Ecology

Possingham, H. P. et al. Limits to the use of threatened species lists. Trends Ecol. Evol. 17, 503–507 (2002).Article 

Google Scholar 
Duarte, C. M. et al. Rebuilding marine life. Nature 580, 39–51 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Knowlton, N. Ocean optimism: Moving beyond the obituaries in marine conservation. Annu. Rev. Mar. Sci. 13, 13 (2021).Article 

Google Scholar 
Cinner, J. E. et al. Bright spots among the world’s coral reefs. Nature 535, 416–419 (2016).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Ripple, W. J. et al. Status and ecological effects of the world’s largest carnivores. Science 343, 1241484 (2014).PubMed 
Article 
CAS 

Google Scholar 
Estes, J. A. et al. Trophic downgrading of planet earth. Science 333, 301–306 (2011).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Hammerschlag, N. et al. Ecosystem function and services of aquatic predators in the anthropocene. Trends Ecol. Evol. 34(4), 369–383 (2019).PubMed 
Article 

Google Scholar 
Ritchie, E. G. et al. Ecosystem restoration with teeth: What role for predators?. Trends Ecol. Evol. 27, 265–271 (2012).PubMed 
Article 

Google Scholar 
Young, H. S., McCauley, D. J., Galetti, M. & Dirzo, R. Patterns, causes, and consequences of anthropocene defaunation. Annu. Rev. Ecol. Evol. Syst. 47, 333–358 (2016).Article 

Google Scholar 
Marshall, K. N., Stier, A. C., Samhouri, J. F., Kelly, R. P. & Ward, E. J. Conservation challenges of predator recovery. Conserv. Lett. 9, 70–78 (2016).Article 

Google Scholar 
Gregr, E. J. et al. Cascading social-ecological costs and benefits triggered by a recovering keystone predator. Science 368, 1243–1247 (2020).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Jones, K. R. et al. The location and protection status of earth’s diminishing marine wilderness. Curr. Biol. 28, 2506-2512.e3 (2018).CAS 
PubMed 
Article 

Google Scholar 
Dirzo, R. et al. Defaunation in the anthropocene. Science 345, 401–406 (2014).ADS 
CAS 
PubMed 
Article 

Google Scholar 
McCauley, D. J. et al. Marine defaunation: Animal loss in the global ocean. Science 347, 1255641 (2015).PubMed 
Article 
CAS 

Google Scholar 
Nielsen, M. R., Meilby, H., Smith-Hall, C., Pouliot, M. & Treue, T. The importance of wild meat in the global south. Ecol. Econ. 146, 696–705 (2018).Article 

Google Scholar 
Ripple, W. J. et al. Are we eating the world’s megafauna to extinction?. Conserv. Lett. 12, e12627 (2019).Article 

Google Scholar 
Pacoureau, N. et al. Half a century of global decline in oceanic sharks and rays. Nature 589, 567–571 (2021).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Carrizo, S. F. et al. Freshwater megafauna: Flagships for freshwater biodiversity under threat. Bioscience 67, 919–927 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Luskin, M. S., Albert, W. R. & Tobler, M. W. Sumatran tiger survival threatened by deforestation despite increasing densities in parks. Nat. Commun. 8, 1783 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Desforges, J.-P. et al. Predicting global killer whale population collapse from PCB pollution. Science 361, 1373–1376 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Alava, J. J., Cheung, W. W. L., Ross, P. S. & Sumaila, U. R. Climate change–contaminant interactions in marine food webs: Toward a conceptual framework. Glob. Change Biol. 23, 3984–4001 (2017).Article 

Google Scholar 
Chapron, G. et al. Recovery of large carnivores in Europe’s modern human-dominated landscapes. Science 346, 1517–1519 (2014).ADS 
CAS 
PubMed 
Article 

Google Scholar 
House, P. H., Clark, B. L. & Allen, L. G. The return of the king of the kelp forest: Distribution, abundance, and biomass of Giant sea bass (Stereolepis gigas) off Santa Catalina Island, California, 2014–2015. Bull. South. Calif. Acad. Sci. 115, 1–14 (2016).
Google Scholar 
Waterhouse, L. et al. Recovery of critically endangered Nassau grouper (Epinephelus striatus) in the Cayman Islands following targeted conservation actions. Proc. Natl. Acad. Sci. 117, 1587–1595 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Balmford, A. & Knowlton, N. Why Earth Optimism? (American Association for the Advancement of Science, 2017).Book 

Google Scholar 
Sutherland, W. J., Pullin, A. S., Dolman, P. M. & Knight, T. M. The need for evidence-based conservation. Trends Ecol. Evol. 19, 305–308 (2004).PubMed 
Article 

Google Scholar 
Adams, W. M. & Sandbrook, C. Conservation, evidence and policy. Oryx 47, 329–335 (2013).Article 

Google Scholar 
Faith, J. T. & Surovell, T. A. Synchronous extinction of North America’s Pleistocene mammals. Proc. Natl. Acad. Sci. 106, 20641–20645 (2009).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Davis, S. J., Peters, G. P. & Caldeira, K. The supply chain of CO2 emissions. Proc. Natl. Acad. Sci. https://doi.org/10.1073/pnas.1107409108 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Visconti, P. et al. Projecting global biodiversity indicators under future development scenarios. Conserv. Lett. 9, 5–13 (2016).Article 

Google Scholar 
Lotze, H. K., Coll, M., Magera, A. M., Ward-Paige, C. & Airoldi, L. Recovery of marine animal populations and ecosystems. Trends Ecol. Evol. 26, 595–605 (2011).PubMed 
Article 

Google Scholar 
Queiroz, N. et al. Global spatial risk assessment of sharks under the footprint of fisheries. Nature https://doi.org/10.1038/s41586-019-1444-4 (2019).Article 
PubMed 

Google Scholar 
Pimiento, C. et al. Functional diversity of marine megafauna in the anthropocene. Sci. Adv. 6, 7650 (2020).ADS 
Article 

Google Scholar 
Estes, J. A., Heithaus, M., McCauley, D. J., Rasher, D. B. & Worm, B. Megafaunal impacts on structure and function of ocean ecosystems. Annu. Rev. Environ. Resour. 41, 83–116 (2016).Article 

Google Scholar 
Hoffmann, M. et al. The impact of conservation on the status of the world’s vertebrates. Science 330, 1503–1509 (2010).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Tom Gelatt (National Marine Mammal Laboratory, A. F. S. C. & Sweeney, K. IUCN red list of threatened species: Eumetopias jubatus. IUCN Red List of Threatened Species. https://www.iucnredlist.org/en (2016).Taylor, M. F. J., Suckling, K. F. & Rachlinski, J. J. The effectiveness of the endangered species act: A quantitative analysis. Bioscience 55, 360–367 (2005).Article 

Google Scholar 
Hejny, J. The Trump administration and environmental policy: Reagan redux?. J. Environ. Stud. Sci. 8, 197–211 (2018).Article 

Google Scholar 
Sanderson, F. J. et al. Assessing the performance of EU nature legislation in protecting target bird species in an era of climate change. Conserv. Lett. 9, 172–180 (2016).Article 

Google Scholar 
Donald, P. F. et al. International conservation policy delivers benefits for birds in Europe. Science 317, 810–813 (2007).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Cuthbert, R. J. et al. Continuing mortality of vultures in India associated with illegal veterinary use of diclofenac and a potential threat from nimesulide. Oryx 50, 104–112 (2016).Article 

Google Scholar 
Margalida, A. & Oliva-Vidal, P. The shadow of diclofenac hangs over European vultures. Nat. Ecol. Evol. 1, 1050 (2017).PubMed 
Article 

Google Scholar 
Williams, D. R., Balmford, A. & Wilcove, D. S. The past and future role of conservation science in saving biodiversity. Conserv. Lett. 13, e12720 (2020).Article 

Google Scholar 
Barnes, M. D. et al. Wildlife population trends in protected areas predicted by national socio-economic metrics and body size. Nat. Commun. 7, 12747 (2016).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sala, E. & Giakoumi, S. No-take marine reserves are the most effective protected areas in the ocean. ICES J. Mar. Sci. 75, 1166–1168 (2018).Article 

Google Scholar 
Watson, J. E. M., Dudley, N., Segan, D. B. & Hockings, M. The performance and potential of protected areas. Nature 515, 67–73 (2014).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Juffe-Bignoli, D. et al. Protected Planet Report 2014: Tracking Progress Towards Global Targets for Protected Areas (Springer, 2014).
Google Scholar 
Turnbull, J. W., Johnston, E. L. & Clark, G. F. Evaluating the social and ecological effectiveness of partially protected marine areas. Conserv. Biol. 35, 921–932 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Barnosky, A. D. et al. Merging paleobiology with conservation biology to guide the future of terrestrial ecosystems. Science 355, 1–10 (2017).Article 
CAS 

Google Scholar 
White, T. D. et al. Assessing the effectiveness of a large marine protected area for reef shark conservation. Biol. Conserv. 207, 64–71 (2017).Article 

Google Scholar 
Geldmann, J. et al. Effectiveness of terrestrial protected areas in reducing habitat loss and population declines. Biol. Conserv. 161, 230–238 (2013).Article 

Google Scholar 
Daskin, J. H. & Pringle, R. M. Warfare and wildlife declines in Africa’s protected areas. Nature 553, 328–332 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Pringle, R. M. Upgrading protected areas to conserve wild biodiversity. Nature 546, 91–99 (2017).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Redpath, S. M. et al. Don’t forget to look down: Collaborative approaches to predator conservation. Biol. Rev. 92, 2157–2163 (2017).PubMed 
Article 

Google Scholar 
Hazzah, L. et al. Efficacy of two lion conservation programs in Maasailand, Kenya. Conserv. Biol. 28, 851–860 (2014).PubMed 
Article 

Google Scholar 
Zarfl, C. et al. Future large hydropower dams impact global freshwater megafauna. Sci. Rep. 9, 18531 (2019).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Arthington, A. H., Dulvy, N. K., Gladstone, W. & Winfield, I. J. Fish conservation in freshwater and marine realms: Status, threats and management. Aquat. Conserv. Mar. Freshw. Ecosyst. 26, 838–857 (2016).Article 

Google Scholar 
Castello, L. & Macedo, M. N. Large-scale degradation of Amazonian freshwater ecosystems. Glob. Change Biol. 22, 990–1007 (2016).ADS 
Article 

Google Scholar 
Safford, R. et al. Vulture conservation: The case for urgent action. Bird Conserv. Int. 29, 1–9 (2019).Article 

Google Scholar 
Ogada, D. et al. Another continental vulture crisis: Africa’s vultures collapsing toward extinction. Conserv. Lett. 9, 89–97 (2016).ADS 
Article 

Google Scholar 
Buechley, E. R. & Şekercioğlu, Ç. H. The avian scavenger crisis: Looming extinctions, trophic cascades, and loss of critical ecosystem functions. Biol. Conserv. 198, 220–228 (2016).Article 

Google Scholar 
Hammerschlag, N. & Gallagher, A. J. Extinction risk and conservation of the earth’s national animal symbols. Bioscience 67, 744–749 (2017).Article 

Google Scholar 
Sutherland, W. J., Dicks, L. V., Ockendon, N. & Smith, R. K. What Works in Conservation 2015 (Open Book Publishers, 2015).Book 

Google Scholar 
Dulvy, N. K. et al. Challenges and priorities in shark and ray conservation. Curr. Biol. 27, R565–R572 (2017).CAS 
PubMed 
Article 

Google Scholar 
Finucci, B., Duffy, C. A. J., Francis, M. P., Gibson, C. & Kyne, P. M. The extinction risk of New Zealand chondrichthyans. Aquat. Conserv. Mar. Freshw. Ecosyst. 29, 783–797 (2019).Article 

Google Scholar 
Creel, S. et al. Questionable policy for large carnivore hunting. Science 350, 1473–1475 (2015).ADS 
CAS 
PubMed 
Article 

Google Scholar 
González, L. M. et al. Causes and spatio-temporal variations of non-natural mortality in the Vulnerable Spanish imperial eagle Aquila adalberti during a recovery period. Oryx 41, 495–502 (2007).Article 

Google Scholar 
Morandini, V., de Benito, E., Newton, I. & Ferrer, M. Natural expansion versus translocation in a previously human-persecuted bird of prey. Ecol. Evol. 7, 3682–3688 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Goodrich, J. M. et al. Panthera tigris, Tiger. IUCN Red List Threat. Species (2015).Wikramanayake, E. et al. A landscape-based conservation strategy to double the wild tiger population. Conserv. Lett. 4, 219–227 (2011).Article 

Google Scholar 
Bhattarai, B. R., Wright, W., Morgan, D., Cook, S. & Baral, H. S. Managing human-tiger conflict: Lessons from Bardia and Chitwan National Parks, Nepal. Eur. J. Wildl. Res. 65, 34 (2019).Article 

Google Scholar 
Pinsky, M. L. et al. Preparing ocean governance for species on the move. Science 360, 1189–1191 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Courchamp, F. et al. The paradoxical extinction of the most charismatic animals. PLoS Biol. 16, e2003997 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Nyhus, P. J. Human-wildlife conflict and coexistence. Annu. Rev. Environ. Resour. 41, 143–171 (2016).Article 

Google Scholar 
Carter, N. H. & Linnell, J. D. C. Co-adaptation is key to coexisting with large carnivores. Trends Ecol. Evol. 31, 575–578 (2016).PubMed 
Article 

Google Scholar 
Guerra, A. S. Wolves of the sea: Managing human-wildlife conflict in an increasingly tense ocean. Mar. Policy 99, 369–373 (2019).Article 

Google Scholar 
Das, C. S. Pattern and characterisation of human casualties in Sundarban by tiger attacks, India. Sustain. For. 1, 1–10 (2018).
Google Scholar 
Packer, C. et al. Conserving large carnivores: Dollars and fence. Ecol. Lett. 16, 635–641 (2013).CAS 
PubMed 
Article 

