More stories

  • in

    Perspectives in machine learning for wildlife conservation

    1.Ceballos, G., Ehrlich, P. R. & Raven, P. H. Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction. Proc. Natl Acad. Sci. USA 117, 13596–13602 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    2.Committee, T. I. R. L. The IUCN Red List of Threatened Species – Strategic Plan 2017-2020. Tech. Rep., IUCN (2017).3.Witmer, G. W. Wildlife population monitoring: some practical considerations. Wild. Res. 32, 259–263 (2005).
    Google Scholar 
    4.McEvoy, J. F., Hall, G. P. & McDonald, P. G. Evaluation of unmanned aerial vehicle shape, flight path and camera type for waterfowl surveys: disturbance effects and species recognition. PeerJ 4, e1831 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    5.Burghardt, G. M. et al. Perspectives–minimizing observer bias in behavioral studies: a review and recommendations. Ethology 118, 511–517 (2012).
    Google Scholar 
    6.Giese, M. Effects of human activity on Adelie penguin Pygoscelis adeliae breeding success. Biol. Conserv. 75, 157–164 (1996).
    Google Scholar 
    7.Köndgen, S. et al. Pandemic human viruses cause decline of endangered great apes. Curr. Biol. 18, 260–264 (2008).PubMed 

    Google Scholar 
    8.Weissensteiner, M. H., Poelstra, J. W. & Wolf, J. B. W. Low-budget ready-to-fly unmanned aerial vehicles: an effective tool for evaluating the nesting status of canopy-breeding bird species. J. Avian Biol. 46, 425–430 (2015).
    Google Scholar 
    9.Sasse, D. B. Job-related mortality of wildlife workers in the united states, 1937–2000. Wildl. Soc. Bull. 31, 1015–1020 (2003).10.Kays, R., Crofoot, M. C., Jetz, W. & Wikelski, M. Terrestrial animal tracking as an eye on life and planet. Science 348, aaa2478 (2015).11.Altmann, J. Observational study of behavior: sampling methods. Behaviour 49, 227–266 (1974).CAS 
    PubMed 

    Google Scholar 
    12.Hodgson, J. C. et al. Drones count wildlife more accurately and precisely than humans. Methods Ecol. Evolution 9, 1160–1167 (2018).
    Google Scholar 
    13.Betke, M. et al. Thermal imaging reveals significantly smaller Brazilian free-tailed bat colonies than previously estimated. J. Mammal. 89, 18–24 (2008).
    Google Scholar 
    14.Rollinson, C. R. et al. Working across space and time: nonstationarity in ecological research and application. Front. Ecol. Environ. 19, 66–72 (2021).
    Google Scholar 
    15.Junker, J. et al. A severe lack of evidence limits effective conservation of the world’s primates. BioScience 70, 794–803 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    16.Sherman, J., Ancrenaz, M. & Meijaard, E. Shifting apes: Conservation and welfare outcomes of Bornean orangutan rescue and release in Kalimantan, Indonesia. J. Nat. Conserv. 55, 125807 (2020).
    Google Scholar 
    17.O’Donoghue, P. & Rutz, C. Real-time anti-poaching tags could help prevent imminent species extinctions. J. Appl. Ecol. 53, 5–10 (2016).PubMed 

    Google Scholar 
    18.Lahoz-Monfort, J. J. & Magrath, M. J. L. A comprehensive overview of technologies for species and habitat monitoring and conservation. BioScience biab073. https://academic.oup.com/bioscience/advance-article/doi/10.1093/biosci/biab073/6322306 (2021).19.Gottschalk, T., Huettmann, F. & Ehlers, M. Thirty years of analysing and modelling avian habitat relationships using satellite imagery data: a review. Int. J. Remote Sens. 26, 2631–2656 (2005).
    Google Scholar 
    20.Steenweg, R. et al. Scaling-up camera traps: monitoring the planet’s biodiversity with networks of remote sensors. Front. Ecol. Environ. 15, 26–34 (2017).
    Google Scholar 
    21.Hausmann, A. et al. Social media data can be used to understand tourists’ preferences for nature-based experiences in protected areas. Conserv. Lett. 11, e12343 (2018).
    Google Scholar 
    22.Sugai, L. S. M., Silva, T. S. F., Ribeiro, J. W. & Llusia, D. Terrestrial passive acoustic monitoring: review and perspectives. BioScience 69, 15–25 (2018).
    Google Scholar 
    23.Wikelski, M. et al. Going wild: what a global small-animal tracking system could do for experimental biologists. J. Exp. Biol. 210, 181–186 (2007).PubMed 

    Google Scholar 
    24.Belyaev, M. Y. et al. Development of technology for monitoring animal migration on Earth using scientific equipment on the ISS RS. in 2020 27th Saint Petersburg International Conference on Integrated Navigation Systems (ICINS), 1–7 (IEEE, 2020).25.Harel, R., Loftus, J. C. & Crofoot, M. C. Locomotor compromises maintain group cohesion in baboon troops on the move. Proc. R. Soc. B 288, 20210839 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    26.Farley, S. S., Dawson, A., Goring, S. J. & Williams, J. W. Situating ecology as a big-data science: current advances, challenges, and solutions. BioScience 68, 563–576 (2018).
    Google Scholar 
    27.Lasky, M. et al. Candid critters: Challenges and solutions in a large-scale citizen science camera trap project. Citizen Science: Theory and Practice 6, https://doi.org/10.5334/cstp.343 (2021).28.Hastie, T., Tibshirani, R. & Friedman, J. The Elements of Statistical Learning: Data Mining, Inference, and Prediction (Springer, 2001).29.Christin, S., Hervet, É. & Lecomte, N. Applications for deep learning in ecology. Methods Ecol. Evolution 10, 1632–1644 (2019).
    Google Scholar 
    30.Kwok, R. Ai empowers conservation biology. Nature 567, 133–135 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    31.Kwok, R. Deep learning powers a motion-tracking revolution. Nature 574, 137–139 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    32.LeCun, Y., Bengio, Y. & Hinton, G. Deep learning. Nature 521, 436–444 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    33.Pichler, M., Boreux, V., Klein, A.-M., Schleuning, M. & Hartig, F. Machine learning algorithms to infer trait-matching and predict species interactions in ecological networks. Methods Ecol. Evolution 11, 281–293 (2020).
    Google Scholar 
    34.Knudby, A., LeDrew, E. & Brenning, A. Predictive mapping of reef fish species richness, diversity and biomass in Zanzibar using IKONOS imagery and machine-learning techniques. Remote Sens. Environ. 114, 1230–1241 (2010).ADS 

    Google Scholar 
    35.Rey, N., Volpi, M., Joost, S. & Tuia, D. Detecting animals in African savanna with UAVs and the crowds. Remote Sens. Environ. 200, 341–351 (2017).ADS 

    Google Scholar 
    36.Beery, S., Morris, D. & Yang, S. Efficient pipeline for camera trap image review. in Proceedings of the Workshop Data Mining and AI for Conservation, Conference for Knowledge Discovery and Data Mining (2019).37.Kellenberger, B., Marcos, D. & Tuia, D. When a few clicks make all the difference: improving weakly-supervised wildlife detection in UAV images. in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (2019).38.Schofield, D. et al. Chimpanzee face recognition from videos in the wild using deep learning. Sci. Adv. 5, eaaw0736 (2019).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Ditria, E. M. et al. Automating the analysis of fish abundance using object detection: optimizing animal ecology with deep learning. Front. Mar. Sci. 7, 429 (2020).
    Google Scholar 
    40.Kellenberger, B., Veen, T., Folmer, E. & Tuia, D. 21 000 birds in 4.5 h: efficient large-scale seabird detection with machine learning. Remote Sens. Ecol. Conserv. 7, 445–460 (2021).
    Google Scholar 
    41.Ahumada, J. A. et al. Wildlife insights: a platform to maximize the potential of camera trap and other passive sensor wildlife data for the planet. Environ. Conserv. 47, 1–6 (2020).MathSciNet 

    Google Scholar 
    42.Eikelboom, J. A. J. et al. Improving the precision and accuracy of animal population estimates with aerial image object detection. Methods Ecol. Evolution 10, 1875–1887 (2019).
    Google Scholar 
    43.Weinstein, B. G. A computer vision for animal ecology. J. Anim. Ecol. 87, 533–545 (2018).PubMed 

    Google Scholar 
    44.Valletta, J. J., Torney, C., Kings, M., Thornton, A. & Madden, J. Applications of machine learning in animal behaviour studies. Anim. Behav. 124, 203–220 (2017).
    Google Scholar 
    45.Peters, D. P. C. et al. Harnessing the power of big data: infusing the scientific method with machine learning to transform ecology. Ecosphere 5, art67 (2014).
    Google Scholar 
    46.Yu, Q. et al. Study becomes insight: ecological learning from machine learning. Methods Ecol. Evol. 12, 2117–2128 (2021).47.Lucas, T. C. D. A translucent box: interpretable machine learning in ecology. Ecol. Monogr. 90, https://doi.org/10.1002/ecm.1422 (2020).48.Reichstein, M. et al. Deep learning and process understanding for data-driven Earth system science. Nature 566, 195–204 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    49.Camps-Valls, G., Tuia, D., Zhu, X. X. & Reichstein, M. Deep Learning for the Earth Sciences: A Comprehensive Approach to Remote Sensing, Climate Science and Geosciences (Wiley & Sons, 2021).50.Karpatne, A. et al. Theory-guided data science: A new paradigm for scientific discovery from data. IEEE Trans. Knowl. Data Eng. 29, 2318–2331 (2017).
    Google Scholar 
    51.Oliver, R. Y., Meyer, C., Ranipeta, A., Winner, K. & Jetz, W. Global and national trends, gaps, and opportunities in documenting and monitoring species distributions. PLoS Biol 19, e3001336 https://doi.org/10.1371/journal.pbio.3001336 (2021).52.Beery, S., Wu, G., Rathod, V., Votel, R. & Huang, J. Context R-CNN: long term temporal context for per-camera object detection. in 2020 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 13075–13085 (2020).53.Norouzzadeh, M. S. et al. Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning. Proc. Natl Acad. Sci. USA 115, E5716–E5725 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    54.Schneider, S., Taylor, G. W., Linquist, S. & Kremer, S. C. Past, present and future approaches using computer vision for animal re-identification from camera trap data. Methods Ecol. Evolution 10, 461–470 (2019).
    Google Scholar 
    55.Beery, S., Van Horn, G. & Perona, P. Recognition in terra incognita. in 2018 European Conference on Computer Vision (ECCV), 456–473 (2018).56.Sugai, L. S. M., Silva, T. S. F., Ribeiro Jr, J. W. & Llusia, D. Terrestrial passive acoustic monitoring: review and perspectives. BioScience 69, 15–25 (2019).
    Google Scholar 
    57.Wrege, P. H., Rowland, E. D., Keen, S. & Shiu, Y. Acoustic monitoring for conservation in tropical forests: examples from forest elephants. Methods Ecol. Evolution 8, 1292–1301 (2017).
    Google Scholar 
    58.Desjonquères, C., Gifford, T. & Linke, S. Passive acoustic monitoring as a potential tool to survey animal and ecosystem processes in freshwater environments. Freshw. Biol. 65, 7–19 (2020).
    Google Scholar 
    59.Davis, G. E. et al. Long-term passive acoustic recordings track the changing distribution of North Atlantic right whales (eubalaena glacialis) from 2004 to 2014. Sci. Rep. 7, 1–12 (2017).
    Google Scholar 
    60.Wood, C. M. et al. Detecting small changes in populations at landscape scales: a bioacoustic site-occupancy framework. Ecol. Indic. 98, 492–507 (2019).
    Google Scholar 
    61.Kahl, S., Wood, C. M., Eibl, M. & Klinck, H. Birdnet: a deep learning solution for avian diversity monitoring. Ecol. Inform. 61, 101236 (2021).
    Google Scholar 
    62.Stowell, D., Wood, M. D., Pamuła, H., Stylianou, Y. & Glotin, H. Automatic acoustic detection of birds through deep learning: the first bird audio detection challenge. Methods Ecol. Evolution 10, 368–380 (2019).
    Google Scholar 
    63.Ford, J. K. B. in Encyclopedia of Marine Mammals 253–254 (Elsevier, 2018).64.Hughey, L. F., Hein, A. M., Strandburg-Peshkin, A. & Jensen, F. H. Challenges and solutions for studying collective animal behaviour in the wild. Philos. Trans. R. Soc. B: Biol. Sci. 373, 20170005 (2018).
    Google Scholar 
    65.Williams, H. J. et al. Optimizing the use of biologgers for movement ecology research. J. Anim. Ecol. 89, 186–206 (2020).PubMed 

