Ecology

Pörtner, H. O. et al. Climate Change 2022: Impacts, Adaptation and Vulnerability (IPCC, 2022).Patz, J. A., Campbell-Lendrum, D., Holloway, T. & Foley, J. A. Impact of regional climate change on human health. Nature 438, 310–317 (2005).CAS 
Article 

Google Scholar 
Smith, K. et al. in Climate Change 2014: Impacts, Adaptation, and Vulnerability (eds Field, C. B. et al.) 709–754 (Cambridge Univ. Press, 2014).Mora, C. et al. Broad threat to humanity from cumulative climate hazards intensified by greenhouse gas emissions. Nat. Clim. Change 8, 1062–1071 (2018).CAS 
Article 

Google Scholar 
Altizer, S., Ostfeld, R. S., Johnson, P. T., Kutz, S. & Harvell, C. D. Climate change and infectious diseases: from evidence to a predictive framework. Science 341, 514–519 (2013).CAS 
Article 

Google Scholar 
Epstein, P. The ecology of climate change and infectious diseases: comment. Ecology 91, 925–928 (2010).Article 

Google Scholar 
IPCC Climate Change 2014: Synthesis Report (eds Core Writing Team, Pachauri, R. K. & Meyer, L. A.) (IPCC, 2014).Jaenisch, T. & Patz, J. Assessment of associations between climate and infectious diseases: a comparison of the reports of the Intergovernmental Panel on Climate Change (IPCC), the National Research Council (NRC), and United States Global Change Research Program (USGCRP). Glob. Change Hum. Health 3, 67–72 (2002).Article 

Google Scholar 
Hellberg, R. S. & Chu, E. Effects of climate change on the persistence and dispersal of foodborne bacterial pathogens in the outdoor environment: a review. Crit. Rev. Microbiol. 42, 548–572 (2016).Article 

Google Scholar 
Tabachnick, W. J. Climate change and the arboviruses: lessons from the evolution of the dengue and yellow fever viruses. Ann. Rev. Virol 29, 125–145 (2016).Article 
CAS 

Google Scholar 
Khasnis, A. A. & Nettleman, M. D. Global warming and infectious disease. Arch. Med. Res. 36, 689–696 (2005).Article 

Google Scholar 
McMichael, A. J. Extreme weather events and infectious disease outbreaks. Virulence 6, 543–547 (2015).Article 

Google Scholar 
Ahern, M., Kovats, R. S., Wilkinson, P., Few, R. & Matthies, F. Global health impacts of floods: epidemiologic evidence. Epidemiol. Rev. 27, 36–46 (2005).Article 

Google Scholar 
Hunter, P. R. Climate change and waterborne and vector‐borne disease. J. Appl. Microbiol. 94, 37–46 (2003).Article 

Google Scholar 
Gage, K. L., Burkot, T. R., Eisen, R. J. & Hayes, E. B. Climate and vector borne diseases. Am. J. Prev. Med. 35, 436–450 (2008).Article 

Google Scholar 
Semenza, J. C. et al. Climate change impact assessment of food- and waterborne diseases. Crit. Rev. Environ. Sci. Technol. 42, 857–890 (2012).Article 

Google Scholar 
Nichols, G., Lake, I. & Heaviside, C. Climate change and water-related infectious diseases. Atmosphere 9, 385 (2018).Article 

Google Scholar 
Cunliffe, J. A proliferation of pathogens through the 20th century. Scand. J. Immunol. 68, 120–128 (2008).CAS 
Article 

Google Scholar 
Cecchi, L. et al. Projections of the effects of climate change on allergic asthma: the contribution of aerobiology. Allergy 65, 1073–1081 (2010).CAS 

Google Scholar 
Demain, J. G. Climate change and the impact on respiratory and allergic disease: 2018. Curr. Allergy Asthma Rep. 18, 22 (2018).Article 

Google Scholar 
Andersen, L. K. & Davis, M. D. The effects of the El Niño Southern Oscillation on skin and skin-related diseases: a message from the International Society of Dermatology Climate Change Task Force. Int. J. Dermatol. 54, 1343–1351 (2015).Article 

Google Scholar 
Guenther, A. B., Zimmerman, P. R., Harley, P. C., Monson, R. K. & Fall, R. Isoprene and monoterpene emission rate variability: model evaluations and sensitivity analyses. J. Geophys. Res. Atmos 98, 12609–12617 (1993).Article 

Google Scholar 
Metcalf, C. J. E. & Lessler, J. Opportunities and challenges in modeling emerging infectious diseases. Science 357, 149–152 (2017).CAS 
Article 

Google Scholar 
Chen, I.-C., Hill, J. K., Ohlemüller, R., Roy, D. B. & Thomas, C. D. Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).CAS 
Article 

Google Scholar 
Nava, A., Shimabukuro, J. S., Chmura, A. A. & Luz, S. L. B. The impact of global environmental changes on infectious disease emergence with a focus on risks for Brazil. ILAR J. 58, 393–400 (2017).CAS 
Article 

Google Scholar 
Gray, J. S., Dautel, H., Estrada-Peña, A., Kahl, O. & Lindgren, E. Effects of climate change on ticks and tick-borne diseases in Europe. Interdiscip. Perspect. Infect. Dis. 2009, 593232 (2009).CAS 
Article 

Google Scholar 
Ngongeh, L. A., Idika, I. K. & Ibrahim Shehu, A. R. warming and its impacts on parasitology/entomology. Open Parasitol. J 5, 1–11 (2014).Article 

Google Scholar 
LaDeau, S. L., Calder, C. A., Doran, P. J. & Marra, P. P. West Nile virus impacts in American crow populations are associated with human land use and climate. Ecol. Res. 26, 909–916 (2011).Article 

Google Scholar 
Gale, P., Drew, T., Phipps, L. P., David, G. & Wooldridge, M. The effect of climate change on the occurrence and prevalence of livestock diseases in Great Britain: a review. J. Appl. Microbiol. 106, 1409–1423 (2009).CAS 
Article 

Google Scholar 
Lancien, J., Muguwa, J., Lannes, C. & Bouvier, J. B. Tsetse and human trypanosomiasis challenge in south eastern Uganda. Int. J. Trop. Insect Sci. 11, 411–416 (1990).Article 

Google Scholar 
Karesh, W. B. et al. Ecology of zoonoses: natural and unnatural histories. Lancet 380, 1936–1945 (2012).Article 

Google Scholar 
Vezzulli, L., Colwell, R. R. & Pruzzo, C. Ocean warming and spread of pathogenic vibrios in the aquatic environment. Microb. Ecol. 65, 817–825 (2013).Article 

Google Scholar 
Arriaza, B. T., Reinhard, K. J., Araújo, A. G., Orellana, N. C. & Standen, V. G. Possible influence of the ENSO phenomenon on the pathoecology of diphyllobothriasis and anisakiasis in ancient Chinchorro populations. Mem. Inst. Oswaldo Cruz 105, 66–72 (2010).Article 

Google Scholar 
Kaffenberger, B. H., Shetlar, D., Norton, S. A. & Rosenbach, M. The effect of climate change on skin disease in North America. J. Am. Acad. Dermatol. 76, 140–147 (2017).Article 

Google Scholar 
Coates, S. J., Enbiale, W., Davis, M. D. & Andersen, L. K. The effects of climate change on human health in Africa, a dermatologic perspective: a report from the International Society of Dermatology Climate Change Committee. Int. J. Dermatol. 59, 265–278 (2020).Article 

Google Scholar 
Patz, J. A. et al. Unhealthy landscapes: policy recommendations on land use change and infectious disease emergence. Environ. Health Perspect. 112, 1092–1098 (2004).Article 

Google Scholar 
Nagy, G. J. et al. in Climate Change and Health (ed Leal, W) 475–514 (Springer, 2016).Kontra, J. M. Zombie infections and other infectious disease complications of global warming. J. Lancaster Gen. Hosp. 12, 12–16 (2017).
Google Scholar 
Charron, D., Fleury, M., Lindsay, L. R., Ogden, N. & Schuster, C. J. in Human Health in a Changing Climate (ed Séguin, J) 173–210 (Health Canada, 2008).Butler, C. D. & Harley, D. Primary, secondary and tertiary effects of eco-climatic change: the medical response. Postgrad. Med. J. 86, 230–234 (2010).Article 

Google Scholar 
Quarles, W. Global warming means more pathogens. IPM Pract. 35, 1–8 (2017).
Google Scholar 
Patz, J. A., Engelberg, D. & Last, J. The effects of changing weather on public health. Ann. Rev. Public Health 21, 271–307 (2000).CAS 
Article 

Google Scholar 
Yavarian, J., Shafiei-Jandaghi, N. Z. & Mokhtari-Azad, T. Possible viral infections in flood disasters: a review considering 2019 spring floods in Iran. Iran. J. Microbiol. 11, 85–89 (2019).
Google Scholar 
Boxall, A. B. A. et al. Impacts of climate change on indirect human exposure to pathogens and chemicals from agriculture. Environ. Health Perspect. 117, 508–514 (2009).CAS 
Article 

Google Scholar 
Wu, R., Trubl, G., Taş, N. & Jansson, J. K. Permafrost as a potential pathogen reservoir. One Earth 5, 351–360 (2022).Article 

Google Scholar 
Gross, M. Permafrost thaw releases problems. Curr. Biol. 29, R39–R41 (2019).CAS 
Article 

Google Scholar 
Baker-Austin, C. et al. Heat wave-associated vibriosis, Sweden and Finland, 2014. Emerg. Infect. Dis. 22, 1216 (2016).CAS 
Article 

Google Scholar 
Ghanchi, N. K. et al. Case series of Naegleria fowleri primary ameobic meningoencephalitis from Karachi, Pakistan. Am. J. Trop. Med. Hyg. 97, 1600–1602 (2017).Article 

Google Scholar 
Waits, A., Emelyanova, A., Oksanen, A., Abass, K. & Rautio, A. Human infectious diseases and the changing climate in the Arctic. Environ. Int. 121, 703–713 (2018).Article 

Google Scholar 
Oskorouchi, H. R., Nie, P. & Sousa-Poza, A. The effect of floods on anemia among reproductive age women in Afghanistan. PLoS ONE 13, e0191726 (2018).Article 
CAS 

Google Scholar 
Caminade, C., McIntyre, K. M. & Jones, A. E. Impact of recent and future climate change on vector‐borne diseases. Ann. N. Y. Acad. Sci. 1436, 157 (2019).Article 

Google Scholar 
Clegg, J. Influence of climate change on the incidence and impact of arenavirus diseases: a speculative assessment. Clin. Microbiol. Infect. 15, 504–509 (2009).CAS 
Article 

Google Scholar 
Nguyen, H. Q., Huynh, T. T. N., Pathirana, A. & Van der Steen, P. Microbial risk assessment of tidal-induced urban flooding in Can Tho City (Mekong Delta, Vietnam). Int. J. Environ. Res. Public. Health 14, 1485 (2017).Article 
CAS 

Google Scholar 
Ivers, L. C. & Ryan, E. T. Infectious diseases of severe weather-related and flood-related natural disasters. Curr. Opin. Infect. Dis. 19, 408–414 (2006).Article 

Google Scholar 
Cornell, K. Climate change and infectious disease patterns in the United States: public health preparation and ecological restoration as a matter of justice. MSc thesis, Goucher College (2016).Mishra, V. et al. Climate change and its impacts on global health: a review. Pharma Innov. 8, 316–326 (2019).
Google Scholar 
Lemonick, D. M. Epidemics after natural disasters. Am. J. Clin. Med. 8, 144–152 (2011).
Google Scholar 
Khan, A. E., Xun, W. W., Ahsan, H. & Vineis, P. Climate change, sea-level rise, and health impacts in Bangladesh. Environ. Sci. Policy Sustain. Dev. 53, 18–33 (2011).Article 

Google Scholar 
Jones, B. A. et al. Zoonosis emergence linked to agricultural intensification and environmental change. Proc. Natl Acad. Sci. USA 110, 8399–8404 (2013).CAS 
Article 

Google Scholar 
Zell, R., Krumbholz, A. & Wutzler, P. Impact of global warming on viral diseases: what is the evidence? Curr. Opin. Biotechnol. 19, 652–660 (2008).CAS 
Article 

Google Scholar 
McFarlane, R. A., Sleigh, A. C. & McMichael, A. J. Land-use change and emerging infectious disease on an island continent. Int. J. Environ. Res. Public. Health 10, 2699–2719 (2013).Article 

Google Scholar 
White, R. J. & Razgour, O. Emerging zoonotic diseases originating in mammals: a systematic review of effects of anthropogenic land‐use change. Mammal. Rev. 50, 336–352 (2020).Article 

Google Scholar 
Myers, S. S. et al. Human health impacts of ecosystem alteration. Proc. Natl Acad. Sci. USA 110, 18753–18760 (2013).CAS 
Article 

Google Scholar 
Munang’andu, H. M. et al. The effect of seasonal variation on anthrax epidemiology in the upper Zambezi floodplain of western Zambia. J. Vet. Sci. 13, 293–298 (2012).Article 

Google Scholar 
Liu, Q. et al. Changing rapid weather variability increases influenza epidemic risk in a warming climate. Environ. Res. Lett. 15, 044004 (2020).Article 

Google Scholar 
Kapoor, R. et al. God is in the rain: the impact of rainfall-induced early social distancing on COVID-19 outbreaks. J. Health Econ. 81, 102575 (2020).
Google Scholar 
Raza, A., Khan, M. T. I., Ali, Q., Hussain, T. & Narjis, S. Association between meteorological indicators and COVID-19 pandemic in Pakistan. Environ. Sci. Pollut. Res. 28, 40378–40393 (2021).CAS 
Article 

Google Scholar 
Nichols, G. L. et al. Coronavirus seasonality, respiratory infections and weather. BMC Infect. Dis. 21, 1101 (2021).El-Sayed, A. & Kamel, M. Climatic changes and their role in emergence and re-emergence of diseases. Environ. Sci. Pollut. Res. 27, 22336–22352 (2020).CAS 
Article 

Google Scholar 
Ruszkiewicz, J. A. et al. Brain diseases in changing climate. Environ. Res. 177, 108637 (2019).CAS 
Article 

Google Scholar 
Herrador, B. R. G. et al. Analytical studies assessing the association between extreme precipitation or temperature and drinking water-related waterborne infections: a review. Environ. Health 14, 29 (2015).Article 

Google Scholar 
Burge, C. A. et al. Climate Change influences on marine infectious diseases: implications for management and society. Ann. Rev. Mar. Sci. 6, 249–277 (2014).Article 

Google Scholar 
Mills, J. N., Gage, K. L. & Khan, A. S. Potential influence of climate change on vector-borne and zoonotic diseases: a review and proposed research plan. Environ. Health Perspect. 118, 1507–1514 (2010).Article 

Google Scholar 
Gubler, D. J. et al. Climate variability and change in the United States: potential impacts on vector-and rodent-borne diseases. Environ. Health Perspect. 109, 223–233 (2001).
Google Scholar 
Dayrit, J. F., Bintanjoyo, L., Andersen, L. K. & Davis, M. D. P. Impact of climate change on dermatological conditions related to flooding: update from the International Society of Dermatology Climate Change Committee. Int. J. Dermatol. 57, 901–910 (2018).Article 

Google Scholar 
Myaing, T. T. Climate change and emerging zoonotic diseases. KKU Vet. J. 21, 172–182 (2011).
Google Scholar 
Kimes, N. E. et al. Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J. 6, 835–846 (2012).CAS 
Article 

Google Scholar 
Oh, M. H., Lee, S. M., Lee, D. H. & Choi, S. H. Regulation of the Vibrio vulnificus hupA gene by temperature alteration and cyclic AMP receptor protein and evaluation of its role in virulence. Infect. Immun. 77, 1208–1215 (2009).CAS 
Article 

