More stories

  • in

    Assessing mammal trapping standards in wild boar drop-net capture

    Dubois, S. et al. International consensus principles for ethical wildlife control. Conserv. Biol. 31(4), 753–760 (2017).PubMed 
    Article 

    Google Scholar 
    Frank, B. & Glikman, J. A. Human–wildlife conflicts and the need to include coexistence. In Human–Wildlife Interactions (eds Frank, B. et al.) 1–19 (Cambridge University Press, 2019).
    Google Scholar 
    Meng, X. J., Lindsay, D. S. & Sriranganathan, N. Wild boars as sources for infectious diseases in livestock and humans. Philos. Trans. R. Soc. B Biol. Sci. 364, 2697–2707 (2009).CAS 
    Article 

    Google Scholar 
    Massei, G., Roy, S. & Bunting, R. Too many hogs? A review of methods to mitigate impact by wild boar and feral hogs. Hum. Wildl. Interact. 5, 79–99 (2011).
    Google Scholar 
    Carpio, A. J., Apollonio, M. & Acevedo, P. Wild ungulate overabundance in Europe: Contexts, causes, monitoring and management recommendations. Mamm. Rev. 51, 95–108 (2021).Article 

    Google Scholar 
    Stillfried, M. et al. Secrets of success in a landscape of fear: Urban wild boar adjust risk perception and tolerate disturbance. Front. Ecol. Evol. 5, 157 (2017).Article 

    Google Scholar 
    Castillo-Contreras, R. et al. Urban wild boars prefer fragmented areas with food resources near natural corridors. Sci. Total Environ. 615, 282–288 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Keuling, O., Strauß, E. & Siebert, U. Regulating wild boar populations is ‘somebody else’s problem’!—Human dimension in wild boar management. Sci. Total Environ. 554–555, 311–319 (2016).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Vajas, P. et al. Many, large and early: Hunting pressure on wild boar relates to simple metrics of hunting effort. Sci. Total Environ. 698, 134251. https://doi.org/10.1016/j.scitotenv.2019.134251 (2020).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Licoppe, A. et al. Wild boar/feral pig in (peri-)urban areas. Managing wild boar in human-dominated landscapes. in International Union of Game Biologists (IUGB)—Congress IUGB 2013, 1–31 (2013).Torres-Blas, I. et al. Assessing methods to live-capture wild boars (Sus scrofa) in urban and peri-urban environments. Vet. Rec. 187, e85. https://doi.org/10.1136/vr.105766 (2020).Article 
    PubMed 

    Google Scholar 
    Adams, C. E. Urban Wildlife Management (CRC Press, 2016).
    Google Scholar 
    Conejero, C. et al. Past experiences drive citizen perception of wild boar in urban areas. Mamm. Biol. 96, 68–72 (2019).Article 

    Google Scholar 
    Lewis, J. S., VerCauteren, K. C., Denkhaus, R. M. & Mayer, J. J. Wild pig populations along the urban gradient. In Invasive Wild Pigs in North America (eds VerCauteren, K. C. et al.) 439–463 (CRC Press, 2019).Chapter 

    Google Scholar 
    Massei, G. et al. Effect of the GnRH vaccine GonaCon on the fertility, physiology and behaviour of wild boar. Wildl. Res. 35, 540–547 (2008).CAS 
    Article 

    Google Scholar 
    Náhlik, A. et al. Wild boar management in Europe: Knowledge and practice. In Ecology, Conservation and Management of Wild Pigs and Peccaries (eds Melletti, M. & Meijaard, E.) 339–353 (Cambridge University Press, 2017).Chapter 

    Google Scholar 
    Croft, S., Franzetti, B., Gill, R. & Massei, G. Too many wild boar? Modelling fertility control and culling to reduce wild boar numbers in isolated populations. PLoS One 15, e0238429. https://doi.org/10.1371/journal.pone.0238429 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    González-Crespo, C. et al. Stochastic assessment of management strategies for a Mediterranean peri-urban wild boar population. PLoS One 13, e0202289. https://doi.org/10.1371/journal.pone.0202289 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schemnitz, S. D., Batcheller, G. R., Lovallo, M. J., White, H. B. & Fall, M. W. Capturing and handling wild animals. In Research and Management Techniques for Wildlife and Habitats (ed. Silvy, N. J.) 232–269 (John Hopkins University Press, 2009).
    Google Scholar 
    ECGCGRF (European Community, Government of Canada, and Government of the Russian Federation). Agreement on international humane trapping standards. Off. J. Eur. Communities 42, 43–57 (1997).
    Google Scholar 
    Anonymous. International agreement in the form of an agreed minute between the European Community and the United States of America on humane trapping standards. Off. J. Eur. Communities L219, 26–37 (1998).
    Google Scholar 
    ISO 10990-4. Methods for testing killing trap systems used on land and underwater. in Animal (Mammal) Traps—Part 4 (International Organization for Standardization, 1999).ISO 10990-5. Methods for testing restraining traps. in Animal (Mammal) Traps—Part 5 (International Organization for Standardization, 1999).Proulx, G., Cattet, M., Serfass, T. L. & Baker, S. E. Updating the AIHTS trapping standards to improve animal welfare and capture efficiency and selectivity. Animals 10, 1–26 (2020).Article 

    Google Scholar 
    Proulx, G. Mammal Trapping—Wildlife Management, Animal Welfare and International Standards (Alpha Wildlife Publications, 2022).
    Google Scholar 
    Iossa, G., Soulsbury, C. & Harris, S. Mammal trapping: A review of animal welfare standards of killing and restraining traps. Anim. Welf. 16, 335–352 (2007).CAS 

    Google Scholar 
    Muñoz-Igualada, J., Shivik, J. A., Domínguez, F. G., Lara, J. & González, L. M. Evaluation of cage-traps and cable restraint devices to capture red foxes in Spain. J. Wildl. Manag. 72, 830–836 (2008).Article 

    Google Scholar 
    Trap Research and Development Committee. Best Trapping Practices (Fur Institute of Canada, 2018).
    Google Scholar 
    Virgós, E. et al. A poor international standard for trap selectivity threatens global carnivore and biodiversity conservation. Biodivers. Conserv. 25, 1409–1419 (2016).Article 

    Google Scholar 
    Barasona, J. A., López-Olvera, J. R., Beltrán-Beck, B., Gortázar, C. & Vicente, J. Trap-effectiveness and response to tiletamine-zolazepam and medetomidine anaesthesia in Eurasian wild boar captured with cage and corral traps. BMC Vet. Res. 9, 107 (2013).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Shury, T. Physical capture and restraint. In Zoo Animal and Wildlife Immobilization and Anesthesia (eds West, G. et al.) 109–124 (Wiley Blackwell, 2015).
    Google Scholar 
    Webb, S. L., Lewis, J. S., Hewitt, D. G., Hellickson, M. W. & Bryant, F. C. Assessing the helicopter and net gun as a capture technique for white-tailed deer. J. Wildl. Manag. 72, 310–314 (2008).Article 

    Google Scholar 
    López-Olvera, J. R. et al. Comparative evaluation of effort, capture and handling effects of drive nets to capture roe deer (Capreolus capreolus), Southern chamois (Rupicapra pyrenaica) and Spanish ibex (Capra pyrenaica). Eur. J. Wildl. Res. 55, 193–202 (2009).Article 

    Google Scholar 
    Breed, D. et al. Conserving wildlife in a changing world: Understanding capture myopathy—A malignant outcome of stress during capture and translocation. Conserv. Physiol. 7, 1–21 (2019).Article 
    CAS 

    Google Scholar 
    Mentaberre, G. et al. Azaperone and sudden death of drive net-captured southern chamois. Eur. J. Wildl. Res. 58, 489–493 (2012).Article 

    Google Scholar 
    Gaskamp, J. A., Gee, K. L., Campbell, T. A., Silvy, N. J. & Webb, S. L. Effectiveness and efficiency of corral traps, drop nets and suspended traps for capturing wild pigs (Sus scrofa). Animals 11, 1565 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Baker, S. E., Macdonald, D. W. & Ellwood, S. A. Double standards in spring trap welfare. In Proceedings of the Ninth International Conference on Urban Pests (eds Daivies, C. & Pfeiffer, W. H.) 139–145 (Pureprint Group, 2017).
    Google Scholar 
    López-Olvera, J. R., Castillo-Contreras, R., González-Crespo, C., Conejero, C. & Mentaberre, G. Wild boar is not welcome in the city. Barcelona Metròpolis 103, 22–23 (2017).
    Google Scholar 
    Conejero, C. et al. Conflicto o habituación: las dos caras de la percepción social del jabalí urbano. in Proceedings of XIV Congreso de la Sociedad Española para la Conservación y Estudio de los Mamíferos (SECEM, 2019).Conferencia Sectorial de Medio Ambiente. Directrices Técnicas para la Captura de Especies Cinegéticas Predadoras: Homologación de Métodos y Acreditación de Usuarios (Ministerio para la Transición Ecológica y el Reto Demográfico de España, 2011).Generalitat de Catalunya—Government of Catalonia. Decret 56/2014 relatiu a l’homologació de mètodes de captura en viu d’espècies cinegètiques depredadores i d’espècies exòtiques invasores depredadores i l’acreditació de les persones que en són usuàries. Diari Oficial de la Generalitat de Catalunya 6609 (2014).Fahlman, Å. et al. Wild boar behaviour during live-trap capture in a corral-style trap: Implications for animal welfare. Acta Vet. Scand. 62, 1–11 (2020).Article 

    Google Scholar 
    Sharp, T. & Saunders, G. A Model for Assessing the Relative Humaneness of Pest Animal Control Methods (Australian Government—Department of Agriculture, Fisheries and Forestry [New Millennium Print], 2011).
    Google Scholar 
    Ziegler, L., Fischer, D., Nesseler, A. & Lierz, M. Validation of the live trap ‘Krefelder Fuchsfalle’ in combination with electronic trap sensors based on AIHTS standards. Eur. J. Wildl. Res. 64, 17 (2018).Article 

    Google Scholar 
    Marco, I. et al. Capture myopathy in little bustards after trapping and marking. J. Wildl. Dis. 42, 889–891 (2006).ADS 
    PubMed 
    Article 

    Google Scholar 
    Rideout, C. B. Comparison of techniques for capturing mountain goats. J. Wildl. Manag. 38, 573 (1974).Article 

    Google Scholar 
    Jedrzejewski, W. & Kamler, J. F. Modified drop-net for capturing ungulates. Wildl. Soc. Bull. 32, 1305–1308 (2004).Article 

    Google Scholar 
    Gaskamp, J. A. Use of drop-nets for wild pig damage and disease abatement. Master’s thesis, available electronically from https://hdl.handle.net/1969.1/148198 (Texas A&M University, 2012).Lavelle, M. J. et al. When pigs fly: Reducing injury and flight response when capturing wild pigs. Appl. Anim. Behav. Sci. 215, 21–25 (2019).Article 

    Google Scholar 
    Masilkova, M. et al. Observation of rescue behaviour in wild boar (Sus scrofa). Sci. Rep. 11, 16217 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Podgórski, T. et al. Spatiotemporal behavioral plasticity of wild boar (Sus scrofa) under contrasting conditions of human pressure: Primeval forest and metropolitan area. J. Mammal. 94, 109–119 (2013).Article 

    Google Scholar 
    Manfredo, M., Teel, T. & Bright, A. Why are public values toward wildlife changing?. Hum. Dimens. Wildl. 8, 287–306 (2003).Article 

    Google Scholar 
    Cahill, S., Llimona, F., Cabañeros, L. & Calomardo, F. Characteristics of wild boar (Sus scrofa) habituation to urban areas in the Collserola Natural Park (Barcelona) and comparison with other locations. Anim. Biodivers. Conserv. 35, 221–233 (2012).Article 

    Google Scholar  More

  • in

    Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt

    Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jackson, R. B. et al. The ecology of soil carbon: pools, vulnerabilities, and biotic and abiotic controls. Annu. Rev. Ecol. Evol. Syst. 48, 419–445 (2017).Article 

    Google Scholar 
    Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science 333, 988–993 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403, 853–858 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    IPCC. Climate Change 2021: The Physical Science Basis. (eds Masson-Delmotte, V. et al.) (Cambridge Univ. Press, in press).Mora, C. et al. The projected timing of climate departure from recent variability. Nature 502, 183–187 (2013).Wood, T. E. et al. in Ecosystem Consequences of Soil Warming: Microbes, Vegetation, Fauna and Soil Biogeochemistry (ed. Mohan, J.) Ch. 14 (Academic Press, 2019).Davidson, E. A. & Janssens, I. A. Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    van Gestel, N. et al. Predicting soil carbon loss with warming. Nature 554, E4–E5 (2018).PubMed 
    Article 
    CAS 

    Google Scholar 
    Melillo, J. M. et al. Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science 358, 101–104 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Romero-Olivares, A. L., Allison, S. D. & Treseder, K. K. Soil microbes and their response to experimental warming over time: a meta-analysis of field studies. Soil Biol. Biochem. 107, 32–40 (2017).CAS 
    Article 

    Google Scholar 
    Anderson-Teixeira, K. J., Wang, M. M. H., McGarvey, J. C. & LeBauer, D. S. Carbon dynamics of mature and regrowth tropical forests derived from a pantropical database (TropForC-db). Glob. Change Biol. 22, 1690–1709 (2016).Article 

    Google Scholar 
    Nottingham, A. T., Meir, P., Velasquez, E. & Turner, B. L. Soil carbon loss by experimental warming in a tropical forest. Nature 584, 234–237 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Kimball, B. A. et al. Infrared heater system for warming tropical forest understory plants and soils. Ecol. Evol. 8, 1932–1944 (2018).DeAngelis, K. M. et al. Long-term forest soil warming alters microbial communities in temperate forest soils. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.00104 (2015)Bååth, E. Temperature sensitivity of soil microbial activity modeled by the square root equation as a unifying model to differentiate between direct temperature effects and microbial community adaptation. Glob. Change Biol. 24, 2850–2861 (2018).Article 

    Google Scholar 
    Wieder, W. R., Bonan, G. B. & Allison, S. D. Global soil carbon projections are improved by modelling microbial processes. Nat. Clim. Change 3, 909–912 (2013).CAS 
    Article 

    Google Scholar 
    Ratkowsky, D. A., Olley, J., Mcmeekin, T. A. & Ball, A. Relationship between temperature and growth-rate of bacterial cultures. J. Bacteriol. 149, 1–5 (1982).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rinnan, R., Rousk, J., Yergeau, E., Kowalchuk, G. A. & Bååth, E. Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming. Glob. Change Biol. 15, 2615–2625 (2009).Article 

    Google Scholar 
    Nottingham, A. T., Bååth, E., Reischke, S., Salinas, N. & Meir, P. Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes. Glob. Change Biol. https://doi.org/10.1111/gcb.14502 (2019).Li, J. Q., Bååth, E., Pei, J. M., Fang, C. M. & Nie, M. Temperature adaptation of soil microbial respiration in alpine, boreal and tropical soils: an application of the square root (Ratkowsky) model. Glob. Change Biol. 27, 1281–1292 (2021).CAS 
    Article 

    Google Scholar 
    Rousk, J., Frey, S. D. & Bååth, E. Temperature adaptation of bacterial communities in experimentally warmed forest soils. Glob. Change Biol. 18, 3252–3258 (2012).Article 

    Google Scholar 
    Nottingham, A. T. et al. Annual to decadal temperature adaptation of the soil bacterial community after translocation across an elevation gradient in the Andes. Soil Biol. Biochem. 158, 108217 (2021).CAS 
    Article 

    Google Scholar 
    Nottingham, A. T. et al. Microbial responses to warming enhance soil carbon loss following translocation across a tropical forest elevation gradient. Ecol. Lett. 22, 1889–1899 (2019).PubMed 
    Article 

    Google Scholar 
    Donhauser, J., Niklaus, P. A., Rousk, J., Larose, C. & Frey, B. Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils. Soil Biol. Biochem. 148, 107873 (2020).CAS 
    Article 