    Google Scholar 
    66.Korpela, J. et al. Machine learning enables improved runtime and precision for bio-loggers on seabirds. Commun. Biol. 3, 1–9 (2020).
    Google Scholar 
    67.Yu, H. An evaluation of machine learning classifiers for next-generation, continuous-ethogram smart trackers. Mov. Ecol. 9, 14 (2021).
    Google Scholar 
    68.Browning, E. et al. Predicting animal behaviour using deep learning: GPS data alone accurately predict diving in seabirds. Methods Ecol. Evolution 9, 681–692 (2018).
    Google Scholar 
    69.Liu, Z. Y.-C. et al. Deep learning accurately predicts white shark locomotor activity from depth data. Anim. Biotelemetry 7, 1–13 (2019).
    Google Scholar 
    70.Wang, G. Machine learning for inferring animal behavior from location and movement data. Ecol. Inform. 49, 69–76 (2019).
    Google Scholar 
    71.Wijeyakulasuriya, D. A., Eisenhauer, E. W., Shaby, B. A. & Hanks, E. M. Machine learning for modeling animal movement. PLoS ONE 30, e0235750 (2020).72.Linchant, J., Lisein, J., Semeki, J., Lejeune, P. & Vermeulen, C. Are unmanned aircraft systems (UASs) the future of wildlife monitoring? A review of accomplishments and challenges. Mammal. Rev. 45, 239–252 (2015).
    Google Scholar 
    73.Hodgson, J. C., Baylis, S. M., Mott, R., Herrod, A. & Clarke, R. H. Precision wildlife monitoring using unmanned aerial vehicles. Sci. Rep. 6, 1–7 (2016).
    Google Scholar 
    74.Mathis, A. et al. DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nat. Neurosci. 21, 1281–1289 (2018).CAS 
    PubMed 

    Google Scholar 
    75.Graving, J. M. et al. DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning. Elife 8, e47994 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    76.Mathis, A., Schneider, S., Lauer, J. & Mathis, M. W. A primer on motion capture with deep learning: principles, pitfalls, and perspectives. Neuron 108, 44–65 (2020).CAS 
    PubMed 

    Google Scholar 
    77.Kellenberger, B., Marcos, D. & Tuia, D. Detecting mammals in UAV images: best practices to address a substantially imbalanced dataset with deep learning. Remote Sens. Environ. 216, 139–153 (2018).ADS 

    Google Scholar 
    78.Kellenberger, B., Veen., T., Folmer, E. & Tuia, D. 21,000 birds in 4.5 hours: efficient large-scale seabird detection with machine learning. Remote Sens. Ecol. Conserv. https://doi.org/10.1002/rse2.200 (2021).79.Andrew, W., Greatwood, C. & Burghardt, T. Aerial animal biometrics: individual Friesian cattle recovery and visual identification via an autonomous UAV with onboard deep inference. in International Conference on Intelligent Robots and Systems (IROS) (2019).80.Schroeder, N. M., Panebianco, A., Gonzalez Musso, R. & Carmanchahi, P. An experimental approach to evaluate the potential of drones in terrestrial mammal research: a gregarious ungulate as a study model. R. Soc. open Sci. 7, 191482 (2020).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    81.Bennitt, E., Bartlam-Brooks, H. L. A., Hubel, T. Y. & Wilson, A. M. Terrestrial mammalian wildlife responses to Unmanned Aerial Systems approaches. Sci. Rep. 9, 1–10 (2019).CAS 

    Google Scholar 
    82.Deneu, B., Servajean, M., Botella, C. & Joly, A. Evaluation of deep species distribution models using environment and co-occurrences. in International Conference of the Cross-Language Evaluation Forum for European Languages, 213–225 (Springer, 2019).83.Zhu, X. et al. Deep learning in remote sensing: A comprehensive review and list of resources. IEEE Geosci. Remote Sens. Mag. 5, 8–36 (2017).
    Google Scholar 
    84.Guirado, E., Tabik, S., Rivas, M. L., Alcaraz-Segura, D. & Herrera, F. Whale counting in satellite and aerial images with deep learning. Sci. Rep. 9, 1–12 (2019).CAS 

    Google Scholar 
    85.Duporge, I., Isupova, O., Reece, S., Macdonald, D. W. & Wang, T. Using very-high-resolution satellite imagery and deep learning to detect and count African elephants in heterogeneous landscapes. Remote Sens. Ecol. Conserv. https://doi.org/10.1002/rse2.195 (2020).86.Fretwell, P. T. & Trathan, P. N. Discovery of new colonies by Sentinel2 reveals good and bad news for emperor penguins. Remote Sens. Ecol. Conserv. https://doi.org/10.1002/rse2.176 (2020).87.Brodrick, P. G., Davies, A. B. & Asner, G. P. Uncovering ecological patterns with convolutional neural networks. Trends Ecol. Evolution 34, 734–745 (2019).
    Google Scholar 
    88.Audebert, N., Le Saux, B. & Lefèvre, S. Deep learning for classification of hyperspectral data: a comparative review. IEEE Geosci. Remote Sens. Mag. 7, 159–173 (2019).
    Google Scholar 
    89.McKinley, D. C. et al. Citizen science can improve conservation science, natural resource management, and environmental protection. Biol. Conserv. 208, 15–28 (2017).
    Google Scholar 
    90.Wäldchen, J. & Mäder, P. Machine learning for image based species identification. Methods Ecol. Evolution 9, 2216–2225 (2018).MATH 

    Google Scholar 
    91.Torney, C. J. et al. A comparison of deep learning and citizen science techniques for counting wildlife in aerial survey images. Methods Ecol. Evolution 10, 779–787 (2019).
    Google Scholar 
    92.Parham, J., Crall, J., Stewart, C., Berger-Wolf, T. & Rubenstein, D. I. Animal population censusing at scale with citizen science and photographic identification. in AAAI Spring Symposium-Technical Report (2017).93.Kühl, H. S. & Burghardt, T. Animal biometrics: quantifying and detecting phenotypic appearance. Trends Ecol. Evolution 28, 432–441 (2013).
    Google Scholar 
    94.Yu, X. et al. Automated identification of animal species in camera trap images. EURASIP J. Image Video Process. 2013, 1–10 (2013).ADS 

    Google Scholar 
    95.Mac Aodha, O. et al. Bat detective–deep learning tools for bat acoustic signal detection. PLoS Computat. Biol. 14, e1005995 (2018).
    Google Scholar 
    96.Schindler, F. & Steinhage, V. Identification of animals and recognition of their actions in wildlife videos using deep learning techniques. Ecol. Inform. 61, 101215 (2021).97.Avise, J. C. Molecular Markers, Natural History and Evolution (Springer Science & Business Media, 2012).98.Vidal, M., Wolf, N., Rosenberg, B., Harris, B. P. & Mathis, A. Perspectives on Individual Animal Identification from Biology and Computer Vision. Integr. Comp. Biol. 61, 900–916 https://doi.org/10.1093/icb/icab107 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    99.Berger-Wolf, T. Y. et al. Wildbook: crowdsourcing, computer vision, and data science for conservation. Preprint at https://arxiv.org/abs/1710.08880 (2017).100.Parham, J. et al. An animal detection pipeline for identification. in IEEE Winter Conference on Applications of Computer Vision (WACV), 1075–1083 (IEEE, 2018).101.Weideman, H. et al. Extracting identifying contours for African elephants and humpback whales using a learned appearance model. in Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) (2020).102.Brust, C.-A. et al. Towards automated visual monitoring of individual gorillas in the wild. in 2017 IEEE International Conference on Computer Vision Workshops (ICCVW), 2820–2830 (2017).103.Li, S., Li, J., Tang, H., Qian, R. & Lin, W. ATRW: a benchmark for Amur tiger re-identification in the wild. in 2020 ACM International Conference on Multimedia, 2590–2598 (2020).104.Bendale, A. & Boult, T. E. Towards open set deep networks. in 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 1563–1572 (2016).105.Mathis, M. W. & Mathis, A. Deep learning tools for the measurement of animal behavior in neuroscience. Curr. Opin. Neurobiol. 60, 1–11 (2020).CAS 
    PubMed 

    Google Scholar 
    106.Sanakoyeu, A., Khalidov, V., McCarthy, M. S., Vedaldi, A. & Neverova, N. Transferring dense pose to proximal animal classes. in 2020 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 5233–5242 (2020).107.Zuffi, S., Kanazawa, A., Jacobs, D. W. & Black, M. J. 3D menagerie: modeling the 3D shape and pose of animals. in 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 6365–6373 (2017).108.Biggs, B., Roddick, T., Fitzgibbon, A. & Cipolla, R. Creatures great and smal: recovering the shape and motion of animals from video. in 2018 Asian Conference on Computer Vision (ACCV), 3–19 (Springer, 2018).109.Biggs, B., Boyne, O., Charles, J., Fitzgibbon, A. & Cipolla, R. Who left the dogs out? 3D animal reconstruction with expectation maximization in the loop. in 2020 European Conference on Computer Vision (ECCV), 195–211 (Springer, 2020).110.Zuffi, S., Kanazawa, A., Berger-Wolf, T. & Black, M. J. Three-D safari: learning to estimate zebra pose, shape, and texture from images” in the wild”. in 2019 IEEE International Conference on Computer Vision (ICCV), 5359–5368 (2019).111.Wang, Y., Kolotouros, N., Daniilidis, K. & Badger, M. Birds of a feather: capturing avian shape models from images. in 2021 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 14739–14749 (2021).112.Haalck, L., Mangan, M., Webb, B. & Risse, B. Towards image-based animal tracking in natural environments using a freely moving camera. J. Neurosci. methods 330, 108455 (2020).PubMed 

    Google Scholar 
    113.Pettorelli, N. et al. Satellite remote sensing for applied ecologists: opportunities and challenges. J. Appl. Ecol. 51, 839–848 (2014).
    Google Scholar 
    114.Davies, A. B., Tambling, C. J., Kerley, G. I. H. & Asner, G. P. Effects of vegetation structure on the location of lion kill sites in African thicket. PLoS ONE 11, e0149098 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    115.Froidevaux, J. S. P., Zellweger, F., Bollmann, K., Jones, G. & Obrist, M. K. From field surveys to LiDAR: shining a light on how bats respond to forest structure. Remote Sens. Environ. 175, 242–250 (2016).ADS 

    Google Scholar 
    116.Risse, B., Mangan, M., Stürzl, W. & Webb, B. Software to convert terrestrial LiDAR scans of natural environments into photorealistic meshes. Environ. Model. Softw. 99, 88–100 (2018).
    Google Scholar 
    117.Haalck, L. & Risse, B. Embedded dense camera trajectories in multi-video image mosaics by geodesic interpolation-based reintegration. in 2021 IEEE Winter Conference on Applications of Computer Vision (WACV), 1849–1858 (2021).118.Schonberger, J. L. & Frahm, J.-M. Structure-from-motion revisited. in 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 4104–4113 (2016).119.Mur-Artal, R. & Tardós, J. D. ORB-SLAM2: an open-source SLAM system for monocular, stereo, and RGB-D cameras. IEEE Trans. Robot. 33, 1255–1262 (2017).
    Google Scholar 
    120.Kuppala, K., Banda, S. & Barige, T. R. An overview of deep learning methods for image registration with focus on feature-based approaches. Int. J. Image Data Fusion 11, 113–135 (2020).ADS 

    Google Scholar 
    121.Lisein, J., Linchant, J., Lejeune, P., Bouché, P. & Vermeulen, C. Aerial surveys using an unmanned aerial system (UAS): comparison of different methods for estimating the surface area of sampling strips. Tropical Conserv. Sci. 6, 506–520 (2013).
    Google Scholar 
    122.Wu, C. Critical configurations for radial distortion self-calibration. in 2014 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 25–32 (2014).123.Ferrer, J., Elibol, A., Delaunoy, O., Gracias, N. & Garcia, R. Large-area photo-mosaics using global alignment and navigation data. in Mts/IEEE Oceans Conference, 1–9 (2007).124.Guisan, A. & Zimmermann, N. E. Predictive habitat distribution models in ecology. Ecol. Model. 135, 147–186 (2000).
    Google Scholar 
    125.Lehmann, A., Overton, J. M. & Austin, M. P. Regression models for spatial prediction: their role for biodiversity and conservation. Biodivers. Conserv. 11, 2085–2092 (2002).126.Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).MATH 

