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    Effects of oceanographic environment on the distribution and migration of Pacific saury (Cololabis saira) during main fishing season

    NPFC. 8th Meeting of the Small Scientific Committee on Pacific Saury Report. NPFC-2021-SSC PS08-Final Report. Preprint at https://www.npfc.int/meetings/8th-ssc-ps-meeting (2021).Hubbs, C. L. & Wisner, R. L. Revision of the sauries (Pisces, Scomberesocidae) with descriptions of two new genera and one new species. Fish. Bull. 77, 521–566 (1980).
    Google Scholar 
    Tian, Y., Akamine, T. & Suda, M. Variations in the abundance of Pacific saury (Cololabis saira) from the northwestern Pacific in relation to oceanic-climate changes. Fish. Res. 60, 439–454 (2003).Article 

    Google Scholar 
    Huang, W. B. Comparisons of monthly and geographical variations in abundance and size composition of Pacific saury between the high-seas and coastal fishing grounds in the northwestern Pacific. Fish. Sci. 76, 21–31 (2010).CAS 
    Article 

    Google Scholar 
    Watanabe, Y., Builer, J. L. & Mori, T. Growth of Pacific saury, Cololabis saira, in the northeastern and northwestern Pacific Ocean. Fish. Bull. 86, 489–498 (1988).
    Google Scholar 
    Nakaya, M. et al. Growth and maturation of Pacific saury Cololabis saira under laboratory conditions. Fish. Sci. 76, 45–53 (2010).CAS 
    Article 

    Google Scholar 
    Kosaka, S. Life history of Pacific saury Cololabis saira in the Northwest Pacific and consideration of resource fluctuation based on it. Bull. Tohoku Natl. Fish. Res. Inst. 63, 1–96 (2000).
    Google Scholar 
    Suyama, S. Study on the age, growth, and maturation process of Pacific saury Cololabis saira (Brevoort) in the north Pacific. Bull. Fish. Res. Agen. 5, 68–113 (2002).
    Google Scholar 
    Huang, W. B., Lo, N. C. H., Chiu, T. S. & Chen, C. S. Geographical distribution and abundance of Pacific saury fishing stock in the Northwestern Pacific in relation to sea temperature. Zool. Stud. 46, 705–716 (2007).
    Google Scholar 
    Liu, S. et al. Using novel spawning ground indices to analyze the effects of climate change on Pacifc saury abundance. J. Mar. Syst. 191, 13–23 (2019).Article 

    Google Scholar 
    Tian, Y., Akamine, T. & Suda, M. Long-term variability in the abundance of Pacific Saury in the Northwestern Pacific Ocean and climate changes during the last century. Bull. Jpn. Soc. Fish. Oceanogr. 66, 16–25 (2002).
    Google Scholar 
    Tian, Y., Ueno, Y., Suda, M. & Akamine, T. Decadal variability in the abundance of Pacific saury and its response to climatic/oceanic regime shifts in the northwestern subtropical Pacific during the last half century. J. Mar. Syst. 52, 235–257 (2004).Article 

    Google Scholar 
    Yasuda, I. & Watanabe, T. Chlorophyll a variation in the Kuroshio Extension revealed with a mixed-layer tracking float: Implication on the long-term change of Pacific saury (Cololabis saira). Fish. Oceanogr. 16, 482–488 (2007).Article 

    Google Scholar 
    Fuji, T., Kurita, Y., Suyama, S. & Ambe, D. Estimating the spawning ground of Pacific saury Cololabis saira by using the distribution and geographical variation in maturation status of adult fish during the main spawning season. Fish. Oceanogr. 30, 382–396 (2020).Article 

    Google Scholar 
    Yasuda, I. & Watanabe, Y. On the relationship between the Oyashio front and saury fishing grounds in the northewestern Pacific: A forecasting method for fishing ground locations. Fish. Oceanogr. 3, 172–181 (1994).Article 

    Google Scholar 
    Kuroda, H. & Yokouchi, K. Interdecadal decrease in potential fishing areas for Pacific saury off the southeastern coast of Hokkaido, Japan. Fish. Oceanogr. 26, 439–454 (2017).Article 

    Google Scholar 
    Fukushima, S. Synoptic analysis of migration and fishing conditions of saury in the northwestern Pacific Ocean. Bull. Tohoku. Reg. Fish. Res. Lab 41, 1–70 (1979).
    Google Scholar 
    Sugisaki, H. & Kurita, Y. Daily rhythm and seasonal variation of feeding habit of Pacific saury (Cololabis saira) in relation to their migration and oceanographic conditions off Japan. Fish. Oceanogr. 13, 63–73 (2004).Article 

    Google Scholar 
    Huang, W. B. & Huang, Y. C. Maturity characteristics of Pacific saury during fishing season in the Northwest pacific. J. Mar. Sci. Tech. 23, 819–826 (2015).
    Google Scholar 
    Tseng, C. T. et al. Influence of climate-driven sea surface temperature increase on potential habitats of the Pacific saury (Cololabis saira). ICES J. Mar. Sci. 68, 1105–1113 (2011).Article 

    Google Scholar 
    Tseng, C. T. et al. Sea surface temperature fronts affect distribution of Pacific saury (Cololabis saira) in the Northwestern Pacific Ocean. Deep Sea Res II Top. Stud. Oceanogr. 107, 15–21 (2014).ADS 
    Article 

    Google Scholar 
    Hua, C., Li, F., Zhu, Q., Zhu, G. & Meng, L. Habitat suitability of Pacific saury (Cololabis saira) based on a yield-density model and weighted analysis. Fish. Res. 221, 105408. https://doi.org/10.1016/j.fishres.2019.105408 (2020).Article 

    Google Scholar 
    Mugo, R., Saitoh, S. I., Nihira, A. & Kuroyama, T. Habitat characteristics of skipjack tuna (Katsuwonus pelamis) in the western North Pacific: A remote sensing perspective. Fish. Oceanogr. 19, 382–396 (2010).Article 

    Google Scholar 
    Yu, W., Chen, X., Chen, Y., Yi, Q. & Zhang, Y. Effects of environmental variations on the abundance of western winter-spring cohort of neon flying squid (Ommastrephes bartramii) in the Northwest Pacific Ocean. Acta Oceanol. Sin. 34, 43–51 (2015).CAS 
    Article 

    Google Scholar 
    Kakehi, S. et al. Forecasting Pacific saury (Cololabis saira) fishing grounds off Japan using a migration model driven by an ocean circulation model. Ecol. Model. 431, 109150. https://doi.org/10.1016/j.ecolmodel.2020.109150 (2020).Article 

    Google Scholar 
    Swain, D. P. & Wade, E. J. Spatial distribution of catch and effort in a fishery for snow crab (Chionoecetes opilio): Tests of predictions of the ideal free distribution. Can. J. Fish. Aquat. Sci. 60, 897–909 (2003).Article 

    Google Scholar 
    Chang, Y. J. et al. Modelling the impacts of environmental variation on habitat suitability for Pacific saury in the Northwestern Pacific Ocean. Fish. Oceanogr. 28, 291–304 (2018).Article 

    Google Scholar 
    Bakun, A. Fronts and eddies as key structures in the habitat of marine fish larvae: Opportunity, adaptive response and competitive advantage. Sci. Mar. 70, 105–122 (2006).Article 

    Google Scholar 
    Oozeki, Y., Watanabe, Y. & Kitagawa, D. Environmental factors affecting larval growth of Pacific saury, Cololabis saira, in the northwestern Pacific Ocean. Fish. Oceanogr. 13, 44–53 (2004).Article 

    Google Scholar 
    Ito, S. I. et al. Initial design for a fish bioenergetics model of Pacific saury coupled to a lower trophic ecosystem model. Fish. Oceanogr. 13, 111–124 (2004).Article 

    Google Scholar 
    Miyamoto, H. et al. Geographic variation in feeding of Pacific saury Cololabis saira in June and July in the North Pacific Ocean. Fish. Oceanogr. 29, 558–571 (2020).CAS 
    Article 

    Google Scholar 
    Tseng, C. T. et al. Spatial and temporal variability of the Pacific saury (Cololabis saira) distribution in the northwestern Pacific Ocean. ICES J. Mar. Sci. 70, 991–999 (2013).Article 

    Google Scholar 
    Ichii, T. et al. Oceanographic factors affecting interannual recruitment variability of Pacific saury (Cololabis saira) in the central and western North Pacific. Fish. Oceanogr. 27, 445–457 (2018).Article 

    Google Scholar 
    Coletto, J. L., Pinho, M. P. & Madureira, L. S. P. Operational oceanography applied to skipjack tuna (Katsuwonus pelamis) habitat monitoring and fishing in south-western Atlantic. Fish. Oceanogr. 28, 82–93 (2018).Article 

    Google Scholar 
    Shi, Y., Zhu, Q., Hua, C. & Zhang, Y. Evaluation of saury stick-held net performance between model test and on-sea measurements. Haiyang Xuebao 41, 123–133 (2019).CAS 

