animal health practices among Maasai pastoralists and implications for antimicrobial use and antimicrobial resistance. Prev. Vet. Med. 188, 105266 (2021).PubMed 
    Article 

    Google Scholar 
    Essack, S. Water, sanitation and hygiene in national action plans for antimicrobial resistance. Bull. World Health Organ. 99, 606–608 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aarestrup, F. M. et al. Effect of abolishment of the use of antimicrobial agents for growth promotion on occurrence of antimicrobial resistance in fecal enterococci from food animals in Denmark. Antimicrob. Agents Chemother. 45, 2054–2059 (2001).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Funtowicz, S. & Ravetz, J. in Handbook of Transdisciplinary Research (eds Hadorn, G. H. et al.) 361–368 (Springer, 2008); https://doi.org/10.1007/978-1-4020-6699-3Theuretzbacher, U., Outterson, K., Engel, A. & Karlén, A. The global preclinical antibacterial pipeline. Nat. Rev. Microbiol. 185, 275–285 (2019).
    Google Scholar 
    Lacotte, Y., Årdal, C. & Ploy, M. C. Infection prevention and control research priorities: what do we need to combat healthcare-associated infections and antimicrobial resistance? Results of a narrative literature review and survey analysis. Antimicrob. Resist. Infect. Control 9, 142 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kennedy, D. A. & Read, A. F. Why the evolution of vaccine resistance is less of a concern than the evolution of drug resistance. Proc. Natl Acad. Sci. USA 115, 12878 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Vekemans, J. et al. Leveraging vaccines to reduce antibiotic use and prevent antimicrobial resistance: a World Health Organization action framework. Clin. Infect. Dis. 73, E1011–E1017 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Micoli, F., Bagnoli, F., Rappuoli, R. & Serruto, D. The role of vaccines in combatting antimicrobial resistance. Nat. Rev. Microbiol. 195, 287–302 (2021).Article 
    CAS 

    Google Scholar 
    Massella, E. et al. Antimicrobial resistance profile and ExPEC virulence potential in commensal Escherichia coli of multiple sources. Antibiotics 10, 351 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Huttner, A. et al. Safety, immunogenicity, and preliminary clinical efficacy of a vaccine against extraintestinal pathogenic Escherichia coli in women with a history of recurrent urinary tract infection: a randomised, single-blind, placebo-controlled phase 1b trial. Lancet Infect. Dis. 17, 528–537 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Frenck, R. W. et al. Safety and immunogenicity of a vaccine for extra-intestinal pathogenic Escherichia coli (ESTELLA): a phase 2 randomised controlled trial. Lancet Infect. Dis. 19, 631–640 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Patel, R. & Fang, F. C. Diagnostic stewardship: opportunity for a laboratory-infectious diseases partnership. Clin. Infect. Dis. 67, 799–801 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Okeke, I. N. Divining Without Seeds: The Case for Strengthening Laboratory Medicine in Africa (Cornell Univ. Press, 2011).Loosli, K., Davis, A., Muwonge, A. & Lembo, T. Addressing antimicrobial resistance by improving access and quality of care—a review of the literature from East Africa. PLoS Negl. Trop. Dis. 15, e0009529 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chokshi, A., Sifri, Z., Cennimo, D. & Horng, H. Global contributors to antibiotic resistance. J. Glob. Infect. Dis. 11, 36–42 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Adedapo, A. D. & Akunne, O. O. Patterns of antimicrobials prescribed to patients admitted to a tertiary care hospital: a prescription quality audit. Cureus 13, e15896 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    Kumarasamy, K. K. et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect. Dis. 10, 597–602 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Davenport, M. et al. New and developing diagnostic technologies for urinary tract infections. Nat. Rev. Urol. 14, 298–310 (2017).Article 

    Google Scholar 
    van Dongen, J. E. et al. Point-of-care CRISPR/Cas nucleic acid detection: recent advances, challenges and opportunities. Biosens. Bioelectron. 166, 112445 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Nielsen, T. B. et al. Monoclonal antibody therapy against Acinetobacter baumannii. Infect. Immun. 89, e0016221 (2021).PubMed 
    Article 

    Google Scholar 
    Dwivedi, P., Narvi, S. S. & Tewari, R. P. Application of polymer nanocomposites in the nanomedicine landscape: envisaging strategies to combat implant associated infections. J. Appl. Biomater. Funct. Mater. 11, 129–142 (2013).
    Google Scholar 
    Song, M., Wu, D., Hu, Y., Luo, H. & Li, G. Characterization of an Enterococcus faecalis bacteriophage vB_EfaM_LG1 and its synergistic effect with antibiotic. Front. Cell. Infect. Microbiol. 11, 636 (2021).
    Google Scholar 
    Dhama, K. et al. Growth promoters and novel feed additives improving poultry production and health, bioactive principles and beneficial applications: the trends and advances—a review. Int. J. Pharmacol. 10, 129–159 (2014).CAS 
    Article 

