Ecology

Franklin, J. F., Shugart, H. H. & Harmon, M. E. Tree death as an ecological process. Bioscience 37, 550–556 (1987).Article 

Google Scholar 
Harmon, M. E. et al. Ecology of coarse woody debris in temperate ecosystems. In Advances in Ecological Research (eds MacFadyen, A. & Ford, E. D.) 133–302 (Academic Press, 1986).Chapter 

Google Scholar 
Harmon, M. E. & Bell, D. M. Mortality in forested ecosystems: suggested conceptual advances. Forests 11, 572 (2020).Article 

Google Scholar 
van Mantgem, P. J. et al. Widespread increase of tree mortality rates in the Western United States. Science 323, 521–524 (2009).ADS 
Article 

Google Scholar 
Kinnucan, H. W. Timber price dynamics after a natural disaster: Hurricane Hugo revisited. J. For. Econ. 25, 115–129 (2016).
Google Scholar 
Marsinko, A. P., Straka, T. J. & Haight, R. G. The effect of a large-scale natural disaster on regional timber supply. J. World For. Resour. Manag. 8, 75–85 (1997).
Google Scholar 
Lugo, A. E. Visible and invisible effects of hurricanes on forest ecosystems: an international review. Austral Ecol. 33, 368–398 (2008).Article 

Google Scholar 
Shifley, S. R., Brookshire, B. L., Larsen, D. R. & Herbeck, L. A. Snags and down wood in missouri old-growth and mature second-growth forests. North. J. Appl. For. 14, 165–172 (1997).Article 

Google Scholar 
Bobiec, A. Living stands and dead wood in the Białowieża forest: suggestions for restoration management. For. Ecol. Manag. 165, 125–140 (2002).Article 

Google Scholar 
Spetich, M. A., Shifley, S. R. & Parker, G. R. Regional distribution and dynamics of coarse woody debris in midwestern old-growth forests. For. Sci. 45, 302–313 (1999).
Google Scholar 
Rimle, A., Heiri, C. & Bugmann, H. Deadwood in Norway spruce dominated mountain forest reserves is characterized by large dimensions and advanced decomposition stages. For. Ecol. Manag. 404, 174–183 (2017).Article 

Google Scholar 
Ruokolainen, A., Shorohova, E., Penttilä, R., Kotkova, V. & Kushnevskaya, H. A continuum of dead wood with various habitat elements maintains the diversity of wood-inhabiting fungi in an old-growth boreal forest. Eur. J. For. Res. 137, 707–718 (2018).Article 

Google Scholar 
Ranius, T. & Kindvall, O. Modelling the amount of coarse woody debris produced by the new biodiversity-oriented silvicultural practices in Sweden. Biol. Conserv. 119, 51–59 (2004).Article 

Google Scholar 
Bouget, C. & Duelli, P. The effects of windthrow on forest insect communities: a literature review. Biol. Conserv. 118, 281–299 (2004).Article 

Google Scholar 
Svensson, M. et al. The relative importance of stand and dead wood types for wood-dependent lichens in managed boreal forests. Fungal Ecol. 20, 166–174 (2016).Article 

Google Scholar 
Bahuguna, D., Mitchell, S. J. & Nishio, G. R. Post-harvest windthrow and recruitment of large woody debris in riparian buffers on Vancouver Island. Eur. J. For. Res. 131, 249–260 (2012).Article 

Google Scholar 
Fortin, M. & DeBlois, J. Modeling tree recruitment with zero-inflated models: the example of hardwood stands in southern Quebec Canada. For. Sci. 53, 529–539 (2007).
Google Scholar 
Herrero, C., Pando, V. & Bravo, F. Modelling coarse woody debris in Pinus spp. Plantations. A case study in Northern Spain. Ann. For. Sci. 67, 708–708 (2010).Article 

Google Scholar 
Arekhi, S. Modeling spatial pattern of deforestation using GIS and logistic regression: a case study of northern Ilam forests, Ilam province Iran. Afr. J. Biotechnol. 10, 16236–16249 (2011).
Google Scholar 
Kumar, R., Nandy, S., Agarwal, R. & Kushwaha, S. P. S. Forest cover dynamics analysis and prediction modeling using logistic regression model. Ecol. Indic. 45, 444–455 (2014).Article 

Google Scholar 
Podur, J. J., Martell, D. L. & Stanford, D. A compound poisson model for the annual area burned by forest fires in the province of Ontario. Environmetrics 21, 457–469 (2010).MathSciNet 

Google Scholar 
Tobler, W. R. A computer movie simulating urban growth in the Detroit Region. Econ. Geogr. 46, 234–240 (1970).Article 

Google Scholar 
Griffith, D. & Chun, Y. Spatial autocorrelation and spatial filtering. In Handbook of regional science 1477–1507 (eds Fischer, M. M. & Nijkamp, P.) (Springer, 2014). https://doi.org/10.1007/978-3-642-23430-9_72.Chapter 

Google Scholar 
Li, T. & Meng, Q. Forest dynamics in relation to meteorology and soil in the Gulf Coast of Mexico. Sci. Total Environ. 702, 134913 (2019).ADS 
Article 

Google Scholar 
Brunsdon, C., Fotheringham, A. S. & Charlton, M. E. Geographically weighted regression: a method for exploring spatial nonstationarity. Geogr. Anal. 28, 281–298 (1996).Article 

Google Scholar 
Fotheringham, A. S., Charlton, M. E. & Brunsdon, C. Geographically weighted regression: a natural evolution of the expansion method for spatial data analysis. Environ. Plan. A 30, 1905–1927 (1998).Article 

Google Scholar 
Yang, C., Fu, M., Feng, D., Sun, Y. & Zhai, G. Spatiotemporal changes in vegetation cover and its influencing factors in the loess Plateau of China based on the geographically weighted regression model. Forests 12, 673 (2021).Article 

