More stories

  • in

    Global warming is shifting the relationships between fire weather and realized fire-induced CO2 emissions in Europe

    Jolly, W. M. et al. Climate-induced variations in global wildfire danger from 1979 to 2013. Nat. Commun. 6, 1–11 (2015).CAS 
    Article 

    Google Scholar 
    Abatzoglou, J. T., Williams, A., Boschetti, L., Zubkova, M. & Kolden, C. A. Global patterns of interannual climate-fire relationships. Glob. Change Biol. 24, 5164–5175 (2018).ADS 
    Article 

    Google Scholar 
    Giorgi, F. Climate change hot-spots. Geophys. Res. Lett. 33, L08707 (2006).ADS 
    Article 

    Google Scholar 
    Andela, N. et al. A human-driven decline in global burned area. Science 356, 1356–1362 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    IPCC In Climate Change 2021: The Physical Science Basis (eds Masson-Delmotte, V. et al.) (Cambridge University Press, 2021).
    Google Scholar 
    Dupuy, J. et al. Climate change impact on future wildfire danger and activity in southern Europe: A review. Ann. For. Sci. 77, 35 (2020).Article 

    Google Scholar 
    Turco, M. et al. Decreasing fires in mediterranean Europe. PLoS ONE 11, e0150663 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Turco, M. et al. Exacerbated fires in Mediterranean Europe due to anthropogenic warming projected with non-stationary climate-fire models. Nat. Commun. 9, 1–9 (2018).Article 
    CAS 

    Google Scholar 
    Ruffault, J. et al. Increased likelihood of heat-induced large wildfires in the Mediterranean Basin. Sci. Rep. 10, 13790 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Moreira, F. et al. Wildfire management in Mediterranean-type regions: Paradigm change needed. Environ. Res. Lett. 15, 011001 (2020).ADS 
    Article 

    Google Scholar 
    Di Giuseppe, F. et al. Fire Weather Index: The skill provided by the European Centre for Medium-Range Weather Forecasts ensemble prediction system. Nat. Hazards Earth Syst. Sci. 20, 2365–2378 (2020).ADS 
    Article 

    Google Scholar 
    Van Wagner, C. E. Development and structure of the Canadian forest fireweather index system. Canadian Forestry Service, Forestry Technical Report 35 (1987).de Groot, W. J. et al. Development of the Indonesian and Malaysian fire danger rating systems. Mitig. Adapt. Strat. Global Change. 12, 165–180 (2007).Article 

    Google Scholar 
    Venäläinen, A. et al. Temporal variations and change in forest fire danger in Europe for 1960–2012. Nat. Hazards Earth Syst. Sci. 14, 1477–1490 (2014).ADS 
    Article 

    Google Scholar 
    Bowman, D. M. et al. Human exposure and sensitivity to globally extreme wildfire events. Nat. Ecol. Evol. 1, 1–6 (2017).Article 

    Google Scholar 
    Abatzoglou, J. T. et al. Global emergence of anthropogenic climate change in fire weather indices. Geophys. Res. Lett. 46, 326–336 (2019).ADS 
    Article 

    Google Scholar 
    Jain, P. et al. Observed increases in extreme fire weather driven by atmospheric humidity and temperature. Nat. Clim. Change 12, 63–70 (2022).ADS 
    Article 

    Google Scholar 
    Calheiros, T. et al. Recent evolution of spatial and temporal patterns of burnt areas and fire weather risk in the Iberian Peninsula. Agr. For. Meteorol. 287, 107923 (2020).Article 

    Google Scholar 
    Abatzoglou, J. T. et al. Increasing synchronous fire danger in forests of the western United States. Geophys. Res. Lett. 48, e2020GL091377 (2021).ADS 

    Google Scholar 
    Kaiser, J. W. et al. Biomass burning emissions estimated with a global fire assimilation system based on observed fire radiative power. Biogeosciences 9, 527–554 (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    Peuch, V. H. et al. The use of satellite data in the Copernicus atmosphere monitoring service. In IEEE International Geoscience and Remote Sensing Symposium (ed Moreno, J.) 1594–1596 (IEEE, 2018).Carnicer, J. et al. Regime shifts of Mediterranean forest carbon uptake and reduced resilience driven by multidecadal ocean surface temperatures. Glob. Change Biol. 25, 2825–2840 (2019).ADS 
    Article 

    Google Scholar 
    Williams, A. P. et al. Observed impacts of anthropogenic climate change on wildfire in California. Earth’s Fut. 7, 892–910 (2019).ADS 
    Article 

    Google Scholar 
    Rogers, B. M. et al. Focus on changing fire regimes: Interactions with climate, ecosystems, and society. Environ. Res. Lett. 15, 030201 (2020).ADS 
    Article 

    Google Scholar 
    Duane, A. et al. Towards a comprehensive look at global drivers of novel extreme wildfire events. Clim. Change 165, 1–21 (2021).ADS 
    Article 

    Google Scholar 
    Ellis, T. M. et al. Global increase in wildfire risk due to climate-driven declines in fuel moisture. Glob. Change Biol. 28, 1544–1559 (2022).Article 

    Google Scholar 
    Grassi, G. et al. On the realistic contribution of European forests to reach climate objectives. Carbon Balance Manag. 14, 1–5 (2019).CAS 
    Article 

    Google Scholar 
    Pilli, R., Alkama, R., Cescatti, A., Kurz, W. A. & Grassi, G. The European forest Carbon budget under future climate conditions and current management practices. Biogeosci. Discuss. 1, 33 (2022).
    Google Scholar 
    Migliavacca, M. et al. Modeling biomass burning and related carbon emissions during the 21st century in Europe. J. Geophys. Res. Biogeosci. 118, 1732–1747 (2013).CAS 
    Article 

    Google Scholar 
    Resco de Dios, V. et al. Climate change induced declines in fuel moisture may turn currently fire-free Pyrenean mountain forests into fire-prone ecosystems. Sci. Total Environ. 797, 149104 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Pausas, J. G. & Keeley, J. E. Wildfires and global change. Front. Ecol. Environ. 19, 387–395 (2021).Article 

    Google Scholar 
    Peñuelas, J. et al. Shifting from a fertilization-dominated to a warming-dominated period. Nat. Ecol. Evol. 1, 1438–1445 (2017).PubMed 
    Article 

    Google Scholar 
    Wang, S. et al. Recent global decline of CO2 fertilization effects on vegetation photosynthesis. Science 370, 1295–1300 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Carnicer, J. et al. Widespread crown condition decline, food web disruption, and amplified tree mortality with increased climate change-type drought. Proc. Natl. Acad. Sci. 108, 1474–1478 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Seidl, R., Schelhaas, M. J., Rammer, W. & Verkerk, P. J. Increasing forest disturbances in Europe and their impact on carbon storage. Nat. Clim. Change 4, 806–810 (2014).ADS 
    CAS 
    Article 

    Google Scholar 
    Forzieri, G. et al. Vulnerability of European forests to climate risks. Geophys. Res. Abstr. 21, 1 (2019).
    Google Scholar 
    Senf, C. & Seidl, R. Mapping the forest disturbance regimes of Europe. Nat. Sustain. 4, 63–70 (2021).Article 

    Google Scholar 
    Carnicer, J. et al. Forest resilience to global warming is strongly modulated by local-scale topographic, microclimatic and biotic conditions. J. Ecol. 109, 3322–3339 (2021).Article 

    Google Scholar 
    Sanginés de Cárcer, P. et al. Vapor–pressure deficit and extreme climatic variables limit tree growth. Glob. Change Biol. 24, 1108–1122 (2018).ADS 
    Article 

    Google Scholar 
    Yuan, W. et al. Increased atmospheric vapor pressure deficit reduces global vegetation growth. Sci. Adv. 5, eaax1396 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Carnicer, J., Barbeta, A., Sperlich, D., Coll, M. & Peñuelas, J. Contrasting trait syndromes in angiosperms and conifers are associated with different responses of tree growth to temperature on a large scale. Front. Plant Sci. 4, 409 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lee, H. et al. Implementing land-based mitigation to achieve the Paris Agreement in Europe requires food system transformation. Environ. Res. Lett. 14, 104009 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    Bednar-Friedl, B. et al. Europe. In Climate Change 2022: Impacts, Adaptation and Vulnerability. IPCC-WMO.Luyssaert, S. et al. Trade-offs in using European forests to meet climate objectives. Nature 562, 259–262 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nabuurs, G. J. et al. By 2050 the mitigation effects of EU forests could nearly double through climate smart forestry. Forests 8, 484 (2017).Article 

    Google Scholar 
    Vizzarri, M., Pilli, R., Korosuo, A., Frate, L. & Grassi, G. The role of forests in climate change mitigation: The EU context. In Climate-Smart Forestry in Mountain Regions (eds Tognetti, R. et al.) 507–520 (Springer, 2022).Chapter 

    Google Scholar 
    Tognetti, R., Smith, M. & Panzacchi, P. Climate-Smart Forestry in Mountain Regions 574 (Springer, 2022).Book 

    Google Scholar 
    Ali, E. et al. Mediterranean Region. In Climate Change 2022: Impacts, Adaptation and Vulnerability. IPCC-WMO.IPCC, 2021. Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (Cambridge University Press) (in press).Boer, M. M. et al. Changing weather extremes call for early warning of potential for catastrophic fire. Earth’s Fut. 5, 1196–1202 (2017).ADS 
    Article 

    Google Scholar 
    Drobyshev, I. et al. Trends and patterns in annually burned forest areas and fire weather across the European boreal zone in the 20th and early 21st centuries. Agric. For. Meteorol. 306, 108467 (2021).ADS 
    Article 

    Google Scholar 
    Chen, Y., Morton, D. C., Andela, N., Giglio, L. & Randerson, J. T. How much global burned area can be forecast on seasonal time scales using sea surface temperatures?. Environ. Res. Lett. 11, 045001 (2016).ADS 
    Article 

    Google Scholar 
    McCarty, J. L., Smith, T. E. & Turetsky, M. R. Arctic fires re-emerging. Nat. Geosci. 13, 658–660 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    Witze, A. The Arctic is burning like never before—And that’s bad news for climate change. Nature 585, 336–338 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Scholten, R. C., Jandt, R., Miller, E. A., Rogers, B. M. & Veraverbeke, S. Overwintering fires in boreal forests. Nature 593, 399–404 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Smith, T., McCarty, J., Turetsky, M. & Parrington, M. Geospatial analysis of Arctic fires in the MODIS era: 2003–2020. In EGU General Assembly Conference Abstracts (2021).Lehtonen, I., Venäläinen, A., Kämäräinen, M., Peltola, H. & Gregow, H. Risk of large-scale fires in boreal forests of Finland under changing climate. Nat. Hazards Earth Syst. Sci. 16, 239–253 (2016).ADS 
    Article 

    Google Scholar 
    Fernandes, P. M., Pereira Pacheco, A., Almeida, R. & Claro, J. The role of fire-suppression force in limiting the spread of extremely large forest fires in Portugal. Eur. J. For. Res. 135, 253–262 (2016).Article 

    Google Scholar 
    Vitolo, C. et al. ERA5-based global meteorological wildfire danger maps. Sci. Data 7, 216 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    San-Miguel-Ayanz, M. et al. In Comprehensive Monitoring of Wildfires in Europe: The European Forest Fire Information System (EFFIS) (ed. Tiefenbacher, J.) 87–108 (InTech, Croatia, 2012).
    Google Scholar 
    Harvey, D. A., Alexander, M. E. & Janz, B. A comparison of fire-weather severity in northern Alberta during the 1980 and 1981 fire seasons. For. Chron. 62, 507–513 (1986).Article 

    Google Scholar 
    Copernicus Climate Change Service. Fire Danger Indicators for Europe from 1970 to 2098 Derived from Climate Projections (2020). https://doi.org/10.24381/CDS.CA755DE7.Flannigan, M. D. et al. Fuel moisture sensitivity to temperature and precipitation: Climate change implications. Clim. Change 134, 59–71 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    Fargeon, H. et al. Projections of fire danger under climate change over France: Where do the greatest uncertainties lie?. Clim. Change 160, 479–493 (2020).ADS 
    Article 

    Google Scholar 
    Rovithakis, A. et al. Future climate change impact on wildfire danger over the Mediterranean: The case of Greece. Environ. Res. Lett. 17, 045022 (2022).ADS 
    Article 