    Google Scholar 
    Vieco-Saiz, N. et al. Benefits and inputs from lactic acid bacteria and their bacteriocins as alternatives to antibiotic growth promoters during food-animal production. Front. Microbiol. 10, 57 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ng, W. K. & Koh, C. B. The utilization and mode of action of organic acids in the feeds of cultured aquatic animals. Rev. Aquac. 9, 342–368 (2017).Article 

    Google Scholar 
    Mattioli, G. A. et al. Effects of parenteral supplementation with minerals and vitamins on oxidative stress and humoral immune response of weaning calves. Animals 10, 1298 (2020).PubMed Central 
    Article 

    Google Scholar 
    Mwangi, S., Timmons, J., Fitz-Coy, S. & Parveen, S. Characterization of Clostridium perfringens recovered from broiler chicken affected by necrotic enteritis. Poult. Sci. 98, 128–135 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Prendergast, A. J. et al. Putting the ‘A’ into WaSH: a call for integrated management of water, animals, sanitation, and hygiene. Lancet Planet. Health 3, e336–e337 (2019).PubMed 
    Article 

    Google Scholar 
    Martinelli, M. et al. Probiotics’ efficacy in paediatric diseases: which is the evidence? A critical review on behalf of the Italian Society of Pediatrics. Ital. J. Pediatr. 46, 104 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rasko, D. A. & Sperandio, V. Anti-virulence strategies to combat bacteria-mediated disease. Nat. Rev. Drug Discov. 9, 117–128 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rodrigues, M., McBride, S. W., Hullahalli, K., Palmer, K. L. & Duerkop, B. A. Conjugative delivery of CRISPR–Cas9 for the selective depletion of antibiotic-resistant enterococci. Antimicrob. Agents Chemother. 63, e01454-19 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Casu, B., Arya, T., Bessette, B. & Baron, C. Fragment-based screening identifies novel targets for inhibitors of conjugative transfer of antimicrobial resistance by plasmid pKM101. Sci. Rep. 7, 14907 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Denyer Willis, L. & Chandler, C. Quick fix for care, productivity, hygiene and inequality: reframing the entrenched problem of antibiotic overuse. BMJ Glob. Health 4, e001590 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wilkinson, A., Ebata, A. & Macgregor, H. Interventions to reduce antibiotic prescribing in LMICs: a scoping review of evidence from human and animal health systems. Antibiotics 8, 2 (2018).Torres, N. F., Chibi, B., Middleton, L. E., Solomon, V. P. & Mashamba-Thompson, T. P. Evidence of factors influencing self-medication with antibiotics in low and middle-income countries: a systematic scoping review. Public Health 168, 92–101 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Potgieter, N., Banda, N. T., Becker, P. J. & Traore-Hoffman, A. N. WASH infrastructure and practices in primary health care clinics in the rural Vhembe District municipality in South Africa. BMC Fam. Pract. 22, 8 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Humphreys, G. Reinventing the toilet for 2.5 billion in need. Bull. World Health Organ. 92, 470–471 (2014).PubMed 
    Article 

    Google Scholar 
    Yam, P., Fales, D., Jemison, J., Gillum, M. & Bernstein, M. Implementation of an antimicrobial stewardship program in a rural hospital. Am. J. Health Syst. Pharm. 69, 1142–1148 (2012).PubMed 
    Article 

    Google Scholar 
    Sartelli, M. et al. Antibiotic use in low and middle-income countries and the challenges of antimicrobial resistance in surgery. Antibiotics 9, 497 (2020).PubMed Central 
    Article 

    Google Scholar 
    Büdel, T. et al. On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat. J. Antimicrob. Chemother. 75, 2432–2441 (2020).PubMed 
    Article 
    CAS 

    Google Scholar 
    Finch, M. J., Morris, J. G., Kaviti, J., Kagwanja, W. & Levine, M. M. Epidemiology of antimicrobial resistant cholera in Kenya and East Africa. Am. J. Trop. Med. Hyg. 39, 484–490 (1988).CAS 
    PubMed 
    Article 

    Google Scholar 
    Mutreja, A. et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477, 462–465 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Weill, F. X. et al. Genomic history of the seventh pandemic of cholera in Africa. Science 358, 785–789 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Opintan, J. A., Newman, M. J., Nsiah-Poodoh, O. A. & Okeke, I. N. Vibrio cholerae O1 from Accra, Ghana carrying a class 2 integron and the SXT element. J. Antimicrob. Chemother. 62, 929–933 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Garbern, S. C. et al. Clinical and socio-environmental determinants of multidrug-resistant Vibrio cholerae 01 in older children and adults in Bangladesh. Int. J. Infect. Dis. 105, 436–441 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Mintz, E. D. & Guerrant, R. L. A lion in our village—the unconscionable tragedy of cholera in Africa. N. Engl. J. Med. https://doi.org/10.1056/NEJMp0810559 (2009).Gibani, M. M. et al. The impact of vaccination and prior exposure on stool shedding of Salmonella typhi and Salmonella paratyphi in 6 controlled human infection studies. Clin. Infect. Dis. 68, 1265–1273 (2019).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    California wildfire spread derived using VIIRS satellite observations and an object-based tracking system