Google Scholar 
Monjarás-Vega, N. et al. Predicting forest fire kernel density at multiple scales with geographically weighted regression in Mexico. Sci. Total Environ. 718, 137313 (2020).ADS 
Article 

Google Scholar 
Peng, X., Wu, H. & Ma, L. A study on geographically weighted spatial autoregression models with spatial autoregressive disturbances. Commun. Stat. Theor. Methods 49, 5235–5251 (2020).MathSciNet 
Article 

Google Scholar 
Harris, P. & Brunsdon, C. Exploring spatial variation and spatial relationships in a freshwater acidification critical load data set for Great Britain using geographically weighted summary statistics. Comput. Geosci. 36, 54–70 (2010).ADS 
Article 

Google Scholar 
Li, J., Jin, M. & Li, H. Exploring spatial influence of remotely sensed PM2.5 concentration using a developed deep convolutional neural network model. Int. J. Environ. Res. Public Health 16, 454 (2019).Article 

Google Scholar 
Peng, C., Wang, M. & Chen, W. Spatial analysis of PAHs in soils along an urban-suburban-rural gradient: scale effect, distribution patterns, diffusion and influencing factors. Sci. Rep. 6, 37185 (2016).ADS 
CAS 
Article 

Google Scholar 
Wu, S. et al. Geographically and temporally neural network weighted regression for modeling spatiotemporal non-stationary relationships. Int. J. Geogr. Inf. Sci. 35, 582–608 (2021).Article 

Google Scholar 
Wu, S. et al. Modeling spatially anisotropic nonstationary processes in coastal environments based on a directional geographically neural network weighted regression. Sci. Total Environ. 709, 136097 (2020).ADS 
CAS 
Article 

Google Scholar 
Du, Z., Wang, Z., Wu, S., Zhang, F. & Liu, R. Geographically neural network weighted regression for the accurate estimation of spatial non-stationarity. Int. J. Geogr. Inf. Sci. 34, 1353–1377 (2020).Article 

Google Scholar 
Sun, Y., Ao, Z., Jia, W., Chen, Y. & Xu, K. A geographically weighted deep neural network model for research on the spatial distribution of the down dead wood volume in liangshui national nature reserve (China). IForest 14, 353–361 (2021).Article 

Google Scholar 
Wilkinson, L. Tests of significance in stepwise regression. Psychol. Bull. 86, 168–174 (1979).Article 

Google Scholar 
Henderson, D. A. & Denison, D. R. Stepwise regression in social and psychological research. Psychol. Rep. 64, 251–257 (1989).Article 

Google Scholar 
Carl, G. & Kühn, I. Analyzing spatial autocorrelation in species distributions using Gaussian and logit models. Ecol. Model. 207, 159–170 (2007).Article 

Google Scholar 
Wu, W. & Zhang, L. Comparison of spatial and non-spatial logistic regression models for modeling the occurrence of cloud cover in north-eastern Puerto Rico. Appl. Geogr. 37, 52–62 (2013).Article 

Google Scholar 
Ozdemir, A. Using a binary logistic regression method and GIS for evaluating and mapping the groundwater spring potential in the Sultan Mountains (Aksehir, Turkey). J. Hydrol. 405, 123–136 (2011).ADS 
Article 

Google Scholar 
Pineda Jaimes, N. B., Bosque Sendra, J., Gómez Delgado, M. & Franco, Plata R. Exploring the driving forces behind deforestation in the state of Mexico (Mexico) using geographically weighted regression. Appl. Geogr. 30, 576–591 (2010).Article 

Google Scholar 
Tutmez, B., Kaymak, U., Erhan Tercan, A. & Lloyd, C. D. Evaluating geo-environmental variables using a clustering based areal model. Comput. Geosci. 43, 34–41 (2012).ADS 
Article 

Google Scholar 
Li, X., Wu, P., Guo, F.-T. & Hu, X. A geographically weighted regression approach to detect divergent changes in the vegetation activity along the elevation gradients over the last 20 years. For. Ecol. Manag. 490, 119089 (2021).Article 

Google Scholar 
Que, X., Ma, C., Ma, X. & Chen, Q. Parallel computing for fast spatiotemporal weighted regression. Comput. Geosci. 150, 104723 (2021).Article 

Google Scholar 
Wu, L. et al. Spatial analysis of severe fever with thrombocytopenia syndrome virus in China using a geographically weighted logistic regression model. Int. J. Environ. Res. Public Health 13, 1125 (2016).Article 

Google Scholar 
Liu, Y. et al. Geographical variations in maternal lifestyles during pregnancy associated with congenital heart defects among live births in Shaanxi province Northwestern China. Sci. Rep. 10, 12958 (2020).ADS 
CAS 
Article 

Google Scholar 
Saefuddin, A., Saepudin, D. & Kusumaningrum, D. Geographically weighted poisson regression (GWPR) for analyzing the malnutrition data in java-Indonesia (European Regional Science Association (ERSA), 2013).
Google Scholar 
Lecun, Y., Bengio, Y. & Hinton, G. Deep learning. Nature 521, 436–444 (2015).ADS 
CAS 
Article 

Google Scholar 
Ketkar, N. Introduction to Keras. In Deep learning with python: a hands-on introduction (ed. Ketkar, N.) 97–111 (Apress, 2017). https://doi.org/10.1007/978-1-4842-2766-4_7.Chapter 

Google Scholar 
Tsomokos, D. I., Ashhab, S. & Nori, F. Fully connected network of superconducting qubits in a cavity. New J. Phys. 10, 113020 (2008).ADS 
Article 

Google Scholar 
Hu, T. et al. Study on the estimation of forest volume based on multi-source data. Sensors 21, 7796 (2021).ADS 
Article 

Google Scholar 
Chen, L., Ren, C., Zhang, B., Wang, Z. & Xi, Y. Estimation of forest above-ground biomass by geographically weighted regression and machine learning with sentinel imagery. Forests 9, 582 (2018).Article 