    Google Scholar 
    Mangan, S. A. et al. Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466, 752–755 (2010).Pold, G., Melillo, J. M. & DeAngelis, K. M. Two decades of warming increases diversity of a potentially lignolytic bacterial community. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.00480 (2015).Zhou, J. Z. et al. Temperature mediates continental-scale diversity of microbes in forest soils. Nat. Commun. 7, 12083 (2016).Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).Wu, L. et al. Reduction of microbial diversity in grassland soil is driven by long-term climate warming. Nat. Microbiol. 7, 1054–1062 (2022).Oliverio, A. M., Bradford, M. A. & Fierer, N. Identifying the microbial taxa that consistently respond to soil warming across time and space. Glob. Change Biol. 23, 2117–2129 (2017).Article 

    Google Scholar 
    Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Spracklen, D. V., Baker, J. C. A., Garcia-Carreras, L. & Marsham, J. H. The effects of tropical vegetation on rainfall. Annu. Rev. Env. Resour. 43, 193–218 (2018).Article 

    Google Scholar 
    Bradford, M. A. Thermal adaptation of decomposer communities in warming soils. Front. Microbiol. https://doi.org/10.3389/Fmicb.2013.00333 (2013).Pietikäinen, J., Pettersson, M. & Bååth, E. Comparison of temperature effects on soil respiration and bacterial and fungal growth rates. FEMS Microbiol. Ecol. 52, 49–58 (2005).PubMed 
    Article 
    CAS 

    Google Scholar 
    Mori, A. S. et al. Biodiversity–productivity relationships are key to nature-based climate solutions. Nat. Clim. Change 11, 543–550 (2021).Article 

    Google Scholar 
    Delgado-Baquerizo, M. et al. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat. Ecol. Evol. 4, 210–220 (2020).PubMed 
    Article 

    Google Scholar 
    Wagg, C., Bender, S. F., Widmer, F. & van der Heijden, M. G. A. Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc. Natl Acad. Sci. USA 111, 5266–5270 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nottingham, A. T. et al. Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes. Ecology 99, 2455–2466 (2018).PubMed 
    Article 

    Google Scholar 
    Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).Article 

    Google Scholar 
    Brown, J. H. Why are there so many species in the tropics? J. Biogeogr. 41, 8–22 (2014).PubMed 
    Article 

    Google Scholar 
    LaManna, J. A. et al. Plant diversity increases with the strength of negative density dependence at the global scale. Science 356, 1389–1392 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bagchi, R. et al. Pathogens and insect herbivores drive rainforest plant diversity and composition. Nature 506, 85–88 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lapebie, P., Lombard, V., Drula, E., Terrapon, N. & Henrissat, B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat. Commun. https://doi.org/10.1038/s41467-019-10068-5 (2019).Makhalanyane, T. P. et al. Microbial ecology of hot desert edaphic systems. FEMS Microbiol. Rev. 39, 203–221 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Aydogan, E. L., Moser, G., Muller, C., Kampfer, P. & Glaeser, S. P. Long-term warming shifts the composition of bacterial communities in the phyllosphere of Galium album in a permanent grassland field-experiment. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.00144 (2018).Hu, D. Y., Zang, Y., Mao, Y. J. & Gao, B. L. Identification of molecular markers that are specific to the class thermoleophilia. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.01185 (2019).Mohan, J. E. et al. Mycorrhizal fungi mediation of terrestrial ecosystem responses to global change: mini-review. Fungal Ecol. 10, 3–19 (2014).Article 

    Google Scholar 
    Manzoni, S., Taylor, P., Richter, A., Porporato, A. & Agren, G. I. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 196, 79–91 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Allison, S. D., Wallenstein, M. D. & Bradford, M. A. Soil-carbon response to warming dependent on microbial physiology. Nat. Geosci. 3, 336–340 (2010).CAS 
    Article 

    Google Scholar 
    Reed, S. C. et al. Soil biogeochemical responses of a tropical forest to warming and hurricane disturbance. Adv. Ecol. Res. 62, 225–252 (2020).Article 

    Google Scholar 
    Nottingham, A. T., Turner, B. L., Stott, A. W. & Tanner, E. V. J. Nitrogen and phosphorus constrain labile and stable carbon turnover in lowland tropical forest soils. Soil Biol. Biochem. 80, 26–33 (2015).CAS 
    Article 

    Google Scholar 
    Walker, T. W. N. et al. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nat. Clim. Change 8, 885–889 (2018).Kemmitt, S. J. et al. Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass—a new perspective. Soil Biol. Biochem. 40, 61–73 (2008).CAS 
    Article 

    Google Scholar 
    Nannipieri, P., Trasar-Cepeda, C. & Dick, R. P. Soil enzyme activity: a brief history and biochemistry as a basis for appropriate interpretations and meta-analysis. Biol. Fert. Soils 54, 11–19 (2018).CAS 
    Article 

    Google Scholar 
    Wallenstein, M., Allison, S., Ernakovich, J., Steinweg, J. M. & Sinsabaugh, R. in Soil Enzymology. Soil Biology Vol. 22 (eds Shukla, G. & Varma, A.) Ch. 13 (Springer, 2011).Zhou, X. Y., Chen, L., Xu, J. M. & Brookes, P. C. Soil biochemical properties and bacteria community in a repeatedly fumigated-incubated soil. Biol. Fert. Soils 56, 619–631 (2020).CAS 
    Article 

    Google Scholar 
    Sanchez-Julia, M. & Turner, B. L. Abiotic contribution to phenol oxidase activity across a manganese gradient in tropical forest soils. Biogeochemistry https://doi.org/10.1007/s10533-021-00764-0 (2021).Razavi, B. S., Liu, S. B. & Kuzyakov, Y. Hot experience for cold-adapted microorganisms: temperature sensitivity of soil enzymes. Soil Biol. Biochem. 105, 236–243 (2017).CAS 
    Article 

    Google Scholar 
    Pinney, M. M. et al. Parallel molecular mechanisms for enzyme temperature adaptation. Science 371, eaay2784 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Fanin, N. et al. Soil enzymes in response to climate warming: mechanisms and feedbacks. Funct. Ecol. https://doi.org/10.1111/1365-2435.14027 (2022).Hall, S. J. & Silver, W. L. Iron oxidation stimulates organic matter decomposition in humid tropical forest soils. Glob. Change Biol. 19, 2804–2813 (2013).Article 

    Google Scholar 
    Freeman, C., Ostle, N. & Kang, H. An enzymic ‘latch’ on a global carbon store. Nature 409, 149 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    Sarmiento, C. et al. Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proc. Natl Acad. Sci. USA 114, 11458–11463 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Condit, R., Perez, R., Lao, S., Aguilar, S. & Hubbell, S. P. Demographic trends and climate over 35 years in the Barro Colorado 50 ha plot. For. Ecosyst. https://doi.org/10.1186/s40663-017-0103-1 (2017).Woodring, W. P. Geology of Barro Colorado Island. Smithson. Misc. Collect. 135, 1–39 (1958).
    Google Scholar 
    Sanchez, P. A. & Logan, T. J. Myths and science about the chemistry and fertility of soils in the tropics. SSSA Spec. Publ. 29, 35–46 (1992).CAS 

    Google Scholar 
    Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Brookes, P. C., Landman, A., Pruden, G. & Jenkinson, D. S. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol. Biochem. 17, 837–842 (1985).CAS 
    Article 

    Google Scholar 
    Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 19, 703–707 (1987).CAS 
    Article 

    Google Scholar 
    Jenkinson, D. S., Brookes, P. C. & Powlson, D. S. Measuring soil microbial biomass. Soil Biol. Biochem. 36, 5–7 (2004).CAS 
    Article 

    Google Scholar 
    Kouno, K., Tuchiya, Y. & Ando, T. Measurement of soil microbial biomass phosphorus by an anion-exchange membrane method. Soil Biol. Biochem. 27, 1353–1357 (1995).CAS 
    Article 

    Google Scholar 
    Tabatabai, M. A. in Methods of Soil Analysis. Part 2. Microbiological and Biochemical Properties (ed. Page, A.L.) 778–833 (SSSA, 1994).Marx, M. C., Wood, M. & Jarvis, S. C. A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil Biol. Biochem. 33, 1633–1640 (2001).CAS 
    Article 

    Google Scholar 
    Price, N. & Stevens, L. Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins (Oxford Univ. Press, 1999).Hagerty, S. B., Allison, S. D. & Schimel, J. P. Evaluating soil microbial carbon use efficiency explicitly as a function of cellular processes: implications for measurements and models. Biogeochemistry 140, 269–283 (2018).CAS 
    Article 

    Google Scholar 
    Frey, S. D., Lee, J., Melillo, J. M. & Six, J. The temperature response of soil microbial efficiency and its feedback to climate. Nat. Clim. Change 3, 395–398 (2013).CAS 
    Article 

    Google Scholar 
    Spohn, M. et al. Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland. Soil Biol. Biochem. 97, 168–175 (2016).CAS 
    Article 

    Google Scholar 
    Sinsabaugh, R. L. et al. Stoichiometry of microbial carbon use efficiency in soils. Ecol. Monogr. 86, 172–189 (2016).Article 

    Google Scholar 
    Geyer, K. M., Dijkstra, P., Sinsabaugh, R. & Frey, S. D. Clarifying the interpretation of carbon use efficiency in soil through methods comparison. Soil Biol. Biochem. 128, 79–88 (2019).CAS 
    Article 

    Google Scholar 
    Bååth, E., Pettersson, M. & Söderberg, K. H. Adaptation of a rapid and economical microcentrifugation method to measure thymidine and leucine incorporation by soil bacteria. Soil Biol. Biochem. 33, 1571–1574 (2001).Article 

    Google Scholar 
    Bárcenas-Moreno, G., Gomez-Brandon, M., Rousk, J. & Bååth, E. Adaptation of soil microbial communities to temperature: comparison of fungi and bacteria in a laboratory experiment. Glob. Change Biol. 15, 2950–2957 (2009).Article 

    Google Scholar 
    Smirnova, E., Huzurbazar, S. & Jafari, F. PERFect: PERmutation Filtering test for microbiome data. Biostatistics 20, 615–631 (2019).PubMed 
    Article 

    Google Scholar 
    Alberdi, A. & Gilbert, M. T. P. hilldiv: an R package for the integral analysis of diversity based on Hill numbers. Preprint at bioRxiv https://doi.org/10.1101/545665 (2019).Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169–172 (2011).PubMed 
    Article 

    Google Scholar 
    Oksanen, J. et al. vegan: Community ecology package, R Package version 2 https://cran.r-project.org/web/packages/vegan/ (2018).Dufrene, M. & Legendre, P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67, 345–366 (1997).
    Google Scholar 
    Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. https://doi.org/10.1186/gb-2011-12-6-r60 (2011).Roesch, L. F. W. et al. PIME: a package for discovery of novel differences among microbial communities. Mol. Ecol. Resour. 20, 415–428 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Roberts, D.W. labdsv: Ordination and multivariate analysis for ecology. R package version 2.0-1 https://cran.r-project.org/web/packages/labdsv/ (2019).Cao, Y. et al. microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. Bioinformatics 38, 4027–4029 (2022).Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. Peerj 3, e1319 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Peterson, R. A. & Cavanaugh, J. E. Ordered quantile normalization: a semiparametric transformation built for the cross-validation era. J. Appl. Stat. 47, 2312–2327 (2020).PubMed 
    Article 

    Google Scholar  More

  • in

    A Cryptochrome adopts distinct moon- and sunlight states and functions as sun- versus moonlight interpreter in monthly oscillator entrainment