    Google Scholar 
    Semedi, B., Saitoh, S., Saitoh, K. & Yoneta, K. Application of multi-sensor satellite remote sensing for determining distribution and movement of Pacific saury, Cololabis saira. Fish. Sci. 68, 1781–1784 (2002).Article 

    Google Scholar 
    Syah, A. F., Saitoh, S. I., Alabia, I. D. & Hirawake, T. Detection of potential fishing zone for Pacific saury (Cololabis saira) using generalized additive model and remotely sensed data. IOP Conf. Ser. Earth Env. Sci. 54, 012074. https://doi.org/10.1088/1755-1315/54/1/012074 (2017).Article 

    Google Scholar 
    Xing, Q. et al. Application of a fish habitat model considering mesoscale oceanographic features in evaluating climatic impact on distribution and abundance of Pacific saury (Cololabis saira). Prog. Oceanogr. 201, 102743. https://doi.org/10.1016/j.pocean.2022.102743 (2022).Article 

    Google Scholar 
    Tittensor, D. P. et al. Global patterns and predictors of marine biodiversity across taxa. Nature 466, 1098–1101 (2010).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Prants, S. V., Budyansky, M. V. & Uleysky, M. Y. Identifying Lagrangian fronts with favourable fishery conditions. Deep Sea Res. Part I Oceanogr. Res. Pap. 90, 27–35 (2014).ADS 
    Article 

    Google Scholar 
    Saito, H., Tsuda, A. & Kasai, H. Nutrient and plankton dynamics in the Oyashio region of the western subarctic Pacific Ocean. Deep Sea Res. II Top. Stud. Oceanogr. 49, 5463–5486 (2002).ADS 
    CAS 
    Article 

    Google Scholar 
    Watanabe, Y., Kurita, Y., Noto, M., Oozeki, Y. & Kitagawa, D. Growth and survival of Pacific Saury Cololabis saira in the Kuroshio-Oyashio transitional waters. J. Oceanogr. 59, 403–414 (2003).Article 

    Google Scholar 
    Bakun, A. Ocean eddies, predator pits and bluefin tuna: Implications of an inferred ‘low risk-limited payoff’ reproductive scheme of a (former) archetypical top predator. Fish Fish. 14, 424–438 (2013).Article 

    Google Scholar 
    Iwahashi, M., Isoda, Y., Ito, S. I., Oozeki, Y. & Suyama, S. Estimation of seasonal spawning ground locations and ambient sea surface temperatures for eggs and larvae of Pacific saury (Cololabis saira) in the western North Pacific. Fish. Oceanogr. 15, 128–138 (2006).Article 

    Google Scholar 
    Oozeki, Y., Okunishi, T., Takasuka, A. & Ambe, D. Variability in transport processes of Pacific saury Cololabis saira larvae leading to their broad dispersal: Implications for their ecological role in the western North Pacific. Prog. Oceanogr. 138, 448–458 (2015).ADS 
    Article 

    Google Scholar 
    Polovina, J. J., Kleiber, P. & Kobayashi, D. R. Application of TOPEX-Poseidon satellite altimetry to simulate transport dynamics of larvae of spiny lobster, Panulirus marginatus, in the Northwestern Hawaiian Islands, 1993–1996. Fish. Bull. 97, 132–143 (1999).
    Google Scholar 
    Kawai, H. Hydrography of the Kuroshio extension. In Kuroshio—Its Physical Aspects (eds Stommel, H. & Yoshida, K.) 235–352 (University of Tokyo, 1972).
    Google Scholar 
    Yamada, F. & Sekine, Y. Variations in sea surface temperature and 500 hPa height over the north Pacific with reference to the occurrence of anomalous southward Oyashio intrusion east of Japan. J. Meteorol. Soc Jpn. Ser. II 75, 995–1000 (1997).Article 

    Google Scholar 
    Ellis, N., Smith, S. J. & Pitcher, C. R. Gradient forests: Calculating importance gradients on physical predictors. Ecology 93, 156–168 (2012).PubMed 
    Article 

    Google Scholar 
    Hastie, T. J. & Tibshirani, R. J. Generalized additive models. Stat. Sci. 1, 297–310 (1986).MathSciNet 
    MATH 

    Google Scholar 
    Litzow, M. A., Hobday, A. J., Frusher, S. D., Dann, P. & Tuck, G. N. Detecting regime shifts in marine systems with limited biological data: An example from southeast Australia. Prog. Oceanogr. 141, 96–108 (2016).ADS 
    Article 

    Google Scholar 
    Pang, Y. et al. Variability of coastal cephalopods in overexploited China Seas under climate change with implications on fisheries management. Fish. Res. 208, 22–33 (2018).Article 

    Google Scholar  More

  • in

    A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

    Lee, J.-W. & McKibbin, W. J. Globalization and disease: the case of SARS. Asian Economic Pap. 3, 113–131 (2004).Article 

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

    Google Scholar 
    Peiris, J. S. M., Guan, Y. & Yuen, K. Y. Severe acute respiratory syndrome. Nat. Med. 10, S88–S97 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Raj, V. S., Osterhaus, A. D. M. E., Fouchier, R. A. M. & Haagmans, B. L. MERS: emergence of a novel human coronavirus. Curr. Opin. Virol. 5, 58–62 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhou, P. et al. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature 556, 255–258 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Zhou, L. et al. The re-emerging of SADS-CoV infection in pig herds in Southern China. Transbound. Emerg. Dis. 66, 2180–2183 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dong, E., Du, H. & Gardner, L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. 20, 533–534 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Daszak, P., Keusch, G. T., Phelan, A. L., Johnson, C. K. & Osterholm, M. T. Infectious disease threats: a rebound to resilience. Health Aff. 40, 204–211 (2021).Article 

    Google Scholar 
    Anthony, S. J. et al. Further evidence for bats as the evolutionary source of Middle East respiratory syndrome coronavirus. mBio 8, e00373-17 (2017).Li, W. D. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679 (2005).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Wang, L. F. & Eaton, B. T. In Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission (eds J. E. Childs, J. S. Mackenzie, & J. A. Richt) 325–344 (Springer Berlin Heidelberg, 2007).Dudas, G., Carvalho, L. M., Rambaut, A. & Bedford, T. MERS-CoV spillover at the camel-human interface. eLife 7, e31257 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ge, X. Y. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535–538 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Menachery, V. D. et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat. Med. 21, 1508–1513 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Menachery, V. D. et al. SARS-like WIV1-CoV poised for human emergence. Proc. Natl Acad. Sci. USA 113, 3048–3053 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Li, H. et al. Human-animal interactions and bat coronavirus spillover potential among rural residents in Southern China. Biosaf. Health 1, 84–90 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, N. et al. Serological evidence of bat SARS-related coronavirus infection in humans, China. Virologica Sin. 33, 104–107 (2018).Article 

    Google Scholar 
    Wasik, B. R. et al. Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover? Philos. Trans. R. Soc. Lond. Ser. B, Biol. Sci. 374, 20190017 (2019).CAS 
    Article 

    Google Scholar 
    Parrish, C. R. et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol. Mol. Biol. Rev. 72, 457–470 (2008).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lloyd-Smith, J. O. et al. Epidemic dynamics at the human-animal interface. Science 326, 1362–1367 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Gray, G. C., Robie, E. R., Studstill, C. J. & Nunn, C. L. Mitigating future respiratory virus pandemics: new threats and approaches to consider. Viruses 13, 637 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Latinne, A. et al. Origin and cross-species transmission of bat coronaviruses in China. Nat. Commun. 11, 4235 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    McFarlane, R., Sleigh, A. & McMichael, T. Synanthropy of wild mammals as a determinant of emerging infectious diseases in the Asian-Australasian region. EcoHealth 9, 24–35 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hu, B. et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLOS Pathog. 13, e1006698 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    IUCN. The IUCN Red List of Threatened Species. Version 2021-1, https://www.iucnredlist.org (2021).Ruiz-Aravena, M. et al. Ecology, evolution and spillover of coronaviruses from bats. Nat. Rev. Microbiol. 20, 299–314 (2022).CAS 
    PubMed 
    Article 

    Google Scholar 
    Coker, R. J., Hunter, B. M., Rudge, J. W., Liverani, M. & Hanvoravongchai, P. Emerging infectious diseases in southeast Asia: regional challenges to control. Lancet 377, 599–609 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Horby, P. W., Pfeiffer, D. & Oshitani, H. Prospects for emerging infections in East and Southeast Asia 10 years after severe acute respiratory syndrome. Emerg. Infect. Dis. 19, 853–860 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wacharapluesadee, S. et al. Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nat. Commun. 12, 972 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Rulli, M. C., D’Odorico, P., Galli, N. & Hayman, D. T. S. Land-use change and the livestock revolution increase the risk of zoonotic coronavirus transmission from rhinolophid bats. Nat. Food 2, 409–416 (2021).CAS 
    Article 

    Google Scholar 
    Delaune, D. et al. A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nat. Commun. 12, 6563 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Zhou, H. et al. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell 184, 4380–4391 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    World Health Organization. WHO-convened global study of origins of SARS-CoV-2: China Part. (2021).Holmes, E. C. et al. The origins of SARS-CoV-2: a critical review. Cell 184, 4848–4856 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brooks, T. M. et al. Measuring terrestrial Area of Habitat (AOH) and its utility for the IUCN Red List. Trends Ecol. Evol. 34, 977–986 (2019).PubMed 
    Article 