Google Scholar 
Srivastava, N., Hinton, G., Krizhevsky, A., Sutskever, I. & Salakhutdinov, R. Dropout: a simple way to prevent neural networks from overfitting. J. Mach. Learn. Res. 15, 1929–1958 (2014).MathSciNet 
MATH 

Google Scholar 
Mastromichalakis, S. ALReLU: A different approach on Leaky ReLU activation function to improve neural networks performance. arXiv:2012.07564 [Cs] arXiv:2012.07564 (2021).Chen, C., Li, Y., Yan, C., Dai, H. & Liu, G. A robust algorithm of multiquadric method based on an improved huber loss function for interpolating remote-sensing-derived elevation data sets. Remote Sens. 7, 3347–3371 (2015).ADS 
Article 

Google Scholar 
de Jong, P., Sprenger, C. & Veen, F. On extreme values of Moran’s I and Geary’s c ( spatial autocorrelation). Geogr. Anal. 16, 17–24 (1984).Article 

Google Scholar 
Fu, W. J., Jiang, P. K., Zhou, G. M. & Zhao, K. L. Using Moran’s i and GIS to study the spatial pattern of forest litter carbon density in a subtropical region of southeastern China. Biogeosciences 11, 2401–2409 (2014).ADS 
Article 

Google Scholar 
Parizi, E., Hosseini, S. M., Ataie-Ashtiani, B. & Simmons, C. T. Normalized difference vegetation index as the dominant predicting factor of groundwater recharge in phreatic aquifers: case studies across Iran. Sci. Rep. 10, 17473 (2020).ADS 
CAS 
Article 

Google Scholar 
Moore, J. R. Differences in maximum resistive bending moments of Pinus radiata trees grown on a range of soil types. For. Ecol. Manag. 135, 63–71 (2000).Article 

Google Scholar 
Lanquaye-Opoku, N. & Mitchell, S. J. Portability of stand-level empirical windthrow risk models. For. Ecol. Manag. 216, 134–148 (2005).Article 

Google Scholar 
Li, X. et al. Response of species and stand types to snow/wind damage in a temperate secondary forest Northeast China. J. For. Res. 29, 395–404 (2018).CAS 
Article 

Google Scholar 
Zhen, Z. et al. Geographically local modeling of occurrence, count, and volume of downwood in Northeast China. Appl. Geogr. 37, 114–126 (2013).Article 

Google Scholar 
Vozmishcheva, A. et al. Strong disturbance impact of tropical cyclone Lionrock (2016) on Korean pine-broadleaved forest in the Middle Sikhote-Alin Mountain range Russian Far East. Forests 10, 15 (2019).Article 

Google Scholar 
Bivand, R., Müller, W. G. & Reder, M. Power calculations for global and local Moran’s I. Comput. Stat. Data Anal. 53, 2859–2872 (2009).MathSciNet 
MATH 
Article 

Google Scholar 
Yuan, J. et al. Dynamics of coarse woody debris characteristics in the Qinling mountain forests in China. Forests 8, 403–403 (2017).MathSciNet 
Article 

Google Scholar 
Næsset, E. Estimating timber volume of forest stands using airborne laser scanner data. Remote Sens. Environ. 61, 246–253 (1997).ADS 
Article 

Google Scholar 
Næsset, E. Determination of mean tree height of forest stands by digital photogrammetry. Scand. J. For. Res. 17, 446–459 (2002).ADS 
Article 

Google Scholar 
Rich, R. L., Frelich, L. E. & Reich, P. B. Wind-throw mortality in the southern boreal forest: effects of species, diameter and stand age. J. Ecol. 95, 1261–1273 (2007).Article 

Google Scholar 
Odhiambo, B. O., Kenduiywo, B. K. & Were, K. Spatial prediction and mapping of soil pH across a tropical afro-montane landscape. Appl. Geogr. 114, 102129 (2020).Article 

Google Scholar  More

Caldeira, K. & Wickett, M. E. Oceanography: Anthropogenic carbon and ocean pH. Nature 425, 365–365 (2003).ADS 
CAS 
Article 

Google Scholar 
Sabine, C. L. et al. The oceanic sink for anthropogenic CO2. Science 305, 367–371 (2004).ADS 
CAS 
Article 

Google Scholar 
IPCC. In IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (eds. Pörtner, H.-O., Roberts, D. C., Masson-Delmotte, V., Zhai, P., Tignor, M., Poloczanska, E., Mintenbeck, K., Alegría, A., Nicolai, M., Okem, A., Petzold, J., Rama, B., Weyer, N. M.) (2019).Kroeker, K. J. et al. Impacts of ocean acidification on marine organisms: Quantifying sensitivities and interaction with warming. Glob. Change Biol. 19, 1884–1896 (2013).ADS 
Article 

Google Scholar 
Ries, J. B., Cohen, A. L. & McCorkle, D. C. Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. Geology 37, 1131–1134 (2014).ADS 
Article 

Google Scholar 
Ramajo, L. et al. Food supply confers calcifiers resistance to ocean acidification. Sci. Rep. 6, 19374 (2016).ADS 
CAS 
Article 

Google Scholar 
Vargas, C. A. et al. Species-specific responses to ocean acidification should account for local adaptation and adaptive plasticity. Nat. Ecol. Evol. 1, 0084 (2017).Article 

Google Scholar 
Kleypas, J. A. & Yates, K. K. Coral reefs and ocean acidification. Oceanography 22, 108–117 (2009).Article 

Google Scholar 
Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737–1742 (2007).ADS 
CAS 
Article 

Google Scholar 
Pandolfi, J. M., Connolly, S. R., Marshall, D. J. & Cohen, A. L. Projecting coral reef futures under global warming and ocean acidification. Science 333, 418–422 (2011).ADS 
CAS 
Article 