    l-cry mutants show higher spawning synchrony than wild-type animals under non-natural light conditionsIn order to test for a functional involvement of L-Cry in monthly oscillator function, we generated two l-cry mutant alleles (Δ34 and Δ11bp) (Fig. 1a) using TALENs28. In parallel, we generated a monoclonal antibody against Platynereis L-Cry. By testing mutant versus wildtype worms with the anti-L-Cry antibody in Western blots (Fig. 1b) and immunohistochemistry (Fig. 1e–j), we verified the absence of L-Cry protein in mutants. Furthermore, we confirmed that the staining of the antibody in wildtype worms (Fig. 1e–h) matches the regions where l-cry mRNA is expressed (Fig. 1d). These tests confirmed that the engineered l-cry mutations result in loss-of-function alleles. In turn, they validate the specificity of the raised anti-L-Cry antibody.Fig. 1: l-cry–/– mutants are loss-of-function alleles.a Overview of the l-cry genomic locus for wt and mutants. Both mutant alleles result in an early frameshift and premature stop codons. The Δ34 allele has an additional 9 bp deletion in exon 3. b Western Blots of P. dumerilii heads probed with anti-L-Cry antibody. In the context of further investigations such Western blots of mutant versus wild types have been performed more than 10 times with highly consistent results. Also see further analyses in this manuscript and ref. 36. c overview of P. dumerilii. d whole mount in situ hybridization against l-cry mRNA on worm head. ae, anterior eye; pe, posterior eye. e–j Immunohistochemistry of premature wild-type (e–h) and mutant (i, j) worm heads sampled at zt19/20 using anti-L-Cry antibody (green) and Hoechst staining (magenta), dorsal views, anterior up. e, f: z-stack images (maximal projections of 50 layers, 1.28 µm each) in the area highlighted by the rectangle in (d), whereas (g–j) are single layer images of the area highlighted by the white rectangles in (e, f). In the context of further investigations such stainings of mutant versus wild types have been performed more than 10 times with highly consistent results. Also see further analyses in this manuscript and ref. 36.Full size imageWe next assessed the circalunar maturation timing of wild types and l-cry mutant populations in conventional culture conditions, i.e. worms grown under typical indoor room lighting (named here artificial sun- and moonlight, Supplementary Fig. 1b).We expected either no phenotype (if L-Cry was not involved in circalunar clock entrainment) or a decreased spawning precision (if L-Cry was functioning as moonlight receptor in circalunar clock entrainment). Instead we observed an increased precision of the entrained worm population:We analyzed the maturation data using two statistical approaches, linear and circular statistics. We used the classical linear plots5 and statistics to compare the monthly spawning data distribution (Fig. 2a–c, i). This revealed a clear difference between mutant animals, which exhibited a stronger spawning peak at the beginning of the NM phase, compared to their wildtype and heterozygous counterparts (Fig. 2a–c, Kolmogorov–Smirnov test on overall data distribution, Fig. 2i).Fig. 2: L-Cry shields the circalunar clock from light that is not naturalistic moonlight.a–d, j Spawning of l-cry +/+ (a), l-cry +/– (Δ34) (b) and l-cry −/−(Δ34/ Δ34) (c) animals over the lunar month in the lab with 8 nights of artificial moonlight (a–c), under natural conditions in the sea (d, replotted from ref. 34,50,) and in the lab using naturalistic sun- and moonlight (j, 8 nights moonlight). e–h, k Data as in (a–d, j) as circular plot. 360° correspond to 30 days of the lunar month. The arrow represents the mean vector, characterized by the direction angle µ and r (length of µ). r indicates phase coherence (measure of population synchrony). p-values inside the plots: result of Rayleigh Tests. Significance indicates non-random distribution of data points. The inner circle represents the Rayleigh critical value (p = 0.05). i–l Results of two-sided multisample statistics on spawning data shown in (a–h, j, k). The phase differences in days can be calculated from the angle between the two mean vectors (i.e. 12°= 1 day).Full size imageWe then analyzed the same data using circular statistics (as the monthly cycle is repeating, see details in Methods section), which allowed us to describe the data with the mean vector (defined by the direction angle µ and its length r, shown as arrows in Fig. 2e–g). The phase coherence r (ranging from 0 to 1) serves as a measure for synchrony of the population data. As expected for entrained populations, all genotypes distributed their spawning across a lunar month significantly different from random (Fig. 2e–g, p values in circles, Rayleigh’s Uniformity test29). In line with the observed higher spawning peak of the l-cry−/− mutants in the linear plots, the circular analysis revealed a significant difference in spawning distribution (Mardia–Watson-Wheeler test, for details see Methods section) and higher spawning synchrony of mutants (r = 0.614) than in wild types and heterozygotes (r = 0.295 and r = 0.222) (Fig. 2i). The specificity of this phenotype of higher spawning precision for l-cry homozygous mutants was confirmed by analyses on trans-heterozygous l-cry (Δ34/Δ11) mutants (Supplementary Fig. 2), and by the fact that such a phenotype is not detectable in any other light receptor mutant available in Platynereis (r-opsin130: Supplementary Fig. 3a, b, e, f, i; c-opsin131: Supplementary Fig. 3c, d, g, h, i, Go-opsin: refs. 32, 33).The higher spawning synchrony of l-cry mutants under artificial light mimics the spawning precision of wild-type at its natural habitatThis increased spawning precision of l-cry mutants under artificial (but conventional indoor) laboratory light conditions let us wonder about the actual population synchrony of the worms under truly natural conditions. The lunar spawning synchrony of P. dumerilii at the Bay of Naples (the origin of our lab culture) has been worked on for more than 100 y. This allowed us to re-investigate very detailed spawning data records from the worms’ natural habitat published prior to environmental/light pollution. For better accessibility and comparability we combined all months and replotted the data published in 192934 (Fig. 2d, h, I; see details in Methods section; r = 0.631). This analysis revealed that the higher spawning synchrony in l-cry–/– worms mimics the actual spawning synchrony of P. dumerillii populations in their natural habitat34 (compare Fig. 2c, g with 2d, h.)Given that recent, non-inbred isolates from the same habitat as our lab inbred strains (which is the same habitat as the data collected in ref. 34) exhibit a broad spawning distribution under standard worm culture light conditions (which includes the bright artificial moonlight)35, we hypothesized that the difference in spawning synchrony between wildtype laboratory cultures and populations in their natural habitat is caused by the rather bright nocturnal light stimulus typically used for the standard laboratory culture (Supplementary Fig. 1a vs. b).Lunar spawning precision of wild-type animals depends on naturalistic moonlight conditionsWe next tested the resulting prediction that naturalistic moonlight should increase the spawning precision of the wildtype population, using naturalistic sun- and moonlight devices we specifically designed based on light measurements at the natural habitat of P. dumerilii31 (Supplementary Fig. 1a, c). We assessed the impact of the naturalistic sun- and moonlight (Supplementary Fig. 1a, c) on wildtype animals, maintaining the temporal aspects of the lab light regime (i.e. 8 nights of “full moon”). Indeed, merely adjusting the light intensity to naturalistic conditions increased the precision and phase coherence of population-wide reproduction: After several months under naturalistic sun- and moonlight, wildtype worms spawned with a major peak highly comparable to the wildtype precision reported at its natural habitat (Fig. 2d, h vs. j, k), and also exhibited an increased population synchrony (r = 0.398 compared to r = 0.295 under standard worm room light conditions). This increased similarity to the spawning distribution at the natural habitat (“Sea”) is confirmed by statistical analyses (Fig. 2l): The phase difference (angle between the two mean vectors) is only one day (corresponding to 12°). In contrast, the spawning distribution of wild types under standard worm room light versus naturalistic light conditions is highly significantly different in linear and circular statistical tests and has a phase difference of 7.7 days (Fig. 2l).These findings show that it is the naturalistic light that is critical for a highly precise entrainment of the monthly clock of wild-type worms. Given that l-cry–/– animals reach this high precision with the artificial light (i.e. standard lab light) implies that in wildtype L-Cry blocks artificial, but not naturalistic full-moonlight from efficiently synchronizing the circalunar clock. This block is removed in l-cry–/– animals, leading to a better synchronization of the l-cry–/– population. This finding suggests that L-Cry’s major role could be that of a gatekeeper controlling which ambient light is interpreted as full-moonlight stimulus for circalunar clock entrainment.
    l-cry functions as a light signal gatekeeper for circalunar clock entrainmentA prediction of this hypothesis is that mutants should entrain better to an artificial full-moonlight stimulus provided out-of-phase than their wild type counterparts (in which L-Cry should block the “wrong” moonlight at least partially from re-entraining the circalunar oscillator).We thus compared the spawning rhythms of l-cry+/+ and l-cry–/– worms under a re-entrainment paradigm, where we provided our bright artificial culture full-moonlight at the time of the subjective new moon phase (Fig. 3a). In order to compare the spawning data distribution relative to the initial full moon (FM) stimulus, as well as to the new full moon stimulus (i.e. new FM), we used two nomenclatures for the months: months with numbers are analyzed relative to the initial nocturnal light stimulus (i.e. FM), whereas months with letters are analyzed relative to the new (phase-shifted) nocturnal light stimulus (i.e. new FM, Fig. 3a). When the nocturnal light stimulus is omitted (to test for the oscillator function) we then refer to ‘free-running FM’ (FR-FM) or ‘new free-running FM’ (new FR-FM), respectively (Fig. 3a). Using these definitions, the efficiency of circalunar clock re-entrainment will be reflected in the similarity of spawning data distributions between month 1 and month D, i.e. the more similar the distribution, the more the population has shifted to the new phase.Fig. 3: l-cry−/− mutants entrain the circalunar clock faster than wt to a high-intensity artificial moonlight stimulus.a Nocturnal moonlight exposure protocol of lunar phase shift (entrained by 8 nights, phased shifted by 6 nights of artificial culture moon, light green). b, c Number of mature animals (percent per month, rolling mean with a window of 3 days) of l-cry wild-type (b) and homozygous mutant (c) animals. p-values indicate results of Kolomogorov–Smirnov tests. Dark blue arrowheads- old FM phase: wt show a spawning minimum, indicative that the worms are not properly phase shifted. Mutants spawn in high numbers, but don’t spawn at the old NM indicated by light blue arrowhead. Also compare to initial FM and NM in months 1,2. d, e Circular plots of the data shown in (b) and (c). Each circle represents one lunar month. Each dot represents one mature worm. The arrow represents the mean vector characterized by the direction angle µ and r. r (length of µ) indicates phase coherence (measure of population synchrony). The inner circle represents the Rayleigh critical value (p = 0.05). f, g Results of two-sided multisample statistics of data in (d, e). Phase differences in days can be calculated from the angle between the two mean vectors (i.e. 12°= 1 day).Full size imageWhen using the artificial nocturnal light conditions, the re-entrainment of l-cry–/– animals was both faster and more complete than for their wildtype relatives, as predicted from our gate keeper hypothesis. This is evident from the linear data analysis and Kolmogorov–Smirnov tests when comparing the month before the entrainment (month 1) with two months that should be shifted after the entrainment (months C,D, Fig. 3b, c, f, g).Most notably, while l-cry−/− worms were fully shifted in month D (Fig. 3c: compare boxes and see complete lack of spawning at the light blue arrowhead indicating the old NM/new FR-FM phase versus massive spawning at new NM phase around dark blue arrowhead), wildtype animals were still mostly spawning according to the initial lunar phase (Fig. 3b: compare boxes and see spawning at the light blue arrowhead versus almost lack of spawning at dark blue arrowhead). The faster re-entrainment of l-cry–/–, compared to l-cry+/+ animals is also confirmed by the Mardia–Watson-Wheeler test (see Methods section for details). For l-cry+/+ animals, the comparisons of the spawning distributions before and after re-entrainment show a 1000-fold (months 1 versus C) and tenfold (months 1 versus D) higher statistical significance difference than the corresponding comparisons for l-cry−/− worms (Fig. 3f, g). Consistently, the phase differences in days calculated from the angle between the two mean vectors from the circular analysis is smaller in the mutants than in the wild types when comparing the phase of the month before the entrainment (month 1) with two months after the entrainment (months C, D) (Fig. 3d–g). The fact that there are still differences in the mutant population before and after entrainment is likely due to the fact that even the mutants are not fully re-entrained. However, they have shifted more robustly in response to an artificial nocturnal light stimulus than the wild types. This provides further evidence that in wildtype worms L-Cry indeed blocks the “wrong” light from entering into the circalunar clock and thus functions as a light gatekeeper.L-Cry functions mainly as light interpreter, while its contribution as direct moonlight entraining photoreceptor is (at best) minorWe next tested to which extent L-Cry is itself a sensor for the re-entrainment signal under naturalistic light conditions. Based on the finding that l-cry−/− worms can still re-entrain the circalunar oscillator (see above), it is clear that even if L-Cry also directly contributed to the entrainment, it cannot be the only moonlight receptor mediating entrainment. With the experiments below, we aimed to test if L-Cry has any role as an entraining photoreceptor to the monthly oscillator.Thus, we tested how the circalunar clock is shifted in response to a re-entrainment with naturalistic moonlight in Platynereis wt versus l-cry−/− worms. For this, animals initially raised and entrained under standard worm room light conditions of artificial sun- and moonlight (Supplementary Fig. 1b, e) were challenged by a deviating FM stimulus of 8 nights of naturalistic moonlight (Fig. 4a, Supplementary Fig. 1c, e). This re-entraining stimulus was repeated for three consecutive months (Fig. 4a).Fig. 4: l-cry has a minor contribution as entraining photoreceptor to circalunar clock entrainment.a Nocturnal moonlight exposure protocol of lunar phase shift with 8 nights of naturalistic moonlight (dark green). Number of mature animals (percent per month, rolling mean with a window of 3 days) of l-cry wild-type (b) and mutant (c) animals. p-values: Kolomogorov–Smirnov tests. Black arrowheads indicate spawning-free intervals of the wildtype, which shifted to the position of the new FM (under free-running conditions: FR-FM). d, e Data as in (b, c) plotted as circular data. 360° correspond to 30 days of the lunar month. The arrow represents the mean vector characterized by the direction angle µ and r. r (length of µ) indicates phase coherence (measure of population synchrony). p values are results of Rayleigh Tests: Significance indicates non-random distribution of data points. The inner circle represents the Rayleigh critical value (p = 0.05). f, g Results of two-sided multisample statistics on spawning data shown in (a–e). Phase differences in days can be calculated from the angle between the two mean vectors (i.e. 12°= 1 day).Full size imageThe resulting spawning distribution was analyzed for the efficacy of the naturalistic moonlight to phase-shift the circalunar oscillator. In order to test if the animals had shifted their spawning to the new phase, we again compared the spawning pattern before the exposure to the new full moon stimulus (months with numbers: data distribution analyzed relative to the initial/old FM, see Fig. 4a for an overview) to the spawning pattern after the exposure to the new full moon stimulus (months with letters: data distribution analyzed relative to the new FM, Fig. 4a). The more similar the data distributions of month 1 is to the months C, D, the more the population was shifted to the new phase.The first re-entraining full moon stimulus (Fig. 4b, first dark green box) is given in the middle of the main spawning period. The nocturnal light itself does not cause immediate effects on the number of spawning worms (Fig. 4b, see also Fig. 2b, c), but the repeated exposure resulted in a noticeable shift of the spawning distribution indicating a phase shift of the monthly oscillator in wildtype. Already at the third re-entraining full moon stimulus, wildtype animals exhibited a completely shifted spawning pattern (Fig. 4b, d-d″, month 1, 2 vs. month C). This is supported by statistical analyses: When comparing the months 1 and 2 (relative to the old FM before the shift) to the month C (relative to the new FM after the shift), both the Kolmogorov–Smirnov test (Fig. 4b: gray rectangles, 4f) and the Mardia–Watson–Wheeler test of the same data were non-significant (Fig. 4f), indicative of the population shifting to the new phase. Consistently, the direction angle (µ) of the mean vectors before and after the shift was highly similar, resulting in a phase difference of only 0.2 days between months 1 and C and 0.5 days between month 2 and month C (Fig. 4f, for details see methods). The month under circalunar free-running conditions (month D) supports this observation, albeit with lower statistical support (Fig. 4b, d″, f).Of note, wild-type worms would eventually reach the high spawning precision found under naturalistic moonlight only after several more months based on independent experiments (Fig. 2j, k).When we analyzed the spawning distribution of l-cry mutants in the same way as the wild types, we found that the data distribution exhibited significant differences in the linear Kolmogorov–Smirnov test when comparing months 1 and 2 before the shift to the months C and D after the shift (Fig. 4c: gray rectangles, Fig. 4g); as well as in the phase distribution in the circular analyses when comparing the months before the shift (months 1 and 2) with the last months of the shift (months C,D) (Fig. 4e, e′ versus e″, e‴, g). The populations also exhibited a noticeable phase difference of ≥3.5 days (Fig. 4g).Based on the statistical significant difference in the re-entrainment of l-cry–/–, but not wild-type populations under a naturalistic sun- and moonlight regime, we conclude that L-Cry also likely contributes to circalunar entrainment as a photoreceptor. However, as these differences are rather minor, compared to the much stronger differences seen under artificial light regime, we conclude that its major role is the light gatekeeping function.In an independent study that focused on the impact of moonlight on daily timing, we identified r-Opsin1 as a lunar light receptor that mediates moonlight effects on the worms’ ~24 h clock36. We tested if r-opsin1 is similarly important for mediating the moonlight effects on the monthly oscillator of the worm, analyzed here. This is not the case. r-opsin1–/– animals re-entrain as well as wildtype worms under naturalistic light conditions (Supplementary Fig. 4). This adds to and is also consistent with our above observation that the spawning distribution is un-altered between r-opsin1–/– and wildtype animals under artificial light conditions (Supplementary Fig. 3a, b, e, f). This finding also further enforces the notion that monthly and daily oscillators use distinct mechanisms, but both require L-Cry as light interpreter.L-Cry discriminates between naturalistic sun- and moonlight by forming differently photoreduced statesGiven that the phenotype of l-cry–/– animals suggests a role of L-Cry as light gatekeeper, i.e. only allowing the ‘right’ light to most efficiently impact on the circalunar oscillator, we next investigated how this could function on the biochemical and cell biological level.While we have previously shown that Pdu-L-Cry is degraded upon light exposure in S2 cell culture15, it has remained unclear if L-Cry has the spectral properties and sensitivity to sense moonlight and whether this would differ from sunlight sensation. To test this, we purified full length L-Cry from insect cells (Supplementary Fig. 5a–c). Multi-angle light scattering (SEC-MALS) analyses of purified dark-state L-Cry revealed a molar mass of about 130 kDa, consistent with the formation of an L-Cry homodimer (theoretical molar mass of L-Cry monomer is 65.6 kDa) (Fig. 5a). Furthermore, purified L-Cry binds Flavin Adenine Dinucleotide (FAD) as its chromophore (Supplementary Fig. 5d, e). We then used UV/Vis absorption spectroscopy to analyze the FAD photoreaction of purified L-Cry in presence of 1 mM TCEP to prevent protein oxidation. The absorption spectrum of dark-state L-Cry showed maxima at 450 nm and 475 nm, consistent with the presence of oxidized FAD (Supplementary Fig. 5f, black line). As basic starting point to analyze its photocycle, L-Cry was photoreduced using a LED (PerkinElmer ACULED Dyo) with a blue-light dominated spectrum and spectral peak at 450 nm (Supplementary Fig. 1d, d′, henceforth referred to as “blue-light”) for 110 s37. The light-activated spectrum showed that blue-light irradiation of L-Cry leads to the complete conversion of FADox into an anionic FAD radical (FADo-) with characteristic FADo- absorption maxima at 370 nm and 404 nm and reduced absorbance at 450 nm (Supplementary Fig. 5f, blue spectrum, black arrows). In darkness, L-Cry reverted back to the dark-state with time constants of 2 min (18 °C), 4 min (6 °C) and 4.7 min (ice) (Supplementary Fig. 5g–k).Fig. 5: L-Cry forms differently photoreduced sunlight- and moonlight states.a Multi-Angle Light Scattering (MALS) analyses of dark-state L-Cry fractionated by size exclusion chromatography (SEC). Black dashed line: normalized UV absorbance, solid line: normalized scattering signal. The molar mass of about 130 kDa derived from MALS (mass signal shown in red) corresponds to an L-Cry homodimer. b Absorption spectrum of L-Cry in darkness (black) and after sunlight exposure (orange). Additional timepoints: Supplementary Fig. 6a. c Dark recovery of L-Cry after 20 min sunlight on ice. Absorbance at 450 nm in Supplementary Fig. 6b. d, e Absorption spectra of L-Cry after exposure to naturalistic moonlight for different durations. f Full spectra of dark recovery after 6 h moonlight. Absorbance at 450 nm: Supplementary Fig. 6d. g Absorption spectrum of L-Cry after 6 h of moonlight followed by 20 min of sunlight. h Absorption spectrum of L-Cry after 20 min sunlight followed by moonlight first results in dark-state recovery. Absorbance at 450 nm: Supplementary Fig. 6e. i Absorption spectrum of L-Cry after 20 min sunlight followed by 4 h and 6 h moonlight builds up the moonlight state. j Model of L-Cry responses to sunlight (orange), moonlight (green) and darkness (black). Only transitions between stably accumulating states are shown. Absorbances in (b–i) were normalized when a shift in the baseline occurred between different measurements of the same measurement set, which is then indicated on the Y-axis as “normalized absorbance”.Full size imageWe then investigated the response of L-Cry to ecologically relevant light, i.e. sun- and moonlight using naturalistic sun- and moonlight devices that we designed based on light measurements at the natural habitat of P. dumerilii31 (Supplementary Fig. 1a, c, e). Upon naturalistic sunlight illumination, FAD was photoreduced to FADo-, but with slower kinetics than under the stronger blue-light source, likely due to the intensity differences between the two lights (Supplementary Fig. 1c–e).While blue-light illumination led to a complete photoreduction within 110 s (Supplementary Fig. 5f), sunlight induced photoreduction to FADo- was completed after 5–20 min (Fig. 5b) and did not further increase upon continued illumation for up to 2 h (Supplementary Fig. 6a). Dark recovery kinetics had time constants of 3.2 min (18 °C) and 5 min (ice) (Fig. 1c, Supplementary Fig. 6b, c).As the absorbance spectrum of L-Cry overlaps with that of moonlight at the Platynereis natural habitat (Supplementary Fig. 1a), L-Cry has the principle spectral prerequisite to sense moonlight. However, the most striking characteristic of moonlight is its very low intensity (5.8 × 1010 photons/cm2/s at −5m, Supplementary Fig. 1a–e). To test if Pdu-L-Cry is sensitive enough for moonlight, we illuminated purified L-Cry with our custom-built naturalistic moonlight, closely resembling full-moonlight intensity and spectrum at the Platynereis natural habitat (Supplementary Fig. 1a, c, e). Naturalistic moonlight exposure up to 2.75 h did not markedly photoreduce FAD, notably there was no difference between 1 h and 2.75 h (Fig. 5d). However, further continuous naturalistic moonlight illumination of 4 h and longer resulted in significant changes (Fig. 5d), whereby the spectrum transitioned towards the light activated state of FADo- (note peak changes at 404 nm and at 450 nm). This photoreduction progressed further until 6 h naturalistic moonlight exposure (Fig. 5d). No additional photoreduction could be observed after 9 h and 12 h of naturalistic moonlight exposure (Fig. 5e), indicating a distinct state induced by naturalistic moonlight that reaches its maximum after ~6 h, when about half of the L-Cry molecules are photoreduced. This time of ~6 h is remarkably consistent with classical work showing that a minimum of ~6 h of continuous nocturnal light is important for circalunar clock entrainment, irrespective of the preceding photoperiod5. The dark recovery of L-Cry after 6 h moonlight exposure occurred with a time constant of 6.7 min at 18 °C (Fig. 5f, Supplementary Fig. 6d). Given that both sunlight and moonlight cause FAD photoreduction, but with different kinetics and different final FADo- product/FADox educt ratios, we wondered how purified L-Cry would react to transitions between naturalistic sun- and moonlight (i.e. during “sunrise” and “sunset”).Mimicking the sunrise scenario, L-Cry was first illuminated with naturalistic moonlight for 6 h followed by 20 min of sunlight exposure. This resulted in an immediate enrichment of the FADo- state (Fig. 5g). Hence, naturalistic sunlight immediately photoreduces remaining oxidized flavin molecules, that are characteristic of moonlight activated L-Cry, to FADo-, to reach a distinct fully reduced sunlight state.In contrast, when we next mimicked the day-night transition (“sunset”) by first photoreducing with naturalistic sunlight (or strong blue-light) and subsequently exposed L-Cry to moonlight, L-Cry first returned to its full dark-state within about 30 min (naturalistic sunlight: τ = 7 min (ice), Fig. 5h, Supplementary Fig. 6e; blue-light: τ = 9 min (ice), Supplementary Fig. 6f–h), despite the continuous naturalistic moonlight illumination. Prolonged moonlight illumination then led to the conversion of dark-state L-Cry to the moonlight state (Fig. 5i, Supplementary Fig. 6f). Hence, fully photoreduced sunlight-state L-Cry first has to return to the dark-state before accumulating the moonlight state characterized by the stable presence of the partial FADo- product/FADox educt. In contrast to sunlight-state L-Cry, moonlight-state L-Cry does not return to the oxidized (dark) state under naturalistic moonlight (Fig. 5e), i.e. moonlight maintains the moonlight state, but not the sunlight state. We note, that a partially photoreduced L-Cry state may be formed transiently during dark-state recovery of the sunlight state under moonlight. However, this transiently occurring partially photoreduced L-Cry state would differ from the “true” moonlight state (e.g. by an allosteric change) preventing its accumulation (see discussion and Supplementary Fig. 6i).Given that L-Cry forms a homodimer and moonlight photoreduces about half of the FAD molecules, we propose that the moonlight state corresponds to a half-reduced FADo- FADox dimer, where FAD is only photoreduced in one L-Cry monomer, whereas in the sunlight state both monomers are photoreduced (FADo- FADo-) (Fig. 5j). This implies that the quantum yield for FADox to FADo- photoreduction differs between the two L-Cry monomers. One monomer (referred to as “A” in Fig. 5j) acts as “very low intensity light sensor” with a high quantum yield ΦA. Hence, the very low photon number provided after 6 h of moonlight illumination is sufficient to photoreduce its flavin co-factor, resulting in the partially photoreduced FADo- FADox moonlight state (Fig. 5j).For direct comparison, our naturalistic moonlight’s emission (in the main absorbance range of L-Cry: 330 nm–510 nm) is 5.4 × 1010 photons/cm2/s (Supplementary Fig. 1e), which accumulates to ~1.2 × 1015 photons/cm2 in the 6 h required to reach the half-reduced moonlight state (Fig. 5d, e). For naturalistic sunlight, emitting ~7.5 × 1014 photons/cm2/s (330–510 nm), at least 5 min of sunlight illumination (i.e. > ~1.8 × 1017 photons/cm2) are required to photoreduce the flavin in both L-Cry monomers in order to reach the fully photoreduced FADo- FADo- sunlight state (Fig. 5b, j). Thus, the second L-Cry monomer (monomer “B” in Fig. 5j) has a significantly lower quantum yield ΦB for FAD photoreduction (ΦB  More

