Philippa Kaur

Bengtsson, J. Biological control as an ecosystem service: partitioning contributions of nature and human inputs to yield. Ecol. Entomol. 40, 45–44 (2015).Article 

Google Scholar 
Zalucki, M., Furlong, M. J., Schellhorn, N. A., Macfadyen, S. & Davies, A. P. Assessing the impact of natural enemies in agroecosystems: toward “real” IPM or in quest of Holy Grail? Insect. Sci. 22, 1–5 (2015).PubMed 
Article 

Google Scholar 
Van Lenteren, J. C., Bolckmans, K., Kohl, J., Ravensberg, W. J. & Urabaneja, A. Biological control using invertebrates and microorganisms: plenty of new opportunities. BioControl 63, 39–59 (2018).Article 

Google Scholar 
Symondson, W. O. C., Sunderland, K. D. & Greenstone, M. H. Can generalist predators be effective biological control agents. Annu. Rev. Entomol. 47, 561–594 (2002).CAS 
PubMed 
Article 

Google Scholar 
Bianchi, F. J. J. A., Booij, C. J. H. & Tscharntke, T. Sustainable pest regulation in agricultural landscapes: a review on landscape composition, biodiversity and natural pest control. Proc. R. Soc. B. 273, 1715–1727 (2006).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Van Nouhuys, S., Niemikapee, S. & Hanski, I. Variation in a host-parasitoid interaction across independent populations. Insects 3, 1236–1256 (2012).PubMed 
PubMed Central 
Article 

Google Scholar 
Hedlund, K., Vet, L. E. M. & Dicke, M. Generalist and specialist parasitoid strategies of using odours of adult drosophilid flies when searching for larval hosts. Oikos 77, 390–398 (1996).Article 

Google Scholar 
Evans, E. W., Stevenson, A. T. & Richards, D. R. Essential versus alternative foods of insect predators: benefits of a mixed diet. Oelcologia 121, 107–112 (1999).Article 

Google Scholar 
Lovei, G. L. & Sunderland, K. M. Ecology and behavior of ground beetles (Coleoptera: Carabidae). Annu. Rev. Entomol. 41, 231–256 (1996).CAS 
PubMed 
Article 

Google Scholar 
Kromp, B. Carabid beetles in sustainable agriculture: a review on pest control efficacy, cultivation impacts and enhancement. Agric. Ecosyt. Environ. 74, 187–228 (1999).Article 

Google Scholar 
Tuf, H., Dedek, P. & Vesley, M. Does the diurnal activity pattern of carabid beetles depend on season, ground temperature, or habitat? Arch. Biol. Sci. 64, 721–732 (2012).Article 

Google Scholar 
Firlej, A., Doyon, J., Harwood, J. D. & Brodeur, J. A multi-approach study to delineate interaction between carabid beetles and soybean aphids. Environ. Entomol. 42, 89–96 (2013).PubMed 
Article 

Google Scholar 
Clark, M. S., Luna, J. M., Stone, N. D. & Youngman, R. R. Generalist predator consumption of armyworm (Lepidoptera: Noctuidae) and effect of predator removal and damage in no-till corn. Environ. Entomol. 23, 617–622 (1994).Article 

Google Scholar 
Floate, K. D., Doane, J. F. & Gillot, C. Carabid predators of the wheat midge (Diptera: Cecidomyiidae) in Saskatchewan. Environ. Entomol. 19, 1503–1511 (1990).Article 

Google Scholar 
Barsics, F., Haubruge, E. & Verheggen, F. J. Wireworms’ management: an overview of the existing methods, with particular regards to Agriotis spp. (Coleoptera: Elateridae). Insects 4, 117–152 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Oberholzer, F., Escher, N. & Frank, T. The potential of carabid beetles (Coleoptera) to reduce slug damage to oilseed rape in the laboratory. Eur. J. Entomol. 100, 81–85 (2003).Article 

Google Scholar 
Honek, A., Martinkova, Z. & Jarosik, V. Ground beetles Carabidae as seed predators. Eur. J. Entomol. 100, 531–544 (2003).Article 

Google Scholar 
Lundgren, J. G. Relationship of Natural Enemies and Non-prey Foods 1–460 (Springer, 2009).Carbonne, B. et al. The resilience of weed seedbank regulation by carabid beetles, at continental scales, to alternative prey. Sci. Rep. 10, 1935 (2020).Article 
CAS 

Google Scholar 
Wilder, S. M., Norris, M., Lee, R. W., Raubenheimer, D. & Simpson, S. J. Arthropod food webs become increasingly lipid-limited at higher trophic levels. Ecol. Lett. 16, 895–902 (2013).PubMed 
Article 

Google Scholar 
Denno, R. F. & Fagan, W. F. Might nitrogen limitation promote omnivory among carnivorous arthropods? Ecology 84, 2522–2531 (2003).Article 

Google Scholar 
Saska, P. & Jarosik, V. Laboratory study of larval food requirements in nine species of Amara (Coleoptera: Carabidae). Plant Prot. 37, 103–110 (2001).
Google Scholar 
Saska, P., Van der Werf, W. & Westerman, P. Spatial and temporal patterns of carabid activity-density in cereals do not explain levels of weed seed predation. Bull. Entomological Res. 98, 169–181 (2008).CAS 
Article 

Google Scholar 
Talarico, F., Giglio, A., Pizzolotto, R. & Brandmayr, P. P. A synthesis of the feeding habits and reproductive rhythms in Italian seed feeding ground beetles (Coleoptera: Carabidae). Eur. J. Entomol. 113, 325–336 (2016).Article 

Google Scholar 
Fawki, S., Bak, S. S. & Toft, S. Food preference and food value for the carabid beetles Pterostichus melanarius, P. versicolor, and Carabus nemoralis. Eur. Carabidol. 114, 99–109 (2003).
Google Scholar 
Frei, B., Guenay, Y., Bohan, B. A., Traugett, M. & Wallinger, C. Molecular analysis indicates high levels of carabid weed seed consumption in cereal fields across central Europe. J. Plant Sci. 92, 935–942 (2019).
Google Scholar 
Kulkarni, S. S., Dosdall, L. M., Spence, J. R. & Willenborg, C. J. Brassicaceous weed seed predation by ground beetles (Coleoptera: Carabidae). Weed. Sci. 64, 294–302 (2016).Article 

Google Scholar 
Saska, P., Honek, A., Foffova, H. & Martinkova, Z. Burial-induced changes in the seed preferences of carabid beetles (Coleoptera: Carabidae). Eur. J. Entomol. 116, 113–140 (2019).Article 

Google Scholar 
Saska, P., Honek, A. & Martinkova, Z. Preference of carabid beetles (Coleoptera: Carabidae) for herbaceous seeds. Acta Zool. Acad. Sci. Hung. 65, 57–76 (2019).Article 

Google Scholar 
Sih, A. & Christensen, B. Optimal diet theory: when does it work, and when and why does it fail? Anim. Behav. 61, 379–390 (2001).Article 

Google Scholar 
Barron, A. B., Gurney, K. N., Meah, L. F. S., Vasilaki, E. & Marshall, J. A. R. Decision-making and action selection in insects: inspiration from vertebrate-based theories. Front. Behav. Neurosci. 9, 216 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Kulkarni, S. S., Dosdall, L. M., Spence, J. R. & Willenborg, C. J. C. J. The role of ground beetles (Coleoptera: Carabidae) in weed seed consumption: a review. Weed. Sci. 63, 355–376 (2015).Article 

Google Scholar 
Kulkarni, S. S., Dosdall, L. M., Spence, J. R. & Willenborg, C. J. Seed detection and discrimination by ground beetles (Coleoptera: Carabidae) are associated with olfactory cues. PLoS One 12, e0170593 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Law, J. J. & Gallagher, R. S. The role of imbibition on seed selection by Harpalus pensylvanicus. Appl. Soil. Ecol. 87, 118–124 (2015).Article 

Google Scholar 
Davis, A. S., Schutte, B. J., Iannuzzi, J. & Renner, K. A. Chemical and physical defenses of weed seeds in relation to soil seedbank persistence. Weed Sci. 56, 676–684 (2008).CAS 
Article 

Google Scholar 
Ali, K. A. & Willneborg., C. J. C. J. The biology of seed discrimination and its role in shaping the foraging ecology of carabids: a review. Ecol. Evol. 11, 13702–13722 (2021).PubMed 
PubMed Central 
Article 

Google Scholar 
Wheater, C. P. Prey detection by some predatory Coleoptera (Carabidae and Staphylinidae). J. Zool. 215, 171–185 (1989).Article 

Google Scholar 
Mundy, C. A., Aleen-Williams, L. J., Underwood, N. & Warrington, S. Prey selection and foraging behavior by Pterostichus cupreus L. (Col., Carabidae) under laboratory conditions. J. Appl. Entomol. 124, 349–358 (2000).Article 

Google Scholar 
Kielty, J. P., Allen-Williams, L. J., Underwood, N. & Eastwood, E. A. Behavioral responses of three species of ground beetles (Carabidae: Coloeptera) to olfactory cues associated with prey and habitat. J. Insect. Behav. 9, 237–249 (1996).Article 

Google Scholar 
Tréfás, H., Canning, H., McKinlay, R. G., Armstrong, G. & Bujaki, G. Preliminary experiments on the olfactory responses of Pterostichus melanarius Illiger (Coleoptera:Carabidae) to intact plants. Agric. Entomol. 3, 71–76 (2001).Article 

Google Scholar 
McKemey, A. R., Symondson, W. O. C. & Glen, D. M. Predation and prey size choice by the carabid Pterostichus melanarius (Coleoptera: Carabidae): the dangers of extrapolating from laboratory to field. Bull. Entomol. Res. 93, 227–234 (2003).CAS 
PubMed 
Article 

Google Scholar 
Thomas, R. S., Glen, D. M. & Symondson, W. O. C. Prey detection through olfaction by the soil-dwelling larvae of the carabid predator Pterostichus melanarius. Soil Biol. Biochem. 40, 207–216 (2008).CAS 
Article 

Google Scholar 
Talarico, F. et al. Electrophysiological and behavioral analyses on prey selecting in the myrmecophagous carabid beetle Siagona europaea Dejean 1826 (Coleoptera: Carabidae). Etho. Ecol. Evol. 22, 375–384 (2010).Article 

Google Scholar 
Dessaint, F., Chadoeuf, R. & Barrales, G. Spatial pattern analysis of weed seeds in the cultivated soil seed bank. J. Appl. Ecol. 28, 721–730 (1991).Article 

Google Scholar 
Oster, M., Smith, L., Beck, J. J., Howard, A. & Field, C. B. Orientational behavior of predaceous ground beetle species in response to volatile emissions identified from yellow starthistle damaged by an invasive slug. Arthropod-Plant. Inte. 8, 429–437 (2014).Article 

Google Scholar 
Srinivasan, M. V., Poteser, M. & Karl, K. Motion detection in insect orientation and navigation. Vis. Res. 39, 2749–2766 (1999).CAS 
PubMed 
Article 

Google Scholar 
Sato, K. & Touhara, K. Insect olfaction: receptors, signal transduction, and behavior. Cell 47, 121–138 (2009).CAS 

Google Scholar 
Leal, W. S. Odorant reception in insects: roles of receptors, binding proteins, and degrading enzymes. Ann. Rev. Entomol. 58, 373–391 (2013).CAS 
Article 

Google Scholar 
Schmidt, H. R. & Benton, R. Molecular mechanisms of olfactory detection in insects: beyond receptors. Open Biol. 10, 200252 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Prokopy, R. J. & Owens, E. D. Visual detection of plants by herbivorous insects. Ann. Rev. Entomol. 28, 337–364 (1983).Article 

Google Scholar 
Ploomi, A. et al. Antennal sensilla in ground beetles (Coleoptera: Carabidae). Agron. Res. 1, 221–228 (2003).
Google Scholar 
Merivee, E. et al. Electrophysiological responses from neurons of antennal taste sensilla in the polyphagous predatory ground beetle Pterostichus oblongopunctatus (Fabricius 1787) to plant sugars and amin acids. J. Insect. Physiol. 54, 1213–1219 (2008).CAS 
PubMed 
Article 