    OverviewIn this study, we used VIIRS active fire detections to track the dynamic evolution of all fires in California from 2012 to 2020 (Fig. 1). We developed an approach that has the following steps. First, after reading the satellite fire pixel data at each 12-hour time step, the new fire pixels are aggregated into multiple clusters using the fire pixel locations and an automatic clustering algorithm. These clusters are then spatially compared to existing fire objects. If a cluster is not close to any existing active fire object, we use all fire pixels within the cluster to form a new fire object. If a cluster is located near an existing fire object which is still active, we view the cluster as an extension of the existing fire. In this case, we append all pixels within the cluster to the corresponding existing fire object, allowing the existing object to grow. When a fire expands and gets close enough (within a pre-defined distance threshold) to an existing active fire object, we merge the two objects. For each time step (12 hours in this case for the two overpasses), we derive or update a suite of attributes and status indicators associated with each fire event, including pixel-level attributes of fire and surface properties, vector geometries related to the fire shape, and meta-attributes characterizing the entire fire object.Data inputSatellite remote sensing instruments provide active fire detections with accurate geographical location and broad spatial coverage. The primary data for this fire tracking system are active fire locations and the fire radiative power (FRP) recorded by the VIIRS instrument aboard the Suomi National Polar-orbiting Partnership (Suomi-NPP) satellite24. VIIRS observes Earth’s surface twice each day in low and mid latitude regions, with local overpass times of approximately 1:30 am and 1:30 pm. Compared to its predecessor, the MODIS sensors on the Terra and Aqua satellites, VIIRS has a higher spatial resolution and can detect smaller and cooler fires24. Also, the VIIRS instrument provides a more consistent pixel area across the image swath25, resulting in more accurate estimates of active fire location. Therefore, compared with MODIS, the VIIRS active fire products can be used to map fire event progression with higher accuracy21. Two streams of VIIRS active fire data are operationally produced using a contextual fire detection algorithm24, drawing upon VIIRS moderate resolution band (M-band) and imaging band (I-band) reflectance and radiance data layers. In this fire tracking system, we used the Suomi-NPP VIIRS I-band fire location data product (VNP14IMGML, Collection 1 Version 4) that contains the centre location, FRP, scan angle, and other attribute fields associated with each pixel. The I-band fire detection product has a 375-m spatial resolution at nadir (the sub-satellite point) and an average resolution across the full swath of about 470 m. Theoretical estimates of fire detection efficiency for the VIIRS sensor indicate that during the day, VIIRS can detect 700 K fires with 50% probability that have a size of about 200 m2 (a 15 m × 15 m fire area)24. During night, the detection efficiency increases, and VIIRS can detect 700 K fires as small as 40 m2. From a fire spread tracking perspective, these detection efficiencies imply that in many instances, the area of a fire pixel that is covered with flaming fire combustion is several orders of magnitude smaller than the overall pixel size. The VNP14IMGML data, available from 2012 onwards, were downloaded from the University of Maryland VIIRS Active Fire website (https://viirsfire.geog.umd.edu/).Land cover data are an additional input in the system required to classify different fire types and determine the spatial connectivity threshold. Here we use the U.S. National Land Cover Database (NLCD 2016)26 that is available from the Multi-Resolution Land Characteristics (MRLC) Consortium website (https://www.mrlc.gov/national-land-cover-database-nlcd-2016). We aggregated the original 30-m data to match the spatial resolution of VIIRS active fire data, and merged the original 16 classes into several groups: ‘Water’, ‘Urban’, ‘Barren’, ‘Forest’, ‘Shrub’, ‘Grassland’, and ‘Agriculture’. We used the 1000-hour dead fuel moisture from the high-resolution (4 km) gridMET product27 for the purpose of separating wildfires and management fires. This gridMET dataset was computed from 7–day average conditions composed of day length, hours of rain, and daily temperature and humidity ranges. Regularly updated gridMET data are available from the Climatology Lab website (http://www.climatologylab.org/gridmet.html).Other ancillary and validation datasets used in this study included a shapefile of California borders and fire perimeters from the California Forestry and Fire Protection’s Fire and Resource Assessment Program (FRAP) dataset (https://frap.fire.ca.gov/mapping/maps/).Fire object hierarchyFire detections from VIIRS are dynamically tracked within the framework of a three-level object hierarchy (Fig. 1). The lowest level is the fire pixel object, which includes the geographical location (latitude and longitude), the FRP value, and the origin (first assigned fire object id). The second level is the fire object, which includes all attributes associated with each individual fire event at a particular time step (Table 2). Each fire object includes one or more fire pixel objects, a unique identification number (id), and a set of attributes associated with the whole fire. Two types of fire attributes are derived and recorded for each fire object. The first type encompasses temporal (e.g., ignition time, duration) and spatial (e.g., centroid, ignition location) characteristics of the object as well as general properties (e.g., size, type, active status). The second type is the geometric information related to the fire object, including the fire perimeter, the active fire front line, and the newly detected fire pixel locations (stored as vectors). All fire objects in the State of California are combined to form an allfires object, to characterize the whole-region fire situation at a specific time step. The allfires object comprises a list of fire objects, and also contains meta information representing the statistics of all fires and the records describing fire evolution. A full list of the attributes associated with the pixel object, the fire object, and the allfires object is presented in Table 2.Table 2 List of main attributes associated with pixel, fire and allfires objects.Full size tableFire event trackingThe fire records (locations and FRPs) from the monthly VIIRS active fire location products (VNP14IMGML) are read into the system at each half-daily time step (roughly 1:30 am and 1:30 pm local time). We apply spatial and temporal filters to the data to extract active fire pixels recorded in California during each 12-hour time interval. We also apply quality flag filters (thermal anomaly type of ‘0: presumed vegetation fire’ in VNP14IMGML)) to ensure the use of only pixels likely associated with vegetation fires. The fire location and FRP values are used to create fire pixel objects. To speed up the calculation, the newly detected active fire pixels after filtering are first aggregated to specific clusters using the distances between them and an automatic clustering algorithm. In this initial aggregation algorithm, a ball tree28 is created to partition all newly detected active fire pixels into a nested set