Google Scholar 
Casadevall, A. Climate change brings the specter of new infectious diseases. J. Clin. Invest. 130, 553–555 (2020).CAS 
Article 

Google Scholar 
Beyer, R. M., Manica, A. & Mora, C. Shifts in global bat diversity suggest a possible role of climate change in the emergence of SARS-CoV-1 and SARS-CoV-2. Sci. Total Environ. 767, 145413 (2021).CAS 
Article 

Google Scholar 
Warburton, E. M., Pearl, C. A. & Vonhof, M. J. Relationships between host body condition and immunocompetence, not host sex, best predict parasite burden in a bat–helminth system. Parasitol. Res. 115, 2155–2164 (2016).Article 

Google Scholar 
Plowright, R. K. et al. Reproduction and nutritional stress are risk factors for Hendra virus infection in little red flying foxes (Pteropus scapulatus). Proc. R. Soc. B 275, 861–869 (2008).Article 

Google Scholar 
Beldomenico, P. M. & Begon, M. Disease spread, susceptibility and infection intensity: vicious circles? Trends Ecol. Evol. 25, 21–27 (2010).Article 

Google Scholar 
Mora, C. et al. Suitable days for plant growth disappear under projected climate change: potential human and biotic vulnerability. PLoS Biol. 13, e1002167 (2015).Article 
CAS 

Google Scholar 
Mora, C. et al. Biotic and human vulnerability to projected changes in ocean biogeochemistry over the 21st century. PLoS Biol. 11, e1001682 (2013).CAS 
Article 

Google Scholar 
Thiault, L. et al. Escaping the perfect storm of simultaneous climate change impacts on agriculture and marine fisheries. Sci. Adv. 5, eaaw9976 (2019).CAS 
Article 

Google Scholar 
Myers, S. S. et al. Increasing CO2 threatens human nutrition. Nature 510, 139–142 (2014).CAS 
Article 

Google Scholar 
Tirado, M. C., Clarke, R., Jaykus, L., McQuatters-Gollop, A. & Frank, J. Climate change and food safety: a review. Food Res. Int. 43, 1745–1765 (2010).Article 

Google Scholar 
Greene, M. Impact of the Sahelian drought in Mauritania, West Africa. Lancet 303, 1093–1097 (1974).Article 

Google Scholar 
Cabrol, J.-C. War, drought, malnutrition, measles—a report from Somalia. N. Engl. J. Med. 365, 1856–1858 (2011).CAS 
Article 

Google Scholar 
Cohen, S. et al. Chronic stress, glucocorticoid receptor resistance, inflammation, and disease risk. Proc. Natl Acad. Sci. USA 109, 5995–5999 (2012).CAS 
Article 

Google Scholar 
Calow, R. C., MacDonald, A. M., Nicol, A. L. & Robins, N. S. Ground water security and drought in Africa: linking availability, access, and demand. Groundwater 48, 246–256 (2010).CAS 
Article 

Google Scholar 
Salvador, C., Nieto, R., Linares, C., Díaz, J. & Gimeno, L. Effects of droughts on health: diagnosis, repercussion, and adaptation in vulnerable regions under climate change. Challenges for future research. Sci. Total Environ. 703, 134912 (2020).CAS 
Article 

Google Scholar 
Alhoot, M. A., Tong, W. T., Low, W. Y. & Sekaran, S. D. in Climate Change and Human Health Scenario in South and Southeast Asia (ed Akhtar, R) 243–268 (Springer, 2016).Yusa, A. et al. Climate change, drought and human health in Canada. Int. J. Environ. Res. Public Health 12, 8359–8412 (2015).CAS 
Article 

Google Scholar 
Ligon, B. L. Infectious Diseases that Pose Specific Challenges After Natural Disasters: A Review. Semin. Pediatr. Infect. Dis. 17, 36–45 (2006).Article 

Google Scholar 
Nsuami, M. J., Taylor, S. N., Smith, B. S. & Martin, D. H. Increases in gonorrhea among high school students following hurricane Katrina. Sex. Transm. Infect. 85, 194–198 (2009).CAS 
Article 

Google Scholar 
Jochelson, K. HIV and syphilis in the Republic of South Africa: the creation of an epidemic. Afr. Urban Q. 6, 20–34 (1991).
Google Scholar 
Sobral, M. F. F., Duarte, G. B., da Penha Sobral, A. I. G., Marinho, M. L. M. & de Souza Melo, A. Association between climate variables and global transmission of SARS-CoV-2. Sci. Total Environ. 729, 138997 (2020).CAS 
Article 

Google Scholar 
Liu, J. et al. Impact of meteorological factors on the COVID-19 transmission: a multi-city study in China. Sci. Total Environ. 726, 138513 (2020).CAS 
Article 

Google Scholar 
Chua, P. L. et al. Global projections of temperature-attributable mortality due to enteric infections: a modelling study. Lancet Planet. Health 5, e436–e445 (2021).Article 

Google Scholar 
McCreesh, N. & Booth, M. Challenges in predicting the effects of climate change on Schistosoma mansoni and Schistosoma haematobium transmission potential. Trends Parasitol. 29, 548–555 (2013).Article 

Google Scholar 
Wu, X., Tian, H., Zhou, S., Chen, L. & Xu, B. Impact of global change on transmission of human infectious diseases. Sci. China Earth Sci. 57, 189–203 (2014).Article 

Google Scholar 
Moreno, A. R. Climate change and human health in Latin America: drivers, effects, and policies. Reg. Environ. Change 6, 157–164 (2006).Article 

Google Scholar 
McCann, D. G., Moore, A. & Walker, M.-E. The water/health nexus in disaster medicine: I. drought versus flood. Curr. Opin. Environ. Sustain. 3, 480–485 (2011).Article 

Google Scholar 
Cutler, D. M. & Summers, L. H. The COVID-19 pandemic and the $16 trillion virus. JAMA 324, 1495–1496 (2020).CAS 
Article 

Google Scholar 
Vos, T. et al. Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet 396, 1204–1222 (2020).Article 

Google Scholar 
Hsiao, M.-H. et al. Environmental factors associated with the prevalence of animal bites or stings in patients admitted to an emergency department. J. Acute Med. 2, 95–102 (2012).Article 

Google Scholar 
Jones, N. E. & Baker, M. D. Toxicologic exposures associated with natural disasters: gases, kerosene, ash, and bites. Clin. Pediatr. Emerg. Med. 13, 317–323 (2012).Article 

Google Scholar  More

Agricultural and Horticultural Land Use (StatsNZ, 2021); https://www.stats.govt.nz/indicators/agricultural-and-horticultural-land-useThom, E. R. Hill Country Symposium Grassland Research and Practice Series No. 16 (New Zealand Grassland Association, 2016).Wardle, P. Vegetation of New Zealand (Cambridge Univ. Press, 1991).Maxwell, T. M. R., Moir, J. L. & Edwards, G. R. Grazing and soil fertility effect on naturalized annual clover species in New Zealand high country. Rangel. Ecol. Manage. 69, 444–448 (2016).Article 

Google Scholar 
Maxwell, T., Moir, J. & Edwards, G. Influence of environmental factors on the abundance of naturalised annual clovers in the South Island hill and high country. J. N. Z. Grassl. 72, 165–170 (2010).
Google Scholar 
Nölke, I., Tonn, B., Komainda, M., Heshmati, S. & Isselstein, J. The choice of the white clover population alters overyielding of mixtures with perennial ryegrass and chicory and underlying processes. Sci. Rep. 12, 1155 (2022).Article 

Google Scholar 
Fay, P. A. et al. Grassland productivity limited by multiple nutrients. Nat. Plants 1, 15080 (2015).CAS 
Article 

Google Scholar 
Zhang, W., Maxwell, T. M. R., Robinson, B. & Dickinson, N. Legume nutrition is improved by neighbouring grasses. Plant Soil (in the press).Smith, S. E. & Read, D. J. Mycorrhizal Symbiosis (Academic Press, 2008)Phoenix, G. K., Johnson, D. A., Muddimer, S. P., Leake, J. R. & Cameron, D. D. Niche differentiation and plasticity in soil phosphorus acquisition among co-occurring plants. Nat. Plants 6, 349–354 (2020).CAS 
Article 

Google Scholar 
Lambers, H., Clements, J. C. & Nelson, M. N. How a phosphorus-acquisition strategy based on carboxylate exudation powers the success and agronomic potential of lupines (Lupinus, Fabaceae). Am. J. Bot. 100, 263–288 (2013).CAS 
Article 

Google Scholar 
Li, X. et al. Long-term increased grain yield and soil fertility from intercropping. Nat. Sustain. 4, 943–950 (2021).Article 

Google Scholar 
Homulle, Z., George, T. & Karley, A. Root traits with team benefits: understanding belowground interactions in intercropping systems. Plant Soil 471, 1–26 (2021).Article 

Google Scholar 
Burrows, C. J. Processes of Vegetation Change (Unwin Hyman, 1990).Fornara, D. & Tilman, D. Plant functional composition influences rates of soil carbon and nitrogen accumulation. J. Ecol. 96, 314–322 (2008).CAS 
Article 

Google Scholar 
Lynch, J. P., Strock, C. F., Schneider, H. M., Sidhu, J. S. & Ajmera, I. Root anatomy and soil resource capture. Plant Soil 466, 21–63 (2021).CAS 
Article 

Google Scholar 
Lambers, H., Wright, I. J., Caio, G. & Pereira, P. J. Leaf manganese concentrations as a tool to assess belowground plant functioning in phosphorus-impoverished environments. Plant Soil 461, 43–61 (2021).CAS 
Article 

Google Scholar 
Liu, G. & Martinoia, E. How to survive on low potassium. Nat. Plants 6, 332–333 (2020).Article 

Google Scholar 
Anke, M. & Seifert, M. The biological and toxicological importance of molybdenum in the environment and in the nutrition of plants, animals and man. Part 1: molybdenum in plants. Acta Biol. Hung. 58, 311–324 (2007).CAS 
Article 

Google Scholar 
Gylfadóttir, T., Helgadóttir, Á. & Høgh-Jensen, H. Consequences of including adapted white clover in northern European grassland: transfer and deposition of nitrogen. Plant Soil 297, 93–104 (2007).Article 

Google Scholar 
Maxwell, T. M. L. R. Ecology and Management of Adventive Annual Clover Species in the South Island Hill and High Country of New Zealand. PhD thesis, Lincoln Univ. (2013).Li, C. et al. Syndromes of production in intercropping impact yield gains. Nat. Plants 6, 653–660 (2020).Article 

Google Scholar 
McLaren, R. G. & Cameron, K. C. Soil Science: Sustainable Production and Environmental Science (Oxford Univ. Press, 1996).Chang, X., Duan, C. & Wang, H. Root excretion and plant resistance to metal toxicity. J. Appl. Ecol. 11, 315–320 (2000).CAS 
Article 

Google Scholar 
Puschenreiter, M., Gruber, B. & Wenzel, W. W. Phytosiderophore-induced mobilization and uptake of Cd, Cu, Fe, Ni, Pb and Zn by wheat plants grown on metal-enriched soils. Environ. Exp. Bot. 138, 67–76 (2017).CAS 
Article 

Google Scholar 
Lu, J. Y. et al. Rhizosphere priming effects of Lolium perenne and Trifolium repens depend on phosphorus fertilization and biological nitrogen fixation. Soil Biol. Biochem. 150, 108805 (2020).Article 

Google Scholar 
Wang, L., Chen, F. & Wan, K. Y. Research progress and prospects of plant growth efficiency and its evaluation. Soils 42, 164–170 (2010).CAS 

Google Scholar 
Tian, X. Y. et al. Physiological and molecular advances in magnesium nutrition of plants. Plant Soil 468, 1–17 (2021).CAS 
Article 

Google Scholar 
Wainwright, M. Sulfur oxidation in soils. Adv. Agron. 37, 349–376 (1984).CAS 
Article 

Google Scholar 
Kaiser, B. N., Gridley, K. L., Ngaire Brady, J., Phillips, T. & Tyerman, S. D. The role of molybdenum in agricultural plant production. Ann. Bot. 96, 745–754 (2005).CAS 
Article 

Google Scholar 
Khobra, R. & Singh, B. Phytosiderophore release in relation to multiple micronutrient metal deficiency in wheat. J. Plant Nutr. 41, 679–688 (2018).CAS 
Article 

Google Scholar 
Erenoglu, B., Eker, S., Cakmak, I., Derici, R. & Römheld, V. Effect of iron and zinc deficiency on release of phytosiderophores in barley cultivars differing in zinc efficiency. J. Plant Nutr. 23, 1645–1656 (2000).CAS 
Article 

Google Scholar 
Chen, C., Chaudhary, A. & Mathys, A. Nutritional and environmental losses embedded in global food waste. Resour. Conserv. Recycl. 160, 104912 (2020).Article 

Google Scholar 
Nyfeler, D., Huguenin-Elie, O., Suter, M., Frossard, E. & Lüscher, A. Grass–legume mixtures can yield more nitrogen than legume pure stands due to mutual stimulation of nitrogen uptake from symbiotic and non-symbiotic sources. Agric. Ecosyst. Environ. 140, 155–163 (2011).Article 

Google Scholar 
Zhang, C., Postma, J. A., York, L. M. & Lynch, J. P. Root foraging elicits niche complementarity-dependent yield advantage in the ancient ‘three sisters’ (maize/bean/squash) polyculture. Ann. Bot. 114, 1719–1733 (2014).CAS 
Article 

Google Scholar 
Ghestem, M., Sidle, R. C. & Stokes, A. The influence of plant root systems on subsurface flow: implications for slope stability. BioScience 61, 869–879 (2011).Article 

Google Scholar 
Huo, C., Luo, Y. & Cheng, W. Rhizosphere priming effect: a meta-analysis. Soil Biol. Biochem. 111, 78–84 (2017).CAS 
Article 

Google Scholar 
Coskun, D., Britto, D. T., Shi, W. & Kronzucker, H. J. How plant root exudates shape the nitrogen cycle. Trends Plant Sci. 22, 661–673 (2017).CAS 
Article 

Google Scholar 
Grelet, G. et.al. Regenerative Agriculture in Aotearoa New Zealand: Research Pathways to Build Science-Based Evidence and National Narratives (Landcare Research New Zealand, 2021).Sergei Schaub, R. F. et al. Plant diversity effects on forage quality, yield and revenues of semi-natural grasslands. Nat. Commun. 11, 768 (2020).Article 

Google Scholar 
Brooker, R. W. et al. Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology. N. Phytol. 206, 107–117 (2015).Article 

Google Scholar 
Bardgett, R. D. et al. Combatting global grassland degradation. Nat. Rev. Earth Environ. 2, 720–735 (2021).Article 

Google Scholar  More

Elith, J. & Leathwick, J. R. Species distribution models: Ecological explanation and prediction across space and time. Annu. Rev. Ecol. Evol. Syst. 40, 677–697 (2009).Article 

Google Scholar 
Guisan, A. & Thuiller, W. Predicting species distribution: Offering more than simple habitat models. Ecol. Lett. 8, 993–1009 (2005).PubMed 
Article 

Google Scholar 
Guisan, A. & Zimmermann, N. E. Predictive habitat distribution models in ecology. Ecol. Model. 135, 147–186 (2000).Article 

Google Scholar 
Wilkinson, D. P., Golding, N., Guillera-Arroita, G., Tingley, R. & McCarthy, M. A. A comparison of joint species distribution models for presence–absence data. Methods Ecol. Evol. 10, 198–211 (2018).Article 