    Google Scholar 
    Hosseini, P. R. et al. Does the impact of biodiversity differ between emerging and endemic pathogens? The need to separate the concepts of hazard and risk. Philos. Trans. R. Soc. B: Biol. Sci. 372, 20160129 (2017).Article 

    Google Scholar 
    Dobson, A. P. et al. Ecology and economics for pandemic prevention. Science 369, 379–381 (2020).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Petrovan, S. O. et al. Post COVID-19: a solution scan of options for preventing future zoonotic epidemics. Biol. Rev. 96, 2694–2715 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Roche, B. et al. Was the COVID-19 pandemic avoidable? A call for a “solution-oriented” approach in pathogen evolutionary ecology to prevent future outbreaks. Ecol. Lett. 23, 1557–1560 (2020).PubMed 
    Article 

    Google Scholar 
    Naguib, M. M., Ellström, P., Järhult, J. D., Lundkvist, Å. & Olsen, B. Towards pandemic preparedness beyond COVID-19. Lancet Microbe 1, e185–e186 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Muylaert, R. L. et al. Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health. Proc. Roy. Soc. B., 289, 20220397 (2022).Carroll, D. et al. The global virome project. Science 359, 872–874 (2018).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Zhou, H. et al. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Curr. Biol. 30, 2196–2203.e2193 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Li, L.-L. et al. A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China. Emerg. Microbes Infect. 10, 1683–1690 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pormohammad, A. et al. Comparison of confirmed COVID-19 with SARS and MERS cases – Clinical characteristics, laboratory findings, radiographic signs and outcomes: A systematic review and meta-analysis. Rev. Med. Virol. 30, e2112 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brehm, T. T. et al. Comparison of clinical characteristics and disease outcome of COVID-19 and seasonal influenza. Sci. Rep. 11, 5803 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Wolfe, N. D., Dunavan, C. P. & Diamond, J. Origins of major human infectious diseases. Nature 447, 279–283 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Wolfe, N. D. et al. Emergence of unique primate T-lymphotropic viruses among central African bushmeat hunters. Proc. Natl Acad. Sci. USA 102, 7994–7999 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Nikolay, B. et al. Transmission of Nipah virus—14 Years of investigations in Bangladesh. N. Engl. J. Med. 380, 1804–1814 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Byrne, A. W. et al. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases. BMJ Open 10, e039856 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wolfe, N. D. et al. Naturally acquired simian retrovirus infections in central African hunters. Lancet 363, 932–937 (2004).PubMed 
    Article 

    Google Scholar 
    Mildenstein, T., Tanshi, I. & Racey, P. A. Exploitation of bats for bushmeat and medicine. In Bats in the Anthropocene: Conservation of Bats in a Changing World (eds Voigt, C. C. & Kingston, T.) Ch. 12, 325–375 (Springer International Publishing, 2016).Low, M.-R. et al. Bane or blessing? Reviewing cultural values of bats across the Asia-Pacific region. J. Ethnobiol. 41, 18–34 (2021).Article 

    Google Scholar 
    Kingston, T. Cute, creepy, or crispy—How values, attitudes, and norms shape human behavior toward bats. In Bats in the Anthropocene: Conservation of Bats in a Changing World (eds Voigt, C. C. & Kingston, T.) 571–595 (Springer International Publishing, 2016).Li, H. et al. Knowledge, attitude, and practice regarding zoonotic risk in wildlife trade, Southern China. EcoHealth 18, 95–106 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jung, K. & Threlfall, C. G. Urbanisation and its effects on bats—A global meta-analysis. In Bats in the Anthropocene: Conservation of Bats in a Changing World (eds Voigt, C. C. & Kingston, T.) Ch. 2, 13–33 (Springer International Publishing, 2016).Latinne, A. et al. Characterizing and quantifying the wildlife trade network in Sulawesi, Indonesia. Glob. Ecol. Conserv. 21, e00887 (2020).Article 

    Google Scholar 
    Huong, N. Q. et al. Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013–2014. PLOS ONE 15, e0237129 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Virachith, S. et al. Low seroprevalence of COVID-19 in Lao PDR, late 2020. Lancet Regional Health – West. Pac. 13, 100197 (2021).Article 

    Google Scholar 
    Letko, M., Seifert, S. N., Olival, K. J., Plowright, R. K. & Munster, V. J. Bat-borne virus diversity, spillover and emergence. Nat. Rev. Microbiol. 18, 461–471 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Swadling, L. et al. Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2. Nature 601, 110–117 (2022).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Liu, K. et al. Binding and molecular basis of the bat coronavirus RaTG13 virus to ACE2 in humans and other species. Cell 184, 3438–3451.e3410 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Le Bert, N. et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 584, 457–462 (2020).PubMed 
    Article 
    CAS 

    Google Scholar 
    Philavong, C. et al. Perception of health risks in Lao market vendors. Zoonoses Public Health 67, 796–804 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Carlson, C. J. et al. The future of zoonotic risk prediction. Philos. Trans. R. Soc. B: Biol. Sci. 376, 20200358 (2021).CAS 
    Article 

    Google Scholar 
    Bell, D., Roberton, S. & Hunter, P. R. Animal origins of SARS coronavirus: possible links with the international trade in small carnivores. Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci. 359, 1107–1114 (2004).Article 

    Google Scholar 
    He, J. F. et al. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science 303, 1666–1669 (2004).CAS 
    Article 
    ADS 

    Google Scholar 
    Tu, C. et al. Antibodies to SARS-Coronavirus in Civets. Emerg. Infect. Dis. 10, 2244–2248 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Guan, Y. et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China. Science 302, 276–278 (2003).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Freuling, C. et al. Susceptibility of raccoon dogs for experimental SARS-CoV-2 infection. Emerg. Infect. Dis. 26, 2982–2985 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    OIE-World Organisation for Animal Health. Infection with SARS-CoV-2 in animals. https://www.oie.int/app/uploads/2021/11/en-factsheet-sars-cov-2-20211025.pdf (2021).Oreshkova, N. et al. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020. Eurosurveillance 25, 2001005 (2020).PubMed Central 
    Article 

    Google Scholar 
    Oude Munnink, B. B. et al. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science 371, 172–177 (2021).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Daszak, P. et al. Workshop Report on Biodiversity and Pandemics of the Intergovernmental Platform on Biodiversity and Ecosystem Services. (Bonn, Germany, 2020).Chinese Academy of Engineering. Report on sustainable development strategy of China’s wildlife farming industry. (2017).Becker, D. J. et al. Optimising predictive models to prioritise viral discovery in zoonotic reservoirs. The Lancet Microbe, https://doi.org/10.1016/S2666-5247(21)00245-7 (2022).Wacharapluesadee, S. et al. Longitudinal study of age-specific pattern of coronavirus infection in Lyle’s flying fox (Pteropus lylei) in Thailand. Virol. J. 15, 38 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Luo, Y. et al. Longitudinal surveillance of Betacoronaviruses in fruit bats in Yunnan Province, China during 2009–2016. Virologica Sin. 33, 87–95 (2018).CAS 
    Article 

    Google Scholar 
    Maganga, G. D. et al. Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon. Sci. Rep. 10, 7314 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    Epstein, J. H. et al. Nipah virus dynamics in bats and implications for spillover to humans. Proc. Natl Acad. Sci. USA 117, 29190 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Thompson, C. W. et al. Preserve a voucher specimen! The critical need for integrating natural history collections in infectious disease studies. mBio 12, e02698–02620 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Phelps, K. L. et al. Bat research networks and viral surveillance: gaps and opportunities in Western Asia. Viruses 11, 240 (2019).PubMed Central 
    Article 

    Google Scholar 
    Gibb, R. et al. Zoonotic host diversity increases in human-dominated ecosystems. Nature 584, 398–402 (2020).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    Robertson, K. et al. Rabies-related knowledge and practices among persons at risk of bat exposures in Thailand. Plos Negl. Trop. Dis. 5, e1054 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wacharapluesadee, S. et al. Group C Betacoronavirus in bat guano fertilizer, Thailand. Emerg. Infect. Dis. 19, 1349–1352 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Suwannarong, K. et al. Risk factors for bat contact and consumption behaviors in Thailand; a quantitative study. BMC Public Health 20, 841 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Valitutto, M. T. et al. Detection of novel coronaviruses in bats in Myanmar. PLoS ONE 15, e0230802 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Phelps, K., Jose, R., Labonite, M. & Kingston, T. Assemblage and species threshold responses to environmental and disturbance gradients shape bat diversity in disturbed cave landscapes. Diversity 10, 55 (2018).Article 

    Google Scholar 
    Quibod, M. N. R. M. et al. Diversity and threats to cave-dwelling bats in a small island in the southern Philippines. J. Asia-Pac. Biodivers. 12, 481–487 (2019).Article 