of hyperspheres in a 2-D space (latitude and longitude). This space partitioning data structure can be used to expedite nearest neighbours search29 and allow for quick cluster grouping. Here we refer to a cluster as a collection of pixel objects that are recorded at the same time step and are also spatially nearby. In the following steps, all pixels within a cluster are considered as a whole for fire merging and creation.We define an extended area for every existing fire object as the fire vector perimeter (see the section of Calculating and recording fire attributes for detail) plus a radial buffer that depends on the fire type property of the object. The buffer is set to 5 km for forest fires and 1 km for other fire types (shrub, crop, urban), considering that the fire spread rate can differ across biomes13. We then evaluate the spatial distance between the perimeters of a newly classified cluster and all existing active fire objects (a fire object keeps an active status if one or more active fire pixels associated with it are detected during the past 5 days), and calculate the shortest distance. If the shortest distance is smaller than the buffer of the associated existing active fire (i.e., new cluster overlaps with the extended area of an existing fire object), we assume all fire pixels in the new cluster are associated with the growth of the existing fire object at the current time step (Fig. 2). The existing fire object is updated by appending all fire pixel objects within the new cluster. If a newly classified cluster does not overlap with the extended area of any existing active fire object, we assume this is a new fire. A new fire object (by assigning a new fire id) is created using all fire pixel objects in the cluster.With the addition of new fire pixels, an existing fire object may expand and touch the extended area of another existing active fire object. If this happens, we assume that these two existing fire objects merge into a single object at this time step. All fire pixels in the fire object with a higher id number (a later start date, termed as the ‘source fire’) are appended to the fire object with lower id number (earlier start date, termed as the ‘target fire’) in this case. We record the id of the target fire in a list of fire mergers, and update all attributes associated with this fire (Fig. 3). In order to avoid double counting, the source fire object (with all pixels being transferred to the target fire object) is flagged as invalid, and is excluded from statistical analysis of fire events.Fig. 3The time series of growth for the SCU Lightning Complex fire (2020). Panel (b) shows the fire size of the SCU fire (total area within the fire object perimeter) at half-daily time steps. A fraction of the fire growth (shown in orange) was due to the addition of newly detected fire pixels. Panel (a) shows the number of new fire pixels (associated with the SCU fire object) detected at each time step. The other part of the fire growth (shown in red) was due to the merging with existing fire objects. Panel (c) shows the number of fire pixels in the existing objects that were merged to the SCU fire object.Full size imageCalculating and recording fire attributesOther than individual fire pixels contained in a fire object, several core attributes (properties and geometries) are also dynamically updated at each time step and are used for fire tracking and characterization.Important time-related attributes include the fire ignition time (the time step at which the first fire pixel within the fire object was detected), the fire end time (the latest time step with an active fire observation), and the fire duration (the time difference between the ignition time and end time). If a fire object does not have new active fire pixels appended during 5 consecutive days (i.e., the fire end time is more than 5 days before the present time step), its status is set to inactive. Once inactive, a fire object is no longer evaluated for use in future clustering (i.e., new active fire detections later will form new fire objects, even if they are spatially close to the inactive fire object).Each fire object is assigned to a specific fire type. The fire type is identified using the major land cover type within the fire perimeter (Table 3). In an initial analysis, we found that prescribed fires, on average, have higher coarse fuel moisture levels than wildfires. Therefore, we also record the 1000-hour fuel moisture (fm1000) from the gridMET dataset27 for each fire object (corresponding to the ignition time step) and use this value to divide forest and shrub fires further to wildfire and prescribed types.Table 3 Classification of fire types based on dominant land cover type (from the US National Land Cover Database) within each fire perimeter and the 1000-hr fuel moisture (FM-1000, from gridMET dataset) at the time of ignition.Full size tableAn essential step in this object-based fire tracking system is to determine the vector shape of the fire perimeter. In this system, we use an alpha shape30 algorithm to derive bounding polygons containing fire pixels in a fire object. For an alpha shape, the radius of the disks forming the curves in the polygon is determined by the alpha parameter α. Compared with the commonly used convex hull, the alpha shape hull is able to capture the irregular shapes around the fire perimeter more accurately22.To identify the optimal values for the α parameter, we performed the following analysis. First, we derived the final fire perimeters for all large fires that occurred in California during the 2018 wildfire season using a set of α values ranging from 500 m to 10 km and compared the results with more refined fire perimeters from the Fire and Resource Assessment Program (FRAP) dataset (Fig. 4). Large magnitude α values tended to overestimate the total burned area, while small α values often fragmented a large fire event. We found that a value of α = 1 km was optimal in terms of balancing the ability of the hull to catch the boundary shape and to keep the integrity of a fire object. For each time step, we applied the alpha shape algorithm to all fire pixel locations associated with a fire object since the time of ignition. This processing step resulted in a concave hull with the shape of polygon or multipolygon. To account for the pixel size, we expanded the concave hull to the fire perimeter using a buffer size equal to half of the VIIRS nadir cross-track pixel width (187.5 m). The alpha shape algorithm does not work when the total number of fire pixels (npix) is less than 4. If npix equals 3, we used a convex hull algorithm and the same 187.5 m buffer to determine a polygon perimeter. If npix is 1 or 2, circles centered on the fire pixel location with radius of 187.5 m were used.Fig. 4Optimization of the alpha shape parameter (α). For all large fires (final size  > 4 km2) in California during 2018, fire perimeters were estimated using VIIRS active fires and different alpha parameters. By comparing (a) the burned area (BA) and (b) the number of fire objects with the FRAP data, an optimal alpha parameter of 1 km was identified for use in this study (shown in red). The vertical bars and lines show the mean and 1-std variability from all fires. The dashed blue lines indicate the ideal values when compared to FRAP. Panels (c)–(h) show the fire perimeters derived using different alpha shape parameters for two sample fires in 2018. The shapes with pink color are