Google Scholar 
Dudley, S. F. J. A comparison of the shark control programs of New South Wales and Queensland (Australia) and KwaZulu-Natal (South Africa). Ocean Coast. Manag. 34, 1–27 (1997).Article 

Google Scholar 
O’Connell, C. P., Andreotti, S., Rutzen, M., Meӱer, M. & Matthee, C. A. Testing the exclusion capabilities and durability of the Sharksafe Barrier to determine its viability as an eco-friendly alternative to current shark culling methodologies. Aquat. Conserv. Mar. Freshw. Ecosyst. 28, 252–258 (2018).Article 

Google Scholar 
Gailey, G. et al. Effects of sea ice on growth rates of an endangered population of gray whales. Sci. Rep. 10, 1553 (2020).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hazen, E. L. et al. A dynamic ocean management tool to reduce bycatch and support sustainable fisheries. Sci. Adv. 4, 3001 (2018).ADS 
Article 

Google Scholar 
Ingeman, K. E., Samhouri, J. F. & Stier, A. C. Ocean recoveries for tomorrow’s Earth: Hitting a moving target. Science 363, 6425 (2019).Article 

Google Scholar 
Sánchez-Hernández, J. & Amundsen, P.-A. Ecosystem type shapes trophic position and omnivory in fishes. Fish Fish. 19, 1003–1015 (2018).Article 

Google Scholar 
Gainsbury, A. M., Tallowin, O. J. S. & Meiri, S. An updated global data set for diet preferences in terrestrial mammals: testing the validity of extrapolation. Mammal Rev. 48, 160–167 (2018).Article 

Google Scholar 
Faurby, S. et al. PHYLACINE 1.2: The phylogenetic atlas of mammal macroecology. Ecology 99, 2626–2626 (2018).PubMed 
Article 

Google Scholar 
Costello, M. J. et al. Marine biogeographic realms and species endemicity. Nat. Commun. 8, 1057 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Olson, D. M. et al. Terrestrial ecoregions of the world: A new map of life on earth: A new global map of terrestrial ecoregions provides an innovative tool for conserving biodiversity. Bioscience 51, 933–938 (2001).Article 

Google Scholar 
Rodrigues, A. S. L., Pilgrim, J. D., Lamoreux, J. F., Hoffmann, M. & Brooks, T. M. The value of the IUCN red list for conservation. Trends Ecol. Evol. 21, 71–76 (2006).PubMed 
Article 

Google Scholar  More

Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard
Provided by the Springer Nature SharedIt content-sharing initiative More

Ioannidis, J. P. A., Fanelli, D., Dunne, D. D. & Goodman, S. N. Meta-research: evaluation and improvement of research methods and practices. PLoS Biol. 13, e1002264 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Hampton, S. E. et al. The Tao of open science for ecology. Ecosphere 6, art120 (2015).Article 

Google Scholar 
Rothstein, H. R., Sutton, A. J. & Borenstein, M. Publication Bias in Meta-Analysis: Prevention, Assessment and Adjustments (John Wiley & Sons, 2005).Sutton, A. J. in The Handbook of Research Synthesis and Meta-Analysis (eds Cooper, H. et al.) 435–452 (Russell Sage Foundation, 2009).Nakagawa, S., Koricheva, J., Macleod, M. & Viechtbauer, W. Introducing our series: research synthesis and meta-research in biology. BMC Biol. 18, 20 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Nakagawa, S. et al. A new ecosystem for evidence synthesis. Nat. Ecol. Evol. 4, 498–501 (2020).PubMed 
Article 

Google Scholar 
Coolidge, H. J. & Lord, R. H. in Archibald Cary Coolidge: Life and Letters 308 (Houghton Mifflin Harcourt, 1932).Nickerson, R. S. Confirmation bias: a ubiquitous phenomenon in many guises. Rev. Gen. Psychol. 2, 175–220 (1998).Article 

Google Scholar 
Touchon, J. C. & McCoy, M. W. The mismatch between current statistical practice and doctoral training in ecology. Ecosphere 7, e01394 (2016).Article 

Google Scholar 
Begley, C. G. & Ellis, L. M. Raise standards for preclinical cancer research. Nature 483, 531–533 (2012).CAS 
PubMed 
Article 

Google Scholar 
Aarts, A. A. et al. Estimating the reproducibility of psychological science. Science 349, aac4716 (2015).Article 
CAS 

Google Scholar 
Camerer, C. F. et al. Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015. Nat. Hum. Behav. 2, 637–644 (2018).PubMed 
Article 

Google Scholar 
Fraser, H., Parker, T., Nakagawa, S., Barnett, A. & Fidler, F. Questionable research practices in ecology and evolution. PLoS ONE 13, e0200303 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Culina, A., van den Berg, I., Evans, S. & Sánchez-Tójar, A. Low availability of code in ecology: a call for urgent action. PLoS Biol. 18, e3000763 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Jennions, M. D. & Møller, A. P. Publication bias in ecology and evolution: an empirical assessment using the ‘trim and fill’ method. Biol. Rev. Camb. Philos. Soc. 77, 211–222 (2002).PubMed 
Article 

Google Scholar 
Jennions, M. D. & Møller, A. P. A survey of the statistical power of research in behavioral ecology and animal behavior. Behav. Ecol. 14, 438–445 (2003).Article 

Google Scholar 
Cassey, P., Ewen, J. G., Blackburn, T. M. & Møller, A. P. A survey of publication bias within evolutionary ecology. Proc. Biol. Sci. 271, S451–S454 (2004).PubMed 
PubMed Central 
Article 

Google Scholar 
Kardish, M. R. et al. Blind trust in unblinded observation in ecology, evolution, and behavior. Front. Ecol. Evol. 3, 51 (2015).Article 

Google Scholar 
Jennions, M. D. & Møller, A. P. Relationships fade with time: a meta-analysis of temporal trends in publication in ecology and evolution. Proc. Biol. Sci. 269, 43–48 (2002).PubMed 
PubMed Central 
Article 

Google Scholar 
Baker, M. 1,500 scientists lift the lid on reproducibility. Nature 533, 452–454 (2016).CAS 
PubMed 
Article 

Google Scholar 
Chalmers, I. & Glasziou, P. Avoidable waste in the production and reporting of research evidence. Lancet 374, 86–89 (2009).PubMed 
Article 

Google Scholar 
Altman, D. G. The scandal of poor medical research. BMJ 308, 283–284 (1994).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Glasziou, P. & Chalmers, I. Is 85% of health research really ‘wasted’? BMJ Opinion (14 January 2016).Glasziou, P. & Chalmers, I. Research waste is still a scandal. BMJ 363, k4645 (2018).Article 

Google Scholar 
Chalmers, I. et al. How to increase value and reduce waste when research priorities are set. Lancet 383, 156–165 (2014).PubMed 
Article 

Google Scholar 
Kunin, W. E. Robust evidence of declines in insect abundance and biodiversity. Nature 574, 641–642 (2019).CAS 
PubMed 
Article 

Google Scholar 
Christie, A. P. et al. Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences. Nat. Commun. 11, 6377 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Campbell, H. A. et al. Finding our way: on the sharing and reuse of animal telemetry data in Australasia. Sci. Total Environ. 534, 79–84 (2015).CAS 
PubMed 
Article 

Google Scholar 
Koricheva, J. Non-significant results in ecology: a burden or a blessing in disguise? Oikos 102, 397–401 (2003).Article 

Google Scholar 
Bennett, L. T. & Adams, M. A. Assessment of ecological effects due to forest harvesting: approaches and statistical issues. J. Appl. Ecol. 41, 585–598 (2004).Article 

Google Scholar 
Duval, S. & Tweedie, R. A nonparametric ‘trim and fill’ method of accounting for publication bias in meta-analysis. J. Am. Stat. Assoc. 95, 89–98 (2012).
Google Scholar 
Brlík, V. et al. Weak effects of geolocators on small birds: a meta-analysis controlled for phylogeny and publication bias. J. Anim. Ecol. 89, 207–220 (2020).PubMed 
Article 

Google Scholar 
Hurlbert, S. H. Pseudoreplication and the design of ecological field experiments. Ecol. Monogr. 54, 187–211 (1984).Article 

Google Scholar 
Jennions, M. D. & Møller, A. P. A survey of the statistical power of research in behavioral ecology and animal behaviour. Behav. Ecol. 14, 438–445 (2003).Article 

Google Scholar 
Culina, A., Purgar, M. & Klanjscek, T. Datasets and codes for Purgar et al. 2022: quantifying research waste in ecology. Zenodo https://zenodo.org/record/6566100#.YrLWB-zMIqs (2022).Ferguson, C. et al. Europe PMC in 2020. Nucleic Acids Res. 49, D1507–D1514 (2021).CAS 
PubMed 
Article 

Google Scholar 
Huang, C.-K. et al. Meta-Research: Evaluating the impact of open access policies on research institutions. eLife 9, e57067 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Ross-Hellauer, T. Open science, done wrong, will compound inequities. Nature 603, 363 (2022).CAS 
PubMed 
Article 

Google Scholar 
Smith, A. C. et al. Assessing the effect of article processing charges on the geographic diversity of authors using Elsevier’s ‘Mirror journal’ system. Quant. Sci. Stud. 2, 1123–1143 (2021).Article 

Google Scholar 
Christie, A. P. et al. Reducing publication delay to improve the efficiency and impact of conservation science. PeerJ 9, e12245 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Desjardins-Proulx, P. et al. The case for open preprints in biology. PLoS Biol. 11, e1001563 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Munafò, M. R. et al. A manifesto for reproducible science. Nat. Hum. Behav. 1, 0021 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
O’Dea, R. E. et al. Towards open, reliable, and transparent ecology and evolutionary biology. BMC Biol. 19, 68 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Culina, A. et al. Navigating the unfolding open data landscape in ecology and evolution. Nat. Ecol. Evol. 2, 420–426 (2018).PubMed 
Article 

Google Scholar 
Culina, A., Crowther, T. W., Ramakers, J. J. C., Gienapp, P. & Visser, M. E. How to do meta-analysis of open datasets. Nat. Ecol. Evol. 2, 1053–1056 (2018).PubMed 
Article 

Google Scholar 
Roche, D. G., Kruuk, L. E. B., Lanfear, R. & Binning, S. A. Public data archiving in ecology and evolution: how well are we doing? PLoS Biol. 13, e1002295 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Grainger, M. J., Bolam, F. C., Stewart, G. B. & Nilsen, E. B. Evidence synthesis for tackling research waste. Nat. Ecol. Evol. 4, 495–497 (2020).PubMed 
Article 

Google Scholar 
Nørgaard, B. et al. Systematic reviews are rarely used to inform study design—a systematic review and meta-analysis. J. Clin. Epidemiol. 145, 1–13 (2022).PubMed 
Article 

Google Scholar 
Webb, J. A. et al. Weaving common threads in environmental causal assessment methods: toward an ideal method for rapid evidence synthesis. Freshw. Sci. 36, 250–256 (2017).Article 

Google Scholar 
Collins, A., Coughlin, D., Miller, J. & Kirk, S. The Production of Quick Scoping Reviews and Rapid Evidence Assessments: A How to Guide (Joint Water Evidence Group, 2015).Carrick, J. et al. Is planting trees the solution to reducing flood risks? J. Flood Risk Manag. 12, e12484 (2019).Article 

Google Scholar 
Nuñez, M. A. & Amano, T. Monolingual searches can limit and bias results in global literature reviews. Nat. Ecol. Evol. 5, 264 (2021).PubMed 
Article 

Google Scholar 
Morrison, A. et al. The effect of English-language restriction on systematic review-based meta-analyses: a systematic review of empirical studies. Int. J. Technol. Assess. Health Care 28, 138–144 (2012).PubMed 
Article 

Google Scholar 
Wu, T., Li, Y., Bian, Z., Liu, G. & Moher, D. Randomized trials published in some Chinese journals: how many are randomized? Trials 10, 46 (2009).PubMed 
PubMed Central 
Article 

Google Scholar 
Vorobeichik, E. L. & Kozlov, M. V. Impact of point polluters on terrestrial ecosystems: methodology of research, experimental design, and typical errors. Russ. J. Ecol. 43, 89–96 (2012).Article 

Google Scholar 
Simmons, J. P., Nelson, L. D. & Simonsohn, U. False-positive psychology: undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychol. Sci. 22, 1359–1366 (2011).PubMed 
Article 

Google Scholar 
Transforming Our World: the 2030 Agenda for Sustainable Development (United Nations, 2015).MacCoun, R. & Perlmutter, S. Blind analysis: hide results to seek the truth. Nature 526, 187–189 (2015).CAS 
PubMed 
Article 

Google Scholar 
Parker, T. H. et al. Transparency in ecology and evolution: real problems, real solutions. Trends Ecol. Evol. 31, 711–719 (2016).PubMed 
Article 

Google Scholar 
Announcement: reducing our irreproducibility. Nature 496, 398 (2013).Moher, D. et al. Increasing value and reducing waste in biomedical research: who’s listening? Lancet 387, 1573–1586 (2016).PubMed 
Article 

Google Scholar 
Smaldino, P. E. & McElreath, R. The natural selection of bad science. R. Soc. Open Sci. 3, 160384 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Vrieze, J. Landmark research integrity survey finds questionable practices are surprisingly common. ScienceInsider https://www.sciencemag.org/news/2021/07/landmark-research-integrity-survey-finds-questionable-practices-are-surprisingly-common (2021).Woolston, C. Impact factor abandoned by Dutch university in hiring and promotion decisions. Nature 595, 462 (2021).CAS 
PubMed 
Article 