    Google Scholar 
    127.Parravicini, V. et al. Global patterns and predictors of tropical reef fish species richness. Ecography 36, 1254–1262 (2013).
    Google Scholar 
    128.Smoliński, S. & Radtke, K. Spatial prediction of demersal fish diversity in the baltic sea: comparison of machine learning and regression-based techniques. ICES J. Mar. Sci. 74, 102–111 (2017).
    Google Scholar 
    129.Čandek, K., Čandek, U. P. & Kuntner, M. Machine learning approaches identify male body size as the most accurate predictor of species richness. BMC Biol. 18, 1–16 (2020).
    Google Scholar 
    130.Baltensperger, A. P. & Huettmann, F. Predictive spatial niche and biodiversity hotspot models for small mammal communities in Alaska: applying machine-learning to conservation planning. Landscape Ecol. 30, 681–697 (2015).131.Faisal, A., Dondelinger, F., Husmeier, D. & Beale, C. M. Inferring species interaction networks from species abundance data: a comparative evaluation of various statistical and machine learning methods. Ecol. Inform. 5, 451–464 (2010).
    Google Scholar 
    132.Van Horn, G. et al. The inaturalist species classification and detection dataset. in 2018 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 8769–8778 (2018).133.Copas, K. et al. Training machines to improve species identification using GBIF-mediated datasets. in AGU Fall Meeting Abstracts, Vol. 2019, IN53C–0758 (2019).134.Lennox, R. J. et al. A novel framework to protect animal data in a world of ecosurveillance. BioScience 70, 468–476 (2020).
    Google Scholar 
    135.Strubell, E., Ganesh, A. & McCallum, A. Energy and policy considerations for deep learning in NLP. in Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics, 3645–3650 (2019).136.Samek, W., Montavon, G., Vedaldi, A., Hansen, L. K. & Müller, K.-R. Explainable AI: Interpreting, Explaining and Visualizing Deep Learning, Vol. 11700 (Springer Nature, 2019).137.Swanson, A. et al. Snapshot Serengeti, high-frequency annotated camera trap images of 40 mammalian species in an African savanna. Sci. data 2, 1–14 (2015).
    Google Scholar 
    138.de Lutio, R. et al. Digital taxonomist: identifying plant species in community scientists’ photographs. ISPRS J. Photogramm. Remote Sens. 182, 112–121 (2021).139.Mac Aodha, O., Cole, E. & Perona, P. Presence-only geographical priors for fine-grained image classification. in Proceedings of the IEEE/CVF International Conference on Computer Vision, 9596–9606 (2019).140.Gurumurthy, S. et al. Exploiting Data and Human Knowledge for Predicting Wildlife Poaching. in Proceedings of the 1st ACM SIGCAS Conference on Computing and Sustainable Societies, 1–8, https://doi.org/10.1145/3209811.3209879 (ACM, 2018).141.Datta, S., Anderson, D., Branson, K., Perona, P. & Leifer, A. Computational neuroethology: a call to action. Neuron 104, 11–24 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    142.Joska, D. et al. AcinoSet: a 3D pose estimation dataset and baseline models for Cheetahs in the wild. 2021 IEEE International Conference on Robotics and Automation (ICRA) Preprint at https://arxiv.org/abs/2103.13282 (IEEE, Xi’an, China, 2021).143.Chen, Q. & Koltun, V. Photographic image synthesis with cascaded refinement networks. in 2019 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 1511–1520 (2017).144.Lee, J., Hwangbo, J., Wellhausen, L., Koltun, V. & Hutter, M. Learning quadrupedal locomotion over challenging terrain. Sci. Robot. 5, eabc5986 (2020).145.Botella, C., Joly, A., Bonnet, P., Munoz, F. & Monestiez, P. Jointly estimating spatial sampling effort and habitat suitability for multiple species from opportunistic presence-only data. Methods Ecol. Evolution 12, 933–945 (2021).
    Google Scholar 
    146.Beery, S., Cole, E., Parker, J., Perona, P. & Winner, K. Species distribution modeling for machine learning practitioners: a review. in Proceedings of the 4th ACM SIGCAS Conference on Computing and Sustainable Societies (2021).147.Arzoumanian, Z., Holmberg, J. & Norman, B. An astronomical pattern-matching algorithm for computer-aided identification of whale sharks Rhincodon typus. J. Appl. Ecol. 42, 999–1011 (2005).
    Google Scholar 
    148.de Knegt, H. J., Eikelboom, J. A. J., van Langevelde, F., Spruyt, W. F. & Prins, H. H. T. Timely poacher detection and localization using sentinel animal movement. Sci. Rep. 11, 1–11 (2021).
    Google Scholar 
    149.Walter, T. & Couzin, I. D. TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields. eLife 10, e64000 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    150.Kellenberger, B., Tuia, D. & Morris, D. AIDE: accelerating image-based ecological surveys with interactive machine learning. Methods Ecol. Evolution 11, 1716–1727 (2020).
    Google Scholar 
    151.Settles, B. Active learning. Synth. lectures Artif. Intell. Mach. Learn. 6, 1–114 (2012).MathSciNet 
    MATH 

    Google Scholar 
    152.Ofli, F. et al. Combining human computing and machine learning to make sense of big (aerial) data for disaster response. Big Data 4, 47–59 (2016).PubMed 

    Google Scholar 
    153.Simpson, R., Page, K. R. & De Roure, D. Zooniverse: observing the world’s largest citizen science platform. in Proceedings of the 23rd International Conference on World Wide Web 1049–1054 (2014).154.Pocock, M. J. O., Roy, H. E., Preston, C. D. & Roy, D. B. The biological records centre: a pioneer of citizen science. Biol. J. Linn. Soc. 115, 475–493 (2015).
    Google Scholar  More

  • in

    Estimating mangrove forest gross primary production by quantifying environmental stressors in the coastal area