  • in

    A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States

    Smol, J. P. & Stoermer, E. F. The Diatoms: Application for the Environmental and Earth Sciences (Cambridge University Press, 2010).Charles, D. F. Relationships between surface sediment diatom assemblages and lake water characteristics in Adirondack lakes. Ecology 66, 994–111 (1985).Article 

    Google Scholar 
    Whitehead, D. R., Charles, D. F., Jackson, S. T., Reed S. E. & Sheehan, M. C. In Diatoms and Lake Acidity (eds J. P. Smol et al.) 251–274 (W. Junk, 1986).Whitehead, D. R. et al. The developmental history of Adirondack (N.Y.) lakes. J. Paleolimnol. 2, 185–206 (1989).ADS 
    Article 

    Google Scholar 
    Whitehead, D. R., Charles, D. F. & Goldstein, R. A. The PIRLA project (Paleoecological Investigation of Recent Lake Acidification): an introduction to the synthesis of the project. J. Paleolimnol. 3, 187–194 (1990).ADS 
    Article 

    Google Scholar 
    Dixit, S. S. et al. Diatom assemblages from Adirondack lakes (New York, USA) and the development of inference models for retrospective environmental assessment. J. Paleolimnol. 8, 27–47 (1993).ADS 
    Article 

    Google Scholar 
    Dixit, S. S. & Smol, J. P. Diatom evidence of past water quality changes in Adirondack seepage lakes (New York, USA). Diatom Res. 1, 113–129 (1995).Article 

    Google Scholar 
    Allen, A. P. et al. Concordance of taxonomic composition patterns across multiple lake assemblages: effects of scale, body size, and land use. Can. J. Fish. Aquat. 56, 2029–2040 (1999).Article 

    Google Scholar 
    Pither, J. & Aarssen, L. W. The evolutionary species pool hypothesis and patterns of freshwater diatom diversity along a pH gradient. J. Biogeogr. 32, 503–513 (2005).Article 

    Google Scholar 
    Winegardner, A. K., Legendre, P., Beisner, B. E. & Gregory-Eaves, I. Diatom diversity patterns over the past c. 150 years across the conterminous United States of America: Identifying mechanisms behind beta diversity. Global Ecol. Biogeogr. 26, 1303–1315 (2017).Article 

    Google Scholar 
    Dixit, S. S. & Smol, J. P. Diatoms as indicators in the Environmental Monitoring and Assessment Program-Surface Waters (EMAP-SW). Environ. Monit. Assess. 31, 275–37 (1994).PubMed 

    Google Scholar 
    Dixit, S. S. et al. Assessing water quality changes in the lakes of the northeastern United States using sediment diatoms. Can. J. Fish. Aquatic Sci. 56, 131–152 (1999).Article 

    Google Scholar 
    Stevenson, R. J., Zalack, J. & Wolin, J. A multimetric index of lake diatom condition using surface sediment assemblages. Freshw. Sci. 32, 1005–1025 (2013).Article 

    Google Scholar 
    Liu, B. & Stevenson, R. J. Improving assessment accuracy for lake biological condition by classifying lakes with diatom typology, varying metrics and modeling multimetric indices. Sci. Total Environ. 609, 263–271 (2017).ADS 
    Article 

    Google Scholar 
    Herlihy, A. T. et al. Using multiple approaches to develop nutrient criteria for lakes in the conterminous USA. Freshw. Sci. 32, 367–384 (2013).Article 

    Google Scholar 
    Bachmann, R. W., Hoyer, M. V. & Canfield, D. E. The extent that natural lakes in the United States of America have been changed by cultural eutrophication. Limnol. Oceanogr. 58, 945–950 (2013).ADS 
    Article 

    Google Scholar 
    McDonald, C. P. et al. Comment on Bachmann et al. (2013): A nonrepresentative sample cannot describe the extent of cultural eutrophication of natural lakes in the United States. Limnol. Oceanogr. 59, 2226–2230 (2014).ADS 
    Article 

    Google Scholar 
    Smith, V. H. et al. Comment: Cultural eutrophication of natural lakes in the United States is real and widespread. Limnol. Oceanogr. 59, 2217–2225 (2014).ADS 
    Article 

    Google Scholar 
    Bachmann, R. W., Hoyer, M. V. & Canfield, D. E. Response to comments: Quantification of the extent of cultural eutrophication of natural lakes in the United States. Limnol. Oceanogr. 59, 2231–2239 (2014).ADS 
    Article 

    Google Scholar 
    Bachmann, R. W., Hoyer, M. V., Croteau, A. C. & Canfield, D. E. Factors related to Secchi depths and their stability over time as determined from a probability sample of US lakes. Environ. Monit. Assess. 189, 206 (2017).Article 

    Google Scholar 
    Stager, J. C., Leavitt, P. R. & Dixit, S. S. Assessing impacts of past human activity on the water quality of Upper Saranac lake, New York. Lake Reserv. Manag. 13, 175–184 (1997).Article 

    Google Scholar 
    Dixit, S. S., Dixit, A. S., Smol, J. P., Hughes, R. M. & Paulsen, S. G. Water Quality Changes from Human Activities in Three Northeastern USA Lakes. Lake Reserv. Manag. 16, 35–321 (2000).Article 

    Google Scholar 
    Köster, D. et al. Paleolimnological assessment of human-induced impacts on Walden Pond (Massachusetts, USA) using diatoms and stable isotopes. Aquat. Ecosyst. Health 8, 117–131 (2005).Article 

    Google Scholar 
    Enache, M. D., Charles, D. F., Belton, T. J. & Callinan, C. W. Total phosphorus changes in New York and New Jersey lakes (USA) inferred from sediment cores. Lake Reserv. Manag. 28, 293–310 (2012).Article 

    Google Scholar 
    Rowell, H. C. et al. Quantitative paleolimnological inference models applied to a high-resolution biostratigraphic study of lake degradation and recovery, Onondaga Lake, New York (USA). J Paleolimnol. 55, 241–258 (2016).Article 

    Google Scholar 
    Tyree, M. A., Bishop, I. W., Hawkins, C. P., Mitchell, R. & Spaulding, S. A. Reduction of taxonomic bias in diatom species data. Limnol. Oceanogr. Methods 18, 271–279 (2020).Article 

    Google Scholar 
    Stribling, J. B., Pavlik, K. L., Holdsworth, S. M. & Leppo, E. W. Data quality, performance, and uncertainty in taxonomic identification for biological assessments. J. North Am. Benthol. Soc. 27, 906–919 (2008).Article 

    Google Scholar 
    Thomson, S. A. et al. Towards a global list of accepted species II. Consequences of inadequate taxonomic list governance. Org. Divers. Evol. 21, 623–630 (2021).Article 

    Google Scholar 
    Spaulding, S. A. et al. Diatoms of North America https://diatoms.org/ (2020).Lee, S. S., Bishop, I. W., Spaulding, S. A., Mitchell, R. M. & Yuan, L. L. Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets. Ecol. Indic. 102, 166–174 (2019).Article 

    Google Scholar 
    Cumming, B. F. et al. How Much Acidification Has Occurred in Adirondack Region Lakes (New York, USA) since Preindustrial Times? Can. J. Fish. Aquat. 49, 128–141 (1992).Article 

    Google Scholar 
    Larsen, D. P., Stevens, D. L., Selle, A. R. & Paulsen, S. G. Environmental Monitoring and Assessment Program, EMAP-Surface Waters: A northeast lakes pilot. Lake Reserv. Manag. 7, 1–11 (1991).Article 

    Google Scholar 
    Hughes, R. M., Paulsen, S. G. & Stoddard, J. L. EMAP-surface waters: A multiassemblage, probability survey of ecological integrity in the USA. Hydrobiologia 422, 429–443 (2000).Article 

    Google Scholar 
    Larsen, D. P., Thornton, K. W., Urquhart, N. S. & Paulsen, S. G. The role of sample surveys for monitoring the condition of the nation’s lakes. Environ. Monit. Assess. 32, 101–34 (1994).Article 

    Google Scholar 
    U.S. Environmental Protection Agency. Environmental Monitoring & Assessment Program. Northeast Lakes 1991-94 Data Sets. https://archive.epa.gov/emap/archive-emap/web/html/nelakes.html (2016).U.S. Environmental Protection Agency. National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes. Report No. EPA-841-R-09-001. (U.S. Environmental Protection Agency, 2009).U.S. Environmental Protection Agency. 2012 National Lakes Assessment. Field Operations Manual. Report No. EPA 841-B-11-003. (U.S. Environmental Protection Agency, 2011)Charles, D. F., Knowles, C. & Davis, R. S. Protocols for the Analysis of Algal Samples Collected as Part of the U.S. Geological Survey National Water-Quality Assessment Program. https://water.usgs.gov/nawqa/protocols/algprotocol/algprotocol.pdf Report (2002).Krammer, K. Diatoms of Europe V. 1. (Gantner Verlag, 2000)Lange-Bertalot, H. Diatoms of Europe V. 2. (Gantner Verlag, 2001)Krammer, K. Diatoms of Europe V. 3. (Gantner Verlag, 2002)Krammer, K. Diatoms of Europe V. 4. (Gantner Verlag, 2003)Siver, P. A. & Hamilton, P. B. Iconographia Diatomologica V. 22. (Gantner Verlag, 2011).Levkov, Z., Metzeltin, D. & Pavlov, A. Diatoms of Europe V. 7. (Gantner Verlag, 2013)Levkov, Z., Mitić-Kopanja, D. & Reichardt, E. Diatoms of Europe V. 8. (Koeltz Botanical Books, 2016).Lange-Bertalot, H., Hofmann, G., Werum, M. & Cantonati, M. Freshwater Benthic Diatoms of Central Europe (Koeltz Botanical Books, 2017).Guiry, M. D. & Guiry, G. M. AlgaeBase https://www.algaebase.org (2021).Kociolek, J. P. et al. DiatomBase http://www.diatombase.org (2021).De Cáceres, M. Package ‘indicspecies’ https://cran.r-project.org/web/packages/indicspecies/indicspecies.pdf (2020).Legendre, P. & Birks, H. J. B. In Tracking Environmental Change Using Lake Sediments. V. 5: Data Handling and Numerical Techniques (eds Birks H. J. B. et al.) 201–248 (Springer Dordrecht, 2012).Legendre, P. & Gallagher, E. D. Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271–280 (2001).ADS 
    Article 