Google Scholar 
Cornwall, C. E. et al. Global declines in coral reef calcium carbonate production under ocean acidification and warming. Proc. Natl. Acad. Sci. 118, e2015265118 (2021).CAS 
Article 

Google Scholar 
Langer, M. R., Silk, M. T. & Lipps, J. H. Global ocean carbonate and carbon dioxide production: The role of reef foraminifera. J. Foraminifer. Res. 27, 271–277 (1997).Article 

Google Scholar 
Langer, M. R. Assessing the contribution of foraminiferan protists to global ocean carbonate production. J. Eukaryot. Microbiol. 55, 163–169 (2008).Article 

Google Scholar 
Hallock, P. Symbiont-bearing Foraminifera. In Modern Foraminifera (ed. Sen Gupta, B. K.) 123–139 (Springer Netherlands, 2003). https://doi.org/10.1007/0-306-48104-9_8.BouDagher-Fadel, M. K. Biology and evolutionary history of larger benthic foraminifera. In Evolution and Geological Significance of Larger Benthic Foraminifera 1–44 (UCL Press, 2018).Köhler-Rink, S. & Kühl, M. Microsensor studies of photosynthesis and respiration in larger symbiotic foraminifera. I The physico-chemical microenvironment of Marginopora vertebralis, Amphistegina lobifera and Amphisorus hemprichii. Mar. Biol. 137, 473–486 (2000).Article 

Google Scholar 
Glas, M. S., Fabricius, K. E., de Beer, D. & Uthicke, S. The O2, pH and Ca2+ microenvironment of benthic foraminifera in a high CO2 world. PLoS One 7, e50010 (2012).ADS 
CAS 
Article 

Google Scholar 
De Nooijer, L. J., Toyofuku, T. & Kitazato, H. Foraminifera promote calcification by elevating their intracellular pH. Proc. Natl. Acad. Sci. U. S. A. 106, 15374–15378 (2009).ADS 
Article 

Google Scholar 
Glas, M., Langer, G. & Keul, N. Calcification acidifies the microenvironment of a benthic foraminifer (Ammonia sp.). J. Exp. Mar. Biol. Ecol. 424–425, 53–58 (2012).Article 

Google Scholar 
Toyofuku, T. et al. Proton pumping accompanies calcification in foraminifera. Nat. Commun. 8, 14145 (2017).ADS 
CAS 
Article 

Google Scholar 
Hallock, P., Lidz, B. H., Cockey-Burkhard, E. M. & Donnelly, K. B. Foraminifera as bioindicators in coral reef assessment and monitoring: The FORAM Index. Environ. Monit. Assess. 81, 221–238 (2003).Article 

Google Scholar 
Uthicke, S., Thompson, A. & Schaffelke, B. Effectiveness of benthic foraminiferal and coral assemblages as water quality indicators on inshore reefs of the Great Barrier Reef, Australia. Coral Reefs 29, 209–225 (2010).ADS 
Article 

Google Scholar 
Prazeres, M., Martínez-Colón, M. & Hallock, P. Foraminifera as bioindicators of water quality: The FoRAM Index revisited. Environ. Pollut. 257, 113612 (2020).CAS 
Article 

Google Scholar 
Sen Gupta, B. K. Modern Foraminifera. (Springer Science & Business Media, 2003).Morse, J. W., Andersson, A. J. & Mackenzie, F. T. Initial responses of carbonate-rich shelf sediments to rising atmospheric pCO2 and “ocean acidification”: Role of high Mg-calcites. Geochim. Cosmochim. Acta 70, 5814–5830 (2006).ADS 
CAS 
Article 

Google Scholar 
Andersson, A. J., Mackenzie, F. T. & Bates, N. R. Life on the margin: Implications of ocean acidification on Mg-calcite, high latitude and cold-water marine calcifiers. Mar. Ecol. Prog. Ser. 373, 265–273 (2008).ADS 
CAS 
Article 

Google Scholar 
Van Dijk, I., De Nooijer, L. J. & Reichart, G.-J. Trends in element incorporation in hyaline and porcelaneous foraminifera as a function of pCO2. Biogeosciences 14, 497–510 (2017).ADS 
Article 

Google Scholar 
Not, C., Thibodeau, B. & Yokoyama, Y. Incorporation of Mg, Sr, Ba, U, and B in high-Mg calcite benthic foraminifers cultured under controlled pCO2. Geochem. Geophys. Geosyst. 19, 83–98 (2018).ADS 
CAS 
Article 

Google Scholar 
Levi, A., Müller, W. & Erez, J. Intrashell variability of trace elements in benthic foraminifera grown under high CO2 levels. Front. Earth Sci. 7, 247 (2019).ADS 
Article 

Google Scholar 
Doo, S. S., Fujita, K., Byrne, M. & Uthicke, S. Fate of calcifying tropical symbiont-bearing large benthic foraminifera: Living sands in a changing ocean. Biol. Bull. 226, 169–186 (2014).CAS 
Article 

Google Scholar 
Fujita, K. et al. Effects of ocean acidification on calcification of symbiont-bearing reef foraminifers. Biogeosciences 8, 2089–2098 (2011).ADS 
Article 

Google Scholar 
Hikami, M. et al. Contrasting calcification responses to ocean acidification between two reef foraminifers harboring different algal symbionts. Geophys. Res. Lett. 38, L19601 (2011).ADS 
Article 

Google Scholar 
Vogel, N. & Uthicke, S. Calcification and photobiology in symbiont-bearing benthic foraminifera and responses to a high CO2 environment. J. Exp. Mar. Biol. Ecol. 424–425, 15–24 (2012).Article 

Google Scholar 
McIntyre-Wressnig, A., Bernhard, J. M., McCorkle, D. C. & Hallock, P. Non-lethal effects of ocean acidification on the symbiont-bearing benthic foraminifer Amphistegina gibbosa. Mar. Ecol. Prog. Ser. 472, 45–60 (2013).ADS 
CAS 
Article 