    The improved performance of the mangrove LUE model considering coastal environments in this study was mainly attributed to the determination of environmental scalars. Parameters determining environmental stressors (e.g., Topt, Tmin, Tmax, VPDmin, and VPDmax) were set based on the general characteristics of mangroves worldwide. It may not be as accurate for the mangroves in our study sites, but it generally reflects the response of mangroves to environmental changes. Furthermore, as can be seen in Fig. S1, it is applicable to our study sites. Despite the specific characteristics of each mangrove ecosystem at different sites being preferred, this study first offers the possibility to estimate mangrove productivity at a larger scale to track GPP, thus emphasizing the role of mangrove ecosystems nationally or worldwide.The validation results showed that the LUE values of the mangrove model agreed well with those estimated by EC method (Fig. 3) and indicated improved performance (slope = 0.8218–1.0108, intercept = -0.0006–0.0052, R2 = 0.54–0.64, RMSE = 0.0051–0.0068, Pearson’s r = 0.73–1), compared to the MOD17 model (slope = 0.4993–0.5566, intercept = 0.0311–0.0313, R2 = 0.24–0.45, RMSE = 0.0217–0.0220, Pearson’s r = 0.45–0.49). Firstly, the RS-based LUE model for terrestrial ecosystems (MOD17) considers only the environmental stressors of Tair and VPD. The photosynthesis in mangrove forests is influenced by other unique environmental factors caused by tidal inundation. According to Fig. S3, PAR caused the most significant effect on LUE, which is consistent with previous studies14,30,32. The impact of SST has not been quantitatively assessed, however, SST is a critical control that determines the upper latitudinal range of mangrove ecosystems12,33. In our study, the effects of SST and salinity on the mangrove LUE were quantified and helped improve LUE modeling.Secondly, LUEmax was typically defined for different land covers, however, there were no specific values for mangrove forests. In this study, the LUEmax of mangroves was first determined. It is worth noting that daytime NEE responses to PAR vary depending on the Tair23,30,34 so that LUEmax was determined separately at high, optimal, and low temperatures. The results showed that LUEmax reached a maximum when Tair was within the optimal range for mangroves, which represents the high productivity of mangrove ecosystems. Furthermore, the estimated LUEmax of mangrove forests (0.057) was larger than most terrestrial forests35,36,37, which could contribute to the high production and carbon sequestration in mangrove forests.Lastly, the relatively low stomatal conductance of mangroves leads to low LSP compared with terrestrial forests, which could result in the high-irradiance stress for photosynthesis38,39. Mangrove LSP ranges from about 0.2–1.2 mmol/m2/s, depending on the species and environments40,41,42. LUE was relatively low in April and May when seasonal PAR was high, as photosynthesis is more likely to reach saturation. Therefore, we assumed the LUE of mangroves decreased with increasing PAR. In addition, we found that the downscaling effect of PAR on LUE was not constant, but varied with increasing PAR. As follows, different PAR scalars were set for mangroves according to different PAR values. This is a first attempt at refining PARscalar considering different solar radiation, which represents a significant departure from the assumption of a constant downscaling effect of PAR in RS-driven models14,43. The accuracy of the LUE model was improved by refining the PARscalar with different downscaling slopes, especially in periods of high PAR values.Compared with the results obtained from flux-tower measurements, the modeled GPP was basically within the confidence interval of the measured results. The annual averages of GPP in Zhangjiang were 1729 g C/m2/year and 1924 g C/m2/year, in 2012 and 2016, and the annual mean value of GPP in Zhanjiang was 1434 g C/m2/year in 2015. The previous study showed that the GPP in Zhangjiang ranged from 1763 to 1919 g C/m2/year with a mean value of 1871 g C/m2/year32,44,45, which is in good agreement with the estimated values obtained in this study. Liu and Lai46 reported that the GPP of the Mai Po mangrove reserve was 2827 g C/m2/year. Rodda, et al.20 found a GPP value of 1271 g C/m2/year for Sunderbans mangroves in India. Gnanamoorthy, et al.47 estimated a GPP of 2305 g C/m2/year for Pichavaram mangroves. Variations in these estimates across sites were possibly caused by different climate-hydrological conditions, mangrove species, and ages. Differences in the same location may be due to different time scales and different methods of data gap filling and flux partitioning.In a similar way to the GPP model for terrestrial ecosystems48, the effect of the mangrove GPP model on the accuracy of GPP estimates can vary considerably under different environmental conditions. However, in comparison with the accuracy of models built for other vegetation types, the GPP model in this study performed substantially in two sites with RMSE of 2.54–3.41 g C/m2/day. Wang et al.49 adopted different models to estimate GPP for global vegetation and validation results showed the RMSE ranged from 1.79 to 2.33 g C/m2/day. Xiao, et al.50 demonstrated that the deviation between observed and predicted GPP was about 35–282 g C/m2 in an evergreen needleleaf forest. Also, the absolute GPP errors were 7.94–20.92% and 9.97–13.70% for maize cropland and degraded grassland36. Despite the discrepancy, our results were generally consistent with previous studies and were verified by field observations near the flux towers.The comparison of MODIS GPP and EC-estimated GPP showed that the MODIS GPP had a large fluctuation and weakly reflected productivity, being overestimated in 2012 and underestimated in 2015. Different meteorological inputs, different environmental scalars and fraction of absorbed photosynthetic active radiation (fAPAR) products in MODIS GPP and our mangrove GPP model can explain their different results. However, the improvements in our GPP model may help to obtain more accurate GPP estimates. The response of mangrove productivity to Tair has not been well-calibrated in the MODIS GPP product, which may partly account for the poor correlation between the MODIS GPP and EC estimates. Besides, MODIS GPP product was developed based on the International Geosphere-Biosphere Programme (IGBP) land cover map, which doesn’t include mangroves as a specific land cover37. Therefore, LUEmax and environmental parameters were not defined for mangroves, which varied with different environments. This may lead to uncertainty in MODIS GPP product for mangrove forests14. However, the GPP model generated in our study showed similar trends to the field measurements, capturing seasonal variations. The increase in the difference between MODIS GPP and EC estimates may be due to the assumption that the increase in GPP is linear with respect to PAR. In our model, the response of GPP to PAR was suppressed, resulting in seasonal changes in GPP that better match the observations. In addition, the GPP derived from this study was in higher agreement with measured values compared with GPP estimated from the vegetation photosynthesis model (VPM), as shown in Fig. S4. The improvement of this model was more obvious in winter (December to February), which may be due to the environmental stress of SST and PAR. The VPM without considering SSTscalar and PARscalar overestimated GPP in winter. It is indicated that the performance of the mangrove GPP model in this study varied with season. It is recommended to improve the estimation of GPP in the future by considering the seasonal variation of mangrove forests when determining environmental variables.Most studies provide EC-based estimates of GPP that are measurements from a limited footprint. It is possible to extrapolate results across similar vegetation types and geographic settings, but not to areas of heterogeneous vegetation. The RS-based GPP model offers spatial-scale estimates that can be directly incorporated into ecosystem-type models. PAR, SST, and salinity are the key environmental parameters of this RS-based mangrove GPP model. SST and salinity data were derived from the satellite images, while PAR was generated from the reconstructed PAR data, since it is more accurate than the existing RS data and has historical year data. However, PAR products from Hamawari-8, MERIS, and SeaWiFS are available now, which provide an opportunity to obtain large-scale PAR data using RS in the future. In addition to this, GPP of two mangrove forests was assessed and validated with three-year measurements. Validation at different sites and years showed similar results, which indicated the model has similar performance across mangrove forests. Nonetheless, these estimates need to be corroborated with EC databases, which are relatively accurate and provide many additional variables that are currently beyond the scope of higher spatial-resolution RS estimates. The proposed GPP model considering coastal environments was well suited to extend the study area by incorporating RS information and meteorological data. Currently, there are still few mangrove carbon flux towers worldwide. The LUE and GPP models proposed in this study are difficult to validate with measurements from flux towers in other countries. However, local measurements are available in many countries with large mangrove forests, such as Thailand, Vietnam, India, and Bangladesh. Therefore, it is expected that comparisons with measurements from previous studies can be conducted to show the consistency and applicability.The LUE model considering the effects of SST, salinity, and PAR performed well, however, the GPP estimated from the LUE, fAPAR, and PAR showed discrepancies and were generally lower than the measured values. Although the results are better than MODIS GPP products, limitations exist still.Firstly, the effects of salinity and SST on mangrove productivity were directly related to tidal activities. The soil pore water and surface water salinity could affect the osmotic pressure of mangroves especially for the submerged parts which would control the stomatal conductance. In the same way, SST could influence the temperature of mangrove root systems and soil sediments which has impacts on mangrove roots’ respiration and transpiration. Although, theoretically, salinity and SST should be considered as environmental variables affecting mangrove LUE, our results (Fig. S3) indicated that salinity and SST have little influence on mangrove productivity51. To date, the quantitative impact of SST has not been comprehensively unfolded, but it is a global control that determines the upper limit of the latitudinal range of mangroves12,33. The weak relationships between salinity, SST, and mangrove GPP could be due to the uncertainty caused by tidal inundation. Tide duration, tide height, and tide cycle would determine the effect of salinity and SST on the mangrove LUE and GPP. However, quantifying the influence from the tidal cycle remains a challenging task, which could result in the relatively poor performance of Salinityscalar and SSTscalar as shown in Fig. S3. Quantifying the soil temperature and surface water salinity considering the tidal cycle will contribute to model the LUE and GPP of mangrove forests.Secondly, mangroves of different species and ages exhibit diverse structural and physical conditions, resulting in different LUEmax, and optimal growing conditions such as Topt and VPDmin. The environmental settings would also vary from region to region. Liu and Lai46 found that LUE increased slightly with the increasing salinity below 15 ppt (R2 = 0.16). However, it was noted that photosynthetic activity of mangroves would be inhibited when the surface water salinity was high30,51,52,53. Probably, the mutual relationship between LUE and salinity depends on the salinity level and mangrove species. However, we have not specified the variables for different mangrove species, ages and locations which could be improved in the future. Besides, there are multicollinearities between different environmental variables. For example, Tair may have effects on SST and VPD, but as shown in Fig. S5, they are all important for mangrove photosynthesis. However, the correlations between them are not clear and need to be quantified in the future.Thirdly, the relatively low spatial and temporal resolution of the environmental data from RS would influence the accuracy of the model. The datasets have a relatively coarse resolution (usually 500 m–1 km and daily) and are thereby less suitable for smaller nature reserves, especially in the narrow patches of mangrove areas that are rapidly being exploited in coastal China. Moreover, the variability in LUE decreases with increasing temporal scale54. In our study, we determined the PARscalar based on the response of LUE to hourly-scale PAR and found the different down-regulation effects with increasing PAR. However, this phenomenon is not obvious in previous studies. Most RS-based LUE models were developed at a daily or 8-day temporal scale6,50,55,56,57. In terrestrial forests, the light saturated effect caused by increasing PAR was neglectable with coarse temporal scale because the average PAR was usually lower than the LSP. However, as the time scale increases, the effect of light saturation on LUE becomes more pronounced32,58,59. More importantly, this effect is more obvious in mangroves due to their lower LSP18,38, which makes it important in mangrove LUE modeling. The results in Fig. 3 show similar performances of LUE model on hourly and daily scale. Thus, we suggested that our model can be adopted in hourly and daily temporal resolution. However, the PARscalar developed in this study was based on the mangrove forests in one study site which may be influenced by the mangrove species with different LSP and light conditions. What’s more, VPD was on a monthly scale, which cannot reflect environmental dynamics. However, the hourly and daily VPD data are currently not available for coastal areas in China. Therefore, we used monthly averages to represent daily VPD, which may lead to uncertainty in the derived GPP estimates (Figs. 6 and 7). Besides, porewater salinity is controlled by sea surface salinity, precipitation, and river discharge. However, currently, pore water salinity was expressed in terms of sea surface salinity, which may lead to an underestimation of Salinityscalar. More systematic study is necessary to make it more applicable and accurate on a large scale, of which modeling the LUE for different mangrove species and locations is inevitable. However, serving as a fundamental and preliminary step, our study aims to provide a framework for RS-based mangrove GPP modeling. Recently, with the advancement of satellite imagery, hourly-scale RS data for PAR, temperature and SST are available. It can be expected that our current work could be further improved by investigating the light saturation effects in different mangrove forests and adopt higher temporal resolution RS products such as Himawari-8 and GCOM-C in the future.Lastly, the overall underestimation of GPP was mainly caused by the underestimation of fAPAR. Even though the fAPAR computed from Sentinel-2 had higher resolution and accuracy than MODIS fAPAR products, future improvements are still needed. Sentinel-2 fAPAR products (fAPAR-S2) was calculated as the instantaneous fAPAR obtained at 10:00 local solar time which only roughly represented the daily average but was not accurate. Besides, RS-derived fAPAR only considers the absorptions by living green vegetation elements, whereas the ground measured fAPAR refers to the contributions from all absorbing components60. The lower fAPAR-S2 values in mangrove forests may be due to the exposed-to-air root systems which absorb the radiation. Moreover, the spatial distribution of PAR was determined by Co-Kriging interpolation. The elevation was taken as the covariate to estimate spatial PAR. There are many other variables affecting the incoming PAR (e.g., slope and clearness)61. A more comprehensive set of variables needs to be included in the Co-kriging interpolation to improve the PAR estimation.The spatial and seasonal variations of the mangrove GPP were related to environmental changes along the shoreline. The low summer GPP was explained by the lower fAPAR in summer compared with other seasons, which was principally due to the underestimation of fAPAR in summer. Furthermore, PARscalar took a mean value of LSP as 1 mmol/m2/s, however, LSP varied with different species and environmental conditions. In summer, mangroves are more likely to obtain light saturation, and thus PARscalar may lead to an underestimation of LUE and thus GPP. On the contrary, PAR values in winter were relatively low but increased slightly with decreasing latitude. Thus, the inhibitory effect of PAR on LUE was not significant, and GPP increased with decreasing latitude. Salinity and VPD were more stable across years and locations and had no noticeable effect on the mangrove LUE and GPP. The seasonal latitudinal patterns and effects on mangrove productivity were similar for Tair and SST. Tair and SST were lower in winter, especially at high latitudes where mangroves were more sensitive to cold weather. Therefore, the GPP of mangroves at high latitudes in winter was the lowest throughout the year. However, hot weather in summer also limited the photosynthesis in mangroves, especially at low latitudes, where Tair and SST were higher. Nevertheless, there were some correlations among these environmental constants. For example, the Tair affects the vapor pressure and SST. There was a positive correlation between PAR and Tair. The multicollinearity among these variables and the various conditions of mangroves may affect the performance of the model and show variations along the coastline, which would be improved in future studies.Additionally, the GPP of mangroves increased from 2007 to 2018, which was mainly due to the expansion of mangrove forests in the coastal areas. As mangroves grow, canopy size and tree density increase, which may lead to higher LUE and less underestimation of fAPAR, thus contributing to high productivity. However, Zhejiang province (27° 02′ N–31° 11′ N) experienced extremely cold weather in January 2016 caused by the East Asia cold wave62,63, and large areas of mangrove forests died or became sick, leading to a decline in the mangrove GPP at high latitudes in 2018. More

  • in

    Narrowly distributed taxa are disproportionately informative for conservation planning

    1.Balmford, A. & Gaston, K. J. Why biodiversity surveys are good value How the ‘terror crocodile’ grew so big. Nature 398, 204–205 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    2.Rondinini, C., Marco, M. D., Visconti, P., Butchart, S. H. M. & Boitani, L. Update or outdate: Long-term viability of the IUCN Red List Making the Red List financially. Conserv. Lett. 7, 126–130 (2014).Article 

    Google Scholar 
    3.Braithwaite, M. E. & Walker, K. J. 50 Years of Mapping the British and Irish Flora 1962–2012 (Botanical Society of the British Isles, 2012).
    Google Scholar 
    4.Barrett, G., Silcocks, A., Barry, S., Cunningham, R. & Poulter, R. The New Atlas of Australian Birds (Royal Australasian Ornithologists Union, 2003).
    Google Scholar 
    5.Biodiversity Center of Japan. Animal Distribution Atlas of Japan (Ministry of Environment Japan, 2010).
    Google Scholar 
    6.McGowan, K. & Corwin, K. The Second Atlas of Breeding Birds in New York State (Comstock Publishing Associates, 2008).
    Google Scholar 
    7.Rhoads, A. F. & Klein, W. M. J. The vascular Flora of Pennsylvenia: Annoted Checklist and Atlas (American Philosophical Society, 1993).
    Google Scholar 
    8.Baker, H. et al. Population estimates of birds in Great Britain and the United Kingdom British Birds. Br. Birds 99, 25–44 (2006).
    Google Scholar 
    9.Bonn, A., Rodrigues, A. S. L. & Gaston, K. J. Threatened and endemic species: Are they good indicators of patterns of biodiversity on a national scale?. Ecol. Lett. 5, 733–741 (2002).Article 

    Google Scholar 
    10.Albuquerque, F. & Beier, P. Rarity-weighted richness: A simple and reliable alternative to integer programming and heuristic algorithms for minimum set and maximum coverage problems in conservation planning. PLoS ONE 10, e0119905 (2015).Article 

    Google Scholar 
    11.Williams, P. et al. A comparison of richness hotspots, rarity hotspots, and complementary areas for conserving diversity of British birds. Conserv. Biol. 10, 155–174 (1996).Article 

    Google Scholar 
    12.Platts, P. J. et al. Conservation implications of omitting narrow-ranging taxa from species distribution models, now and in the future. Divers. Distrib. 20, 1307-1320. (2014).Article 

    Google Scholar 
    13.Kujala, H., Moilanen, A. & Gordon, A. Spatial characteristics of species distributions as drivers in conservation prioritization. Methods Ecol. Evol. 9, 1121–1132 (2018).Article 

    Google Scholar 
    14.Kukkala, A. S. & Moilanen, A. Core concepts of spatial prioritisation in systematic conservation planning. Biol. Rev. Camb. Philos. Soc. 88, 443–464 (2013).Article 

    Google Scholar 
    15.Lawler, J. J., White, D., Sifneos, J. C. & Master, L. L. Rare species and the use of indicator groups for conservation planning. Conserv. Biol. 17, 875–882 (2003).Article 

    Google Scholar 
    16.Kujala, H., Lahoz-Monfort, J. J., Elith, J. & Moilanen, A. Not all data are equal: Influence of data type and amount in spatial conservation prioritisation. Methods Ecol. Evol. 9, 2249–2261 (2018).Article 

    Google Scholar 
    17.Grantham, H. S. et al. Diminishing return on investment for biodiversity data in conservation planning. Conserv. Lett. 1, 190–198 (2008).Article 

    Google Scholar 
    18.Margules, C. R. & Pressey, R. L. Systematic conservation planning. Nature 405, 243–253 (2000).CAS 
    Article 

    Google Scholar 
    19.Moilanen, A., Wilson, K. A. & Possingham, H. Spatial Conservation Prioritization: Quantitative Methods and Computational Tools (Oxford University Press, 2009).
    Google Scholar 
    20.Akasaka, M., Kadoya, T., Ishihama, F., Fujita, T. & Fuller, R. A. Smart protected area placement decelerates biodiversity loss: A representation-extinction feedback leads rare species to extinction. Conserv. Lett. 10, 539–546 (2017).Article 

    Google Scholar 
    21.Boakes, E., McGowan, P. & Fuller, R. Distorted views of biodiversity: spatial and temporal bias in species occurrence data. PLoS Biol. 8, e1000385 (2010).Article 

    Google Scholar 
    22.Williams, P. H., Margules, C. R. & Hilbert, D. W. Data requirements and data sources for biodiversity priority area selection. J. Biosci. 27, 327–338 (2002).CAS 
    Article 

    Google Scholar 
    23.Da Fonseca, G. A. B. et al. … following Africa’s lead Community groups could. Nature 405, 393–394 (2000).Article 

    Google Scholar 
    24.Possingham, H. P., Grantham, H. & Rondinini, C. How can you conserve species that haven’t been found? Commentary. J. Biogeogr. 34, 758–759 (2007).Article 