Google Scholar 
Merivee, E., Ploomi, A., Luik, A., Rahi, M. & Smmelselg, V. Antennal sensilla of the ground beetle Platynus dorsalis (Pontoppidan, 1763) (Coleoptera: Carabidae). Micros. Res. Tech. 55, 339–349 (2001).CAS 
Article 

Google Scholar 
Merivee, E. et al. Antennal sensilla of the ground beetle Bembidion properans Steph. (Coleoptera: Carabidae). Micron 33, 429–440 (2002).PubMed 
Article 

Google Scholar 
Giglio, A., Perotta, E., Talarico, F., Brandmayr, T. E. & Ferrera, E. A. Sensilla on the maxillary and labial palps in a helicophagous ground beetle larva (Coleoptera: Carabidae). Acta Zool. 200, 1463–6393 (2013).
Google Scholar 
Van Naters, W. V. D. G. & Carlson, J. R. J. R. Receptors and neurons for fly odors in Drosophila. Curr. Biol. 17, 606–612 (2007).Article 
CAS 

Google Scholar 
Amrein, H. & Throne, N. Gustatory perception and behavior in Dropsophila melanogaster. Curr. Biol. 15, R673–R684 (2005).CAS 
PubMed 
Article 

Google Scholar 
Su, C. Y., Menuz, K. & Carlson, J. R. Olfactory perception: receptors, cells, and circuits. Cell 139, 45–59 (2009).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Krieger, J. & Breer, H. Olfactory receptors in invertebrates. Science 286, 720–723 (1999).CAS 
PubMed 
Article 

Google Scholar 
Chapman, R. F. The Insects: Structure and Function 4th edn, 1–584 (Cambridge University Press, 1998).Bhandari, S. R., Jo, J. S. & Lee, J. G. Comparisons of glucosinolate profiles in different tissues of nine Brassica crops. Molecules 20, 15827–15841 (2015).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Reifenrath, K., Riederer, M. & Muller, M. Leaf surface wax layers of Brassicaceae lack feeding stimulants for Phaedon cochleariae. Entomol. Exp. Appl. 115, 41–50 (2005).CAS 
Article 

Google Scholar 
Stadler, E. & Reifenrath, K. Glucosinolates on the leaf surface perceived by insect herbivores: review of ambiguous results and new investigations. Phytoch. Rev. 8, 207–225 (2009).Article 
CAS 

Google Scholar 
Sharma, A., Sandhi, R. K. & Reddy, G. V. P. A review of interactions between insect biological control agents and semiochemicals. Insects 10, 439 (2019).PubMed Central 
Article 

Google Scholar 
Warwick, S. I., Francis, A. & Susko, D. J. The biology of Canadian weeds. 9. Thlaspi arvense L. (updated). Can. J. Plant. Sci. 82, 803–823 (2002).Article 

Google Scholar 
Moyna, P. & Garcia, M. Chemical composition of oat seed epicuticular lipids. J. Sci. Food Agric. 34, 209–211 (1983).CAS 
PubMed 
Article 

Google Scholar 
Kunst, L. & Samuels, A. L. Biosynthesis and secretion of plant cuticular wax. Prog. Lipid Res. 42, 51–80 (2003).CAS 
PubMed 
Article 

Google Scholar 
Eigenbrode, S. D. & Espelie, K. E. Effects of plants epicuticular lipids on insect herbivores. Annu. Rev. Entomol. 40, 171–194 (1995).Article 

Google Scholar 
Finch, S. Volatile plant chemicals and their effect on host plant by the cabbage root fly (Delia brassicae). Entomol. Exp. Appl. 24, 350–359 (1978).CAS 
Article 

Google Scholar 
Udayagiri, S. & Mason, C. E. Epicuticular wax chemicals in Zea mays influence oviposition in Ostrinia nubilalis. J. Chem. Ecol. 23, 1675–1687 (1997).CAS 
Article 

Google Scholar 
Adati, T. & Matsuda, K. The effect of leaf surface wax on feeding of the strawberry leaf beetle, Galerucella vittaticollis, with reference to host plant preference. Tohoku. J. Agric. Res. 50, 57–61 (2000).
Google Scholar 
Damon, S. J., Groves, R. L. & Harvey, M. J. Variation for epicuticular waxes on onion foliage and impacts on numbers of onion thrips. J. Am. Soc. Hortic. Sci. 139, 495–501 (2014).CAS 
Article 

Google Scholar 
Braccini, C. L., Vega, A. S., Chludil, H. D., Leicach, S. R. & Fernandez, P. C. Host selection, oviposition behavior and leaf traits in a specialist willow sawfly on species of Salix (Salicaceae). Ecol. Entomol. 38, 617–626 (2013).Article 

Google Scholar 
Wojcicka, A. Effects of epicuticular waxes from triticale on the feeding behaviour and mortality of the grain aphid, Sitobion avenae (Fabricius) (Hemiptera: Aphididae). J. Plant. Prot. Res. 56, 39–44 (2016).CAS 
Article 

Google Scholar 
Medina, E. et al. Taxonomic significance of the epicuticular wax composition in species of genus Clusia from Panama. Biochem. Syst. Ecol. 34, 319–326 (2006).CAS 
Article 

Google Scholar 
Schulz-Bohm, K., Martin-Sanchez, L. & Garbeva, P. Microbial volatiles: small molecules with an inter-kingdom interactions. Front. Microbiol. 8, 2484 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Ali, K. A. Mechanisms of Seed Discrimination and Selective Seed Foraging in Carabid Weed Seed Predators. https://harvest.usask.ca/bitstream/handle/10388/13815/ALI-DISSERTATION-2022.pdf?sequence=1&isAllowed=y (2022).Webster, B., Qvarfordt, E., Olsson, U. & Glinwood, R. Different roles for innate and learnt behavioral responses to odors in insect host location. Behav. Ecol. 24, 366–372 (2013).Article 

Google Scholar 
Luff, M. L. Adult and larval feeding habits of Pterostichus madidus (F.) (Carabidae: Coleoptera). J. Nat. Hist. 8, 403–409 (1974).Article 

Google Scholar 
Blubaugh, C. K. & Kaplan, I. Invertebrate seed predators reduce weed emergence following seed rain. Weed Sci. 64, 80–86 (2016).Article 

Google Scholar 
Blubaugh, C. K., Hagler, J. R., Machtley, S. A. & Kaplan, I. Cover crops increase foraging activity of omnivorous predators in seed patches and facilitate weed biological control. Agric. Ecosyst. Environ. 231, 264–270 (2016).Article 

Google Scholar 
Foffova, H. et al. Which seed properties determine the preferences of carabid beetles seed predators? Insects 11, 757 (2020).Petit, S., Boursault, A. & Bohan, D. A. Weed seed choice by carabid beetles (Coleoptera: Carabidae): linking field measurements and laboratory diet assessments. Eur. J. Entomol. 111, 615–620 (2014).Article 

Google Scholar 
Carbonne, B. et al. Direct and indirect effects of landscape and field management intensity on carabids through trophic resources and weeds. J. Appl. Ecol. 59, 176–187 (2022).Article 

Google Scholar 
Foffova, H., Bohan, D. A. & Saska, P. Do properties and species of weed seeds affect their consumption by carabid beetles? Acta Zool. Acad. Sci. Hung. 66, 37–48 (2020b).Article 

Google Scholar 
De Heij, S. E. & Willenborg, C. J. Connected carabids: network interactions and their impact on biocontrol by carabid beetles. Bioscience 70, 90–500 (2020).Article 

Google Scholar 
Honek, A., Martinkova, Z., Saska, P. & Pekar, S. Size and taxonomic constraints determine seed preference of Carabidae (Coleoptera). Basic Appl. Ecol. 8, 343–353 (2007).Article 

Google Scholar 
Spence, J. R. & Niemela, J. K. Sampling carabid assemblages with pitfall traps: the madness and the method. Can. Entomol. 126, 881–884 (1994).Article 

Google Scholar 
Lindroth, C. H. The Ground Beetles (Carabidae, excluding Cicindelinae) of Canada and Alaska. Supplement 20, 24, 29, 33, 34, 35. Part I, pages I–XLVIII, 1969. Part II, pages 1–200, 1961. Part III, pages 201–408, 1963. Part IV, pages 409–648, 1966. Part V, pages 649–944, 1968. Part VI, pages 945–1192 (Opusca Entomology, 1961–1969).White, S. S., Renner, K. A., Menalled, F. D. & Landis, D. A. Feeding preferences of weed seed predators and effect on weed emergence. Weed. Sci. 55, 606–612 (2007).CAS 
Article 

Google Scholar 
Glinwood, R., Ahmed, E., Ovarfordt, E. & Ninkovic, V. Olfactory learning of plant genotypes by a polyphagous predator. Oecologia 166, 637–647 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Sablon, L., Dickens, J. C., Haubruge, E. H. & Verhggen., F. J. Chemical ecology of the Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae), and potential for alternative control methods. Insects 4, 31–54 (2013).Article 

Google Scholar 
Zhang, L., Li, H. & Zhang, L. Two olfactory pathways to detect aldehydes on locust mouthpart. Int. J. Biol. Sci. 13, 759–771 (2017).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pekar, S. & Hruskova, M. M. How granivorous Coreus marginatus (Hemiptera: Cereidae) recognizes its food. Acta Ethol. 9, 26–30 (2006).Article 

Google Scholar 
Ardenghi, N., Mulch, A., Pross, J. & Niedermeyer, E. M. Leaf wax n-alkane extraction: an optimized procedure. Org. Geochem. 113, 283–292 (2017).CAS 
Article 

Google Scholar 
Takahashi, S. & Gassa, A. Roles of cuticular hydrocarbons in intra- and interspecific recognition behavior of two Rhinotermitidae species. J. Chem. Ecol. 21, 1837–1845 (1995).CAS 
PubMed 
Article 

Google Scholar 
Bates, D., Machler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 
CAS 

Google Scholar 
Nobre, J. S. & Singer, J. D. M. Residual analysis for linear mixed models. Biom. J. 49, 863–875 (2007).PubMed 
Article 

Google Scholar 
Schielzeth, H. et al. Robustness of linear mixed-effects models to violations of distributional assumptions. Methods Ecol. Evol. 11, 1141–1152 (2020).Article 

Google Scholar  More

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Google Scholar  More

Wanger, T. C. et al. Integrating agroecological production in a robust post-2020 Global Biodiversity Framework. Nat. Ecol. Evol. 4, 1150–1152 (2020).PubMed 
Article 

Google Scholar 
Newbold, T. et al. Global effects of land use on local terrestrial biodiversity. Nature 520, 45–50 (2015).CAS 
PubMed 
Article 

Google Scholar 
Amundson, R. et al. Soil and human security in the 21st century. Science 348, 1261071 (2015).PubMed 
Article 
CAS 

Google Scholar 
Robertson, G. P. & Vitousek, P. M. Nitrogen in agriculture: balancing the cost of an essential resource. Annu. Rev. Environ. Resour. 34, 97–125 (2009).Article 

Google Scholar 
Campbell, B. M. et al. Agriculture production as a major driver of the Earth system exceeding planetary boundaries. Ecol. Soc. 22, 8 (2017).Article 

Google Scholar 
Kremen, C. & Merenlender, A. M. Landscapes that work for biodiversity and people. Science 362, eaau6020 (2018).PubMed 
Article 
CAS 

Google Scholar 
Krebs, A. V. The Corporate Reapers: The Book of Agribusiness (Essential Books, 1992).Mortensen, D. A. & Smith, R. G. Confronting barriers to cropping system diversification. Front. Sustain. Food Syst. 4, 564197 (2020).Article 

Google Scholar 
2017 Census of Agriculture – 2019 Organic Survey (USDA NASS, 2020); https://www.nass.usda.gov/Publications/AgCensus/2017/index.phpFarms and Land in Farms 2019 Summary (USDA NASS, 2020); https://usda.library.cornell.edu/concern/publications/5712m6524Reganold, J. P. & Wachter, J. M. Organic agriculture in the twenty-first century. Nat. Plants 2, 15221 (2016).PubMed 
Article 