    Google Scholar 
    Oksanen, J. et al. Package ‘vegan’ https://cran.r-project.org/web/packages/vegan/vegan.pdf (2020).Spaulding, S. A. Diatom Laboratory: Research Labs & Groups: INSTAAR: CU-Boulder https://instaar.colorado.edu/research/labs-groups/diatom-laboratory//research-detail (2021).Conservation Gateway. Northeast Lake and Pond Classification System. http://www.conservationgateway.org/ConservationByGeography/NorthAmerica/UnitedStates/edc/reportsdata/freshwater/Pages/Northeast-Lakes.aspx (2021).Soranno, P. & Cheruvelil, K. LAGOS-NE-LIMNO v1.087.3: A module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925–2013. Environmental Data Initiative https://doi.org/10.6073/pasta/08c6f9311929f4874b01bcc64eb3b2d7 (2019).U.S. Geological Survey. National Hydrography Dataset (NHD). USGS Unnumbered Series. (U.S. Geological Survey, 2001).Potapova, M. G., Lee, S. S., Spaulding, S. A. & Schulte, N. O. A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States. U.S. EPA Office of Research and Development (ORD) https://doi.org/10.23719/1524246 (2022).U.S. Environmental Protection Agency. National Aquatic Resource Surveys. National Lakes Assessment 2007 (data and metadata files) https://www.epa.gov/national-aquatic-resource-surveys/data-national-aquatic-resource-surveys (2010).U.S. Environmental Protection Agency. National Aquatic Resource Surveys. National Lakes Assessment 2017 (data and metadata files). http://www.epa.gov/national-aquatic-resource-surveys/data-national-aquatic-resource-surveys (2021). More

  • in

    Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups

    Smith, D. C., Simon, M., Alldredge, A. L. & Azam, F. Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution. Nature 359, 139–142. https://doi.org/10.1038/359139a0 (1992).ADS 
    CAS 
    Article 

    Google Scholar 
    Alldredge, A. L. & Gotschalk, C. C. Direct observations of the mass flocculation of diatom blooms: Characteristics, settling velocities and formation of diatom aggregates. Deep Sea Res. A 36, 159–171. https://doi.org/10.1016/0198-0149(89)90131-3 (1989).ADS 
    CAS 
    Article 

    Google Scholar 
    Jackson, G. A. A model of the formation of marine algal flocs by physical coagulation processes. Deep Sea Res. A 37, 1197–1211. https://doi.org/10.1016/0198-0149(90)90038-w (1990).ADS 
    CAS 
    Article 

    Google Scholar 
    Kiørboe, T., Lundsgaard, C., Olesen, M. & Hansen, J. L. S. Aggregation and sedimentation processes during a spring phytoplankton bloom: A field experiment to test coagulation theory. J. Mar. Res. 52, 297–323. https://doi.org/10.1357/0022240943077145 (1994).Article 

    Google Scholar 
    Jackson, G. Coagulation Theory and Models of Oceanic Plankton Aggregation (CRC Press, 2005).
    Google Scholar 
    Grossart, H. P., Kiorboe, T., Tang, K. & Ploug, H. Bacterial colonization of particles: Growth and interactions. Appl. Environ. Microb. 69, 3500–3509. https://doi.org/10.1128/aem.69.6.3500-3509.2003 (2003).ADS 
    CAS 
    Article 

    Google Scholar 
    Kiorboe, T., Tang, K., Grossart, H. P. & Ploug, H. Dynamics of microbial communities on marine snow aggregates: Colonization, growth, detachment, and grazing mortality of attached bacteria. Appl. Environ. Microbiol. 69, 3036–3047. https://doi.org/10.1128/AEM.69.6.3036 (2003).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martin, J. H., Knauer, G. A., Karl, D. M. & Broenkow, W. W. VERTEX: Carbon cycling in the northeast pacific. Deep Sea Res. A 34, 267–285. https://doi.org/10.1016/0198-0149(87)90086-0 (1987).ADS 
    CAS 
    Article 

    Google Scholar 
    Buesseler, K. O. et al. VERTIGO (vertical transport in the global ocean): A study of particle sources and flux attenuation in the North Pacific. Deep Sea Res. II 55, 1522–1539. https://doi.org/10.1016/j.dsr2.2008.04.024 (2008).ADS 
    Article 

    Google Scholar 
    Grossart, H. P., Tang, K. W., Kiorboe, T. & Ploug, H. Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages. FEMS Microbiol. Lett. 266, 194–200. https://doi.org/10.1111/j.1574-6968.2006.00520.x (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    Martinez, J., Smith, D. C., Steward, G. F. & Azam, F. Variability in ectohydrolytic enzyme activities of pelagic marine bacteria and its significance for substrate processing in the sea. Aquat. Microb. Ecol. 10, 223–230. https://doi.org/10.3354/ame010223 (1996).Article 

    Google Scholar 
    Kellogg, C. T. E. et al. Evidence for microbial attenuation of particle flux in the Amundsen Gulf and Beaufort Sea: Elevated hydrolytic enzyme activity on sinking aggregates. Polar Biol. 34, 2007–2023. https://doi.org/10.1007/s00300-011-1015-0 (2011).Article 

    Google Scholar 
    Jiao, N. et al. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean. Nat. Rev. Microbiol. 8, 593–599. https://doi.org/10.1038/nrmicro2386 (2010).CAS 
    Article 
    PubMed 

    Google Scholar 
    Jiao, N. & Zheng, Q. The microbial carbon pump: From genes to ecosystems. Appl. Environ. Microbiol. 77, 7439–7444. https://doi.org/10.1128/AEM.05640-11 (2011).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Buchan, A., LeCleir, G. R., Gulvik, C. A. & Gonzalez, J. M. Master recyclers: Features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698. https://doi.org/10.1038/nrmicro3326 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Smriga, S., Fernandez, V. I., Mitchell, J. G. & Stocker, R. Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria. Proc. Natl. Acad. Sci. USA 113, 1576–1581. https://doi.org/10.1073/pnas.1512307113 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Secchi, E. et al. The effect of flow on swimming bacteria controls the initial colonization of curved surfaces. Nat. Commun. 11, 2851. https://doi.org/10.1038/s41467-020-16620-y (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Acinas, S. G., Antón, J. & Rodríguez-Valera, F. Diversity of free-living and attached bacteria in offshore Western Mediterranean Waters as depicted by analysis of genes encoding 16S rRNA. Appl. Environ. Microb. 65, 514–522 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    Grossart, H. P., Levold, F., Allgaier, M., Simon, M. & Brinkhoff, T. Marine diatom species harbour distinct bacterial communities. Environ. Microbiol. 7, 860–873. https://doi.org/10.1111/j.1462-2920.2005.00759.x (2005).CAS 
    Article 
    PubMed 

    Google Scholar 
    Mestre, M. et al. Sinking particles promote vertical connectivity in the ocean microbiome. Proc. Natl. Acad. Sci. USA 115, E6799–E6807. https://doi.org/10.1073/pnas.1802470115 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rieck, A., Herlemann, D. P., Jurgens, K. & Grossart, H. P. Particle-associated differ from free-living bacteria in surface waters of the Baltic Sea. Front. Microbiol. 6, 1297. https://doi.org/10.3389/fmicb.2015.01297 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ziervogel, K., Steen, A. D. & Arnosti, C. Changes in the spectrum and rates of extracellular enzyme activities in seawater following aggregate formation. Biogeosciences 7, 1007–1015. https://doi.org/10.5194/bg-7-1007-2010 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    Stocker, R., Seymour, J. R., Samadani, A., Hunt, D. E. & Polz, M. F. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc. Natl. Acad. Sci. USA 105, 4209–4214. https://doi.org/10.1073/pnas.0709765105 (2008).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lopez-Perez, M. et al. Genomes of surface isolates of Alteromonas macleodii: The life of a widespread marine opportunistic copiotroph. Sci. Rep. 2, 696. https://doi.org/10.1038/srep00696 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thiele, S., Fuchs, B. M., Amann, R. & Iversen, M. H. Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow. Appl. Environ. Microbiol. 81, 1463–1471. https://doi.org/10.1128/AEM.02570-14 (2015).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bachmann, J. et al. Environmental drivers of free-living vs particle-attached bacterial community composition in the mauritania upwelling system. Front. Microbiol. 9, 2836. https://doi.org/10.3389/fmicb.2018.02836 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kirchman, D. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 39, 91–100. https://doi.org/10.1016/s0168-6496(01)00206-9 (2002).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bizic-Ionescu, M. et al. Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization. Environ. Microbiol. 17, 3500–3514. https://doi.org/10.1111/1462-2920.12466 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhao, Z., Baltar, F. & Herndl, G. J. Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Sci. Adv. 6, 4354. https://doi.org/10.1126/sciadv.aaz4354 (2020).ADS 
    CAS 
    Article 

    Google Scholar 
    Baumas, C. M. J. et al. Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions. ISME J. 15, 1695–1708. https://doi.org/10.1038/s41396-020-00880-z (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ploug, H., Grossart, H. P., Azam, F. & Jørgensen, B. B. Photosynthesis, respiration, and carbon turnover in sinking marine snow from surface waters of Southern California Bight: Implications for the carbon cycle in the ocean. Mar. Ecol. Prog. Ser. 179, 1–11. https://doi.org/10.3354/meps179001 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    Ploug, H. & Grossart, H.-P. Bacterial growth and grazing on diatom aggregates: Respiratory carbon turnover as a function of aggregate size and sinking velocity. Limnol. Oceanogr. 45, 1467–1475. https://doi.org/10.4319/lo.2000.45.7.1467 (2000).ADS 
    CAS 
    Article 

    Google Scholar 
    Ebrahimi, A., Schwartzman, J. & Cordero, O. X. Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria. Proc. Natl. Acad. Sci. USA 116, 23309–23316. https://doi.org/10.1073/pnas.1908512116 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grossart, H.-P. & Ploug, H. Microbial degradation of organic carbon and nitrogen on diatom aggregates. Limnol. Oceanogr. 46, 267–277. https://doi.org/10.4319/lo.2001.46.2.0267 (2001).ADS 
    CAS 
    Article 

    Google Scholar 
    Datta, M. S., Sliwerska, E., Gore, J., Polz, M. F. & Cordero, O. X. Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat. Commun. 7, 11965. https://doi.org/10.1038/ncomms11965 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kiorboe, T., Grossart, H. P., Ploug, H. & Tang, K. Mechanisms and rates of bacterial colonization of sinking aggregates. Appl. Environ. Microbiol. 68, 3996–4006. https://doi.org/10.1128/AEM.68.8.3996-4006.2002 (2002).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vaqué, D., Duarte, C. M. & Marrasé, C. Influence of algal population dynamics on phytoplankton colonization by bacteria: Evidence from two diatom species. Mar. Ecol. Prog. Ser. 65, 201–203. https://doi.org/10.3354/meps065201 (1990).ADS 
    Article 

    Google Scholar 
    Grossart, H.-P. & Ploug, H. Bacterial production and growth efficiencies: Direct measurements on riverine aggregates. Limnol. Oceanogr. 45, 436–445. https://doi.org/10.4319/lo.2000.45.2.0436 (2000).ADS 
    CAS 
    Article 

    Google Scholar 
    Duhamel, S. et al. Growth and specific P-uptake rates of bacterial and phytoplanktonic communities in the Southeast Pacific (BIOSOPE cruise). Biogeosciences 4, 941–956. https://doi.org/10.5194/bg-4-941-2007 (2007).ADS 
    Article 

    Google Scholar 
    Kirchman, D. L. Growth rates of microbes in the oceans. Annu. Rev. Mar. Sci. 8, 285–309. https://doi.org/10.1146/annurev-marine-122414-033938 (2016).ADS 
    Article 

    Google Scholar 
    Brumley, D. R. et al. Cutting through the noise: Bacterial chemotaxis in marine microenvironments. Front. Mar. Sci. 7, 527. https://doi.org/10.3389/fmars.2020.00527 (2020).Article 

    Google Scholar 
    Thomas, T. et al. Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS ONE 3, e3252. https://doi.org/10.1371/journal.pone.0003252 (2008).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Varbanets, L. D. et al. The black sea bacteria-producers of hydrolytic enzymes. Mikrobiol. Z. 73, 9–15 (2011).CAS 
    PubMed 

    Google Scholar 
    Sapp, M. et al. Species-specific bacterial communities in the phycosphere of microalgae?. Microb. Ecol. 53, 683–699. https://doi.org/10.1007/s00248-006-9162-5 (2007).Article 
    PubMed 

    Google Scholar 
    Sarmento, H. & Gasol, J. M. Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton. Environ. Microbiol. 14, 2348–2360. https://doi.org/10.1111/j.1462-2920.2012.02787.x (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Gram, L., Grossart, H. P., Schlingloff, A. & Kiorboe, T. Possible quorum sensing in marine snow bacteria: Production of acylated homoserine lactones by Roseobacter strains isolated from marine snow. Appl. Environ. Microbiol. 68, 4111–4116. https://doi.org/10.1128/AEM.68.8.4111 (2002).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Arandia-Gorostidi, N. et al. Warming the phycosphere: Differential effect of temperature on the use of diatom-derived carbon by two copiotrophic bacterial taxa. Environ. Microbiol. 22, 1381–1396. https://doi.org/10.1111/1462-2920.14954 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Sarmento, H., Morana, C. & Gasol, J. M. Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: Quantity is more important than quality. ISME J 10, 2582–2592. https://doi.org/10.1038/ismej.2016.66 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Grossart, H. P. & Simon, M. Bacterial colonization and microbial decomposition of limnetic organic aggregates (lake snow). Aquat. Microb. Ecol. 15, 127–140. https://doi.org/10.3354/ame015127 (1998).Article 

    Google Scholar 
    Kiørboe, T. & Jackson, G. A. Marine snow, organic solute plumes, and optimal chemosensory behavior of bacteria. Limnol. Oceanogr. 46, 1309–1318. https://doi.org/10.4319/lo.2001.46.6.1309 (2001).ADS 
    Article 

    Google Scholar 
    Chakraborty, S. et al. Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles. Nat. Commun. 12, 4085. https://doi.org/10.1038/s41467-021-23875-6 (2021).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hygum, B. H., Petersen, J. W. & Søndergaard, M. Dissolved organic carbon released by zooplankton grazing activity-a high-quality substrate pool for bacteria. J. Plankton Res. 19, 97–111. https://doi.org/10.1093/plankt/19.1.97 (1997).CAS 
    Article 

    Google Scholar 
    Suttle, C. A. Marine viruses–major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812. https://doi.org/10.1038/nrmicro1750 (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bizic-Ionescu, M., Ionescu, D. & Grossart, H. P. Organic particles: Heterogeneous hubs for microbial interactions in aquatic ecosystems. Front. Microbiol. 9, 2569. https://doi.org/10.3389/fmicb.2018.02569 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Arandia-Gorostidi, N., Weber, P. K., Alonso-Saez, L., Moran, X. A. & Mayali, X. Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment. ISME J. 11, 641–650. https://doi.org/10.1038/ismej.2016.156 (2017).CAS 
    Article 
    PubMed 

    Google Scholar 
    Worrich, A. et al. Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments. Nat. Commun. 8(1), 15472. https://doi.org/10.1038/ncomms15472 (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Iversen, M. H. & Ploug, H. Ballast minerals and the sinking carbon flux in the ocean: Carbon-specific respiration rates and sinking velocity of marine snow aggregates. Biogeosciences 7, 2613–2624. https://doi.org/10.5194/bg-7-2613-2010 (2010).ADS 
    CAS 
    Article 

    Google Scholar 
    Baltar, F., Arístegui, J., Gasol, J. M., Sintes, E. & Herndl, G. J. Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the subtropical North Atlantic. Limnol. Oceanogr. 54, 182–193. https://doi.org/10.4319/lo.2009.54.1.0182 (2009).ADS 
    CAS 
    Article 

    Google Scholar 
    Schneider, B., Schlitzer, R., Fischer, G. & Nöthig, E.-M. Depth-dependent elemental compositions of particulate organic matter (POM) in the ocean. Glob. Biogeochem. Cycles https://doi.org/10.1029/2002gb001871 (2003).Article 