    Google Scholar 
    25.Ohlemuller, R. et al. The coincidence of climatic and species rarity: High risk to small-range species from climate change. Biol. Lett. 4, 568–572 (2008).Article 

    Google Scholar 
    26.Kier, G. et al. A global assessment of endemism and species richness across island and mainland regions. Proc. Natl. Acad. Sci. USA. 106, 9322–9327 (2009).ADS 
    CAS 
    Article 

    Google Scholar 
    27.Raes, N., Roos, M. C., Slik, J. W. F., Van Loon, E. E. & Steege, H. T. Botanical richness and endemicity patterns of Borneo derived from species distribution models. Ecography (Cop.) 32, 180–192 (2009).Article 

    Google Scholar 
    28.Tulloch, A. I. T., Mustin, K., Possingham, H. P., Szabo, J. K. & Wilson, K. A. To boldly go where no volunteer has gone before: predicting volunteer activity to prioritize surveys at the landscape scale. Divers. Distrib. 19, 465–480 (2013).Article 

    Google Scholar 
    29.Rodewald, A. D., Strimas-Mackey, M., Schuster, R. & Arcese, P. Tradeoffs in the value of biodiversity feature and cost data in conservation prioritization. Sci. Rep. 9, 5921 (2019).Article 

    Google Scholar 
    30.Rabinowitz, D. Seven forms of rarity. In The biological aspects of rare plant conservation. (ed. Synge, H.) 205–217 (Wiley, Chichester, 1981).
    Google Scholar 
    31.Ministry of Environment. Red Data Book 2014: Plants I (Gyousei, 2015).
    Google Scholar 
    32.Ministry of Environment. Red Data Book 2014: Plants II (Gyousei, 2015).
    Google Scholar 
    33.Yahara, T. et al. Red list of Japanese vascular plants: Summary of methods and results. Proc. Japan. Soc. Plant Taxon. 13, 89–96 (1998).
    Google Scholar 
    34.Ball, I. R., Possingham, H. P. & Watts, M. Marxan and relatives: Software for spatial conservation prioritisation. In Spatial Conservation Prioritisation: Quantitative Methods and Computational Tools (eds Moilanen, A. et al.) 185–195 (Oxford University Press, 2009).
    Google Scholar 
    35.Yoshioka, A., Akasaka, M. & Kadoya, T. Spatial prioritization for biodiversity restoration: A simple framework referencing past species distributions. Restor. Ecol. 22, 185–195 (2014).Article 

    Google Scholar 
    36.Naidoo, R. et al. Integrating economic costs into conservation planning. Trends Ecol. Evol. 21, 681–687 (2006).Article 

    Google Scholar 
    37.Japan Statistics. Population of Japan: Final Report of the 2005 Population Census. (Statistics Japan, 2010).38.R Core Team. R 4.0.0. (R Foundation for Statistical Computing, 2020).39.Zweig, M. H. & Campbell, G. Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine. Clin. Chem. 39, 561–577 (1993).CAS 
    Article 

    Google Scholar 
    40.Hermoso, V., Ward, D. P. & Kennard, M. J. Using water residency time to enhance spatio-temporal connectivity for conservation planning in seasonally dynamic freshwater ecosystems. J. Appl. Ecol. 49, 1028–1035 (2012).Article 

    Google Scholar 
    41.Beyer, H. L., Dujardin, Y., Watts, M. E. & Possingham, H. P. Solving conservation planning problems with integer linear programming. Ecol. Modell. 328, 14–22 (2016).Article 

    Google Scholar 
    42.Schuster, R., Hanson, J. O., Strimas-Mackey, M. & Bennett, J. R. Integer linear programming outperforms simulated annealing for solving conservation planning problems. PeerJ 8, e9258. https://doi.org/10.7717/peerj.9258 (2020).Article 

    Google Scholar  More

  • in

    Consider fungal friends

    Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
    the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
    Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
    and JavaScript. More

  • in

    Pantanal fires

    Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
    the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
    Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
    and JavaScript. More

  • in

    Giant sponge grounds of Central Arctic seamounts are associated with extinct seep life

    1.Maldonado, M. et al. in Marine Animal Forests: The Ecology of Benthic Biodiversity Hotspots (eds. Rossi, S., Bramanti, L., Gori, A. & del Valle, C.) (Springer, 2016).2.de Goeij, J. M. et al. Surviving in a marine desert: the sponge loop retains resources within coral reefs. Science 342, 108–110 (2013).ADS 
    PubMed 

    Google Scholar 
    3.Beazley, L., Kenchington, E., Yashayaev, I. & Murillo, F. J. Drivers of epibenthic megafaunal composition in the sponge grounds of the Sackville Spur, northwest. Atl. Deep. Res. Part I 98, 102–114 (2015).
    Google Scholar 
    4.Klitgaard, A. B. & Tendal, O. S. Progress in oceanography distribution and species composition of mass occurrences of large-sized sponges in the northeast Atlantic. Prog. Oceanogr. 61, 57–98 (2004).ADS 

    Google Scholar 
    5.Kazanidis, G. et al. Distribution of deep-sea sponge aggregations in an area of multisectoral activities and changing oceanic conditions. Front. Mar. Sci. 6, 163 (2019).
    Google Scholar 
    6.Hanz, U., Roberts, E. M., Duineveld, G., Davies, A. & Rapp, H. T. Long – term observations reveal environmental conditions and food supply mechanisms at an Arctic deep-sea sponge ground. J. Geophisical. Res. 126, 1–18 (2021).
    Google Scholar 
    7.Roberts, E. et al. Water masses constrain the distribution of deep-sea sponges in the North Atlantic Ocean and Nordic Seas. Mar. Ecol. Prog. Ser. 659, 75–96 (2021).ADS 

    Google Scholar 
    8.Cathalot, C. et al. Cold-water coral reefs and adjacent sponge grounds: hotspots of benthic respiration and organic carbon cycling in the deep sea. Front. Mar. Sci. 2, 37 (2015).
    Google Scholar 
    9.Kahn, A. S., Yahel, G., Chu, J. W. F., Tunnicliffe, V. & Leys, S. P. Benthic grazing and carbon sequestration by deep-water glass sponge reefs. Limnol. Oceanogr. 60, 78–88 (2015).ADS 

    Google Scholar 
    10.Morganti, T., Coma, R., Yahel, G. & Ribes, M. Trophic niche separation that facilitates co-existence of high and low microbial abundance sponges is revealed by in situ study of carbon and nitrogen fluxes. Limnol. Oceanogr. 62, 1963–1983 (2017).ADS 
    CAS 

    Google Scholar 
    11.Kutti, T., Bannister, R. J. & Fosså, J. H. Community structure and ecological function of deep-water sponge grounds in the Traenadypet MPA — Northern Norwegian continental shelf. Cont. Shelf Res. 69, 21–30 (2013).ADS 

    Google Scholar 
    12.Bart, M. C. et al. Dissolved organic carbon (DOC) is essential to balance the metabolic demands of four dominant North-Atlantic deep-sea sponges. Limnol. Oceanogr. 9999, 1–14 (2020).
    Google Scholar 
    13.Gloeckner, V. et al. The HMA-LMA dichotomy revisited: an electron microscopical survey of 56 sponge species. Biol. Bull. 227, 78–88 (2014).PubMed 

    Google Scholar 
    14.Bruck, T. B., Self, W. T., Reed, J. K., Nitecki, S. S. & McCarthy, P. J. Comparison of the anaerobic microbiota of deep-water Geodia spp. and sandy sediments in the Straits of Florida. ISME J. 4, 686–699 (2010).PubMed 

    Google Scholar 
    15.Schottner, S. et al. Relationships between host phylogeny, host type and bacterial community diversity in cold-water coral reef sponges. PLoS ONE 8, 1–11 (2013).
    Google Scholar 
    16.Hoffmann, F. et al. An anaerobic world in sponges. Geomicrobiol. J. 22, 1–10 (2005).
    Google Scholar 
    17.Schlindwein, V. & Schmid, F. Mid-ocean-ridge seismicity reveals extreme types of ocean lithosphere. Nature 535, 276–279 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    18.Cochran, J. R. Seamount volcanism along the Gakkel Ridge. Arct. Ocean. Geophys. J. Int. 174, 1153–1173 (2008).ADS 

    Google Scholar 
    19.Arrigo, K. R., van Dijken, G. & Pabi, S. Impact of a shrinking Arctic ice cover on marine primary production. Geophys. Res. Lett. 35, L19603 (2008).ADS 

    Google Scholar 
    20.Wassmann, P., Slagstad, D. & Ellingsen, I. Primary production and climatic variability in the European sector of the Arctic Ocean prior to 2007: preliminary results. Polar Biol. 33, 1641–1650 (2010).
    Google Scholar 
    21.Wiedmann, I. et al. What feeds the Benthos in the Arctic Basins? Assembling a carbon budget for the deep Arctic Ocean. Front. Mar. Sci. 7, 224 (2020).
    Google Scholar 
    22.Boetius, A. & Purser, A. The Expedition PS101 of the Research Vessel POLARSTERN to the Arctic Ocean in 2016, Berichte zur Polar- und Meeresforschung = Reports on polar and marine research, Bremerhaven, Alfred Wegener Institute for Polar and Marine Research. (2017).23.Alvizu, A., Xavier, J. R. & Rapp, H. T. Description of new chiactine-bearing sponges provides insights into the higher classification of Calcaronea (Porifera: Calcarea). Zootaxa 4615, 201–251 (2019).
    Google Scholar 
    24.Rybakova, E., Kremenetskaia, A., Vedenin, A., Boetius, A. & Gebruk, A. Deep-sea megabenthos communities of the Eurasian Central Arctic are influenced by ice-cover and sea-ice algal falls. PLoS ONE 14, 1–27 (2019).
    Google Scholar 
    25.Astrom, E. K. L. et al. Methane cold seeps as biological oases in the high-Arctic deep sea. Limnol. Oceanogr. 63, 209–231 (2018).
    Google Scholar 
    26.Sen, A., Didriksen, A., Hourdez, S., Svenning, M. M. & Rasmussen, T. L. Frenulate siboglinids at high Arctic methane seeps and insight into high latitude frenulate distribution. Ecol. Evol. 10, 1339–1351 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    27.Henrich, R. et al. Facies belts and communities of the arctic Vesterisbanken Seamount (Central Greenland Sea). Facies 27, 71 (1992).
    Google Scholar 
    28.Leys, S. P., Kahn, A. S., Fang, J. K. H., Kutti, T. & Bannister, R. J. Phagocytosis of microbial symbionts balances the carbon and nitrogen budget for the deep-water boreal sponge Geodia barretti. Limnol. Oceanogr. 63, 187–202 (2018).ADS 
    CAS 

    Google Scholar 
    29.Druffel, E. R. M., Griffin, S., Glynn, C. S., Benner, R. & Walker, B. D. Radiocarbon in dissolved organic and inorganic carbon of the Arctic Ocean. Geophys. Res. Lett. 44, 2369–2376 (2017).ADS 
    CAS 

    Google Scholar 
    30.Mehrshad, M., Rodriguez-Valera, F., Amoozegar, M. A., López-García, P. & Ghai, R. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME J. 12, 655–668 (2018).CAS 
    PubMed 

    Google Scholar 
    31.Petersen, J. M., Wentrup, C., Verna, C., Knittel, K. & Dubilier, N. Origins and evolutionary flexibility of chemosynthetic symbionts from deep-sea animals. Biol. Bull. 223, 123–137 (2012).CAS 
    PubMed 

    Google Scholar 
    32.Rubin-Blum, M. et al. Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts. ISME J. 13, 1209–1225 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Bayer, K., Jahn, M. T., Slaby, B. M., Moitinho-Silva, L. & Hentschel, U. Marine sponges as chloroflexi hot spots: genomic insights and high-resolution visualization of an abundant and diverse symbiotic clade. mSystems 3, e00150–18 (2018).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    34.Kamke, J. et al. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J. 7, 2287–2300 (2013).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    35.Bayer, K. et al. Microbial strategies for survival in the glass sponge Vazella pourtalesii. mSystems 5, e00473–20 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    36.Van Duyl, F. C., Hegeman, J., Hoogstraten, A. & Maier, C. Dissolved carbon fixation by sponge-microbe consortia of deep water coral mounds in the northeastern Atlantic Ocean. Mar. Ecol. Prog. Ser. 358, 137–150 (2008).ADS 