Google Scholar 
Muller, A. et al. Strategies for feeding the world more sustainably with organic agriculture. Nat. Commun. 8, 1290 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Lori, M., Symnaczik, S., Mäder, P., De Deyn, G. & Gattinger, A. Organic farming enhances soil microbial abundance and activity—a meta-analysis and meta-regression. PLoS ONE 12, e0180442 (2017).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Seufert, V. & Ramankutty, N. Many shades of gray—the context-dependent performance of organic agriculture. Sci. Adv. 3, e1602638 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
USDA AMS. National Organic Program; Final Rule, 7 CFR Part 205. Fed. Regist. 65, 80547–80684 (2000).
Google Scholar 
Wezel, A. et al. Agroecology as a science, a movement and a practice. A review. Agron. Sustain. Dev. 29, 503–515 (2009).Article 

Google Scholar 
Tamburini, G. et al. Agricultural diversification promotes multiple ecosystem services without compromising yield. Sci. Adv. 6, eaba1715 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Kleijn, D. et al. Ecological intensification: bridging the gap between science and practice. Trends Ecol. Evol. 34, 154–166 (2019).PubMed 
Article 

Google Scholar 
Bommarco, R., Kleijn, D. & Potts, S. G. Ecological intensification: harnessing ecosystem services for food security. Trends Ecol. Evol. 28, 230–238 (2013).PubMed 
Article 

Google Scholar 
Kremen, C. & Miles, A. Ecosystem services in biologically diversified versus conventional farming systems: benefits, externalities, and trade-offs. Ecol. Soc. 17, 40 (2012).
Google Scholar 
Bowles, T. M. et al. Long-term evidence shows that crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America. One Earth 2, 284–293 (2020).Article 

Google Scholar 
Wood, S. A. et al. Functional traits in agriculture: agrobiodiversity and ecosystem services. Trends Ecol. Evol. 30, 531–539 (2015).PubMed 
Article 

Google Scholar 
Faucon, M.-P., Houben, D. & Lambers, H. Plant functional traits: soil and ecosystem services. Trends Plant Sci. 22, 385–394 (2017).CAS 
PubMed 
Article 

Google Scholar 
D’Hose, T. et al. The positive relationship between soil quality and crop production: a case study on the effect of farm compost application. Appl. Soil Ecol. 75, 189–198 (2014).Article 

Google Scholar 
Fließbach, A., Oberholzer, H.-R., Gunst, L. & Mäder, P. Soil organic matter and biological soil quality indicators after 21 years of organic and conventional farming. Agric. Ecosyst. Environ. 118, 273–284 (2007).Article 

Google Scholar 
Francioli, D. et al. Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front. Microbiol. 7, 1446 (2016).PubMed 
PubMed Central 
Article 

Google Scholar 
Nunes, M. R., Karlen, D. L., Veum, K. S., Moorman, T. B. & Cambardella, C. A. Biological soil health indicators respond to tillage intensity: a US meta-analysis. Geoderma 369, 114335 (2020).CAS 
Article 

Google Scholar 
Blanco-Canqui, H. & Ruis, S. J. No-tillage and soil physical environment. Geoderma 326, 164–200 (2018).Article 

Google Scholar 
Willekens, K., Vandecasteele, B., Buchan, D. & De Neve, S. Soil quality is positively affected by reduced tillage and compost in an intensive vegetable cropping system. Appl. Soil Ecol. 82, 61–71 (2014).Article 

Google Scholar 
Dainese, M. et al. A global synthesis reveals biodiversity-mediated benefits for crop production. Sci. Adv. 5, eaax0121 (2019).PubMed 
PubMed Central 
Article 

Google Scholar 
Albrecht, M. et al. The effectiveness of flower strips and hedgerows on pest control, pollination services and crop yield: a quantitative synthesis. Ecol. Lett. 23, 1488–1498 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Chaplin-Kramer, R., de Valpine, P., Mills, N. J. & Kremen, C. Detecting pest control services across spatial and temporal scales. Agric. Ecosyst. Environ. 181, 206–212 (2013).Article 

Google Scholar 
Martin, E. A. et al. The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agroecosystem services across Europe. Ecol. Lett. 22, 1083–1094 (2019).PubMed 
Article 

Google Scholar 
Karp, D. S. et al. Crop pests and predators exhibit inconsistent responses to surrounding landscape composition. Proc. Natl Acad. Sci. USA 115, E7863–E7870 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, X., Liu, X., Zhang, M., Dahlgren, R. A. & Eitzel, M. A review of vegetated buffers and a meta-analysis of their mitigation efficacy in reducing nonpoint source pollution. J. Environ. Qual. 39, 76–84 (2010).CAS 
PubMed 
Article 

Google Scholar 
Eyhorn, F. et al. Sustainability in global agriculture driven by organic farming. Nat. Sustain. 2, 253–255 (2019).Article 

Google Scholar 
Buck, D., Getz, C. & Guthman, J. From farm to table: the organic vegetable commodity chain of northern California. Sociol. Rural. 37, 3–20 (1997).Article 

Google Scholar 
Guthman, J. Raising organic: an agro-ecological assessment of grower practices in California. Agric. Hum. Values 17, 257–266 (2000).Article 

Google Scholar 
Guthman, J. The trouble with ‘organic lite’ in California: a rejoinder to the ‘conventionalisation’ debate. Sociol. Rural. 44, 301–316 (2004).Article 

Google Scholar 
Darnhofer, I., Lindenthal, T., Bartel-Kratochvil, R. & Zollitsch, W. Conventionalisation of organic farming practices: from structural criteria towards an assessment based on organic principles. A review. Agron. Sustain. Dev. 30, 67–81 (2010).Article 

Google Scholar 
Constance, D. H., Choi, J. Y. & Lyke-Ho-Gland, H. Conventionalization, bifurcation, and quality of life: certified and non-certified organic farmers in Texas. J. Rural Soc. Sci. 23, 208–234 (2008).
Google Scholar 
2017 Census of Agriculture – United States Summary and State Data (USDA NASS, 2019); https://www.nass.usda.gov/Publications/AgCensus/2017/index.php2017 Census of Agriculture: Characteristics of All Farms and Farms with Organic Sales (USDA NASS, 2019); https://www.nass.usda.gov/Publications/AgCensus/2017/index.phpPonisio, L. C. et al. Diversification practices reduce organic to conventional yield gap. Proc. R. Soc. B 282, 20141396 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Wezel, A. et al. Agroecological practices for sustainable agriculture. A review. Agron. Sustain. Dev. 34, 1–20 (2014).Article 

Google Scholar 
Gomiero, T., Pimentel, D. & Paoletti, M. G. Environmental impact of different agricultural management practices: conventional vs. organic agriculture. Crit. Rev. Plant Sci. 30, 95–124 (2011).Article 

Google Scholar 
Tittonell, P. et al. Agroecology in large scale farming—a research agenda. Front. Sustain. Food Syst. 4, 584605 (2020).Article 

Google Scholar 
Haan, N. L., Zhang, Y. & Landis, D. A. Predicting landscape configuration effects on agricultural pest suppression. Trends Ecol. Evol. 35, 175–186 (2020).PubMed 
Article 

Google Scholar 
Martin, E. A., Seo, B., Park, C.-R., Reineking, B. & Steffan-Dewenter, I. Scale-dependent effects of landscape composition and configuration on natural enemy diversity, crop herbivory, and yields. Ecol. Appl. 26, 448–462 (2016).PubMed 
Article 

Google Scholar 
Tscharntke, T. et al. Landscape moderation of biodiversity patterns and processes – eight hypotheses. Biol. Rev. 87, 661–685 (2012).PubMed 
Article 

Google Scholar 
Olimpi, E. M. et al. Evolving food safety pressures in California’s central coast region. Front. Sustain. Food Syst. 3, 102 (2019).Article 

Google Scholar 
Karp, D. S. et al. The unintended ecological and social impacts of food safety regulations in California’s central coast region. BioScience 65, 1173–1183 (2015).Article 

Google Scholar 
Bovay, J., Ferrier, P. & Zhen, C. Estimated Costs for Fruit and Vegetable Producers To Comply With the Food Safety Modernization Act’s Produce Rule, EIB-195 (U.S. Department of Agriculture, Economic Research Service, 2018).Coombes, B. & Campbell, H. Dependent reproduction of alternative modes of agriculture: organic farming in New Zealand. Sociol. Rural. 38, 127–145 (1998).Article 

Google Scholar 
Hughner, R. S., McDonagh, P., Prothero, A., Shultz, C. J. & Stanton, J. Who are organic food consumers? A compilation and review of why people purchase organic food. J. Consum. Behav. 6, 94–110 (2007).Article 

Google Scholar 
Smith, E. & Marsden, T. Exploring the ‘limits to growth’ in UK organics: beyond the statistical image. J. Rural Stud. 20, 345–357 (2004).Article 

Google Scholar 
Howard, P. H. Concentration and Power in the Food System: Who Controls What We Eat? (Bloomsbury, 2016).Arcuri, A. The transformation of organic regulation: the ambiguous effects of publicization. Regul. Gov. 9, 144–159 (2015).Article 

Google Scholar 
Seufert, V., Ramankutty, N. & Mayerhofer, T. What is this thing called organic? – How organic farming is codified in regulations. Food Policy 68, 10–20 (2017).Article 

Google Scholar 
Guthman, J. in Alternative Food Politics: From the Margins to the Mainstream (eds. Phillipov, M. & Kirkwood, K.) 23–36 (Routledge, 2019).Jaffee, D. & Howard, P. H. Corporate cooptation of organic and fair trade standards. Agric. Hum. Values 27, 387–399 (2010).Article 

Google Scholar 
Campbell, H. & Rosin, C. After the ‘organic industrial complex’: an ontological expedition through commercial organic agriculture in New Zealand. J. Rural Stud. 27, 350–361 (2011).Article 

Google Scholar 
Lockie, S. & Halpin, D. The ‘conventionalisation’ thesis reconsidered: structural and ideological transformation of Australian organic agriculture. Sociol. Rural. 45, 284–307 (2005).Article 

Google Scholar 
Prokopy, L. S. et al. Adoption of agricultural conservation practices in the United States: evidence from 35 years of quantitative literature. J. Soil Water Conserv. 74, 520–534 (2019).Article 

Google Scholar 
Pretty, J. et al. Global assessment of agricultural system redesign for sustainable intensification. Nat. Sustain. 1, 441–446 (2018).Article 

Google Scholar 
Gliessman, S. Transforming food systems with agroecology. Agroecol. Sustain. Food Syst. 40, 187–189 (2016).Article 

Google Scholar 
Hill, S. B. Redesigning the food system for sustainability. Alternatives 12, 32–36 (1985).
Google Scholar 
Padel, S., Levidow, L. & Pearce, B. UK farmers’ transition pathways towards agroecological farm redesign: evaluating explanatory models. Agroecol. Sustain. Food Syst. 44, 139–163 (2020).Article 

Google Scholar 
Esquivel, K. E. et al. The ‘sweet spot’ in the middle: why do mid-scale farms adopt diversification practices at higher rates? Front. Sustain. Food Syst. 5, 734088 (2021).Article 

Google Scholar 
Brislen, L. Meeting in the middle: scaling-up and scaling-over in alternative food networks. Cult. Agric. Food Environ. 40, 105–113 (2018).Article 

Google Scholar 
De Master, K. New inquiries into the agri-cultures of the middle. Cult. Agric. Food Environ. 40, 130–135 (2018).Article 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).Article 

Google Scholar 
Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 
CAS 

Google Scholar 
Lenth, R. V. emmeans: Estimated marginal means, aka least-squares means. R package version 1.7.4-1 https://CRAN.R-project.org/package=emmeans (2021).Wasserstein, R. L. & Lazar, N. A. The ASA statement on p-values: context, process, and purpose. Am. Stat. 70, 129–133 (2016).Article 