final FEDS fire perimeters derived from VIIRS active fires using the alpha shape algorithm. The blue shapes represent the corresponding fire perimeters from the FRAP dataset. Overlap between FRAP and FEDS is shown in purple.Full size imageWe also calculate the active front line for each fire object at each time step. The active fire front consists of the segments of the fire perimeter that are actively burning and releasing energy and emissions. The position of the active fire line is critical in evaluating the fire risk, estimating the fire emissions, and predicting fire spread. We derive the active portion of the fire perimeter as segments that are within a 500 m radius of newly detected fire pixel locations. We found that this threshold allowed for a continuous projection of the active fire front in rapidly expanding areas of large wildfires during the 2018 fire season; this threshold may be optimized in future work to maximize performance metrics for fire model forecasts. The resulting active line for each fire at each time step has the shape of a linestring (object representing a sequence of points and the line segments connecting them), a multi-linestring (a collection of multiple linestrings), or a linear ring (closed linestring). Figure 5 shows an example map of the fire perimeters and active fire front lines on September 8 during the 2020 wildfire season.Fig. 5An example map of fire perimeters and fire active fronts in California. The map was created using the fire event data suite (FEDS) as of the Suomi-NPP afternoon overpass (~1:30 pm local time) of Sep 8, 2020. The background is the Aqua MODIS Corrected Reflectance Imagery (true color) recorded at the same day (provided by the NASA Global Imagery Browse Services). The active front line of a fire is shown in yellow, active fire areas are shown in red, and the area of inactive (extinguished) fires are shown in dark red.Full size imageAdditional fire properties, such as the fire area and active fire line length, are also derived using these geometries of the fire object (see Table 2). Note this list can be easily expanded to include more user-defined properties with the help of the fire object core vector data.The allfires object contains a list of all existing fire objects at a time step. This object also records the ids of fire objects that have been modified (including fires newly formed, fires that expanded with new pixel additions, fires with pixels addition due to merging, and fires that just became invalid) at the current time step.Creating the fire event data suite (FEDS)By tracking the spatiotemporal evolution of all fire objects in California, we derived a complete dataset of fire events for each calendar year (Jan 1 am – Dec 31 pm) during the Suomi-NPP VIIRS era (2012–2020). The dataset contains four products that represent the fire information in California at multiple spatial scales and from different perspectives (Fig. 1 and Table 4), ranging from the most detailed and memory-intensive data format (Pickle) to the most high-level format (CSV).Table 4 Data structure of the FEDS.Full size tableThe first product is the direct serialization result of the allfires object at each time step (twice per day). The product is stored as a Pickle file31 which allows for analysis of the complex allfires object structure (including all attributes associated with all fire objects it contains). This file also serves as the restart file for continued fire tracking at any time step, which is essential for the operational mode using the near-real-time fire data. By restoring an exact copy of the previously pickled allfires object, any attribute in the allfires object can be deserialized from the saved files. The Pickle file is the most basic data product in the dataset, and is created at each half-day time step.The second product (Snapshot) represents a more accessible and self-explanatory variant of the Pickle serialization product. In this product, we tabulated important diagnostic attributes for each fire and saved them in GeoPackage32 data files. Each GeoPackage file includes three data layers: one contains the properties and the fire perimeter geometry, another contains the active fire line geometry, and a third contains the new fire pixel location geometry. This product, created at a half-daily time step, allows for a more straightforward interpretation of regional fire status at a particular time step. We also created a GeoPackage file that summarizes the final fire perimeters and attributes for all fires during the whole study period (2012–2020).The third product (Largefire) focuses on the temporal evolution of individual large fires with an area greater than 4 km2. At each time step, the time series of properties and geometries (fire perimeter, active fire line, and new fire pixel locations) for each of the large fires are extracted and saved to GeoPackage files. This product facilitates the visualization and analysis for an individual targeted fire (Fig. 6) and is particularly useful in the near-real-time evaluation, forecasting, and policy making.Fig. 6The spatiotemporal evolution of the Creek fire (2020). Contours and dots reflect the fire perimeters and newly detected fire pixels at each 12-hour time step. Data for the period of Sep 5 am–Nov 6 am, 2020 are shown.Full size imageThe fourth product (Summary), which is stored as NetCDF and CSV files and created at the end of a fire season, records the all-year time series of fire statistics (including major fire attributes such as number, size, duration, fire line length, etc.) over the whole State of California. This product provides a feasible regional summary of the temporal evolution of fires.Potential for near-real-time (NRT) fire event trackingWhile the main objective of this paper is to apply the object-based fire tracking system to historical VIIRS fire detections and create a retrospective multi-year FEDS, we note that this system has the potential to be used for tracking fire events in near-real-time, providing rich and valuable information for fire management and short-term risk assessment. We have experimented with the use of this system for NRT fire event tracking in California using the daily NRT Suomi-NPP VIIRS active fire detection product (VNP14IMGTDL, collection 6) as the main data source. The VNP14IMGTDL product is routinely produced and is publicly available at the NASA Fire Information for Resource Management System (FIRMS). Since the NRT product undergoes less rigorous quality assurance, we use only fires with ‘nominal’ or ‘high’ confidence levels from the NRT product for fire tracking. Some active fire detections from the NRT data are potentially associated with static non-vegetation fires (e.g., fires from gas flaring in oil and gas or landfill industries or false detections due to reflection from solar panels) and are not the main interest for vegetation fire studies. To avoid the unnecessary computation associated with these static fires, we record and evaluate the fire pixel density for each fire object at each time step. When a small fire ( 20 per km2), it is considered to be a static fire and subsequently labelled as invalid.Similar to the retrospective FEDS, we use the active fire detections to create an object serialization product, a regional snapshot GIS product, and a time series product of large fire evolution twice daily. This experimental NRT data will be available upon publication through a university hosted server. More