    Google Scholar 
    37.Leitner, A. B., Neuheimer, A. B. & Drazen, J. C. Evidence for long-term seamount-induced chlorophyll enhancements. Sci. Rep. 10, 12729 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    38.von Appen, W.-J., Latarius, K. & Kanzow, T. Physical oceanography and current meter data from mooring F6-17. Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven (2017). https://doi.org/10.1594/PANGAEA.870845.39.Woodgate, R. Arctic ocean circulation: going around at the top of the world. Nat. Educ. Knowl. 4, 8 (2013).
    Google Scholar 
    40.White, M., Bashmachnikov, I., Arístegui, J. & Martins, A. in Seamounts: Ecology, Fisheries & Conservation (eds Pitcher, T. J. et al.) Ch. 4 (Wiley, 2007).41.Buchs, D. M., Hoernle, K. & Grevemeyer, I. In Encyclopedia of Marine Geosciences (eds Harff, J., Meschede, M., Petersen, S. & Thiede, J.) (Springer, Dordrecht, 2015). https://doi.org/10.1007/978-94-007-6644-0_34-2.42.Emerson, D. & Moyer, C. Microbiology of seamounts: common patterns observed in community structure. Oceanography 23, 148–163 (2010).
    Google Scholar 
    43.Rimskaya-Korsakova, N. N. et al. First discovery of pogonophora (Annelida, Siboglinidae) in the Kara Sea coincide with the area of high methane concentration. Dokl. Biol. Sci. 490, 25–27 (2020).CAS 
    PubMed 

    Google Scholar 
    44.Cardenas, P. & Rapp, H. T. Demosponges from the Northern mid-Atlantic ridge shed more light on the diversity and biogeography of North Atlantic deep-sea sponges. J. Mar. Biol. Assoc. U. Kindom 95, 1475–1516 (2015).
    Google Scholar 
    45.Meyer, H. K., Roberts, E. M., Rapp, H. T. & Davies, A. J. Spatial patterns of arctic sponge ground fauna and demersal fish are detectable in autonomous underwater vehicle (AUV) imagery. Deep. Res. Part I Oceanogr. Res. Pap. 153, 103137 (2019).
    Google Scholar 
    46.Grebmeier, J. M. et al. Ecosystem characteristics and processes facilitating persistent macrobenthic biomass hotspots and associated benthivory in the Pacific Arctic. Prog. Oceanogr. 136, 92–114 (2015).ADS 

    Google Scholar 
    47.Oevelen, D. Van et al. The cold-water coral community as a hot spot for carbon cycling on continental margins: a food-web analysis from Rockall Bank (northeast Atlantic). Limnol. Oceanogr. 54, 1829–1844 (2009).ADS 

    Google Scholar 
    48.Hammel, J. U., Herzen, J., Beckmann, F. & Nickel, M. Sponge budding is a spatiotemporal morphological patterning process: insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma. Front. Zool. 6, 19 (2009).PubMed 
    PubMed Central 

    Google Scholar 
    49.Witte, U. & Graf, G. Metabolism of deep-sea sponges in the Greenland- Norwegian Sea. Mar. Biol. 198, 223–235 (1996).
    Google Scholar 
    50.Rovelli, L. et al. Benthic O2 uptake of two cold-water coral communities estimated with the non-invasive eddy correlation technique. Mar. Ecol. Prog. Ser. 525, 97–104 (2015).ADS 

    Google Scholar 
    51.De Clippele, L. H. et al. Mapping cold-water coral biomass: an approach to derive ecosystem functions. Coral Reefs 40, 215–231 (2021).
    Google Scholar 
    52.de Kluijver, A. et al. An integrative model of carbon and nitrogen metabolism in a common deep-sea sponge (Geodia barretti). Front. Mar. Sci. 7, 1–18 (2021).
    Google Scholar 
    53.Lalande, C., Nothig, E.-M. & Fortier, L. Algal export in the Arctic ocean in times of global warming. Geophys. Res. Lett. 46, 1–9 (2019).
    Google Scholar 
    54.Boetius, A. et al. Export of algal biomass from the melting Arctic sea ice. Science 339, 1430–1433 (2013).55.Maier, S. R. et al. Survival under conditions of variable food availability: Resource utilization and storage in the cold-water coral Lophelia pertusa. Limnol. Oceanogr. 64, 1651–1671 (2019).ADS 
    CAS 

    Google Scholar 
    56.Rix, L. et al. Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses. ISME J. 14, 2554–2567 (2020).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    57.Hansell, D. A. Recalcitrant dissolved organic carbon fractions. Ann. Rev. Mar. Sci. 5, 421–445 (2013).PubMed 

    Google Scholar 
    58.Bart, M. C. et al. Differential processing of dissolved and particulate organic matter by deep-sea sponges and their microbial symbionts. Sci. Rep. 10, 1–13 (2020).
    Google Scholar 
    59.Anderson, L. G. & Amon, R. M. W. DOM in the Arctic Ocean. In Biogeochemistry of Marine Dissolved Organic Matter (eds Hansell, D. A. & Carlson, C. A.) Ch. 14 (Academic Press, 2015).60.Rossel, P. E., Bienhold, C., Boetius, A. & Dittmar, T. Dissolved organic matter in pore water of Arctic Ocean sediments: environmental influence on molecular composition. Org. Geochem. 97, 41–52 (2016).CAS 

    Google Scholar 
    61.Landry, Z., Swan, B. K., Herndl, G. J., Stepanauskas, R. & Giovannoni, S. J. SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. MBio 8, e00413–e00417 (2017).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    62.Radax, R. et al. Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ. Microbiol. 14, 1308–1324 (2012).63.Busch, K. et al. Chloroflexi dominate the deep-sea golf ball sponges Craniella zetlandica and Craniella infrequens throughout different life stages. Front. Mar. Sci. 7, 1–13 (2020).
    Google Scholar 
    64.Raimundo, I. et al. Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes. Microbiome 9, 1–18 (2021).
    Google Scholar 
    65.Hoffmann, F. et al. Complex nitrogen cycling in the sponge Geodia barretti. Environ. Microbiol. 11, 2228–2243 (2009).CAS 
    PubMed 

    Google Scholar 
    66.Radax, R., Hoffmann, F., Rapp, H. T., Leininger, S. & Schleper, C. Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges. Environ. Microbiol. 14, 909–923 (2012).CAS 
    PubMed 

    Google Scholar 
    67.Kahn, A. S., Chu, J. W. F. & Leys, S. P. Trophic ecology of glass sponge reefs in the Strait of Georgia, British Columbia. Sci. Rep. 8, 756 (2018).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    68.Thiel, V. et al. Mid-chain branched alkanoic acids from “living fossil” demosponges: a link to ancient sedimentary lipids? Org. Geochem. 30, 1–14 (1999).CAS 

    Google Scholar 
    69.de Kluijver, A. et al. Bacterial precursors and unsaturated long-chain fatty acids are biomarkers of North-Atlantic deep-sea demosponges. PLoS ONE 16, 1–18 (2021).
    Google Scholar 
    70.Parnell, A. C., Inger, R., Bearhop, S. & Jackson, A. L. Source partitioning using stable isotopes: coping with too much variation. PLoS ONE 5, e9672 (2010).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    71.Freeman, C. J. et al. Microbial symbionts and ecological divergence of Caribbean sponges: a new perspective on an ancient association. ISME J. 14, 1571–1583 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    72.Middelburg, J. J. Stable isotopes dissect aquatic food webs from the top to the bottom. Biogeosciences 11, 2357–2371 (2014).ADS 

    Google Scholar 
    73.Åström, E. et al. Chemosynthesis influences food web and community structure in high-Arctic benthos. Mar. Ecol. Prog. Ser. 629, 19–42 (2019).ADS 

    Google Scholar 
    74.Ravaux, J. et al. Comparative degradation rates of chitinous exoskeletons from deep-sea environments. Mar. Biol. 143, 405–412 (2003).CAS 

    Google Scholar 
    75.Gooday, G. W. The Ecology of Chitin Degradation. In Advances in Microbial Ecology, (ed. Marshall, K. C.) vol 11. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-7612-5_10.76.Schwarz, J. R., Yayanos, A. A. & Colwell, R. R. Metabolic activities of the intestinal microflora of a deep-sea invertebrate. Appl. Environ. Microbiol. 31, 46 LP–46 48 (1976).ADS 

    Google Scholar 
    77.Godefroy, N. et al. Sponge digestive system diversity and evolution: filter feeding to carnivory. Cell Tissue Res. 377, 341–351 (2019).PubMed 

    Google Scholar 
    78.Ehrlich, H. et al. First evidence of chitin as a component of the skeletal fibers of marine sponges. Part I. Verongidae (demospongia: Porifera). J. Exp. Zool. Part B Mol. Dev. Evol. 308B, 347–356 (2007).CAS 

    Google Scholar 
    79.Bowden, D. A. et al. Cold seep epifaunal communities on the Hikurangi Margin, New Zealand: composition, succession, and vulnerability to human activities. PLoS ONE 8, e76869 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    80.Georgieva, M. N. et al. Identification of fossil worm tubes from Phanerozoic hydrothermal vents and cold seeps. J. Syst. Palaeontol. 17, 287–329 (2017).
    Google Scholar 
    81.Morganti, T. M. et al. In situ observation of sponge trails suggests common sponge locomotion in the deep central Arctic. Curr. Biol. 31, R368–R370 (2021).CAS 
    PubMed 

    Google Scholar 
    82.Maldonado, M. An experimental approach to the ecological significance of microhabitat-scale movement in an encrusting sponge. Mar. Ecol. Prog. Ser. 185, 239–255 (1999).ADS 

    Google Scholar 
    83.Rice, A. L., Thurston, M. H. & New, A. L. Dense aggregations of a hexactinellid sponge, Pheronema carpenteri, in the Porcupine Seabight (northeast Atlantic Ocean), and possible causes. Prog. Oceanogr. 24, 179–196 (1990).ADS 

    Google Scholar 
    84.Roberts, E. M. et al. Oceanographic setting and short-timescale environmental variability at an Arctic seamount sponge ground. Deep. Res. Part I Oceanogr. Res. Pap. 138, 98–113 (2018).ADS 

    Google Scholar 
    85.Purser, A. et al. Ocean floor observation and bathymetry system (OFOBS): a new towed camera/sonar system for deep-sea habitat surveys. IEEE J. Ocean. Eng. 44, 1–13 (2019).
    Google Scholar 
    86.Marcon, Y. & Purser, A. PAPARA(ZZ)I: an open-source software interface for annotating photographs of the deep-sea. SoftwareX 6, 69–80 (2017).ADS 

    Google Scholar 
    87.Morganti, T. M., Ribes, M., Yahel, G. & Coma, R. Size is the major determinant of pumping rates in marine sponges. Front. Physiol. 10, 1474 (2019).PubMed 
    PubMed Central 

    Google Scholar 
    88.Zelles, L. Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 35, 275–294 (1997).ADS 
    CAS 
    PubMed 

    Google Scholar 
    89.Volkman, J. K., Jeffrey, S. W., Nichols, P. D., Rogers, G. I. & Garland, C. D. Fatty acid and lipid composition of 10 species of microalgae used in mariculture. J. Exp. Mar. Bio. Ecol. 128, 219–240 (1989).CAS 

    Google Scholar 
    90.Koopmans, M. et al. Seasonal variation of fatty acids and stable carbon isotopes in sponges as indicators for nutrition: biomarkers in sponges identified. Mar. Biotechnol. 17, 43–54 (2015).CAS 

    Google Scholar 
    91.Mollenhauer, G., Grotheer, H., Gentz, T., Bonk, E. & Hefter, J. Standard operation procedures and performance of the MICADAS radiocarbon laboratory at Alfred Wegener Institute (AWI). Ger. Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 496, 45–51 (2021).ADS 
    CAS 

    Google Scholar 
    92.Fallon, S. J., James, K., Norman, R., Kelly, M. & Ellwood, M. J. A simple radiocarbon dating method for determining the age and growth rate of deep-sea sponges. Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 268, 1241–1243 (2010).ADS 
    CAS 

    Google Scholar 
    93.Griffith, D. R. et al. Carbon dynamics in the western Arctic Ocean: insights from full-depth carbon isotope profiles of DIC, DOC, and POC. Biogeosciences 9, 1217–1224 (2012).ADS 
    CAS 

    Google Scholar 
    94.Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    95.Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).PubMed 
    PubMed Central 

    Google Scholar 
    96.Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    97.Li, D. et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102, 3–11 (2016).CAS 
    PubMed 

    Google Scholar 
    98.Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    99.Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    100.Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–W37 (2011).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    101.Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).CAS 
    PubMed 

    Google Scholar 
    102.Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    103.De Anda, V. et al. MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. Gigascience 6, 1–17 (2017).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    104.Benner, R., Benitez-Nelson, B., Kaiser, K. & Amon, R. M. W. Export of young terrigenous dissolved organic carbon from rivers to the Arctic Ocean. Geophys. Res. Lett. 31, 10–13 (2004).
    Google Scholar 
    105.Thibodeau, B., Bauch, D. & Voss, M. Nitrogen dynamic in Eurasian coastal Arctic ecosystem: Insight from nitrogen isotope. Glob. Biogeochem. Cycles 31, 836–849 (2017).ADS 
    CAS 