Google Scholar 
Zimmermann, N. E., Edwards, T. C., Graham, C. H., Pearman, P. B. & Svenning, J.-C. New trends in species distribution modelling. Ecography (Cop.) 33, 985–989 (2010).Article 

Google Scholar 
Elith, J. et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography (Cop.) 29, 129–151 (2006).Article 

Google Scholar 
Kass, J. M. et al. Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods Ecol. Evol. 9, 1151–1156 (2018).Article 

Google Scholar 
Morisette, J. T. et al. VisTrails SAHM: Visualization and workflow management for species habitat modeling. Ecography (Cop.) 36, 129–135 (2013).Article 

Google Scholar 
Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M. B. BIOMOD—A platform for ensemble forecasting of species distributions. Ecography (Cop.) 32, 369–373 (2009).Article 

Google Scholar 
Guisan, A. et al. Predicting species distributions for conservation decisions. Ecol. Lett. 16, 1424–1435 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Syfert, M. M. et al. Using species distribution models to inform IUCN Red List assessments. Biol. Conserv. 177, 174–184 (2014).Article 

Google Scholar 
Robinson, A. P., Walshe, T., Burgman, M. A. & Nunn, M. Invasive Species: Risk Assessment and Management (Cambridge University Press, 2017).Book 

Google Scholar 
Fontaine, J. J. Improving our legacy: Incorporation of adaptive management into state wildlife action plans. J. Environ. Manag. 92, 1403–1408 (2011).Article 

Google Scholar 
Gantchoff, M., Conlee, L. & Belant, J. Conservation implications of sex-specific landscape suitability for a large generalist carnivore. Divers. Distrib. 25, 1488–1496 (2019).Article 

Google Scholar 
Camaclang, A. E., Maron, M., Martin, T. G. & Possingham, H. P. Current practices in the identification of critical habitat for threatened species. Conserv. Biol. 29, 482–492 (2014).PubMed 
Article 

Google Scholar 
Schwartz, M. W. The Performance of the Endangered Species Act. Annu. Rev. Ecol. Evol. Syst. 39, 279–299 (2008).Article 

Google Scholar 
Acevedo, P. et al. Generalizing and transferring spatial models: A case study to predict Eurasian badger abundance in Atlantic Spain. Ecol. Model. 275, 1–8 (2014).Article 

Google Scholar 
Werkowska, W., Márquez, A. L., Real, R. & Acevedo, P. A practical overview of transferability in species distribution modeling. Environ. Rev. 25, 127–133 (2017).Article 

Google Scholar 
Barbosa, A. M., Real, R. & MarioVargas, J. Transferability of environmental favourability models in geographic space: The case of the Iberian desman (Galemys pyrenaicus) in Portugal and Spain. Ecol. Model. 220, 747–754 (2009).Article 

Google Scholar 
Randin, C. F. et al. Are niche-based species distribution models transferable in space?. J. Biogeogr. 33, 1689–1703 (2006).Article 

Google Scholar 
Jiménez-Valverde, A. et al. Use of niche models in invasive species risk assessments. Biol. Invasions 13, 2785–2797 (2011).Article 

Google Scholar 
Torres, R. T. et al. Favourableness and connectivity of a Western Iberian landscape for the reintroduction of the iconic Iberian ibex Capra pyrenaica. Oryx 51, 709–717 (2016).Article 

Google Scholar 
Luoto, M., Kuussaari, M. & Toivonen, T. Modelling butterfly distribution based on remote sensing data. J. Biogeogr. 29, 1027–1037 (2002).Article 

Google Scholar 
Cerasoli, F. et al. Determinants of habitat suitability models transferability across geographically disjunct populations: Insights from Vipera ursinii urs inii. Ecol. Evol. 11, 3991–4011 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Dobrowski, S. Z. et al. Modeling plant ranges over 75 years of climate change in California, USA: Temporal transferability and species traits. Ecol. Monogr. 81, 241–257 (2011).Article 

Google Scholar 
Townsend Peterson, A., Papeş, M. & Eaton, M. Transferability and model evaluation in ecological niche modeling: A comparison of GARP and Maxent. Ecography (Cop.) 30, 550–560 (2007).Article 

Google Scholar 
Qiao, H. et al. An evaluation of transferability of ecological niche models. Ecography (Cop.) 42, 521–534 (2018).Article 

Google Scholar 
Wenger, S. J. & Olden, J. D. Assessing transferability of ecological models: An underappreciated aspect of statistical validation. Methods Ecol. Evol. 3, 260–267 (2012).Article 

Google Scholar 
Gantchoff, M., Conlee, L. & Belant, J. L. Planning for carnivore recolonization by mapping sex-specific landscape connectivity. Glob. Ecol. Conserv. 21, e00869 (2020).Article 

Google Scholar 
Gantchoff, M. G. et al. Potential distribution and connectivity for recolonizing cougars in the Great Lakes region, USA. Biol. Conserv. 257, 109144 (2021).Article 

Google Scholar 
Boudreau, M. et al. Spatial prioritization of public outreach in the face of carnivore recolonization. J. Appl. Ecol. 59, 757–767 (2002).Article 

Google Scholar 
Chapron, G. et al. Recovery of large carnivores in Europe’s modern human-dominated landscapes. Science 80(346), 1517–1519 (2014).ADS 
Article 
CAS 

Google Scholar 
Laliberte, A. S. & Ripple, W. J. Range contractions of North American carnivores and ungulates. Bioscience 54, 123 (2004).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 
Gompper, M. E., Belant, J. L. & Kays, R. Carnivore coexistence: America’s recovery. Science 347, 382–383 (2015).CAS 
PubMed 
Article 

Google Scholar 
Mech, L. D. Where can wolves live and how can we live with them?. Biol. Conserv. 210, 310–317 (2017).Article 

Google Scholar 
United States Fish and Wildlife Service (USFWS). Endangered and threatened wildlife and plants; Removing the gray wolf (Canis lupus) from the list of endangered and threatened wildlife. Fed. Reg. 85(213), 69778–69895 (2020).
Google Scholar 
Gehring, T. M. & Potter, B. A. Wolf habitat analysis in Michigan: An example of the need for proactive land management for carnivore species. Wild. Soc. Bull. 33, 1237–1244 (2005).Article 

Google Scholar 
Falcucci, A., Maiorano, L., Tempio, G., Boitani, L. & Ciucci, P. Modeling the potential distribution for a range-expanding species: Wolf recolonization of the Alpine range. Biol. Conserv. 158, 63–72 (2013).Article 

Google Scholar 
Torres, L. G. et al. Poor transferability of species distribution models for a pelagic predator, the grey petrel, indicates contrasting habitat preferences across ocean basins. PLoS One 10, e0120014 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Olson, L. E. et al. Improved prediction of Canada lynx distribution through regional model transferability and data efficiency. Ecol. Evol. 11, 1667–1690 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Carroll, C., Rohlf, D. J., vonHoldt, B. M., Treves, A. & Hendricks, S. A. Wolf delisting challenges demonstrate need for an improved framework for conserving intraspecific variation under the endangered species act. Bioscience 71, 73–84 (2020).PubMed 
PubMed Central 

Google Scholar 
Yang, L. et al. A new generation of the United States National Land Cover Database: Requirements, research priorities, design, and implementation strategies. ISPRS J. Photogramm. Remote Sens. 146, 108–123 (2018).ADS 
Article 

Google Scholar 
Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: How, where and how many?. Methods Ecol. Evol. 3, 327–338 (2012).Article 

Google Scholar 
Marmion, M., Parviainen, M., Luoto, M., Heikkinen, R. K. & Thuiller, W. Evaluation of consensus methods in predictive species distribution modelling. Divers. Distrib. 15, 59–69 (2009).Article 

Google Scholar 
Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: Prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).Article 

Google Scholar 
Paton, R. S. & Matthiopoulos, J. Defining the scale of habitat availability for models of habitat selection. Ecology https://doi.org/10.1890/14-2241.1 (2015).Article 

Google Scholar 
Derville, S., Torres, L. G., Iovan, C. & Garrigue, C. Finding the right fit: Comparative cetacean distribution models using multiple data sources and statistical approaches. Divers. Distrib. 24, 1657–1673 (2018).Article 

Google Scholar 
Warren, D. L., Glor, R. E. & Turelli, M. Environmental niche equivalency versus conservatism: Quantitative approaches to niche evolution. Evolution 62, 2868–2883 (2008).PubMed 
Article 

Google Scholar 
Warren, D. L., Glor, R. E. & Turelli, M. ENMTools: A toolbox for comparative studies of environmental niche models. Ecography https://doi.org/10.1111/j.1600-0587.2009.06142.x (2010).Article 

Google Scholar 
Arntzen, J. W. From descriptive to predictive distribution models: A working example with Iberian amphibians and reptiles. Front. Zool. 3, 1–11 (2006).Article 

Google Scholar 
Conway, K. Wolf recovery—GIS facilitates habitat mapping in the Great Lake States. GIS WORLD 9, 54–57 (1996).
Google Scholar 
Boitani, L. Wolf conservation and recovery. In Wolves: Behavior, Ecology, and Conservation (eds Mech, L. D. & Boitani, L.) (University of Chicago Press, 2007).
Google Scholar 
Mladenoff, D. J., Sickley, T. A., Haight, R. G. & Wydeven, A. P. A regional landscape analysis and prediction of favorable gray wolf habitat in the northern Great Lakes region. Conserv. Biol. 9, 279–294 (1995).Article 

Google Scholar 
Treves, A., Martin, K. A., Wiedenhoeft, J. E. & Wydeven, A. P. Dispersal of gray wolves in the Great Lakes region. In Recovery of Gray Wolves in the Great Lakes Region of the United States 191–204 (Springer, 2009).Chapter 

Google Scholar 
Nelson, M. E. Winter range arrival and departure of white-tailed deer in northeastern Minnesota. Can. J. Zool. 73, 1069–1076 (1995).Article 

Google Scholar 
Droghini, A. & Boutin, S. Snow conditions influence grey wolf (Canis lupus) travel paths: The effect of human-created linear features. Can. J. Zool. 96, 39–47 (2018).Article 

Google Scholar 
Beyer, D. E., Peterson, R. O., Vucetich, J. A. & Hammill, J. H. Wolf population changes in Michigan. In Recovery of Gray Wolves in the Great Lakes Region of the United States 65–85 (Springer, 2009).Chapter 

Google Scholar 
Claeys, G. B. Wolves in the Lower Peninsula of Michigan: Habitat modeling, evaluation of connectivity, and capacity estimation (Doctoral dissertation, Duke University) (2010)..Gehring, T. M. & Potter, B. A. Wolf habitat analysis in Michigan: An example of the need for proactive land management for carnivore species. Wildl. Soc. Bull. 33, 1237–1244 (2005).Article 

Google Scholar 
Mancinelli, S., Falco, M., Boitani, L. & Ciucci, P. Social, behavioural and temporal components of wolf (Canis lupus) responses to anthropogenic landscape features in the central Apennines, Italy. J. Zool. 309, 114–124 (2019).Article 

Google Scholar 
Potvin, M. J. et al. Monitoring and habitat analysis for wolves in upper Michigan. J. Wildl. Manag. 69, 1660–1669 (2005).Article 

Google Scholar 
Whittington, J. et al. Caribou encounters with wolves increase near roads and trails: A time-to-event approach. J. Appl. Ecol. 48, 1535–1542 (2011).Article 

Google Scholar 
Zimmermann, B., Nelson, L., Wabakken, P., Sand, H. & Liberg, O. Behavioral responses of wolves to roads: Scale-dependent ambivalence. Behav. Ecol. 25, 1353–1364 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Kojola, I. et al. Wolf visitations close to human residences in Finland: The role of age, residence density, and time of day. Biol. Conserv. 198, 9–14 (2016).Article 

Google Scholar 
Gaynor, K. M., Hojnowski, C. E., Carter, N. H. & Brashares, J. S. The influence of human disturbance on wildlife nocturnality. Science 360, 1232–1235 (2018).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Kautz, T. M. et al. Large carnivore response to human road use suggests a landscape of coexistence. Glob. Ecol. Conserv. 30, e01772 (2021).Article 

Google Scholar 
Thuiller, W., Brotons, L., Araújo, M. B. & Lavorel, S. Effects of restricting environmental range of data to project current and future species distributions. Ecography (Cop.) 27, 165–172 (2004).Article 

Google Scholar 
Václavík, T. & Meentemeyer, R. K. Equilibrium or not? Modelling potential distribution of invasive species in different stages of invasion. Divers. Distrib. 18, 73–83 (2011).Article 

Google Scholar 
VanDerWal, J., Shoo, L. P., Graham, C. & Williams, S. E. Selecting pseudo-absence data for presence-only distribution modeling: How far should you stray from what you know?. Ecol. Model. 220, 589–594 (2009).Article 

Google Scholar 
Brum, F. T. et al. Global priorities for conservation across multiple dimensions of mammalian diversity. Proc. Natl. Acad. Sci. U.S.A. 114, 7641–7646 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rosauer, D. F., Pollock, L. J., Linke, S. & Jetz, W. Phylogenetically informed spatial planning is required to conserve the mammalian tree of life. Proc. Biol. Sci. 284, 20170627 (2017).PubMed 
PubMed Central 

Google Scholar 
Guillera-Arroita, G. et al. Is my species distribution model fit for purpose? Matching data and models to applications. Glob. Ecol. Biogeogr. 24, 276–292 (2015).Article 

Google Scholar  More

IPCC. Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (2021).Giorgi, F. & Lionello, P. Climate change projections for the Mediterranean region. Glob. Planet. Change 63, 90–104 (2008).Article 

Google Scholar 
Post, E. et al. The polar regions in a 2 °C warmer world. Sci. Adv. 5, eaaw9883 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Körner, C. Alpine Plant Life (Springer International Publishing, 2021).Graven, H. D. et al. Enhanced seasonal exchange of CO2 by northern ecosystems since 1960. Science 341, 1085–1089 (2013).CAS 
PubMed 
Article 

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

Google Scholar 
Gamm, C. M. et al. Declining growth of deciduous shrubs in the warming climate of continental western Greenland. J. Ecol. 106, 640–654 (2018).CAS 
Article 

Google Scholar 
AMAP. Arctic Climate Change Update 2021: Key Trends and Impacts. Arctic Monitoring and Assessment Programme (2021).Elmendorf, S. C. et al. Plot-scale evidence of tundra vegetation change and links to recent summer warming. Nat. Clim. Change 2, 453–457 (2012).Article 

Google Scholar 
Bjorkman, A. D. et al. Plant functional trait change across a warming tundra biome. Nature 562, 57–62 (2018).CAS 
PubMed 
Article 

Google Scholar 
Zhang, W. et al. Self‐amplifying feedbacks accelerate greening and warming of the arctic. Geophys. Res. Lett. 45, 7102–7111 (2018).Article 

Google Scholar 
Körner, C. Treelines will be understood once the functional difference between a tree and a shrub is. Ambio 41, 197–206 (2012).PubMed 
PubMed Central 
Article 

Google Scholar 
Pellizzari, E. et al. Diverging shrub and tree growth from the Polar to the Mediterranean biomes across the European continent. Glob. Change Biol. 23, 3169–3180 (2017).Article 

Google Scholar 
Dobbert, S., Pape, R. & Löffler, J. How does spatial heterogeneity affect inter‐ and intraspecific growth patterns in tundra shrubs. J. Ecol. 7, 1 (2021).
Google Scholar 
Ackerman, D., Griffin, D., Hobbie, S. E. & Finlay, J. C. Arctic shrub growth trajectories differ across soil moisture levels. Glob. Change Biol. 23, 4294–4302 (2017).Article 