    Google Scholar 
    Iturbide, M. et al. An update of IPCC climate reference regions for subcontinental analysis of climate model data: Definition and aggregated datasets. Earth Syst. Sci. Data 12, 2959–2970 (2020).ADS 
    Article 

    Google Scholar  More

  • in

    Honey bee symbiont buffers larvae against nutritional stress and supplements lysine

    Dolezal AG, Toth AL. Feedbacks between nutrition and disease in honey bee health. Curr Opin Insect Sci. 2018;26:114–9.PubMed 
    Article 

    Google Scholar 
    Scofield HN, Mattila HR. Honey bee workers that are pollen stressed as larvae become poor foragers and waggle dancers as adults. PLoS ONE. 2015;10:e0121731.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    McFall-Ngai M, Hadfield MG, Bosch TCG, Carey HV, Domazet-Lošo T, Douglas AE, et al. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA. 2013;110:3229–36.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Akman Gündüz E, Douglas AE. Symbiotic bacteria enable insect to use a nutritionally inadequate diet. Proc R Soc B Biol Sci. 2009;276:987–91.Article 
    CAS 

    Google Scholar 
    Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, et al. Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters. PLoS Biol 2006;4:e188.Bing X, Attardo GM, Vigneron A, Aksoy E, Scolari F, Malacrida A, et al. Unravelling the relationship between the tsetse fly and its obligate symbiont Wigglesworthia: transcriptomic and metabolomic landscapes reveal highly integrated physiological networks. Proc R Soc B Biol Sci. 2017; 284:20170360.Itoh H, Jang S, Takeshita K, Ohbayashi T, Ohnishi N, Meng X-Y, et al. Host–symbiont specificity determined by microbe–microbe competition in an insect gut. Proc Natl Acad Sci USA. 2019;116:22673–82.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Flórez LV, Scherlach K, Miller IJ, Rodrigues A, Kwan JC, Hertweck C, et al. An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles. Nat Commun. 2018;9:2478.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Kaltenpoth M, Göttler W, Herzner G, Strohm E. Symbiotic bacteria protect wasp larvae from fungal infestation. Curr Biol. 2005;15:475–9.CAS 
    PubMed 
    Article 

    Google Scholar 
    Oliver KM, Degnan PH, Hunter MS, Moran NA. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 2009;325:992–4.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Shin SC, Kim SH, You H, Kim B, Kim AC, Lee KA, et al. Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science 2011;334:670–4.CAS 
    PubMed 
    Article 

    Google Scholar 
    Dedeine F, Vavre F, Fleury F, Loppin B, Hochberg ME, Boulétreau M. Removing symbiotic Wolbachia bacteria specifically inhibits oogenesis in a parasitic wasp. Proc Natl Acad Sci USA. 2001;98:6247–52.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Koropatnick TA, Engle JT, Apicella MA, Stabb EV, Goldman WE, McFall-Ngai MJ. Microbial factor-mediated development in a host-bacterial mutualism. Science 2004;306:1186–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Chun CK, Troll JV, Koroleva I, Brown B, Manzella L, Snir E, et al. Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association. Proc Natl Acad Sci USA. 2008;105:11323–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Shikuma NJ, Pilhofer M, Weiss GL, Hadfield MG, Jensen GJ, Newman DK. Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 2014;343:529–33.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X. Molecular basis of symbiosis between Rhizobium and legumes. Nature 1997;387:394–401.CAS 
    PubMed 
    Article 

    Google Scholar 
    Médigue C, Masson-Boivin C, Gilbert LB, Cruveiller S, Gris C, Batut J, et al. Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biol. 2010;8:e1000280.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Brucker RM, Bordenstein SR. Speciation by symbiosis. Trends Ecol Evol. 2012;27:443–51.PubMed 
    Article 

    Google Scholar 
    Moran NA, McCutcheon JP, Nakabachi A. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. 2008;42:165–90.CAS 
    PubMed 
    Article 

    Google Scholar 
    Moran NA, Tran P, Gerardo NM. Symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum Bacteroidetes. Appl Environ Microbiol. 2005;71:8802–10.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lee FJ, Miller KI, McKinlay JB, Newton ILG. Differential carbohydrate utilization and organic acid production by honey bee symbionts. FEMS Microbiol Ecol. 2018;94:fiy113.CAS 
    Article 

    Google Scholar 
    Lee FJ, Rusch DB, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environ Microbiol. 2015;17:796–815.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zheng H, Nishida A, Kwong WK, Koch H, Engel P, Steele MI, et al. Metabolism of toxic sugars by strains of the bee gut symbiont Gilliamella apicola. MBio 2016;7:e01326–16.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kešnerová L, Mars RAT, Ellegaard KM, Troilo M, Sauer U, Engel P. Disentangling metabolic functions of bacteria in the honey bee gut. PLoS Biol. 2017;15:e2003467.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Gallai N, Salles JM, Settele J, Vaissière BE. Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol Econ. 2009;68:810–21.Article 

    Google Scholar 
    Brodschneider R, Gray A, Adjlane N, Ballis A, Brusbardis V, Charrière JD, et al. Multi-country loss rates of honey bee colonies during winter 2016/2017 from the COLOSS survey. J Apic Res. 2018;57:452–7.Article 

    Google Scholar 
    Kulhanek K, Steinhauer N, Rennich K, Caron DM, Sagili RR, Pettis JS, et al. A national survey of managed honey bee 2015-6 annual colony losses in the USA. J Apic Res. 2017;56:328–40.Article 

    Google Scholar 
    Goulson D, Nicholls E, Botías C, Rotheray EL. Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 2015;347:1255957.PubMed 
    Article 
    CAS 

    Google Scholar 
    Dolezal AG, Carrillo-Tripp J, Judd TM, Allen Miller W, Bonning BC, Toth AL. Interacting stressors matter: Diet quality and virus infection in honeybee health. R Soc Open Sci. 2019;6:81803.Article 
    CAS 

    Google Scholar 
    St Clair AL, Zhang G, Dolezal AG, O’Neal ME, Toth AL, et al. Diversified farming in a monoculture landscape: effects on honey bee health and wild bee communities. Environ Entomol. 2020;49:753–64.Article 

    Google Scholar 
    Naug D. Nutritional stress due to habitat loss may explain recent honeybee colony collapses. Biol Conserv. 2009;142:2369–72.Article 

    Google Scholar 
    Taha EKA, Al-Kahtani S, Taha R. Protein content and amino acids composition of bee-pollens from major floral sources in Al-Ahsa, eastern Saudi Arabia. Saudi J Biol Sci. 2019;26:232–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    de Groot AP. Amino acid requirements for growth of the honeybee (Apis mellifica L.). Experientia 1952;8:192–4.Article 

    Google Scholar 
    Brodschneider R, Crailsheim K. Nutrition and health in honey bees. Apidologie 2010;41:278–94.Article 

    Google Scholar 
    Keller I, Fluri P, Imdorf A. Pollen nutrition and colony development in honey bees – Part II. Bee World. 2005;86:27–34.Article 

    Google Scholar 
    Huang Z. Pollen nutrition affects honey bee stress resistance. Terr Arthropod Rev. 2012;5:175–89.Article 

    Google Scholar 
    van Dooremalen C, Stam E, Gerritsen L, Cornelissen B, van der Steen J, van Langevelde F, et al. Interactive effect of reduced pollen availability and Varroa destructor infestation limits growth and protein content of young honey bees. J Insect Physiol. 2013;59:487–93.PubMed 
    Article 
    CAS 

    Google Scholar 
    Feldhaar H, Straka J, Krischke M, Berthold K, Stoll S, Mueller MJ, et al. Nutritional upgrading for omnivorous carpenter ants by the endosymbiont Blochmannia. BMC Biol. 2007;5:48.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Sannino DR, Dobson AJ, Edwards K, Angert ER, Buchon N. The Drosophila melanogaster gut microbiota provisions thiamine to its host. MBio 2018;9:e00155–18.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hammer TJ, Moran NA. Links between metamorphosis and symbiosis in holometabolous insects. Philos Trans R Soc B Biol Sci. 2019;374:20190068.CAS 
    Article 

    Google Scholar 
    Kowallik V, Mikheyev AS. Honey bee larval and adult microbime life stages are effectively decoupled with vertical transmisson overcoming early life perturbations. mBio 2021;12:e02966–21.CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Storelli G, Defaye A, Erkosar B, Hols P, Royet J, Leulier F. Lactobacillus plantarum promotes Drosophila systemic growth by modulating hormonal signals through TOR-dependent nutrient sensing. Cell Metab. 2011;14:403–14.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wright GA, Nicolson SW, Shafir S. Nutritional physiology and ecology of honey bees. Annu Rev Entomol. 2017;63:327–44.PubMed 
    Article 
    CAS 

    Google Scholar 
    Tarpy DR, Mattila HR, Newton ILG. Development of the honey bee gut microbiome throughout the queen-rearing process. Appl Environ Microbiol. 2015;81:3182–91.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Corby-Harris V, Snyder LA, Schwan MR, Maes P, McFrederick QS, Anderson KE. Origin and effect of Alpha 2.2 Acetobacteraceae in honey bee larvae and description of Parasaccharibacter apium gen. nov., sp. nov. Appl Environ Microbiol. 2014;80:7460–72.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Vojvodic S, Rehan SM, Anderson KE. Microbial gut diversity of Africanized and European honey bee larval instars. PLoS ONE. 2013;8:72106.Article 
    CAS 

    Google Scholar 
    Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, et al. Dynamic microbiome evolution in social bees. Sci Adv. 2017;3:e1600513.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T. GLOOME: Gain loss mapping engine. Bioinformatics 2010;26:2914–5.CAS 
    PubMed 
    Article 

    Google Scholar 
    Price MN, Deutschbauer AM, Arkin AP. GapMind: Automated annotation of amino acid biosynthesis. mSystems 2020;5:e00291–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schmehl DR, Tomé HVV, Mortensen AN, Martins GF, Ellis JD. Protocol for the in vitro rearing of honey bee (Apis mellifera L.) workers. J Apic Res. 2016;55:113–29.Article 

    Google Scholar 
    Li H, Tennessen JM. Preparation of Drosophila larval samples for gas chromatography-mass spectrometry (GC-MS)-based metabolomics. J Vis Exp. 2018;136:e57847.
    Google Scholar 
    Rortais A, Arnold G, Halm MP, Touffet-Briens F. Modes of honeybees exposure to systemic insecticides: Estimated amounts of contaminated pollen and nectar consumed by different categories of bees. Apidologie 2005;36:71–83.CAS 
    Article 

    Google Scholar 
    Buttstedt A, Mureşan CI, Lilie H, Hause G, Ihling CH, Schulze SH, et al. How honeybees defy gravity with royal jelly to raise queens. Curr Biol. 2018;28:1095–1100.CAS 
    PubMed 
    Article 

    Google Scholar 
    Fratini F, Cilia G, Mancini S, Felicioli A. Royal jelly: An ancient remedy with remarkable antibacterial properties. Microbiol Res. 2016;192:130–41.CAS 
    PubMed 
    Article 

    Google Scholar 
    Fontana R, Mendes MA, De Souza BM, Konno K, César LMM, Malaspina O, et al. Jelleines: A family of antimicrobial peptides from the royal jelly of honeybees (Apis mellifera). Peptides 2004;25:919–28.CAS 
    PubMed 
    Article 

    Google Scholar 
    Rokop ZP, Horton MA, Newton ILG. Interactions between cooccurring lactic acid bacteria in honey bee hives. Appl Environ Microbiol. 2015;81:7261–70.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Crailsheim K, Brodschneider R, Aupinel P, Behrens D, Genersch E, Vollmann J, et al. Standard methods for artificial rearing of Apis mellifera larvae. J Apic Res. 2013;52:1–16.Article 

    Google Scholar 
    Smith EA, Newton ILG. Genomic signatures of honey bee association in an acetic acid symbiont. Genome Biol Evol. 2020;12:1882–94.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kaftanoglu O, Linksvayer TA, Page RE. Rearing honey bees, Apis mellifera, in vitro 1: Effects of sugar concentrations on survival and development. J Insect Sci. 2011;11:96.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aupinel P, Fortini D, Dufour H, Tasei J-N, Michaud B, Odoux J-F, et al. Improvement of artificial feeding in a standard in vitro method for rearing Apis mellifera larvae. Bull Insectol. 2005;58:107–11.
    Google Scholar 
    Hansen AK, Moran NA. Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. Proc Natl Acad Sci USA. 2011;108:2849–54.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    McCutcheon JP, McDonald BR, Moran NA. Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci USA. 2009;106:15394–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. Aps Nat. 2000;407:81–86.CAS 