Google Scholar 
Kuroyanagi, A., Kawahata, H., Suzuki, A., Fujita, K. & Irie, T. Impacts of ocean acidification on large benthic foraminifers: Results from laboratory experiments. Mar. Micropaleontol. 73, 190–195 (2009).ADS 
Article 

Google Scholar 
Knorr, P. O., Robbins, L. L., Harries, P. J., Hallock, P. & Wynn, J. Response of the Miliolid Archaias angulatus to simulated ocean acidification. J. Foraminifer. Res. 45, 109–127 (2015).Article 

Google Scholar 
Prazeres, M., Uthicke, S. & Pandolfi, J. M. Ocean acidification induces biochemical and morphological changes in the calcification process of large benthic foraminifera. Proc. R. Soc. B Biol. Sci. 282, 20142782 (2015).Article 

Google Scholar 
Reymond, C., Lloyd, A., Kline, D., Dove, S. & Pandolfi, J. Decline in growth of foraminifer Marginopora rossi under eutrophication and ocean acidification scenarios. Glob. Change Biol. 19, 291–302 (2013).ADS 
Article 

Google Scholar 
Sinutok, S., Hill, R., Doblin, M. A., Wuhrer, R. & Ralph, P. J. Warmer more acidic conditions cause decreased productivity and calcification in subtropical coral reef sediment-dwelling calcifiers. Limnol. Oceanogr. 56, 1200–1212 (2011).ADS 
CAS 
Article 

Google Scholar 
Sinutok, S., Hill, R., Kühl, M., Doblin, M. A. & Ralph, P. J. Ocean acidification and warming alter photosynthesis and calcification of the symbiont-bearing foraminifera Marginopora vertebralis. Mar. Biol. 161, 2143–2154 (2014).CAS 
Article 

Google Scholar 
Schmidt, C., Kucera, M. & Uthicke, S. Combined effects of warming and ocean acidification on coral reef Foraminifera Marginopora vertebralis and Heterostegina depressa. Coral Reefs 33, 805–818 (2014).ADS 
Article 

Google Scholar 
Engel, B., Hallock, P., Price, R. & Pichler, T. Shell dissolution in larger benthic foraminifers exposed to pH and temperature extremes: Results from an in situ experiment. J. Foraminifer. Res. 45, 190–203 (2015).Article 

Google Scholar 
Marques, J. A., de Barros Marangoni, L. F. & Bianchini, A. Combined effects of sea water acidification and copper exposure on the symbiont-bearing foraminifer Amphistegina gibbosa. Coral Reefs 36, 489–501 (2017).ADS 
Article 

Google Scholar 
Uthicke, S. & Fabricius, K. E. Productivity gains do not compensate for reduced calcification under near-future ocean acidification in the photosynthetic benthic foraminifer species Marginopora vertebralis. Glob. Change Biol. 18, 2781–2791 (2012).ADS 
Article 

Google Scholar 
Uthicke, S., Momigliano, P. & Fabricius, K. E. High risk of extinction of benthic foraminifera in this century due to ocean acidification. Sci. Rep. 3, 1–5 (2013).Article 

Google Scholar 
Pettit, L. R., Smart, C. W., Hart, M. B., Milazzo, M. & Hall-Spencer, J. M. Seaweed fails to prevent ocean acidification impact on foraminifera along a shallow-water CO2 gradient. Ecol. Evol. 5, 1784–1793 (2015).Article 

Google Scholar 
Martinez, A., Hernández-Terrones, L., Rebolledo-Vieyra, M. & Paytan, A. Impact of carbonate saturation on large Caribbean benthic foraminifera assemblages. Biogeosciences 15, 6819–6832 (2018).ADS 
CAS 
Article 

Google Scholar 
Pettit, L. R. et al. Benthic foraminifera show some resilience to ocean acidification in the northern Gulf of California, Mexico. Mar. Pollut. Bull. 73, 452–462 (2013).CAS 
Article 

Google Scholar 
Charrieau, L. M. et al. The effects of multiple stressors on the distribution of coastal benthic foraminifera: A case study from the Skagerrak-Baltic Sea region. Mar. Micropaleontol. 139, 42–56 (2018).ADS 
Article 

Google Scholar 
Narayan, G. R. et al. Response of large benthic foraminifera to climate and local changes: Implications for future carbonate production. Sedimentology https://doi.org/10.1111/sed.12858 (2021).Article 

Google Scholar 
Le Cadre, V., Debenay, J.-P. & Lesourd, M. Low pH effect on Ammonia beccarii test deformation: Implications for using test deformations as a pollution indicator. J. Foraminifer. Res. 33, 1–9 (2003).Article 

Google Scholar 
Kurtarkar, S. R., Nigam, R., Saraswat, R. & Linshy, V. N. Regeneration and abnormality in benthic foraminifer Rosalina leei: Implications in reconstructing past salinity changes. Riv. Ital. Paleontol. E Stratigr. 117(1), 189–196 (2011).
Google Scholar 
Haynert, K., Schönfeld, J., Polovodova-Asteman, I. & Thomsen, J. The benthic foraminiferal community in a naturally CO2-rich coastal habitat of the southwestern Baltic Sea. Biogeosciences 9, 4421–4440 (2012).ADS 
CAS 
Article 

Google Scholar 
Lee, J. J. ‘Living Sands’—Larger foraminifera and their endosymbiotic algae. Symbiosis 25, 71–100 (1997).CAS 

Google Scholar 
Parker, J. Ultrastructure of the test wall in modern porcelaneous foraminifera: Implications for the classification of the Miliolida. J. Foraminifer. Res. 47, 136–174 (2017).ADS 
Article 

Google Scholar 
Erez, J. The source of ions for biomineralization in foraminifera and their implications for paleoceanographic proxies. Rev. Mineral. Geochem. 54, 115–149 (2003).CAS 
Article 