Google Scholar 
Krueger, J. I. & Heck, P. R. Putting the P-value in its place. Am. Stat. 73, 122–128 (2019).Article 

Google Scholar 
Wasserstein, R. L., Schirm, A. L. & Lazar, N. A. Moving to a world beyond ‘p < 0.05’. Am. Stat. 73(Suppl. 1), 1–19 (2019).Article  Google Scholar  Agresti, A. Categorical Data Analysis (Wiley, 2013). More

Our long-term surveillance of SARS-CoV-2 in Austria demonstrated that WBE alone yields a time-resolved map of the genetic dynamics during a pandemic. Yet one task of pathogenomic surveillance is to link genetic pathogen information with clinical manifestation and the immunological status of patients. WBE is limited in that regard since the available data are anonymized to start with. Nonetheless, WBE provides invaluable population-level guidance on epidemiological developments, which complements case-based surveillance and provides information for optimal resource allocation. This notion can also be transferred to a global perspective. WBE provides a tool to shed light on blind spots of pathogen surveillance in places and communities with poor healthcare accessibility. If carefully set up and used in respectful and coequal terms, WBE of infectious diseases could make an important contribution to global safety.To this end, several challenges must be overcome. Current WBE methods need to be expanded to other pathogens beyond SARS-CoV-2 and validated with case-based epidemiological data. Furthermore, current methods must be adapted and optimized to be applicable in locations without a centralized sewer infrastructure5. Finally, international sharing of wastewater-based pathogen sequencing data will be needed to unleash the full potential of WBE for global pathogen surveillance.We are confident that our study will support initiatives already working in these directions, as well as encouraging intensified efforts to exploit such population-level surveillance approaches in the global fight against infectious diseases.
Fabian Amman
1
& Andreas Bergthaler
2

1
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

2
Medical University Vienna, Vienna, Austria More

Field-data collectionFieldwork was conducted in DRC between January 2018 and March 2020. Ten transects (4–11 km long) were installed, identical to the approach in ref. 9, in locations that were highly likely to be peatland. These were selected to help test hypotheses about the role of vegetation, surface wetness, nutrient status and topography in peat accumulation (Fig. 1a and Supplementary Table 1). A further eight transects (0.5–3 km long) were installed to assess our peat mapping capabilities (Fig. 1a and Supplementary Table 1).Every 250 m along each transect, land cover was classified as one of six classes: water, savannah, terra firme forest, non-peat-forming seasonally inundated forest, hardwood-dominated peat swamp forest or palm-dominated peat swamp forest. Peat swamp forest was classified as palm dominated when >50% of the canopy, estimated by eye, was palms (commonly Raphia laurentii or Raphia sese). In addition, several ground-truth points were collected at locations in the vicinity of each transect from the clearly identifiable land-cover classes water, savannah and terra firme forest.Peat presence/absence was recorded every 250 m along all transects, and peat thickness (if present) was measured by inserting metal poles into the ground until the poles were prevented from going any further by the underlying mineral layer, identical to the pole method of ref. 9. In addition, a core of the full peat profile was extracted every kilometre along the ten hypothesis-testing transects, if peat was present, with a Russian-type corer (52 mm stainless steel Eijkelkamp model); these 63 cores were sealed in plastic for laboratory analysis.Peat-thickness laboratory measurementsPeat was defined as having an organic matter (OM) content of ≥65% and a thickness of ≥0.3 m (sensu ref. 9). Therefore, down-core OM content of all 63 cores was analysed to measure peat thickness. The organic matter content of each 0.1-m-thick peat sample was estimated via loss on ignition (LOI), whereby samples were heated at 550 °C for 4 h. The mass fraction lost after heating was used as an estimate of total OM content (% of mass). Peat thickness was defined as the deepest 0.1 m with OM ≥ 65%, after which there is a transition to mineral soil. Samples below this depth were excluded from further analysis. Rare mineral intrusions into the peat layer above this depth, where OM 4× the mean Cook’s distance were excluded as influential outliers. Mean pole-method offset was significantly higher along the DRC transects (0.94 m) than along those in ROC (0.48 m; P  More

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Darling, E. S., Alvarez-Filip, L., Oliver, T. A., McClanahan, T. R. & Côté, I. M. Evaluating life-history strategies of reef corals from species traits. Ecol. Lett. 15, 1378–1386 (2012).PubMed 

Google Scholar 
Bridge, T. C. L. et al. Incongruence between life-history traits and conservation status in reef corals. Coral Reefs 39, 271–279 (2020).
Google Scholar 
Raja, N. B. et al. Morphological traits of reef corals predict extinction risk but not conservation status. Glob. Ecol. Biogeogr. 30, 1597–1608 (2021).
Google Scholar 
Orzechowski, E. A. et al. Marine extinction risk shaped by trait–environment interactions over 500 million years. Glob. Change Biol. 21, 3595–3607 (2015).ADS 

Google Scholar 
Pietsch, C., Mata, S. A. & Bottjer, D. J. High temperature and low oxygen perturbations drive contrasting benthic recovery dynamics following the end-Permian mass extinction. Palaeogeogr. Palaeoclimatol. Palaeoecol. 399, 98–113 (2014).
Google Scholar 
Wagner, P. J. & Estabrook, G. F. Trait-based diversification shifts reflect differential extinction among fossil taxa. Proc. Natl. Acad. Sci. 111, 16419–16424 (2014).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kiessling, W. Geologic and Biologic Controls on the Evolution of Reefs. Annu. Rev. Ecol. Evol. Syst. 40, 173–192 (2009).
Google Scholar 
Kiessling, W. Reef expansion during the Triassic: Spread of photosymbiosis balancing climatic cooling. Palaeogeogr. Palaeoclimatol. Palaeoecol. 290, 11–19 (2010).
Google Scholar 
Foden, W. B. et al. Identifying the World’s Most Climate Change Vulnerable Species: A Systematic Trait-Based Assessment of all Birds, Amphibians and Corals. PLOS ONE 8, e65427 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hughes, A. D. & Grottoli, A. G. Heterotrophic Compensation: A Possible Mechanism for Resilience of Coral Reefs to Global Warming or a Sign of Prolonged Stress? PLOS ONE 8, e81172 (2013).ADS 
PubMed 
PubMed Central 

Google Scholar 
Stanley, G. D. Jr & Helmle, K. P. Middle Triassic Coral Growth Bands and Their Implication for Photosymbiosis. PALAIOS 25, 754–763 (2010).ADS 

Google Scholar 
van Woesik, R. et al. Hosts of the Plio-Pleistocene past reflect modern-day coral vulnerability. Proc. R. Soc. B Biol. Sci. 279, 2448–2456 (2012).
Google Scholar 
Madin, J. S. et al. The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Sci. Data 3, 160017 (2016).PubMed 
PubMed Central 

Google Scholar 
Madin, J. S. et al. A Trait-Based Approach to Advance Coral Reef Science. Trends Ecol. Evol. 31, 419–428 (2016).PubMed 

Google Scholar 
Riedel, P. Korallen in der Trias der Tethys:. Stratigraphische Reichweiten, Diversitätsmuster, Entwicklungstrends und Bedeutung als Rifforganismen. Mitteilungen Ges. Geol.- Bergbaustud. Österr. 37, 97–118 (1991).
Google Scholar 
Budd, A. F., Adrain, T. S., Park, J. W., Klaus, J. S. & Johnson, K. G. The Neogene Marine Biota of Tropical America (“NMITA”) Database: Integrating Data from the Dominican Republic Project. in Evolutionary Stasis and Change in the Dominican Republic Neogene (eds. Nehm, R. H. & Budd, A. F.) 301–310, https://doi.org/10.1007/978-1-4020-8215-3_13 (Springer Netherlands, 2008).Budd, A. F., Foster, C. T., Dawson, J. P. & Johnson, K. G. The Neogene Marine Biota of Tropical America (“NMITA”) database: Accounting for biodiversity in paleontology. J. Paleontol. 75, 743–751 (2001).
Google Scholar 
Scotese, C. R. PALEOMAP PaleoAtlas for GPlates and the PaleoData Plotter Program. https://www.earthbyte.org/paleomap-paleoatlas-for-gplates/ (2016).Johnson, K. G., Budd, A. F. & Stemann, T. A. Extinction selectivity and ecology of Neogene Caribbean reef corals. Paleobiology 21, 52–73 (1995).
Google Scholar 
Pinzón, J. H. et al. Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia). J. Biogeogr. 40, 1595–1608 (2013).
Google Scholar 
Lathuilière, B. Coraux constructeurs du Bajocien inférieur de France: 2ème partie. Geobios 33, 153–181 (2000).
Google Scholar 
Kiessling, W. & Kocsis, Á. T. Biodiversity dynamics and environmental occupancy of fossil azooxanthellate and zooxanthellate scleractinian corals. Paleobiology 41, 402–414 (2015).
Google Scholar 
Raja, N. B., Dimitrijević, D., Krause, M. C. & Kiessling, W. Ancient Reef Traits Database. Zenodo https://doi.org/10.5281/zenodo.5717611 (2022).Mannani, M. Late Triassic scleractinian corals from Nayband Formation, southwest Ardestan, Central Iran. Bol. Soc. Geológica Mex. 72, A090619 (2020).
Google Scholar 
Löser, H., Stemann, T. A. & Mitchell, S. Oldest scleractinian fauna from Jamaica (Hauterivian, Benbow Inlier). J. Paleontol. 83, 333–349 (2009).
Google Scholar 
Löser, H. Morphology, Taxonomy and Distribution of the Cretaceous coral genus Aulastraeopora (Late Barremian-Early Cenomanian; Scleractinia). Riv. Ital. Paleontol. E Stratigr. 114, (2008).Löser, H. Revision of Actinastrea, the most common Cretaceous coral genus. Paläontol. Z. 86, 15–22 (2012).
Google Scholar 
Löser, H., Werner, W. & Darga, R. A Middle Cenomanian coral fauna from the Northern Calcareous Alps (Bavaria, Southern Germany) – new insights into the evolution of Mid-Cretaceous corals. Zitteliana 53, 37–76 (2013).
Google Scholar 
Löser, H. & Bilotte, M. Taxonomy of a platy coral association from the Late Cenomanian of the southern Corbières (Aude, France). Ann. Paléontol. 103, 3–17 (2017).
Google Scholar 
Löser, H., Steuber, T. & Löser, C. Early Cenomanian coral faunas from Nea Nikopoli (Kozani, Greece; Cretaceous). Carnets Géologie Noteb. Geol. 18, 23–121 (2018).
Google Scholar 
Löser, H. Early evolution of the family Siderastraeidae (Scleractinia; Cretaceous-extant). Paläontol. Z. 90, 1–17 (2016).
Google Scholar 
Kiessling, W. et al. Massive corals in Paleocene siliciclastic sediments of Chubut (Argentina). Facies 51, 233–241 (2005).
Google Scholar 
Stolarski, J. & Vertino, A. First Mesozoic record of the scleractinian Madrepora from the Maastrichtian siliceous limestones of Poland. Facies 53, 67–78 (2007).
Google Scholar 
Yabe, H. & Sugiyama, T. 5. Younger Cenozoic Reef-corals from the Nabire Beds of Nabire, Dutch New Guinea. Proc. Imp. Acad. 18, 16–23 (1942).
Google Scholar 
Wilson, M. A., Vinn, O. & Palmer, T. J. Bivalve borings, bioclaustrations and symbiosis in corals from the Upper Cretaceous (Cenomanian) of southern Israel. Palaeogeogr. Palaeoclimatol. Palaeoecol. 414, 243–245 (2014).
Google Scholar 
Tomás, S., Löser, H. & Salas, R. Low-light and nutrient-rich coral assemblages in an Upper Aptian carbonate platform of the southern Maestrat Basin (Iberian Chain, eastern Spain). Cretac. Res. 29, 509–534 (2008).
Google Scholar 
Baron-Szabo, R. C. Scleractinian corals from the upper Berriasian of central Europe and comparison with contemporaneous coral assemblages. Zootaxa 4383, 1 (2018).Kiessling, W., Roniewicz, E., Villier, L., Leonide, P. & Struck, U. An early Hettangian coral reef in southern France: Implications for the end-Triassic reef crisis. PALAIOS 24, 657–671 (2009).ADS 