Google Scholar 
Stendel, M., Christensen, J. H. & Petersen, D. in High-Arctic Ecosystem Dynamics in a Changing Climate (eds. Meltofte, H.) 13–43 (Elsevier, 2008).Prislan, P. et al. Annual cambial rhythm in Pinus halepensis and Pinus sylvestris as indicator for climate adaptation. Front. Plant Sci. 7, 1923 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Gazol, A. & Camarero, J. J. Mediterranean dwarf shrubs and coexisting trees present different radial-growth synchronies and responses to climate. Plant Ecol. 213, 1687–1698 (2012).Article 

Google Scholar 
Olano, J. M., Almería, I., Eugenio, M. & Arx, G. V. Under pressure: how a Mediterranean high-mountain forb coordinates growth and hydraulic xylem anatomy in response to temperature and water constraints. Funct. Ecol. 27, 1295–1303 (2013).Article 

Google Scholar 
Voltas, J. et al. A retrospective, dual-isotope approach reveals individual predispositions to winter-drought induced tree dieback in the southernmost distribution limit of Scots pine. Plant, Cell Environ. 36, 1435–1448 (2013).CAS 
Article 

Google Scholar 
Hanewinkel, M., Cullmann, D. A., Schelhaas, M.-J., Nabuurs, G.-J. & Zimmermann, N. E. Climate change may cause severe loss in the economic value of European forest land. Nat. Clim. Change 3, 203–207 (2013).Article 

Google Scholar 
Castagneri, D., Battipaglia, G., Arx, G. V., Pacheco, A. & Carrer, M. Tree-ring anatomy and carbon isotope ratio show both direct and legacy effects of climate on bimodal xylem formation in Pinus pinea. Tree Physiol. 38, 1098–1109 (2018).CAS 
PubMed 
Article 

Google Scholar 
Cabon, A., Peters, R. L., Fonti, P., Martínez-Vilalta, J. & Cáceres, M. Temperature and water potential co-limit stem cambial activity along a steep elevational gradient. N. Phytologist 226, 1325–1340 (2020).CAS 
Article 

Google Scholar 
Camarero, J. J., Valeriano, C., Gazol, A., Colangelo, M. & Sánchez-Salguero, R. Climate differently impacts the growth of coexisting trees and shrubs under semi-arid mediterranean conditions. Forests 12, 381 (2021).Article 

Google Scholar 
García-Cervigón Morales, A. I., Olano Mendoza, J. M., Eugenio Gozalbo, M. & Camarero Martínez, J. J. Arboreal and prostrate conifers coexisting in Mediterranean high mountains differ in their climatic responses. Dendrochronologia 30, 279–286 (2012).Article 

Google Scholar 
Oladi, R., Emaminasab, M. & Eckstein, D. The dendroecological potential of shrubs in north Iranian semi-deserts. Dendrochronologia 44, 94–102 (2017).Article 

Google Scholar 
McMahon, S. M. & Parker, G. G. A general model of intra-annual tree growth using dendrometer bands. Ecol. Evolution 5, 243–254 (2015).Article 

Google Scholar 
Drew, D. M., Downes, G. M. & Battaglia, M. CAMBIUM, a process-based model of daily xylem development in Eucalyptus. J. Theor. Biol. 264, 395–406 (2010).PubMed 
Article 

Google Scholar 
Delpierre, N., Berveiller, D., Granda, E. & Dufrêne, E. Wood phenology, not carbon input, controls the interannual variability of wood growth in a temperate oak forest. N. Phytologist 210, 459–470 (2016).CAS 
Article 

Google Scholar 
Rathgeber, C. B. K., Cuny, H. E. & Fonti, P. Biological basis of tree-ring formation: a crash course. Front. Plant Sci. 7, 734 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Körner, C. Carbon limitation in trees. J. Ecol. 91, 4–17 (2003).Article 

Google Scholar 
Thompson, J. D. Plant Evolution in the Mediterranean (Oxford University Press, 2005).Rossi, S. et al. Pattern of xylem phenology in conifers of cold ecosystems at the Northern Hemisphere. Glob. Change Biol. 22, 3804–3813 (2016).Article 

Google Scholar 
Löffler, J. & Pape, R. Thermal niche predictors of alpine plant species. Ecology 101, e02891 (2020).PubMed 
Article 

Google Scholar 
Zweifel, R. et al. Why trees grow at night. N. Phytologist 231, 2174–2185 (2021).Article 

Google Scholar 
González-Rodríguez, Á. M. et al. Seasonal cycles of sap flow and stem radius variation of Spartocytisus supranubius in the alpine zone of Tenerife, Canary Islands. Alp. Bot. 127, 97–108 (2017).Article 

Google Scholar 
Zweifel, R., Haeni, M., Buchmann, N. & Eugster, W. Are trees able to grow in periods of stem shrinkage. N. Phytologist 211, 839–849 (2016).Article 

Google Scholar 
Rossi, S., Deslauriers, A., Anfodillo, T. & Carraro, V. Evidence of threshold temperatures for xylogenesis in conifers at high altitudes. Oecologia 152, 1–12 (2007).PubMed 
Article 

Google Scholar 
Myers-Smith, I. H. et al. Climate sensitivity of shrub growth across the tundra biome. Nat. Clim. Change 5, 887–891 (2015).Article 

Google Scholar 
Mitrakos, K. A Theory for Mediterranean Plant Life (Acta oecologica, 1980).Camarero, J. J., Olano, J. M. & Parras, A. Plastic bimodal xylogenesis in conifers from continental Mediterranean climates. N. Phytologist 185, 471–480 (2010).Article 

Google Scholar 
Alday, J. G., Camarero, J. J., Revilla, J. & Resco de Dios, V. Similar diurnal, seasonal and annual rhythms in radial root expansion across two coexisting Mediterranean oak species. Tree Physiol. 40, 956–968 (2020).PubMed 
Article 

Google Scholar 
Lockhart, J. A. An analysis of irreversible plant cell elongation. J. Theor. Biol. 8, 264–275 (1965).CAS 
PubMed 
Article 

Google Scholar 
Descals, A. et al. Soil thawing regulates the spring growth onset in tundra and alpine biomes. Sci. total Environ. 742, 140637 (2020).CAS 
PubMed 
Article 

Google Scholar 
Morgner, E., Elberling, B., Strebel, D. & Cooper, E. J. The importance of winter in annual ecosystem respiration in the High Arctic: effects of snow depth in two vegetation types. Polar Res. 29, 58–74 (2010).CAS 
Article 

Google Scholar 
Weijers, S., Beckers, N. & Löffler, J. Recent spring warming limits near-treeline deciduous and evergreen alpine dwarf shrub growth. Ecosphere 9, e02328 (2018).Article 

Google Scholar 
Bret-Harte, M. S. et al. Developmental plasticity allows Betula nana to dominate tundra subjected to an altered environment. Ecology 82, 18–32 (2001).Article 

Google Scholar 
Wang, Y. et al. Warming‐induced shrubline advance stalled by moisture limitation on the Tibetan Plateau. Ecography 44, 1631–1641 (2021).Article 

Google Scholar 
Tape, K. D., Hallinger, M., Welker, J. M. & Ruess, R. W. Landscape heterogeneity of shrub expansion in Arctic Alaska. Ecosystems 15, 711–724 (2012).CAS 
Article 

Google Scholar 
Francon, L., Corona, C., Till-Bottraud, I., Carlson, B. Z. & Stoffel, M. Some (do not) like it hot: shrub growth is hampered by heat and drought at the alpine treeline in recent decades. Am. J. Bot. 107, 607–617 (2020).PubMed 
Article 

Google Scholar 
Lu, X., Liang, E., Babst, F., Camarero, J. J. & Büntgen, U. Warming-induced tipping points of Arctic and alpine shrub recruitment. Proc. Natl Acad. Sci. USA 119, e2118120119 (2022).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sabater, A. M. et al. Transpiration from subarctic deciduous woodlands: environmental controls and contribution to ecosystem evapotranspiration. Ecohydrology 13, e2190 (2019).
Google Scholar 
Larson, P. R. The indirect effect of photoperiod on tracheid diameter in Pinus resinosa. Am. J. Bot. 49, 132–137 (1962).Article 

Google Scholar 
Jackson, S. D. Plant responses to photoperiod. N. Phytologist 181, 517–531 (2009).CAS 
Article 

Google Scholar 
Waisel, Y. & Fahn, A. The effects of environment on wood formation and cambial activity in Robina Pseudacacia L. N. Phytologist 64, 436 (1965).Article 

Google Scholar 
Pasho, E., Camarero, J. J. & Vicente-Serrano, S. M. Climatic impacts and drought control of radial growth and seasonal wood formation in Pinus halepensis. Trees 26, 1875–1886 (2012).Article 

Google Scholar 
Gričar, J. et al. Plasticity in variation of xylem and phloem cell characteristics of Norway spruce under different local conditions. Front. Plant Sci. 6, 730 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Zellweger, F. et al. Forest microclimate dynamics drive plant responses to warming. Science 368, 772–775 (2020).CAS 
PubMed 
Article 

Google Scholar 
Oberhuber, W., Sehrt, M. & Kitz, F. Hygroscopic properties of thin dead outer bark layers strongly influence stem diameter variations on short and long time scales in Scots pine (Pinus sylvestris L.). Agric. For. Meteorol. 290, 108026 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Sonntag, D. Important new values of the physical constants of 1986, vapour pressure formulations based on ITS-90, and psychrometer formulae. Z. f.ür. Meteorologie 70, 340–344 (1990).
Google Scholar 
Löffler, J., Dobbert, S., Pape, R. & Wundram, D. Dendrometer measurements of arctic-alpine dwarf shrubs and micro-environmental drivers of plant growth—Dataset from long-term alpine ecosystem research in central Norway. Erdkunde 75, DP311201 (2021).
Google Scholar 
Löffler, J., Albrecht, E. C., Dobbert, S., Pape, R. & Wundram, D. Dendrometer measurements of Mediterranean-alpine dwarf shrubs and micro-environmental drivers of plant growth—Dataset from long-term alpine ecosystem research in the Sierra Nevada, Spain (LTAER-ES). Erdkunde 76, DP311202 (2022).Article 

Google Scholar 
R Core Team. A Language and Environment for Statistical Computing. https://www.R-project.org/ (2020).Wood, S. N. Generalized Additive Models. An introduction with R (2nd edition) (Chapman & Hall/CRC, 2017).Wood, S. N. Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J. R. Stat. Soc.: Ser. B 73, 3–36 (2011).Article 

Google Scholar 
Byun, J. G. et al. Radial growth response of Pinus densiflora and Quercus spp. to topographic and climatic factors in South Korea. J. Plant Ecol. 6, 380–392 (2013).Article 

Google Scholar 
Yee, T. W. & Mitchell, N. D. Generalized additive models in plant ecology. J. Vegetation Sci. 2, 587–602 (1991).Article 

Google Scholar 
Gasparrini, A., Scheipl, F., Armstrong, B. & Kenward, M. G. A penalized framework for distributed lag non-linear models. Biometrics 73, 938–948 (2017).PubMed 
Article 

Google Scholar 
Scott, E. R., Uriarte, M. & Bruna, E. M. Delayed effects of climate on vital rates lead to demographic divergence in Amazonian forest fragments. https://doi.org/10.1101/2021.06.28.450186 (2021).Almon, S. The distributed lag between capital appropriations and expenditures. Econometrica 33, 178 (1965).Article 

Google Scholar 
Vanoni, M., Bugmann, H., Nötzli, M. & Bigler, C. Drought and frost contribute to abrupt growth decreases before tree mortality in nine temperate tree species. For. Ecol. Manag. 382, 51–63 (2016).Article 

Google Scholar 
Pukienė, R., Vitas, A., Kažys, J. & Rimkus, E. Four-decadal series of dendrometer measurements reveals trends in Pinus sylvestris L. inter- and intra-annual growth response to climatic conditions. Can. J. For. Res. 51, 445–454 (2020).Article 

Google Scholar 
Gasparrini, A., Armstrong, B. & Kenward, M. G. Distributed lag non-linear models. Stat. Med. 29, 2224–2234 (2010).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gasparrini, A. Distributed lag linear and non-linear models in R: the package dlnm. J. Stat. Softw. 43, https://doi.org/10.18637/jss.v043.i08 (2011).Kartverket. Terrain Map. https://www.norgeskart.no/ (Norwegian Mapping Authority, 2008).Autonomous body National Center for Geographic Information (CNIG). Digital Terrain Model – DTM25. http://centrodedescargas.cnig.es/ (2009). More

Luck, G. W., Daily, G. C. & Ehrlich, P. R. Population diversity and ecosystem services. Trends Ecol. Evol. 18, 331–336. https://doi.org/10.1016/S0169-5347(03)00100-9 (2003).Article 

Google Scholar 
Schindler, D. E. et al. Population diversity and the portfolio effect in an exploited species. Nature 465, 609–612. https://doi.org/10.1038/nature09060 (2010).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Moore, J. W., Yeakel, J. D., Peard, D., Lough, J. & Beere, M. Life-history diversity and its importance to population stability and persistence of a migratory fish: Steelhead in two large North American watersheds. J. Anim. Ecol. 83, 1035–1046. https://doi.org/10.1111/1365-2656.12212 (2014).Article 
PubMed 

Google Scholar 
Barrett, R. D. H. et al. Linking a mutation to survival in wild mice. Science 363, 499. https://doi.org/10.1126/science.aav3824 (2019).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Jones, F. C. et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484, 55. https://doi.org/10.1038/nature10944 (2012).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Savage, A. E. & Zamudio, K. R. MHC genotypes associate with resistance to a frog-killing fungus. Proc. Natl. Acad. Sci. 108, 16705. https://doi.org/10.1073/pnas.1106893108 (2011).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Hofinger, B. J. et al. An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Mol. Ecol. 20, 3653–3668. https://doi.org/10.1111/j.1365-294X.2011.05201.x (2011).CAS 
Article 
PubMed 

Google Scholar 
Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines. Proc. Natl. Acad. Sci. 114, E6089. https://doi.org/10.1073/pnas.1704949114 (2017).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Hughes, J. B., Daily, G. C. & Ehrlich, P. R. Population diversity: its extent and extinction. Science 278, 689. https://doi.org/10.1126/science.278.5338.689 (1997).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Fernández-Llamazares, Á. et al. Scientists’ warning to humanity on threats to indigenous and local knowledge systems. J. Ethnobiol. 41(144–169), 126 (2021).
Google Scholar 
Womble, J. N., Willson, M. F., Sigler, M. F., Kelly, B. P. & VanBlaricom, G. R. Distribution of Steller sea lions (Eumetopias jubatus) in relation to spring-spawning fish in SE Alaska. Mar. Ecol. Prog. Ser. 294, 271–282 (2005).ADS 
Article 

Google Scholar 
Thomas, G. L. & Thorne, R. E. Night-time predation by Steller sea lions. Nature 411, 1013–1013. https://doi.org/10.1038/35082745 (2001).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Chamberlin, J. W., Beckman, B. R., Greene, C. M., Rice, C. A. & Hall, J. E. How relative size and abundance structures the relationship between size and individual growth in an ontogenetically piscivorous fish. Ecol. Evol. 7, 6981–6995. https://doi.org/10.1002/ece3.3218 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Hatch, S. A. Kittiwake diets and chick production signal a 2008 regime shift in the Northeast Pacific. Mar. Ecol. Prog. Ser. 477, 271–284 (2013).ADS 
Article 

Google Scholar 
Schrimpf, M. B., Parrish, J. K. & Pearson, S. F. Trade-offs in prey quality and quantity revealed through the behavioral compensation of breeding seabirds. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps09750 (2012).Article 