  • in

    Incorporation of machine learning and deep neural network approaches into a remote sensing-integrated crop model for the simulation of rice growth

    Jones, J. W. et al. The DSSAT cropping system model. Eur. J. Agron. 18, 235–265 (2003).Article 

    Google Scholar 
    van Diepen, C. A., Wolf, J., van Keulen, H. & Rappoldt, C. WOFOST: a simulation model of crop production. Soil Use Manag. 5, 16–24 (1989).Article 

    Google Scholar 
    Cao, J. et al. Integrating multi-source data for rice yield prediction across China using machine learning and deep learning approaches. Agric. For. Meteorol. 297, 108275 (2021).ADS 
    Article 

    Google Scholar 
    Khanal, S., Kushal, K. C., Fulton, J. P., Shearer, S. & Ozkan, E. Remote sensing in agriculture—accomplishments, limitations, and opportunities. Remote Sens. 12, 3783 (2020).ADS 
    Article 

    Google Scholar 
    Maas, S. J. Parameterised model of gramineous crop growth: II. within-season simulation calibration. Agron. J. 85, 354–358 (1993).Article 

    Google Scholar 
    Nguyen, V., Jeong, S., Ko, J., Ng, C. & Yeom, J. Mathematical integration of remotely-sensed information into a crop modelling process for mapping crop productivity. Remote Sens. 11, 2131 (2019).Article 

    Google Scholar 
    Huang, J. et al. Assimilation of remote sensing into crop growth models: current status and perspectives. Agric. For. Meteorol. 276–277, 107609 (2019).ADS 
    Article 

    Google Scholar 
    Jin, X. et al. A review of data assimilation of remote sensing and crop models. Eur. J. Agron. 92, 141–152 (2018).Article 

    Google Scholar 
    Shawon, A. R. et al. Assessment of a proximal sensing-integrated crop model for simulation of soybean growth and yield. Remote Sens. 12, 410 (2020).ADS 
    Article 

    Google Scholar 
    Shawon, A. R. et al. Two-dimensional simulation of barley growth and yield using a model integrated with remote-controlled aerial imagery. Remote Sens. 12, 3766 (2020).ADS 
    Article 