Google Scholar 
Stanley, G. D. & Beauvais, L. Middle Jurassic corals from the Wallowa terrane, west-central Idaho. J. Paleontol. 64, 352–362 (1990).
Google Scholar 
Gretz, M., Lathuilière, B., Martini, R. & Bartolini, A. The Hettangian corals of the Isle of Skye (Scotland): An opportunity to better understand the palaeoenvironmental conditions during the aftermath of the Triassic–Jurassic boundary crisis. Palaeogeogr. Palaeoclimatol. Palaeoecol. 376, 132–148 (2013).
Google Scholar 
Reolid, M., Molina, J. M., Löser, H., Navarro, V. & Ruiz-Ortiz, P. A. Coral biostromes of the Middle Jurassic from the Subbetic (Betic Cordillera, southern Spain): facies, coral taxonomy, taphonomy, and palaeoecology. Facies 55, 575–593 (2009).
Google Scholar 
Pandey, D. K., Lathuilière, B., Fürsich, F. T. & Kuldeep, S. The oldest Jurassic cyathophorid coral (Scleractinia) from siliciclastic environments of the Kachchh Basin, western India. Paläontol. Z. 76, 347–356 (2002).
Google Scholar 
Löser, H. & Heinrich, M. New coral genera and species from the Rußbach and Gosau area (Upper Cretaceous; Austria). Palaeodiversity 11, 127–149 (2018).
Google Scholar 
Stanley, G. D. & Whalen, M. T. Triassic corals and spongiomorphs from Hells Canyon, Wallowa terrane, Oregon. J. Paleontol. 63, 800–819 (1989).
Google Scholar 
Gill, G. A., Santantonio, M. & Lathuilière, B. The depth of pelagic deposits in the Tethyan Jurassic and the use of corals: an example from the Apennines. Sediment. Geol. 166, 311–334 (2004).ADS 

Google Scholar 
Baron-Szabo, R. C., Hamedani, A. & Senowbari-Daryan, B. Scleractinian corals from lower cretaceous deposits north of Esfahan (central Iran). Facies 48, 199–215 (2003).
Google Scholar 
Lathuilière, B., Baron-Szabo, R. C., Charbonnier, S. & Pacaud, J.-M. The Mesozoic scleractinian genus Adelocoenia (Stylinidae) and its Jurassic species. Carnets Géologie Noteb. Geol. 20, 367–406 (2020).
Google Scholar 
Roniewicz, E. & Stanley, G. D. Middle Triassic cnidarians from the New Pass Range, Central Nevada. J. Paleontol. 72, 246–256 (1998).
Google Scholar 
Shepherd, H. M. E., Stanley, G. D. & Amirhassankhani, F. Norian to Rhaetian scleractinian corals in the Ferdows Patch Reef (Nayband Formation, east central Iran). J. Paleontol. 86, 801–812 (2012).
Google Scholar 
Budd, A. F. & Wallace, C. C. First record of the Indo-Pacific reef coral genus Isopora in the Caribbean Region: two new species from the Neogene of Curaçao, Netherlands Antilles. Palaeontology 51, 1387–1401 (2008).
Google Scholar 
Pandolfi, J. M. A new, extinct pleistocene reef coral from the Montastraea “annularis” species complex. J. Paleontol. 81, 472–482 (2007).
Google Scholar 
El-Asa’ad, G. M. A. Oxfordian hermatypic corals from Central Saudi Arabia. Geobios 24, 267–287 (1991).
Google Scholar 
Masse, J.-P., Morycowa, E. & Fenerci-Masse, M. Valanginian-Hauterivian scleractinian coral communities from the Marseille region (SE France). Cretac. Res. 30, 178–192 (2009).
Google Scholar 
El-Sorogy, A. S. & Al-Kahtany, K. M. Contribution to the scleractinian corals of Hanifa Formation, Upper Jurassic, Jabal Al-Abakkayn, central Saudi Arabia. Hist. Biol. 27, 90–102 (2015).
Google Scholar 
Beauvais, L. & Stump, T. E. Corals, molluscs, and paleogeography of late Jurassic strata of the Cerro Pozo Serna, Sonora, Mexico. Palaeogeogr. Palaeoclimatol. Palaeoecol. 19, 275–301 (1976).
Google Scholar 
Roniewicz, E., Stanley, G. D., da Costa Monteiro, F. & Grant-Mackie, J. A. Late Triassic (Carnian) corals from Timor-Leste (East Timor): their identity, setting, and biogeography. Alcheringa Australas. J. Palaeontol. 29, 287–303 (2005).
Google Scholar 
Stanley, G. D. & Onoue, T. Upper Triassic reef corals from the Sambosan Accretionary Complex, Kyushu, Japan. Facies 61, 1 (2015).
Google Scholar 
Melnikova, G. K. & Roniewicz, E. Early Jurassic corals with dominating solitary growth forms from the Kasamurg Mountains, Central Asia. Palaeoworld 26, 124–148 (2017).
Google Scholar 
Stanley, G. D. & Beauvais, L. Corals from an Early Jurassic coral reef in British Columbia: refuge on an oceanic island reef. Lethaia 27, 35–47 (1994).
Google Scholar 
Caruthers, A. H. & Stanley, G. D. Systematic analysis of Upper Triassic silicified scleractinian corals from Wrangellia and the Alexander Terrane, Alaska and British Columbia. J. Paleontol. 82, 470–491 (2008).
Google Scholar 
Roniewicz, E. & Stanley, G. D. Upper Triassic corals from Nevada, western North America, and the implications for paleoecology and paleogeography. J. Paleontol. 87, 934–964 (2013).
Google Scholar 
Lathuilière, B. Coraux constructeurs du Bajocien inférieur de France. 1ere partie. Geobios 33, 51–72 (2000).
Google Scholar 
Morycowa, E. Supplemental data on Triassic (Anisian) corals from Upper Silesia (Poland). Ann. Soc. Geol. Pol. https://doi.org/10.14241/asgp.2018.001 (2018).Budd, A. F. & Bosellini, F. R. Revision of Oligocene Mediterranean meandroid corals in the scleractinian families Mussidae, Merulinidae and Lobophylliidae. J. Syst. Palaeontol. 14, 771–798 (2016).
Google Scholar 
Roniewicz, E. Early Norian (Triassic) Corals from the Northern Calcareous Alps, Austria, and the Intra-Norian Faunal Turnover. Acta Palaeontol. Pol. 56, 401–428 (2011).
Google Scholar 
Budd, A. F., Adrain, T. S., Park, J. W., Klaus, J. S. & Johnson, K. G. The Neogene Marine Biota of Tropical America (“NMITA”) Database: Integrating Data from the Dominican Republic Project. in Evolutionary Stasis and Change in the Dominican Republic Neogene (eds. Nehm, R. H. & Budd, A. F.) vol. 30 301–310 (Springer Netherlands, 2008).Mielnikova, G. Monstroseris, a new Upper Triassic scleractinian coral from Iran. Acta Palaeontol. Pol. 34, 71–74 (1989).
Google Scholar 
Löser, H. Taxonomy, stratigraphic distribution and palaeobiogeography of the Early Cretaceous coral genus Holocystis. Rev. Mex. Cienc. Geológicas 23, 288–301 (2006).
Google Scholar 
Löser, H. Corals from the Maastrichtian Ocozocoautla Formation (Chiapas, Mexico)-a closer look. Rev. Mex. Cienc. Geológicas 29, 534–550 (2012).
Google Scholar 
Löser, H. The Barremian coral fauna of the Serre de Bleyton mountain range (Drôme, SE France). Ann. Naturhistorischen Mus. Wien Ser. Für Mineral. Petrogr. Geol. Paläontol. Anthropol. Prähistorie 112, 575–612 (2010).
Google Scholar 
Löser, H., García-Barrera, P., Mendoza-Rosales, C. C. & Ortega-Hernández, J. Corals from the Early Cretaceous (Barremian – Early Albian) of Puebla (Mexico) – Introduction and Family Stylinidae. Rev. Mex. Cienc. Geológicas 30, 385–403 (2013).
Google Scholar 
Morycowa, E., Masse, J.-P., Arias, C. & Minondo, L. V. Montlivaltia multiformis Toula (Scleractinia) from the Aptian of the Prebetic domain (SE Spain). Span. J. Palaeontol. 16, 131–144 (2001).
Google Scholar 
Morycowa, E. & Masse, J.-P. Actinaraeopsis ventosiana, a new scleractinian species from the Lower Cretaceous of Provence (SE France). Ann. Soc. Geol. Pol. 77, 141–145 (2007).
Google Scholar 
Stolarski, J. & Taviani, M. Oligocene scleractinian corals from CRP- 3 drillhole, McMurdo Sound (Victoria Land Basin, Antarctica). Terra Antarct. 8, 1–4 (2001).
Google Scholar 
Morycowa, E. & Marcopoulou-Diacantoni, A. Albian corals from the Subpelagonian zone of Central Greece (Agrostylia, Parnassos region). Ann. Soc. Geol. Pol. 72, 1–65 (2002).
Google Scholar 
Morycowa, E. & Roniewicz, E. Revision of the genus Cladophyllia and description of Apocladophyllia gen. n.(Cladophylliidae fam. n., Scleractinia). Acta Palaeontol. Pol. 35, 165–190 (1990).
Google Scholar 
Morycowa, E. & Masse, J.-P. Lower Cretaceous Microsolenina (Scleractinia) from Provence (southern France). Ann. Soc. Geol. Pol. 79, 97–140 (2009).
Google Scholar 
Squires, R. L. & Demetrion, R. A. Paleontology of the Eocene Bateque Formation, Baja California Sur, Mexico. Contrib. Sci. 434, 1–55 (1992).
Google Scholar 
Wells, J. W. Cretaceous, Tertiary, and Recent Corals, a Sponge, and an Alga from Venezuela. J. Paleontol. 18, 429–447 (1944).
Google Scholar 
Morycowa, E. & Decrouez, D. Early Aptian scleractinian corals from the Upper Schrattenkalk of Hergiswil (Lucerne region, Helvetic Zone of central Switzerland). Rev. Paléobiol. 25, 791 (2006).
Google Scholar 
Stolarski, J. Paleogene corals from Seymour Island, Antarctic Peninsula. Palaeontol. Pol. 55, 1–63 (1996).
Google Scholar 
Vaughan, T. W. New Corals: One Recent, Alaska; Three Eocene, Alabama and Louisiana. J. Paleontol. 15, 280–284 (1941).
Google Scholar 
Stolarski, J. & Russo, A. Microstructural diversity of the stylophyllid [Scleractinia] skeleton. Acta Palaeontol. Pol. 47, (2002).Roniewicz, E. Jurassic scleractinian coral Thamnoseris Etallon, 1864 (Scleractinia), and its homeomorphs. Acta Palaeontol. Pol. 24, 51–70 (1979).
Google Scholar 
Lathuilière, B., Charbonnier, S. & Pacaud, J.-M. Nomenclatural and taxonomic acts and remarks for the revision of Jurassic corals. Zitteliana 89, 133–150 (2017).
Google Scholar 
Roniewicz, E. Upper Kimmeridgian Scleractinia of Pomerania (Poland). Ann. Soc. Geol. Pol. 47, 613–622 (1977).
Google Scholar 
Roniewicz, E. Scleractinia from the Upper Portlandian of Tisbury, Wiltshire, England. Acta Palaeontol. Pol. 15, 519–541 (1970).
Google Scholar 
Roniewicz, E. Kimmeridgian-Valanginian reef corals from the Moesian platform from Bulgaria. Ann. Soc. Geol. Pol. 78, 91–134 (2008).
Google Scholar 
Ricci, C., Lathuiliere, B. & Rusciadelli, G. Coral communities, zonation and paleoecology of an Upper Jurassic reef complex (Ellipsactinia Limestones, Central Apennines, Italy). Riv. Ital. Paleontol. E Stratigr. 124, 433–508 (2018).
Google Scholar 
Pandey, D. K. et al. Jurassic corals from southern Tunisia. Zitteliana A45, 3–34 (2005).
Google Scholar 
Pandey, D. K. et al. Jurassic corals from the Shemshak Formation of the Alborz Mountains, Iran. Zitteliana A46, 41–74 (2006).
Google Scholar 
Pandey, D. K. & Fürsich, F. T. Contributions to the Jurassic of Kachchh, Western India I. The coral fauna. Beringeria 8, 3–69.Morycowa, E. & Mišík, M. Upper Jurassic shallow-water scleractinian corals from the Pieniny Klippen Belt (Western Carpathians, Slovakia). Geol. Carpathica 56, (2005).Pandey, D. K. et al. Lower Cretaceous corals from the Koppeh Dagh, NE-Iran. Zitteliana A47, 3–52 (2007).
Google Scholar 
Morycowa, E. Corals from the Tithonian carbonate complex in the Dąbrowa Tarnowska–Szczucin area (Polish Carpathian Foreland). Ann. Soc. Geol. Pol. 82, 1–38 (2012).
Google Scholar 
Baron-Szabo, R. Corals of the Theresienstein reef (Upper Turonian-Coniacian, Salzburg, Austria). Proc. Biol. Soc. Wash. 10, 257–268 (2001).
Google Scholar 
Morycova, E. Middle Triassic Scleractinia from the Cracow-Silesia region, Poland. Acta Palaeontol. Pol. 33, 91–121 (1988).
Google Scholar 
El-Asa’ad, G. M. A. Callovian colonial corals from the Tuwaiq Mountain Limestone of Saudi Arabia. Paleontology 32, 675–684 (1989).
Google Scholar 
Roniewicz, E. & Michalik, J. Rhaetian scleractinian corals in the Western Carpathians. Geol. Carpathica 49, 391–399 (1998).
Google Scholar 
Roniewicz, E. & Michalik, J. Carnian corals from the Male Karpaty Mountains, Western Carpathians, Slovakia. Geol. Carpathica 53, 149–157 (2002).
Google Scholar 
Roniewicz, E. Rhaetian corals of the Tatra Mts. Acta Geol. Pol. 24, 97–116 (1974).
Google Scholar 
Turnšek, D. et al. Contributions to the fauna (corals, brachiopods) and stable isotopes of the Late Triassic Steinplatte reef/basin-complex, Northern Calcareous Alps, Austria. Abh. Geol. Bundensanstalt 56, 121–142 (1999).
Google Scholar 
Roniewicz, E. Upper Triassic Solitary Corals from the Gosaukamm and other North Alpine Regions. Sitzungsberichte Biol. Wiss. Erdwissenschaften 3–41 (1995).Wells, J. W. & Jenks, W. F. Mesozoic invertebrate faunas of Peru. Part 3, Lower Jurassic corals from the Arequipa region. Am. Mus. Novit. 1631 (1953).Turnšek, D. & Senowbari-Daryan, B. Upper Triassic (Carnian-Lowermost Norian) Corals from the Pantokrator Limestone of Hydra (Greece). AbhGeolB-A 50, (1994).Wells, J. W. Jurassic Corals from the Smackover Limestone, Arkansas. J. Paleontol. 16, 126–129 (1942).
Google Scholar 
Turnšek, D., Buser, S. & Debeljak, I. Liassic coral patch reef above the” Lithiotid limestone” on Trnovski gozd plateau, west Slovenia: Liasni koralni kopasti greben na” litiotidnem apnencu” v Trnovskem gozdu, zahodna Slovenija. Razpr. IV Razreda SAZU XLIV–1, 285–331 (2003).
Google Scholar 
Turnšek, D. & Košir, A. Early Jurassic corals from Krim Mountain, Slovenia. Razpr. IV Razreda SAZU XLI–1, 81–113 (2000).
Google Scholar 
Roniewicz, E. Triassic scleractinian corals of the Zlambach Beds, Northern Calcareous Alps, Austria. Denkschr Osterr Akad Wiss Math Nat K1 126, 1–152 (1989).
Google Scholar 
Roniewicz, E. Les scléractiniaires du Jurassique supérieur de la Dobrogea centrale, Roumanie. Palaeontol. Pol. 34, 17–121 (1976).
Google Scholar 
Kiessling, W., Kumar Pandey, D., Schemm-Gregory, M., Mewis, H. & Aberhan, M. Marine benthic invertebrates from the Upper Jurassic of northern Ethiopia and their biogeographic affinities. J. Afr. Earth Sci. 59, 195–214 (2011).ADS 