    Google Scholar 
    Furey, N. M. & Racey, P. A. Conservation ecology of cave bats. In Bats in the Anthropocene: Conservation of Bats in a Changing World (eds C. C. Voigt & T. Kingston) 463–500 (Springer International Publishing, 2016).Herkt, K. M. B., Skidmore, A. K. & Fahr, J. Macroecological conclusions based on IUCN expert maps: a call for caution. Glob. Ecol. Biogeogr. 26, 930–941 (2017).Article 

    Google Scholar 
    Jung, M. et al. A global map of terrestrial habitat types. Sci. Data 7, 256 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jung, M. et al. A global map of terrestrial habitat types (Version 001), https://doi.org/10.5281/zenodo.3666246 (2020).Faust, C. L. et al. Null expectations for disease dynamics in shrinking habitat: dilution or amplification. Philos. Trans. R. Soc. B: Biol. Sci. 372, 20160173 (2017).Article 

    Google Scholar 
    Redding, D. W., Moses, L. M., Cunningham, A. A., Wood, J. & Jones, K. E. Environmental-mechanistic modelling of the impact of global change on human zoonotic disease emergence: a case study of Lassa fever. Methods Ecol. Evol. 7, 646–655 (2016).Article 

    Google Scholar 
    Hassell, J. M. et al. Towards an ecosystem model of infectious disease. Nat. Ecol. Evol. 5, 907–918 (2021).PubMed 
    Article 

    Google Scholar 
    Winter, D. J. rentrez: An R package for the NCBI eUtils API. R. J. 9, 520–526 (2017).Article 

    Google Scholar 
    South, A. rworldmap: A New R package for Mapping Global Data. R. J. 3, 35–43 (2011).Article 

    Google Scholar 
    Olival, K. J. et al. Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: a case study of bats. PLOS Pathog. 16, e1008758 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Anthony, S. J. et al. Global patterns in coronavirus diversity. Virus Evolution 3, vex012 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Murakami, S. et al. Detection and characterization of Bat Sarbecovirus phylogenetically related to SARS-CoV-2, Japan. Emerg. Infect. Dis. 26, 3025–3029 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, L. et al. Multilocus phylogeny and species delimitation within the philippinensis group (Chiroptera: Rhinolophidae). Zoologica Scr. 47, 655–672 (2018).Article 

    Google Scholar 
    Wilson, D. E. & Mittermeier, R. A. Handbook of the Mammals of the World. Vol. 9. Bats. (Lynx Edicions, 2019).Srinivasulu, B. & Srinivasulu, C. In plain sight: Bacular and noseleaf morphology supports distinct specific status of Roundleaf Bats Hipposideros pomona Andersen, 1918 and Hipposideros gentilis Andersen, 1918 (Chiroptera: Hipposideridae). J. Threatened Taxa 10, 12018–12026 (2018).Article 

    Google Scholar 
    Rondinini, C. et al. Global habitat suitability models of terrestrial mammals. Philos. Trans. R. Soc. B: Biol. Sci. 366, 2633–2641 (2011).Article 

    Google Scholar 
    IUCN. Habitats Classification Scheme (Version 3.1), https://www.iucnredlist.org/resources/habitat-classification-scheme (2021).Williams, P. & Fong, Y. T. World Map of Carbonate Rock Outcrops v3.0 (ed The University of Auckland) (2010).Ross, N. fasterize: Fast Polygon to Raster Conversion. R package version 1.0.3 (2020).Hijmans, R. J. raster: Geographic Data Analysis and Modeling. R package version 3.4-5. (2020).Chamberlain, S. & Boettiger, C. R Python, and Ruby clients for GBIF species occurrence data. PeerJ Preprints 5, https://doi.org/10.7287/peerj.preprints.3304v1 (2017).Chamberlain, S. et al. rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.6.0 (2022).GBIF.org. GBIF Occurrence Download, https://doi.org/10.15468/dl.8w26d8 (2021).Feng, X. et al. A checklist for maximizing reproducibility of ecological niche models. Nat. Ecol. Evol. 3, 1382–1395 (2019).PubMed 
    Article 

    Google Scholar 
    Zizka, A. et al. CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods Ecol. Evol. 10, 744–751 (2019).Article 

    Google Scholar 
    WorldPop. Unconstrained global mosaic 2020 (1km resolution), https://doi.org/10.5258/SOTON/WP00647 (2018).Greenberg, J. A. & Mattiuzzi, M. gdalUtils: Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities. R package version 2.0.3.2. (2020).Carnell, R. lhs: Latin Hypercube Samples. R package version 1.1.1. (2020).Signorell, A. et al. DescTools: Tools for Descriptive Statistics v. 0.99.41 (2021).Delignette-Muller, M. L. & Dutang, C. fitdistrplus: an R Package for fitting distributions. J. Stat. Softw. 64, 1–34 (2015).Article 

    Google Scholar 
    Tan, C. W. et al. A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2–spike protein–protein interaction. Nat. Biotechnol. 38, 1073–1078 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Tang, F. et al. Lack of peripheral memory B cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study. J. Immunol. 186, 7264 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sobol, I. M. Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates. Math. Computers Simul. 55, 271–280 (2001).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Iooss, B., Da Veiga, S., Janon, A. & Pujol, G. sensitivity: Global Sensitivity Analysis of Model Outputs. R package version 1.25.0. (2021).Monod, H., Naud, C. & Makowski, D. Uncertainty and sensitivity analysis for crop models. In Working with Dynamic Crop Models: Evaluation, Analysis, Parameterization, and Applications (eds Wallach, D., Makowski, D. & Jones, J.) (Elsevier Science, 2006).Janon, A., Klein, T., Lagnoux, A., Nodet, M. & Prieur, C. Asymptotic normality and efficiency of two Sobol index estimators. ESAIM: Probab. Stat. 18, 342–364 (2014).MathSciNet 
    MATH 
    Article 

    Google Scholar  More

  • in

    Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas

    Roberson, L. A., Watson, R. A. & Klein, C. J. Over 90 endangered fish and invertebrates are caught in industrial fisheries. Nat. Commun. 11, 1–8 (2020).Article 
    CAS 

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

    Google Scholar 
    Dulvy, N. K. et al. Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Curr. Biol. 31, 1–15 (2021).Article 
    CAS 

    Google Scholar 
    MacNeil, M. A. et al. Global status and conservation potential of reef sharks. Nature 583, 801–806 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Dent, F. & Clarke, S. State of the global market for shark products. FAO Fish. Aquac. Tech. Pap. No. 590. 187 (2015).FAO. 2008. The State of World Fisheries and Aquaculture. Food and Agriculture Organization of the United Nations, Rome (2008).Davidson, L. N. K., Krawchuk, M. A. & Dulvy, N. K. Why have global shark and ray landings declined: improved management or over fishing? Fish Fish 17, 438–458 (2016).Article 

    Google Scholar 
    Clarke, S. C. et al. Global estimates of shark catches using trade records from commercial markets. Ecol. Lett. 9, 1115–1126 (2006).PubMed 
    Article 

    Google Scholar 
    Dulvy, N. K. et al. Extinction risk and conservation of the world’ s sharks and rays. Elife 3, 1–35 (2014).Article 

    Google Scholar 
    FAO. The State of World Fisheries and Aquaculture. Sustainability in action. Rome https://doi.org/10.4060/ca9229en (2020).Smith, H. et al. Ecology and the science of small-scale fisheries: A synthetic review of research effort for the Anthropocene. Biol. Conserv. 254, 108895 (2021).Article 

    Google Scholar 
    Worm, B. et al. Global catches, exploitation rates, and rebuilding options for sharks. Mar. Policy 40, 194–204 (2013).Article 

    Google Scholar 
    Queiroz, N. et al. Global spatial risk assessment of sharks under the footprint of fisheries. Nature 572, 461–466 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Leurs, G. et al. Industrial fishing near West African marine protected areas and its potential effects on mobile marine predators. Fron. Mar. Sci. 8, 1–13 (2021).ADS 

    Google Scholar 
    White, W. T. et al. Shark longline fishery of Papua New Guinea: Size and species composition and spatial variation of the catches. Mar. Freshw. Res. 71, 662–669 (2020).Article 

    Google Scholar 
    Jacquet, J. & Pauly, D. Funding priorities: Big barriers to small-scale fisheries. Conserv. Biol. 22, 832–835 (2008).PubMed 
    Article 

    Google Scholar 
    Moore, J. E. et al. An interview-based approach to assess marine mammal and sea turtle captures in artisanal fisheries. Biol. Conserv. 143, 795–805 (2010).Article 

    Google Scholar 
    Soykan, C. U. et al. Why study bycatch? An introduction to the Theme Section on fisheries bycatch. Endanger. Species Res. 5, 91–102 (2008).Article 

    Google Scholar 
    Haque, A. B. et al. Socio-ecological approach on the fishing and trade of rhino rays (Elasmobranchii: Rhinopristiformes) for their biological conservation in the Bay of Bengal, Bangladesh. Ocean Coast. Manag. 210, 105690 (2021).Article 

    Google Scholar 
    Barausse, A. et al. The role of fisheries and the environment in driving the decline of elasmobranchs in the nor-thern Adriatic Sea. ICES J. Mar. Sci. 71, 1593–1603 (2014).Article 