    Google Scholar 
    Gil R, Silva FJ, Zientz E, Delmotte F, González-Candelas F, Latorre A, et al. The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes. Proc Natl Acad Sci USA. 2003;100:9388–93.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 2012;10:13–26.CAS 
    Article 

    Google Scholar 
    Wernegreen JJ, Lazarus AB, Degnan PH. Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle. Microbiology 2002;148:2551–6.CAS 
    PubMed 
    Article 

    Google Scholar 
    McCutcheon JP, Moran NA. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc Natl Acad Sci USA. 2007;104:19392–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bennett GM, Mccutcheon JP, Macdonald BR, Romanovicz D, Moran NA. Differential genome evolution between companion symbionts in an insect-bacterial symbiosis. mBio 2014;5:e01697–14.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Husnik F, Nikoh N, Koga R, Ross L, Duncan RP, Fujie M, et al. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell 2013;153:1567.CAS 
    PubMed 
    Article 

    Google Scholar 
    Bao XY, Yan JY, Yao YL, Wang Y, Bin, Visendi P, Seal S, et al. Lysine provisioning by horizontally acquired genes promotes mutual dependence between whitefly and two intracellular symbionts. PLOS Pathog. 2021;17:e1010120.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cotte JF, Casabianca H, Giroud B, Albert M, Lheritier J, Grenier-Loustalot MF. Characterization of honey amino acid profiles using high-pressure liquid chromatography to control authenticity. Anal Bioanal Chem. 2004;378:1342–50.CAS 
    PubMed 
    Article 

    Google Scholar 
    Baker HG. Non-sugar chemical constituents of nectar. Apidologie 1977;8:349–56.Article 

    Google Scholar 
    Nyholm SV, McFall-Ngai MJ. The winnowing: Establishing the squid – Vibrios symbiosis. Nat Rev Microbiol. 2004;2:632–42.CAS 
    PubMed 
    Article 

    Google Scholar 
    Kikuchi Y, Hosokawa T, Fukatsu T. Insect-microbe mutualism without vertical transmission: a stinkbug acquires a beneficial gut symbiont from the environment every generation. Appl Environ Microbiol. 2007;73:4308–16.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Itoh H, Jang S, Takeshita K, Ohbayashi T, Ohnishi N, Meng XY, et al. Host–symbiont specificity determined by microbe–microbe competition in an insect gut. Proc Natl Acad Sci USA. 2019;116:22673–82.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Oono R, Anderson CG, Denison RF. Failure to fix nitrogen by non-reproductive symbiotic rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proc R Soc B Biol Sci. 2011;278:2698–703.Article 

    Google Scholar 
    Brown BP, Wernegreen JJ. Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae. BMC Genom. 2019;20:1–15.CAS 
    Article 

    Google Scholar 
    Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 2004;20:44–50.CAS 
    PubMed 
    Article 

    Google Scholar 
    Meijuan X, Rao Z, Yang J, Dou W, Xu Z. The effect of a LYSE exporter overexpression on L-arginine production in Corynebacterium crenatum. Curr Microbiol. 2013;67:271–8.Article 
    CAS 

    Google Scholar 
    Indurthi SM, Chou H-T, Lu C-D. Molecular characterization of lysR-lysXE, gcdR-gcdHG and amaR-amaAB operons for lysine export and catabolism: a comprehensive lysine catabolic network in Pseudomonas aeruginosa PAO1. Microbiology 2016;162:876–88.CAS 
    Article 

    Google Scholar 
    Pathania A, Sardesai AA. Distinct paths for basic amino acid export in Escherichia coli: YbjE (LysO) mediates export of L-lysine. J Bacteriol. 2015;197:2036–47.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Miller DL, Smith EA, Newton ILG. A bacterial symbiont protects honey bees from fungal disease. mBio 2021;12:e00503–21.CAS 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Appraisal of growth inhibitory, biochemical and genotoxic effects of Allyl Isothiocyanate on different developmental stages of Zeugodacus cucurbitae (Coquillett) (Diptera: Tephritidae)

    Wink, M. Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective. Phytochemistry 64, 3–19 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    Khare, S. et al. Plant secondary metabolites synthesis and their regulations under biotic and abiotic constraints. J. Plant Biol. 63, 203–216 (2020).CAS 
    Article 

    Google Scholar 
    Gajger, I. T. & Dar, S. A. Plant allelochemicals as sources of insecticides. Insects 12, 189 (2021).Article 

    Google Scholar 
    Vig, A. P., Rampal, G., Thind, T. S. & Arora, S. Bio-protective effects of glucosinolates: A review. LWT Food Sci. Technol. 42, 1561–1572 (2009).CAS 
    Article 

    Google Scholar 
    Sikorska-Zimny, K. & Beneduce, L. The glucosinolates and their bioactive derivatives in Brassica: A review on classification, biosynthesis and content in plant tissues, fate during and after processing, effect on the human organism and interaction with the gut microbiota. Crit. Rev. Food Sci. Nutr. 61, 2544–2571. https://doi.org/10.1080/10408398.2020.1780193 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Radojčić Redovniković, I., Glivetić, T., Delonga, K. & Vorkapić-Furač, J. Glucosinolates and their potential role in plant. Period. Biol. 110, 297–309 (2008).
    Google Scholar 
    Wittstock, U., Kliebenstein, D. J., Lambrix, V., Reichelt, M. & Gershenzon, J. Chapter five glucosinolate hydrolysis and its impact on generalist and specialist insect herbivores. Recent Adv. Phytochem. 37, 101–125 (2003).CAS 
    Article 

    Google Scholar 
    Noret, N. et al. Palatability of Thlaspi caerulescens for snails: Influence of zinc and glucosinolates. New Phytol. 165, 763–772 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hopkins, R. J., Van Dam, N. M. & Van Loon, J. J. A. Role of glucosinolates in Insect-plant relationships and multitrophic interactions. Annu. Rev. Entomol. 54, 57–83 (2008).Article 
    CAS 

    Google Scholar 
    Guleria, S. & Tiku, A. K. Botanicals in pest management: Current status and future perspectives. Integr. Pest Manag. 1, 317–329 (2009).
    Google Scholar 
    Clay, N. K., Adio, A. M., Denoux, C., Jander, G. & Ausubel, F. M. Glucosinolate metabolites required for an Arabidopsis innate immune response. Science 323, 95–101 (2009).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Yang, B. et al. Inhibitory effect of allyl and benzyl isothiocyanates on ochratoxin a producing fungi in grape and maize. Food Microbiol. 100, 103865 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Agrawal, A. A. & Kurashige, N. S. A role for isothiocyanates in plant resistance against the specialist herbivore Pieris rapae. J. Chem. Ecol. 296(29), 1403–1415 (2003).Article 

    Google Scholar 
    Müller, C. et al. The role of the glucosinolate-myrosinase system in mediating greater resistance of Barbarea verna than B. vulgaris to Mamestra brassicae Larvae. J. Chem. Ecol. 44, 1190–1205 (2018).PubMed 
    Article 
    CAS 

    Google Scholar 
    Kegley, S. E., Hill, B. R., Orme, S. & Choi, A. H. PAN Pesticide Database (Pesticide Action Network, 2000).
    Google Scholar 
    Worfel, R. C., Schneider, K. S. & Yang, T. C. S. Suppressive effect of allyl isothiocyanate on populations of stored grain insect pests. J. Food Process. Preserv. 21, 9–19 (1997).CAS 
    Article 

    Google Scholar 
    Wu, H., Zhang, G. A., Zeng, S. & Lin, K. C. Extraction of allyl isothiocyanate from horseradish (Armoracia rusticana) and its fumigant insecticidal activity on four stored-product pests of paddy. Pest Manag. Sci. 65, 1003–1008 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bhushan, S., Gupta, S., Kaur Sohal, S., Arora, S. & Saroj Arora, C. Assessment of insecticidal action of 3-Isothiocyanato-1-propene on the growth and development of Spodoptera litura (Fab.) (Lepidoptera: Noctuidae). J. Entomol. Zool. Stud. 4, 1068–1073 (2016).
    Google Scholar 
    Dhillon, M. K., Naresh, J. S., Singh, R. & Sharma, N. K. Reaction of different bitter gourd (Momordica charantia L.) genotypes to melon fruit fly, Bactrocera cucurbitae (Coquillett). Int. J. Plant Prot. 33, 55–59 (2005).
    Google Scholar 
    Ekesi, S., Nderitu, P. W. & Chang, C. L. Adaptation to and small-scale rearing of invasive fruit fly Bactrocera invadens (Diptera: Tephritidae) on artificial diet. Ann. Entomol. Soc. Am. 100, 562–567 (2007).Article 

    Google Scholar 
    Jakhar, S. et al. Estimation losses due to fruit fly, Bactrocera cucurbitae (Coquillett) on long melon in semi-arid region of Rajasthan. J. Entomol. Zool. Stud. 8, 632–635 (2020).MathSciNet 

    Google Scholar 
    Ladania, M. S. Physiological Disorders and Their Management. Citrus Fruit: Biology, Technology and Evaluation 451–463 (Academic press, 2008).
    Google Scholar 
    Du, Y., Grodowitz, M. J. & Chen, J. Insecticidal and enzyme inhibitory activities of isothiocyanates against red imported fire ants, Solenopsis invicta. Biomolecules 10, 716 (2020).CAS 
    PubMed Central 
    Article 

    Google Scholar 
    Tsao, R., Reuber, M., Johnson, L. & Coats, J. R. Insecticidal toxicities of glucosinolate· containing extracts from crambe seeds. J. Agric. Urban Entomol. 13, 109–120 (1996).CAS 

    Google Scholar 
    Li, Q., Eigenbrode, S. D., Stringam, G. R. & Thiagarajah, M. R. Feeding and growth of Plutella xylostella and Spodoptera eridania on Brassica juncea with varying glucosinolate concentrations and myrosinase activities. J. Chem. Ecol. 26, 2401–2419 (2000).CAS 
    Article 

    Google Scholar 
    Noble, R. R., Harvey, S. G. & Sams, C. E. Toxicity of Indian mustard and allyl isothiocyanate to masked chafer beetle larvae. Plant Health Prog. 3, 9 (2002).Article 

    Google Scholar 
    Sousa, A. H., Faroni, L. R. A., Pimentel, M. A. G. & Freitas, R. S. Relative toxicity of mustard essential oil to insect-pests of stored products. Rev. Caatinga 27, 222–226 (2014).
    Google Scholar 
    de Souza, L. P., Faroni, L. R. D. A., Lopes, L. M., de Sousa, A. H. & Prates, L. H. F. Toxicity and sublethal effects of allyl isothiocyanate to Sitophilus zeamais on population development and walking behavior. J. Pest Sci. 91, 761–770 (2018).Article 

    Google Scholar 
    Freitas, R. C. P., Faroni, L. R. D. A., Haddi, K., Jumbo, L. O. V. & Oliveira, E. E. Allyl isothiocyanate actions on populations of Sitophilus zeamais resistant to phosphine: Toxicity, emergence inhibition and repellency. J. Stored Prod. Res. 69, 257–264 (2016).Article 