Google Scholar 
Directorate-General for Research and Innovation (European Commission). Towards a Reform of the Research Assessment System. Scoping Report (Publications Office, 2021).Athena Research & Innovation Center, Directorate-General for Research and Innovation (European Commission), PPMI, UNU-MERIT. Monitoring the Open Access Policy of Horizon 2020. Final report (European Commission, 2021).Kwon, D. University of California and Elsevier forge open-access deal. TheScientist https://www.the-scientist.com/news-opinion/university-of-california-and-elsevier-forge-open-access-deal–68557 (2021).Vines, T. H. et al. Mandated data archiving greatly improves access to research data. FASEB J. 27, 1304–1308 (2013).CAS 
PubMed 
Article 

Google Scholar 
NPQIP Collaborative Group. Did a change in Nature journals’ editorial policy for life sciences research improve reporting? BMJ Open Sci. 3, e000035 (2019).Article 

Google Scholar 
Glasziou, P. et al. Reducing waste from incomplete or unusable reports of biomedical research. Lancet 383, 267–276 (2014).PubMed 
Article 

Google Scholar 
Fecher, B. & Friesike, S. in Opening Science: the Evolving Guide on How the Internet is Changing Research, Collaboration and Scholarly Publishing (eds Bartling, S. & Friesike, S.) 17–47 (Springer International Publishing, 2014).Hardwicke, T. E. et al. Calibrating the scientific ecosystem through meta-research. Annu. Rev. Stat. Appl. 7, 11–37 (2020).Article 

Google Scholar 
McKiernan, E. C. et al. How open science helps researchers succeed. eLife 5, e16800 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Fidler, F. et al. Metaresearch for evaluating reproducibility in ecology and evolution. Bioscience 67, 282–289 (2017).PubMed 
PubMed Central 

Google Scholar 
Cornwall, C. E. & Hurd, C. L. Experimental design in ocean acidification research: problems and solutions. ICES J. Mar. Sci. 73, 572–581 (2016).Article 

Google Scholar 
Fidler, F., Burgman, M. A., Cumming, G., Buttrose, R. & Thomason, N. Impact of criticism of null-hypothesis significance testing on statistical reporting practices in conservation biology. Conserv. Biol. 20, 1539–1544 (2006).PubMed 
Article 

Google Scholar 
Forstmeier, W. & Schielzeth, H. Cryptic multiple hypotheses testing in linear models: overestimated effect sizes and the winner’s curse. Behav. Ecol. Sociobiol. 65, 47–55 (2011).PubMed 
Article 

Google Scholar 
Gillespie, B. R., Desmet, S., Kay, P., Tillotson, M. R. & Brown, L. E. A critical analysis of regulated river ecosystem responses to managed environmental flows from reservoirs. Freshw. Biol. 60, 410–425 (2015).Article 

Google Scholar 
Haddaway, N. R., Styles, D. & Pullin, A. S. Evidence on the environmental impacts of farm land abandonment in high altitude/mountain regions: a systematic map. Environ. Evid. 3, 17 (2014).Article 

Google Scholar 
Heffner, R. A., Butler, M. J. & Reilly, C. K. Pseudoreplication revisited. Ecology 77, 2558–2562 (1996).Article 

Google Scholar 
Holman, L., Head, M. L., Lanfear, R. & Jennions, M. D. Evidence of experimental bias in the life sciences: why we need blind data recording. PLoS Biol. 13, e1002190 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Hurlbert, S. H. & White, M. D. Experiments with freshwater invertebrate zooplanktivores: quality of statistical analyses. Bull. Mar. Sci. 53, 128–153 (1993).
Google Scholar 
Johnson, W. T.3rd & Freeberg, T. M. Pseudoreplication in use of predator stimuli in experiments on antipredator responses. Anim. Behav. 119, 161–164 (2016).Article 

Google Scholar 
Kozlov, M. V. Pseudoreplication in ecological research: the problem overlooked by Russian scientists. Zh. Obshch. Biol. 64, 292–307 (2003).CAS 
PubMed 

Google Scholar 
Kozlov, M. V. Plant studies on fluctuating asymmetry in Russia: mythology and methodology. Russ. J. Ecol. 48, 1–9 (2017).Article 

Google Scholar 
McDonald, S., Cresswell, T., Hassell, K. & Keough, M. Experimental design and statistical analysis in aquatic live animal radiotracing studies: a systematic review. Crit. Rev. Environ. Sci. Technol. 52, 2772–2801 (2021).Article 

Google Scholar 
Møller, A. P., Thornhill, R. & Gangestad, S. W. Direct and indirect tests for publication bias: asymmetry and sexual selection. Anim. Behav. 70, 497–506 (2005).Article 

Google Scholar 
Mrosovsky, N. & Godfrey, M. H. The path from grey literature to Red Lists. Endang. Species Res. 6, 185–191 (2008).
Google Scholar 
O’Brien, C., van Riper, C.3rd & Myers, D. E. Making reliable decisions in the study of wildlife diseases: using hypothesis tests, statistical power, and observed effects. J. Wildl. Dis. 45, 700–712 (2009).PubMed 
Article 

Google Scholar 
Parker, T. H. What do we really know about the signalling role of plumage colour in blue tits? A case study of impediments to progress in evolutionary biology. Biol. Rev. Camb. Philos. Soc. 88, 511–536 (2013).PubMed 
Article 

Google Scholar 
Ramage, B. S. et al. Pseudoreplication in tropical forests and the resulting effects on biodiversity conservation. Conserv. Biol. 27, 364–372 (2013).PubMed 
Article 

Google Scholar 
Sallabanks, R., Arnett, E. B. & Marzluff, J. M. An evaluation of research on the effects of timber harvest on bird populations. Wildl. Soc. Bull. 28, 1144–1155 (2000).
Google Scholar 
Sánchez-Tójar, A. et al. Meta-analysis challenges a textbook example of status signalling and demonstrates publication bias. eLife 7, e37385 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Waller, B., Warmelink, L., Liebal, K., Micheletta, J. & Slocombe, K. Pseudoreplication: a widespread problem in primate communication research. Anim. Behav. 86, 483–488 (2013).Article 

Google Scholar 
Van Wilgenburg, E. & Elgar, M. A. Confirmation bias in studies of nestmate recognition: a cautionary note for research into the behaviour of animals. PLoS ONE 8, e53548 (2013).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yoccoz, N. G. Use, overuse, and misuse of significance tests in evolutionary biology and ecology. Bull. Ecol. Soc. Am. 72, 106–111 (1991).
Google Scholar 
Zaitsev, A. S., Gongalsky, K. B., Malmström, A., Persson, T. & Bengtsson, J. Why are forest fires generally neglected in soil fauna research? A mini-review. Appl. Soil Ecol. 98, 261–271 (2016).Article 

Google Scholar 
Zvereva, E. L. & Kozlov, M. V. Biases in studies of spatial patterns in insect herbivory. Ecol. Monogr. 89, e01361 (2019).Article 

Google Scholar 
RStudio Team. RStudio: Integrated Development for R (RStudio, 2020).Viechtbauer, W. Conducting meta-analyses in R with the metafor package. J. Stat. Softw. 36, 1–48 (2010).Article 

Google Scholar  More

Rockström, J. et al. Planetary boundaries: exploring the safe operating space for humanity. Ecol. Soc. 461, 472–475 (2009).Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015).PubMed 
Article 
CAS 

Google Scholar 
Pimm, S. L. et al. The biodiversity of species and their rates of extinction, distribution, and protection. Science 344, 1246752 (2014).CAS 
PubMed 
Article 

Google Scholar 
Wake, D. B. & Vredenburg, V. T. Are we in the midst of the sixth mass extinction? A view from the world of amphibians. Proc. Natl Acad. Sci. USA 105, 11466–11473 (2008).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sweet, M., Burian, A. & Bulling, M. Corals as canaries in the coalmine: towards the incorporation of marine ecosystems into the ‘One Health’ concept. J. Invertebr. Pathol. 186, 107538 (2021).PubMed 
Article 

Google Scholar 
Flandroy, L. et al. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci. Total Environ. 627, 1018–1038 (2018).CAS 
PubMed 
Article 

Google Scholar 
Cardinale, B. J. et al. Biodiversity loss and its impact on humanity. Nature 486, 59–67 (2012).CAS 
PubMed 
Article 

Google Scholar 
Oliver, T. H. et al. Declining resilience of ecosystem functions under biodiversity loss. Nat. Commun. 6, 10122 (2015).PubMed 
Article 
CAS 

Google Scholar 
Loreau, M. & de Mazancourt, C. Biodiversity and ecosystem stability: a synthesis of underlying mechanisms. Ecol. Lett. 16, 106–115 (2013).PubMed 
Article 

Google Scholar 
Doering, T. et al. Towards enhancing coral heat tolerance: a ‘microbiome transplantation’ treatment using inoculations of homogenized coral tissues. Microbiome 9, 102 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rosado, P. M. et al. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 13, 921–936 (2019).CAS 
PubMed 
Article 

Google Scholar 
Santos, H. F. et al. Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota. Sci. Rep. 5, 18268 (2015).Article 
CAS 

Google Scholar 
Santoro, E. P. et al. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci. Adv. 7, eabg3088 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Silva, D. P. et al. Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites. Microbiome 9, 118 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hoyt, J. R. et al. Field trial of a probiotic bacteria to protect bats from white-nose syndrome. Sci. Rep. 9, 9158 (2019).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Bletz, M. C. et al. Mitigating amphibian chytridiomycosis with bioaugmentation: characteristics of effective probiotics and strategies for their selection and use. Ecol. Lett. 16, 807–820 (2013).PubMed 
Article 

Google Scholar 
Daisley, B. A. et al. Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees. Commun. Biol. 3, 534 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Powell, J. E., Carver, Z., Leonard, S. P. & Moran, N. A. Field-realistic tylosin exposure impacts honey bee microbiota and pathogen susceptibility, which is ameliorated by native gut probiotics. Microbiol. Spectr. 9, e0010321 (2021).PubMed 
Article 

Google Scholar 
Borges, D., Guzman-Novoa, E. & Goodwin, P. H. Effects of prebiotics and probiotics on honey bees (Apis mellifera) infected with the microsporidian parasite Nosema ceranae. Microorganisms 9, 481 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Daisley, B. A. et al. Novel probiotic approach to counter Paenibacillus larvae infection in honey bees. ISME J. 14, 476–491 (2020).CAS 
PubMed 
Article 

Google Scholar 
Trinder, M. et al. Probiotic Lactobacillus rhamnosus reduces organophosphate pesticide absorption and toxicity to Drosophila melanogaster. Appl. Environ. Microbiol. 82, 6204–6213 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Enquist, B. J., Abraham, A. J., Harfoot, M. B. J., Malhi, Y. & Doughty, C. E. The megabiota are disproportionately important for biosphere functioning. Nat. Commun. 11, 699 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Knowlton, N. et al. Rebuilding Coral Reefs: A Decadal Grand Challenge. (International Coral Reef Society, Future Earth Coasts, 2021).Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Jaspers, C. et al. Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology 133, 81–87 (2019).PubMed 
Article 

Google Scholar 
Bosch, T. C. G. & McFall-Ngai, M. J. Metaorganisms as the new frontier. Zoology 114, 185–190 (2011).PubMed 
Article 

Google Scholar 
Wilkins, L. G. E. et al. Host-associated microbiomes and their roles in marine ecosystem functions. PLoS Biol. 17, e3000533 (2019).Humphreys, C. P. et al. Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants. Nat. Commun. 1, 103 (2010).PubMed 
Article 
CAS 

Google Scholar 
Koskella, B. & Bergelson, J. The study of host-microbiome (co)evolution across levels of selection. Phil. Trans. R. Soc. Lond. B 375, 20190604 (2020).Article 

Google Scholar 
Keller-Costa, T. et al. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. Microbiome 9, 72 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Guerra, C. A. et al. Global projections of the soil microbiome in the Anthropocene. Glob. Ecol. Biogeogr. 30, 987–999 (2021).PubMed 
Article 

Google Scholar 
Weinbauer, M. G. & Rassoulzadegan, F. Extinction of microbes: evidence and potential consequences. Endanger. Species Res. 3, 205–215 (2007).Article 

Google Scholar 
Petersen, C. & Round, J. L. Defining dysbiosis and its influence on host immunity and disease. Cell. Microbiol. 16, 1024–1033 (2014).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hanski, I. et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc. Natl Acad. Sci. USA 109, 8334–8339 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).CAS 
PubMed 
Article 

Google Scholar 
Balbín-Suárez, A. et al. Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis. FEMS Microbiol. Ecol. 97, fiab031 (2021).Erlacher, A., Cardinale, M., Grosch, R., Grube, M. & Berg, G. The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome. Front. Microbiol. 5, 175 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Shahi, F., Redeker, K. & Chong, J. Rethinking antimicrobial stewardship paradigms in the context of the gut microbiome. JAC Antimicrob. Resist. 1, dlz015 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Voolstra, C. R. & Ziegler, M. Adapting with microbial help: microbiome flexibility facilitates rapid responses to environmental change. Bioessays 42, e2000004 (2020).PubMed 
Article 

Google Scholar 
McBurney, M. I. et al. Establishing what constitutes a healthy human gut microbiome: state of the science, regulatory considerations, and future directions. J. Nutr. 149, 1882–1895 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Voolstra, C. R. et al. Extending the natural adaptive capacity of coral holobionts. Nat. Rev. Earth Environ. 2, 747–762 (2021).Article 

Google Scholar 
Woodhams, D. C. et al. Prodigiosin, violacein, and volatile organic compounds produced by widespread cutaneous bacteria of amphibians can inhibit two Batrachochytrium fungal pathogens. Microb. Ecol. 75, 1049–1062 (2018).CAS 
PubMed 
Article 

Google Scholar 
Voyles, J. et al. Shifts in disease dynamics in a tropical amphibian assemblage are not due to pathogen attenuation. Science 359, 1517–1519 (2018).CAS 
PubMed 
Article 

Google Scholar 
Harris, R. N. et al. Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus. ISME J. 3, 818–824 (2009).CAS 
PubMed 
Article 