Google Scholar 
Dissard, D., Nehrke, G., Reichart, G. J. & Bijma, J. Impact of seawater pCO2 on calcification and Mg/Ca and Sr/Ca ratios in benthic foraminifera calcite: results from culturing experiments with Ammonia tepida. Biogeosciences 7, 81–93 (2010).ADS 
CAS 
Article 

Google Scholar 
McIntyre-Wressnig, A., Bernhard, J. M., Wit, J. C. & Mccorkle, D. C. Ocean acidification not likely to affect the survival and fitness of two temperate benthic foraminiferal species: Results from culture experiments. J. Foraminifer. Res. 44, 341–351 (2014).Article 

Google Scholar 
Charrieau, L. M. et al. Decalcification and survival of benthic foraminifera under the combined impacts of varying pH and salinity. Mar. Environ. Res. 138, 36–45 (2018).CAS 
Article 

Google Scholar 
Saraswat, R. et al. Effect of salinity induced pH/alkalinity changes on benthic foraminifera: A laboratory culture experiment. Estuar. Coast. Shelf Sci. 153, 96–107 (2015).ADS 
CAS 
Article 

Google Scholar 
Buzas-Stephens, P. & Buzas, M. A. Population dynamics and dissolution of foraminifera in Nueces Bay, Texas. J. Foraminifer. Res. 35, 248–258 (2005).Article 

Google Scholar 
Cesbron, F. et al. Vertical distribution and respiration rates of benthic foraminifera: Contribution to aerobic remineralization in intertidal mudflats covered by Zostera noltei meadows. Estuar. Coast. Shelf Sci. 179, 23–38 (2016).CAS 
Article 

Google Scholar 
Lee, J. J. et al. Nutritional and related experiments on laboratory maintenance of three species of symbiont-bearing, large foraminifera. Mar. Biol. 109, 417–425 (1991).Article 

Google Scholar 
Yanko, V., Arnold, A. J. & Parker, W. C. Effects of marine pollution on benthic Foraminifera. In Modern Foraminifera 217–235 (Springer Netherlands, 1999). https://doi.org/10.1007/0-306-48104-9_13.Polovodova Asteman, I. & Schönfeld, J. Foraminiferal test abnormalities in the western Baltic Sea. J. Foraminifer. Res. 38, 318–336 (2008).Article 

Google Scholar 
Boltovskoy, E. & Wright, R. The test. In Recent Foraminifera (eds. Boltovskoy, E. & Wright, R.) 51–93 (Springer Netherlands, 1976). https://doi.org/10.1007/978-94-017-2860-7_3.Kaczmarek, K. et al. Boron incorporation in the foraminifer Amphistegina lessonii under a decoupled carbonate chemistry. Biogeosciences 12, 1753–1763 (2015).ADS 
Article 

Google Scholar 
Allen, K. et al. Controls on boron incorporation in cultured tests of the planktic foraminifer Orbulina universa. Earth Planet. Sci. Lett. 309, 291–301 (2011).ADS 
CAS 
Article 

Google Scholar 
Allen, K., Hönisch, B., Eggins, S. & Rosenthal, Y. Environmental controls on B/Ca in calcite tests of the tropical planktic foraminifer species Globigerinoides ruber and Globigerinoides sacculifer. Earth Planet. Sci. Lett. s351–352, 270–280 (2012).ADS 
Article 

Google Scholar 
Howes, E. L. et al. Decoupled carbonate chemistry controls on the incorporation of boron into Orbulina universa. Biogeosciences 14, 415–430 (2017).ADS 
CAS 
Article 

Google Scholar 
Lea, D. W. Trace elements in foraminiferal calcite. In Modern Foraminifera 259–277 (Springer Netherlands, 2003).Quigg, A. Micronutrients. In The Physiology of Microalgae (eds. Borowitzka, M. A., Beardall, J. & Raven, J. A.) 211–231 (Springer International Publishing, 2016). https://doi.org/10.1007/978-3-319-24945-2_10.Jennings, D. Culturing Benthic Foraminifera to Understand the Effects of Changing Seawater Chemistry and Temperature on Foraminiferal Shell Chemistry. (2015).Van Dijk, I., De Nooijer, L. J., Barras, C. & Reichart, G.-J. Mn Incorporation in large benthic foraminifera: Differences between species and the impact of pCO2. Front. Earth Sci. https://doi.org/10.3389/feart.2020.567701 (2020).Article 

Google Scholar 
Raitzsch, M., Dueñas-Bohórquez, A., Reichart, G.-J., de Nooijer, L. J. & Bickert, T. Incorporation of Mg and Sr in calcite of cultured benthic foraminifera: Impact of calcium concentration and associated calcite saturation state. Biogeosciences 7, 869–881 (2010).ADS 
CAS 
Article 

Google Scholar 
Holzmann, M., Hohenegger, J., Hallock, P., Piller, W. E. & Pawlowski, J. Molecular phylogeny of large miliolid foraminifera (Soritacea Ehrenberg 1839). Mar. Micropaleontol. 43, 57–74 (2001).ADS 
Article 

Google Scholar 
Hottinger, L., Halicz, E. & Reiss, Z. Recent Foraminiferida from the Gulf of Aqaba, Red Sea. vol. 33 (Slovenska Akademija Znanosti in Umetnosti, Dela Opera, Classis IV: Historia Naturalis, 1993).Langer, M., Makled, W., Pietsch, S. & Weinmann, A. Asynchronous calcification in juvenile megalospheres: An ontogenetic window into the life cycle and polymorphism of Peneroplis. J. Foraminifer. Res. 39, 8–14 (2009).Article 

Google Scholar 
Dissard, D., Nehrke, G., Reichart, G.-J. & Bijma, J. The impact of salinity on the Mg/Ca and Sr/Ca ratio in the benthic foraminifera Ammonia tepida: Results from culture experiments. Geochim. Chosmocimica Acta 74, 928–940 (2010).ADS 
CAS 
Article 