    Google Scholar 
    Jabeen, A., Zaitoon, A., Lim, L. T. & Scott-Dupree, C. Toxicity of five plant volatiles to adult and egg stages of Drosophila suzukii matsumura (Diptera: Drosophilidae), the spotted-wing Drosophila. J. Agric. Food Chem. 69, 9511–9519 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Wu, H., Liu, X. R., Yu, D. D., Zhang, X. & Feng, J. T. Effect of allyl isothiocyanate on ultra-structure and the activities of four enzymes in adult Sitophilus zeamais. Pestic. Biochem. Physiol. 109, 12–17 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang, C., Wu, H., Zhao, Y., Ma, Z. & Zhang, X. Comparative studies on mitochondrial electron transport chain complexes of Sitophilus zeamais treated with allyl isothiocyanate and calcium phosphide. Pestic. Biochem. Physiol. 126, 70–75 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    Jeschke, V. et al. How glucosinolates affect generalist lepidopteran larvae: Growth, development and glucosinolate metabolism. Front Plant Sci. 8, 1995. https://doi.org/10.3389/fpls.2017.01995 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Agnihotri, A. R., Hulagabali, C. V., Adhav, A. S. & Joshi, R. S. Mechanistic insight in potential dual role of sinigrin against Helicoverpa armigera. Phytochemistry 145, 121–127. https://doi.org/10.1016/j.phytochem.2017.10.014 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Jeschke, V. et al. So much for glucosinolates: A generalist does survive and develop on Brassicas, but at what cost?. Plants 10, 962. https://doi.org/10.3390/plants10050962 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Benrey, B. & Denno, R. F. The slow-growth-high-mortality hypothesis: A test using the cabbage butterfly. Ecology 78, 987–999 (1997).
    Google Scholar 
    Shroff, R., Vergara, F., Muck, A., Svatoš, A. & Gershenzon, J. Nonuniform distribution of glucosinolates in Arabidopsis thaliana leaves has important consequences for plant defense. Proc. Natl. Acad. Sci 05, 6196–6201 (2008).ADS 
    Article 
    CAS 

    Google Scholar 
    Bai, P. P. et al. Inhibition of phenoloxidase activity delays development in Bactrocera dorsalis (Diptera: Tephritidae). Fla. Entomol. 97, 477–485. https://doi.org/10.1653/024.097.0218 (2014).Article 

    Google Scholar 
    Datta, R., Kaur, A., Saraf, I., Singh, I. P. & Kaur, S. Effect of ethyl acetate extract and purified compounds of Alpinia galanga (L.) on Immune Response of a Polyphagous Lepidopteran pest, Spodoptera litura (Fabricius). Asian J. Adv. Basic Sci. 6, 16–21 (2018).CAS 

    Google Scholar 
    Hartzer, K. L., Zhu, K. Y. & Baker, J. E. Phenoloxidase in larvae of Plodia interpunctella (Lepidoptera: Pyralidae): Molecular cloning of the proenzyme cDNA and enzyme activity in larvae paralyzed and parasitized by Habrobracon hebetor (Hymenoptera: Braconidae). Arch. Insect Biochem. Physiol. 59, 67–79 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    Silva, C. J. M. et al. Immune response triggered by the ingestion of polyethylene microplastics in the dipteran larvae Chironomus riparius. J. Hazard. Mater. 414, 125401. https://doi.org/10.1016/j.jhazmat.2021.125401 (2021).CAS 
    Article 
    PubMed 

    Google Scholar 
    Aucoin, R. R., Philogène, B. J. R. & Arnason, J. T. Antioxidant enzymes as biochemical defenses against phototoxin induced oxidative stress in three species of herbivorous Lepidoptera. Arch. Insect Biochem. Physiol. 16, 139–152 (1991).CAS 
    Article 

    Google Scholar 
    Wang, Y., Branicky, R., Noë, A. & Hekimi, S. Superoxide dismutases: Dual roles in controlling ROS damage and regulating ROS signaling. Int. J. Cell Biol. 217, 1915–1928. https://doi.org/10.1083/jcb.201708007 (2018).CAS 
    Article 

    Google Scholar 
    Zhang, C., Ma, Z., Zhang, X. & Wu, H. Transcriptomic alterations in Sitophilus zeamais in response to allyl isothiocyanate fumigation. Pest. Biochem. Physiol. 137, 62–70. https://doi.org/10.1016/j.pestbp.2016.10.001 (2017).CAS 
    Article 

    Google Scholar 
    Felton, G. W. & Summers, C. B. Antioxidant systems in insects. Arch. Insect Biochem. Physiol. 29, 187–197. https://doi.org/10.1002/arch.940290208 (1995).CAS 
    Article 
    PubMed 

    Google Scholar 
    Cadenas, E. Mechanisms of oxygen activation and reactive oxygen species detoxification. In Oxidative Stress and Antioxidant Defenses in Biology (ed. Ahmad, S.) 1–46 (Chapman & Hall, 1995). https://doi.org/10.1007/978-1-4615-9689-9_1.Chapter 

    Google Scholar 
    Schramm, K., Vassão, D. G., Reichelt, M., Gershenzon, J. & Wittstock, U. Metabolism of glucosinolate- derived isothiocyanates to glutathione conjugates in generalist lepidopteran herbivores. Insect Biochem. Mol. Biol. 42, 174–182. https://doi.org/10.1016/j.ibmb.2011.12.002 (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Falk, K. L. et al. The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluscan herbivores. Mol. Ecol. 23, 1188–1203. https://doi.org/10.1111/mec.12610 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gloss, A. D. et al. Evolution in an ancient detoxification pathway is coupled with a transition to herbivory in the Drosophilidae. Mol. Biol. Evol. 31, 2441–3245. https://doi.org/10.1093/molbev/msu201 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bhatt, P., Zhou, X., Huang, Y., Zhang, W. & Chen, S. Characterization of the role of esterases in the biodegradation of organophosphate, carbamate, and pyrethroid pesticides. J. Hazard. Mater. 1, 125026. https://doi.org/10.1016/j.jhazmat.2020.125026 (2021).CAS 
    Article 

    Google Scholar 
    Murfadunnisa, S. et al. Larvicidal and enzyme inhibition of essential oil from Spheranthus amaranthroids (Burm.) against lepidopteran pest Spodoptera litura (Fab.) and their impact on non-target earthworms. Biocatal. Agric. Biotechnol. 21, 101324. https://doi.org/10.1016/j.bcab.2019.101324 (2019).Article 

    Google Scholar 
    Sengottayan, S. N. Physiological and biochemical effect of neem and other Meliaceae plants secondary metabolites against Lepidopteran insects. Front. Physiol. 4, 359. https://doi.org/10.3389/fphys.2013.00359 (2013).Article 

    Google Scholar 
    Augustyniak, M., Gladysz, M. & Dziewięcka, M. The Comet assay in insects: Status, prospects and benefits for science. Mutat. Res. Rev. Mutat. Res. 767, 67–76. https://doi.org/10.1016/j.mrrev.2015.09.001Get (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Foster, E. R. & Downs, J. A. Histone H2A phosphorylation in DNA double strand break repair. FEBS J. 272, 3231–3240. https://doi.org/10.1111/j.1742-4658.2005.04741.x (2005).CAS 
    Article 
    PubMed 

    Google Scholar 
    Porichha, S. K., Sarangi, P. K. & Prasad, R. Genotoxic effect of chlorpyrifosin Channa punctatus. Cytol. Genet. 9, 631–638 (1998).
    Google Scholar 
    Kalita, M. K., Haloi, K. & Devi, D. Larval exposure to chlorpyrifos affects nutritional physiology and induces genotoxicity in silkworm Philosamia ricini (Lepidoptera: Saturniidae). Front. physiol. 7, 1–14. https://doi.org/10.3389/fphys.2016.00535 (2016).Article 

    Google Scholar 
    Datta, R. et al. Assessment of genotoxic and biochemical effects of purified compounds of Alpinia galanga on a polyphagous lepidopteran pest Spodoptera litura (Fabricius). Phytoparasitica 48, 501–511. https://doi.org/10.1007/s12600-020-00813-8 (2020).CAS 
    Article 

    Google Scholar 
    Afify, A. & Negm, A. A. K. H. Genotoxic effect of insect growth regulators on different stages of peach fruit fly, Bactrocera zonata (Saunders)(Diptera: Tephritidae). Afr. Entomol. 26, 154–161 (2018).Article 

    Google Scholar 
    Gupta, J. N., Verma, A. N. & Kashyap, R. K. An improved method for mass rearing for melon fruit fly Dacus cucurbitae Coquillett. Indian J. Entomol. 40, 470–471 (1978).
    Google Scholar 
    Srivastava, B. G. A chemically defined diet for Dacus cucurbitae (Coq.) larvae under aseptic conditions. Entomol. News Lett. 5, 24 (1975).
    Google Scholar 
    Kumar, A., Sood, S., Mehta, V., Nadda, G. & Shanker, A. Biology of Thysanoplusia orichalcea (Fab.) in relation to host preference and suitability for insect culture and bioefficacy. Indian J. Appl. Entomol. 18, 16–21 (2004).
    Google Scholar 
    Martinez, S. S. & Emden, H. F. V. Growth disruption, abnormalities and mortality of Spodoptera littoralis (Boisduval) (Lepidoptera: Noctuidae) caused by azadirachtin. Neotrop. Entomol. 30, 113–125 (2001).CAS 
    Article 

    Google Scholar 
    Khan, Z. R. & Saxena, R. C. Behavioural and physiological responses of Sogatella furcifera (Homoptera: Delphacidae) to selected resistant and susceptible rice cultivars. J. Econ. Entomol. 78, 1280–1286 (1985).Article 

    Google Scholar 
    Zimmer, M. Phenol oxidation. In Methods to Study Litter Decomposition (eds Graça, M. A. et al.) (Springer, 2005).
    Google Scholar 
    Kono, Y. Generation of superoxide radical during auto-oxidation of hydroxylamine and an assay for superoxide dismutase. Arch. Biochem. Biophys. 186, 189–195. https://doi.org/10.1016/0003-9861(78)90479-4 (1978).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bergmeyer, H. U. Reagents for enzymatic analysis. In Methods of Enzymatic Analysis (eds Bergmeyer, H. U. & Gawehn, K.) 438 (Verlag Chemie, 1974).
    Google Scholar 
    Chien, C. & Dauterman, W. C. Studies on glutathione S-transferases in Helicoverpa (=Heliothis) zea. Insect Biochem. 21, 857–864. https://doi.org/10.1016/0020-1790(91)90092-S (1991).CAS 
    Article 

    Google Scholar 
    Katzenellenbogen, B. & Kafatos, F. C. General esterases of silk worm moth moulting fluid: Preliminary characterization. J. Insect Physiol. 17, 1139–1151. https://doi.org/10.1016/0022-1910(71)90016-3 (1971).CAS 
    Article 

    Google Scholar 
    Mac Intyre, R. J. A method for measuring activities of acid phosphatases separated by acrylamide gel electrophoresis. Biochem. Genet. 5, 45–56 (1971).CAS 
    Article 

    Google Scholar 
    Singh, N. P., McCoy, M. T., Tice, R. R. & Schneider, E. L. A simple technique for quantitation of low levels of DNA damage in individual cells. Exp. Cell Res. 175, 184–191 (1988).CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Alternative transcript splicing regulates UDP-glucosyltransferase-catalyzed detoxification of DIMBOA in the fall armyworm (Spodoptera frugiperda)