    Google Scholar 
    Pérez-Jiménez, J. C. & Mendez-Loeza, I. The small-scale shark fisheries in the southern Gulf of Mexico: Understanding their heterogeneity to improve their management. Fish. Res. 172, 96–104 (2015).Article 

    Google Scholar 
    Saidi, B., Enajjar, S. & Bradai, M. N. Elasmobranch captures in shrimps trammel net fishery off the Gulf of Gabès (Southern Tunisia, Mediterranean Sea). J. Appl. Ichthyol. 32, 421–426 (2016).Article 

    Google Scholar 
    Vögler, R., González, C. & Segura, A. M. Spatio-temporal dynamics of the fish community associated with artisanal fisheries activities within a key marine protected area of the Southwest Atlantic (Uruguay). Ocean Coast. Manag. 190, 105175 (2020).Dulvy, N. K. et al. Challenges and priorities in Shark and Ray conservation. Curr. Biol. 27, R565–R572 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Davidson, L. N. K. & Dulvy, N. K. Global marine protected areas to prevent extinctions. Nat. Ecol. Evol. 1, 1–6 (2017).Article 

    Google Scholar 
    Edgar, G. J. et al. Global conservation outcomes depend on marine protected areas with five key features. Nature 506, 216–220 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Giakoumi, S. et al. Ecological effects of full and partial protection in the crowded Mediterranean Sea: A regional meta-analysis. Sci. Rep. 7, 1–12 (2017).ADS 
    CAS 
    Article 

    Google Scholar 
    Grorud-Colvert, K. et al. The MPA Guide: A framework to achieve global goals for the ocean. Science 373, 6560 (2021).Article 
    CAS 

    Google Scholar 
    Di Franco, A. et al. Five key attributes can increase marine protected areas performance for small-scale fisheries management. Sci. Rep. 6, 38135 (2016).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Ban, N. C., Kushneryk, K., Falk, J., Vachon, A. & Sleigh, L. Improving compliance of recreational fishers with Rockfish Conservation Areas: community–academic partnership to achieve and evaluate conservation. ICES J. Mar. Sci. 77, 2308–2318 (2019).Di Lorenzo, M., Guidetti, P., Di Franco, A., Calò, A. & Claudet, J. Assessing spillover from marine protected areas and its drivers: A meta-analytical approach. Fish Fish. 15, 1–10 (2020).Belharet, M. et al. Extending full protection inside existing marine protected areas, or reducing fishing effort outside, can reconcile conservation and fisheries goals. J. Appl. Ecol. 57, 1948–1957 (2020).Article 

    Google Scholar 
    McCauley, D. J. et al. Marine defaunation: Animal loss in the global ocean. Science 347, 247–254 (2015).CAS 
    Article 

    Google Scholar 
    Di Franco, A. et al. Linking home ranges to protected area size: The case study of the Mediterranean Sea. Biol. Conserv. 221, 175–181 (2018).MacKeracher, T., Diedrich, A. & Simpfendorfer, C. A. Sharks, rays and marine protected areas: A critical evaluation of current perspectives. Fish Fish 20, 255–267 (2019).Article 

    Google Scholar 
    Ward-Paige, C. A., Keith, D. M., Worm, B. & Lotze, H. K. Recovery potential and conservation options for elasmobranchs. J. Fish. Biol. 80, 1844–1869 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lester, S. E. et al. Biological effects within no-take marine reserves: a global synthesis. MEPS 384, 33–46 (2009).ADS 
    Article 

    Google Scholar 
    O’Leary, B. C. et al. Addressing criticisms of large-scale marine protected areas. Bioscience 68, 359–370 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Collins, C. et al. Understanding persistent non-compliance in a remote, large-scale marine protected area. Front. Mar. Sci. 8, 1–13 (2021).ADS 
    Article 

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

    Google Scholar 
    Speed, C. W., Cappo, M. & Meekan, M. G. Evidence for rapid recovery of shark populations within a coral reef marine protected area. Biol. Conserv. 220, 308–319 (2018).Article 

    Google Scholar 
    Escalle, L. et al. Restricted movements and mangrove dependency of the nervous shark Carcharhinus cautus in nearshore coastal waters. J. Fish. Biol. 87, 323–341 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    O’Leary, B. C. et al. Effective coverage targets for ocean protection. Conserv. Lett. 9, 398–404 (2016).Article 

    Google Scholar 
    Guidetti, P., Danovaro, R., Bottaro, M. & Ciccolella, A. Marine protected areas and endangered shark conservation. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 2671–2672 (2021).Article 

    Google Scholar 
    Lubchenco, J. & Grorud-Colvert, K. Making waves: The science and politics of ocean protection. Science 350, 382–383 (2015).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Zupan, M. et al. Marine partially protected areas: drivers of ecological effectiveness. Front. Ecol. Environ. 16, 381–387 (2018).Article 

    Google Scholar 
    Dulvy, N. K., Allen, D. J., Ralph, G. M. & Walls, R. H. L. The Conservation Status of Sharks, Rays, and Chimaeras in the Mediterranean Sea. IUCN, Malaga, Spain. pp. 236 (2016).Morales-Muñiz, A. & Roselló, E. 20,000 years of fishing in the Strait: archaeological fish and shellfish assemblages from southern Iberia. In Human Impacts on Ancient Marine Ecysosytems: a Global Perspective (eds Torben, R. C. & Erlandson, J. M.), pp. 243–278 (University of California Press, Berkeley, 2008).Coll, M. et al. The biodiversity of the Mediterranean Sea: estimates, patterns, and threats. PLoS One 5, e11842 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Cashion, M. S., Bailly, N. & Pauly, D. Official catch data underrepresent shark and ray taxa caught in Mediterranean and Black Sea fisheries. Mar. Pol. 105, 1–9 (2019).Article 

    Google Scholar 
    Ferretti, F., Myers, R. A., Serena, F. & Lotze, H. K. Loss of large predatory sharks from the Mediterranean Sea. Conserv. Biol. 22, 952–964 (2008).PubMed 
    Article 

    Google Scholar 
    Colloca, F., Enea, M., Ragonese, S. & Di Lorenzo, M. A century of fishery data documenting the collapse of smooth-hounds (Mustelus spp.) in the Mediterranean Sea. Aquat. Conserv. Mar. Freshw. Ecosyst. 27, 1145–1155 (2017).Article 

    Google Scholar 
    Colloca, F., Carrozzi, V., Simonetti, A. & Lorenzo, M. D. Using local ecological knowledge of fishers to reconstruct abundance trends of Elasmobranch populations in the Strait of Sicily. Front. Mar. Sci. 7, 1–8 (2020).Article 

    Google Scholar 
    FAO. The State of World Fisheries and Aquaculture.Contributing to food security and nutrition for all. Rome. pp 200 (2016).Milazzo, M., Cattano, C., Al Mabruk, S. A. A. & Giovos, I. Mediterranean sharks and rays need action. Science 371, 355–356 (2021).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Claudet, J., Loiseau, C., Sostres, M. & Zupan, M. Underprotected marine protected areas in a global biodiversity hotspot. One Earth 2, 380–384 (2020).ADS 
    Article 

    Google Scholar 
    Maynou, F. et al. Estimating trends of population decline in long-lived marine species in the Mediterranean Sea based on fishers’ perceptions. PLoS One 6, e21818 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Serena, F. et al. Species diversity, taxonomy and distribution of Chondrichthyes in the Mediterranean and Black Sea. Eur. Zool. J. 87, 497–536 (2020).Article 

    Google Scholar 
    Morey, G., Moranta, J., Riera, F., Grau, A. M. & Morales-NIN, B. Elasmobranchs in trammel net fishery associated to marine reserves in the Balearic Islands (NW Mediterranean). Cybium 30, 125–132 (2006).
    Google Scholar 
    Temple, A. J. et al. Marine megafauna interactions with small-scale fisheries in the southwestern Indian Ocean: a review of status and challenges for research and management. Rev. Fish. Biol. Fish. 28, 89–115 (2018).Article 

    Google Scholar 
    Siskey, M. R., Shipley, O. N. & Frisk, M. G. Skating on thin ice: Identifying the need for species- ­ specific data and defined migration ecology of Rajidae spp. Fish Fish 20, 286–302 (2019).Article 

    Google Scholar 
    Chapman, D. D., Feldheim, K. A., Papastamatiou, Y. P. & Hueter, R. E. There and back again: a review of residency and return migrations in Sharks, with implications for population structure and management. Ann. Rev. Mar. Sci. 7, 547–570 (2015).PubMed 
    Article 

    Google Scholar 
    Heupel, M. R., Carlson, J. K. & Simpfendorfer, C. A. Shark nursery areas: Concepts, definition, characterization and assumptions. Mar. Ecol. Prog. Ser. 337, 287–297 (2007).ADS 
    Article 

    Google Scholar 
    Speed, C., Field, I., Meekan, M. & Bradshaw, C. Complexities of coastal shark movements and their implications for management. Mar. Ecol. Prog. Ser. 408, 275–293 (2010).ADS 
    Article 