Google Scholar 
Willson, M. F. & Womble, J. N. Vertebrate exploitation of pulsed marine prey: A review and the example of spawning herring. Rev. Fish Biol. Fisheries 16, 183–200. https://doi.org/10.1007/s11160-006-9009-7 (2006).Article 

Google Scholar 
Sandell, T., Lindquist, A., Dionne, P. & Lowry, D. 2016 Washington State herring stock status report (Washington Department of Fish and Wildlife, 2019).Petrou, E. L. et al. Functional genetic diversity in an exploited marine species and its relevance to fisheries management. Proc. R. Soc. B Biol. Sci. 288, 20202398. https://doi.org/10.1098/rspb.2020.2398 (2021).CAS 
Article 

Google Scholar 
Chamberlin, J. et al. Phenological diversity of a prey species supports life-stage specific foraging opportunity for a mobile consumer. ICES J. Mar. Sci. 78, 3089–3100. https://doi.org/10.1093/icesjms/fsab176 (2021).Article 

Google Scholar 
Lok, E. K. et al. Spatiotemporal associations between Pacific herring spawn and surf scoter spring migration: Evaluating a silver wave hypothesis. Mar. Ecol. Prog. Ser. 457, 139–150 (2012).ADS 
Article 

Google Scholar 
Armstrong, J. B., Takimoto, G., Schindler, D. E., Hayes, M. M. & Kauffman, M. J. Resource waves: Phenological diversity enhances foraging opportunities for mobile consumers. Ecology 97, 1099–1112. https://doi.org/10.1890/15-0554.1 (2016).Article 
PubMed 

Google Scholar 
McKechnie, I. et al. Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability. Proc. Natl. Acad. Sci. https://doi.org/10.1073/pnas.1316072111 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Moss, M. L., Rodrigues, A. T., Speller, C. F. & Yang, D. Y. The historical ecology of Pacific herring: Tracing Alaska Native use of a forage fish. J. Archaeol. Sci. Rep. https://doi.org/10.1016/j.jasrep.2015.10.005 (2016).Article 

Google Scholar 
Kopperl, R. E. Herring use in southern Puget Sound: Analysis of fish remains at 45-KI-437. Northwest Anthropol. Res. Notes 35, 1–20 (2001).
Google Scholar 
McKechnie, I. & Moss, M. L. Meta-analysis in zooarchaeology expands perspectives on Indigenous fisheries of the Northwest Coast of North America. J. Archaeol. Sci. Rep. 8, 470–485. https://doi.org/10.1016/j.jasrep.2016.04.006 (2016).Article 

Google Scholar 
Caldwell, M. E. et al. A bird’s eye view of northern Coast Salish intertidal resource management features, southern British Columbia, Canada. J. Isl. Coast. Archaeol. 7, 219–233. https://doi.org/10.1080/15564894.2011.586089 (2012).Article 

Google Scholar 
Eells, M. & Castile, G. P. The Indians of Puget Sound: The Notebooks of Myron Eells (University of Washington Press, 1985).
Google Scholar 
Smith, M. W. The Puyallup-Nisqually (Columbia University Press, 1940).Book 

Google Scholar 
Thornton, T. F. & Moss, M. L. Herring and People in the North Pacific: Sustaining a Keystone Species (University of Washington Press, 2021).
Google Scholar 
Powell, M. Divided waters: Heiltsuk spatial management of herring fisheries and the politics of native sovereignty. West. Hist. Q. 43, 463–484. https://doi.org/10.2307/westhistquar.43.4.0463 (2012).Article 

Google Scholar 
Gauvreau, A. M., Lepofsky, D., Rutherford, M. & Reid, M. “Everything revolves around the herring”: The Heiltsuk–herring relationship through time. Ecol. Soc. https://doi.org/10.5751/ES-09201-220210 (2017).Article 

Google Scholar 
von der Porten, S., Lepofsky, D., McGregor, D. & Silver, J. Recommendations for marine herring policy change in Canada: Aligning with Indigenous legal and inherent rights. Mar. Policy 74, 68–76. https://doi.org/10.1016/j.marpol.2016.09.007 (2016).Article 

Google Scholar 
Hammond, J. Fish in puget sound. Am. Angler 25, 392–393 (1886).
Google Scholar 
Bargmann, G. Forage fish management plan (Washington Department of Fish and Wildlife, 1998).Stick, K. C. & Lindquist, A. 2008 Washington State herring stock status report (Washington Department of Fish and Wildlife, 2009).Erlandson, J. M. & Rick, T. C. Archaeology meets marine ecology: The antiquity of maritime cultures and human impacts on marine fisheries and ecosystems. Ann. Rev. Mar. Sci. 2, 231–251. https://doi.org/10.1146/annurev.marine.010908.163749 (2009).Article 

Google Scholar 
Hadly, E. A. & Barnosky, A. D. in Conservation Paleobiology: Using the Past to Manage for the Future Vol. 15 (eds Dietl, G. P. & Flessa, K. W.) 39–59 (Paleontological Society Papers, 2009).Wolverton, S. & Lyman, R. L. in Conservation Biology and Applied Zooarchaeology (eds Wolverton, S. & Lyman, R. L.) 1–22 (University of Arizona Press, 2012).Rogers, L. A. et al. Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries. Proc. Natl. Acad. Sci. 110, 1750. https://doi.org/10.1073/pnas.1212858110 (2013).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Wright, C. A., Dallimore, A., Thomson, R. E., Patterson, R. T. & Ware, D. M. Late Holocene paleofish populations in Effingham Inlet, British Columbia, Canada. Palaeogeogr. Palaeoclimatol. Palaeoecol. 224, 367–384. https://doi.org/10.1016/j.palaeo.2005.03.041 (2005).Article 

Google Scholar 
Thompson, T. Q. et al. Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations. Proc. Natl. Acad. Sci. 116, 177. https://doi.org/10.1073/pnas.1811559115 (2019).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Halffman, C. M. et al. Early human use of anadromous salmon in North America at 11,500 y ago. Proc. Natl. Acad. Sci. 112, 12344–12348. https://doi.org/10.1073/pnas.1509747112 (2015).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Quinn, T. An environmental and historical overview of the Puget Sound ecosystem (U.S. Geological Survey, 2010).Kopperl, R. E., Taylor, A. K., Miss, C. J., Ames, K. M. & Hodges, C. M. The Bear Creek Site (45KI839), a Late Pleistocene-Holocene transition occupation in the Puget Sound lowland, King County, Washington. PaleoAmerica 1, 116–120. https://doi.org/10.1179/2055556314Z.0000000004 (2015).Article 

Google Scholar 
Gunther, E. Klallam Ethnography (University of Washington Press, 1927).
Google Scholar 
Elmendorf, W. W. & Kroeber, A. L. The Structure of Twana Culture (Washington State University Press, 1992).
Google Scholar 
The Suquamish Tribe. Fish consumption survey of the Suquamish Indian tribe of the Port Madison Indian Reservation, Puget Sound Region (Suquamish, WA, 2000).Suttles, W. P. The Economic Life of the Coast Salish of Haro and Rosario Straits (Garland Publishing, 1974).
Google Scholar 
Lane, B. The Indian herring fishery from the earliest times to the mid-nineteenth century (United States Depatment of the Interior, 1974).Stein, J. K. in Vashon Island Archaeology: A View from Burton Acres Shell Midden (eds Stein, J. K. & Phillips, L. S.) 5–16 (Burke Musseum, 2002).Lewarch, D. E. et al. Data recovery excavations at the Bay Street Shell Midden (45KP115), Kitsap County, Washington (Larson Anthropological Archaeological Services Limited, 2002).De Danaan, L. in Vashon Island Archaeology: A View from Burton Acres Shell Midden (eds Stein, J. K. & Phillips, L. S.) 17–31 (Burke Museum, 2002).Stein, J. K. in Vashon Island Archaeology: A View from Burton Acres Shell Midden (eds Stein, J. K. & Phillips, L. S.) 47–64 (Burke Musseum, 2002).Yang, D. Y. & Watt, K. Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci. 32, 331–336. https://doi.org/10.1016/j.jas.2004.09.008 (2005).Article 

Google Scholar 
Yang, D. Y., Liu, L., Chen, X. & Speller, C. F. Wild or domesticated: DNA analysis of ancient water buffalo remains from north China. J. Archaeol. Sci. 35, 2778–2785. https://doi.org/10.1016/j.jas.2008.05.010 (2008).Article 

Google Scholar 
Maddox, D. M. et al. A mutation in Syne2 causes early retinal defects in photoreceptors, secondary neurons, and Müller Glia. Invest. Ophthalmol. Vis. Sci. 56, 3776–3787. https://doi.org/10.1167/iovs.14-16047 (2015).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Han, F. et al. Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci. Elife 9, e61076. https://doi.org/10.7554/eLife.61076 (2020).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Smith, M. J. et al. Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales. Mol. Ecol. Resour. 11, 268–277. https://doi.org/10.1111/j.1755-0998.2010.02965.x (2011).Article 
PubMed 

Google Scholar 
Speller, C. F. et al. High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation. PLoS ONE 7, e51122. https://doi.org/10.1371/journal.pone.0051122 (2012).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Weir, B. & Cockerham, C. Estimating F-Statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).CAS 
PubMed 

Google Scholar 
Archer, F. I., Adams, P. E. & Schneiders, B. B. stratag: An r package for manipulating, summarizing and analysing population genetic data. Mol. Ecol. Resour. 17, 5–11. https://doi.org/10.1111/1755-0998.12559 (2017).CAS 
Article 
PubMed 

Google Scholar 
Jombart, T. adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).CAS 
Article 

Google Scholar 
Rousset, F. Genepop’007: A complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x (2008).Article 
PubMed 

Google Scholar 
Moran, B. M. & Anderson, E. C. Bayesian inference from the conditional genetic stock identification model. Can. J. Fish. Aquat. Sci. 76, 551–560. https://doi.org/10.1139/cjfas-2018-0016 (2018).Article 

Google Scholar 
Moss, M. L. Understanding variability in Northwest Coast faunal assemblages: Beyond economic intensification and cultural complexity. J. Isl. Coast. Archaeol. 7, 1–22. https://doi.org/10.1080/15564894.2011.586090 (2012).Article 

Google Scholar 
Greene, C., Kuehne, L., Rice, C., Fresh, K. & Penttila, D. Forty years of change in forage fish and jellyfish abundance across greater Puget Sound, Washington (USA): Anthropogenic and climate associations. Mar. Ecol. Prog. Ser. 525, 153–170 (2015).ADS 
Article 

Google Scholar 
Rice, C. A., Duda, J. J., Greene, C. M. & Karr, J. R. Geographic patterns of fishes and jellyfish in Puget Sound surface waters. Mar. Coast. Fish. 4, 117–128. https://doi.org/10.1080/19425120.2012.680403 (2012).Article 

Google Scholar 
Haegele, C. W. & Schweigert, J. F. Distribution and characteristics of herring spawning grounds and description of spawning behavior. Can. J. Fish. Aquat. Sci. 42, s39–s55. https://doi.org/10.1139/f85-261 (1985).Article 

Google Scholar 
Gao, Y. W., Joner, S. H. & Bargmann, G. G. Stable isotopic composition of otoliths in identification of spawning stocks of Pacific herring (Clupea pallasi) in Puget Sound. Can. J. Fish. Aquat. Sci. 58, 2113–2120. https://doi.org/10.1139/f01-146 (2001).Article 

Google Scholar 
West, J. E., O’Neill, S. M. & Ylitalo, G. M. Spatial extent, magnitude, and patterns of persistent organochlorine pollutants in Pacific herring (Clupea pallasi) populations in the Puget Sound (USA) and Strait of Georgia (Canada). Sci. Total Environ. 394, 369–378. https://doi.org/10.1016/j.scitotenv.2007.12.027 (2008).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Moss, M. L. The nutritional value of Pacific herring: An ancient cultural keystone species on the Northwest Coast of North America. J. Archaeol. Sci. Rep. 5, 649–655. https://doi.org/10.1016/j.jasrep.2015.08.041 (2016).Article 

Google Scholar 
Brown, F. & Brown, Y. K. Staying the course, staying alive- Coastal First Nations fundamental truths: Biodiversity, stewardship and sustainability 82 (2009).Dugmore, A. J. et al. Cultural adaptation, compounding vulnerabilities and conjunctures in Norse Greenland. Proc. Natl. Acad. Sci. 109, 3658. https://doi.org/10.1073/pnas.1115292109 (2012).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Nunn, P. D. et al. Times of plenty, times of less: Last-millennium societal disruption in the Pacific Basin. Hum. Ecol. 35, 385–401. https://doi.org/10.1007/s10745-006-9090-5 (2007).Article 

Google Scholar 
Rose, K. A., Megrey, B. A., Hay, D., Werner, F. & Schweigert, J. Climate regime effects on Pacific herring growth using coupled nutrient-phytoplankton-zooplankton and bioenergetics models. Trans. Am. Fish. Soc. 137, 278–297. https://doi.org/10.1577/T05-152.1 (2008).Article 

Google Scholar 
Rosenthal, Y., Linsley, B. K. & Oppo, D. W. Pacific ocean heat content during the past 10,000 years. Science 342, 617. https://doi.org/10.1126/science.1240837 (2013).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Hopt, J. & Grier, C. Continuity amidst change: Village organization and fishing subsistence at the Dionisio Point locality in coastal southern British Columbia. J. Isl. Coast. Archaeol. 13, 21–42. https://doi.org/10.1080/15564894.2016.1257526 (2018).Article 

Google Scholar 
Butler, V. L., Campbell, S. K., Bovy, K. M. & Etnier, M. A. Exploring ecodynamics of coastal foragers using integrated faunal records from Čḯxwicən village (Strait of Juan de Fuca, Washington, U.S.A.). J. Archaeol. Sci. Rep. 23, 1143–1167. https://doi.org/10.1016/j.jasrep.2018.09.031 (2019).Article 

Google Scholar 
Lamichhaney, S. et al. Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean. Proc. Natl. Acad. Sci. 114, E3452–E3461 (2017).CAS 
Article 

Google Scholar 
Carpenter, M. L. et al. Pulling out the 1%: Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93, 852–864. https://doi.org/10.1016/j.ajhg.2013.10.002 (2013).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Oosting, T. et al. Unlocking the potential of ancient fish DNA in the genomic era. Evol. Appl. 12, 1513–1522. https://doi.org/10.1111/eva.12811 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Abrahms, B. et al. Emerging perspectives on resource tracking and animal movement ecology. Trends Ecol. Evol. 36, 308–320. https://doi.org/10.1016/j.tree.2020.10.018 (2021).Article 
PubMed 

Google Scholar 
Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360. https://doi.org/10.1017/S0033822200033865 (2009).Article 

Google Scholar 
Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757. https://doi.org/10.1017/RDC.2020.41 (2020).CAS 
Article 

Google Scholar 
Deo, J. N., Stone, J. O. & Stein, J. K. Building confidence in shell: Variations in the marine radiocarbon reservoir correction for the Northwest Coast over the past 3,000 years. Am. Antiq. 69, 771–786. https://doi.org/10.2307/4128449 (2004).Article 

Google Scholar  More

Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: Integrating terrestrial and oceanic components. Science. 281, 237–240 (1998).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Knapp, A. K. & Smith, M. D. Variation among biomes in temporal dynamics of aboveground primary production. Science. 291, 481–484 (2001).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Gillman, L. N. et al. Latitude, productivity and species richness. Glob. Ecol. Biogeogr. 24, 107–117 (2015).Article 

Google Scholar 
Anav, A. et al. Spatiotemporal patterns of terrestrial gross primary production: A review. Rev. Geophys. 53, 1–34 (2015).Article 