    Insects and plantsLarvae of fall armyworm (FAW, Spodoptera frugiperda) were cultured at the Department of Entomology at the Max Planck Institute for Chemical Ecology, and reared on a semi-artificial diet based on pinto bean59, and maintained under controlled light and temperature conditions (12:12 h light/dark, 21 °C).Feeding experiments3rd–4th instar FAW larvae were utilized for all experiments. Insects were starved overnight prior to feeding experiments. The following day insects were fed with a semi-artificial, pinto bean-based diet or put on maize leaves in small plastic cups and allowed to feed on the respective diets for a day. Insects were dissected in cold phosphate buffered saline (PBS, pH = 7.4) to harvest larval tissues (guts, Malphigian tubules, fat bodies, cuticle), which were stored at − 80 °C until further use. For droplet feeding, 12.5 mM DIMBOA was prepared by dissolving the compound in DMSO. This DIMBOA solution was further diluted in 10% aqueous sucrose solution. The larvae were stimulated with forceps to encourage regurgitation, and 2 μL DIMBOA-sucrose solution was administered directly to the larval mouthparts. Insects were then fed on semi-artificial diet for up to 6 h; following which gut tissue was dissected using cold phosphate buffer and the tissue samples were stored at − 80 °C until further use.Insect cell culturesSpodoptera frugiperda Sf9 cells and Trichoplusia ni Hi5 cells were cultured in Sf-900 II serum-free medium (Gibco) and ExpressFive serum-free medium (Gibco), respectively. Adherent cultures were maintained at 27 °C, and sub-cultured every 3–4 days.Cell treatmentsInsect cells were seeded in 6 well culture plates (Corning) and left at 27 °C overnight. For transcript stability tests, a fresh cycloheximide (CHX) stock (50 mg/mL) was prepared in ethanol and added to the cultured cells at a concentration of 50 µg/mL. Incubations with CHX were performed up to 6 h. For testing substrate specificity, cells were then treated with the following compounds for 1 h—DIMBOA (25–100 μM), indole (50–100 μM), quercetin (50–100 μM), and esculetin (50–100 μM). All the stocks were prepared in DMSO and cells treated with the corresponding volume of pure DMSO served as a control. The range of concentrations used for the substrates was based on previous work38.RNA extraction, reverse transcription and real time-PCR analysisTissue samples from the larvae were homogenized and total RNA extracted using the innuPREP RNA Mini Kit (Analytik Jena). Cell cultures used for RNA extraction were obtained during sub-culturing at full confluency, and centrifuged at 500×g for 5 min. The culture medium was discarded, and the fresh pellets were directly used for RNA extraction. RNA concentrations were measured with the NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific). First strand cDNA was synthesized from 1 μg total RNA using SuperScript III Reverse Transcriptase and OligodT primers from Invitrogen. Sequences were successfully amplified using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 35 cycles of 10 s at 98 °C, 20 s at 55 °C, 45 s at 72 °C; and 5 min at 72 °C). The PCR products were purified with a PCR cleanup kit (Qiagen) and cloned into pCR-Blunt II-TOPO vector (Life Technologies) and transformed into NEB cells (Life Technologies), which were plated on selective LB agar medium containing 100 μg/mL ampicillin and incubated overnight at 37 °C. Positive colonies were identified by PCR using vector-specific M13 primers. Positive clones were confirmed by sequencing. Real time PCR analyses were carried out using Brilliant III SYBR Master Mix, employing SYBR Green chemistry. Relative quantification of the transcript levels was done using the 2−∆∆Ct method60. SfRPL10 was used as reference gene for all analyses. The primer pairs used for distinguishing between the variants are listed in Supplementary Table 1. As the expression of full-length and variants of SfUGT33F28 differed according to the strains, tissues, and treatments being analyzed, variant expression is reported as ratios relative to the canonical transcript to facilitate comparisons.Preparation of minigenes for alternative splicing studiesGenomic DNA was isolated from S. frugiperda larvae using the cetyl trimethyl ammonium bromide (CTAB) protocol61. DNA concentration was measured with the NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific). The minigene was amplified using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 35 cycles of 10 s at 98 °C, 30 s at 55–60 °C, 1 min 30 s at 72 °C; and 10 min at 72 °C), cloned into a pCR-Blunt II-TOPO vector (Life Technologies) and sequenced using M13 primers. The confirmed sequence was eventually cloned into a pIB/V5-His-TOPOvector (Life Technologies) and transformed into NEB cells (Life Technologies). Positive colonies were identified by colony PCR using vector-specific OpIE2 primers, sub-cultured overnight at 37 °C in liquid LB medium containing 100 μg/mL ampicillin and used for plasmid DNA purification with the NucleoSpin Plasmid kit (Macherey-Nagel). Concentration and purity of the obtained construct was assessed by the NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific) and the correct orientation of the PCR products was confirmed by DNA sequencing.Nuclear protein isolationNuclear proteins were isolated from insect cells62 using the protocol originally described with few modifications. Cells grown to concentrations of up to 1 × 106 cells/well were harvested and washed with PBS (pH 7.4). The extracts were centrifuged at 12,000×g for 10 min and pellets were re-suspended in 400 μL cell lysis buffer (10 mM HEPES, pH 7.5, 10 mM KCl, 0.1 mM EDTA pH 8.0, 1 mM DTT, 0.5% Nonidet-40 and 10 μL protease inhibitor cocktail). Cells were allowed to swell on ice for 20 min with intermittent mixing. Suspensions were vortexed to disrupt the cell membranes and then centrifuged at 12,000×g for 10 min at 4 °C. Pelleted nuclei were washed thrice with cell lysis buffer, re-suspended in 50 μL nuclear extraction buffer (20 mM HEPES pH 7.5, 400 mM KCl, 1 mM EDTA pH 8.0, 1 mM DTT, 10% glycerol and protease inhibitor) and incubated on ice for 30 min. Nuclear fractions were collected by centrifugation at 12,000g for 15 min at 4 °C. Protein concentrations were measured by Bradford and extracts were stored at − 80 °C until further use.Electrophoretic mobility shift assay (EMSA)EMSA was performed using the LightShift Chemiluminescent EMSA kit (Thermo Scientific) following the manufacturer’s instructions. Genomic DNA fragments of 20–25 bp corresponding to the 5′ flanking region of UGT33F28 exon 1 (with and without AhR-ARNT motif deletion) were synthesized with covalently linked biotin (Sigma). The DNA probes used in the experiment are listed in Supplementary Table 6. EMSA was performed in 20 µL reactions containing 20 fmol biotinylated DNA probe with 3.5–4 µg nuclear protein extracted from insect cells, according to manufacturer’s instructions. A reaction comprising the above along with the excess of unlabeled canonical DNA probe (200 molar excess) was further employed as a control. The reaction was assembled at room temperature and incubated for 30 min. The reactions were separated on a 5% TBE gel in 0.5X TBE at 100 V for 60 min. The samples were then transferred to a positively charged nylon membrane (Hybond N+, Amersham Bioscience) using semi-dry transfer at 15 V for 30 min. The membrane was cross-linked for 1 min using the auto cross-link function on the UV cross-linker (Stratagene). The biotinylated DNA–protein complex was detected by the streptavidin–horseradish peroxidase conjugated antibody provided in the kit. The membrane was washed and incubated with the chemiluminescence substrate for 5 min and the signals were developed by exposing the membrane to an X-ray film for 1 min.Streptavidin affinity purificationStreptavidin agarose (Sigma-Aldrich) was employed for protein purification. Briefly, 50–100 μL of agarose was packed into a 1.5 mL Eppendorf tube for each sample. The agarose was allowed to settle with a short centrifugation (500×g, 5 min) and the supernatant was discarded. The agarose was washed 4–5 times with binding buffer (PBS containing 1 mM EDTA, 1 mM DTT, 4 µg poly dI. dC as non-specific competitor DNA and protease inhibitor). Simultaneously, the binding reaction with the nuclear protein fraction and the DNA probe was assembled as described above. A 100 μg amount of total nuclear protein was incubated with 4 μg of biotinylated DNA probe at room temperature for 20 min. The reaction was loaded onto the streptavidin column equilibrated with the binding buffer and incubated for another 1 h at room temperature with gentle shaking. Subsequently, the agarose was washed 4–5 times with the binding buffer. After the final wash, the supernatant was aspirated and 10 μL was left above the beads. For protein separation, 20–30 μL pf the SDS loading buffer was added onto the agarose, boiled at 95 °C for 5 min and the sample thus obtained was utilized for electrophoresis.Deletion mutagenesisFor deletion mutagenesis, a pair of primers flanking the sequence to be deleted (non-overlapping) was designed. The pCR-Blunt II-TOPO vector (Life Technologies) clone for the SfUGT33F28 exon 1–2 minigene was utilized as a template. Sequence was successfully amplified using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 20 cycles of 10 s at 98 °C, 30 s at 55–60 °C, 4 min at 72 °C; and 10 min at 72 °C). A DpnI digest was performed to remove the background DNA, followed by ligation and transformation into fresh cells. The sequence of the mutant TOPO clone was then confirmed and utilized as a template for cloning into pIB/V5-His-TOPO vector (Life Technologies) for transfection into insect cells.Cloning and heterologous expression of SfUGTsSequences were amplified from S. frugiperda gut cDNA samples using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 35 cycles of 10 s at 98 °C, 20 s at 55–60 °C, 45 s at 72 °C; and 5 min at 72 °C). The resulting amplified products were purified with a PCR cleanup kit (Qiagen) and incubated with GoTaq DNA polymerase (Promega) for 15 min at 72 °C in order to add A overhangs. The products were cloned into the pIB/V5-His-TOPO vector (Life Technologies) and transformed into NEB cells (Life Technologies), which were plated on selective LB agar medium containing 100 μg/mL ampicillin and incubated overnight