    Google Scholar 
    Shin, T. et al. Simulation of wheat productivity using a model integrated with proximal and remotely controlled aerial sensing information. Front. Plant Sci. https://doi.org/10.3389/fpls.2021.649660 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Huang, J. et al. Assimilating a synthetic Kalman filter leaf area index series into the WOFOST model to improve regional winter wheat yield estimation. Agric. For. Meteorol. 216, 188–202 (2016).ADS 
    Article 

    Google Scholar 
    Khaki, S., Wang, L. & Archontoulis, S. V. A CNN-RNN framework for crop yield prediction. Front. Plant Sci. https://doi.org/10.3389/fpls.2019.01750 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kim, N. et al. An artificial intelligence approach to prediction of corn yields under extreme weather conditions using satellite and meteorological data. Appl. Sci. 10, 3785 (2020).CAS 
    Article 

    Google Scholar 
    Kumar, P. et al. Comprehensive evaluation of soil moisture retrieval models under different crop cover types using C-band synthetic aperture radar data. Geocarto Int. 34, 1022–1041 (2019).Article 

    Google Scholar 
    Everingham, Y., Sexton, J., Skocaj, D. & Inman-Bamber, G. Accurate prediction of sugarcane yield using a random forest algorithm. Agron. Sustain. Dev. 36, 27 (2016).Article 

    Google Scholar 
    Feng, P., Wang, B., Li Liu, D., Waters, C. & Yu, Q. Incorporating machine learning with biophysical model can improve the evaluation of climate extremes impacts on wheat yield in south-eastern Australia. Agric. For. Meteorol. 275, 100–113 (2019).ADS 
    Article 

    Google Scholar 
    Shahhosseini, M., Hu, G., Huber, I. & Archontoulis, S. V. Coupling machine learning and crop modeling improves crop yield prediction in the US Corn Belt. Sci. Rep. 11, 1606 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cai, Y. et al. Detecting in-season crop nitrogen stress of corn for field trials using UAV- and CubeSat-based multispectral sensing. IEEE J. Sel. Top. Appl. Earth Obs. Remote Sens. 12, 5153–5166 (2019).ADS 
    Article 

    Google Scholar 
    van Klompenburg, T., Kassahun, A. & Catal, C. Crop yield prediction using machine learning: a systematic literature review. Comput. Electron. Agric. 177, 105709 (2020).Article 

    Google Scholar 
    Kamilaris, A. & Prenafeta-Boldú, F. X. Deep learning in agriculture: a survey. Comput. Electron. Agric. 147, 70–90 (2018).Article 

    Google Scholar 
    Bui, D. T., Tsangaratos, P., Nguyen, V.-T., Liem, N. V. & Trinh, P. T. Comparing the prediction performance of a deep learning neural network model with conventional machine learning models in landslide susceptibility assessment. CATENA 188, 104426 (2020).Article 

    Google Scholar 
    Sahoo, A. K., Pradhan, C. & Das, H. Performance evaluation of different machine learning methods and deep-learning based convolutional neural network for health decision making. In Nature Inspired Computing for Data Science (eds Rout, M. et al.) (Springer International Publishing, 2020).
    Google Scholar 
    Jeong, S. et al. Development of Variable Threshold Models for detection of irrigated paddy rice fields and irrigation timing in heterogeneous land cover. Agric. Water Manag. 115, 83–91 (2012).Article 

    Google Scholar 
    Peng, D., Huete, A. R., Huang, J., Wang, F. & Sun, H. Detection and estimation of mixed paddy rice cropping patterns with MODIS data. Int. J. Appl. Earth Obs. Geoinf. 13, 13–23 (2011).ADS 

    Google Scholar 
    Jeong, S., Ko, J. & Yeom, J.-M. Nationwide projection of rice yield using a crop model integrated with geostationary satellite imagery: a case study in South Korea. Remote Sens. 10, 1665 (2018).ADS 
    Article 

    Google Scholar 
    Xiao, X. et al. Mapping paddy rice agriculture in South and Southeast Asia using multi-temporal MODIS images. Remote Sens. Environ. 100, 95–113 (2006).ADS 
    Article 

    Google Scholar 
    Ozdogan, M. & Gutman, G. A new methodology to map irrigated areas using multi-temporal MODIS and ancillary data: an application example in the continental US. Remote Sens. Environ. 112, 3520–3537 (2008).ADS 
    Article 

    Google Scholar 
    Yeom, J.-M., Jeong, S., Deo, R. C. & Ko, J. Mapping rice area and yield in northeastern Asia by incorporating a crop model with dense vegetation index profiles from a geostationary satellite. GISci. Remote Sens. 58, 1–27 (2021).Article 

    Google Scholar 
    Yeom, J.-M. et al. Monitoring paddy productivity in North Korea employing geostationary satellite images integrated with GRAMI-rice model. Sci. Rep. 8, 16121 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Jeong, S., Ko, J., Choi, J., Xue, W. & Yeom, J.-M. Application of an unmanned aerial system for monitoring paddy productivity using the GRAMI-rice model. Int. J. Remote Sens. 39, 2441–2462 (2018).Article 