    Google Scholar 
    Jannasch, H. W. & Wirsen, C. O. Microbial activities in undecompressed and decompressed deep-seawater samples. Appl. Environ. Microbiol. 43, 1116–1124. https://doi.org/10.1128/AEM.43.5.1116-1124.1982 (1982).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Tamburini, C., Garcin, J., Ragot, M. & Bianchi, A. Biopolymer hydrolysis and bacterial production under ambient hydrostatic pressure through a 2000m water column in the NW Mediterranean. Deep Sea Res. II(49), 2109–2123. https://doi.org/10.1016/s0967-0645(02)00030-9 (2002).ADS 
    Article 

    Google Scholar 
    Iversen, M. H. & Ploug, H. Temperature effects on carbon-specific respiration rate and sinking velocity of diatom aggregates: Potential implications for deep ocean export processes. Biogeosciences 10, 4073–4085. https://doi.org/10.5194/bg-10-4073-2013 (2013).ADS 
    Article 

    Google Scholar 
    Guillard, R. R. & Ryther, J. H. Studies of marine planktonic diatoms I Cyclotella nana Hustedt, and Detonula confervacea (cleve) Gran. Can. J. Microbiol. 8, 229–239. https://doi.org/10.1139/m62-029 (1962).CAS 
    Article 
    PubMed 

    Google Scholar 
    Pernthaler, A., Pernthaler, J. & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68, 3094–3101 (2002).ADS 
    CAS 
    Article 

    Google Scholar 
    Amann, R. I., Krumholz, L. & Stahl, D. A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172, 762–770 (1990).CAS 
    Article 

    Google Scholar 
    Daims, H., Brühl, A., Amann, R., Schleifer, K. & Wagner, M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: Development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22, 11 (1999).Article 

    Google Scholar 
    Eilers, H., Pernthaler, J., Glockner, F. O. & Amann, R. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66, 3044–3051 (2000).ADS 
    CAS 
    Article 

    Google Scholar 
    Manz, W., Amann, R., Vancanneyt, M., Schleifer, K.-H. & Ludwig, W. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142, 1097–1106. https://doi.org/10.1099/13500872-142-5-1097 (1996).CAS 
    Article 
    PubMed 

    Google Scholar 
    Amann, R. I., Ludwig, W. & Schleifer, K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169. https://doi.org/10.1128/mr.59.1.143-169.1995 (1995).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919–1925. https://doi.org/10.1128/AEM.56.6.1919-1925.1990 (1990).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Musat, N. et al. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Natl. Acad. Sci. USA 105, 17861–17866. https://doi.org/10.1073/pnas.0809329105 (2008).ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Polerecky, L. et al. Look@NanoSIMS: A tool for the analysis of nanoSIMS data in environmental microbiology. Environ. Microbiol. 14, 1009–1023. https://doi.org/10.1111/j.1462-2920.2011.02681.x (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Musat, N. et al. The effect of FISH and CARD-FISH on the isotopic composition of (13)C- and (15)N-labeled Pseudomonas putida cells measured by nanoSIMS. Syst. Appl. Microbiol. 37, 267–276. https://doi.org/10.1016/j.syapm.2014.02.002 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Meyer, N. R., Fortney, J. L. & Dekas, A. E. NanoSIMS sample preparation decreases isotope enrichment: Magnitude, variability and implications for single-cell rates of microbial activity. Environ. Microbiol. https://doi.org/10.1111/1462-2920.15264 (2020).Article 
    PubMed 

    Google Scholar  More

  • in

    Revisiting implementation of multiple natural enemies in pest management

    Model equationsOur host-parasite mathematical model involves the following host population components: ‘susceptible’ hosts denoted by (S), and hosts infected by k distinct types of parasites ((k=1,2,…,n)), the corresponding population numbers of infected hosts are denoted by (I_{i_1,i_2,…,i_k}), where each index (i_j) can take a value from 1, …, n (to avoid repeated counting of the same infection configuration, we require throughout the paper that (i_1 More

  • in

    Multiproxy study of 7500-year-old wooden sickles from the Lakeshore Village of La Marmotta, Italy

    Snir, A. et al. The origin of cultivation and proto-weeds, long before Neolithic farming. PLoS ONE 10(7), e0131422. https://doi.org/10.1371/journal.pone.0131422 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Groman-Yaroslavski, I., Weiss, E. & Nadel, D. Composite sickles and cereal harvesting methods at 23,000-years-old Ohalo II Israel. PLoS ONE 11(11), e0167151. https://doi.org/10.1371/journal.pone.0167151 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Edwards, P. C. A 14000 year-old hunter-gatherer’s toolkit. Antiquity 81(314), 865–876. https://doi.org/10.1017/S0003598X0009596X (2007).Article 

    Google Scholar 
    Le Dosseur, G. Bone Objects in the Southern Levant from the Thirteenth to the Fourth Millennia. Bulletin du Centre de recherche français à Jérusalem 12, 111–125 (2003).
    Google Scholar 
    Garrard, A., & Yazbeck, C. The Natufian of Moghr el-Ahwal in the Qadisha valley, northern Lebanon. in Natufian Foragers in the Levant. International Monographs in Prehistory (eds. Bar-Yosef, O. & Valla, F. R.). 17–47. (Michigan, Ann Arbor, 2013).Belfer-Cohen, A. The Natufian in the Levant. Annu. Rev. Anthropol. 20, 167–186. https://doi.org/10.1146/annurev.an.20.100191.001123 (1991).Article 

    Google Scholar 
    Stordeur, D. Le Natoufien et son évolution à travers les artefacts en os in Natufian Foragers in the Levant. International Monographs in Prehistory (eds. Bar-Yosef, O. & Valla, F. R.). 457–482. (Michigan, Ann Arbor, 2013).Rosen, S. A. Lithics after the Stone Age: a handbook of stone tools from the Levant. (Rowman Altamira, 1997).Anderson, P. C. Prehistory of agriculture: new experimental and ethnographic approaches. (Cotsen Institute of Archaeology Press, 1999).Ibáñez, J. J., González Urquijo, J. E., & Rodríguez, A. The evolution of technology during the PPN in the Middle euphrates. A view from use wear analysis of lithic tools. in Systèmes techniques et communautés du Néolithique Préceramique au Proche Orient. Technical Systems and Near Eastern PPN Communities (eds. Astruc, L., Binder, D. & Briois, F.) 153–165 (Editions APDCA, 2007).Maeda, O., Lucas, L., Silva, F., Tanno, K. I. & Fuller, D. Q. Narrowing the harvest: Increasing sickle investment and the rise of domesticated cereal agriculture in the Fertile Crescent. Quatern. Sci. Rev. 145, 226–237. https://doi.org/10.1016/j.quascirev.2016.05.032 (2016).ADS 
    Article 

    Google Scholar 
    Pichon, F. Exploitation of the cereals during the Pre-pottery Neolithic of Dja’de-el-Mughara: Preliminary results of the functional study of the glossy blades. Quatern. Int. 427, 138–151. https://doi.org/10.1016/j.quaint.2016.01.064 (2017).Article 

    Google Scholar 
    Borrell, F., & Molist, M. Projectile Points, Sickle Blades and Glossed Points. Tools and Hafting Systems at Tell Halula (Syria) during the 8th millennium cal. BC Paléorient, 33(2), 59–77 (2007). https://doi.org/10.2307/41496812.Douka, K., Efstratiou, N., Hald, M., Henriksen, P. & Karetsou, A. Dating Knossos and the arrival of the earliest Neolithic in the southern Aegean. Antiquity 91(356), 304–321. https://doi.org/10.15184/aqy.2017.29 (2017).Article 

    Google Scholar 
    Perlès, C. From the Near East to Greece: Let’s reverse the focus. Cultural elements that didn’t transfer. in How did farming reach Europe? (ed. Lichter, C.) 275–290 (Istanbul, Ege Yayınları, 2005).Gijn A.L. van & Wentink K. The role of flint in mediating identities: The microscopic evidence. in Mobilty, meaning & transformations of things, shifting contexts of material culture through time and space. (eds. Hahn, H.P. & Weiss, H.) 120–132 (Oxford, Oxbow Books, 2013).Guilaine, J. The neolithic transition: From the Eastern to the Western Mediterranean. in Times of Neolithic Transition along the Western Mediterranenn. (eds. O., García-Puchol & D. C., Salazar-García) 15–31 (New York, Springer, 2017). https://doi.org/10.1007/978-3-319-52939-4_2.Forenbaher, S. & Miracle, P. T. The spread of farming in the Eastern Adriatic. Antiquity 79(305), 514–528 (2005).Article 

    Google Scholar 
    Gabriele, M. et al. Long-distance mobility in the North-Western Mediterranean during the Neolithic transition using high resolution pottery sourcing. J. Archaeol. Sci. Rep. 28, 102050. https://doi.org/10.1016/j.jasrep.2019.102050 (2019).Article 

    Google Scholar 
    Manen, C., Perrin, T., Guilaine, J., Bouby, L., Bréhard, S., Briois, F., Durand, F., Marinval, P. & Vigne, J. D. The Neolithic transition in the western Mediterranean: A complex and non-linear diffusion process—the radiocarbon record revisited. Radiocarbon 61(2), 531–571 (2019). https://doi.org/10.1017/RDC.2018.98Ibáñez, J. J., Clemente Conte, I., Gassin, B., Gibaja, J. F., Gonzáles Urquijo, J. E., Márquez, B., Philibert, S., Rodríguez Rodríguez, A. Harvesting technology during the Neolithic in south-west Europe. in Prehistoric technology 40 years later: functional studies and the Russian legacy (eds. Longo L. & Skakun, N.) 183–95 (Oxford, Archaeopress, 2008).Gibaja, J. F., Ibáñez, J. J., González Urquijo, J. E. Neolithic Sickles in the Iberian Peninsula. in Exploring and Explaining Diversity in Agricultural Technology, EARTH 2 (eds. van Gijn, A., Whittaker, P. & Anderson, P.) 112–118 (Oxford, Oxbow Books, 2014).Mazzucco, N., Capuzzo, G., Petrinelli-Pannocchia, C., Ibáñez, J. J., Gibaja, J. F. Harvesting tools and the spread of the Neolithic into the Central-Western Mediterranean area. Quat. Int. 470(Part B), 511–528 (2018). https://doi.org/10.1016/j.quaint.2017.04.018.Mazzucco, N., Guilbeau, D., Kačar, S., Podrug, E., Forenbaher, S., Radić, D., Moore, A. T. M. The time is ripe for a change. The evolution of harvesting technologies in Central Dalmatia during the Neolithic period (6th millennium cal BC). J. Anthropol. Archaeol. 51, 88–103 (2018). https://doi.org/10.1016/j.jaa.2018.06.003Mazzucco, N. et al. Migration, adaptation, innovation: The spread of Neolithic harvesting technologies in the Mediterranean. PLoS ONE 15(4), e0232455. https://doi.org/10.1371/journal.pone.0232455 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fugazzola Delpino, M. A., D’Eugenio, G. & Pessina, A. “La Marmotta” (Anguillara Sabazia, RM): Scavi 1989—un abitato perilacustre di età Neolitica. Bull. Paletnol. Ital. 84, 181–315 (1993).
    Google Scholar 
    Fugazzola Delpino, M. A., Pessina, A. Le village néolithique submergé de La Marmotta (lac de Bracciano, Rome). in Le Néolithique du Nord-Ouest méditerranéen (ed. Vaquer, J.) 35–38 (Société préhistorique française, Paris, 1999)Fugazzola Delpino, M. A. La Marmotta. in Le ceramiche impresse nel Neolitico antico. Italia e Mediterraneo (eds. Fugazzola, M.A., Pessina, A. & Tiné, V) 373–395 (Istituto Poligrafico e Zecca dello Stato, Roma, 2002).Grantham, G. L. faucille et la faux. Études rurales 151–152, 103–131 (1999).Article 

    Google Scholar 
    Sigaut, F. Identification des techniques de récolte des graines alimentaires. J. Agric. Trad. Bot. Appl. 25(3), 145–161 (1978).
    Google Scholar 
    Anderson, P. C., Sigaut, F. Introduction: reasons for variability in harvesting techniques and tools. in Exploring and Explaining Diversity in Agricultural Technology, EARTH 2 (eds. van Gijn, A., Whittaker, P. & Anderson, P.) 85–93 (Oxford, Oxbow Books, 2014).Halstead, P. Two oxen ahead: Pre-mechanized farming in the Mediterranean (John Wiley & Sons, 2014).Book 

    Google Scholar 
    Fugazzola Delpino, M. A. & Mineo, M. La piroga neolitica di Bracciano (La Marmotta 1). Bull. Paletnol. Ital. 86, 197–266 (1995).
    Google Scholar 
    Fugazzola Delpino, M. A., Tinazzi, O. Dati di cronologia da un villaggio del Neolitico Antico. Le indagini dendrocronologiche condotte sui legni de La Marmotta (lago di Bracciano-Roma). in Miscellanea in ricordo di Francesco Nicosia, 1–10 (Studia Erudita, Fabrizio Serra Editore, 2010).Salavert, A. et al. Direct dating reveals the early history of opium poppy in western Europe. Sci. Rep. 10, 20263. https://doi.org/10.1038/s41598-020-76924-3 (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ghiselli, L. et al. Nutritional characteristics of ancient Tuscan varieties of Triticum aestivum L. Ital. J. Agron. 11(4), 237–245 (2016).Article 

    Google Scholar 
    Pichon, F. Une moisson expérimentale de céréales, Séranon (août 2016), ArchéOrient – Le Blog, 14 octobre2016, (2016). https://archeorient.hypotheses.org/6667.Banks, W. E. & Kay, M. High-resolution casts for lithic use-wear analysis. Lithic Technol. 28(1), 27–34. https://doi.org/10.1080/01977261.2003.11721000 (2003).Article 

    Google Scholar 
    Ibáñez, J. J., Anderson, P. C., Gonzalez-Urquijo, J. & Gibaja, J. Cereal cultivation and domestication as shown by microtexture analysis of sickle gloss through confocal microscopy. J. Archaeol. Sci. 73, 62–81. https://doi.org/10.1016/j.jas.2016.07.011 (2016).Article 

    Google Scholar 
    Caruso Fermé, L. Modalidades de adquisición y uso del material leñoso entre grupos cazadores-recolectores patagónicos (Argentina). Métodos y técnicas de estudios del material leñoso arqueológico. PhD Dissertation (Universidad Autónoma de Barcelona, Barcelona, 2012).Caruso Fermé, L., Clemente, I., Civalero, M.T. A use-wear analysis of wood technology of patagonian hunter-gatherers. The case of Cerro Casa de Piedra 7, Argentina. J. Archaeol. Sci. 15, 315–321 (2015). https://doi.org/10.1016/j.jas.2015.03.015.Caruso Fermé, L., Aschero, C. Manufacturing and use of the wooden artifacts. A use-wear analysis of wood technology in hunter-gatherer groups (Cerro Casa de Piedra 7 site, Argentina). J. Archaeol. Sci. 31, 102291 (2020). https://doi.org/10.1016/j.quaint.2020.10.067.Schweingruber, F. H. Anatomy of European wood: An atlas for the identification of European trees, shrubs and dwarf shrubs (Paul Haupt, 1990).
    Google Scholar 
    Rageot, M. et al. Birch bark tar production: Experimental and biomolecular approaches to the study of a common and widely used prehistoric adhesive. J. Archaeol. Method Theory 26, 276–312. https://doi.org/10.1007/s10816-018-9372-4 (2019).Article 