    Google Scholar 
    106.Jackson, A. L., Inger, R., Parnell, A. C. & Bearhop, S. Comparing isotopic niche widths among and within communities: SIBER – Stable Isotope Bayesian Ellipses in R. J. Anim. Ecol. 80, 595–602 (2011). More

  • in

    Characterization and phylogeny of fungi isolated from industrial wastewater using multiple genes

    1.Ramganesh, S., Timothy, S., Sudharshan, S. & Willem, A. J. N. Industrial effluents harbor a unique diversity of fungal community structures as revealed by high-throughput sequencing analysis. Pol. J. Environ. Stud. 28(4), 2353–2362. https://doi.org/10.15244/pjoes/90791 (2019).Article 

    Google Scholar 
    2.Hailemariam, A. A. et al. Diversity, co-occurrence and implications of fungal communities in wastewater treatment plants. Sci. Rep. 9, 14056. https://doi.org/10.1038/s41598-019-50624-z (2019).CAS 
    Article 

    Google Scholar 
    3.Maza-Márquez, P., Lee, M. D. & Bebout, B. M. The abundance and diversity of fungi in a hypersaline microbial mat from Guerrero Negro, Baja California, México. J. Fungi 7, 210. https://doi.org/10.3390/jof7030210 (2021).CAS 
    Article 

    Google Scholar 
    4.Ma, X., Baron, J. L., Vikram, A., Stout, J. E. & Bibby, K. Fungal diversity and presence of potentially pathogenic fungi in a hospital hot water system treated with on-site monochloramine. Water Res. 71, 197–206 (2015).CAS 
    Article 

    Google Scholar 
    5.Wei, Z. et al. The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants. Sci. Total Environ. 628, 969–978 (2018).ADS 
    Article 

    Google Scholar 
    6.Ekowati, Y. et al. Clinically relevant fungi in water and on surfaces in an indoor swimming pool facility. Int. J. Hyg. Environ. Health. 220, 1152–1160 (2017).Article 

    Google Scholar 
    7.Manoharachary, C., Kunwar, I. K. & Reddy, S. V. Biodiversity, phylogeny and evolution of fungi. In Nature at Work: Ongoing Saga of Evolution (ed. Sharma, V. P.) (Springer, New Delhi, 2010). https://doi.org/10.1007/978-81-8489-992-4_10.Chapter 

    Google Scholar 
    8.Raja, H. A., Miller, A. N., Pearce, C. J. & Oberlies, N. H. Fungal identification using molecular tools: A primer for the natural products research community. J. Nat. Prod. 80, 756–770. https://doi.org/10.1021/acs.jnatprod.6b01085 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    9.Liu, J., Li, J., Tao, Y., Sellamuthu, B. & Walsh, R. Analysis of bacterial, fungal and archaeal populations from a municipal wastewater treatment plant developing an innovative aerobic granular sludge process. World J. Microbiol. Biotechnol. 33, 14 (2017).Article 

    Google Scholar 
    10.Simeos, M. F. et al. Soil and rhizosphere associated fungi in gray Mangroves (Avicennia marina) from the Red Sea—A metagenomic approach. Genom. Proteom. Bioinform. 13, 310–320. https://doi.org/10.1016/j.gpb.2015.07.002 (2015).Article 

    Google Scholar 
    11.Helal, G. A., Mostafa, M. H. & El-Said, M. A. Fungi in the sewage-treatment Zeinein plant, Cairo, Egypt. J. Basic Appl. Mycol. 2(2011), 69–82 (2011).
    Google Scholar 
    12.Mishra, S. & Mishra, A. To study the diversity of fungal species in sewage water of Durg district. IOSR J. Environ. Sci. Toxicol. Food Technol. 1(6), 45–49 (2015).
    Google Scholar 
    13.Das, S., Dash, H. R., Mangwani, N., Chakraborty, J. & Kumari, S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J. Microbiol. Methods 103, 80–100. https://doi.org/10.1016/j.mimet.2014.05.013 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    14.Yin, G., Zhang, Y., Pennerman, K. K., Wu, G. & Hua, S. S. T. Characterization of Blue Mold Penicillium Species isolated from stored fruits using multiple highly conserved loci. J. Fungi. 3, 1–10. https://doi.org/10.3390/jof3010012 (2017).CAS 
    Article 

    Google Scholar 
    15.Rajeshkumar, K. C., Yilmaz, N. & Marathe, S. D. Morphology and multigene phylogeny of Talaromyces amyrossmaniae, a new synnematous species belonging to the section Trachyspermi from India. Mycokeys 45, 41–56. https://doi.org/10.3897/mycokeys.45.32549 (2019).Article 

    Google Scholar 
    16.Adeniyi, M. et al. Molecular identification of some wild Nigerian mushrooms using internal transcribed spacer: Polymerase chain reaction. AMB Express 8, 1–9. https://doi.org/10.1186/s13568-018-0661-9 (2018).CAS 
    Article 

    Google Scholar 
    17.Houbraken, J. & Samson, R. A. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud. Mycol. 70, 1–51. https://doi.org/10.3114/sim.2011.70.01 (2011).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    18.Visagie, C. M. et al. Studies in mycology. Stud. Mycol. 78, 343–371. https://doi.org/10.1016/j.simyco.2014.09.001 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    19.Asan, A., Kolanlarli, T. K., Sen, B. & Okten, S. Biodiversity of Penicillium species isolated from Edirne Söğütlük Forest soil (Turkey ). Nisan 10, 26–39 (2019).
    Google Scholar 
    20.De Carvalho, M. J. A. et al. Functional and genetic characterization of calmodulin from the dimorphic and pathogenic fungus Paracoccidioides brasiliensis. Fungal Genet. Biol. 39, 204–210. https://doi.org/10.1016/S1087-1845(03)00044-6 (2003).CAS 
    Article 
    PubMed 

    Google Scholar 
    21.De Cassia Garcia Simao, R. & Gomes, S. L. Structure, expression, and functional analysis of the gene coding for calmodulin in the chytridiomycete Blastocladiella emersonii. J. Bacteriol. 183, 2280–2288. https://doi.org/10.1128/JB.183.7.2280-2288.2001 (2001).Article 

    Google Scholar 
    22.Gerber, A., Ito, K., Chu, C. N. & Roeder, R. G. Induced RPB1 depletion reveals a direct gene-specific control of RNA Polymerase III function by RNA Polymerase II. Mol. Cell 78, 765–778. https://doi.org/10.1016/j.molcel.2020.03.023 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Malkus, A. et al. RNA polymerase II gene (RPB2) encoding the second largest protein subunit in Phaeosphaeria nodorum and P. avenaria. Mycol. Res. 110, 1152–1164 (2006).CAS 
    Article 

    Google Scholar 
    24.Vetrovsky, T., Kolarik, M., Zifcakova, L., Zelenka, T. & Baldrian, P. The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities. Mol. Ecol. Resour. 16, 388–401. https://doi.org/10.1111/1755-0998.12456 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    25.Machido, D. A., Ezeonuegbu, B. A. & Yakubu, S. E. Resistance to some heavy metals among fungal flora of raw refinery effluent. J. Appl. Sci. Environ. Manag. 18, 623–627. https://doi.org/10.4314/jasem.v18i4.10 (2014).CAS 
    Article 

    Google Scholar 
    26.Ezeonuegbu, B. A., Machido, D. A. & Yakubu, S. E. Resistance of some heavy metals among fungal flora of raw refinery effluent. J. Appl. Sci. Environ. Manag. 18, 623–627 (2014).CAS 

    Google Scholar 
    27.Barnett, H. L. & Hunter, B. B. Illustrated Genera of Imperfect Fungi 4th edn. (Prentice Hall, 1999).
    Google Scholar 
    28.Hakeem, A. S. & Bhatnagar, B. Heavy metal reduction of pulp and paper mill effluent by indigenous microbes. Asian J. Exp. Biol. Sci. 1, 203–210 (2010).
    Google Scholar 
    29.Viegas, C., Sabino, R., Botelho, D., Santos, M. & Gomes, A. Q. Assessment of exposure to Penicillium glabrum complex in cork industry using complementing methods. Arch. Ind. Hyg. Toxicol. 66, 203–207. https://doi.org/10.1515/aiht-2015-66-2614 (2015).Article 

    Google Scholar 
    30.Khandavilli, R., Meena, R. & Bd, S. Fungal phylogenetic diversity in estuarine sediments of Gautami. Curr. Res. Environ. Appl. Mycol. 6, 268–276. https://doi.org/10.5943/cream/6/4/4 (2016).Article 

    Google Scholar 
    31.Houbraken, J., Frisvad, J. C. & Samson, R. A. Sex in penicillium series roqueforti. IMA Fungus 1, 171–180 (2010).Article 

    Google Scholar 
    32.Goujon, M. et al. A new bioinformatics analysis tools framework at EMBL_EBI. Nucleic Acids Res. 38, W695–W699 (2010).CAS 
    Article 

    Google Scholar 
    33.Kumar, S., Stecher, G. & Tamura, K. MEGA 7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870 (2015).Article 

    Google Scholar 
    34.Sidiq, F., Hoostal, M. & Rogers, S. O. Rapid identification of fungi in culture – negative clinical blood and respiratory samples by DNA sequence analyses. BMC. Res. Notes 9, 1–8. https://doi.org/10.1186/s13104-016-2097-0 (2016).CAS 
    Article 

    Google Scholar 
    35.Oyebanji, E. O., Adekunle, A. A., Coker, H. A. B. & Adebami, G. E. Mycotic loads’ determination of non-sterile pharmaceuticals in lagos state and 16s rdna identification of the fungal isolates. J. Appl. Pharm. Res. 6, 16–28. https://doi.org/10.18231/2348-0335.2018.0007 (2018).CAS 
    Article 

    Google Scholar 
    36.Tiwari, P., Kumar, B., Kaur, G. & Kaur, H. Phytochemical screening and extraction: A review. Int. Pharm. Sci. 1, 98–106 (2011).
    Google Scholar 
    37.Ozdil, S., Asan, A., Sen, B. & Okten, S. Biodiversity of Airborne Fungi in the Indoor Environment of Refrigerators Used in Houses. J. Fungus. 8, 109–124. https://doi.org/10.15318/fungus.2017.41 (2017).Article 

    Google Scholar 
    38.Ashtiani, N. M., Kachuei, R., Yalfani, R. & Harchegani, A. B. Identification of Aspergillus sections Flavi, Nigri, and Fumigati and their differentiation using specific primers. Infez. Med. 2, 127–132 (2017).
    Google Scholar 
    39.Eulalia, M. M., Agnieszka, F. & Zalewska, E. D. Aspergillus penicillioides Speg. Implicated in Keratomycosis. Pol. J. Microbiol. 67, 407–416 (2018).Article 

    Google Scholar 
    40.Kamarudin, N. A. & Zakaria, L. Characterization of two xerophilic Aspergillus spp. from peanuts (Arachis hypogaea) Nur. Malays. J. Microbiol. 14, 41–48 (2018).CAS 

    Google Scholar 
    41.Samson, R. A. et al. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud. Mycol. 78, 141–173. https://doi.org/10.1016/j.simyco.2014.07.004 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    42.Wolski, E. A., Barrera, V., Castellari, C. & Gonzalez, J. F. Biodegradation of phenol in static cultures by Penicillium chrysogenum EK1: catalytic abilities and residual photo toxicity. Rev. Argent. Microbiol. 44, 113–121 (2012).CAS 
    PubMed 

    Google Scholar  More

  • in

    Beyond Demonstrators—tackling fundamental problems in amplifying nature-based solutions for the post-COVID-19 world

    1.Rosenbloom, D. & Markard, J. A COVID-19 recovery for climate. Science 368, 447 (2020).CAS 

    Google Scholar 
    2.European Commission. Towards an EU Research and Innovation policy agenda for nature-based solutions and renaturing cities. Final Report of the Horizon 2020 expert group on nature-based solutions and re-naturing cities, (European Commission, Brussels, 2015).3.Cohen-Shacham, E. et al. Core principles for successfully implementing and upscaling nature-based solutions. Environ. Sci. Policy 98, 20–29 (2019).
    Google Scholar 
    4.Seddon, N., Turner, B., Berry, P., Chausson, A. & Girardin, C. A. J. Grounding nature-based climate solutions in sound biodiversity science. Nat. Clim. Change 9, 84–87 (2019).
    Google Scholar 
    5.Keeler, B. L. et al. Social-ecological and technological factors moderate the value of urban nature. Nat. Sustain 2, 29–38 (2019).
    Google Scholar 
    6.Escobedo, F. J., Giannico, V., Jim, C. Y., Sanesi, G. & Lafortezza, R. Urban forests, ecosystem services, green infrastructure and nature-based solutions: Nexus or evolving metaphors? Urban For. Urban Greening 37, 3–12 (2019).
    Google Scholar 
    7.Pan, H., Page, J., Cong, C., Barthel, S. & Kalantari, Z. How ecosystems services drive urban growth: Integrating nature-based solutions. Anthropocene 35, 100297 (2021).
    Google Scholar 
    8.Keesstra, S. et al. The superior effect of nature based solutions in land management for enhancing ecosystem services. Sci. Total Environ. 610-611, 997–1009 (2018).CAS 