Google Scholar 
Peixoto, R. S., Harkins, D. M. & Nelson, K. E. Advances in microbiome research for animal health. Annu. Rev. Anim. Biosci. 9, 289–311 (2021).CAS 
PubMed 
Article 

Google Scholar 
Blanck, H. & Wängberg, S.-Å. Induced community tolerance in marine periphyton established under arsenate stress. Can. J. Fish. Aquat. Sci. 45, 1816–1819 (1988).Article 

Google Scholar 
French, E., Kaplan, I., Iyer-Pascuzzi, A., Nakatsu, C. H. & Enders, L. Emerging strategies for precision microbiome management in diverse agroecosystems. Nat. Plants 7, 256–267 (2021).PubMed 
Article 

Google Scholar 
Borges, N. et al. Bacteriome structure, function, and probiotics in fish larviculture: the good, the bad, and the gaps. Annu. Rev. Anim. Biosci. 9, 423–452 (2021).CAS 
PubMed 
Article 

Google Scholar 
De Schryver, P. & Vadstein, O. Ecological theory as a foundation to control pathogenic invasion in aquaculture. ISME J. 8, 2360–2368 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Sonnenschein, E. C., Jimenez, G., Castex, M. & Gram, L. The Roseobacter-group bacterium Phaeobacter as a safe probiotic solution for aquaculture. Appl. Environ. Microbiol. 87, e0258120 (2021).PubMed 
Article 

Google Scholar 
Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Peixoto, R. S., Sweet, M. & Bourne, D. G. Customized medicine for corals. Front. Mar. Sci. 6, 686 (2019).Quraishi, M. N. et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment. Pharmacol. Ther. 46, 479–493 (2017).CAS 
PubMed 
Article 

Google Scholar 
Henrick, B. M. et al. Bifidobacteria-mediated immune system imprinting early in life. Cell 184, 3884–3898.e11 (2021).CAS 
PubMed 
Article 

Google Scholar 
Freedman, S. B. et al. Multicenter trial of a combination probiotic for children with gastroenteritis. N. Engl. J. Med. 379, 2015–2026 (2018).CAS 
PubMed 
Article 

Google Scholar 
Cabana, M. D. et al. Early probiotic supplementation for eczema and asthma prevention: a randomized controlled trial. Pediatrics 140, e20163000 (2017).Matsumoto, H. et al. Bacterial seed endophyte shapes disease resistance in rice. Nat. Plants 7, 60–72 (2021).CAS 
PubMed 
Article 

Google Scholar 
D’Alvise, P. W. et al. Phaeobacter gallaeciensis reduces Vibrio anguillarum in cultures of microalgae and rotifers, and prevents vibriosis in cod larvae. PLoS ONE 7, e43996 (2012).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Dittmann, K. K. et al. Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens. Appl. Environ. Microbiol. 86, e00499-20 (2020).Metchnikoff, E. The Prolongation of Life: Optimistic Studies (Heinemann, 1907).Khanna, S., Jones, C., Jones, L., Bushman, F. & Bailey, A. Increased microbial diversity found in successful versus unsuccessful recipients of a next-generation FMT for recurrent Clostridium difficile infection. Open Forum Infect. Dis 5, 304–309(2015).Kachrimanidou, M. & Tsintarakis, E. Insights into the role of human gut microbiota in Clostridioides difficile infection. Microorganisms 8, 200 (2020).Aggarwala, V. et al. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nat. Microbiol. 6, 1309–1318 (2021).Zachow, C., Müller, H., Tilcher, R., Donat, C. & Berg, G. Catch the best: novel screening strategy to select stress protecting agents for crop plants. Agronomy 3, 794–815 (2013).Article 
CAS 

Google Scholar 
Berg, G., Kusstatscher, P., Abdelfattah, A., Cernava, T. & Smalla, K. Microbiome modulation-toward a better understanding of plant microbiome response to microbial inoculants. Front. Microbiol. 12, 650610 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Ehlers, R.-U. in Regulation of Biological Control Agents (ed. Ehlers, R.-U.) 3–23 (Springer Netherlands, 2011).CDC. V-Safe After Vaccination Health Checker https://www.cdc.gov/coronavirus/2019-ncov/vaccines/safety/vsafe.html (2022).Bok, K., Sitar, S., Graham, B. S. & Mascola, J. R. Accelerated COVID-19 vaccine development: milestones, lessons, and prospects. Immunity 54, 1636–1651 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Vestal, R. Fecal microbiota transplant. Hosp. Med. Clin. 5, 58–70 (2016).Article 

Google Scholar 
Jansen, J. W. Fecal microbiota transplant vs oral vancomycin taper: important undiscussed limitations. Clin. Infect. Dis. 64, 1292–1293 (2017).PubMed 
Article 

Google Scholar 
Basson, A. R., Zhou, Y., Seo, B., Rodriguez-Palacios, A. & Cominelli, F. Autologous fecal microbiota transplantation for the treatment of inflammatory bowel disease. Transl. Res. 226, 1–11 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
DeFilipp, Z. et al. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N. Engl. J. Med. 381, 2043–2050 (2019).PubMed 
Article 

Google Scholar 
Slatko, B. E., Luck, A. N., Dobson, S. L. & Foster, J. M. Wolbachia endosymbionts and human disease control. Mol. Biochem. Parasitol. 195, 88–95 (2014).CAS 
PubMed 
Article 

Google Scholar 
Ahantarig, A. & Kittayapong, P. Endosymbiotic Wolbachia bacteria as biological control tools of disease vectors and pests. J. Appl. Entomol. 135, 479–486 (2011).Article 

Google Scholar 
Turner, J. et al. Extreme temperatures in the Antarctic. J. Clim. 34, 2653–2668 (2021).Article 

Google Scholar 
Schoennagel, T. et al. Adapt to more wildfire in western North American forests as climate changes. Proc. Natl Acad. Sci. USA 114, 4582–4590 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Di Virgilio, G. et al. Climate change increases the potential for extreme wildfires. Geophys. Res. Lett. 46, 8517–8526 (2019).Article 

Google Scholar 
Liu, Y., Stanturf, J. & Goodrick, S. Trends in global wildfire potential in a changing climate. Ecol. Manage. 259, 685–697 (2010).Article 

Google Scholar 
Zhou, J. et al. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc. Natl Acad. Sci. USA 111, E836–E845 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Wittebole, X., De Roock, S. & Opal, S. M. A historical overview of bacteriophage therapy as an alternative to antibiotics for the treatment of bacterial pathogens. Virulence 5, 226–235 (2014).PubMed 
Article 

Google Scholar 
Sieiro, C. et al. A hundred years of bacteriophages: can phages replace antibiotics in agriculture and aquaculture? Antibiotics 9, 493 (2020).Rulkens, W. Increasing the environmental sustainability of sewage treatment by mitigating pollutant pathways. Environ. Eng. Sci. 23, 650–665 (2006).Obotey Ezugbe, E. & Rathilal, S. Membrane technologies in wastewater treatment: a review. Membranes 10, 89 (2020).Lee, C. S., Robinson, J. & Chong, M. F. A review on application of flocculants in wastewater treatment. Process Saf. Environ. Prot. 92, 489–508 (2014).Guo, W.-Q., Yang, S.-S., Xiang, W.-S., Wang, X.-J. & Ren, N.-Q. Minimization of excess sludge production by in-situ activated sludge treatment processes–a comprehensive review. Biotechnol. Adv. 31, 1386–1396 (2013).CAS 
PubMed 
Article 

Google Scholar 
Alvarez-Filip, L., Estrada-Saldívar, N., Pérez-Cervantes, E., Molina-Hernández, A. & González-Barrios, F. J. A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 7, e8069 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Meiling, S. S. et al. Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure. Front. Mar. Sci. 8, 670829 (2021).Hunt, P. R. The C. elegans model in toxicity testing. J. Appl. Toxicol. 37, 50–59 (2017).Tkaczyk, A., Bownik, A., Dudka, J., Kowal, K. & Ślaska, B. Daphnia magna model in the toxicity assessment of pharmaceuticals: a review. Sci. Total Environ. 763, 143038 (2021).CAS 
PubMed 
Article 

Google Scholar 
Microbiota Vault. A Vault for Humanity https://www.microbiotavault.org/ (2021).Health and Nutritional Properties of Probiotics in Food Including Powder Milk with Live Lactic Acid Bacteria (FAO, WHO, 2001).Sanders, M. E., Merenstein, D. J., Reid, G., Gibson, G. R. & Rastall, R. A. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nat. Rev. Gastroenterol. Hepatol. 16, 605–616 (2019).PubMed 
Article 

Google Scholar 
Gibson, G. R. et al. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat. Rev. Gastroenterol. Hepatol. 14, 491–502 (2017).PubMed 
Article 

Google Scholar 
Salminen, S. et al. The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat. Rev. Gastroenterol. Hepatol. 18, 649–667 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Liu, A. et al. Adjunctive probiotics alleviates asthmatic symptoms via modulating the gut microbiome and serum metabolome. Microbiol. Spectr. 9, e0085921 (2021).PubMed 
Article 

Google Scholar 
Bagga, D. et al. Probiotics drive gut microbiome triggering emotional brain signatures. Gut Microbes 9, 486–496 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Patel, R. M. & Underwood, M. A. Probiotics and necrotizing enterocolitis. Semin. Pediatr. Surg. 27, 39–46 (2018).PubMed 
Article 

Google Scholar 
Tobias, J. et al. Bifidobacterium longum subsp. infantis EVC001 administration is associated with a significant reduction in the incidence of necrotizing enterocolitis in very low birth weight infants. J. Pediatr. https://doi.org/10.1016/j.jpeds.2021.12.070 (2022).Koziol, L. et al. The plant microbiome and native plant restoration: the example of native mycorrhizal fungi. Bioscience 68, 996–1006 (2018).Article 

Google Scholar 
Cabello, F. C. et al. Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. Environ. Microbiol. 15, 1917–1942 (2013).PubMed 
Article 

Google Scholar 
Evensen, Ø. & Leong, J.-A. C. DNA vaccines against viral diseases of farmed fish. Fish. Shellfish Immunol. 35, 1751–1758 (2013).CAS 
PubMed 
Article 

Google Scholar 
Burridge, L., Weis, J. S., Cabello, F., Pizarro, J. & Bostick, K. Chemical use in salmon aquaculture: a review of current practices and possible environmental effects. Aquaculture 306, 7–23 (2010).CAS 
Article 

Google Scholar 
Kesarcodi-Watson, A., Kaspar, H., Lategan, M. J. & Gibson, L. Probiotics in aquaculture: the need, principles and mechanisms of action and screening processes. Aquaculture 274, 1–14 (2008).Article 

Google Scholar 
Irianto, A. & Austin, B. Probiotics in aquaculture. J. Fish. Dis. 25, 633–642 (2002).Article 

Google Scholar 
Assefa, A. & Abunna, F. Maintenance of fish health in aquaculture: review of epidemiological approaches for prevention and control of infectious disease of fish. Vet. Med. Int. 2018, 5432497 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Hoseinifar, S. H., Sun, Y.-Z., Wang, A. & Zhou, Z. Probiotics as means of diseases control in aquaculture, a review of current knowledge and future perspectives. Front. Microbiol. 9, 2429 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Castex, M., Leclercq, E., Lemaire, P. & Chim, L. Dietary probiotic Pediococcus acidilactici MA18/5M improves the growth, feed performance and antioxidant status of penaeid shrimp Litopenaeus stylirostris: a growth-ration-size approach. Animals 11, 3451 (2021).Goulson, D., Nicholls, E., Botías, C. & Rotheray, E. L. Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 347, 1255957 (2015).Daisley, B. A., Chmiel, J. A., Pitek, A. P., Thompson, G. J. & Reid, G. Missing microbes in bees: how systematic depletion of key symbionts erodes immunity. Trends Microbiol. 28, 1010–1021 (2020).CAS 
PubMed 
Article 

Google Scholar 
Chmiel, J. A., Daisley, B. A., Burton, J. P. & Reid, G. Deleterious effects of neonicotinoid pesticides on Drosophila melanogaster immune pathways. Mbio 10, e01395-19 (2019).Daisley, B. A. et al. Microbiota-mediated modulation of organophosphate insecticide toxicity by species-dependent interactions with lactobacilli in a Drosophila melanogaster insect model. Appl. Environ. Microbiol. 84, e02820-17 (2018).Duarte, G. A. S. et al. Heat waves are a major threat to turbid coral reefs in Brazil. Front. Mar. Sci. 7, 179 (2020).Hughes, T. P. et al. Global warming impairs stock-recruitment dynamics of corals. Nature 568, 387–390 (2019).CAS 
PubMed 
Article 

Google Scholar 
Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).CAS 
PubMed 
Article 

Google Scholar 
Barno, A. R., Villela, H. D. M., Aranda, M., Thomas, T. & Peixoto, R. S. Host under epigenetic control: a novel perspective on the interaction between microorganisms and corals. Bioessays 43, e2100068 (2021).PubMed 
Article 
CAS 

Google Scholar 
Welsh, R. M. et al. Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators. PeerJ 5, e3315 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Peixoto, R. S. et al. Coral probiotics: premise, promise, prospects. Annu. Rev. Anim. Biosci. 9, 265–288 (2021).PubMed 
Article 

Google Scholar 
Peixoto, R. S. et al. Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience. Front. Microbiol. 8, 341 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Morgans, C. A., Hung, J. Y. & Bourne, D. G. Symbiodiniaceae probiotics for use in bleaching recovery. Restoration 28, 282–288 (2020).Zhang, Y. et al. Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium. BMC Microbiol. 21, 130 (2021).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Assis, J. M. et al. Delivering beneficial microorganisms for corals: rotifers as carriers of probiotic bacteria. Front. Microbiol. 11, 608506 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Zhou, G. et al. Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification. Sci. Rep. 6, 35971 (2016).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
VanCompernolle, S. E. et al. Antimicrobial peptides from amphibian skin potently inhibit human immunodeficiency virus infection and transfer of virus from dendritic cells to T cells. J. Virol. 79, 11598–11606 (2005).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Scheele, B. C. et al. Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity. Science 363, 1459–1463 (2019).CAS 
PubMed 
Article 