    Google Scholar 
    Knip, D. M., Heupel, M. R. & Simpfendorfer, C. A. Mortality rates for two shark species occupying a shared coastal environment. Fish. Res. 125–126, 184–189 (2012).Article 

    Google Scholar 
    Espinoza, M., Farrugia, T. J. & Lowe, C. G. Habitat use, movements and site fidelity of the gray smooth-hound shark (Mustelus californicus Gill 1863) in a newly restored southern California estuary. J. Exp. Mar. Bio. Ecol. 401, 63–74 (2011).Article 

    Google Scholar 
    Myers, R. A. & Mertz, G. The limits of exploitation: A precautionary approach. Ecol. Appl. 8, 165–169 (1998).Article 

    Google Scholar 
    Ferretti, F., Osio, G., Jenkins, C., Rosenberg, A. A. & Lotze, H. K. Long-term change in a meso-predator community in response to prolonged and heterogeneous human impact. Sci. Rep. 3, 1057 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Lotze, H. K. et al. Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312, 1806–1809 (2006).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Di Lorenzo, M. et al. Ontogenetic trophic segregation between two threatened smooth ‑ hound sharks in the Central Mediterranean Sea. Sci. Rep. 10, 1–15 (2020).Article 
    CAS 

    Google Scholar 
    Mulas, A. et al. Resource partitioning among sympatric elasmobranchs in the central-western Mediterranean continental shelf. Mar. Biol. 166, 1–16 (2019).Article 

    Google Scholar 
    Silva, P. M., Teixeira, C. M., Pita, C., Cabral, H. N. & França, S. Portuguese artisanal fishers’ knowledge about Elasmobranchs—A case study. Front. Mar. Sci. 8, 1–9 (2021).
    Google Scholar 
    Cortés, E. & Brooks, E. N. Stock status and reference points for sharks using data-limited methods and life history. Fish Fish 19, 1110–1129 (2018).Article 

    Google Scholar 
    Prince, J. D. Gauntlet fisheries for elasmobranchs – The secret of sustainable shark fisheries. J. Northwest Atl. Fish. 37, 407–416 (2005).Article 

    Google Scholar 
    Booth, H., Squires, D. & Milner-Gulland, E. J. The neglected complexities of shark fisheries, and priorities for holistic risk-based management. Ocean Coast. Manag. 182, 104994 (2019).Article 

    Google Scholar 
    Juhel, J. B. et al. Reef accessibility impairs the protection of sharks. J. Appl. Ecol. 55, 673–683 (2018).Article 

    Google Scholar 
    Espinoza, M., Cappo, M., Heupel, M. R., Tobin, A. J. & Simpfendorfer, C. A. Quantifying shark distribution patterns and species-habitat associations: Implications of Marine Park zoning. PLoS One 9, e106885 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Cattano, C., Turco, G., Di Lorenzo, M., Visconti, G. & Milazzo, M. Sandbar shark aggregation in the central Mediterranean Sea and potential effects of tourism. Aquat. Conserv. Mar. Freshw. Ecosyst. 31, 1420–1428 (2021).Article 

    Google Scholar 
    O’Connell, C. P., Stroud, E. M. & He, P. The emerging field of electrosensory and semiochemical shark repellents: Mechanisms of detection, overview of past studies, and future directions. Ocean Coast. Manag. 97, 2–11 (2014).Article 

    Google Scholar 
    Barbato, M. et al. The use of fishers’ Local Ecological Knowledge to reconstruct fish behavioural traits and fishers’ perception of conservation relevance of elasmobranchs in the Mediterranean Sea. Mediterr. Mar. Sci. 22, 603–622 (2021).Article 

    Google Scholar 
    Gill, D. A. et al. Capacity shortfalls hinder the performance of marine protected areas globally. Nature 543, 665–669 (2017).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Booth, H., Squires, D. & Milner-Gulland, E. J. The mitigation hierarchy for sharks: A risk-based framework for reconciling trade-offs between shark conservation and fisheries objectives. Fish Fish 21, 269–289 (2020).Article 

    Google Scholar 
    Sala, E. et al. Author correction: protecting the global ocean for biodiversity, food and climate. Nature 592, 397–402 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Di Franco, A. et al. Improving marine protected area governance through collaboration and co-production. J. Environ. Manag. 269, 110757 (2020).Article 

    Google Scholar 
    Abràmoff, M. D., Magalhães, P. J. & Ram, S. J. Image processing with imageJ. Biophotonics Int 11, 36–41 (2004).
    Google Scholar 
    Froese, R., & Pauly, D. FishBase. https://www.fishbase.org (2021).Micheli, F. et al. Cumulative human impacts on Mediterranean and Black Sea marine ecosystems: assessing current pressures and opportunities. PLoS ONE 8, e79889 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Atwood, T. B. et al. Herbivores at the highest risk of extinction among mammals, birds, and reptiles. Sci. Adv. 6, eabb8458 (2020).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Munstermann, M. J. et al. A global ecological signal of extinction risk in terrestrial vertebrates. Cons. Biol. 36, 1–13 (2021).
    Google Scholar 
    Martin, T. G., Wintle, A., Rhodes, J. R., Field, A. & Low-choy, S. J. REVIEWS AND Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecol. Lett. 8, 1235–1246 (2005).PubMed 
    Article 

    Google Scholar 
    Rigby, R. A., Stasinopoulos, D. M. & Lane, P. W. Generalized additive models for location, scale and shape. J. R. Stat. Soc. Ser. C. Appl. Stat. 54, 507–554 (2005).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Wickham, H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org (2016).Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. 1, 3–14 (2010).Article 

    Google Scholar 
    Akaike, H. A new look at the Statistical Model Identification. IEEE Trans. Autom. Contr. 19, 716–723 (1974).ADS 
    MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Kariya, T. Institute of Mathematical Statistics is collaborating with JSTOR to digitize, preserve, and extend access to The Annals of Statistics. Ann. Stat. 19, 1403–1433, www.jstor.org (1991). ®.
    Google Scholar 
    Stasinopoulos, D. M. & Rigby, R. A. Generalized additive models for location scale and shape (GAMLSS) in R. J. Stat. Softw. 23, 1–46 (2007).Article 

    Google Scholar 
    Van Buuren, S. & Fredriks, M. Worm plot: A simple diagnostic device for modelling growth reference curves. Stat. Med. 20, 1259–1277 (2001).PubMed 
    Article 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. (2020).Legendre, P. & Legendre, L. Numerical ecology, 2nd English edn. Elsevier, Amsterdam (1998).Peres-Neto, P. R., Legendre, P., Dray, S. & Borcard, D. Variation partitioning of species data matrices: Estimation and comparison of fractions. Ecology 87, 2614–2625 (2006).PubMed 
    Article 

    Google Scholar 
    Oksanen, A. J. et al. Vegan: Community Ecology Package. R package Version 2.0-2 (2011). Available at: http://cran.r-project.org/. (2012).Di Lorenzo et al. Dataset1: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318878.v1 (2022).Di Lorenzo et al. Dataset2: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318881.v3 (2022).Di Lorenzo et al. Dataset3: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare. https://doi.org/10.6084/m9.figshare.18318884.v1 (2022).Di Lorenzo et al. Dataset4: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare. https://doi.org/10.6084/m9.figshare.18318887.v1 (2022).Di Lorenzo et al. Code1: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318875.v2 (2022).Di Lorenzo et al. Code2: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318890.v1 (2022).Di Lorenzo et al. Code3: Small-scale fisheries catch more threatened elasmobranchs inside partially protected areas than in unprotected areas. Figshare https://doi.org/10.6084/m9.figshare.18318893.v1 (2022). More

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    Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems

    van Elsas JD, Chiurazzi M, Mallon CA, Elhottovā D, Krištůfek V, Salles JF. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci USA 2012;109:1159–64.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bardgett RD, Van Der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.CAS 
    PubMed 
    Article 

    Google Scholar 
    George PB, Lallias D, Creer S, Seaton FM, Kenny JG, Eccles RM, et al. Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. Nat Commun. 2019;10:1–11.Article 
    CAS 

    Google Scholar 
    Delgado-Baquerizo M, Reich PB, Trivedi C, Eldridge DJ, Abades S, Alfaro FD, et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol. 2020;4:210–20.PubMed 
    Article 

    Google Scholar 
    Xiao E, Ning Z, Xiao T, Sun W, Jiang S. Soil bacterial community functions and distribution after mining disturbance. Soil Biol Biochem. 2021;157:108232.CAS 
    Article 

    Google Scholar 
    Jiao S, Zhang Z, Yang F, Lin Y, Chen W, Wei G. Temporal dynamics of microbial communities in microcosms in response to pollutants. Mol Ecol. 2017;26:923–36.CAS 
    PubMed 
    Article 

    Google Scholar 
    Fajardo C, Costa G, Nande M, Botías P, García-Cantalejo J, Martín M. Pb, Cd, and Zn soil contamination: monitoring functional and structural impacts on the microbiome. Appl Soil Ecol. 2019;135:56–64.Article 