Google Scholar 
Schiebel, R. & Hemleben, C. Planktic Foraminifers in the Modern Ocean. (Springer, 2017).Culberson, C. H., Pytkowicz, R. M. & Hawley, J. E. Seawater alkalinity determination by the pH method. J. Mar. Res. 28, 15–21 (1970).CAS 

Google Scholar 
Dickson, A. G. & Goyet, C. DOE. Handbook of Methods for the Analysis of the Various Parameters of the Carbon Dioxide System in Sea Water, Version 2. (eds., ORNL/CDIAC-74., 1994).Suga, H., Sakai, S., Toyofuku, T. & Ohkouchi, N. A simplified method for determination of total alkalinity in seawater based on the small sample one-point titration method. JAMSTEC Rep. Res. Dev. 17, 23–33 (2013).Article 

Google Scholar 
Robbins, L. L., Hansen, M. E., Kleypas, J. A. & Meylan, S. C. CO2calc: A User-Friendly Seawater Carbon Calculator for Windows, Mac OS X, and iOS (iPhone): U.S. Geological Survey Open-File Report 2010–1280. 17 (2010).Lueker, T. J., Dickson, A. G. & Keeling, C. D. Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: Validation based on laboratory measurements of CO2 in gas and seawater at equilibrium. Mar. Chem. 70, 105–119 (2000).CAS 
Article 

Google Scholar 
Uppström, L. R. The boron/chlorinity ratio of deep-sea water from the Pacific Ocean. Deep Sea Res. Oceanogr. Abstr. 21, 161–162 (1974).ADS 
Article 

Google Scholar 
Orr, J. C., Epitalon, J.-M. & Gattuso, J.-P. Comparison of ten packages that compute ocean carbonate chemistry. Biogeosciences 12, 1483–1510 (2015).ADS 
Article 

Google Scholar 
Fontanier, C. et al. Living (stained) deep-sea foraminifera from the Sea of Marmara: A preliminary study. Deep Sea Res. Part II Top. Stud. Oceanogr. 153, 61 (2018).ADS 
CAS 
Article 

Google Scholar 
Gaffey, S. & Bronnimann, C. Effects of bleaching on organic and mineral phases in biogenic carbonates. J. Sediment. Res. 63, 752–754 (1993).ADS 
Article 

Google Scholar 
Jochum, K. P. et al. Determination of reference values for NIST SRM 610–617 glasses following ISO guidelines. Geostand. Geoanal. Res. 35, 397–429 (2011).CAS 
Article 

Google Scholar  More

Aune, J. B. & Lal, R. Agricultural productivity in the tropics and critical limits of properties of Oxisols, Ultisols, Alfisols. Trop. Agric. (Trinidad and Tobago) 74, 96–103 (1997).
Google Scholar 
Bauer, A. & Black, A. L. Quantification of the effect of soil organic matter content on soil productivity. Soil Sci. Soc. Am. J. 58, 185–193 (1994).ADS 
Article 

Google Scholar 
Hamamoto, T., Chirwa, M., Nyambe, I. & Uchida, Y. Small-scale variability in the soil microbial community structure in a semideveloped farm in Zambia. Appl. Environ. Soil Sci. 2018, 1–6 (2018).Article 

Google Scholar 
Mapanda, F., Wuta, M., Nyamangara, J. & Rees, R. M. Effects of organic and mineral fertilizer nitrogen on greenhouse gas emissions and plant-captured carbon under maize cropping in Zimbabwe. Plant Soil 343, 67–81 (2011).CAS 
Article 

Google Scholar 
Lal, R. Soil carbon sequestration impacts on global climate change and food security. Science 304, 1623–1627 (2004).ADS 
CAS 
Article 

Google Scholar 
Swanepoel, C. M., van der Laan, M., Weepener, H. L., du Preez, C. C. & Annandale, J. G. Review and meta-analysis of organic matter in cultivated soils in southern Africa. Nutr. Cycl. Agroecosyst. 104, 107–123 (2016).CAS 
Article 

Google Scholar 
Zingore, S., Manyame, C., Nyamugafata, P. & Giller, K. E. Long-term changes in organic matter of woodland soils cleared for arable cropping in Zimbabwe. Eur. J. Soil Sci. 56, 727–736 (2005).CAS 

Google Scholar 
Sakala, W. D., Cadisch, G. & Giller, K. E. Interactions between residues of maize and pigeonpea and mineral N fertilizers during decomposition and N mineralization. Soil Biol. Biochem. 32, 679–688 (2000).CAS 
Article 

Google Scholar 
Lal, R. & Stewart, B. A. (eds) Food security and soil quality (CRC Press, 2010).
Google Scholar 
Aparna, K., Pasha, M. A., Rao, D. L. N. & Krishnaraj, P. U. Organic amendments as ecosystem engineers: microbial, biochemical and genomic evidence of soil health improvement in a tropical arid zone field site. Ecol. Eng. 71, 268–277 (2014).Article 

Google Scholar 
Dhull, S., Goyal, S., Kapoor, K. & Mundra, M. Microbial biomass carbon and microbial activities of soils receiving chemical fertilizers and organic amendments. Arch. Agron. Soil Sci. 50, 641–647 (2004).CAS 
Article 

Google Scholar 
Zhong, W. et al. The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 326, 511–522 (2010).CAS 
Article 

Google Scholar 
Janssen, B. H. Simple models and concepts as tools for the study of sustained soil productivity in long-term experiments. I. New soil organic matter and residual effect of P from fertilizers and farmyard manure in Kabete, Kenya. Plant Soil 339, 3–16 (2011).CAS 
Article 

Google Scholar 
Ge, G. et al. Soil biological activity and their seasonal variations in response to long-term application of organic and inorganic fertilizers. Plant Soil 326, 31 (2010).CAS 
Article 

Google Scholar 
Crowther, T. W. et al. The global soil community and its influence on biogeochemistry. Science 365, 6455 (2019).Article 