Google Scholar 
Goldman, C. R., Jassby, A. & Powell, T. Interannual fluctuations in primary production: Meteorological forcing at two subalpine lakes. Limnol. Oceanogr. 34, 310–323 (1989).ADS 
CAS 
Article 

Google Scholar 
Sayers, M. J., Fahnenstiel, G. L., Shuchman, R. A. & Bosse, K. R. A new method to estimate global freshwater phytoplankton carbon fixation using satellite remote sensing: initial results. Int. J. Remote Sens. 42, 3708–3730 (2021).Article 

Google Scholar 
Behrenfeld, M. J. et al. Climate-driven trends in contemporary ocean productivity. Nature 444, 752–755 (2006).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Uitz, J., Claustre, H., Gentili, B. & Stramski, D. Phytoplankton class-specific primary production in the world’s oceans: Seasonal and interannual variability from satellite observations. Global Biogeochem. Cycles 24, GB3016 (2010).ADS 
Article 
CAS 

Google Scholar 
Holt, J. et al. Modelling the global coastal ocean. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 367, 939–951 (2009).ADS 
MATH 
Article 

Google Scholar 
Duarte, C. M., Losada, I. J., Hendriks, I. E., Mazarrasa, I. & Marbà, N. The role of coastal plant communities for climate change mitigation and adaptation. Nat. Clim. Chang. 3, 961–968 (2013).ADS 
CAS 
Article 

Google Scholar 
Saba, V. S. et al. An evaluation of ocean color model estimates of marine primary productivity in coastal and pelagic regions across the globe. Biogeosciences 8, 489–503 (2011).ADS 
CAS 
Article 

Google Scholar 
Duarte, C. M. et al. Seagrass community metabolism: Assessing the carbon sink capacity of seagrass meadows. Global Biogeochem. Cycles 24, 1–8 (2010).Article 
CAS 

Google Scholar 
Charpy-Roubaud, C. & Sournia, A. The comparative estimation of phytoplanktonic, microphytobenthic and macrophytobenthic primary production in the oceans. Mar. Microb. Food Webs 4, 31–57 (1990).
Google Scholar 
Duarte, C. M. et al. Global estimates of the extent and production of macroalgal forests. Global Ecology and Biogeography. 31(7), 1422–1439, https://doi.org/10.1111/geb.13515 (2022).Duggins, D. O. & Estes, J. A. Magnification of secondary production by kelp detritus in coastal marine ecosystems. Science. 245, 170–173 (1989).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Dunton, K. H. & Schell, D. M. Dependence of consumers on macroalgal (Laminaria solidungula) carbon in an arctic kelp community: 13C evidence. Mar. Biol. 625, 615–625 (1987).Article 

Google Scholar 
Krumhansl, K. A. & Scheibling, R. E. Production and fate of kelp detritus. Mar. Ecol. Prog. Ser. 467, 281–302 (2012).ADS 
Article 

Google Scholar 
Ortega, A. et al. Important contribution of macroalgae to oceanic carbon sequestration. Nat. Geosci. 12, 748–754 (2019).ADS 
CAS 
Article 

Google Scholar 
Krause-Jensen, D. & Duarte, C. M. Substantial role of macroalgae in marine carbon sequestration. Nat. Geosci. 9, 737–742 (2016).ADS 
CAS 
Article 

Google Scholar 
Bach, L. T. et al. Testing the climate intervention potential of ocean afforestation using the Great Atlantic Sargassum belt. Nat. Commun. 12, 2556 (2021).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Duarte, C. M., Wu, J., Xiao, X., Bruhn, A. & Krause-Jensen, D. Can Seaweed Farming Play a Role in Climate Change Mitigation and Adaptation? Front. Mar. Sci. 4 (2017).Kanwisher, J. W. Photosynthesis and respiration in some seaweeds. in Some contemporary studies in marine science:: a collection of original scientific papers presented to Dr. S.M. Marshall, O.B.E., F.R.S. in recognition of her contribution with the late Dr. A.P. Orr to marine biological progress (eds. Barnes, H. & Marshall, S. M.) 407 (Allen & Unwin, 1966).Blinks, L. R. Photosynthesis and productivity of littoral marine algae. J. Mar. Res. 14, 363–373 (1955).
Google Scholar 
Printz, H. Seasonal growth and production of dry matter in Ascophyllum nodosum. Avh. Utg. Av Det Nor. Videnskaps-akademi i Oslo. I. Mat. Klasse 4, 1–15 (1950).
Google Scholar 
Rassweiler, A., Reed, D. C., Harrer, S. L. & Nelson, J. C. Improved estimates of net primary production, growth and standing crop of Macrosystis pryifera in Southern California. Ecology 99, 2132 (2018).PubMed 
Article 

Google Scholar 
Littler, M. M. & Arnold, K. E. Primary Productivity of Marine Macroalgal Functional-Form Groups From Southwestern North America. Journal of Phycology 18, 307–311 (1982).Article 

Google Scholar 
Krause-Jensen, D. et al. Seasonal sea ice cover as principal driver of spatial and temporal variation in depth extension and annual production of kelp in Greenland. Glob. Chang. Biol. 18, 2981–2994 (2012).ADS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Smale, D. A. et al. Environmental factors influencing primary productivity of the forest – forming kelp Laminaria hyperborea in the northeast Atlantic. Sci. Rep. 10, 12161 (2020).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pessarrodona, A. et al. Global seaweed productivity. Science Advances https://doi.org/10.1126/sciadv.abn2465 (2022) (in press).Assis, J. et al. Bio-ORACLE v2.0: Extending marine data layers for bioclimatic modelling. Glob. Ecol. Biogeogr. 27, 277–284 (2018).Article 

Google Scholar 
Fulton, C. J. et al. Form and function of tropical macroalgal reefs in the Anthropocene. Funct. Ecol. 33, 989–999 (2019).Article 

Google Scholar 
Tebbett, S. B. & Bellwood, D. R. Algal turf productivity on coral reefs: A meta-analysis. Mar. Environ. Res. 168, 105311 (2021).CAS 
PubMed 
Article 

Google Scholar 
Wernberg, T., Krumhansl, K., Filbee-Dexter, K. & Pedersen, M. F. Status and trends for the world’s kelp forests. in World Seas: An Environmental Evaluation: Ecological Issues and Environmental Impacts (ed. Sheppard, C.) 57–78, https://doi.org/10.1016/B978-0-12-805052-1.00003-6 (Academic Press, 2019).Gómez, I. et al. Light and temperature demands of marine benthic microalgae and seaweeds in polar regions. Bot. Mar. 52, 593–608 (2009).Article 

Google Scholar 
Kindig, A. C. & Littler, M. M. Growth and primary productivity of marine macrophytes exposed to domestic sewage effluents. Mar. Environ. Res. 3, 81–100 (1980).Article 

Google Scholar 
Wanders, J. B. W. The role of benthic algae in the shallow reef of Curaçao (Netherlands Antilles) III: The significance of grazing. Aquat. Bot. 3, 357–390 (1977).Article 

Google Scholar 
Hatcher, B. G. Reef primary productivity: a beggar’s banquet. Trends Ecol. Evol. 3, 106–111 (1988).CAS 
PubMed 
Article 

Google Scholar 
Odum, H. T. & Odum, E. P. Trophic Structure and Productivity of a Windward Coral Reef Community on Eniwetok Atoll. Ecol. Monogr. 25, 291–320 (1955).Article 

Google Scholar 
Owen, D. P., Long, M. H., Fitt, W. K. & Hopkinson, B. M. Taxon-specific primary production rates on coral reefs in the Florida Keys. Limnol. Oceanogr. 1–14, https://doi.org/10.1002/lno.11627 (2020).Attard, K. M. et al. Benthic oxygen exchange in a live coralline algal bed and an adjacent sandy habitat: An eddy covariance study. Mar. Ecol. Prog. Ser. 535, 99–115 (2015).ADS 
CAS 
Article 

Google Scholar 
Attard, K. M. Seasonal metabolism and carbon export potential of a key coastal habitat: The perennial canopy-forming macroalga Fucus vesiculosus. Limnol. Oceanogr. 64, 149–164 (2019).ADS 
Article 

Google Scholar 
Rohatgi, A. WebPlotDigitizer. (2019).Brey, T., Müller-Wiegmann, C., Zittier, Z. M. C. & Hagen, W. Body composition in aquatic organisms – A global data bank of relationships between mass, elemental composition and energy content. J. Sea Res. 64, 334–340 (2010).ADS 
Article 

Google Scholar 
Thom, R. M. Spatial and Temporal Patterns of Fucus distichus ssp. edentatus (de la Pyl.) Pow. (Phaeophyceae: Fucales) in Central Puget Sound. Bot. Mar. 26, 471–486 (1983).Article 

Google Scholar 
Johnston, C. S., Jones, R. G. & Hunter, D. R. A seasonal carbon budget for a laminarian population in a Scottish sea-loch. Helgoländer wissenschaftliche Meeresuntersuchungen 30, 527–545 (1977).ADS 
CAS 
Article 

Google Scholar 
Blain, C. O., Hansen, S. C. & Shears, N. T. Coastal darkening substantially limits the contribution of kelp to coastal carbon cycles. Glob. Chang. Biol. 1–17, https://doi.org/10.1111/gcb.15837 (2021).Randall, J., Wotherspoon, S., Ross, J., Hermand, J. & Johnson, C. An in situ study of production from diel oxygen modelling, oxygen exchange, and electron transport rate in the kelp Ecklonia radiata. Mar. Ecol. Prog. Ser. 615, 51–65 (2019).ADS 
CAS 
Article 

Google Scholar 
Rodgers, K. L., Rees, T. A. V. & Shears, N. T. A novel system for measuring in situ rates of photosynthesis and respiration of kelp. Mar. Ecol. Prog. Ser. 528, 101–115 (2015).ADS 
CAS 
Article 

Google Scholar 
Sanderson, J. C. Subtidal Macroalgal Studies in East and South Eastern Tasmanian Coastal Waters. (University of Tasmania, 1990).Miller, R. J., Reed, D. C. & Brzezinski, M. A. Community structure and productivity of subtidal turf and foliose algal assemblages. Mar. Ecol. Prog. Ser. 388, 1–11 (2009).ADS 
CAS 
Article 

Google Scholar 
Pessarrodona, A. et al. A global dataset of seaweed net primary productivity, Figshare, https://doi.org/10.6084/m9.figshare.14882322 (2021).Berg, P., Huettel, M., Glud, R. N., Reimers, C. E. & Attard, K. M. Aquatic Eddy Covariance: The Method and Its Contributions to Defining Oxygen and Carbon Fluxes in Marine Environments. Ann. Rev. Mar. Sci. 14, 431–455 (2022).PubMed 
Article 

Google Scholar 
Lees, D. C., Houghton, J. P., Erickson, D. E., Driskell, W. B. & Boettcher, D. E. Ecological studies of intertidal and shallow subtidal habitats in lower Cook Inlet, Alaska. (1980).Kelly, E. L. A. et al. A budget of algal production and consumption by herbivorous fish in an herbivore fisheries management area, Maui, Hawaii. Ecosphere 8, e01899 (2017).Article 

Google Scholar 
Pedersen, M. F., Nejrup, L. B., Fredriksen, S., Christie, H. C. & Norderhaug, K. M. Effects of wave exposure on population structure, demography, biomass and productivity of the kelp Laminaria hyperborea. Mar. Ecol. Prog. Ser. 451, 45–60 (2012).ADS 
Article 

Google Scholar 
Kain, J. M. The biology of Laminaria hyperborea X. The effect of depth on some populations. J. Mar. Biol. Assoc. United Kingdom 57, 587–607 (1977).Article 

Google Scholar 
Yatsuya, K., Nishigaki, T., Douke, A., Itani, M. & Wada, Y. Annual net productions of sargassacean species in coastal areas with different environmental characteristics in Kyoto Prefecture, the Sea of Japan. Nippon Suisan Gakkaishi 73, 880–890 (2007).Article 

Google Scholar 
Carter, A. R. & Simons, R. H. Regrowth and Production Capacity of Gelidium pristoides (Gelidiales, Rhodophyta) under Various Harvesting Regimes at Port Alfred, South Africa. Bot. Mar. 30, 227–232 (1987).Article 

Google Scholar 
Santelices, B., Vásquez, J., Ohme, U. & Fonck, E. Managing wild crops of Gracilaria in central Chile. in Eleventh International Seaweed Symposium (eds. Bird, C. J. & Ragan, M. A.) 77–89 (Springer Netherlands, 1984).Pessarrodona, A., Foggo, A. & Smale, D. A. Can ecosystem functioning be maintained despite climate-driven shifts in species composition? Insights from novel marine forests. J. Ecol. 10, 91–104 (2018).
Google Scholar 
Dunton, K. H. An annual carbon budget for an arctic kelp community. in The Alaskan Beaufort Sea: ecosystems and environments. (eds. Barnes, P. W., Schell, D. & Reimnitz, E.) 311–326 (Academic press, 1984).Klumpp, D. W. & McKinnon, A. D. Commmunity structure, biomass and productivity of epilithic algal communities on the Great Barrier Reef; dynamics at different spatial scales. Mar. Ecol. Prog. Ser. 86, 77–89 (1992).ADS 
Article 

Google Scholar 
Westphalen, G. & Cheshire, A. C. Quantum efficiency and photosynthetic production of a temperate turf algal community. Aust. J. Bot. 45, 343–349 (1997).Article 

Google Scholar 
Morrissey, J. Primary productivity of coral reef benthic macroalgae. Proceedings of the 5th International Coral Reef Congress 77–82 (1985).Howard, K. L. & Menzies, R. J. Distribution and Production of Sargassum in the Waters off the Carolina Coast. Bot. Mar. 12, 244–254 (1969).Article 

Google Scholar 
Weigel, B. L. & Pfister, C. A. The dynamics and stoichiometry of dissolved organic carbon release by kelp. Ecology 102, 1–17 (2020).
Google Scholar 
Tait, L. W., South, P. M., Lilley, S. A., Thomsen, M. S. & Schiel, D. R. Assemblage and understory carbon production of native and invasive canopy-forming macroalgae. J. Exp. Mar. Bio. Ecol. 469, 10–17 (2015).CAS 
Article 

Google Scholar 
Rodgers, K. & Shears, N. Modelling kelp forest primary production using in situ photosynthesis, biomass and light measurements. Mar. Ecol. Prog. Ser. 553, 67–79 (2016).ADS 
CAS 
Article 

Google Scholar  More

Vanwonterghem I, Webster NS. Coral reef microorganisms in a changing climate. iScience. 2020;23:100972.PubMed 
PubMed Central 
Article 

Google Scholar 
Voolstra CR, Ziegler M. Adapting with microbial help: microbiome flexibility facilitates rapid responses to environmental change. BioEssays. 2020;42:e2000004.PubMed 
Article 

Google Scholar 
Goulet TL, Erill I, Ascunce MS, Finley SJ, Javan GT. Conceptualization of the holobiont paradigm as it pertains to corals. Front Physiol. 2020;11:566968.PubMed 
PubMed Central 
Article 

Google Scholar 
McDevitt-Irwin JM, Baum JK, Garren M, Vega Thurber RL. Response of coral-associated bacterial communities to local and global stressor. Front Marine Sci. 2017;4:262.Article 

Google Scholar 
Morrow KM, Moss AG, Chadwick NE, Liles MR. Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Appl Environ Microbiol. 2012;78:6438–49.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
O’Brien PA, Smith HA, Fallon S, Fabricius K, Willis BL, Morrow KM, et al. Elevated CO2 has little influence on the bacterial communities associated with the pH-tolerant coral, massive Porites spp. Front Microbiol. 2018;9:2621.PubMed 
PubMed Central 
Article 