at 37 °C. Positive colonies were identified by PCR using vector-specific OpIE2 primers, sub-cultured overnight at 37 °C in liquid LB medium containing 100 μg/mL ampicillin and used for plasmid DNA purification with the NucleoSpin Plasmid kit (Macherey-Nagel). Concentration and purity of the obtained constructs were assessed by NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific) and the correct orientation of the PCR products was confirmed by DNA sequencing.Insect cell transfectionFor transfection, Sf9 cells and Hi5 cells were sub-cultured at full confluency in a 6-well plate in a 1:3 dilution and left overnight to adhere to the flask surface. The medium was replaced, and transfections were carried out using FuGENE HD Transfection Reagent (Promega) in a 1:3 plasmid/lipid ratio (1.7 μg plasmid and 5.0 μL lipid for 3 mL medium). Cells were incubated for 48–72 h at 27 °C and re-suspended in fresh medium containing 50 μg/mL blasticidin for 2 weeks. Stable cell cultures were subsequently maintained at 10 μg/mL blasticidin.Cell lysate preparationCells were obtained from cultures 2 weeks post transfection growing stably on 50 μg/mL blasticidin. A 1 mL quantity of cells was harvested for each construct and re-suspended into 100 µL buffer. Protein concentrations were measured using the Bradford reagent, and 1–2 μg of the cell lysate was used for enzyme assays.Microsome preparationFor microsome extraction, confluent, stably transfected cells from five T-75 flasks (10 mL culture) per recombinant plasmid were harvested by scraping the cells off the bottom using a sterile cell scraper (Sarstedt AG, Nuembrecht, Germany). The obtained cell suspensions were combined into a 50 mL falcon tube and centrifuged at 1000×g for 15 min at 4 °C (AvantiTM J-20 XP Centrifuge, Beckman Coulter, Krefeld, Germany). The supernatant was discarded, the cells were washed twice with ice-cold PBS buffer (pH 7.4) and centrifuged at 1000×g for 15 min. The resulting cell pellet was re-suspended in 10 mL hypotonic buffer (20 mM Tris, 5 mM EDTA, 1 mM DTT, 20% glycerol, pH 7.5), containing 0.1% BenzonaseR nuclease and 100 μL Protease Inhibitor Cocktail (Serva) followed by incubation on ice for 30 min. After cell lysis, the cells were homogenized by 20–30 strokes in a Potter–Elvehjem tissue grinder (Kontes Glass Co., Vineland, USA) and were subsequently mixed with an equal volume of sucrose buffer (20 mM Tris, 5 mM EDTA, 1 mM DTT, 500 mM sucrose, 20% glycerol, pH 7.5). The homogenate was centrifuged at 1200×g and 4 °C for 10 min (AvantiTM J-20 XP Centrifuge, Beckman Coulter), and the supernatant was transferred into Beckman polycarbonate ultracentrifugation bottles (25 × 89 mm) (Beckman Coulter) and centrifuged at 100,000×g and 4 °C for 1.5 h in a fixed angle Type 70 Ti rotor (OptimaTM L-90K Ultracentrifuge, Beckman Coulter). After ultracentrifugation, the clear supernatant, containing the cytosolic fraction, was aliquoted into 1.5 mL Eppendorf tubes. The pellet, containing the microsomal fractions, was re-suspended in 1 mL of phosphate buffer (100 mM K2HPO4, pH 7.0), containing 10 μL Protease Inhibitor Cocktail (Serva) and stored at − 80 °C until further use. Typically, 5–10 μg of the microsome fraction so obtained was utilized for the enzyme assays.Cross-linking assaysCross-linking assays were performed using dimethyl suberimidate (DMS) as the cross-linking agent. A fresh stock of DMS (5 mg/mL) was prepared in 0.2 M triethanolamine (pH 8.0) at the start of each assay. DMS was added to a final concentration of 2.5 mg/mL to insect cell microsomes with gentle shaking up to 3 h, and samples were subsequently stored at − 20 °C until further use. All protein samples were electrophoresed using a 12% Mini-PROTEAN tris glycine gel, blotted onto PVDF membrane using wet transfer at 70 V for 30–45 min, followed by detection using the V5-HRP conjugate.V5-based affinity purificationAnti-V5 agarose affinity gel (Sigma-Aldrich) was employed for protein purification. Briefly, 50–75 μL of the agarose was packed into a 1.5 mL Eppendorf tube for each sample. The agarose was allowed to settle with a short centrifugation and the supernatant was discarded. The agarose was washed 4–5 times with PBS (pH 7.4). Samples to be purified were incubated with 5% digitonin on ice for 20 min and subject to centrifugation at 16,000×g for 30 min. Clarified cell lysate or microsomal extract was added onto the resin (up to 200 μL, volume adjusted by addition of PBS) and incubated for 1.5 h on a shaker. Subsequently, the agarose was washed 4–5 times with PBS. After the final wash, the supernatant was aspirated and 10 μL was left above the beads. This fraction was used for both protein electrophoresis and enzyme assays (separate purifications). For SDS-PAGE, 20–30 μL pf the SDS loading buffer was added onto the agarose, boiled at 95 °C for 5 min and sample thus obtained was utilized for electrophoresis.LC–MS/MS peptide analysisProtein bands of Coomassie Brilliant blue R250 stained gels were cut from the gel matrix and tryptic digestion was carried out63. For LC–MS/MS analysis of the resulting peptides, samples were reconstituted in 20 μL aqueous 1% formic acid, and 1 μL was injected onto an UPLC M-class system (Waters, Manchester, UK) coupled to a Synapt G2-si mass spectrometer (Waters, Manchester, UK). Samples were first pre-concentrated and desalted using a Symmetry C18 trap column (100 Å, 180 µm × 20 mm, 5 µm particle size) at a flow rate of 15 µL/min (0.1% aqueous formic acid). Peptides were eluted onto a ACQUITY UPLC HSS T3 analytical column (100 Å, 75 µm × 200 mm, 1.8 µm particle size) at a flow rate of 350 nL/min with the following gradient: 3–15% over 3 min, 15–20% B over 7 min, 20–40% B over 30 min, 40–50% B over 5 min, 50–70% B over 5 min, 70–95% B over 3 min, isocratic at 95% B for 1 min, and a return to 1% B over 1 min. Phases A and B were composed of 0.1% formic acid and 100% acetonitrile in 0.1% formic acid, respectively). The analytical column was re-equilibrated for 10 min prior to the next injection. The eluted peptides were transferred into the mass spectrometer operated in V-mode with a resolving power of at least 20,000 full width at half height FWHM. All analyses were performed in a positive ESI mode. A 100 fmol/μL sample of human Glu-Fibrinopeptide B in 0.1% formic acid/acetonitrile (1:1 v/v) was infused at a flow rate of 1 μL/min through the reference sprayer every 45 s to compensate for mass shifts in MS and MS/MS fragmentation mode. Data were acquired using data-dependent acquisition (DDA). The acquisition cycle for DDA analysis consisted of a survey scan covering the range of m/z 400–1800 Da followed by MS/MS fragmentation of the ten most intense precursor ions collected at 0.5 s intervals in the range of 50–2000 m/z. Dynamic exclusion was applied to minimize multiple fragmentations for the same precursor ions. MS data were collected using MassLynx v4.1 software (Waters, Manchester, UK).Data processing and protein identificationDDA raw data were processed and searched against a sub-database containing common contaminants (human keratins and trypsin) using ProteinLynx Global Server (PLGS) version 2.5.2 (Waters, Manchester, UK). Spectra remaining unmatched by database searching were interpreted de novo to yield peptide sequences and subjected to homology-based searching using the MS BLAST program64 installed on a local server. MS BLAST searches were performed against a Spodoptera frugiperda database obtained by in silico translation of the S. frugiperda transcriptome37 and against arthropoda database (NCBI). PKL-files of MS/MS spectra were generated and searched against Spodoptera frugiperda database combined with NCBI nr (downloaded on May 24, 2020) using MASCOT software version 2.6.2. The following searching parameters were applied: fixed precursor ion mass tolerance of 15 ppm for the survey peptide, fragment ion mass tolerance of 0.1 Da, 1 missed cleavage, fixed carbamidomethylation of cysteines and possible oxidation of methionine.Enzymatic assaysFor UGT assays, samples from insect cell cultures (transient or stable) were prepared in phosphate buffer (pH 7.0, 100 mM). Typical enzyme reactions included 5–10 µg cell microsomal extracts, 2 μL of 12.5 mM DIMBOA in DMSO (25 nmol), 4 μL of 12.5 mM UDP-glucose in water (50 nmol), and phosphate buffer (pH 7.0, 100 mM) to give an assay volume of 50 μL. Controls containing either boiled enzymatic preparation, or only the protein suspension and buffer were included. After incubation at 30 °C for 60 min, the enzyme reactions were interrupted by adding 50 μL of 1:1 (v:v) methanol/formic acid solution. For enzyme assays involving resin purified microsomal extracts, equal amounts of extracts were employed for resin purification and the enzyme assay (buffer + substrate) was pipetted directly onto the resin. Post incubation, samples were centrifuged, supernatant was collected, and reaction was stopped by addition of methanol/formic acid solution. Assays were centrifuged at 5000g for 5 min and the obtained supernatant was collected and analyzed by LC–MS/MS.Chromatographic methodsFor all analytical chromatography procedures, formic acid (0.05%) in water and acetonitrile were used as mobile phases A and B, respectively, and the column temperature was maintained at 25 °C. Analyses of enzymatic assays and plant samples used a Zorbax Eclipse XDB-C18 column (50 × 4.6 mm, 1.8 μm, Agilent Technologies) with a flow rate of 1.1 mL/min and with the following elution profile: 0–0.5 min, 95% A; 0.5–6 min, 95–67.5% A; 6.02–7 min, 100% B; 7.1–9.5 min, 95% A. LC–MS/MS analyses were performed on an Agilent 1200 HPLC system (Agilent Technologies) coupled to an API 6500 tandem spectrometer (AB Sciex) equipped with a turbospray ion source operating in negative ionization mode. Multiple reaction monitoring (MRM) was used to monitor analyte parent ion to product ion conversion with parameters from the literature for DIMBOA65 and DIMBOA-Glc16. Analyst (version 1.6.3, Applied Biosystems) software was used for data acquisition and processing.Statistical analysisAll statistical analyses were carried out using SigmaPlot 12.0 and R studio (version 3.6.3). Data were tested for homogeneity of variance and normality and were appropriately transformed to meet these criteria where required. The specific statistical method used for each data set is described in the figure legends. More