    Google Scholar 
    Rageot, M. et al. New insights into Early Celtic consumption practices: Organic residue analyses of local and imported pottery from Vix-Mont Lassois. PLoS ONE 14(6), e0218001. https://doi.org/10.1371/journal.pone.0218001 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Arobba, D., Caramiello, R., Martino, G. P. Analisi paleobotaniche di resine dal relitto navale romano del Golfo Dianese. Rivista di Studi Liguri, LXIII-LXIV: 339–355 (1999).Marshall, D. M. Archaeological pollen: extraction from ancient resins. The American Association of Stratigraphic Palynologists. Prog. and Abstr., 38th Ann. Mtg., 34 (2005).Berglund, B. E., Ralska-Jasiewiczowa, M. Pollen analysis and pollen diagrams. in Handbook of Holocene Palaeoecology and Palaeohydrology. (eds. Berglund, B. E.) 455–484 (Chichester, Wiley, 1986).Traverse, A. Paleopalynology. Second Edition, 813 p. (Dordrecht, Springer, 2007).Punt W. (ed.) The Northwest European pollen flora (NEPF), vol. 2 (1980), vol. 3 (1981), vol. 4 (1984) vol. 5 (1988), vol. 6 (1991), vol. 7 (1996), vol. 8 (2003) (Elsevier, Wim Punt, Amsterdam, 1980–2003)Fægri, K. & Iversen, J. Textbook of pollen analysis (John Wiley and Sons, 1989).
    Google Scholar 
    Moore, P. D., Webb, J. A. & Collinson, M. E. Pollen analysis 2nd edn. (Blackwell, 1991).
    Google Scholar 
    Beug, H.-J. Leitfaden der Pollenbestimmung für Mitteleuropa und angrenzende Gebiete (Pfeil, 2004).
    Google Scholar 
    Reille, M. Pollen et spores d’Europe et d’Afrique du Nord. (Marseille, Laboratoire de Botanique Historique et Palynologie, 1992).Katz, O. et al. Rapid phytolith extraction for analysis of phytolith concentrations and assemblages during an excavation: An application at Tell es-Safi/Gath Israel. J. Archaeol. Sci. 37(7), 1557–1563. https://doi.org/10.1016/j.jas.2010.01.016 (2010).Article 

    Google Scholar 
    Brown, D. A. Prospects and limits of a phytolith key for grasses in the central United States. J. Archaeol. Sci. 11, 345–368. https://doi.org/10.1016/0305-4403(84)90016-5 (1984).Article 

    Google Scholar 
    Rosen, A. M. Preliminary identification of silica skeletons from Near Eastern archaeological sites: an anatomical approach. in Phytolith Systematics: Emerging Issues, Advances in Archaeological and Museum Science (eds. Rapp, G. Jr. & Mulholland, S. C.) 129–148 (New York, Plenum Press, 1992)Mulholland, S. C., Rapp Jr. G. A morphological classification of grass silica-bodies. in Phytolith Systematics: Emerging Issues, Advances in Archaeological and Museum Science (eds. Rapp, G. Jr. & Mulholland, S. C.) 65–89 (New York, Plenum Press, 1992)Piperno, D. R. Phytoliths: A comprehensive Guide for Archaeologists and Paleoecologists (Altamira Press, 2006).
    Google Scholar 
    Albert, R. M., & Weiner, S. Study of phytoliths in prehistoric ash layers from Kebara and Tabun caves using a quantitative approach. in Phytoliths: applications in earth sciences and human history, (eds. Meunier, J.D. & Colin, F.) 251–266 (Tokyo, Balkema Publisher, 2001)Albert, R. M. et al. Phytolith-rich layers from the Late Bronze and Iron Ages at Tel Dor (Israel): Mode of formation and archaeological significance. J. Archaeol. Sci. 35(1), 57–75. https://doi.org/10.1016/j.jas.2007.02.015 (2008).Article 

    Google Scholar 
    Albert, R. M., Ruíz, J. A. & Sans, A. PhytCore ODB: A new tool to improve efficiency in the management and exchange of information on phytoliths. J. Archaeol. Sci. 68, 98–105 (2016).Article 

    Google Scholar 
    Portillo, M., Kadowaki, S., Nishiaki, Y. & Albert, R. M. Early Neolithic household behavior at Tell Seker al-Aheimar (Upper Khabur, Syria): A comparison to ethnoarchaeological study of phytoliths and dung spherulites. J. Archaeol. Sci. 42, 107–118 (2014).Article 

    Google Scholar 
    Tsartsidou, G. et al. The phytolith archaeological record: strengths and weaknesses evaluated based on a quantitative modern reference collection from Greece. J. Archaeol. Sci. 34, 1262–1275. https://doi.org/10.1016/j.jas.2006.10.017 (2007).Article 

    Google Scholar 
    Neumann, K., Strömberg , A. E. C., Ball, T., Albert, R. M., Vrydaghs, L. Scott-Cummings, L. (International Committee for Phytolith Taxonomy ICPT). International Code for Phytolith Nomenclature (ICPN) 2.0. Annals of Botany, 124(2): 189–199 (2019).Anderson, P. C. Insight into plant harvesting and other activities at Hatoula, as revealed by microscopic functional analysis of selected chipped stone tools. Le site de Hatoula en Judée occidental. (eds. Lechevallier, M. & Ronen, A.) 277–293 (Paris, Association Paléorient, 1994)Fugazzola Delpino, M.A. La vita quotidiana del Neolitico. Il sito della Marmotta sul Lago di Bracciano. in Settemila anni fa il primo pane. Ambienti e culture delle società neolitiche (eds. Pessina, A. & Muscio G.) 185–192 (Udine, Museo Friulano di Storia Naturale, 1998–1999)Mineo, M. Monossili d’Europa: costruite anche per le rotte marine? in Ubi minor: le isole minori del Mediterraneo centrale: dal Neolitico ai primi contatti coloniali (eds. Guidi, A., Cazzella, A. & Nomi, F.). Scienze dell’Antichità 22, 453–475 (2016)Helwig, K., Monahan, V. & Poulin, J. The identification of hafting adhesive on a slotted antler point from a southwest Yukon ice patch. Am. Antiq. 73, 279–288. https://doi.org/10.1017/S000273160004227X (2008).Article 

    Google Scholar 
    Steigenberger, G. & Herm, C. Natural resins and balsams from an eighteenth-century pharmaceutical collection analysed by gas chromatography/mass spectrometry. Anal. Bioanal. Chem. 401, 1771–1784. https://doi.org/10.1007/s00216-011-5169-y (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    van den Berg, K. J., Boon, J. J., Pastorova, I. & Spetter, L. F. M. Mass spectrometric methodology for the analysis of highly oxidized diterpenoid acids in Old Master paintings. J. Mass Spectrom. 35, 512–533. https://doi.org/10.1002/(SICI)1096-9888(200004)35:4%3c512::AID-JMS963%3e3.0.CO;2-3 (2000).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Behre K. E. Anthropogenic Indicators in Pollen Diagrams, A.A. (Rotterdam, Balkema, 1986).Mercuri, A. M. et al. Anthropogenic Pollen Indicators (API) from archaeological sites as local evidence of human-induced environments in the Italian peninsula. Ann. Bot. 3, 143–153 (2013).
    Google Scholar 
    Andersen, S.-T., Identification of wild grass and cereal pollen. in Danmarks Geologiske Undersøgelse (ed. Aaby, B.) 69–92 (Geological Survey of Denmark, 1978).Bottema, S. Cereal-type pollen in the Near East as indicators of wild or domestic crops. in Préhistoire de l’agriculture: nouvelles approches expérimentales et ethnographiques (ed. Anderson P. C.) 95–106 (Paris, CRA, 1992). https://doi.org/10.1007/BF00217499.Lagerås, P. Long-term history of land-use and vegetation at Femtingagölen—a small lake in the Småland Uplands, southern Sweden. Veg. Hist. Archaeobot. 5, 215–228 (1996).Article 

    Google Scholar 
    Joly, C., Barillé, L., Barreau, M., Mancheron, A. & Visset, L. Grain and annulus diameter as criteria for distinguishing pollen grains of cereals from wild grasses. Rev. Palaeobot. Palynol. 146, 221–233. https://doi.org/10.1016/j.revpalbo.2007.04.003 (2007).Article 

    Google Scholar 
    Punt, W. Umbelliferae. Rev. Palaeobot. Palynol. 42, 155–364 (1984).Article 

    Google Scholar 
    Ellis, M. B. & Ellis, J. P. Microfungi of Land Plants. An Identification Handbook (London, Croom Helm, 1985) (Figure 1270).Ellis, M. B. & Ellis, J. P. Microfungi of Land Plants. An Identification Handbook (London, Croom Helm, 1985) (Figures 174; 176).Rottoli, M., Pessina, A. Neolithic agriculture in Italy: an update of archaeobotanical data with particular emphasis on northern settlements. in The Origins and Spread of Domestic Plants in Southwest Asia and Europe. (eds. Colledge, S. & Conolly, J.) 141–154 (Routledge, New York, 2016)Gurova, M. Prehistoric sickles in the collection of the National Museum of Archaeology in Sofia. in Southeast Europe and Anatolia in Prehistory: Essays in Honor of Vassil Nikolov on his 65th Anniversary (eds. Bacvarov, K. & Gleser, E.) 159–165 (Bonn, Verlag Dr. Rudolf Habelt GmbH, 2016)Sidéra, I. Nouveaux éléments d’origine proche-orientale dans le Néolithique ancien balkanique. in Analyse de l’industrie osseuse. in Préhistoire d’Anatolie. Genèse de deux mondes (ed. Otte, M.), 215–239 (Liège, ERAUL, 1997)Mellaart, J. Excavations at Hacılar: Fourth preliminary report, 1960. Anat. Stud. Anat. Stud. 11, 39–75 (1961).Article 

    Google Scholar 
    Nag, P. K., Goswami, A., Ashtekar, S. P. & Pradhan, C. K. Ergonomics in sickle operation. Appl. Ergon. 19(3), 233–239 (1988).CAS 
    Article 

    Google Scholar 
    Astruc, L., Tkaya, M. B. & Torchy, L. D. l’efficacité des faucilles néolithiques au Proche-Orient: approche expérimentale. Bulletin de la Société préhistorique française 109(4), 671–687 (2012).Article 

    Google Scholar 
    Sigaut, F. Les techniques de récolte des grains : identification, localisation, problèmes d’interprétation. in Rites et rythmes agraires (ed. Cauvin, M.-C.) 31–43 (Lyon, Maison de l’Orient et de la Méditerranée Jean Pouilloux, 1991)Magri, D. Late Quaternary vegetation history at Lagaccione near Lago di Bolsena (central Italy). Rev. Palaeobot. Palynol. 106(3–4), 171–208 (1999).Article 

    Google Scholar 
    Gale, R., & Cutler, D. F. Plants in archaeology: identification manual of vegetative plant materials used in Europe and the Southern Mediterranean to c. 1500 (Westbury and Royal Botanic Gardens, Kew, 2000).Chabal, L. & Feugère, M. L. Le mobilier organique des puits antiques et autres contextes humides de Lattara. Lattara 18, 137–188 (2005).
    Google Scholar 
    Chabal, L. (ed.) Quatre puits de l’agglomération routière gallo-romaine d’Ambrussum (Villetelle, Hérault). Supplément. Revue Archéologique de Narbonnaise, 42: 65–71 (2013).Caruso Fermé, L. & Piqué Huerta, R. Landscape and forest exploitation at the ancient Neolithic site of La Draga (Banyoles, Spain). The Holocene, 24(3): 266 (2014).Boschian, G. Il Riparo “Ermanno de Pompeis” presso l’Eremo di San Bartolomeo di Legio. Scavi 1990–1999. in Atti della XXXVI Riunione Scientifica IIPP, Preistoria e Protostoria dell’Abruzzo, Chieti-Celano, 27–30 settembre 2001, 105–116 (IIPP; Firenze, 2003).Radi, G. & Danese, E. L’abitato di Colle Santo Stefano di Ortucchio (L’Aquila). in Atti della XXXVI Riunione Scientifica IIPP, Preistoria e Protostoria dell’Abruzzo, Chieti-Celano, 27–30 settembre 2001, 145–161 (IIPP; Firenze, 2003).De Francesco, A. M., Bocci, M., Crisci, G. M., & Francaviglia, V. Obsidian provenance at several Italian and Corsican archaeological sites using the non-destructive X-ray fluorescence method. in Obsidian and ancient manufactured glass (eds. Liritzis, I., & Stevenson, C. M.) 115–129 (Albuquerque, UNM Press, 2012).Degano, I. et al. Hafting of Middle Paleolithic tools in Latium (central Italy): New data from Fossellone and Sant’Agostino caves. PLoS ONE 14, e0213473 (2019).CAS 
    Article 

    Google Scholar 
    Nardella, F. et al. Chemical investigations of bitumen from Neolithic archaeological excavations in Italy by GC/MS combined with principal component analysis. Anal. Methods 11, 1449–1459. https://doi.org/10.1039/c8ay02429d (2019).CAS 
    Article 

    Google Scholar 
    Rageot, M. et al. Management systems of adhesive materials throughout the Neolithic in the North-West Mediterranean. J. Archaeol. Sci. 126, 105309 (2021).Article 

    Google Scholar 
    Binder, D., Bourgeois, G., Benoist, F. & Vitry, C. Identification de brai de bouleau (betula) dans le néolithique de Giribaldi (Nice, France) par la spectrométrie de masse. Revue d’Archéométrie 14, 37–42 (1990).Article 

    Google Scholar 
    Vuorela, I. Relative pollen rain around cultivated fields. Acta Bot. Fenn. 102, 1–27 (1973).
    Google Scholar 
    Robinson, M. & Hubbard, R. N. L. B. The transport of pollen in the bracts of hulled cereals. J. Archaeol. Sci. 4(2), 197–199. https://doi.org/10.1016/0305-4403(77)90067-X (1977).Article 

    Google Scholar 
    Hall, V.A., The role of harvesting techniques in the dispersal of pollen grains of Cerealia. Pollen et Spores, XXX, 2, pp. 265–270.Portillo, M., Llergo, Y., Ferrer, A. & Albert, R. M. Tracing microfossil residues of cereal processing in the archaeobotanical record: an experimental approach. Veg. Hist. Archaeobot. 26(1), 59–74. https://doi.org/10.1007/s00334-016-0571-1 (2017).Article 

    Google Scholar 
    Negri, G. Nuovo erbario figurato (Hoepli ed., Milano, 1981).Paris R. R. & Moyse H. Matière Médicale. Vol 2°, (Masson, Paris. 1976).Bulgarelli, G. & Flamigni, S. Le piante tossiche e velenose (Hoepli ed., Milano, 2010).Les, D. H. Aquatic Dicotyledons of North America: Ecology, Life History, and Systematics (CRC Press, 2017).Book 

    Google Scholar 
    Curti, L. Herbarium, un’inedita collezione di piante del XVIII secolo conservata presso l’orto Botanico dell’Università di Padova (Offset Invicta S.p.A., Padova, 1992).Rottoli, M. Zafferanone selvatico (Carthamus lanatus) e cardo della Madonna (Silybum marianum), piante raccolte o coltivate nel Neolitico antico a “La Marmotta”? Bollettino di Paletnologia Italiana, 91–92, 47–61 (2000–2001).Rottoli, M. “La Marmotta”, Anguillara Sabazia (RM), scavi 1989. Analisi paletnobotaniche: prime risultanze. Bullettino di Paletnologia Italiana 84, 305–315 (1993).Van Geel, B. Non-pollen palynomorphs. in Tracking Environmental Change Using Lake Sediments: Terrestrial, vol. 3. (ed. Smol, J. P., Birks, H. J. B., Last W. M.) 99–119 (Algal and Siliceous Indicators, New York, 2001)Hawksworth, David L., van Geel, Bas, Wiltshire, Patricia E. J. The enigma of the Diporotheca palynomorph. Rev. Palaeobot. Palynol. 235, 94–98 (2016). https://doi.org/10.1016/j.revpalbo.2016.09.010.Krug, J. C., Benny, G. L., Keller, H. W. Coprophilous fungi. In Biodiversity of Fungi. Inventory and Monitoring Methods (ed. Foster M., Bill, G.) 467–499 (Elsevier Science, Amsterdam, 2004). More

  • in

    Bacterial ectosymbionts in cuticular organs chemically protect a beetle during molting stages

    Wang C, Wang S. Insect pathogenic fungi: genomics, molecular interactions, and genetic improvements. Annu Rev Entomol. 2017;62:73–90.CAS 
    PubMed 
    Article 

    Google Scholar 
    Lacey LA, Grzywacz D, Shapiro-Ilan DI, Frutos R, Brownbridge M, Goettel MS. Insect pathogens as biological control agents: Back to the future. J Invertebr Pathol. 2015;132:1–41.CAS 
    PubMed 
    Article 

    Google Scholar 
    Butt TM, Coates CJ, Dubovskiy IM, Ratcliffe NA Entomopathogenic fungi: new insights into host-pathogen interactions. Advances in Genetics. 2016. Elsevier Ltd.Lu HL, St. Leger RJ. Insect immunity to entomopathogenic fungi. Adv Genet. 2016;94:251–85.CAS 
    PubMed 
    Article 