Google Scholar 
Rohwer F, Breitbart M, Jara J, Azam F, Knowlton N. Diversity of bacteria associated with the Caribbean coral Montastraea franksi. Coral Reefs. 2001;20:85–91.Article 

Google Scholar 
Rohwer F, Seguritan V, Azam F, Knowlton N. Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series. 2002;243:1–10.Article 

Google Scholar 
Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol. 2007;5:355–62.CAS 
PubMed 
Article 

Google Scholar 
van Oppen MJ, Blackall LL. Coral microbiome dynamics, functions and design in a changing world. Nat Rev Microbiol. 2019;17:557–67.PubMed 
Article 
CAS 

Google Scholar 
Dunphy CM, Gouhier TC, Chu ND, Vollmer SV. Structure and stability of the coral microbiome in space and time. Sci Reports. 2019;9:1–13.
Google Scholar 
Torda G, Donelson JM, Aranda M, Barshis DJ, Bay L, Berumen ML, et al. Rapid adaptive responses to climate change in corals. Nat Clim Change. 2017;7:627–36.Article 

Google Scholar 
Bourne DG, Morrow KM, Webster NS. Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Ann Rev Microbiol. 2016;70:317–40.CAS 
Article 

Google Scholar 
Putnam HM. Avenues of reef-building coral acclimatization in response to rapid environmental change. J Exp Biol. 2021;224:jeb239319.PubMed 
Article 

Google Scholar 
Stocker, TF, Qin, D, Plattner, GK, Alexander, LV, Allen, SK, Bindoff, NL, et al. (2013). Technical summary. In: Climate change 2013. The physical science basis. Contribution of working group I to the fifth assessment report of the intergovernmental panel on climate change [Stocker, TF, Qin, D, Plattner, G-K, Tignor,M, Allen, SK, Doschung, J, Nauels, A, Xia, Y, Bex, V,Midgley, PM (Eds.)]. Cambridge University Press, pp. 33–115.Bindoff, NL, Cheung, WW, Kairo, JG, Arístegui, J, Guinder, VA, Hallberg, R, et al. (2019). Changing ocean, marine ecosystems, and dependent communities. In: IPCC special report on the ocean and cryosphere in a changing climate [Pörtner, H-O, Roberts, DC, Masson-Delmotte, V, Zhai, P, Tignor, M, Poloczanska, E, Mintenbeck, K, Alegría, A, Nicolai, M, Okem, A, Petzold, J, Rama, B, Weyer NM (eds.)]. In press. p. 477–587.Hoegh-Guldberg O, Poloczanska ES, Skirving W, Dove S. Coral reef ecosystems under climate change and ocean acidification. Front Marine Sci. 2017;4:158.Article 

Google Scholar 
Yu T, Chen Y. Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review. Sci Total Environ. 2019;655:865–79.CAS 
PubMed 
Article 

Google Scholar 
Gattuso JP, Magnan A, Billé R, Cheung WW, Howes EL, Joos F, et al. OCEANOGRAPHY. Contrasting futures for ocean and society from different anthropogenic CO2 emissions scenarios. Science. 2015;349:aac4722.PubMed 
Article 
CAS 

Google Scholar 
Kroeker KJ, Kordas RL, Crim RN, Singh GG. Response to technical comment on ‘meta-analysis reveals negative yet variable effects of ocean acidification on marine organisms’. Ecology Lett. 2011;14:E1–E2.Article 

Google Scholar 
Ingrosso G, Abbiati M, Badalamenti F, Bavestrello G, Belmonte G, Cannas R, et al. Mediterranean Bioconstructions Along the Italian Coast. Adv Marine Biology. 2018;79:61–136.Article 

Google Scholar 
Hassenrück C, Fink A, Lichtschlag A, Tegetmeyer HE, de Beer D, Ramette A. Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches. FEMS Microbiology Ecology. 2016;92:fiw027.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Tangherlini M, Corinaldesi C, Ape F, Greco S, Romeo T, Andaloro F, et al. Ocean acidification induces changes in virus-host relationships in Mediterranean benthic ecosystems. Microorganisms. 2021;9:769.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lejeusne C, Chevaldonné P, Pergent-Martini C, Boudouresque CF, Pérez T. Climate change effects on a miniature ocean: the highly diverse, highly impacted Mediterranean Sea. Trends Ecology Evolut. 2010;25:250–60.Article 

Google Scholar 
Fantazzini P, Mengoli S, Pasquini L, Bortolotti V, Brizi L, Mariani M, et al. Gains and losses of coral skeletal porosity changes with ocean acidification acclimation. Nat Commun. 2015;6:1–7.Article 
CAS 

Google Scholar 
Goffredo S, Prada F, Caroselli E, Capaccioni B, Zaccanti F, Pasquini L, et al. Biomineralization control related to population density under ocean acidification. Nat Clim Change. 2014;4:593–7.CAS 
Article 

Google Scholar 
Teixidó N, Caroselli E, Alliouane S, Ceccarelli C, Comeau S, Gattuso JP, et al. Ocean acidification causes variable trait-shifts in a coral species. Global Change Biology. 2020;26:6813–30.PubMed 
Article 

Google Scholar 
Kenkel CD, Moya A, Strahl J, Humphrey C, Bay LK. Functional genomic analysis of corals from natural CO2‐seeps reveals core molecular responses involved in acclimatization to ocean acidification. Global Change Biology. 2018;24:158–71.PubMed 
Article 

Google Scholar 
Morrow KM, Bourne DG, Humphrey C, Botté ES, Laffy P, Zaneveld J, et al. Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges. The ISME J. 2015;9:894–908.CAS 
PubMed 
Article 

Google Scholar 
Biagi E, Caroselli E, Barone M, Pezzimenti M, Teixido N, Soverini M, et al. Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO2 vents. Sci Total Environ. 2020;724:138048.CAS 
PubMed 
Article 

Google Scholar 
Shore A, Day RD, Stewart JA, Burge CA. Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions. Appl Environ Microbiol. 2021;87:e02189–20.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Marcelino VR, Morrow KM, van Oppen MJH, Bourne DG, Verbruggen H. Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef. Mol Ecology. 2017;26:5344–57.CAS 
Article 

Google Scholar 
Goffredo S, Caroselli E, Pignotti E, Mattioli G, Zaccanti F. Variation in biometry and population density of solitary corals with environmental factors in the Mediterranean Sea. Marine Biology. 2007;152:351–61.Article 

Google Scholar 
Webster NS, Negri AP, Botté ES, Laffy PW, Flores F, Noonan S, et al. Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification. Sci Reports. 2016;6:1–9.
Google Scholar 
Klein, SG, Geraldi, NR, Anton, A, Schmidt‐Roach, S, Ziegler, M, Cziesielski, MJ, et al. (2021). Projecting coral responses to intensifying marine heatwaves under ocean acidification. Global change biology, https://doi.org/10.1111/gcb.15818. Advance online publication.Okazaki RR, Towle EK, van Hooidonk R, Mor C, Winter RN, Piggot AM, et al. Species‐specific responses to climate change and community composition determine future calcification rates of Florida Keys reefs. Global Change Biology. 2017;23:1023–35.PubMed 
Article 

Google Scholar 
Maor-Landaw K, Ben-Asher HW, Karako-Lampert S, Salmon-Divon M, Prada F, Caroselli E, et al. Mediterranean versus Red sea corals facing climate change, a transcriptome analysis. Sci Reports. 2017;7:1–8.
Google Scholar 
Prada F, Caroselli E, Mengoli S, Brizi L, Fantazzini P, Capaccioni B, et al. Ocean warming and acidification synergistically increase coral mortality. Sci Reports. 2017;7:40842.CAS 

Google Scholar 
Chen, D, Rojas, M, Samset, BH, Cobb, K, Diongue Niang, A, Edwards, P, et al. (2021). Framing, Context, and Methods. In: Climate change 2021: the physical science basis. Contribution of working group I to the sixth assessment report of the intergovernmental panel on climate change [Masson-Delmotte, V, Zhai, P, Pirani, A, Connors, AL, Péan, C, Berger, S, Caud, N, Chen, Y, Goldfarb, L, Gomis, MI, Huang, M, Leitzell, K, Lonnoy, E, Matthews, JBR, Maycock, TK, Waterfield, T, Yelekçi, O, Yu, R, & Zhou B (eds.)]. In Press.Wall, M, Prada, F, Fietzke, J, Caroselli, E, Dubinsky, Z, Brizi, L, et al. (2019). Linking internal carbonate chemistry regulation and calcification in corals growing at a Mediterranean CO2 vent. Frontiers in marine science, 699.Glasl B, Herndl GJ, Frade PR. The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. ISME J. 2016;10:2280–92.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sweet MJ, Croquer A, Bythell JC. Development of bacterial biofilms on artificial corals in comparison to surface-associated microbes of hard corals. PLoS One. 2011;6:e21195.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Apprill A, Weber LG, Santoro AE. Distinguishing between microbial habitats unravels ecological complexity in coral microbiomes. mSystems. 2016;1:e00143–16.PubMed 
PubMed Central 
Article 

Google Scholar 
Rubio-Portillo E, Santos F, Martínez-García M, de Los Ríos A, Ascaso C, Souza-Egipsy V, et al. Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica. Environ Microbiol. 2016;18:4564–78.CAS 
PubMed 
Article 

Google Scholar 
Palladino G, Biagi E, Rampelli S, Musella M, D’Amico F, Turroni S, et al. Seasonal changes in microbial communities associated with the jewel anemone Corynactis viridis. Front Marine Sci. 2021a;8:57.Article 

Google Scholar 
Palladino G, Rampelli S, Scicchitano D, Musella M, Quero GM, Prada F, et al. Impact of marine aquaculture on the microbiome associated with nearby holobionts: the case of Patella caerulea living in proximity of sea bream aquaculture cages. Microorganisms. 2021b;9:455.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Campbell AM, Fleisher J, Sinigalliano C, White JR, Lopez JV. Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast F lorida. MicrobiologyOpen. 2015;4:390–408.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sadik NJ, Uprety S, Nalweyiso A, Kiggundu N, Banadda NE, Shisler JL, et al. Quantification of multiple waterborne pathogens in drinking water, drainage channels, and surface water in Kampala, Uganda, during seasonal variation. GeoHealth. 2017;1:258–69.PubMed 
PubMed Central 
Article 

Google Scholar 
Su HC, Liu YS, Pan CG, Chen J, He LY, Ying GG. Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: from drinking water source to tap water. Sci Total Environ. 2018;616:453–61.PubMed 
Article 
CAS 

Google Scholar 
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.CAS 
PubMed 
Article 

Google Scholar 
Feehery GR, Yigit E, Oyola SO, Langhorst BW, Schmidt VT, Stewart FJ, et al. A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PloS One. 2013;8:e76096.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for Illumina sequences. BMC Bioinformatics. 2012;13:1–7.Article 
CAS 

Google Scholar 
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:1091.CAS 
PubMed 
Article 

Google Scholar 
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.CAS 
PubMed 
Article 

Google Scholar 
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.PubMed 
PubMed Central 
Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–D596.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Toolkit, P (2019). Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute.Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Andrews, S (2010). Fastqc: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.Liu CM, Li D, Sadakane K, Luo R, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.PubMed 
Article 
CAS 

Google Scholar 
West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res. 2018;28:569–80.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7:1–9.Article 
CAS 

Google Scholar 
Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, et al. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Res. 2013;41:e3.CAS 
PubMed 
Article 

Google Scholar 
Culhane AC, Thioulouse J, Perrière G, Higgins DG. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics. 2005;21:2789–90.CAS 
PubMed 
Article 

Google Scholar 
Meron D, Rodolfo-Metalpa R, Cunning R, Baker AC, Fine M, Banin E. Changes in coral microbial communities in response to a natural pH gradient. ISME J. 2012;6:1775–85.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Tjalsma H, Bolhuis A, Jongbloed JD, Bron S, van Dijl JM. Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol Mol Biology Rev. 2000;64:515–47.CAS 
Article 

Google Scholar 
Kabbara S, Hérivaux A, Dugé de Bernonville T, Courdavault V, Clastre M, Gastebois A, et al. Diversity and evolution of sensor histidine kinases in eukaryotes. Genome Biology Evolut. 2019;11:86–108.CAS 
Article 

Google Scholar 
Campanacci V, Nurizzo D, Spinelli S, Valencia C, Tegoni M, Cambillau C. The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding. FEBS Lett. 2004;562:183–8.CAS 
PubMed 
Article 

Google Scholar 
Pavan ME, López NI, Pettinari MJ. Melanin biosynthesis in bacteria, regulation and production perspectives. Appl Microbiol Biotechnol. 2020;104:1357–70.CAS 
PubMed 
Article 

Google Scholar 
Pérez E, Rubio MB, Cardoza RE, Gutiérrez S, Bettiol W, Monte E, et al. The importance of chorismate mutase in the biocontrol potential of Trichoderma parareesei. Front Microbiol. 2015;6:1181.PubMed 
PubMed Central 
Article 

Google Scholar 
Ohki T, Wakitani Y, Takeo M, Yasuhira K, Shibata N, Higuchi Y, et al. Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities. FEBS Lett. 2006;580:5054–8.CAS 
PubMed 
Article 

Google Scholar 
Velupillaimani D, Muthaiyan A. Potential of Bacillus subtilis from marine environment to degrade aromatic hydrocarbons. Environ Sustainability. 2019;2:381–9.CAS 
Article 

Google Scholar 
Byrne M, Fitzer S. The impact of environmental acidification on the microstructure and mechanical integrity of marine invertebrate skeletons. Conservation Physiol. 2019;7:coz062.CAS 
Article 

Google Scholar 
Godefroid M, Dupont S, Metian M, Hédouin L. Two decades of seawater acidification experiments on tropical scleractinian corals: Overview, meta-analysis and perspectives. Marine Pollut Bull. 2022;178:113552.CAS 
Article 

Google Scholar 
Goffredo S, Arnone S, Zaccanti F. Sexual reproduction in the Mediterranean solitary coral Balanophyllia europaea (Scleractinia, Dendrophylliidae). Marine Ecology Progress Series. 2002;229:83–94.Article 

Google Scholar 
Luo, D, Wang, X, Feng, X, Tian, M, Wang, S, Tang, SL, et al. (2021). Population differentiation of Rhodobacteraceae along with coral compartments. ISME J. https://doi.org/10.1038/s41396-021-01009-6. Advance online publication.Shnit-Orland M, Kushmaro A. Coral mucus-associated bacteria: a possible first line of defense. FEMS Microbiol Ecology. 2009;67:371–80.CAS 
Article 

Google Scholar 
Pollock FJ, McMinds R, Smith S, Bourne DG, Willis BL, Medina M, et al. Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny. Nat Commun. 2018;9:4921.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Glazier A, Herrera S, Weinnig A, Kurman M, Gómez CE, Cordes E. Regulation of ion transport and energy metabolism enables certain coral genotypes to maintain calcification under experimental ocean acidification. Mol Ecology. 2020;29:1657–73.CAS 
Article 

Google Scholar 
Strader ME, Wong JM, Hofmann GE. Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey. Front Zoology. 2020;17:1–23.Article 

Google Scholar 
Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Curr Genet. 2019;65:133–8.CAS 
PubMed 
Article 

Google Scholar 
Contreras-Llano LE, Guerrero-Rubio MA, Lozada-Ramírez JD, García-Carmona F, Gandía-Herrero F. First betalain-producing bacteria break the exclusive presence of the pigments in the plant kingdom. MBio. 2019;10:e00345–19.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Naveed M, Tariq K, Sadia H, Ahmad H, Mumtaz AS. The life history of pyrroloquinoline quinone (PQQ): a versatile molecule with novel impacts on living systems. Int J Mol Biology Open Access. 2016;1:29–46.Article 