Google Scholar 
Harris, R. N., Lauer, A., Simon, M. A., Banning, J. L. & Alford, R. A. Addition of antifungal skin bacteria to salamanders ameliorates the effects of chytridiomycosis. Dis. Aquat. Organ. 83, 11–16 (2009).PubMed 
Article 

Google Scholar 
Loudon, A. H. et al. Interactions between amphibians’ symbiotic bacteria cause the production of emergent anti-fungal metabolites. Front. Microbiol. 5, 441 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Muletz-Wolz, C. R. et al. Inhibition of fungal pathogens across genotypes and temperatures by amphibian skin bacteria. Front. Microbiol. 8, 1551 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Jin Song, S. et al. Engineering the microbiome for animal health and conservation. Exp. Biol. Med. 244, 494–504 (2019).CAS 
Article 

Google Scholar 
Küng, D. et al. Stability of microbiota facilitated by host immune regulation: informing probiotic strategies to manage amphibian disease. PLoS ONE 9, e87101 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Micalizzi, E. W. & Smith, M. L. Volatile organic compounds kill the white-nose syndrome fungus, Pseudogymnoascus destructans, in hibernaculum sediment. Can. J. Microbiol. 66, 593–599 (2020).CAS 
PubMed 
Article 

Google Scholar 
Gabriel, K. T., Joseph Sexton, D. & Cornelison, C. T. Biomimicry of volatile-based microbial control for managing emerging fungal pathogens. J. Appl. Microbiol. 124, 1024–1031 (2018).CAS 
PubMed 
Article 

Google Scholar 
Woodhams, D. C., Bletz, M., Kueneman, J. & McKenzie, V. Managing amphibian disease with skin microbiota. Trends Microbiol. 24, 161–164 (2016).CAS 
PubMed 
Article 

Google Scholar  More

Study sites and swarm characterizationThe survey was conducted in 10 villages in south-western Burkina Faso especially around the district of Bobo-Dioulasso, Santitougou (N11° 17′ 16″, W4° 13′ 04″), Kimidougou (N11° 17′ 53″; W4° 14′ 11″), Nastenga (N10.96871; W003.23477), Zeyama (N10.87638; W 003.26145), Mogobasso (N11° 25′ 31″, W4° 06′ 08″), Synbekuy (N11° 53′ 28″, W3° 44′ 02″), Ramatoulaye (N11° 33′ 39″, W3° 57′ 05″) Syndombokuy (N11° 53′ 06″, W3° 43′ 19″), Lampa (N11.16464; W 003.6374) et Syndounkuy (N11.14541; W 003.05141) (Fig. 1). All villages are located north of Bobo-Dioulasso, on the national road 10 (N10), ranged from 20 and 90 km. The region is characterised by wooded savannah located in south-western Burkina Faso, and the mean annual rainfall is about 1200 mm. The rainy season extends from May to October and the dry season from November to April. Malaria transmission in the area extends from June to November. However, residual transmission may occur beyond this period in specific locations. An. gambiae is the major malaria vector following by An. coluzzii and An. Arabiensis. Villages were chosen to represent similar ecological and entomological settings, they are middle sized and relatively isolated from one another.Figure 1Localization of the study sites in south-western Burkina Faso. This map was created under QGIS version 2.18 Las Palmas. link: https://changelog.qgis.org/en/qgis/version/2.18.0/Full size imageSpray Application Against Mosquito Swarms (SAMS) consisted of spraying diluted insecticide (Actellic 50: tap water with 1:20 concentration) at dusk by trained volunteer teams. They used the innovative technology of targeted swarm spraying with handheld sprayers and conventional broadcast space spray with backpack sprayers to achieve maximum effect. The spraying activities were conducted in eight of the ten villages. The target swarm spray was used in the four villages Kimidougou, Nastenga, Ramatoulaye and Syndombokuy. The broadcast space spray was applied in four other villages, Zeyama, Mogobasso, Lampa and Syndounkuy. The two remaining villages, Santidougou and Synbekuy were chosen as controls (Fig. 1). In each village, the potential swarm markers and the positive swarm sites were identified and geo-referenced using GPS. All concessions also were geo-referenced and labelled using paint.Procedure of the interventionTargeted swam spraying using handheld sprayersTargeted swarm spraying was carried out in four villages. Members of each team and volunteers from the selected villages were trained to target the swarms and apply an appropriate amount of spray each time. After the pre-intervention phase, all swarm sites scattered through the villages were repaired and swarm characteristics recorded. At 30 min before dusk (the estimated swarming time), a volunteer was placed in each compound with a sprayer. The objective of each volunteer was to destroy any swarm in the compound by applying insecticide with the handheld sprayer (Fig. 2A,B). Screening of the compound was continued for about 30 min until it was dark and no mosquitoes were visible. A single operator was able to effectively target 5 to 10 swarms per spray evening, depending on the distribution of swarms across the village. Spraying was carried out for 10 successive days throughout each village. The period of spraying approximately covered the period of pre-imaginal mosquito stages and was renewed after 45 days. The quantity of insecticide used was measured daily, in order to determine with precision the total quantity of insecticide used during targeted spraying.Figure 2Volunteer spraying swarms using handheld sprayers (A,B). Backpack spraying activities (C,D).Full size imageConventional broadcast spraying using Backpack sprayersThe broadcast spraying was also carried out in 4 villages but, unlike the targeted spraying, there was no direct targeting of swarms. At swarming time (estimated around 30 min at dusk) two volunteers with backpack sprayers ran through the entire village along paths between the compounds while spraying insecticide (Fig. 2C,D). As with the targeted spraying procedure, the broadcast spraying was carried out for 10 successive days in all 4 villages simultaneously, and spraying recommenced after 45 days. The quantity of insecticide used was measured daily, in order to determine with precision the total quantity of insecticide used during targeted spraying.Evaluation of the interventionA year prior to the intervention, baseline entomological data was collected in both villages to estimate mosquito density, human biting rate, female insemination rate, age structure of females and entomological inoculation rate29. The same parameters were evaluated immediately before and after intervention. The pre- and post-intervention evaluation of the abovementioned parameters were carried in both control and intervention villages at the same time. In both pre-intervention and post-intervention phases, two methods of mosquito collection were performed in each village, the human landing catch (HLC), indoor and outdoor in 4 houses for 4 successive nights, the pyrethroid spray catch (PSC) in the same10 houses and 10 randomly selected houses. To identify these, all houses in each village were coded and these codes were used to randomly select those to be sampled. All sampled sites were mapped using a global positioning system (GPS). Collected anopheline mosquitoes were sorted by taxonomic status, physiological status, and sex. Approximately, the ovaries of 200 females/month/village (100 females indoor and 100 females outdoor) were dissected to determine the physiological age, and parous females were subsequently subjected to ELISA assays to determine Plasmodium sporozoite rates. Data produced from indoor and outdoor mosquito collections were then used to estimate mosquito densities, their spatial distribution, produce a map identifying hotspots where the highest mosquito densities and biting occurred within the village, female age structure and quantify the intensity of malaria transmission. The impact of the spray was measured to see how it affected each of these parameters in the intervention villages compared to the controls.Statistical analysisThe resting mosquito abundance was assessed as the number of mosquitoes per house, the human biting rate assessed as the number of bites per person per night, the parity rate assessed as the percentage of parous females, and the insemination rate assessed as the percentage of the inseminated females. The list above defined the key entomological parameters to determine the dynamic of An. gambie s.l. populations and malaria transmission. The generalized estimating equation (GEE) method was used to estimate population averaged effect of intervention on various outcome measurements. As the GEE models do not require distributional assumptions but only specification of the mean and variance structure, they are more robust against misspecification of higher-order features of the data, and are useful when the main interest is in population averaged effects of an intervention or treatment. However, because they do not use a full likelihood model, they cannot be used for individual-specific inference30,31. Despite this shortcoming, their robustness to different types of correlation structures in the data (due to temporal ordering of measurements, or other hierarchical structure in data) makes them attractive for analyses of this type. GEE models were run in R version 3.6.232, using the package “geepack”33 for three datasets on insemination and parity rate, number of bites per person per night (NBPN), and density of adult male and female mosquitoes. To clean and plot the data the “tidyverse” family of R packages34 were used.Ethical considerationsThis study did not involve human patients. The full protocol of the study was submitted to the Institutional Ethics Committee of the “Institut de Recherche en Sciences de la Sante” for review and approval (A17-2016/CEIRES). In accordance with the approval, presentations of the project were given to the study site villagers and requests for their participation were made. During these visits the objectives, protocol and expected results were explained and discussed, as well as the implications for the households willing to take part in this study. A written consent form was signed or marked with fingerprint by the head of the households before any activity could take place in his compound. Insecticides used in this study are approved for use by the Burkina Faso insecticide regulation authority. More

Canadell, J. G. et al. Contributions to accelerating atmospheric CO2 growth from economic activity, carbon intensity, and efficiency of natural sinks. Proc. Natl. Acad. Sci. 104, 18866–18870 (2007).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Beer, C. et al. Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate. Science 329, 834–838 (2010).ADS 
CAS 
PubMed 

Google Scholar 
Park, T. et al. Changes in timing of seasonal peak photosynthetic activity in northern ecosystems. Global. Change. Biol. 25, 2382–2395 (2019).ADS 

Google Scholar 
Wang, T. et al. Emerging negative impact of warming on summer carbon uptake in northern ecosystems. Nat. Commun. 9, 5391 (2018).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Farquhar, G. D., Von Caemmerer, S. & Berry, J. A. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149, 78–90 (1980).CAS 
PubMed 

Google Scholar 
Chen, J. M. et al. Effects of foliage clumping on the estimation of global terrestrial gross primary productivity. Global. Biogeochem. Cy 26, GB1019 (2012).ADS 

Google Scholar 
De Pury, D. G. G. & Farquhar, G. D. Simple scaling of photosynthesis from leaves to canopies without the errors of big-leaf models. Plant Cell Environ. 20, 537–557 (1997).
Google Scholar 
Zhang, Y. et al. Development of a coupled carbon and water model for estimating global gross primary productivity and evapotranspiration based on eddy flux and remote sensing data. Agr. Forest. Meteorol. 223, 116–131 (2016).ADS 

Google Scholar 
Monteith, J. L. Climate and the efficiency of crop production in Britain. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 281, 277–294 (1977).ADS 

Google Scholar 
Running, S. W. et al. A continuous satellite-derived measure of global terrestrial primary production. Bioscience. 54, 547–560 (2004).
Google Scholar 
Yuan, W. et al. Global estimates of evapotranspiration and gross primary production based on MODIS and global meteorology data. Remote Sens. Environ. 114, 1416–1431 (2010).ADS 

Google Scholar 
Ruimy, A., Dedieu, G. & Saugier, B. TURC: A diagnostic model of continental gross primary productivity and net primary productivity. Global. Biogeochem. Cy 10, 269–285 (1996).ADS 
CAS 

Google Scholar 
Jung, M. et al. The FLUXCOM ensemble of global land-atmosphere energy fluxes. Sci. Data 6, 190076 (2019).
Google Scholar 
Bodesheim, P., Jung, M., Gans, F., Mahecha, M. D. & Reichstein, M. Upscaled diurnal cycles of land–atmosphere fluxes: a new global half-hourly data product. Earth Syst. Sci. Data 10, 1327–1365 (2018).ADS 

Google Scholar 
Joiner, J. et al. Estimation of Terrestrial Global Gross Primary Production (GPP) with Satellite Data-Driven Models and Eddy Covariance Flux Data. Remote Sens. 10, 1346 (2018).ADS 

Google Scholar 
Xiao, J. et al. Data-driven diagnostics of terrestrial carbon dynamics over North America. Agr. Forest. Meteorol. 197, 142–157 (2014).ADS 

Google Scholar 
Ichii, K. et al. New data-driven estimation of terrestrial CO2 fluxes in Asia using a standardized database of eddy covariance measurements, remote sensing data, and support vector regression. J. Geophys. Res. Biogeosci. 122, 767–795 (2017).CAS 

Google Scholar 
Cai, W. et al. Improved estimations of gross primary production using satellite-derived photosynthetically active radiation. J. Geophys. Res. Biogeosci. 119, 110–123 (2014).
Google Scholar 
Ma, J., Yan, X., Dong, W. & Chou, J. Gross primary production of global forest ecosystems has been overestimated. Sci. Rep. 5, 10820 (2015).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cai, W. et al. Large Differences in Terrestrial Vegetation Production Derived from Satellite-Based Light Use Efficiency Models. Remote Sens. 6, 8945–8965 (2014).ADS 

Google Scholar 
Jung, M. et al. Uncertainties of modeling gross primary productivity over Europe: A systematic study on the effects of using different drivers and terrestrial biosphere models. Global. Biogeochem. Cy 21, GB4021 (2007).ADS 

Google Scholar 
Yuan, W. et al. Global comparison of light use efficiency models for simulating terrestrial vegetation gross primary production based on the LaThuile database. Agr. Forest. Meteorol. 192-193, 108–120 (2014).ADS 

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

Google Scholar 
Joiner, J. et al. Global monitoring of terrestrial chlorophyll fluorescence from moderate-spectral-resolution near-infrared satellite measurements: methodology, simulations, and application to GOME-2. Atmos Meas Tech 6, 2803–2823 (2013).
Google Scholar 
Frankenberg, C. et al. Prospects for chlorophyll fluorescence remote sensing from the Orbiting Carbon Observatory-2. Remote Sens. Environ. 147, 1–12 (2014).ADS 

Google Scholar 
Joiner, J. et al. Filling-in of near-infrared solar lines by terrestrial fluorescence and other geophysical effects: simulations and space-based observations from SCIAMACHY and GOSAT. Atmos Meas Tech 5, 809–829 (2012).CAS 