    Google Scholar 
    9.Hack, J. & Schröter, B. Nature-based solutions for river restoration in metropolitan areas. Brears, R. The Palgrave Encyclopedia of Urban and Regional Futures. 1–10 (Springer International Publishing, Cham, 2021).10.Lam, D. P. M. et al. Scaling the impact of sustainability initiatives: a typology of amplification processes. Urban Transform 2, 3 (2020).
    Google Scholar 
    11.Seddon, N. et al. Global recognition of the importance of nature-based solutions to the impacts of climate change. Glob. Sustain 3, e15 (2020).
    Google Scholar 
    12.Faivre, N., Fritz, M., Freitas, T., de Boissezon, B. & Vandewoestijne, S. Nature-based solutions in the EU: innovating with nature to address social, economic and environmental challenges. Environ. Res. 159, 509–518 (2017).CAS 

    Google Scholar 
    13.Sabel, C. F. & Zeitlin, J. Experimentalist Governance. Levi-Faur, D. The Oxford Handbook of Governance. 169–183 (Oxford Univ. Press, Oxford, 2012).14.Kern, K. Cities as leaders in EU multilevel climate governance: embedded upscaling of local experiments in Europe. Environ. Polit. 28, 125–145 (2019).
    Google Scholar 
    15.Díaz, S. et al. Pervasive human-driven decline of life on Earth points to the need for transformative change. Science 366, eaax3100 (2019).
    Google Scholar 
    16.Chini, C. M., Canning, J. F., Schreiber, K. L., Peschel, J. M. & Stillwell, A. S. The green experiment: cities, green stormwater infrastructure, and sustainability. Sustainability 9 (2017).17.McPhearson, T. et al. Radical changes are needed for transformations to a good Anthropocene. npj Urban Sustain. 1, 5 (2021).
    Google Scholar 
    18.Scoones, I. et al. Transformations to sustainability: combining structural, systemic and enabling approaches. Curr. Opin. Environ. Sustain. 42, 65–75 (2020).
    Google Scholar 
    19.Han, S. & Kuhlicke, C. Reducing hydro-meteorological risk by nature-based solutions: what do we know about people’s perceptions? Water 11, 2599 (2019).
    Google Scholar 
    20.Albert, C. et al. Planning nature-based solutions: principles, steps, and insights. Ambio, 1446–1461 (2020).21.Matthews, T., Lo, A. Y. & Byrne, J. A. Reconceptualizing green infrastructure for climate change adaptation: barriers to adoption and drivers for uptake by spatial planners. Landsc. Urban Planning 138, 155–163 (2015).
    Google Scholar 
    22.Myllyvirta, L. China’s CO2 emissions have surged back from the coronavirus lockdown, rising by 4-5% year-on-year in May, analysis of new government data shows. https://www.carbonbrief.org/analysis-chinas-co2-emissions-surged-past-pre-coronavirus-levels-in-may (2020).23.Samuelsson, K., Barthel, S., Colding, J., Macassa, G. & Giusti, M. Urban nature as a source of resilience during social distancing amidst the coronavirus pandemic. Preprint at https://doi.org/10.31219/osf.io/3wx5a (2020).24.Mahoney, J. Path dependence in historical sociology. Theory Soc. 29, 507–548 (2000).
    Google Scholar 
    25.Davies, C. & Lafortezza, R. Transitional path to the adoption of nature-based solutions. Land Use Policy 80, 406–409 (2019).
    Google Scholar 
    26.Kuzemko, C. et al. Covid-19 and the politics of sustainable energy transitions. Energy Res. Soc. Sci. 68, 101685 (2020).
    Google Scholar 
    27.Kanda, W. & Kivimaa, P. What opportunities could the COVID-19 outbreak offer for sustainability transitions research on electricity and mobility? Energy Res. Soc. Sci. 68, 101666 (2020).
    Google Scholar 
    28.Cohen, M. J. Does the COVID-19 outbreak mark the onset of a sustainable consumption transition? Sustain.: Sci. Pract. Policy 16, 1–3 (2020).
    Google Scholar 
    29.Pearson, R. M., Sievers, M., McClure, E. C., Turschwell, M. P. & Connolly, R. M. COVID-19 recovery can benefit biodiversity. Science 368, 838 (2020).
    Google Scholar 
    30.Everard, M., Johnston, P., Santillo, D. & Staddon, C. The role of ecosystems in mitigation and management of Covid-19 and other zoonoses. Environ. Sci. Policy 111, 7–17 (2020).CAS 

    Google Scholar 
    31.Kavousi, J., Goudarzi, F., Izadi, M. & Gardner, C. J. Conservation needs to evolve to survive in the post-pandemic world. Glob. Change Biol. 26, 4651–4653 (2020).
    Google Scholar 
    32.Lal, R. Home gardening and urban agriculture for advancing food and nutritional security in response to the COVID-19 pandemic. Food Sec., 1–6 (2020).33.Khetan, A. K. COVID-19: why declining biodiversity puts us at greater risk for emerging infectious diseases, and what we can do. J. Gen. Intern. Med. 35, 2746–2747 (2020).
    Google Scholar 
    34.Sugiyama, T. et al. Four Recommendations for Greener, Healthier Cities in the Post-Pandemic. https://www.thenatureofcities.com/2020/06/30/four-recommendations-for-greener-healthier-cities-in-the-post-pandemic/ (2020).35.Thorslund, J. et al. Wetlands as large-scale nature-based solutions: status and challenges for research, engineering and management. Ecol. Eng. 108, 489–497 (2017).
    Google Scholar 
    36.Albert, C. et al. Addressing societal challenges through nature-based solutions: how can landscape planning and governance research contribute? Landsc.Urban Plan. 182, 12–21 (2019).
    Google Scholar 
    37.Albert, C., Von Haaren, C., Othengrafen, F., Krätzig, S. & Saathoff, W. Scaling policy conflicts in ecosystem services governance: a framework for spatial. Analysis. J. Environ. Policy Plan. 19, 574–592 (2017).
    Google Scholar 
    38.Hutchins, M. G. et al. Why scale is vital to plan optimal nature-based solutions for resilient cities. Environ. Res. Lett. 16, 044008 (2021).
    Google Scholar 
    39.Raška, P., Slavíková, L. & Sheehan, J. in Nature-Based Flood Risk Management on Private Land: Disciplinary Perspectives on a Multidisciplinary Challenge 9–20 (Springer International Publishing, 2019).40.Frantzeskaki, N. et al. Nature-based solutions for urban climate change adaptation: linking science, policy, and practice communities for evidence-based decision-making. BioScience 69, 455–466 (2019).
    Google Scholar 
    41.Watkin, L. J., Ruangpan, L., Vojinovic, Z., Weesakul, S. & Torres, A. S. A framework for assessing benefits of implemented nature-based solutions. Sustainability 11, 6788 (2019).
    Google Scholar 
    42.Wurzel, R. K. W., Liefferink, D. & Torney, D. Pioneers, leaders and followers in multilevel and polycentric climate governance. Environ. Polit. 28, 1–21 (2019).
    Google Scholar 
    43.Frantzeskaki, N. et al. Examining the policy needs for implementing nature-based solutions in cities: findings from city-wide transdisciplinary experiences in Glasgow (UK), Genk (Belgium) and Poznań (Poland). Land Use Policy 96, 104688 (2020).
    Google Scholar 
    44.Zingraff-Hamed, A. et al. Governance models for nature-based solutions: cases from Germany. Ambio 50, 1610–1627 (2020).
    Google Scholar 
    45.Toxopeus, H. et al. How ‘just’ is hybrid governance of urban nature-based solutions? Cities 105, 102839 (2020).
    Google Scholar 
    46.Wamsler, C. et al. Environmental and climate policy integration: targeted strategies for overcoming barriers to nature-based solutions and climate change adaptation. J. Clean. Prod. 247, 119154 (2020).
    Google Scholar 
    47.Pérez Rubi, M. & Hack, J. Co-design of experimental nature-based solutions for decentralized dry-weather runoff treatment retrofitted in a densely urbanized area in Central America. Ambio 50, 1498–1513 (2021).
    Google Scholar 
    48.Chapa, F., Pérez, M. & Hack, J. Experimenting transition to sustainable urban drainage systems—identifying constraints and unintended processes in a tropical highly urbanized. Watershed. Water 12, 3554 (2020).
    Google Scholar 
    49.Chen, V., Bonilla Brenes, J. R., Chapa, F. & Hack, J. Development and modelling of realistic retrofitted Nature-based Solution scenarios to reduce flood occurrence at the catchment scale. Ambio 50, 1462–1476 (2021).
    Google Scholar 
    50.Hüesker, F. & Moss, T. The politics of multi-scalar action in river basin management: Implementing the EU Water Framework Directive (WFD). Land Use Policy 42, 38–47 (2015).
    Google Scholar 
    51.WBCSD. Incentives for Natural Infrastructure: review of existing policies, incentives and barriers related to permitting, finance and insurance of natural infrastructure. (World Business Council for Sustainable Development, Geneva, 2017).52.Nesshöver, C. et al. The science, policy and practice of nature-based solutions: an interdisciplinary perspective. Sci. Total Environ. 579, 1215–1227 (2017).
    Google Scholar 
    53.Toxopeus, H. S. Taking Action for Urban Nature: Business Model Catalogue, NATURVATION Guide (2019).54.Duraiappah, A. K. et al. Managing the mismatches to provide ecosystem services for human well-being: a conceptual framework for understanding the New Commons. Curr. Opin.Environ. Sustain 7, 94–100 (2014).
    Google Scholar 
    55.Young, O. R. Vertical interplay among scale-dependent environmental and resource regimes. Ecol. Soc. 11, 27 (2006).
    Google Scholar 
    56.Cumming, G. S., Cumming, D. H. M. & Redman, C. L. Scale mismatches in social-ecological systems: causes, consequences, and solutions. Ecol. Soc. 11, 14 (2006).
    Google Scholar 
    57.Naidoo, R. & Fisher, B. Sustainable development goals: pandemic reset. Nature 583, 198–201 (2020).CAS 

    Google Scholar 
    58.Fyfe, J. C. et al. Quantifying the influence of short-term emission reductions on climate. Sci. Adv. 7, eabf7133 (2021).CAS 

    Google Scholar 
    59.Linnér, B.-O. & Wibeck, V. Conceptualising variations in societal transformations towards sustainability. Environ. Sci.Pol. 106, 221–227 (2020).
    Google Scholar 
    60.Harrabin, R. Coronavirus: Lockdown ‘could boost wild flowers’. https://www.bbc.com/news/science-environment-52215273 (2020).61.Bratman, G. N. et al. Nature and mental health: an ecosystem service perspective. Sci. Adv. 5, eaax0903 (2019).
    Google Scholar 
    62.Honey-Rosés, J. et al. The impact of COVID-19 on public space: an early review of the emerging questions—design, perceptions and inequities. Cities & Health, 1-17(2020).63.Sanyé-Mengual, E., Anguelovski, I., Oliver-Solà, J., Montero, J. I. & Rieradevall, J. Resolving differing stakeholder perceptions of urban rooftop farming in Mediterranean cities: promoting food production as a driver for innovative forms of urban agriculture. Agric. Human Values 33, 101–120 (2016).
    Google Scholar 
    64.PIANC. Guide for applying Working with Nature to navigation infrastructure projects. (Brussels, Belgium, 2018).65.Rijke, J., van Herk, S., Zevenbergen, C. & Ashley, R. Room for the River: delivering integrated river basin management in the Netherlands. Int. J. River Basin Manage. 10, 369–382 (2012). https://doi.org/10.1080/15715124.2012.739173.66.Li, H., Ding, L., Ren, M., Li, C. & Wang, H. Sponge City Construction in China: A Survey of the Challenges and Opportunities. Water (Australia) 9, 594 (2017).67.Kurth, A.-M. & Schirmer, M. Thirty years of river restoration in Switzerland: implemented measures and lessons learned. Environ. Earth Sci. 72, 2065–2079 (2014). https://doi.org/10.1007/s12665-014-3115-y.68.Petty, K. Wildflowers on road verges: an uplifting sight during the coronavirus lockdown. (2020). https://www.plantlife.org.uk/uk/blog/wildflowers-on-road-verges-an-uplifting-sight-during-the-coronavirus-lockdown. More