Google Scholar 
Lathuilière, B. Coraux constructeurs du Bajocien inférieur de France: 2ème partie. Geobios 33, 153–181 (2000).
Google Scholar 
Baron‐Szabo, R. C. Corals of the K/T‐boundary: Scleractinian corals of the suborders Astrocoeniina, Faviina, Rhipidogyrina and Amphiastraeina. J. Syst. Palaeontol. 4, 1–108 (2006).
Google Scholar 
Filkorn, H. F. & Pantoja-Alor, J. NOMENCLATURAL NOTES Mexican Cretaceous coral species (Cnidaria, Anthozoa, Scleractinia) described as new by Filkorn & Pantoja-Alor (2009), but deemed ‘unpublished’ under the International Code of Zoological Nomenclature: republication of data necessary for nomenclatural availability. Bull. Zool. Nomencl. 72, 93–101 (2015).
Google Scholar 
Olden, J. D., Poff, N. L. & Bestgen, K. R. Trait Synergisms and the Rarity, Extirpation, and Extinction Risk of Desert Fishes. Ecology 89, 847–856 (2008).PubMed 

Google Scholar 
Schleuning, M. et al. Trait-Based Assessments of Climate-Change Impacts on Interacting Species. Trends Ecol. Evol. 35, 319–328 (2020).PubMed 

Google Scholar 
Solan, M., Aspden, R. J. & Paterson, D. M. Marine Biodiversity and Ecosystem Functioning: Frameworks, Methodologies, and Integration. (OUP Oxford, 2012).Suding, K. N. et al. Scaling environmental change through the community-level: a trait-based response-and-effect framework for plants. Glob. Change Biol. 14, 1125–1140 (2008).ADS 

Google Scholar 
Finnegan, S. et al. Paleontological baselines for evaluating extinction risk in the modern oceans. Science https://doi.org/10.1126/science.aaa6635 (2015).Yasuhara, M. & Deutsch, C. A. Paleobiology provides glimpses of future ocean. Science https://doi.org/10.1126/science.abn2384 (2022).Cooley, S. et al. Ocean and coastal ecosystems and their services. in Climate change 2022: Impacts, adaptation and vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel of Climate Change (IPCC) (eds. Pörtner, H.-O. et al.) (Cambridge University Press, 2022). More

Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, et al. Antibiotic resistance—the need for global solutions. Lancet Infect Dis. 2013;13:1057–98.PubMed 
Article 

Google Scholar 
Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399:629–55.CAS 
Article 

Google Scholar 
O’Neil J. Antimicrobial resistance: tackling a crisis for the health and wealth of nations. The review on antimicrobial resistance. 2014. https://amr-review.org/sites/default/files/AMRReviewPaper-Tacklingacrisisforthehealthandwealthofnations_1.pdf.Pang Z, Raudonis R, Glick BR, Lin T-J, Cheng Z. Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and alternative therapeutic strategies. Biotechnol Adv. 2019;37:177–92.CAS 
PubMed 
Article 

Google Scholar 
Vandeplassche E, Tavernier S, Coenye T, Crabbé A. Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens. Eur Respir Rev. 2019;28:190041.PubMed 
Article 

Google Scholar 
Wheatley R, Diaz Caballero J, Kapel N, de Winter FHR, Jangir P, Quinn A, et al. Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection. Nat Commun. 2021;12:2460.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Adamowicz EM, Flynn J, Hunter RC, Harcombe WR. Cross-feeding modulates antibiotic tolerance in bacterial communities. ISME J. 2018;12:2723–35.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Allison DG, Matthews MJ. Effect of polysaccharide interactions on antibiotic susceptibility of Pseudomonas aeruginosa. J Appl Bacteriol. 1992;73:484–8.CAS 
PubMed 
Article 

Google Scholar 
Beaudoin T, Yau YCW, Stapleton PJ, Gong Y, Wang PW, Guttman DS, et al. Staphylococcus aureus with Pseudomonas aeruginosa biofilm enhances tobramycin resistance. Npj Biofilms Microbiomes. 2017;3:25.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bottery MJ, Matthews JL, Wood AJ, Johansen HK, Pitchford JW, Friman V-P. Inter-species interactions alter antibiotic efficacy in bacterial communities. ISME J. 2022;16:812–21.CAS 
PubMed 
Article 

Google Scholar 
Elias S, Banin E. Multi-species biofilms: living with friendly neighbors. FEMS Microbiol Rev. 2012;36:990–1004.CAS 
PubMed 
Article 

Google Scholar 
Hoffman LR, Deziel E, D’Argenio DA, Lepine F, Emerson J, McNamara S, et al. Selection for Staphylococcus aureus small-colony variants due to growth in the presence of Pseudomonas aeruginosa. Proc Natl Acad Sci USA. 2006;103:19890–5.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Molina-Santiago C, Daddaoua A, Fillet S, Duque E, Ramos J-L. Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance: Antibiotic resistance. Environ Microbiol. 2014;16:1267–81.CAS 
PubMed 
Article 

Google Scholar 
Orazi G, O’Toole GA. Pseudomonas aeruginosa alters Staphylococcus aureus sensitivity to vancomycin in a biofilm model of cystic fibrosis infection. mBio. 2017;8:e00873–17. https://doi.org/10.1128/mBio.00873-17.Article 
PubMed 
PubMed Central 

Google Scholar 
Perlin MH, Clark DR, McKenzie C, Patel H, Jackson N, Kormanik C, et al. Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations. Proc R Soc B Biol Sci. 2009;276:3759–68.CAS 
Article 

Google Scholar 
Ryan RP, Fouhy Y, Garcia BF, Watt SA, Niehaus K, Yang L, et al. Interspecies signalling via the Stenotrophomonas maltophilia diffusible signal factor influences biofilm formation and polymyxin tolerance in Pseudomonas aeruginosa. Mol Microbiol. 2008;68:75–86.CAS 
PubMed 
Article 

Google Scholar 
Sherrard LJ, McGrath SJ, McIlreavey L, Hatch J, Wolfgang MC, Muhlebach MS, et al. Production of extended-spectrum β -lactamases and the potential indirect pathogenic role of Prevotella isolates from the cystic fibrosis respiratory microbiota. Int J Antimicrob Agents. 2016;47:140–5.CAS 
PubMed 
Article 

Google Scholar 
Tognon M, Köhler T, Gdaniec BG, Hao Y, Lam JS, Beaume M, et al. Co-evolution with Staphylococcus aureus leads to lipopolysaccharide alterations in Pseudomonas aeruginosa. ISME J. 2017;11:2233–43.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Adamowicz EM, Muza M, Chacón JM, Harcombe WR. Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica. PLOS Pathog. 2020;16:e1008700.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Bottery MJ, Pitchford JW, Friman V-P. Ecology and evolution of antimicrobial resistance in bacterial communities. ISME J. 2021;15:939–48.PubMed 
Article 

Google Scholar 
Estrela S, Brown SP. Community interactions and spatial structure shape selection on antibiotic resistant lineages. PLOS Comput Biol. 2018;14:e1006179.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Klümper U, Recker M, Zhang L, Yin X, Zhang T, Buckling A, et al. Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. ISME J. 2019;13:2927–37.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Scheuerl T, Hopkins M, Nowell RW, Rivett DW, Barraclough TG, Bell T. Bacterial adaptation is constrained in complex communities. Nat Commun. 2020;11:754.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sorg RA, Lin L, van Doorn GS, Sorg M, Olson J, Nizet V, et al. Collective resistance in microbial communities by intracellular antibiotic deactivation. PLOS Biol. 2016;14:e2000631.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Kulczycki LL, Kostuch M, Bellanti JA. A clinical perspective of cystic fibrosis and new genetic findings: relationship of CFTR mutations to genotype-phenotype manifestations. Am J Med Genet. 2003;116A:262–7.PubMed 
Article 