Google Scholar 
Köhler, P. et al. Global Retrievals of Solar‐Induced Chlorophyll Fluorescence With TROPOMI: First Results and Intersensor Comparison to OCO‐2. Geophys. Res. Lett. 45, 10,456–410,463 (2018).
Google Scholar 
Joiner, J. et al. First observations of global and seasonal terrestrial chlorophyll fluorescence from space. Biogeosciences 8, 637–651 (2011).ADS 
CAS 

Google Scholar 
Guanter, L. et al. Retrieval and global assessment of terrestrial chlorophyll fluorescence from GOSAT space measurements. Remote Sens. Environ. 121, 236–251 (2012).ADS 

Google Scholar 
Du, S. et al. Retrieval of global terrestrial solar-induced chlorophyll fluorescence from TanSat satellite. Sci. Bull. 63, 1502–1512 (2018).
Google Scholar 
Baker, N. R. Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annu. Rev. Plant Biol. 59, 89–113 (2008).CAS 
PubMed 

Google Scholar 
Drusch, M. et al. The FLuorescence EXplorer Mission Concept—ESA’s Earth Explorer 8. Ieee. T. Geosci. Remote 55, 1273–1284 (2017).ADS 

Google Scholar 
Guanter, L. et al. The TROPOSIF global sun-induced fluorescence dataset from the Sentinel-5P TROPOMI mission. Earth Syst. Sci. Data, 13, 5423–5440 (2021).Roesch, A. Use of Moderate-Resolution Imaging Spectroradiometer bidirectional reflectance distribution function products to enhance simulated surface albedos. J. Geophys. Res. 109 (2004).Wan, Z. New refinements and validation of the collection-6 MODIS land-surface temperature/emissivity product. Remote Sens. Environ. 140, 36–45 (2014).ADS 

Google Scholar 
Sulla-Menashe, D., Gray, J. M., Abercrombie, S. P. & Friedl, M. A. Hierarchical mapping of annual global land cover 2001 to present: The MODIS Collection 6 Land Cover product. Remote Sens. Environ. 222, 183–194 (2019).ADS 

Google Scholar 
Su, W., Charlock, T. P., Rose, F. G. & Rutan, D. Photosynthetically active radiation from Clouds and the Earth’s Radiant Energy System (CERES) products. J. Geophys. Res. 112 (2007).Still, C. J., Berry, J. A., Collatz, G. J. & Defries, R. S. Global distribution of C3and C4vegetation: Carbon cycle implications. Global. Biogeochem. Cy 17, 6-1-6-14 (2003).Zhang, Y. et al. Spatio‐temporal convergence of maximum daily light‐use efficiency based on radiation absorption by canopy chlorophyll. Geophys. Res. Lett. 45, 3508–3519 (2018).ADS 

Google Scholar 
Zhang, Z. et al. The potential of satellite FPAR product for GPP estimation: An indirect evaluation using solar-induced chlorophyll fluorescence. Remote Sens. Environ. 240, 111686 (2020).ADS 

Google Scholar 
Baker, N. R. Chlorophyll Fluorescence: A Probe of Photosynthesis In Vivo. Annu. Rev. Plant. Biol. 59, 89–113 (2008).CAS 
PubMed 

Google Scholar 
Du, S., Liu, L., Liu, X. & Hu, J. Response of canopy solar-induced chlorophyll fluorescence to the absorbed photosynthetically active radiation absorbed by chlorophyll. Remote Sens. 9, 911 (2017).ADS 

Google Scholar 
Rossini, M. et al. Analysis of Red and Far-Red Sun-Induced Chlorophyll Fluorescence and Their Ratio in Different Canopies Based on Observed and Modeled Data. Remote Sens. 8, 412 (2016).ADS 

Google Scholar 
Verrelst, J. et al. Global sensitivity analysis of the SCOPE model: What drives simulated canopy-leaving sun-induced fluorescence? Remote Sens. Environ. 166, 8–21 (2015).ADS 

Google Scholar 
Zhang, Q. et al. Estimating light absorption by chlorophyll, leaf and canopy in a deciduous broadleaf forest using MODIS data and a radiative transfer model. Remote Sens. Environ. 99, 357–371 (2005).ADS 

Google Scholar 
Zhang, Y., Joiner, J., Alemohammad, S. H., Zhou, S. & Gentine, P. A global spatially contiguous solar-induced fluorescence (CSIF) dataset using neural networks. Biogeosciences 15, 5779–5800 (2018).ADS 
CAS 

Google Scholar 
Li, X. & Xiao, J. A Global, 0.05-Degree Product of Solar-Induced Chlorophyll Fluorescence Derived from OCO-2, MODIS, and Reanalysis Data. Remote Sens. 11, 517 (2019).ADS 

Google Scholar 
Yu, L., Wen, J., Chang, C. Y., Frankenberg, C. & Sun, Y. High‐Resolution Global Contiguous SIF of OCO‐2. Geophys. Res. Lett. 46, 1449–1458 (2019).ADS 

Google Scholar 
Ma, Y., Liu, L., Chen, R., Du, S. & Liu, X. Generation of a Global Spatially Continuous TanSat Solar-Induced Chlorophyll Fluorescence Product by Considering the Impact of the Solar Radiation Intensity. Remote Sens. 12, 2167 (2020).ADS 

Google Scholar 
Gentine, P. & Alemohammad, S. H. Reconstructed Solar‐Induced Fluorescence: A Machine Learning Vegetation Product Based on MODIS Surface Reflectance to Reproduce GOME‐2 Solar‐Induced Fluorescence. Geophys. Res. Lett. 45, 3136–3146 (2018).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wen, J. et al. A framework for harmonizing multiple satellite instruments to generate a long-term global high spatial-resolution solar-induced chlorophyll fluorescence (SIF). Remote Sens. Environ. 239, 111644 (2020).ADS 

Google Scholar 
Yang, X. et al. Solar‐induced chlorophyll fluorescence that correlates with canopy photosynthesis on diurnal and seasonal scales in a temperate deciduous forest. Geophys. Res. Lett. 42, 2977–2987 (2015).ADS 
CAS 

Google Scholar 
Hain, C. R., Crow, W. T., Mecikalski, J. R., Anderson, M. C. & Holmes, T. An intercomparison of available soil moisture estimates from thermal infrared and passive microwave remote sensing and land surface modeling. J. Geophys. Res. 116, D15107 (2011).ADS 

Google Scholar 
Anderson, M. C., Norman, J. M., Mecikalski, J. R., Otkin, J. A. & Kustas, W. P. A climatological study of evapotranspiration and moisture stress across the continental United States based on thermal remote sensing: 2. Surface moisture climatology. J. Geophys. Res. 112, D11112 (2007).ADS 

Google Scholar 
Scherrer, D., Bader, M. K.-F. & Körner, C. Drought-sensitivity ranking of deciduous tree species based on thermal imaging of forest canopies. Agr. Forest. Meteorol. 151, 1632–1640 (2011).ADS 

Google Scholar 
Duveiller, G. et al. A spatially downscaled sun-induced fluorescence global product for enhanced monitoring of vegetation productivity. Earth Syst. Sci. Data 12, 1101–1116 (2020).ADS 

Google Scholar 
Zhang, Y. et al. A global moderate resolution dataset of gross primary production of vegetation for 2000–2016. Sci. Data 4, 170165 (2017).PubMed 
PubMed Central 

Google Scholar 
Chen, T. & Guestrin, C. in Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 785-794 (Association for Computing Machinery).Hengl, T. et al. SoilGrids250m: Global gridded soil information based on machine learning. PLOS ONE 12, e0169748 (2017).PubMed 
PubMed Central 

Google Scholar 
Li, Y., Li, M., Li, C. & Liu, Z. Forest aboveground biomass estimation using Landsat 8 and Sentinel-1A data with machine learning algorithms. Sci. Rep. 10, 9952 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tan, W., Wei, C., Lu, Y. & Xue, D. Reconstruction of All-Weather Daytime and Nighttime MODIS Aqua-Terra Land Surface Temperature Products Using an XGBoost Approach. Remote Sens. 13, 4723 (2021).ADS 

Google Scholar 
Adnan, M., Alarood, A. A. S., Uddin, M. I. & Ur Rehman, I. Utilizing grid search cross-validation with adaptive boosting for augmenting performance of machine learning models. PeerJ Comput. Sci. 8, e803 (2022).PubMed 
PubMed Central 

Google Scholar 
Chen, X. A long-term reconstructed TROPOMI solar-induced fluorescence dataset using machine learning algorithms. figshare https://doi.org/10.6084/m9.figshare.19336346.v2 (2022).Guanter, L. et al. Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence. Proc. Natl. Acad. Sci. 111, E1327–E1333 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Pierrat, Z. et al. Diurnal and seasonal dynamics of solar‐induced chlorophyll fluorescence, vegetation indices, and gross primary productivity in the boreal forest. J. Geophys. Res. Biogeosci., e2021JG006588 (2022).Magney, T. S. et al. Mechanistic evidence for tracking the seasonality of photosynthesis with solar-induced fluorescence. Proc. Natl. Acad. Sci. 116, 11640–11645 (2019).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Grossmann, K. et al. PhotoSpec: A new instrument to measure spatially distributed red and far-red Solar-Induced Chlorophyll Fluorescence. Remote Sens. Environ. 216, 311–327 (2018).ADS 

Google Scholar 
Li, Z. et al. Solar-induced chlorophyll fluorescence and its link to canopy photosynthesis in maize from continuous ground measurements. Remote Sens. Environ. 236, 111420 (2020).ADS 

Google Scholar 
Magney, T. S. et al. Mechanistic evidence for tracking the seasonality of photosynthesis with solar-induced fluorescence. Proc. Natl. Acad. Sci. 201900278 (2019).Wei, X., Wang, X., Wei, W. & Wan, W. Use of Sun-Induced Chlorophyll Fluorescence Obtained by OCO-2 and GOME-2 for GPP Estimates of the Heihe River Basin, China. Remote Sens. 10, 2039 (2018).ADS 

Google Scholar 
Walther, S. et al. Satellite chlorophyll fluorescence measurements reveal large‐scale decoupling of photosynthesis and greenness dynamics in boreal evergreen forests. Global. Change. Biol. 22, 2979–2996 (2016).ADS 

Google Scholar 
Köhler, P., Guanter, L. & Joiner, J. A linear method for the retrieval of sun-induced chlorophyll fluorescence from GOME-2 and SCIAMACHY data. Atmos. Meas. Tech. 8, 2589–2608 (2015).
Google Scholar 
Parazoo, N. C. et al. Towards a Harmonized Long‐Term Spaceborne Record of Far‐Red Solar‐Induced Fluorescence. J. Geophys. Res. Biogeosci. 124, 2518–2539 (2019).
Google Scholar 
Pastorello, G. et al. The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data. Sci. Data 7 (2020).Reichstein, M. et al. On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Global. Change. Biol. 11, 1424–1439 (2005).ADS 

Google Scholar 
Lasslop, G. et al. Separation of net ecosystem exchange into assimilation and respiration using a light response curve approach: critical issues and global evaluation. Global. Change. Biol. 16, 187–208 (2010).ADS 

Google Scholar 
Chen, C. et al. China and India lead in greening of the world through land-use management. Nat. Sustain. 2, 122–129 (2019).PubMed 
PubMed Central 

Google Scholar 
Tong, X. et al. Increased vegetation growth and carbon stock in China karst via ecological engineering. Nat. Sustain. 1, 44–50 (2018).
Google Scholar 
Miettinen, J., Shi, C. & Liew, S. C. Deforestation rates in insular Southeast Asia between 2000 and 2010. Global. Change. Biol. 17, 2261–2270 (2011).ADS 

Google Scholar 
De, S. V. et al. Land use patterns and related carbon losses following deforestation in South America. Environ. Res. Lett. 10, 124004 (2015).ADS 

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

Google Scholar 
Still, C. J., Berry, J. A., Collatz, G. J. & Defries, R. S. ISLSCP II C4 Vegetation Percentage, ORNL Distributed Active Archive Center, https://doi.org/10.3334/ORNLDAAC/932 (2009).Pierrat, Z. & Stutz, J. Tower-based solar-induced fluorescence and vegetation index data for Southern Old Black Spruce forest, Zenodo, https://doi.org/10.5281/ZENODO.5884643 (2022).Magney, T. et al. Canopy and needle scale fluorescence data from Niwot Ridge, Colorado 2017-2018, CaltechDATA, https://doi.org/10.22002/D1.1231 (2019).Wan, Z., Hook, S. & Hulley, G. MOD11C1 MODIS/Terra Land Surface Temperature/Emissivity Daily L3 Global 0.05Deg CMG V006, NASA EOSDIS Land Processes DAAC, https://doi.org/10.5067/MODIS/MOD11C1.006 (2015).Friedl, M. & Sulla-Menashe, D. MCD12C1 MODIS/Terra+Aqua Land Cover Type Yearly L3 Global 0.05Deg CMG V006, NASA EOSDIS Land Processes DAAC, https://doi.org/10.5067/MODIS/MCD12C1.006 (2015).Schaaf, C. & Wang, Z. MCD43C4 MODIS/Terra+Aqua BRDF/Albedo Nadir BRDF-Adjusted Ref Daily L3 Global 0.05Deg CMG V006, NASA EOSDIS Land Processes DAAC, https://doi.org/10.5067/MODIS/MCD43C4.006 (2015).Doelling, D. CERES Level 3 SYN1DEG-DAYTerra+Aqua HDF4 file – Edition 4A, NASA Langley Atmospheric Science Data Center DAAC, https://doi.org/10.5067/TERRA+AQUA/CERES/SYN1DEGDAY_L3.004A (2017). More

Descamps, S. et al. Diverging phenological responses of Arctic seabirds to an earlier spring. Glob. Change Biol. 25, 4081–4091 (2019).ADS 
Article 