  • in

    The relative abundances of yeasts attractive to Drosophila suzukii differ between fruit types and are greatest on raspberries

    Six biological replicates each were sampled from four fruit species (blueberries, cherries, raspberries, and strawberries) at four developmental stages. Developmental stages were based on fruit pigmentation ranging from unripe (green) to fully ripe (red/purple/navy; Fig. S1) throughout June to September in 2018. Ten fruits (except blueberries N = 20) were collected for each species per replicate, and this was replicated six times for each ripening stage for each fruit at different sites.Quantitative analysis of fungal communitiesMetabarcoding analysis is generally not quantitative, but the addition of 265 P. cucumerina cells to sub-samples prior to DNA extraction served as an internal standard to attempt an estimation of the size of fungal populations. One replicate spiked with the internal standard of the strawberry stage 3 samples was removed due to poor sequence quality leaving 96 non-spiked and 95 spiked samples which produced a total of 38,445,395 reads that clustered into 1712  > 97% identity Amplicon Sequence Variants (ASV), which from here-in we call phylotypes (Table S1). Blast searches across all phylotypes for matches to the P. cucumerina internal standard’s ITS sequence generated from Sanger sequencing revealed one phylotype that matched with 100% identity. Plectosphaerella cucumerina was naturally present in 21 of the 95 non-spiked samples and comprised of a total of 444 reads. Cherry was the only fruit where the internal standard was reliably recovered: 23 of 24 spiked samples and only one of 24 non-spiked samples contained the internal standard phylotype. After internal standard DNA read normalisation, the mean (± SE) number of fungal cells from each of the useable 23 pairs of cherry replicates was 307,323 (± 39,090) cells. The range of phylotype cell abundance across all cherry samples was 3.9 million for an Aureobasidium phylotype to 3 cells for a phylotype taxonomically assigned no higher level than kingdom. There was no significant change in total fungal cell numbers across cherry maturation stage (Kruskal–Wallis, chi-squared = 2.63, P = 0.45; Fig. S2), but fruit surface areas also increased significantly (Kruskal–Wallis, chi-squared = 19.70, P = 0.0002, Fig. S2). When cell numbers were normalised for surface area this revealed that absolute fungal population sizes remained static across cherry maturation stages (Kruskal–Wallis, chi-squared = 2.49, P = 0.48; Fig. 1A). However, there was a significant change in absolute Saccharomycetales cell numbers when normalised for cherry surface area across maturation (Kruskal–Wallis, chi-squared = 15.30, P = 0.002): stage 1 had significantly greater absolute Saccharomycetales cell numbers than stage 4 (P = 0.0007; Fig. 1B). Six individual Saccharomycetales yeast phylotypes from the genera Debaryomyces, Saccharomyces, Kodamaea, one from the family Pichiaceae, and phylotypes with  > 97% homology to M. pulcherrima and Metschnikowia gruessii, had significantly greater abundances on ripening stage 1 than 4 (P values span 0.045 to 0.006).Figure 1Absolute fungal cell abundances on cherry epicarp. Number of total fungal (A) and Saccharomycetales yeasts (B) cells per mm2 of cherry epicarp (N = 6 except, stage 3 and 4, N = 5) at four ripening stages (1, unripe/green fruit; 2, de-greening fruit; 3, ripening fruit; and 4, fully ripe/harvest fruit) estimated from DNA read abundances normalised to DNA abundances from the deliberate addition of 265 live Plectosphaerella cucumerina cells prior to DNA extraction. Different lower-case letters above bars show significant differences between ripening stages at P  > 0.05, Dunn’s comparisons post-hoc with Benjamini–Hochberg multiple comparison correction.Full size imageOverview of fungal diversity across all fruit samplesThe P. cucumerina internal standard phylotype was removed from all samples, and the sequence data normalised and analysed. A total of 1712 fungal phylotypes was revealed, comprising seven phyla, 25 classes, 96 orders, 197 families, and 280 genera. The most abundant and diverse phylum was Ascomycota, comprising 92.2% of reads and 57.3% of phylotypes, followed by Basidiomycota (7.7% reads and 33.6% phylotypes), Zygomycota (0.1% and 1.1%), Chytridiomycota ( > 0.1% and 0.7%), Mucoromycota ( > 0.1% and 0.3%), Glomeromycota and Rozellomycota (both  > 0.1% and 0.1%; Fig. S3A). A phylotype from the Cladosporium genus was the most common phylotype across all samples, comprising 60.8% of reads. A total of 87 phylotypes from the order Saccharomycetales (budding yeasts) was detected, comprising 1,792,782 DNA reads (4.7% of the total) spanning 10 families and 25 genera. Metschnikowia was the most abundant Saccharomycetales genus (40.0% of Saccharomycetales reads), followed by Hanseniaspora (38.2%), then Pichia (5.2%), with the remaining genera contributing fewer than 3% each. Candida was the most diverse genus within the order Saccharomycetales accounting for 21.8% of phylotypes, despite only comprising 2.4% of reads, followed by Metschnikowia (11.5%), Hanseniaspora (8.0%) and Pichia (6.9%), with each of the remaining genera contributing fewer than 3.5% of phylotypes each (Fig. S3B). The most common Saccharomycetales yeast across all samples was a phylotype from the genus Hanseniaspora with  > 97% homology to H. uvarum and comprised 38.2% of the total Saccharomycetales reads (Fig. S3B).The effect of fruit species and ripening stage on epicarp fungal communitiesWe analysed differences in three biodiversity metrics to evaluate the effect of fruit species and maturation stage on fungal communities: differences in the absolute numbers of phylotypes (richness); differences in the types of phylotypes (i.e. presences/absences); and differences in the relative abundances of phylotypes (community composition) following Morrison-Whittle et al.14 and Morrison‐Whittle and Goddard37.
    Fungal phylotype richnessPhylotype richness was not normally distributed (Shapiro-Wilks, P = 0.008) but square root transformation allowed the data to conform to the assumptions of ANOVA. There was a significant effect of both fruit type and ripening stage on the number of fungal phylotypes, including an interaction between the two (F3,175 = 18.58, P = 1.65 × 10–10; F3,175 = 5.00, P = 0.002 and F9,175 = 6.69, P = 3.25 × 10–8 respectively). Comparisons of effect sizes revealed fruit type (ω2 = 0.30) had a 4.4 times greater effect than ripening stage (ω2 = 0.068) on fungal phylotype richness. Disregarding ripening stage, cherry (mean ± SE number of phylotypes = 98 ± 4.1) had significantly more fungal phylotypes than blueberry (68 ± 3.7), raspberry (72 ± 2.9) and strawberry (76 ± 3.2) (Tukey’s HSD, P  0.05) and there was a significant effect of ripening stage on the number of fungal phylotypes for cherry, raspberry, and strawberry (one-way ANOVA: F3,44 = 4.33, P = 0.0093; F3,44 = 13.56, P = 2.11 × 10–6 and F3,44 = 13.86, P = 1.84 × 10–6, respectively, Fig. 2), but not blueberry (F3,44 = 2.27, P = 0.055). On cherries phylotype numbers increased during ripening, but raspberry and strawberry had greater numbers at intermediate stages of fruit maturation (Fig. 2).Figure 2Number of observed phylotypes across fruit types and maturation stages. Number of fungal phylotypes across four ripening stages (1, unripe/green fruit; 2, de-greening fruit; 3, ripening fruit; and 4, fully ripe/harvest fruit) for blueberry, cherry, raspberry and strawberry (N = 12 except N = 11 for strawberry stage 3). Numbers of fungal phylotypes differ across ripening stages for cherry, raspberry and strawberry but not blueberry (ANOVA, P values shown). Where significant, different lowercase letters represent significant differences in phylotype numbers within each fruit (P  97% homology to Metschnikowia kunwiensis and H. uvarum on raspberry; and phylotypes with  > 97% homology to Kalmanozyma fusiformata (Ustilaginaceae smut fungi) and Podosphaera aphanis on strawberry.Twenty-four of the 195 indicator phylotypes belonged to the Saccharomycetales budding yeasts (Table S13). There were no Saccharomycetales indicator phylotypes for cherry, and just one for blueberry, a fungal phylotype with  > 97% homology to Metschnikowia koreensis. Raspberry had 15 Saccharomycetales indicator phylotypes: three with  > 97% homology to the Metschnikowia and, Candida genera, two Pichia and Schwanniomyces, and one each from Hanseniaspora, Barnettozyma, Debaryomyces, Candida, Geotrichum and Martiniozyma. There were eight indicator phylotypes for strawberry; two Candida and one from each of the Metschnikowia, Starmerella, Kodamaea and Hyphopichia genera and the Pichiaceae family, and a phylotype assigned to the no higher level than fungal kingdom (with  > 97% homology to deposit from Candida genus). The dynamics of Saccharomycetales yeast indicator phylotypes abundances across maturation for raspberry and strawberry is shown in Fig. 6.Figure 6Dynamics of changes in the proportion of budding yeast indicator phylotypes. Mean proportion of reads for the Saccharomycetales budding yeast indicator phylotypes that are significantly overrepresented on (A) raspberry and (B) strawberry (P  97% homology identified by manual Blast searches.Full size imageDifferences of yeast known to be attractive to D. suzukii
    Yeast from the Hanseniaspora, Pichia, Saccharomyces, Candida and Metschnikowia genera and their combinations are attractive to D. suzukii27,28,30,31, and phylotypes belonging to these genera were recovered here. The combined relative read abundances of all phylotypes assigned to these genera were significantly different between fruit types and ripening stages (Kruskal–Wallis chi-squared = 60.54, P = 4.51 × 10–13; chi-squared = 10.11, P = 0.018, respectively). Raspberry had the highest relative abundance of yeast genera known to be attractive to D. suzukii (mean ± SE = 21,539 ± 4339) and this was significantly greater than on the other fruits (P  97% homology to H. uvarum as over-represented on raspberry generally, and especially at later stages (Fig. 6A).Differences of Botrytis cinerea, known to be repulsive to D. suzukii
    The relative read abundances of B. cinerea were significantly different between fruit types and ripening stages (Kruskal–Wallis chi-squared = 73.45, P = 7.80 × 10–16; Kruskal–Wallis chi-squared = 23.81, P = 2.74 × 10–5, respectively). Raspberry had the lowest relative abundance of B. cinerea (mean ± SE = 800 ± 136) and this was significantly lower than strawberry (1994 ± 292) and blueberry (5990 ± 1305) (P  More