    Google Scholar 
    Krabbenhoft DP, Sunderland EM. Global change and mercury. Science. 2013;341:1457–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Obrist D, Kirk JL, Zhang L, Sunderland EM, Jiskra M, Selin NE. A review of global environmental mercury processes in response to human and natural perturbations: Changes of emissions, climate, and land use. Ambio. 2018;47:116–40.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Amos HM, Jacob DJ, Streets DG, Sunderland EM. Legacy impacts of all-time anthropogenic emissions on the global mercury cycle. Global Biogeochem Cycles. 2013;27:410–21.CAS 
    Article 

    Google Scholar 
    Zhang L, Wong MH. Environmental mercury contamination in China: sources and impacts. Environ Int. 2007;33:108–21.CAS 
    PubMed 
    Article 

    Google Scholar 
    Müller AK, Westergaard K, Christensen S, Sørensen SJ. The effect of long-term mercury pollution on the soil microbial community. FEMS Microbiol Ecol. 2001;36:11–9.PubMed 
    Article 

    Google Scholar 
    Liu YR, Wang JJ, Zheng YM, Zhang LM, He JZ. Patterns of bacterial diversity along a long-term mercury-contaminated gradient in the paddy soils. Microb Ecol. 2014;68:575–83.CAS 
    PubMed 
    Article 

    Google Scholar 
    Liu YR, Delgado-Baquerizo M, Bi L, Zhu J, He JZ. Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China. Microbiome. 2018;6:183.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Li D, Li X, Tao Y, Yan Z, Ao Y. Deciphering the bacterial microbiome in response to long-term mercury contaminated soil. Ecotoxicol Environ Saf. 2022;229:113062.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zappelini C, Karimi B, Foulon J, Lacercat-Didier L, Maillard F, Valot B, et al. Diversity and complexity of microbial communities from a chlor-alkali tailings dump. Soil Biol Biochem. 2015;90:101–10.CAS 
    Article 

    Google Scholar 
    Baldrian P, in der Wiesche C, Gabriel J, Nerud F, Zadražil F. Influence of cadmium and mercury on activities of ligninolytic enzymes and degradation of polycyclic aromatic hydrocarbons by Pleurotus ostreatus in soil. Appl Environ Microbiol. 2000;66:2471–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Crane S, Dighton J, Barkay T. Growth responses to and accumulation of mercury by ectomycorrhizal fungi. Fungal Biol. 2010;114:873–80.CAS 
    PubMed 
    Article 

    Google Scholar 
    Johansen JL, Rønn R, Ekelund F. Toxicity of cadmium and zinc to small soil protists. Environ Pollut. 2018;242:1510–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wanner M, Birkhofer K, Fischer T, Shimizu M, Shimano S, Puppe D. Soil testate amoebae and diatoms as bioindicators of an old heavy metal contaminated floodplain in Japan. Microb Ecol. 2020;79:123–33.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhou Y, Sun B, Xie B, Feng K, Zhang Z, Zhang Z, et al. Warming reshaped the microbial hierarchical interactions. Glob Chang Biol. 2021;27:6331–47.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhao ZB, He JZ, Geisen S, Han LL, Wang JT, Shen JP, et al. Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils. Microbiome. 2019;7:33.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, et al. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev. 2018;42:293–323.CAS 
    PubMed 
    Article 

    Google Scholar 
    Jiang Y, Luan L, Hu K, Liu M, Chen Z, Geisen S, et al. Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences. Microbiome. 2020;8:1–14.CAS 
    Article 

    Google Scholar 
    Huang X, Wang J, Dumack K, Liu W, Zhang Q, He Y, et al. Protists modulate fungal community assembly in paddy soils across climatic zones at the continental scale. Soil Biol Biochem. 2021;160:108358.CAS 
    Article 

    Google Scholar 
    Grossmann L, Jensen M, Heider D, Jost S, Glücksman E, Hartikainen H, et al. Protistan community analysis: key findings of a large-scale molecular sampling. ISME J. 2016;10:2269–79.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jassey VE, Signarbieux C, Hättenschwiler S, Bragazza L, Buttler A, Delarue F, et al. An unexpected role for mixotrophs in the response of peatland carbon cycling to climate warming. Sci Rep. 2015;5:1–10.Article 
    CAS 

    Google Scholar 
    Thakur MP, Geisen S. Trophic regulations of the soil microbiome. Trends Microbiol. 2019;27:771–80.CAS 
    PubMed 
    Article 

    Google Scholar 
    Geisen S, Hu S, Dela Cruz TEE, Veen GFC. Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes. ISME J. 2021;15:618–21.CAS 
    PubMed 
    Article 

    Google Scholar 
    Guo S, Xiong W, Hang X, Gao Z, Jiao Z, Liu H, et al. Protists as main indicators and determinants of plant performance. Microbiome. 2021;9:64.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Feng X, Li P, Qiu G, Wang S, Li G, Shang L, et al. Human exposure to methylmercury through rice intake in mercury mining areas, Guizhou Province, China. Environ Sci Technol. 2008;42:326–32.CAS 
    PubMed 
    Article 

    Google Scholar 
    Meng M, Li B, Shao JJ, Wang T, He B, Shi JB, et al. Accumulation of total mercury and methylmercury in rice plants collected from different mining areas in China. Environ Pollut. 2014;184:179–86.CAS 
    PubMed 
    Article 

    Google Scholar 
    Liu YR, Dong JX, Zhang QG, Wang JT, Han LL, Zeng J, et al. Longitudinal occurrence of methylmercury in terrestrial ecosystems of the Tibetan Plateau. Environ Pollut. 2016;218:1342–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Walkley A, Black IA. An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Sci. 1934;37:29–38.CAS 
    Article 

    Google Scholar 
    Jones D, Willett V. Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biol Biochem. 2006;38:991–9.CAS 
    Article 

    Google Scholar 
    Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun. 2016;7:1–8.Article 
    CAS 

    Google Scholar 
    Gardes M, Bruns TD. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol. 1993;2:113–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner H-W, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.CAS 
    PubMed 
    Article 

    Google Scholar 
    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.CAS 
    PubMed 
    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. 2013;41:D590–D6.CAS 
    PubMed 
    Article 

    Google Scholar 
    Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019;47:D259–D64.CAS 
    PubMed 
    Article 

    Google Scholar 
    Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2013;41:D597–604.CAS 
    PubMed 
    Article 

    Google Scholar 
    Oliverio AM, Geisen S, Delgado-Baquerizo M, Maestre FT, Turner BL, Fierer N. The global-scale distributions of soil protists and their contributions to belowground systems. Sci Adv. 2020;6:eaax8787.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Finland MotE: Government decree on the assessment of soil contamination and remediation needs (214/2007). In.: Ministry of the Environment Helsinki (FI); 2007.Carlon C. Derivation methods of soil screening values in europe: A review of national procedures towards harmonisation: A report of the ENSURE action. EUR-OP. 2007.Toth G, Hermann T, Da Silva MR, Montanarella L. Heavy metals in agricultural soils of the European Union with implications for food safety. Environ Int. 2016;88:299–309.CAS 
    PubMed 
    Article 

    Google Scholar 
    De Caceres M, Jansen F. Relationship between species and groups of sites. Package ‘indicspecies’, version 1.7.6. 2016.Frossard A, Donhauser J, Mestrot A, Gygax S, Bååth E, Frey B. Long-and short-term effects of mercury pollution on the soil microbiome. Soil Biol Biochem. 2018;120:191–9.CAS 
    Article 

    Google Scholar 
    Ma B, Wang H, Dsouza M, Lou J, He Y, Dai Z, et al. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J. 2016;10:1891–901.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Langfelder P, Horvath S. Fast R functions for robust correlations and hierarchical clustering. J Stat Softw. 2012;46:1–17.Article 

    Google Scholar 
    Luo F, Zhong J, Yang Y, Scheuermann RH, Zhou J. Application of random matrix theory to biological networks. Phys Lett A. 2006;357:420–3.CAS 
    Article 

    Google Scholar 
    Deng Y, Jiang YH, Yang YF, He ZL, Luo F, Zhou JZ. Molecular ecological network analyses. BMC Bioinform. 2012;13:1–20.Article 

    Google Scholar 
    Benjamini Y, Krieger AM, Yekutieli D. Adaptive linear step-up procedures that control the false discovery rate. Biometrika. 2006;93:491–507.Article 

    Google Scholar 
    Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. Proceedings of the International AAAI Conference on Web and Social Media. 2009;3:361–2.Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1–9.
    Google Scholar 
    Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, O’Hara R, et al. Vegan: community ecology package. Ordination methods, diversity analysis and other functions for community and vegetation ecologists. R Package Ver. 2015;2:3–1.
    Google Scholar 
    Chen B, Xiong W, Qi J, Pan H, Chen S, Peng Z, et al. Trophic interrelationships drive the biogeography of protistan community in agricultural ecosystems. Soil Biol Biochem. 2021;163:108445.CAS 
    Article 

    Google Scholar 
    Jiao S, Lu Y, Wei G. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems. Glob Chang Biol. 2022;28:140–53.Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.PubMed 
    Article 
    CAS 