Google Scholar 
Flume PA, Mogayzel PJ, Robinson KA, Rosenblatt RL, Quittell L, Marshall BC. Cystic fibrosis pulmonary guidelines: pulmonary complications: hemoptysis and pneumothorax. Am J Respir Crit Care Med. 2010;182:298–306.PubMed 
Article 

Google Scholar 
Belkin RA, Henig NR, Singer LG, Chaparro C, Rubenstein RC, Xie SX, et al. Risk factors for death of patients with cystic fibrosis awaiting lung transplantation. Am J Respir Crit Care Med. 2006;173:659–66.PubMed 
Article 

Google Scholar 
Martin C, Hamard C, Kanaan R, Boussaud V, Grenet D, Abély M, et al. Causes of death in French cystic fibrosis patients: the need for improvement in transplantation referral strategies! J Cyst Fibros. 2016;15:204–12.PubMed 
Article 

Google Scholar 
Döring G, Conway SP, Heijerman HGM, Hodson ME, Høiby N, Smyth A, et al. Antibiotic therapy against Pseudomonas aeruginosa in cystic fibrosis: a European consensus. Eur Respir J. 2000;16:749.PubMed 
Article 

Google Scholar 
Marshall B, Faro A, Brown W, Elbert A, Fink A, Cromwell E, et al. Patient registry, annual data report. Bethesda, Maryland: Cystic Fibrosis Foundation; 2020. https://www.cff.org/sites/default/files/2021-11/Patient-Registry-Annual-Data-Report.pdf.Vongthilath R, Richaud Thiriez B, Dehillotte C, Lemonnier L, Guillien A, Degano B, et al. Clinical and microbiological characteristics of cystic fibrosis adults never colonized by Pseudomonas aeruginosa: analysis of the French CF registry. PLOS ONE. 2019;14:e0210201.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zolin A, Orenti A, Jung A, van Rens J. ECFSPR annual report 2019. Denmark: European Cystic Fibrosis Society Patient Registry; 2021. https://www.ecfs.eu/sites/default/files/general-content-files/working-groups/ecfs-patient-registry/ECFSPR_Report_2019_v1_16Feb2022.pdf.Conrad D, Haynes M, Salamon P, Rainey PB, Youle M, Rohwer F. Cystic fibrosis therapy: a community ecology perspective. Am J Respir Cell Mol Biol. 2013;48:150–6.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Filkins LM, Graber JA, Olson DG, Dolben EL, Lynd LR, Bhuju S, et al. Coculture of Staphylococcus aureus with Pseudomonas aeruginosa drives S. aureus towards fermentative metabolism and reduced viability in a cystic fibrosis model. J Bacteriol. 2015;197:2252–64.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA. 2012;109:5809–14.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ballestero S, Vírseda I, Escobar H, Suárez L, Baquero F. Stenotrophomonas maltophilia in cystic fibrosis patients. Eur J Clin Microbiol Infect Dis. 1995;14:728–9.CAS 
PubMed 
Article 

Google Scholar 
Gladman G, Connor PJ, Williams RF, David TJ. Controlled study of Pseudomonas cepacia and Pseudomonas maltophilia in cystic fibrosis. Arch Dis Child. 1992;67:192–5.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Goss CH. Association between Stenotrophomonas maltophilia and lung function in cystic fibrosis. Thorax. 2004;59:955–9.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Parkins MD, Floto RA. Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis. J Cyst Fibros. 2015;14:293–304.CAS 
PubMed 
Article 

Google Scholar 
Goss CH, Otto K, Aitken ML, Rubenfeld GD. Detecting Stenotrophomonas maltophilia does not reduce survival of patients with cystic fibrosis. Am J Respir Crit Care Med. 2002;166:356–61.PubMed 
Article 

Google Scholar 
Alonso A, Martínez JL. Multiple antibiotic resistance in Stenotrophomonas maltophilia. Antimicrob Agents Chemother. 1997;41:1140–2.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhang L, Li XZ, Poole K. Multiple antibiotic resistance in Stenotrophomonas maltophilia: involvement of a multidrug efflux system. Antimicrob Agents Chemother. 2000;44:287–93.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Abda EM, Krysciak D, Krohn-Molt I, Mamat U, Schmeisser C, Förstner KU, et al. Phenotypic heterogeneity affects Stenotrophomonas maltophilia K279a colony morphotypes and β-lactamase expression. Front Microbiol. 2015;6:1373.Okazaki A, Avison MB. Induction of L1 and L2 β-lactamase production in Stenotrophomonas maltophilia is dependent on an AmpR-type regulator. Antimicrob Agents Chemother. 2008;52:1525–8.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Walsh TR, Hall L, Assinder SJ, Nichols WW, Cartwright SJ, MacGowan AP, et al. Sequence analysis of the L1 metallo-β-lactamase from Xanthomonas maltophilia. Biochim Biophys Acta. 1994;1218:199–201.CAS 
PubMed 
Article 

Google Scholar 
Yang Z, Liu W, Cui Q, Niu W, Li H, Zhao X, et al. Prevalence and detection of Stenotrophomonas maltophilia carrying metallo-I2-lactamase blaL1 in Beijing, China. Front Microbiol. 2014;5:692.Kataoka D, Fujiwara H, Kawakami T, Tanaka Y, Tanimoto A, Ikawa S, et al. The indirect pathogenicity of Stenotrophomonas maltophilia. Int J Antimicrob Agents. 2003;22:601–6.CAS 
PubMed 
Article 

Google Scholar 
Winstanley C, O’Brien S, Brockhurst MA. Pseudomonas aeruginosa evolutionary adaptation and diversification in cystic fibrosis chronic lung infections. Trends Microbiol. 2016;24:327–37.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
McGuigan L, Callaghan M. The evolving dynamics of the microbial community in the cystic fibrosis lung. Environ Microbiol. 2015;17:16–28.PubMed 
Article 

Google Scholar 
Wistrand-Yuen E, Knopp M, Hjort K, Koskiniemi S, Berg OG, Andersson DI. Evolution of high-level resistance during low-level antibiotic exposure. Nat Commun. 2018;9:1599.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Mahrt N, Tietze A, Künzel S, Franzenburg S, Barbosa C, Jansen G, et al. Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance. Nat Ecol Evol. 2021;5:1233–1242.Govaert L, Altermatt F, De Meester L, Leibold MA, McPeek MA, Pantel JH, et al. Integrating fundamental processes to understand eco‐evolutionary community dynamics and patterns. Funct Ecol. 2021;35:2138–55.Article 

Google Scholar 
Palmer KL, Aye LM, Whiteley M. Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum. J Bacteriol. 2007;189:8079–87.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Souza Barbosa F, Capra Pezzi L, Tsao M, Oliveira TF, Manoela Dias Macedo S, Schapoval EES, et al. Stability and degradation products of imipenem applying High‐Resolution Mass Spectrometry: an analytical study focused on solutions for infusion. Biomed Chromatogr. 2018;33:4471.Verpooten G, Verbist L, Buntinx A, Entwistle L, Jones K, Broe M. The pharmacokinetics of imipenem (thienamycin-formamidine) and the renal dehydropeptidase inhibitor cilastatin sodium in normal subjects and patients with renal failure. Br J Clin Pharmacol. 1984;18:183–93.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Li H, Luo Y-F, Williams BJ, Blackwell TS, Xie C-M. Structure and function of OprD protein in Pseudomonas aeruginosa: from antibiotic resistance to novel therapies. Int J Med Microbiol. 2012;302:63–8.CAS 
PubMed 
Article 

Google Scholar 
Kousser C, Clark C, Sherrington S, Voelz K, Hall RA. Pseudomonas aeruginosa inhibits Rhizopus microsporus germination through sequestration of free environmental iron. Sci Rep. 2019;9:5714.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Schalk IJ, Guillon L. Pyoverdine biosynthesis and secretion in Pseudomonas aeruginosa: implications for metal homeostasis: pyoverdine biosynthesis. Environ Microbiol. 2013;15:1661–73.CAS 
PubMed 
Article 

Google Scholar 
Duan X, Pan Y, Cai Z, Liu Y, Zhang Y, Liu M, et al. rpoS-mutation variants are selected in Pseudomonas aeruginosa biofilms under imipenem pressure. Cell Biosci. 2021;11:138.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zhu K, Chen S, Sysoeva TA, You L. Universal antibiotic tolerance arising from antibiotic-triggered accumulation of pyocyanin in Pseudomonas aeruginosa. PLOS Biol. 2019;17:e3000573.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
El-Fouly MZ, Sharaf AM, Shahin AAM, El-Bialy HA, Omara AMA. Biosynthesis of pyocyanin pigment by Pseudomonas aeruginosa. J Radiat Res Appl Sci. 2015;8:36–48.CAS 
Article 

Google Scholar 
Baron SS, Rowe JJ. Antibiotic action of pyocyanin. Antimicrob Agents Chemother. 1981;20:814–20.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kimura M, Ohta T. The average number of generations until fixation of a mutant gene in a finite population. Genetics. 1969;61:763–71.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Meirelles LA, Perry EK, Bergkessel M, Newman DK. Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics. PLOS Biol. 2021;19:e3001093.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Hall JPJ, Harrison E, Brockhurst MA. Competitive species interactions constrain abiotic adaptation in a bacterial soil community. Evol Lett. 2018;2:580–9.PubMed 
PubMed Central 
Article 

Google Scholar 
Scanlan PD, Hall AR, Blackshields G, Friman V-P, Davis MR, Goldberg JB, et al. Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations. Mol Biol Evol. 2015;32:1425–35.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Finkel SE. Long-term survival during stationary phase: evolution and the GASP phenotype. Nat Rev Microbiol. 2006;4:113–20.CAS 
PubMed 
Article 

Google Scholar 
Gefen O, Fridman O, Ronin I, Balaban NQ. Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity. Proc Natl Acad Sci. 2014;111:556–61.CAS 
PubMed 
Article 

Google Scholar 
Fang Z, Zhang L, Huang Y, Qing Y, Cao K, Tian G, et al. OprD mutations and inactivation in imipenem-resistant Pseudomonas aeruginosa isolates from China. Infect Genet Evol. 2014;21:124–8.CAS 
PubMed 
Article 

Google Scholar 
Hirabayashi A, Kato D, Tomita Y, Iguchi M, Yamada K, Kouyama Y, et al. Risk factors for and role of OprD protein in increasing minimal inhibitory concentrations of carbapenems in clinical isolates of Pseudomonas aeruginosa. J Med Microbiol. 2017;66:1562–72.CAS 
PubMed 
Article 

Google Scholar 
Huang H, Jeanteur D, Pattus F, Hancock REW. Membrane topology and site-specific mutagenesis of Pseudomonas aeruginosa porin OprD. Mol Microbiol. 1995;16:931–41.CAS 
PubMed 
Article 

Google Scholar 
Fournier D, Richardot C, Müller E, Robert-Nicoud M, Llanes C, Plésiat P, et al. Complexity of resistance mechanisms to imipenem in intensive care unit strains of Pseudomonas aeruginosa. J Antimicrob Chemother. 2013;68:1772–80.CAS 
PubMed 
Article 

Google Scholar 
Kao C-Y, Chen S-S, Hung K-H, Wu H-M, Hsueh P-R, Yan J-J, et al. Overproduction of active efflux pump and variations of OprD dominate in imipenem-resistant Pseudomonas aeruginosa isolated from patients with bloodstream infections in Taiwan. BMC Microbiol. 2016;16:107.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Ocampo-Sosa AA, Cabot G, Rodríguez C, Roman E, Tubau F, Macia MD, et al. Alterations of OprD in carbapenem-intermediate and -susceptible strains of Pseudomonas aeruginosa isolated from patients with bacteremia in a Spanish multicenter study. Antimicrob Agents Chemother. 2012;56:1703–13.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Shu J-C, Kuo A-J, Su L-H, Liu T-P, Lee M-H, Su I-N, et al. Development of carbapenem resistance in Pseudomonas aeruginosa is associated with OprD polymorphisms, particularly the amino acid substitution at codon 170. J Antimicrob Chemother. 2017;72:2489–95.CAS 
PubMed 
Article 