Google Scholar 
Ramp, C., Delarue, J., Palsbøll, P. J., Sears, R. & Hammond, P. S. Adapting to a warmer ocean—seasonal shift of baleen whale movements over three decades. PLoS ONE 10, e0121374 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Insley, S. J., Halliday, W. D., Mouy, X. & Diogou, N. Bowhead whales overwinter in the Amundsen Gulf and Eastern Beaufort Sea. R. Soc. Open Sci. 8, 1 (2021).Article 

Google Scholar 
Heide-Jørgensen, M. P., Laidre, K. L., Quakenbush, L. T. & Citta, J. J. The Northwest Passage opens for bowhead whales. Biol. Lett. 8, 270–273 (2012).PubMed 
Article 

Google Scholar 
Durant, J., Hjermann, D., Ottersen, G. & Stenseth, N. Climate and the match or mismatch between predator requirements and resource availability. Clim. Res. 33, 271–283 (2007).Article 

Google Scholar 
Staudinger, M. D. et al. It’s about time: A synthesis of changing phenology in the Gulf of Maine ecosystem. Fish. Oceanogr. 28, 532–566 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Miller-Rushing, A. J., Høye, T. T., Inouye, D. W. & Post, E. The effects of phenological mismatches on demography. Philos. Trans. R. Soc. B Biol. Sci. 365, 3177–3186 (2010).Article 

Google Scholar 
Edwards, M. & Richardson, A. J. Impact of climate change on marine pelagic phenology and trophic mismatch. Nature 430, 881–884 (2004).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Record, N. et al. Rapid climate-driven circulation changes threaten conservation of endangered North Atlantic right whales. Oceanography 32, 1 (2019).Article 

Google Scholar 
MacLeod, C. Global climate change, range changes and potential implications for the conservation of marine cetaceans: a review and synthesis. Endanger. Species Res. 7, 125–136 (2009).Article 

Google Scholar 
Learmonth, J. A. et al. Potential effects of climate change on marine mammals. Oceanogr. Mar. Biol. Annu. Rev. 44, 431–464 (2006).
Google Scholar 
Pinsky, M. L., Worm, B., Fogarty, M. J., Sarmiento, J. L. & Levin, S. A. Marine taxa track local climate velocities. Science 341, 1239–1242 (2013).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Pershing, A. J. et al. Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery. Science 350, 809–812 (2015).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Gulf of Maine Research Institute. Gulf of Maine Warming Update: 2021 the Hottest Year on Record. (2022).Saba, V. S. et al. Enhanced warming of the Northwest Atlantic Ocean under climate change. J. Geophys. Res. Oceans 121, 118–132 (2016).ADS 
Article 

Google Scholar 
Friedland, K. D. et al. Trends and change points in surface and bottom thermal environments of the US Northeast Continental Shelf Ecosystem. Fish. Oceanogr. 29, 396–414 (2020).Article 

Google Scholar 
Nye, J., Link, J., Hare, J. & Overholtz, W. Changing spatial distribution of fish stocks in relation to climate and population size on the Northeast United States continental shelf. Mar. Ecol. Prog. Ser. 393, 111–129 (2009).ADS 
Article 

Google Scholar 
Kress, S. W., Shannon, P. & O’Neal, C. Recent changes in the diet and survival of Atlantic puffin chicks in the face of climate change and commercial fishing in midcoast Maine, USA. FACETS 1, 27–43 (2017).Article 

Google Scholar 
Davis, G. E. et al. Exploring movement patterns and changing distributions of baleen whales in the western North Atlantic using a decade of passive acoustic data. Glob. Change Biol. 26, 4812–4840 (2020).ADS 
Article 

Google Scholar 
Pace, R. M., Corkeron, P. J. & Kraus, S. D. State-space mark-recapture estimates reveal a recent decline in abundance of North Atlantic right whales. Ecol. Evol. 7, 8730–8741 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Meyer-Gutbrod, E. L. & Greene, C. H. Uncertain recovery of the North Atlantic right whale in a changing ocean. Glob. Change Biol. 24, 455–464 (2018).ADS 
Article 

Google Scholar 
Sorochan, K. A. et al. North Atlantic right whale (Eubalaena glacialis) and its food: (II) interannual variations in biomass of Calanus spp. on western North Atlantic shelves. J. Plankton Res. 41, 687–708 (2019).Article 

Google Scholar 
Friedland, K. D. et al. Spring bloom dynamics and zooplankton biomass response on the US Northeast Continental Shelf. Cont. Shelf Res. 102, 47–61 (2015).ADS 
Article 

Google Scholar 
Meyer-Gutbrod, E., Greene, C., Davies, K. & Johns, D. Ocean regime shift is driving collapse of the North Atlantic right whale population. Oceanography 34, 22–31 (2021).Article 

Google Scholar 
Knowlton, A., Hamilton, P., Marx, M., Pettis, H. & Kraus, S. Monitoring North Atlantic right whale Eubalaena glacialis entanglement rates: A 30 yr retrospective. Mar. Ecol. Prog. Ser. 466, 293–302 (2012).ADS 
Article 

Google Scholar 
Davies, K. T. A. & Brillant, S. W. Mass human-caused mortality spurs federal action to protect endangered North Atlantic right whales in Canada. Mar. Policy 104, 157–162 (2019).Article 

Google Scholar 
Kraus, S. D. & Rolland, R. M. Right whales in the urban ocean. in The urban whale: North Atlantic right whales at the crossroads 1–38 (Harvard University Press, 2010). https://doi.org/10.2307/j.ctv1pnc1q9.Winn, H. E., Price, C. A. & Sorensen, P. W. The distributional biology of the right whale (Eubalaena glacialis) in the western North Atlantic. Rep. Int. Whal. Comm. Spec. 10, 129–138 (1986).
Google Scholar 
Mayo, C. A. & Marx, M. K. Surface foraging behaviour of the North Atlantic right whale, Eubalaena glacialis, and associated zooplankton characteristics. Can. J. Zool. 68, 2214–2220 (1990).Article 

Google Scholar 
Mayo, C. A. et al. Distribution, demography, and behavior of North Atlantic right whales (Eubalaena glacialis) in Cape Cod Bay, Massachusetts, 1998–2013. Mar. Mammal Sci. 34, 979–996 (2018).Article 

Google Scholar 
Pendleton, D. E. et al. Regional-scale mean copepod concentration indicates relative abundance of North Atlantic right whales. Mar. Ecol. Prog. Ser. 378, 211–225 (2009).ADS 
Article 

Google Scholar 
Kenney, R. D., Winn, H. E. & Macaulay, M. C. Cetaceans in the Great South Channel, 1979–1989: right whale (Eubalaena glacialis). Cont. Shelf Res. 15, 385–414 (1995).ADS 
Article 

Google Scholar 
Brown, M. W. et al. Recovery strategy for the North Atlantic right whale (Eubalaena glacialis) in Atlantic Canadian waters. in Species at risk act recovery strategy series (Fisheries and Oceans Canada, 2009).Weinrich, M. T., Kenney, R. D. & Hamilton, P. K. Right whales (Eubalaena glacialis) on Jeffreys Ledge: a habitat of unrecognized importance?. Mar. Mammal Sci. 16, 326–337 (2000).Article 

Google Scholar 
Cole, T. et al. Evidence of a North Atlantic right whale Eubalaena glacialis mating ground. Endanger. Species Res. 21, 55–64 (2013).Article 

Google Scholar 
Ganley, L., Brault, S. & Mayo, C. What we see is not what there is: estimating North Atlantic right whale Eubalaena glacialis local abundance. Endanger. Species Res. 38, 101–113 (2019).Article 

Google Scholar 
Simard, Y., Roy, N., Giard, S. & Aulanier, F. North Atlantic right whale shift to the Gulf of St. Lawrence in 2015, revealed by long-term passive acoustics. Endanger. Species Res. 40, 271–284 (2019).Article 

Google Scholar 
Leiter, S. et al. North Atlantic right whale Eubalaena glacialis occurrence in offshore wind energy areas near Massachusetts and Rhode Island, USA. Endanger. Species Res. 34, 45–59 (2017).Article 

Google Scholar 
Stone, K. M. et al. Distribution and abundance of cetaceans in a wind energy development area offshore of Massachusetts and Rhode Island. J. Coast. Conserv. 21, 527–543 (2017).Article 

Google Scholar 
Vanderlaan, A., Taggart, C., Serdynska, A., Kenney, R. & Brown, M. Reducing the risk of lethal encounters: Vessels and right whales in the Bay of Fundy and on the Scotian Shelf. Endanger. Species Res. 4, 283–297 (2008).Article 

Google Scholar 
National Marine Fisheries Service. Endangered and threatened species; critical habitat for endangered North Atlantic right whale. Fed. Regist. 80, 9314–9345 (2015).
Google Scholar 
National Marine Fisheries Service. Taking of marine mammals incidental to commercial fishing operations; Atlantic large whale take reduction plan regulations; Atlantic coastal fisheries cooperative management act provisions; American lobster fishery. Fed. Regist. 85, 86878–86900 (2020).
Google Scholar 
Reeves, R. R., Breiwick, J. M. & Mitchell, E. D. History of whaling and estimated kill of right whales, Balaena glacialis, in the Northeastern United States, 1620–1924. Mar. Fish. Rev. 36, 1 (1999).
Google Scholar 
Allen, G. M. The whalebone whales of New England. Mem. Boston Soc. Nat. Hist. 8, 107–322 (1915).ADS 

Google Scholar 
CETAP (Cetacean and Turtle Assessment Program). A characterization of marine mammals and turtles in the mid- and North- Atlantic areas of the U.S. Outer Continental Shelf, final report. (1982).Kenney, R. D. & Vigness-Raposa, K. J. Marine mammals and sea turtles of Narragansett Bay, Block Island Sound, Rhode Island Sound, and nearby waters: An analysis of existing data for the Rhode Island Ocean Special Area Management Plan. in Rhode Island Ocean Special Area Management Plan; Volume 2 Appendix A: Technical Reports for the Rhode Island Ocean Special Area Management Plan. 701–1037 (Rhode Island Coastal Resources Management Council, Wakefield, RI, 2010).Pendleton, D. et al. Weekly predictions of North Atlantic right whale Eubalaena glacialis habitat reveal influence of prey abundance and seasonality of habitat preferences. Endanger. Species Res. 18, 147–161 (2012).MathSciNet 
Article 

Google Scholar 
Kraus, S. D., Kenney, R. D. & Thomas, L. A framework for studying the effects of offshore wind development on marine mammals and turtles. (2019). Report prepared for the Massachusetts Clean Energy Center, Boston, MA, and the Bureau of Ocean Energy Management, Office of Renewable Energy Programs, Sterling, VA. Anderson Cabot Center for Ocean Life, New England Aquarium, Boston, MA. 48 pp.Quintana-Rizzo, E. et al. Residency, demographics, and movement patterns of North Atlantic right whales Eubalaena glacialis in an offshore wind energy development area in southern New England, USA. Endanger. Species Res. 45, 251–268 (2021).Article 

Google Scholar 
Taylor, J. K. D., Kenney, R. D., LeRoi, D. J. & Kraus, S. D. Automated vertical photography for detecting pelagic species in multitaxon aerial surveys. Mar. Technol. Soc. J. 48, 36–48 (2014).Article 

Google Scholar 
Hamilton, P. K., Knowlton, A. R. & Marx, M. K. Right whales tell their own stories: the photo-identification catalog. in The urban whale: North Atlantic right whales at the crossroads 75–104 (Harvard University Press, 2010).Buckland, S. T., Anderson, D. R., Burnham, K. P. & Laake, J. L. Distance sampling: Estimating abundance of biological populations Vol. 50 (Chapman and Hall, 1993).MATH 
Book 

Google Scholar 
R: The R Project for Statistical Computing. https://www.r-project.org/.Miller, D. L., Rexstad, E., Thomas, L., Marshall, L. & Laake, J. L. Distance Sampling in R. J. Stat. Softw. 89, 1–28 (2019).Article 

Google Scholar 
Eberhardt, L. L., Chapman, D. G. & Gilbert, J. R. A review of marine mammal census methods. Wildl. Monogr. 1, 3–46 (1979).
Google Scholar 
Durant, S. M. et al. Long-term trends in carnivore abundance using distance sampling in Serengeti National Park, Tanzania: Serengeti carnivore trends. J. Appl. Ecol. 48, 1490–1500 (2011).Article 

Google Scholar 
Reeves, R. R. & Mitchell, E. The Long Island, New York, right whale fishery: 1650–1924. Rep. Int. Whal. Comm. 10, 201–220 (1986).
Google Scholar 
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, 13460 (2017).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Jackson, J. et al. Have whales returned to a historical hotspot of industrial whaling? The pattern of southern right whale Eubalaena australis recovery at South Georgia. Endanger. Species Res. 43, 323–339 (2020).Article 

Google Scholar 
Carroll, E. L. et al. Reestablishment of former wintering grounds by New Zealand southern right whales. Mar. Mammal Sci. 30, 206–220 (2014).Article 

Google Scholar 
Charlton, C. et al. Southern right whales (Eubalaena australis) return to a former wintering calving ground: Fowlers Bay, South Australia. Mar. Mammal Sci. 35, 1438–1462 (2019).Article 

Google Scholar 
Garrigue, C. et al. Searching for humpback whales in a historical whaling hotspot of the Coral Sea, South Pacific. Endanger. Species Res. 42, 67–82 (2020).Article 

Google Scholar 
Clapham, P. J., Aguilar, A. & Hatch, L. T. Determining spatial and temporal scales for management: lessons from whaling. Mar. Mammal Sci. 24, 183–201 (2008).Article 

Google Scholar 
Watkins, W. A. & Schevill, W. E. Right whale feeding and baleen rattle. J. Mammal. 57, 58–66 (1976).Article 