    Google Scholar 
    Revelle WR. psych: Procedures for personality and psychological research. 2017.Archer E. rfPermute: estimate permutation p-values for random forest importance metrics. R package version. 2016;1(2).Wang JT, Zheng YM, Hu HW, Li J, Zhang LM, Chen BD, et al. Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems. Sci Rep. 2016;6:1–7.Article 
    CAS 

    Google Scholar 
    Schermelleh-Engel K, Moosbrugger H, Müller H. Evaluating the fit of structural equation models: Tests of significance and descriptive goodness-of-fit measures. Methods Psychol Res Online. 2003;8:23–74.
    Google Scholar 
    Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, et al. Body size determines soil community assembly in a tropical forest. Mol Ecol. 2019;28:528–43.CAS 
    PubMed 
    Article 

    Google Scholar 
    Stefan G, Cornelia B, Jörg R, Michael B. Soil water availability strongly alters the community composition of soil protists. Pedobiologia. 2014;57:205–13.Article 

    Google Scholar 
    Luan L, Jiang Y, Cheng M, Dini-Andreote F, Sui Y, Xu Q, et al. Organism body size structures the soil microbial and nematode community assembly at a continental and global scale. Nat Commun. 2020;11:6406.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Qi Q, Hu C, Lin J, Wang X, Tang C, Dai Z, et al. Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks. Environ Pollut. 2022;306:119406.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wu W, Lu HP, Sastri A, Yeh YC, Gong GC, Chou WC, et al. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME J. 2018;12:485–94.PubMed 
    Article 

    Google Scholar 
    Villarino E, Watson JR, Jönsson B, Gasol JM, Salazar G, Acinas SG, et al. Large-scale ocean connectivity and planktonic body size. Nat Commun. 2018;9:1–13.CAS 
    Article 

    Google Scholar 
    Mitsch WJ, Gosselink JG Wetlands. John Wiley & Sons; 2015.Margesin R, Feller G, Gerday C, Russell N. The Encyclopedia of Environmental Microbiology. 2002;2.Liu YR, Johs A, Bi L, Lu X, Hu HW, Sun D, et al. Unraveling microbial communities associated with methylmercury production in paddy soils. Environ Sci Technol. 2018;52:13110–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Hall B, St Louis V, Rolfhus K, Bodaly R, Beaty K, Paterson M, et al. Impacts of reservoir creation on the biogeochemical cycling of methyl mercury and total mercury in boreal upland forests. Ecosystems. 2005;8:248–66.CAS 
    Article 

    Google Scholar 
    Clarholm M. Protozoan grazing of bacteria in soil-impact and importance. Microb Ecol. 1981;7:343–50.CAS 
    PubMed 
    Article 

    Google Scholar 
    Asiloglu R, Shiroishi K, Suzuki K, Turgay OC, Harada N. Soil properties have more significant effects on the community composition of protists than the rhizosphere effect of rice plants in alkaline paddy field soils. Soil Biol Biochem. 2021;161:108397.CAS 
    Article 

    Google Scholar 
    Asiloglu R, Kenya K, Samuel SO, Sevilir B, Murase J, Suzuki K, et al. Top-down effects of protists are greater than bottom-up effects of fertilisers on the formation of bacterial communities in a paddy field soil. Soil Biol Biochem. 2021;156:108186.CAS 
    Article 

    Google Scholar 
    Nguyen BAT, Chen QL, He JZ, Hu HW. Livestock manure spiked with the antibiotic tylosin significantly altered soil protist functional groups. J Hazard Mater. 2021;427:127867.Nguyen BAT, Chen QL, He JZ, Hu HW. Oxytetracycline and ciprofloxacin exposure altered the composition of protistan consumers in an agricultural soil. Environ Sci Technol. 2020;54:9556–63.CAS 
    PubMed 
    Article 

    Google Scholar 
    Nguyen BAT, Chen QL, Yan ZZ, Li CY, He JZ, Hu HW. Distinct factors drive the diversity and composition of protistan consumers and phototrophs in natural soil ecosystems. Soil Biol Biochem. 2021;160:108317.CAS 
    Article 

    Google Scholar 
    Wu S, Dong Y, Deng Y, Cui L, Zhuang X. Protistan consumers and phototrophs are more sensitive than bacteria and fungi to pyrene exposure in soil. Sci Total Environ. 2022;822:153539.CAS 
    PubMed 
    Article 

    Google Scholar 
    Potts LD, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, et al. Chronic environmental perturbation influences microbial community assembly patterns. Environ Sci Technol. 2022;56:2300–11.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Ge AH, Liang ZH, Xiao JL, Zhang Y, Zeng Q, Xiong C, et al. Microbial assembly and association network in watermelon rhizosphere after soil fumigation for Fusarium wilt control. Agric Ecosyst Environ. 2021;312:107336.CAS 
    Article 

    Google Scholar 
    Pernthaler J, Sattler B, Simek K, Schwarzenbacher A, Psenner R. Top-down effects on the size-biomass distribution of a freshwater bacterioplankton community. Aquat Microb Ecol. 1996;10:255–63.Article 

    Google Scholar 
    Holtze MS, Ekelund F, Rasmussen LD, Jacobsen CS, Johnsen K. Prey-predator dynamics in communities of culturable soil bacteria and protozoa: differential effects of mercury. Soil Biol Biochem. 2003;35:1175–81.CAS 
    Article 

    Google Scholar 
    Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459:193–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Meisner A, Wepner B, Kostic T, van Overbeek LS, Bunthof CJ, de Souza RSC, et al. Calling for a systems approach in microbiome research and innovation. Curr Opin Biotechnol. 2022;73:171–8.CAS 
    PubMed 
    Article 

    Google Scholar  More

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    IPBES responds to critics of its assessment of wild-species use

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    Nitrogen cycling and microbial cooperation in the terrestrial subsurface

    Distribution of nitrogen-cycling pathways in groundwaterDifferences in nitrogen-cycling processes based on oxygen and nitrate concentrationsSixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3) concentrations (Fig. 1A; Table S1). Nitrate concentrations were pristine (site C) to N-contaminated (sites A, B, D) [4]. Sites A–C were oxic and had low DOC (typical of groundwaters), whereas site D was dysoxic with relatively high DOC. Metagenomes from groundwater wells comprised pairs, representing the planktonic and sediment-attached fractions. Over 70 Gbp of raw sequence was generated per site (390 Gbp overall, 322 Gbp trimmed). However, 2Kb long and only 0.64–8.14% of reads (3.8% on average) mapped to MAGs (Table S4), reflecting the complexity of microbial communities in the terrestrial subsurface [11]. To capture this diversity, metagenomic reads are first used here to determine the distribution of N metabolisms.Fig. 1: Geochemistry and protein-coding sequences (based on reads) involved in nitrogen cycling that are significantly different among sites used for metagenomics.A Bar plots showing geochemical data from groundwater samples, coloured according to site. Solid bar colour = groundwater samples. Grid lines = attached-fraction enriched groundwater. All samples from site D were characterized as dysoxic, although gwj15-16 contained 0.37 mg/L DO, which are near suboxic levels (i.e. More

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    Potato-gene wrangler

    All crops have been modified through some form of improvement, whether to enhance yield, taste, resilience or another factor. My passion is to continue accelerating the development of crop varieties that are more resistant to climate change and pests. This will make food supplies more secure and will also improve the quality of life for small-hold farmers in Africa and Asia, whose livelihoods can be devastated by crop failure.The goal of crop breeding is not only to develop new varieties, but also to produce genetically superior parents with a range of desirable traits that will be useful in future generations. Complex traits, such as yield or climate resilience, are often regulated by many genes. To speed up crop breeding for those traits, we use genomic data to select the best parental combinations, and then cameras and digital tools to identify the best progeny.In this photo, I’m in a greenhouse in Peru owned by my employer, the International Potato Center (CIP), inspecting potential sweet potato (Ipomoea batatas) breeding parents for cross-pollination. CIP is one of 13 gene banks and research facilities around the world, known collectively as One CGIAR, which protect and utilize crop genetic diversity. I’ve worked at CIP since 2016; before then, I worked in industry, where I developed crops such as drought-tolerant corn hybrids.Because potatoes don’t have seeds that can be preserved for decades, we must reproduce them by growing small parts of plant organs, such as a root, a tuber or part of a stem, in tissue culture. Nearly 85% of the unique potato populations stored at CIP are also cryopreserved in liquid nitrogen to maintain a long-term backup.I can’t think of a nobler mission than working on food security. I hope that more young scientists — especially women — will focus their talents on crop breeding for the future. More

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    Don’t dilute the term Nature Positive

    Nature Positive is an aspirational term that is increasingly being used by businesses, governments and NGOs, but there is a danger that its meaning is being diluted away from measurable overall net gain in biodiversity towards merely any action that benefits nature, argues E.J. Milner-Gulland.The term is appealing because it suggests an optimistic, intuitive and clear summary of where society needs to get to, and it can be used equally by business, government and civil society to describe their aspirations to protect and recover nature. However, once terms start gaining traction, particularly relatively general terms like Nature Positive, there is a risk of slippage and loss of meaning. It is already starting to feel like any actions that increase biodiversity anywhere, and by any amount, can be called Nature Positive. This trend has to be resisted. More