Google Scholar 
Pernet E, Guillemot L, Burgel P-R, Martin C, Lambeau G, Sermet-Gaudelus I, et al. Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity. Nat Commun. 2014;5:5105.CAS 
PubMed 
Article 

Google Scholar 
Briaud P, Camus L, Bastien S, Doléans-Jordheim A, Vandenesch F, Moreau K. Coexistence with Pseudomonas aeruginosa alters Staphylococcus aureus transcriptome, antibiotic resistance and internalization into epithelial cells. Sci Rep. 2019;9:16564.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Khare A, Tavazoie S. Multifactorial competition and resistance in a two-species bacterial system. PLOS Genet. 2015;11:e1005715.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Mashburn LM, Jett AM, Akins DR, Whiteley M. Staphylococcus aureus serves as an iron source for Pseudomonas aeruginosa during in vivo coculture. J Bacteriol. 2005;187:554–66.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cirz RT, O’Neill BM, Hammond JA, Head SR, Romesberg FE. Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin. J Bacteriol. 2006;188:7101–10.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
García-Contreras R, Nuñez-López L, Jasso-Chávez R, Kwan BW, Belmont JA, Rangel-Vega A, et al. Quorum sensing enhancement of the stress response promotes resistance to quorum quenching and prevents social cheating. ISME J. 2015;9:115–25.PubMed 
Article 
CAS 

Google Scholar 
Moradali MF, Ghods S, Rehm BHA. Pseudomonas aeruginosa lifestyle: a paradigm for adaptation, survival, and persistence. Front Cell Infect Microbiol 2017;7:39.Vogt SL, Green C, Stevens KM, Day B, Erickson DL, Woods DE, et al. The stringent response is essential for Pseudomonas aeruginosa virulence in the rat lung agar bead and Drosophila melanogaster feeding models of infection. Infect Immun. 2011;79:4094–104.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Baron SS, Terranova G, Rowe JJ. Molecular mechanism of the antimicrobial action of pyocyanin. Curr Microbiol. 1989;18:223–30.CAS 
Article 

Google Scholar 
Castañeda-Tamez P, Ramírez-Peris J, Pérez-Velázquez J, Kuttler C, Jalalimanesh A, Saucedo-Mora MÁ, et al. Pyocyanin restricts social cheating in Pseudomonas aeruginosa. Front Microbiol. 2018;9:1348.PubMed 
PubMed Central 
Article 

Google Scholar 
Fontoura R, Spada JC, Silveira ST, Tsai SM, Brandelli A. Purification and characterization of an antimicrobial peptide produced by Pseudomonas sp. strain 4B. World J Microbiol Biotechnol. 2009;25:205–13.CAS 
Article 

Google Scholar 
Hassan HM, Fridovich I. Mechanism of the antibiotic action pyocyanine. J Bacteriol. 1980;141:156–63.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Machan ZA, Pitt TL, White W, Watson D, Taylor GW, Cole PJ, et al. Interaction between Pseudomonas aeruginosa and Staphylococcus aureus: description of an antistaphylococcal substance. J Med Microbiol. 1991;34:213–7.CAS 
PubMed 
Article 

Google Scholar 
Raji El Feghali PA, Nawas T. Pyocyanin: a powerful inhibitor of bacterial growth and biofilm formation. Madridge J Case Rep Stud. 2018;3:101–7.Article 

Google Scholar 
Saha S, Thavasi R, Jayalakshmi S. Phenazine pigments from Pseudomonas aeruginosa and their application as antibacterial agent and food colourants. Res J Microbiol. 2008;3:122–8.CAS 
Article 

Google Scholar 
Schiessl KT, Hu F, Jo J, Nazia SZ, Wang B, Price-Whelan A, et al. Phenazine production promotes antibiotic tolerance and metabolic heterogeneity in Pseudomonas aeruginosa biofilms. Nat Commun. 2019;10:762.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Jagmann N, Brachvogel H-P, Philipp B. Parasitic growth of Pseudomonas aeruginosa in co-culture with the chitinolytic bacterium Aeromonas hydrophila: parasitic growth of Pseudomonas aeruginosa. Environ Microbiol. 2010;12:1787–802.CAS 
PubMed 
Article 

Google Scholar 
Noto MJ, Burns WJ, Beavers WN, Skaar EP. Mechanisms of pyocyanin toxicity and genetic determinants of resistance in Staphylococcus aureus. J Bacteriol. 2017;199:00221–17.Venkataraman A, Rosenbaum MA, Perkins SD, Werner JJ, Angenent LT. Metabolite-based mutualism between Pseudomonas aeruginosa PA14 and Enterobacter aerogenes enhances current generation in bioelectrochemical systems. Energy Environ Sci. 2011;4:4550.CAS 
Article 

Google Scholar 
Waite RD, Qureshi MR, Whiley RA. Modulation of behaviour and virulence of a high alginate expressing Pseudomonas aeruginosa strain from cystic fibrosis by oral commensal bacterium Streptococcus anginosus. PLOS ONE. 2017;12:e0173741.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Whooley MA, McLoughlin AJ. The regulation of pyocyanin production in Pseudomonas aeruginosa. Eur J Appl Microbiol Biotechnol. 1982;15:161–6.CAS 
Article 

Google Scholar 
Elbargisy RM. Optimization of nutritional and environmental conditions for pyocyanin production by urine isolates of Pseudomonas aeruginosa. Saudi J Biol Sci. 2021;28:993–1000.CAS 
PubMed 
Article 

Google Scholar 
Gupta S, Laskar N, Kadouri DE. Evaluating the effect of oxygen concentrations on antibiotic sensitivity, growth, and biofilm formation of human pathogens. Microbiol Insights. 2016;9. https://doi.org/10.4137/MBI.S40767.Article 
PubMed 
PubMed Central 

Google Scholar 
Worlitzsch D, Tarran R, Ulrich M, Schwab U, Cekici A, Meyer KC, et al. Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J Clin Investig. 2002;109:317–25.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Skurnik D, Roux D, Cattoir V, Danilchanka O, Lu X, Yoder-Himes DR, et al. Enhanced in vivo fitness of carbapenem-resistant oprD mutants of Pseudomonas aeruginosa revealed through high-throughput sequencing. Proc Natl Acad Sci USA. 2013;110:20747–52.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Higgins S, Heeb S, Rampioni G, Fletcher MP, Williams P, Cámara M. Differential regulation of the phenazine biosynthetic operons by quorum sensing in Pseudomonas aeruginosa PAO1-N. Front Cell Infect Microbiol. 2018;8:252.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Dragoš A, Martin M, Falcón García C, Kricks L, Pausch P, Heimerl T, et al. Collapse of genetic division of labour and evolution of autonomy in pellicle biofilms. Nat Microbiol. 2018;3:1451–60.PubMed 
Article 
CAS 

Google Scholar 
Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, et al. Lung function and microbiota diversity in cystic fibrosis. Microbiome. 2020;8:45.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Bruce KD. Characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16S ribosomal DNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol. 2004;42:5176–83.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Workentine ML, Sibley CD, Glezerson B, Purighalla S, Norgaard-Gron JC, Parkins MD, et al. Phenotypic heterogeneity of Pseudomonas aeruginosa populations in a cystic fibrosis patient. PLoS ONE. 2013;8:e60225.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Valdezate S. Persistence and variability of Stenotrophomonas maltophilia in cystic fibrosis patients, Madrid, 1991-8. Emerg Infect Dis. 2001;7:113–22.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Dalbøge CS, Hansen CR, Pressler T, Høiby N, Johansen HK. Chronic pulmonary infection with Stenotrophomonas maltophilia and lung function in patients with cystic fibrosis. J Cyst Fibros. 2011;10:318–25.PubMed 
Article 

Google Scholar 
Jeon YD, Jeong WY, Kim MH, Jung IY, Ahn MY, Ann HW, et al. Risk factors for mortality in patients with Stenotrophomonas maltophilia bacteremia. Medicine. 2016;95:e4375.PubMed 
PubMed Central 
Article 

Google Scholar 
Sherrard LJ, Tunney MM, Elborn JS. Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis. Lancet Lond Engl. 2014;384:703–13.CAS 
Article 

Google Scholar 
Choi K-H, Schweizer HP. Mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa. Nat Protoc. 2006;1:153–61.CAS 
PubMed 
Article 

Google Scholar 
Jelsbak L, Johansen HK, Frost A-L, Thøgersen R, Thomsen LE, Ciofu O, et al. Molecular epidemiology and dynamics of Pseudomonas aeruginosa populations in lungs of cystic fibrosis patients. Infect Immun. 2007;75:2214–24.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Yeung ATY, Parayno A, Hancock REW. Mucin promotes rapid surface motility in Pseudomonas aeruginosa. mBio. 2012;3:300073–12.Kirchner S, Fothergill JL, Wright EA, James CE, Mowat E, Winstanley C. Use of artificial sputum medium to test antibiotic efficacy against Pseudomonas aeruginosa in conditions more relevant to the cystic fibrosis lung. J Vis Exp. 2012;64:3857.Hill DB, Long RF, Kissner WJ, Atieh E, Garbarine IC, Markovetz MR, et al. Pathological mucus and impaired mucus clearance in cystic fibrosis patients result from increased concentration, not altered pH. Eur Respir J. 2018;52:1801297.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Benoni G, Cuzzolin L, Bertrand C, Puchetti V, Velo G. Imipenem kinetics in serum, lung tissue and pericardial fluid in patients undergoing thoracotomy. J Antimicrob Chemother. 1987;20:725–8.CAS 
PubMed 
Article 

Google Scholar 
Radhakrishnan M, Jaganath A, Rao GSU, Kumari HBV. Nebulized imipenem to control nosocomial pneumonia caused by Pseudomonas aeruginosa. J Crit Care. 2008;23:148–50.CAS 
PubMed 
Article 

Google Scholar 
Wenzler E, Fraidenburg DR, Scardina T, Danziger LH. Inhaled antibiotics for gram-negative respiratory infections. Clin Microbiol Rev. 2016;29:581–632.PubMed 
PubMed Central 
Article 

Google Scholar 
The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters.Version 12.0, 2022. http://www.eucast.org.Kang D, Revtovich AV, Chen Q, Shah KN, Cannon CL, Kirienko NV. Pyoverdine-dependent virulence of Pseudomonas aeruginosa isolates from cystic fibrosis patients. Front Microbiol. 2019;10:2048.PubMed 
PubMed Central 
Article 

Google Scholar 
Martin LW, Reid DW, Sharples KJ, Lamont IL. Pseudomonas siderophores in the sputum of patients with cystic fibrosis. BioMetals. 2011;24:1059–67.CAS 
PubMed 
Article 

Google Scholar 
Caldwell CC, Chen Y, Goetzmann HS, Hao Y, Borchers MT, Hassett DJ, et al. Pseudomonas aeruginosa exotoxin pyocyanin causes cystic fibrosis airway pathogenesis. Am J Pathol. 2009;175:2473–88.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
O’Loughlin CT, Miller LC, Siryaporn A, Drescher K, Semmelhack MF, Bassler BL. A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation. Proc Natl Acad Sci USA. 2013;110:17981–6.PubMed 
PubMed Central 
Article 

Google Scholar 
Sass G, Nazik H, Penner J, Shah H, Ansari SR, Clemons KV, et al. Studies of Pseudomonas aeruginosa mutants indicate pyoverdine as the central factor in inhibition of Aspergillus fumigatus biofilm. J Bacteriol. 2018;200:00345–17.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 
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.CAS 
PubMed 
Article 

Google Scholar 
Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. In: Sun L, Shou W, editors. Engineering and Analyzing Multicellular Systems. New York, NY: Springer New York; 2014. p. 165–88.Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.CAS 
PubMed 
Article 

Google Scholar  More