    Google Scholar 
    Jeong, S. et al. Geographical variations in gross primary production and evapotranspiration of paddy rice in the Korean Peninsula. Sci. Total Environ. 714, 136632 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Roger, P., Vermote, E. & Ray, J. MODIS Surface Reflectance User’s Guide. Collection 6 (2015).Scharlemann, J. P. W. et al. Global data for ecology and epidemiology: a novel algorithm for temporal Fourier processing MODIS data. PLoS ONE 3, e1408 (2008).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pede, T. & Mountrakis, G. An empirical comparison of interpolation methods for MODIS 8-day land surface temperature composites across the conterminous Unites States. ISPRS J. Photogramm. Remote Sens. 142, 137–150 (2018).ADS 
    Article 

    Google Scholar 
    Kilibarda, M. et al. Spatio-temporal interpolation of daily temperatures for global land areas at 1 km resolution. J. Geophys. Res. Atmos. 119, 2294–2313 (2014).ADS 
    Article 

    Google Scholar 
    Nunez, M. The development of a satellite-based insolation model for the tropical western Pacific Ocean. Int. J. Climatol. 13, 607–627 (1993).Article 

    Google Scholar 
    Otkin, J. A., Anderson, M. C., Mecikalski, J. R. & Diak, G. R. Validation of GOES-based insolation estimates using data from the U.S. Climate reference network. J. Hydrometeorol. 6, 460–475 (2005).ADS 
    Article 

    Google Scholar 
    Pinker, R. & Laszlo, I. Modeling surface solar irradiance for satellite applications on a global scale. J. Appl. Meteorol. 31, 194–211 (1992).ADS 
    Article 

    Google Scholar 
    Kawamura, H., Tanahashi, S. & Takahashi, T. Estimation of insolation over the Pacific Ocean off the Sanriku coast. J. Oceanogr. 54, 457–464 (1998).Article 

    Google Scholar 
    Yeom, J.-M., Seo, Y.-K., Kim, D.-S. & Han, K.-S. Solar radiation received by slopes using COMS imagery, a physically based radiation model, and GLOBE. J. Sens. 2016, 1–15 (2016).Article 

    Google Scholar 
    Yeom, J.-M., Han, K.-S. & Kim, J.-J. Evaluation on penetration rate of cloud for incoming solar radiation using geostationary satellite data. Asia-Pac. J. Atmos. Sci. 48, 115–123 (2012).ADS 
    Article 

    Google Scholar 
    Kawai, Y. & Kawamura, H. Validation and improvement of satellite-derived surface solar radiation over the Northwestern Pacific Ocean. J. Oceanogr. 61, 79–89 (2005).Article 

    Google Scholar 
    Tanahashi, S., Kawamura, H., Matsuura, T., Takahashi, T. & Yusa, H. A system to distribute satellite incident solar radiation in real-time. Remote Sens. Environ. 75, 412–422 (2001).ADS 
    Article 

    Google Scholar 
    Elbern, H., Schmidt, H., Talagrand, O. & Ebel, A. 4D-variational data assimilation with an adjoint air quality model for emission analysis. Environ. Model. Softw. 15, 539–548 (2000).Article 

    Google Scholar 
    Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. Numerical Recipes: The Art of Scientific Computing (Cambridge University Press, 1992).MATH 

    Google Scholar 
    Ko, J. et al. Simulation and mapping of rice growth and yield based on remote sensing. J. Appl. Remote Sens. 9, 096067 (2015).Article 

    Google Scholar 
    Emami Javanmard, M., Ghaderi, S. F. & Hoseinzadeh, M. Data mining with 12 machine learning algorithms for predict costs and carbon dioxide emission in integrated energy-water optimization model in buildings. Energy Convers. Manag. 238, 114153 (2021).CAS 
    Article 

    Google Scholar 
    Diebold, F. X. & Shin, M. Machine learning for regularized survey forecast combination: partially-egalitarian LASSO and its derivatives. Int. J. Forecast. 35, 1679–1691 (2019).Article 

    Google Scholar 
    Khosla, E., Dharavath, R. & Priya, R. Crop yield prediction using aggregated rainfall-based modular artificial neural networks and support vector regression. Environ. Dev. Sustain. 22, 5687–5708 (2020).Article 

    Google Scholar 
    Wang, S., Azzari, G. & Lobell, D. B. Crop type mapping without field-level labels: random forest transfer and unsupervised clustering techniques. Remote Sens. Environ. 222, 303–317 (2019).ADS 
    Article 

    Google Scholar 
    Ustuner, M. & Balik, S. F. Polarimetric target decompositions and light gradient boosting machine for crop classification: a comparative evaluation. ISPRS Int. J. Geo Inf. 8, 97 (2019).Article 

    Google Scholar 
    Jeong, S., Ko, J. & Yeom, J.-M. Predicting rice yield at pixel scale through synthetic use of crop and deep learning models with satellite data in South and North Korea. Sci. Total Environ. 802, 149726 (2022).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Nash, J. E. & Sutcliffe, J. V. River flow forecasting through conceptual models part I: a discussion of principles. J. Hydrol. 10, 282–290 (1970).ADS 
    Article 

    Google Scholar  More