  • in

    The double-edged sword of inducible defences: costs and benefits of maladaptive switching from the individual to the community level

    In our simulations for the autotrophs, we varied two of the three trade-off properties (level of defence, plasticity costs and defence costs; see Fig. 1b) at a time and kept the third one constant. This results in three constellations reflecting three different trade-offs between these properties (Table 1):

    parallel: trade-off between defence and plasticity costs;

    crossing: trade-off between defence costs and plasticity costs;

    angle: trade-off between defence and defence costs.

    Table 1 Description of the three constellations parallel, crossing, and angle defining the position of the four phenotypes in the trait space of defence and growth rate.Full size tableIn all three constellations, the autotrophic species B spanned the entire defence range, i.e. it had a completely undefended phenotype Bu and a maximally defended phenotype Bd. A either had a more limited defence range (in constellations parallel and angle) or spanned the entire range as well (in constellation crossing), representing three distinct ways that the trade-off between defence, growth rate, and plasticity range may play out. For each constellation, we varied the maximum switching rate χmax over 5 orders of magnitude to investigate the effect of plasticity (Table 1, middle row). This parameter determines how rapidly a species can switch between phenotypes (see “Methods”, “Exchange rates”); higher values indicate faster adaptation. These results were also compared with a non-plastic baseline scenario where both phenotypes of each species are presented but χmax = 0 (Table 1, upper row), as well as a rigid scenario where the species have only a single phenotype (Table 1, bottom row). All parameters and their values can be found in Supplementary Table S1.In the following, we give a detailed description of the results for constellation parallel, where the autotroph species A and B have the same defence costs resulting in parallel trade-off lines between defence and growth rate, while varying the level of defence for A and varying the plasticity costs for B (Table 1, left column). We start with examining patterns for the phenotype biomasses, coexistence and community stability in the non-plastic baseline scenario “parallel 0”, and then compare the corresponding scenarios with a low exchange rate (“parallel 0.01”) and a high exchange rate (“parallel 1”). We next discuss the other two constellations (crossing and angle, Table 1) more briefly. Finally, we generalize across all scenarios and focus on the coexistence, the degree of maladaptive switching, and the consumer and total autotroph biomasses.Non-plastic baseline dynamics: scenario parallel 0
    In this scenario, four single phenotypes unconnected by exchange compete with each other. Thus, species coexistence here depends entirely on phenotype coexistence: the trade-offs have to be such that for each species, at least one phenotype is a good enough competitor to survive. Which phenotypes survive depend on the two trade-off parameters, defence of the defended phenotype of species A (dAu) and plasticity costs for species B (pcB), which thus determine whether coexistence is possible.The defence costs were kept constant at an intermediate value of 0.3 for both species, resulting in parallel trade-off lines (Table 1, scenario “parallel 0”). The undefended phenotype of A, Au, is a growth-specialist with the highest growth rate of all phenotypes. The defended phenotype of the same species, Ad, has a defence between 0 and 0.9 and a relatively high growth rate, and can be viewed as a generalist. Species B has variable plasticity costs that lower the growth rate of both phenotypes. The defended phenotype of species B, Bd, has the lowest growth rate of all phenotypes but is very well-defended, and thus a defence-specialist. Its undefended phenotype, Bu, is as undefended as Au but has a lower growth rate; it is thus always an inferior competitor and inevitably goes extinct (Fig. 2c).Figure 2Biomasses, coexistence and trait space for scenario parallel 0. Biomasses of the four autotrophic phenotypes (a–d), their coexistence patterns (e), the consumer biomass (f) and the autotrophs’ trait values (g–j) (higher biomasses are shown by darker colours). Lines in (a–f) separate the regions I–III of different coexistence patterns. Note that in (a–f), the y-axis is reversed to show increasing fitness along all axes. An exemplary trait combination for every region is shown in (g–j); larger symbols indicate the surviving phenotypes. Shaded areas in (e) depict oscillating systems (quarter-lag predator–prey cycles in dense shading, antiphase cycles in loose shading).Full size imageAs Bu never survives, coexistence of the autotroph species requires the survival of defence-specialist Bd. Bd can only survive if Ad is not too defended, because Ad has a higher growth rate than Bd and will outcompete Bd in the “defended” niche otherwise (region Ib; Fig. 2d,h). A second criterion is that the plasticity costs for B must not be too high, because then the benefits of the defence of Bd no longer outweigh the costs, and it will go extinct even if there are no other highly defended phenotypes around (region Ia; Fig. 2d,g). In the regions where Bd goes extinct, species coexistence is not possible (Fig. 2e). The generalist Ad either survives by itself (region Ia in Fig. 2b,g) if its defence is low to intermediate, or together with the growth-specialist Au if its defence is high (region Ib in Fig. 2a,b,h). In the regions II and III where Bd survives, it never survives on its own, but always together with one of the phenotypes of A. It coexists with the growth-specialist Au if the plasticity costs are very low (region II in Fig. 2,i), and together with Ad if they are low to intermediate (region III in Fig. 2,j). These two regions do support species coexistence (Fig. 2e).In three of the four regions (Ib, II and III in Fig. 2f), consumer biomass is low, because the final community always contains a well-defended phenotype (Ad in region Ib, and Bd in regions II and III); the overall level of defence of the community is relatively high in these regions (Supplementary Figure S1). Conversely, consumer biomass is relatively high in region Ia, because the only surviving autotroph phenotype is relatively fast-growing and fairly undefended (Fig. 2f,g). The regions where a well-defended phenotype survives often show antiphase cycles (Ib, II and III in Fig. 2e). These cycles do not occur in the region where only Ad survives (Ia in Fig. 2e); but regular quarter-lag predator–prey cycles can be found here if Ad is almost entirely undefended.While the community defence (i.e. mean defence of the autotroph community) depends strongly on the coexisting phenotypes, the community growth rate is roughly constant because over the entire trait space, at least one phenotype with a high growth rate always survives (Supplementary Figure S1). The standing variance of the community defence was high when two phenotypes coexist as they occupy different niches along the defence axis (Fig. 2h–j). In contrast, the variance of the community growth rate was very low and almost constant across all regions.Effect of phenotypic plasticityEven a little bit of plasticity in the scenario parallel 0.01 (χmax = 0.01) can change the above patterns for coexistence, stability, and average consumer biomass (Fig. 3a–d). While the autotrophs are intuitively expected to benefit from being plastic, the effect of plasticity on consumer biomass always turned out to be positive (Fig. 3a). This may be explained by the fact that switching was always, on average, maladaptive (Fig. 3c,d), measured by the adaptation index Φ (see Eqs. (11–13) in “Methods”). This index combines information on the net “flow” of individuals due to switching (i.e. whether more undefended individuals switch to defended or vice versa) with the fitness difference between the two phenotypes, and thus measures whether overall, more individuals switch from a low-fitness to a high-fitness phenotype (adaptive) or the reverse (maladaptive). This index can approach zero, but is always negative at equilibrium (see Appendix B), indicating maladaptive switching.Figure 3Consumer biomass, autotroph coexistence and maladaptive switching for the scenarios parallel 0.01 (a–d) and parallel 1 (e–h). Consumer biomass (a,e), the autotroph coexistence patterns (b,f), and the autotrophs’ maladaptive switching Φ (c,d,g,h) (higher biomasses or more intensive maladaptive switching are shown by darker colours). Lines separate the regions I–III of different autotroph coexistence. The y-axis is reversed to follow the pattern of increasing fitness. Grey areas in (c,d,g,h) depict areas where the species was extinct. Shaded areas in b and f depict oscillating systems (quarter-lag predator–prey cycles in dense shading, antiphase cycles in loose shading).Full size imageThe most striking effect of plasticity was on coexistence, which was affected both positively and negatively by plasticity in different regions of the parameter space (Fig. 3b, Supplementary Figure S4a–d). A negative effect on coexistence is seen in region II, where the autotroph species previously coexisted (Fig. 2e), while with plasticity, B outcompeted A (Fig. 3b). Without plasticity, coexistence was possible in this region because Au and Bd survived; importantly, Au outcompeted Bu due to its higher growth rate, even though the difference between their growth rates is very small in this region (Fig. 2i). Plasticity reverses the competitive exclusion pattern between the two undefended phenotypes: Bu receives a constant flow of biomass from the well-defended Bd, which compensates for its slightly lower growth rate and allows it to outcompete Au. Thus, coexistence is reduced as a direct consequence of maladaptive switching.Plasticity can also promote coexistence, as the coexistence region now extends into former region Ib where the generalist Ad is highly defended (Fig. 2b, Supplementary Figure S1a). This is also an effect of maladaptive switching, though in this case the effect is indirect, mediated through the effect of plasticity on consumer biomass. Without plasticity, coexistence was impossible in region Ib because Bd was always outcompeted by Ad: even though the latter had a slightly lower level of defence, this was outweighed by its higher growth rate, making Ad the superior competitor over Bd. However, plasticity changes this because maladaptive switching increases the consumer biomass, which in turn alters the cost/ benefit balance of defence: Bd derives a stronger benefit from its high level of defence, which now outweighs the cost and allows it to survive. Coexistence through this mechanism is not possible when the plasticity costs for B are too high or when Ad is too well-defended, explaining the narrowing of the coexistence “tail” for high defence of Ad (Fig. 3b).While the patterns of coexistence changed when allowing for plasticity, the patterns in the trait values were nearly indistinguishable from the previous scenario (Supplementary Figure S1, S2). Finally, plasticity had a strong impact on the community dynamics, as most of the antiphase cycles were stabilized (Ib, II, III in Fig. 3b). Their area decreased sharply as these cycles were characterized by asynchronous dynamics between the two prey phenotypes, which were reduced by plasticity. In contrast, the area of the quarter-lag predator–prey cycles remained unaffected by plasticity.All the above patterns were found to a far stronger degree with a higher amount of plasticity (χmax = 1; Fig. 3e–h, Supplementary Figure S4e–h). Consumer biomass increased strongly everywhere (cf. Fig. 3a,e), reflecting the strong increase in the degree of maladaptive switching (cf. Fig. 3c,d,g,h). The higher exchange rates led to more synchronization between the phenotypes, extinguishing the antiphase cycles completely (Fig. 3f). It also decreased the biomass of both defended phenotypes (cf. Supplementary Figure S4b,d,f,h). This in turn led to a lower community defence and a higher community growth rate (Supplementary Figure S3) both contributing to a higher consumer biomass. Finally, there was a sharp decrease in the coexistence region for high plasticity (Fig. 3e). Region II, where B outcompetes A through maladaptive switching, doubled in size due to the much higher degree of maladaptive switching (Fig. 3g,h). Region I, where A outcompetes B, now also increased, when the level of defence of Ad is relatively low (Fig. 3e). This is again an indirect effect of maladaptive switching causing a strong increase in consumer biomass, affecting the cost/ benefit balance of defence: while Bd derives a strong benefit from its high level of defence, Bu is completely undefended, and is at an extra disadvantage because of its low growth rate. Thus, while Bd would have been able to survive by itself, the high exchange rate causes a strong source-sink dynamic that drives B extinct.Effect of plasticity in constellations crossing and angle
    In constellation crossing the trade-off lines of both species cross in the trait space, as the level of defence is the same for both defended phenotypes; species B has a lower growth rate for its undefended phenotype than species A due to plasticity costs, while its defence costs are low and thus the growth rate of its defended phenotype is higher than for species A (Table 1, Supplementary Figure S5). Without plasticity the crossing trade-off lines lead to coexistence of both species in all simulations as Au and Bd were always the only survivors, mostly showing antiphase oscillations (Supplementary Figure S5).Allowing for phenotypic plasticity has the same results as were observed for constellation parallel: consumer biomass sharply increases (Fig. 4a,e); antiphase cycles are dampened or absent; and the area of coexistence decreases (Fig. 4b,f). All these changes are more pronounced for higher exchange rates (cf. Fig. 4a,b,e,f). Again, the biomass of the defended phenotypes decreased for high exchange rates (Supplementary Figure S6). Switching was always maladaptive for high exchange rates (Fig. 4g,h), and mostly maladaptive for low exchange rates (Fig. 4c,d). As was seen for constellation parallel, maladaptive switching was the reason for the decrease in coexistence. B can outcompete A when B has low plasticity costs. Bd has a much higher growth rate than Ad, while the undefended phenotypes have similar growth rates. The direction of competitive exclusion between Au and Bu is thus easily reversed by Bd donating biomass to the sink Bu, allowing B to occupy both niches and outcompete A (region II in Fig. 4b,f). The same mechanism happens in reverse for high plasticity and defence costs of B: the differences in growth rate for the undefended phenotypes are high, while the defended phenotypes have very similar growth rates. Au can support Ad, and A outcompetes B (region III in Fig. 4b,f).Figure 4Coexistence and maladaptive switching for scenario crossing 0.01 (a-d) and crossing 1 (e–h). Consumer biomass (a,e), the autotroph coexistence patterns (b,f), and the autotrophs’ maladaptive switching Φ (c,d,g,h) (higher biomasses or more intensive maladaptive switching are shown by darker colours). Lines separate the regions I–III of different autotroph coexistence. The x- and y-axis are reversed to follow the pattern of increasing fitness. Shaded areas in (b) depict antiphase cycles. Grey areas in (c,d,g,h) depict areas where the species was extinct. Shaded grey areas depict areas without simulations (cf. “Methods”). Note that (c,d,g,h) have each a different colour scale.Full size imageIn constellation angle there are no plasticity costs, and thus the undefended phenotypes Au and Bu have identical growth rates. The defended phenotypes take the same places in trait space as in the parallel constellation: Ad is a generalist, with a lower level of defence and a relatively high growth rate due to low defence costs, whereas Bd is a defence-specialist with a high level of defence but a low growth rate. This leads to the trade-off lines forming an angle (see Table 1). Without phenotypic plasticity, the coexistence patterns are the same as in constellation parallel, except that no competitive exclusion occurs between the undefended phenotypes; instead, they (neutrally) coexist in regions Ib, II and III (Supplementary Figure S7; cf. Fig. 2).With plasticity, neutral coexistence vanished: the defended phenotype that survived (Ad in region Ib, Bd in region III) could support the undefended phenotype of its own species, driving the other species extinct (Fig. 5b,f). As in the other constellations, the area of coexistence and the biomasses of the defended phenotypes decreased and antiphase cycles vanished with increasing χmax (Fig. 5b,f, Supplementary Figure S8), while maladaptive switching and the consumer biomass increased (Fig. 5).Figure 5Coexistence and maladaptive switching for scenario angle 0.01 (a–d) and angle 1 (e–h). Consumer biomass (a,e), the autotroph coexistence patterns (b,f), and the autotrophs’ maladaptive switching Φ (c,d,g,h) (higher biomasses or more intensive maladaptive switching are shown by darker colours). Lines separate the regions I–III of different autotroph coexistence. The y-axis is reversed to follow the pattern of increasing fitness. Shaded areas in (b) depict antiphase cycles. Grey areas in (c,d,g,h) depict areas where the species was extinct. Note that (c,d,g,h) have each a different colour scale.Full size imageGeneral resultsAs plasticity had very similar effects across all three constellations, we here generalize our results: we compare the three constellations for exchange rates over 5 orders of magnitude, as well as the non-plastic scenario and the rigid scenario (Table 1). That is, all simulations from one scenario (e.g. parallel 0) were summarized into one bar respective point in Fig. 6.Figure 6General patterns for coexistence, maladapative switching and biomasses. Share of surviving species in percent (A, B, coexistence or neutral coexistence) (a–c), median absolute value of maladaptive switching Φ (d–f) and median of total autotroph biomass (A + B), median consumer biomass C and share of defended phenotypes ((Ad + Bd)/(A + B)) (g–i) for the three constellations and increasing maximum exchange rates χmax. χmax = 0 denotes the non-plastic scenarios; *denotes the rigid scenarios. Maladaptive switching and the share of defended phenotypes do not apply for the rigid scenarios.Full size imageFor all constellations, the fraction of simulation runs leading to coexistence was highest in the non-plastic scenario and decreased with increasing χmax (Fig. 6a–c). In constellation parallel the share of coexistence for increasing χmax continuously decreased from 51 to 3% (Fig. 6a). In crossing, the share decreased from full to no coexistence (Fig. 6b). In angle, the share of coexistence was 88% in the non-plastic scenario when taking also neutral coexistence into account (Fig. 6c). Its share decreased to 9% for a χmax of 10 and increased again to 25% for the rigid scenario. Maladaptive switching increased for both species and all constellations for increasing χmax (Fig. 6d–f). The increased plasticity led to a lower total autotroph biomass and a lower share of defended phenotypes (Fig. 6g–i), which resulted in higher consumer biomass (Fig. 6g–i).Interestingly, and counterintuitively, the above patterns show that increasing the speed of plasticity (by increasing χmax) makes the system behave more like the rigid system. The coexistence patterns in scenarios with high χmax approach those of the rigid scenarios in two of the constellations (Fig. 6a,b). Similarly, the total autotroph and consumer biomasses approach the ones in the rigid scenarios (Fig. 6g–i). Thus, we found the higher χmax make the autotrophs not more adaptive, but behave more like non-adaptive species. More

  • in

    Cyanophages from a less virulent clade dominate over their sister clade in global oceans

    Infection properties of clade A and clade B T7-like cyanophagesWe set out to test the hypothesis that the phylogenetic separation of T7-like cyanophages into two major clades reflects differences in their infection physiology. To do this we investigated a suite of infection properties of three pairs of clade A and B phages, each pair infecting the same Synechococcus host (Table 1) to allow us to control for variability in host genetics and physiology. These six cyanophages are representatives of 3 clade A and 2 clade B cyanophage subclades (SI Appendix, Table S1).Table 1 Summary of infection physiology of three pairs of clade A and clade B cyanophages infecting the same Synechococcus hosts.Full size tableWe began by investigating adsorption kinetics and the length of time taken to produce new phages in the infection cycle, the latent period, from phage growth curve experiments. In all three pairs of phages, adsorption was 7–15-fold more rapid in the clade A phage versus the clade B phage (Fig. 1, Table 1). Furthermore, the clade A phage had a faster infection cycle with a latent period that was 3-5-fold shorter than the clade B phage on the same host (Fig. 1a–c) (Table 1). To determine how representative these findings are for a greater diversity of T7-like cyanophages we report the latent period of nine additional non-paired phages that infect a variety of hosts and span the diversity of this cyanophage genus, measured here and taken from the literature (SI Appendix, Table S1). These phages showed the same pattern as observed between phage pairs, although one clade A phage had a relatively long latent period (see SI Appendix, Table S1). Overall, the 5 clade A phages representative of 5 subclades had a significantly shorter latent period (3.3 ± 3.6 h, n = 5 phages (mean ± SD) than the 10 clade B phages from 7 subclades (7.7 ± 2.0 h, n = 10 phages) (Kruskal-Wallis: χ2 = 4.72, df = 1; p = 0.029, n = 15). No significant differences in the length of the latent period were found for clade B phages that infected Synechococcus and Prochlorococcus (Kruskal-Wallis: χ2 = 1.13, df = 1; p = 0.29, n = 10).Fig. 1: Comparison of the infection physiology between pairs of clade A and clade B T7-like cyanophage infecting the same Synechococcus host.a–c Cyanophage growth curves, d–f burst sizes, g–i virulence as the percentage of lysed host cells, j–l decay as loss of infectivity, m–o plaque sizes. a, d, g, j, m Clade A Syn5 phage and clade B S-TIP37 phage infecting WH8109. b, e, h, k, n Clade A S-CBP42 phage and clade B S-RIP2 phage infecting WH7803. c, f, i, l, o Clade A S-TIP28 phage and clade B S-TIP67 phage infecting CC9605. The host strain is shown at the right of the panels. Red and blue lines or bars show results for clade A and clade B phages, respectively. a–c, g–I Error bars indicate standard deviations. d–f Burst size results are for single cells. j–l The solid line shows the fitted multi-level linear model. m–o The time after infection at which plaques were photographed appears above the images. *p value  More

  • in

    Demand outstripping supply

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