    Google Scholar 
    Yuan S, Tao X, Huang S, Chen S, Xu A. Comparative immune systems in animals. Annu Rev Anim Biosci. 2014;2:235–58.CAS 
    PubMed 
    Article 

    Google Scholar 
    Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms. Nat Prod Rep. 2015;32:904–36.PubMed 
    Article 

    Google Scholar 
    Oliver KM, Smith AH, Russell JA. Defensive symbiosis in the real world – advancing ecological studies of heritable, protective bacteria in aphids and beyond. Funct Ecol. 2014;28:341–55.Article 

    Google Scholar 
    Scarborough CL, Ferrari J, Godfray HC. Aphid protected from pathogen. Science 2005;310:1781.CAS 
    PubMed 
    Article 

    Google Scholar 
    Łukasik P, van Asch M, Guo H, Ferrari J, Charles H. Unrelated facultative endosymbionts protect aphids against a fungal pathogen. Ecol Lett. 2013;16:214–8.PubMed 
    Article 

    Google Scholar 
    Flórez LV, Scherlach K, Gaube P, Ross C, Sitte E, Hermes C, et al. Antibiotic-producing symbionts dynamically transition between plant pathogenicity and insect-defensive mutualism. Nat Commun. 2017;8:15172.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 
    Kroiss J, Kaltenpoth M, Schneider B, Schwinger MG, Hertweck C, Maddula RK, et al. Symbiotic streptomycetes provide antibiotic combination prophylaxis for wasp offspring. Nat Chem Biol. 2010;6:261–3.CAS 
    PubMed 
    Article 

    Google Scholar 
    Kaltenpoth M, Goettler W, Koehler S, Strohm E. Life cycle and population dynamics of a protective insect symbiont reveal severe bottlenecks during vertical transmission. Evol Ecol. 2010;24:463–77.Article 

    Google Scholar 
    Wang X, Yang X, Zhou F, Tian ZQ, Cheng J, Michaud JP, et al. Symbiotic bacteria on the cuticle protect the oriental fruit moth Grapholita molesta from fungal infection. Biol Control. 2022;169:104895.CAS 
    Article 

    Google Scholar 
    Wang L, Feng Y, Tian J, Xiang M, Sun J, Ding J, et al. Farming of a defensive fungal mutualist by an attelabid weevil. ISME J. 2015;9:1793–801.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Currie CR, Stuart AE. Weeding and grooming of pathogens in agriculture by ants. Proc R Soc B Biol Sci. 2001;268:1033–9.CAS 
    Article 

    Google Scholar 
    Currie CR, Scottt JA, Summerbell RC, Malloch D. Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature 1999;398:701–4.CAS 
    Article 

    Google Scholar 
    Currie CR, Bot ANM, Boomsma JJ. Experimental evidence of a tripartite mutualism: Bacteria protect ant fungus gardens from specialized parasites. Oikos 2003;101:91–102.Article 

    Google Scholar 
    Um S, Fraimout A, Sapountzis P, Oh D-CC, Poulsen M. The fungus-growing termite Macrotermes natalensis harbors bacillaene-producing Bacillus sp. that inhibit potentially antagonistic fungi. Sci Rep. 2013;3:3250.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Grubbs KJ, Surup F, Biedermann PHW, McDonald BR, Klassen JL, Carlson CM, et al. Cycloheximide-producing streptomyces associated with xyleborinus saxesenii and xyleborus affinis fungus-farming ambrosia beetles. Front Microbiol. 2020;11:1–12.Article 

    Google Scholar 
    Piel J. Metabolites from symbiotic bacteria. Nat Prod Rep. 2009;26:338–62.CAS 
    PubMed 
    Article 

    Google Scholar 
    Van Arnam EB, Currie CR, Clardy J. Defense contracts: Molecular protection in insect-microbe symbioses. Chem Soc Rev. 2018;47:1638–51.PubMed 
    Article 

    Google Scholar 
    Beemelmanns C, Guo H, Rischer M, Poulsen M. Natural products from microbes associated with insects. Beilstein J Org Chem. 2016;12:314–27.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lackner G, Peters EE, Helfrich EJN, Piel J. Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. Proc Natl Acad Sci USA. 2017;114:E347–E356.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schoenian I, Spiteller M, Ghaste M, Wirth R, Herz H, Spiteller D. Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proc Natl Acad Sci USA. 2011;108:1955–60.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kaltenpoth M, Strupat K, Svatoš A. Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH. ISME J. 2016;10:527–31.PubMed 
    Article 

    Google Scholar 
    Geier B, Sogin EM, Michellod D, Janda M, Kompauer M, Spengler B, et al. Spatial metabolomics of in situ host–microbe interactions at the micrometre scale. Nat Microbiol. 2020;5:498–510.CAS 
    PubMed 
    Article 

    Google Scholar 
    De Roode JC, Lefèvre T. Behavioral immunity in insects. Insects 2012;3:789–820.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kerwin AH, Gromek SM, Suria AM, Samples RM, Deoss DJ, O’Donnell K, et al. Shielding the next generation: Symbiotic bacteria from a reproductive organ protect bobtail squid eggs from fungal fouling. mBio. 2019;10:e02376-19.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Soler JJ, Martín-Vivaldi M, Ruiz-Rodríguez M, Valdivia E, Martín-Platero AM, Martínez-Bueno M, et al. Symbiotic association between hoopoes and antibiotic-producing bacteria that live in their uropygial gland. Funct Ecol. 2008;22:864–71.Article 

    Google Scholar 
    Bunker ME, Elliott G, Martin MO, Arnold AE, Weiss SL. Vertically transmitted microbiome protects eggs from fungal infection and egg failure. Anim Microbiome. 2021;3:43.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nyholm SV. In the beginning: Egg-microbe interactions and consequences for animal hosts: Egg microbiomes in animals. Philos Trans R Soc B Biol Sci. 2020;375:20190593.CAS 
    Article 

    Google Scholar 
    Smith DFQ, Dragotakes Q, Kulkarni M, Hardwick M, Casadevall A, Microbiology M, et al. Melanization is an important antifungal defense mechanism in Galleria mellonella hosts. bioRxiv 2022.04.02.486843.Yokoi K, Hayakawa Y, Kato D, Minakuchi C, Tanaka T, Ochiai M, et al. Prophenoloxidase genes and antimicrobial host defense of the model beetle, Tribolium castaneum. J Invertebr Pathol. 2015;132:190–200.CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhang J, Huang W, Yuan C, Lu Y, Yang B, Wang CY, et al. Prophenoloxidase-mediated ex vivo immunity to delay fungal infection after insect ecdysis. Front Immunol. 2017;8:1–14.
    Google Scholar 
    Zhang J, Lu A, Kong L, Zhang Q, Ling E. Functional analysis of insect molting fluid proteins on the protection and regulation of ecdysis. J Biol Chem. 2014;289:35891–906.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Soluk DA. Postmolt susceptibility of ephemerella larvae to predatory stoneflies: constraints on defensive armour. Oikos 1990;58:336.Article 

    Google Scholar 
    Kanyile SN, Engl T, Kaltenpoth M. Nutritional symbionts enhance structural defence against predation and fungal infection in a grain pest beetle. J Exp Biol. 2022;225:1–9.Article 

    Google Scholar 
    Flórez LV, Kaltenpoth M. Symbiont dynamics and strain diversity in the defensive mutualism between Lagria beetles and Burkholderia. Environ Microbiol. 2017;19:3674–88.PubMed 
    Article 
    CAS 

    Google Scholar 
    Uberti A, Smaniotto MA, Giacobbo CL, Lovatto M, Lugaresi A, Girardi GC. Novo inseto praga na cultura do pessegueiro: biologia de Lagria villosa Fabricius, 1783 (Coleoptera: Tenebrionidae) alimentados com pêssego. Sci Electron Arch. 2017;10:72–76.
    Google Scholar 
    Stammer HJ. Die Symbiose der Lagriiden (Coleoptera). Z für Morphol und Ökologie der Tiere. 1929;15:1–34.Article 

    Google Scholar 
    Boucias DG, Pendland JC Principles of Insect Pathology. 1998. Springer Science + Business Media, LLC, New York.Garcia MA, Pierozzi IJ. Aspectos da biologia e ecologia de Lagria villosa Fabricius, 1781 (Coleoptera, Lagriidae). Rev Bras Biol. 1982;42:415–20.
    Google Scholar 
    Vega FE, Posada F, Catherine Aime M, Pava-Ripoll M, Infante F, Rehner SA. Entomopathogenic fungal endophytes. Biol Control. 2008;46:72–82.Article 

    Google Scholar 
    Kabaluk JT, Ericsson JD. Metarhizium anisopliae seed treatment increases yield of field corn when applied for wireworm control. Agron J. 2007;99:1377–81.Article 

    Google Scholar 
    Hallouti A, Ait Hamza M, Zahidi A, Ait Hammou R, Bouharroud R, Ait Ben Aoumar A, et al. Diversity of entomopathogenic fungi associated with Mediterranean fruit fly (Ceratitis capitata (Diptera: Tephritidae)) in Moroccan Argan forests and nearby area: impact of soil factors on their distribution. BMC Ecol. 2020;20:1–13.Article 
    CAS 

    Google Scholar 
    Iwanicki NS, Pereira AA, Botelho ABRZ, Rezende JM, Moral RDA, Zucchi MI, et al. Monitoring of the field application of Metarhizium anisopliae in Brazil revealed high molecular diversity of Metarhizium spp in insects, soil and sugarcane roots. Sci Rep. 2019;9:1–12.CAS 
    Article 

    Google Scholar 
    Roberts DW, St. Leger RJ. Metarhizium spp., cosmopolitan insect-pathogenic fungi: Mycological aspects. Adv Appl Microbiol. 2004;54:1–70.CAS 
    PubMed 
    Article 

    Google Scholar 
    Wierz JC, Gaube P, Klebsch D, Kaltenpoth M, Flórez LV. Transmission of bacterial symbionts with and without genome erosion between a beetle host and the plant environment. Front Microbiol. 2021;12:715601.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gillespie JP, Bailey AM, Cobb B, Vilcinskas A. Fungi as elicitors of insect immune responses. Arch Insect Biochem Physiol. 2000;44:49–68.CAS 
    PubMed 
    Article 

    Google Scholar 
    Ortiz-Urquiza A, Keyhani NO. Action on the surface: Entomopathogenic fungi versus the insect cuticle. Insects 2013;4:357–74.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Grizanova EV, Coates CJ, Dubovskiy IM, Butt TM. Metarhizium brunneum infection dynamics differ at the cuticle interface of susceptible and tolerant morphs of Galleria mellonella. Virulence 2019;10:999–1012.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Eaton WD, Love DC, Botelho C, Meyers TR, Imamura K, Koeneman T. Preliminary results on the seasonality and life cycle of the parasitic dinoflagellate causing bitter crab disease in Alaskan Tanner crabs (Chionoecetes bairdi). J Invertebr Pathol. 1991;57:426–34.CAS 
    PubMed 
    Article 

    Google Scholar 
    Field RH, Chapman CJ, Taylor AC, Neil DM, Vickerman K. Infection of the Norway lobster Nephrops norvegicus by a Hematodinium-like species of dinoflagellate on the west coast of Scotland. Dis Aquat Organ. 1992;13:1–15.Article 

    Google Scholar 
    Threlkeld ST, Chiavelli DA, Willey RL. The organization of zooplankton epibiont communities. Trends Ecol Evol. 1993;8:317–21.CAS 
    PubMed 
    Article 

    Google Scholar 
    Duneau D, Ebert D. The role of moulting in parasite defence. Proc R Soc B Biol Sci. 2012;279:3049–54.Article 

    Google Scholar 
    Vandenberg JD, Ramos M, Altre JA. Dose-Response and Age- and Temperature-Related Susceptibility of the Diamondback Moth (Lepidoptera: Plutellidae) to Two Isolates of Beauveria bassiana (Hyphomycetes: Moniliaceae). Environ Entomol. 1998;27:1017–21.Article 

    Google Scholar 
    Vey A, Fargues J. Histological and ultrastructural studies of Beauveria bassiana infection in Leptinotarsa decemlineta larvae during ecdysis. J Invertebr Pathol. 1977;30:207–15.Article 

    Google Scholar 
    Reynolds SE, Samuels RI. Physiology and biochemistry of insect moulting fluid. Adv Insect Phys. 1996;26:157–232.CAS 
    Article 

    Google Scholar 
    Lopanik NB. Chemical defensive symbioses in the marine environment. Funct Ecol. 2014;28:328–40.Article 

    Google Scholar 
    Sen R, Ishak HD, Estrada D, Dowd SE, Hong E, Mueller UG. Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants. Proc Natl Acad Sci USA. 2009;106:17805–10.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Currie CR, Poulsen M, Mendenhall J, Boomsma JJ, Billen J. Coevolved crypts and exocrine glands support mutualistic bacteria in fungus-growing ants. Science 2006;311:81–3.CAS 
    PubMed 
    Article 

    Google Scholar 
    Li H, Sosa-Calvo J, Horn HA, Pupo MT, Clardy J, Rabeling C, et al. Convergent evolution of complex structures for ant-bacterial defensive symbiosis in fungus-farming ants. Proc Natl Acad Sci USA. 2018;115:10720–5.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Kaltenpoth M, Roeser-Mueller K, Koehler S, Peterson A, Nechitaylo TY, Stubblefield JW, et al. Partner choice and fidelity stabilize coevolution in a Cretaceous-age defensive symbiosis. Proc Natl Acad Sci. 2014;111:6359–64.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Engl T, Kroiss J, Kai M, Nechitaylo TY, Svatoš A, Kaltenpoth M. Evolutionary stability of antibiotic protection in a defensive symbiosis. Proc Natl Acad Sci USA. 2018;115:E2020–E2029.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Gil-Turnes MS, Hay ME, Fenical W. Symbiotic marine bacteria chemically defend crustacean embryos from a pathogenic fungus. Science 1989;246:116–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Gil-Turnes MS, Fenical W. Embryos of Homarus americanus are protected by epibiotic bacteria. Biol Bull. 1992;182:105–8.CAS 
    PubMed 
    Article 

    Google Scholar 
    Hoffmann KH Insect Molecular Biology and Ecology. 2015. CRC Press.Eisner T, Morgan RC, Attygalle AB, Smedley SR, Herath KB, Meinwald J. Defensive production of quinoline by a phasmid insect (Oreophoetes peruana). J Exp Biol. 1997;200:2493–2500.CAS 
    PubMed 
    Article 

    Google Scholar 
    Waterworth SC, Flórez LV, Rees ER, Hertweck C, Kaltenpoth M, Kwan JC. Horizontal gene transfer to a defensive symbiont with a reduced genome in a multipartite beetle microbiome. mBio. 2020;11:e02430-19.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Niehs SP, Kumpfmüller J, Dose B, Little RF, Ishida K, Flórez LV, et al. Insect‐associated bacteria assemble the antifungal butenolide gladiofungin by non‐canonical polyketide chain termination. Angew Chem. 2020;132:23322–6.Article 

    Google Scholar 
    Dose B, Niehs SP, Scherlach K, Flórez LV, Kaltenpoth M, Hertweck C. Unexpected bacterial origin of the antibiotic icosalide: two-tailed depsipeptide assembly in multifarious Burkholderia symbionts. ACS Chem Biol. 2018;13:2414–20.CAS 
    PubMed 
    Article 

    Google Scholar 
    Parada AE, Needham DM, Fuhrman JA. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.CAS 
    PubMed 
    Article 

    Google Scholar 
    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.CAS 
    PubMed 
    Article 

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

    Google Scholar 
    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:590–6.Article 
    CAS 

    Google Scholar 
    Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and ‘all-species Living Tree Project (LTP)’ taxonomic frameworks. Nucleic Acids Res. 2014;42:643–8.Article 
    CAS 

    Google Scholar 
    Weiss B, Kaltenpoth M. Bacteriome-localized intracellular symbionts in pollen-feeding beetles of the genus Dasytes (Coleoptera, Dasytidae). Front Microbiol. 2016;7:1–10.Article 

    Google Scholar 
    Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990;56:1919–25.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Paschke C, Leisner A, Hester A, Maass K, Guenther S, Bouschen W, et al. Mirion – A software package for automatic processing of mass spectrometric images. J Am Soc Mass Spectrom. 2013;24:1296–306.CAS 
    PubMed 
    Article 

    Google Scholar  More