Google Scholar 
Beardsley, R. C. et al. Spatial variability in zooplankton abundance near feeding right whales in the Great South Channel.. Deep Sea Res Part II Top. Stud. Oceanogr. 43, 1601–1625 (1996).ADS 
Article 

Google Scholar 
Wishner, K. F. et al. Copepod patches and right whales in the Great South Channel off New England. Bull. Mar. Sci. 43, 825–844 (1988).ADS 

Google Scholar 
Baumgartner, M., Cole, T., Clapham, P. & Mate, B. North Atlantic right whale habitat in the lower Bay of Fundy and on the SW Scotian Shelf during 1999–2001. Mar. Ecol. Prog. Ser. 264, 137–154 (2003).ADS 
Article 

Google Scholar 
Moore, M. J. & van der Hoop, J. M. The painful side of trap and fixed net fisheries: Chronic entanglement of large whales. J. Mar. Biol. 2012, 1–4 (2012).Article 

Google Scholar  More

United Nations Framework Convention on Climate Change (UNFCCC). The Paris Agreement. https://unfccc.int/process-and-meetings/the-paris-agreement/the-paris-agreement (2015). Accessed on 16 Dec 2021.Tubiello, F. N. et al. The contribution of agriculture, forestry and other land use activities to global warming, 1990–2012. Glob. Change Biol. 21(7), 2655–2660 (2015).ADS 
Article 

Google Scholar 
Frank, S. et al. Agricultural non-CO2 emission reduction potential in the context of the 15 °C target. Nat. Clim. Change 9(1), 66–72 (2019).ADS 
CAS 
Article 

Google Scholar 
Crippa, M. et al. Food systems are responsible for a third of global anthropogenic GHG emissions. Nat. Food 2, 198–209 (2021).CAS 
Article 

Google Scholar 
Hong, C. et al. Global and regional drivers of land-use emissions in 1961–2017. Nature 589, 554–561 (2021).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Tubiello, F. N. et al. Greenhouse gas emissions from food systems: Building the evidence base. Environ. Res. Lett. 16, 065007 (2021).ADS 
CAS 
Article 

Google Scholar 
Smith, P. et al. Agriculture, forestry and other land use (AFOLU). In Climate Change 2014: Mitigation of Climate Change. Contribution of Working Group III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (eds Edenhofer, O. et al.) (Cambridge University Press, 2014).
Google Scholar 
Schlesinger, W. H. & Andrews, J. A. Soil respiration and the global carbon cycle. Biogeochemistry 78, 7–20 (2000).Article 

Google Scholar 
Smith, K. A. & Conen, F. Impacts of land management on fluxes of trace greenhouse gases. Soil Use Manage. 20, 245–253 (2004).
Google Scholar 
Foley, J. A. et al. Solutions for a cultivated planet. Nature 478, 337–342 (2011).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Jones, S. K. et al. Nitrous oxide emissions from managed grassland: A comparison of eddy covariance and static chamber measurements. Atmos. Meas. Tech. 4, 2179–2194 (2011).CAS 
Article 

Google Scholar 
Chapuis‐Lardy, L., Wrage, N., Metay, A., Chotte, J. L. & Bernoux, M. Soils, a sink for N2O? A review. Glob. Change Biol. 13, 1–17 (2007).ADS 
Article 

Google Scholar 
Sanz-Cobena, A. et al. Do cover crops enhance N2O, CO2 or CH4 emissions from soil in Mediterranean arable systems? Sci. Total Environ. 466, 164–174 (2014).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Kaye, J. P. & Quemada, M. Using cover crops to mitigate and adapt to climate change. A review. Agron. Sustain. Dev. 37(1), 1–17 (2017).Article 

Google Scholar 
Poeplau, C. & Don, A. Carbon sequestration in agricultural soils via cultivation of cover crops—A meta-analysis. Agric. Ecosyst. Environ. 200, 33–41 (2015).CAS 
Article 

Google Scholar 
Guardia, G. et al. Effective climate change mitigation through cover cropping and integrated fertilization: A global warming potential assessment from a 10-year field experiment. J Clean. Prod. 241, 118307 (2019).CAS 
Article 

Google Scholar 
Osipitan, O. A., Dille, J. A., Assefa, Y. & Knezevic, S. Z. Cover crop for early season weed suppression in crops: Systematic review and meta-analysis. Agron. J. 110(6), 2211–2221 (2018).Article 

Google Scholar 
Thapa, R., Mirsky, S. B. & Tully, K. L. Cover crops reduce nitrate leaching in agroecosystems: A global meta-analysis. J. Environ. Qual. 47(6), 1400–1411 (2018).CAS 
PubMed 
Article 

Google Scholar 
Snapp, S. S. et al. Evaluating cover crops for benefits, costs and performance within cropping system niches. Agron. J. 97, 322–332 (2005).Article 

Google Scholar 
Reicks, G. W. et al. Winter cereal rye cover crop decreased nitrous oxide emissions during early spring. Agron. J. 113, 3900–3909 (2021).CAS 
Article 

Google Scholar 
Behnke, G. D. & Villamil, M. B. Cover crop rotations affect greenhouse gas emissions and crop production in Illinois, USA. Field Crops Res. 241, 107580 (2019).Article 

Google Scholar 
Blanco-Canqui, H., Holman, J. D., Schlegel, A. J., Tatarko, J. & Shaver, T. M. Replacing fallow with cover crops in a semi-arid soil: Effects on soil properties. Soil Sci. Soc. Am. J. 77, 1026–1034 (2013).ADS 
CAS 
Article 

Google Scholar 
Basche, A. D., Miguez, F. E., Kaspar, T. C. & Castellano, M. J. Do cover crops increase or decrease nitrous oxide emissions? A meta-analysis. J. Soil Water Conserv. 69, 471–482 (2014).Article 

Google Scholar 
Smith, P. et al. Greenhouse gas mitigation in agriculture. Philos. Trans. R. Soc. B 363, 789–813 (2008).CAS 
Article 

Google Scholar 
Finney, D. M., White, C. M. & Kaye, J. P. Biomass production and carbon nitrogen ratio influence ecosystem services from cover crop mixtures. Agron. J. 108, 39–52 (2016).CAS 
Article 

Google Scholar 
Drost, S. M., Rutgers, M., Wouterse, M., De Boer, W. & Bodelier, P. L. Decomposition of mixtures of cover crop residues increases microbial functional diversity. Geoderma 361, 114060 (2020).ADS 
CAS 
Article 

Google Scholar 
Thapa, V. R., Ghimire, R., Acosta-Martínez, V., Marsalis, M. A. & Schipanski, M. E. Cover crop biomass and species composition affect soil microbial community structure and enzyme activities in semi-arid cropping systems. Appl. Soil Ecol. 157, 103735 (2021).Article 

Google Scholar 
Muhammad, I. et al. Regulation of soil CO2 and N2O emissions by cover crops: A meta-analysis. Soil Till. Res. 192, 103–112 (2019).Article 

Google Scholar 
Sarkodie-Addo, J., Lee, H. C. & Baggs, E. M. Nitrous oxide emissions after application of inorganic fertilizer and incorporation of green manure residues. Soil Use Manage. 19, 331–339 (2006).Article 

Google Scholar 
Guardia, G. et al. Effect of cover crops on greenhouse gas emissions in an irrigated field under integrated soil fertility management. Biogeosciences 13, 5245–5257 (2016).ADS 
CAS 
Article 

Google Scholar 
Mitchell, D. C., Castellano, M. J., Sawyer, J. E. & Pantoja, J. Cover crop effects on nitrous oxide emissions: Role of mineralizable carbon. Soil Sci. Soc. Am. J. 77, 1765 (2013).ADS 
CAS 
Article 

Google Scholar 
Bodner, G., Mentler, A., Klik, A., Kaul, H. P. & Zechmeister-Boltenstern, S. Do cover crops enhance soil greenhouse gas losses during high emission moments under temperate Central Europe conditions? Die Bodenkult J. Land Manage. Food Environ. 68, 171–187 (2018).Article 
CAS 

Google Scholar 
Álvaro-Fuentes, J., Easter, M. & Paustian, K. Climate change effects on organic carbon storage in agricultural soils of northeastern Spain. Agric. Ecosyst. Environ. 155, 87–94 (2012).Article 
CAS 

Google Scholar 
Bronson, K. F. et al. Carbon and nitrogen pools of southern High Plains cropland and grassland soils. Soil Sci. Soc. Am. J. 68, 1695–1704 (2004).ADS 
CAS 
Article 

Google Scholar 
Zhou, X., Talley, M. & Luo, Y. Biomass, litter and soil respiration along a precipitation gradient in Southern Great Plains, USA. Ecosystems 12, 1369–1380 (2009).CAS 
Article 

Google Scholar 
Poulter, B. et al. Contribution of semi-arid ecosystems to interannual variability of the global carbon cycle. Nature 509, 600–603 (2014).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Ahlström, A. et al. The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink. Science 348, 895–899 (2015).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Huang, J., Yu, H., Guan, X., Wang, G. & Guo, R. Accelerated dryland expansion under climate change. Nat. Clim. Change 6, 166–171 (2016).ADS 
Article 

Google Scholar 
Antosh, E., Idowu, J., Schutte, B. & Lehnhoff, E. Winter cover crops effects on soil properties and sweet corn yield in semi-arid irrigated systems. Agron. J. 112, 92–106 (2020).Article 

Google Scholar 
Paye, W. S. et al. Cover crop water use and corn silage production in semi-arid irrigated conditions. Agric. Water Manage. 260, 107275 (2022).Article 

Google Scholar 
Paye, W. S., Acharya, P. & Ghimire, R. Water productivity of forage sorghum in response to winter cover crops in semi-arid irrigated conditions. Field Crops Res. 283, 108552 (2022).Article 

Google Scholar 
Garba, I. I., Bell, L. W. & Williams, A. Cover crop legacy impacts on soil water and nitrogen dynamics, and on subsequent crop yields in drylands: A meta-analysis. Agron. Sustain. Dev. 42(3), 1–21 (2022).Article 
CAS 

Google Scholar 
Gabriel, J. L., Muñoz-Carpena, R. & Quemada, M. The role of cover crops in irrigated systems: Water balance, nitrate leaching and soil mineral nitrogen accumulation. Agric. Ecosyst. Environ. 155, 50–61 (2012).CAS 
Article 

Google Scholar 
Trost, B. et al. Irrigation, soil organic carbon and N2O emissions. A review. Agron. Sustain Dev. 33, 733–749 (2013).CAS 
Article 

Google Scholar 
Nilahyane, A., Ghimire, R., Thapa, V. R. & Sainju, U. M. Cover crop effects on soil carbon dioxide emissions in a semiarid cropping system. Agrosyst. Geosci. Environ. 3, e20012 (2020).
Google Scholar 
Thapa, V. R., Ghimire, R., Duval, B. D. & Marsalis, M. A. Conservation systems for positive net ecosystem carbon balance in semi-arid drylands. Agrosyst. Geosci. Environ. 2, 1–8 (2019).Article 

Google Scholar 
Abdalla, M. et al. A critical review of the impacts of cover crops on nitrogen leaching, net greenhouse gas balance and crop productivity. Glob. Change Biol. 25(8), 2530–2543 (2019).ADS 
Article 

Google Scholar 
Larionova, A. A., Sapronov, D. V., de Gerenyu, V. L., Kuznetsova, L. G. & Kudeyarov, V. N. Contribution of plant root respiration to the CO2 emission from soil. Eurasian Soil Sci. 39, 1127–1135 (2006).ADS 
Article 

Google Scholar 
Hanson, P. J., Edwards, N. T., Garten, C. T. & Andrews, J. A. Separating root and soil microbial contributions to soil respiration: A review of methods and observations. Biogeochemistry 48, 115–146 (2000).CAS 
Article 

Google Scholar 
Rochette, P., Flanagan, L. B. & Gregorich, E. G. Separating soil respiration into plant and soil components using analyses of the natural abundance of carbon-13. Soil Sci. Soc. Am. J. 63, 1207–1213 (1999).ADS 
CAS 
Article 

Google Scholar 
Sainju, U. M., Jabro, J. D. & Stevens, W. B. Soil carbon dioxide emission and carbon content as affected by irrigation, tillage, cropping system, and nitrogen fertilization. J. Environ. Qual. 37, 98–106 (2008).CAS 
PubMed 
Article 

Google Scholar 
Mosier, A. R., Halvorson, A. D., Reule, C. A. & Liu, X. J. Net global warming potential and greenhouse gas intensity in irrigated cropping systems in northeastern Colorado. J. Environ. Qual. 35, 1584–1598 (2006).CAS 
PubMed 
Article 

Google Scholar 
Fan, J. et al. Stover retention rather than no-till decreases the global warming potential of rainfed continuous maize cropland. Field Crops Res. 219, 14–23 (2018).Article 

Google Scholar 
USDA Soil Survey Staff. Web Soil Survey. http://websoilsurvey.sc.egov.usda.gov/App/WebSoilSurvey.aspx (2022). Accessed on 23 Jan 2022.Zibilske, L. M. Carbon mineralization. In Methods of Soil Analysis: Part 2. Microbiological and Biochemical Properties (eds Weaver, R. W. et al.). https://doi.org/10.2136/sssabookser5.2.c38 (Soil Science Society of America Journal, 1994).Chapter 

Google Scholar 
Sainju, U. M. Net global warming potential, and greenhouse gas intensity. Soil Sci. Soc. Am. J. 84, 1393–1404 (2020).ADS 
CAS 
Article 

Google Scholar 
Lal, R. Carbon emission from farm operations. Environ. Int. 30, 981–990 (2004).CAS 
PubMed 
Article 

Google Scholar 
Haile-Mariam, S., Collins, H. P. & Higgins, S. S. Greenhouse gas fluxes from an irrigated sweet corn (Zea mays L.)–potato (Solanum tuberosum L.) rotation. J. Environ. Qual. 37(3), 759–771 (2008).CAS 
PubMed 
Article 

Google Scholar  More