Google Scholar 
Aguilar C, Raina JB, Fôret S, Hayward DC, Lapeyre B, Bourne DG, et al. Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress. BMC Genomics. 2019;20:1–13.Article 

Google Scholar 
Bury-Moné S, Nomane Y, Reymond N, Barbet R, Jacquet E, Imbeaud S, et al. Global analysis of extracytoplasmic stress signaling in Escherichia coli. PLoS Genetics. 2009;5:e1000651.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Chilton SS, Falbel TG, Hromada S, Burton BM. A conserved metal binding motif in the Bacillus subtilis competence protein ComFA enhances transformation. J Bacteriol. 2017;199:e00272–17.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Johnsen AR, Kroer N. Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events. FEMS Microbiology Ecology. 2007;59:718–28.CAS 
PubMed 
Article 

Google Scholar 
Maurer LM, Yohannes E, Bondurant SS, Radmacher M, Slonczewski JL. pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. J Bacteriol. 2005;187:304–19.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ma C, Sim S, Shi W, Du L, Xing D, Zhang Y. Energy production genes sucB and ubiF are involved in persister survival and tolerance to multiple antibiotics and stresses in Escherichia coli. FEMS Microbiol Lett. 2010;303:33–40.CAS 
PubMed 
Article 

Google Scholar 
Toesca I, Perard C, Bouvier J, Gutierrez C, Conter A. The transcriptional activator NhaR is responsible for the osmotic induction of osmCp1, a promoter of the stress-inducible gene osmC in Escherichia coli. Microbiology. 2001;147:2795–803.CAS 
PubMed 
Article 

Google Scholar 
Benner R, Kaiser K. Abundance of amino sugars and peptidoglycan in marine particulate and dissolved organic matter. Limnology Oceanogr. 2003;48:118–28.CAS 
Article 

Google Scholar 
Mills LA, McCormick AJ, Lea-Smith DJ. Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Reports. 2020;40:BSR20193325.CAS 
Article 

Google Scholar 
Labare MP, Bays JT, Butkus MA, Snyder-Leiby T, Smith A, Goldstein A, et al. The effects of elevated carbon dioxide levels on a Vibrio sp. isolated from the deep-sea. Environ Sci Pollut Res Int. 2010;17:1009–15.CAS 
PubMed 
Article 

Google Scholar 
Sogin EM, Putnam HM, Anderson PE, Gates RD. Metabolomic signatures of increases in temperature and ocean acidification from the reef-building coral, Pocillopora damicornis. Metabolomics. 2016;12:71.Article 
CAS 

Google Scholar 
Yang Y, Kadim MI, Khoo WJ, Zheng Q, Setyawati MI, Shin YJ, et al. Membrane lipid composition and stress/virulence related gene expression of Salmonella Enteritidis cells adapted to lactic acid and trisodium phosphate and their resistance to lethal heat and acid stress. Int J Food Microbiol. 2014;191:24–31.CAS 
PubMed 
Article 

Google Scholar 
Diricks M, Gutmann A, Debacker S, Dewitte G, Nidetzky B, Desmet T. Sequence determinants of nucleotide binding in Sucrose Synthase: improving the affinity of a bacterial Sucrose Synthase for UDP by introducing plant residues. Protein Eng Design Select. 2017;30:143–50.CAS 

Google Scholar 
De Carvalho CC, Caramujo MJ. The various roles of fatty acids. Molecules. 2018;23:2583.PubMed Central 
Article 
CAS 

Google Scholar 
Campanacci V, Bishop RE, Blangy S, Tegoni M, Cambillau C. The membrane bound bacterial lipocalin Blc is a functional dimer with binding preference for lysophospholipids. FEBS Lett. 2006;580:4877–83.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zawadzka-Skomiał J, Markiewicz Z, Nguyen-Disteche M, Devreese B, Frere JM, Terrak M. Characterization of the bifunctional glycosyltransferase/acyltransferase penicillin-binding protein 4 of Listeria monocytogenes. J Bacteriol. 2006;188:1875–81.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Wannicke N, Frey C, Law CS, Voss M. The response of the marine nitrogen cycle to ocean acidification. Global Change Biology. 2018;24:5031–43.PubMed 
Article 

Google Scholar 
Burnat M, Herrero A, Flores E. Compartmentalized cyanophycin metabolism in the diazotrophic filaments of a heterocyst-forming cyanobacterium. Proc Natl Acad Sci USA. 2014;111:3823–8.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang H, Yang C. Arginine and nitrogen mobilization in cyanobacteria. Mol Microbiol. 2019;111:863–7.CAS 
PubMed 
Article 

Google Scholar 
Law AM, Lai SW, Tavares J, Kimber MS. The structural basis of beta-peptide-specific cleavage by the serine protease cyanophycinase. J Mol Biol. 2009;392:393–404.CAS 
PubMed 
Article 

Google Scholar 
Flores E, Arévalo S, Burnat M. Cyanophycin and arginine metabolism in cyanobacteria. Algal Res. 2019;42:101577.Article 

Google Scholar 
Bednarz VN, Van De Water JA, Grover R, Maguer JF, Fine M, Ferrier-Pagès C. Unravelling the importance of diazotrophy in corals–combined assessment of nitrogen assimilation, diazotrophic community and natural stable isotope signatures. Front Microbiol. 2021;12:1638.
Google Scholar 
Rädecker N, Pogoreutz C, Voolstra CR, Wiedenmann J, Wild C. Nitrogen cycling in corals: the key to understanding holobiont functioning? Trends Microbiol. 2015;23:490–7.PubMed 
Article 
CAS 

Google Scholar 
Béraud E, Gevaert F, Rottier C, Ferrier-Pagès C. The response of the scleractinian coral Turbinaria reniformis to thermal stress depends on the nitrogen status of the coral holobiont. J Exp Biol. 2013;216:2665–74.PubMed 

Google Scholar 
Tong H, Cai L, Zhou G, Zhang W, Huang H, Qian PY. Correlations between prokaryotic microbes and stress-resistant algae in different corals subjected to environmental stress in Hong Kong. Front Microbiol. 2020;11:686.PubMed 
PubMed Central 
Article 

Google Scholar 
Pogoreutz C, Rädecker N, Cardenas A, Gärdes A, Voolstra CR, Wild C. Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching. Global Change Biol. 2017;23:3838–48.Article 

Google Scholar 
Zhou Y, Tang K, Wang P, Wang W, Wang Y, Wang X. Identification of bacteria-derived urease in the coral gastric cavity. Sci China Earth Sci. 2020;63:1553–63.CAS 
Article 

Google Scholar 
Biscéré T, Ferrier-Pagès C, Grover R, Gilbert A, Rottier C, Wright A, et al. Enhancement of coral calcification via the interplay of nickel and urease. Aquatic Toxicol. 2018;200:247–56.Article 
CAS 

Google Scholar  More

Fischer, C. P. & Romero, L. M. Chronic captivity stress in wild animals is highly species-specific. Conserv. Physiol. 7, coz093 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McGill, I. et al. Isosporoid coccidiosis in translocated cirl buntings (Emberiza cirlus). Vet. Rec. 167, 656–660 (2010).CAS 
PubMed 
Article 

Google Scholar 
Mohajeri, M. H. et al. The role of the microbiome for human health: from basic science to clinical applications. Eur. J. Nutr. 57, 1–14 (2018).PubMed 
PubMed Central 
Article 

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

Google Scholar 
Peters, A., Meredith, A., Skerratt, L., Carver, S. & Raidal, S. Infectious disease and emergency conservation interventions. Conserv. Biol. 34, 784–785 (2020).PubMed 
Article 

Google Scholar 
Northover, A. S. et al. Altered parasite community structure in an endangered marsupial following translocation. Int. J. Parasitol. Parasites Wildl. 10, 13–22 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Daniel, B. M. et al. A bat on the brink? A range-wide survey of the Critically Endangered Livingstone’s fruit bat Pteropus livingstonii. Oryx 51, 742–751 (2017).Article 

Google Scholar 
IUCN. Pteropus livingstonii: Sewall, B.J., Young, R., Trewhella, W.J. & Rodríguez-Clark, K.M. and Granek, E.F. IUCN Red List of Threatened Species (2016) https://doi.org/10.2305/iucn.uk.2016-2.rlts.t18732a22081502.en.IUCN Species Survival Commission. Species action plan for Livingstone’s fruit bat ‘Pteropus livingstonii’. https://portals.iucn.org/library/node/7368 (1995).Haag, A. F., Ross Fitzgerald, J. & Penadés, J. R. Staphylococcus aureus in animals. Gram-Positive Pathog. https://doi.org/10.1128/9781683670131.ch46 (2019).Article 

Google Scholar 
Pirolo, M. et al. Unidirectional animal-to-human transmission of methicillin-resistant Staphylococcus aureus ST398 in pig farming; evidence from a surveillance study in southern Italy. Antimicrob. Resist. Infect. Control 8, 1–10 (2019).Article 

Google Scholar 
Young, B. C. et al. Severe infections emerge from commensal bacteria by adaptive evolution. Elife 6, e30637 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Heaton, C. J., Gerbig, G. R., Sensius, L. D., Patel, V. & Smith, T. C. Staphylococcus aureus epidemiology in wildlife: A systematic review. Antibiotics 9, 89 (2020).PubMed Central 
Article 

Google Scholar 
Sheppard, S. K., Guttman, D. S. & Fitzgerald, J. R. Population genomics of bacterial host adaptation. Nat. Rev. Genet. 19, 549–565 (2018).CAS 
PubMed 
Article 

Google Scholar 
Richardson, E. J. et al. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat. Ecol. Evol. 2, 1468–1478 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Bacigalupe, R., Tormo-Mas, M. Á., Penadés, J. R. & Ross Fitzgerald, J. A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species. Sci. Adv. 5, eaax0063 (2019).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Spoor, L. E. et al. Recombination-mediated remodelling of host–pathogen interactions during Staphylococcus aureus niche adaptation. Microb. Genomics 1(4), e000036. https://doi.org/10.1099/mgen.0.000036 (2015).Article 

Google Scholar 
Tong, S. Y. C., Davis, J. S., Eichenberger, E., Holland, T. L. & Fowler, V. G. Jr. Staphylococcus aureus infections: Epidemiology, pathophysiology, clinical manifestations, and management. Clin. Microbiol. Rev. 28, 603–661 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Fountain, K. et al. Diversity of staphylococcal species cultured from captive Livingstone’s fruit bats (Pteropus livingstonii) and their environment. J. Zoo Wildl. Med. 50, 266–269 (2019).PubMed 
Article 

Google Scholar 
Fountain, K. et al. Fatal exudative dermatitis in island populations of red squirrels (Sciurus vulgaris): spillover of a virulent clone (ST49) from reservoir hosts. Microb. Genom. 7(5), 000565. https://doi.org/10.1099/mgen.0.000565 (2021).CAS 
Article 
PubMed Central 

Google Scholar 
Rohmer, C. & Wolz, C. The role of hlb-converting bacteriophages in Staphylococcus aureus host adaption. Microb. Physiol. 31 109–122. https://doi.org/10.1159/000516645 (2021).
PubMed 
Article 

Google Scholar 
Senghore, M. et al. Transmission of Staphylococcus aureus from humans to green monkeys in The Gambia as revealed by whole-genome sequencing. Appl. Environ. Microbiol. 82, 5910–5917 (2016).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Xue, H., Lu, H. & Zhao, X. Sequence diversities of serine-aspartate repeat genes among Staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer. PLoS ONE 6, e20332 (2011).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Paharik, A. E. et al. The Spl serine proteases modulate protein production and virulence in a rabbit model of pneumonia. mSphere 1, e00208-16 (2016).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Wein, T., Hülter, N. F., Mizrahi, I. & Dagan, T. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nat. Commun. 10, 2595 (2019).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Cheng, A. G., Missiakas, D. & Schneewind, O. The giant protein Ebh is a determinant of Staphylococcus aureus cell size and complement resistance. J. Bacteriol. 196, 971–981 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Lin, Y.-C. et al. Staphylococcal phosphatidylinositol-specific phospholipase C potentiates lung injury via complement sensitisation. Cell. Microbiol. 21, e13085 (2019).PubMed 

Google Scholar 
Siboo, I. R., Chambers, H. F. & Sullam, P. M. Role of SraP, a serine-rich surface protein of Staphylococcus aureus, in binding to human platelets. Infect. Immun. 73, 2273–2280 (2005).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Nakamura, Y. et al. Phosphatidylinositol-specific phospholipase C enhances epidermal penetration by Staphylococcus aureus. Sci. Rep. 10, 17845 (2020).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Peng, X. et al. Flight is the key to postprandial blood glucose balance in the fruit bats Eonycteris spelaea and Cynopterus sphinx. Ecol. Evol. 7, 8804–8811 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, e00088-17 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Pence, M. A. et al. Beta-lactamase repressor BlaI modulates Staphylococcus aureus cathelicidin antimicrobial peptide resistance and virulence. PLoS ONE 10, e0136605 (2015).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Raafat, D. et al. Molecular epidemiology of methicillin-susceptible and methicillin-resistant Staphylococcus aureus in wild, captive and laboratory rats: Effect of habitat on the nasal S. aureus population. Toxins 12, 80 (2020).CAS 
PubMed Central 
Article 

Google Scholar 
National Library of Medicine (US), National Center for Biotechnology Information. Genbank. (1982).PubMLST—Public databases for molecular typing and microbial genome diversity. https://pubmlst.org/.Wick, R. R., Judd, L. M. & Holt, K. E. Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS Comput. Biol. 14, e1006583 (2018).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).ADS 
Article 
CAS 
PubMed 
PubMed Central 

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

Google Scholar 
Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data (2010).Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).MathSciNet 
CAS 
PubMed 
PubMed Central 
Article 

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

Google Scholar 
Seeman, T. MLST. Github https://github.com/tseemann/mlst.Page, A. J. et al. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Seeman, T. Snippy: Fast Bacterial Variant Calling from NGS Reads (2015).Carver, T., Harris, S. R., Berriman, M., Parkhill, J. & McQuillan, J. A. Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28, 464–469 (2012).CAS 
PubMed 
Article 

Google Scholar 
Sievers, F. & Higgins, D. G. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci. 27, 135–145 (2018).CAS 
PubMed 
Article 

Google Scholar 
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2—A multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Seeman, T. Abricate; Mass screening of contigs for antimicrobial resistance or virulence genes. Github https://github.com/tseemann/abricate.Feldgarden, M. et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob. Agents Chemother. 63, e00483-19 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chen, L., Zheng, D., Liu, B., Yang, J. & Jin, Q. VFDB 2016: Hierarchical and refined dataset for big data analysis–10 years on. Nucleic Acids Res. 44, D694–D697 (2016).CAS 
PubMed 
Article 

Google Scholar 
Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Gupta, S. K. et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob. Agents Chemother. 58, 212–220 (2014).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Arndt, D., Marcu, A., Liang, Y. & Wishart, D. S. PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Brief. Bioinform. 20, 1560–1567 (2019).CAS 
PubMed 
Article 

Google Scholar 
Antipov, D. et al. plasmidSPAdes: Assembling plasmids from whole genome sequencing data. Bioinformatics https://doi.org/10.1093/bioinformatics/btw493 (2016).Article 
PubMed 

Google Scholar 
Robertson, J. & Nash, J. H. E. MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb. Genom. 4(8), e000206. https://doi.org/10.1099/mgen.0.000206 (2018).CAS 
Article 

Google Scholar 
Jaillard, M. et al. A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet. 14, e1007758 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar  More