Google Scholar 
Grunwald, D., Kaiser, M. & Ludwig, B. Effect of biochar and organic fertilizers on C mineralization and macro-aggregate dynamics under different incubation temperatures. Soil Tillage Res. 164, 11–17 (2016).Article 

Google Scholar 
Schleuss, P.-M. et al. Stoichiometric controls of soil carbon and nitrogen cycling after long-term nitrogen and phosphorus addition in a mesic grassland in South Africa. Soil Biol. Biochem. 135, 294–303 (2019).CAS 
Article 

Google Scholar 
de Vries, F. T., Hoffland, E., van Eekeren, N., Brussaard, L. & Bloem, J. Fungal/bacterial ratios in grasslands with contrasting nitrogen management. Soil Biol. Biochem. 38, 2092–2103 (2006).Article 

Google Scholar 
Francioli, D. et al. Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front. Microbiol. 7, (2016).Fan, F. et al. Probing potential microbial coupling of carbon and nitrogen cycling during decomposition of maize residue by 13C-DNA-SIP. Soil Biol. Biochem. 70, 12–21 (2014).CAS 
Article 

Google Scholar 
Guo, Z., Han, J., Li, J., Xu, Y. & Wang, X. Effects of long-term fertilization on soil organic carbon mineralization and microbial community structure. PLoS ONE 14, e0211163 (2019).CAS 
Article 

Google Scholar 
Kihara, J. et al. Soil aggregation and total diversity of bacteria and fungi in various tillage systems of sub-humid and semi-arid Kenya. Appl. Soil Ecol. 58, 12–20 (2012).Article 

Google Scholar 
Sugihara, S., Funakawa, S., Kilasara, M. & Kosaki, T. Effects of land management on CO2 flux and soil C stock in two Tanzanian croplands with contrasting soil texture. Soil Biol. Biochem. 46, 1–9 (2012).CAS 
Article 

Google Scholar 
Ouédraogo, E., Brussaard, L. & Stroosnijder, L. Soil fauna and organic amendment interactions affect soil carbon and crop performance in semi-arid West Africa. Biol Fertil Soils 44, 343–351 (2007).Article 

Google Scholar 
Ouédraogo, E., Mando, A. & Brussaard, L. Soil macrofaunal-mediated organic resource disappearance in semi-arid West Africa. Appl. Soil Ecol. 27, 259–267 (2004).Article 

Google Scholar 
Powlson, D. S., Hirsch, P. R. & Brookes, P. C. The role of soil microorganisms in soil organic matter conservation in the tropics. Nutr. Cycl. Agroecosyst. 61, 41–51 (2001).Article 

Google Scholar 
Gentile, R., Vanlauwe, B., Kavoo, A., Chivenge, P. & Six, J. Residue quality and N fertilizer do not influence aggregate stabilization of C and N in two tropical soils with contrasting texture. Nutr. Cycl. Agroecosyst. 88, 121–131 (2010).CAS 
Article 

Google Scholar 
Amato, M. & Ladd, J. N. Decomposition of 14C-labelled glucose and legume material in soils: Properties influencing the accumulation of organic residue C and microbial biomass C. Soil Biol. Biochem. 24, 455–464 (1992).CAS 
Article 

Google Scholar 
Spain, A. V. Influence of environmental conditions and some soil chemical properties on the carbon and nitrogen contents of some tropical Australian rainforest soils. Soil Res. 28, 825–839 (1990).CAS 
Article 

Google Scholar 
Schimel, D. S., Coleman, D. C. & Horton, K. A. Soil organic matter dynamics in paired rangeland and cropland toposequences in North Dakota. Geoderma 36, 201–214 (1985).ADS 
Article 

Google Scholar 
Schimel, D., Stillwell, M. A. & Woodmansee, R. G. Biogeochemistry of C, N, and P in a soil catena of the shortgrass steppe. Ecology 66, 276–282 (1985).CAS 
Article 

Google Scholar 
Macharia, J. M. et al. Soil greenhouse gas fluxes from maize production under different soil fertility management practices in East Africa. J. Geophys. Res. Biogeosci. 125, e2019JG005427 (2020).Ortiz-Gonzalo, D. et al. Multi-scale measurements show limited soil greenhouse gas emissions in Kenyan smallholder coffee-dairy systems. Sci. Total Environ. 626, 328–339 (2018).ADS 
CAS 
Article 

Google Scholar 
De la Cruz-Barrón, M. et al. The bacterial community structure and dynamics of carbon and nitrogen when maize (Zea mays L.) and its neutral detergent fibre were added to soil from zimbabwe with contrasting management practices. Microb. Ecol. 73, 135–152 (2017).Article 

Google Scholar 
Wood, S. A. et al. Agricultural intensification and the functional capacity of soil microbes on smallholder African farms. J. Appl. Ecol. 52, 744–752 (2015).CAS 
Article 

Google Scholar 
Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).ADS 
CAS 
Article 

Google Scholar 
Wagg, C., Dudenhöffer, J.-H., Widmer, F. & van der Heijden, M. G. A. Linking diversity, synchrony and stability in soil microbial communities. Funct. Ecol. 32, 1280–1292 (2018).Article 

Google Scholar 
Nannipieri, P. et al. Microbial diversity and soil functions. Eur. J. Soil Sci. 54, 655–670 (2003).Article 

Google Scholar 
Liu, B. et al. Microbial metabolic efficiency and community stability in high and low fertility soils following wheat residue addition. Appl. Soil Ecol. 159, 103848 (2021).Article 

Google Scholar 
Hamamoto, T., Uchida, Y., von Rein, I. & Mukumbuta, I. Effects of short-term freezing on nitrous oxide emissions and enzyme activities in a grazed pasture soil after bovine-urine application. Sci. Total Environ. 740, 140006 (2020).ADS 
CAS 
Article 

Google Scholar 
Thomsen, I. K., Schjønning, P., Jensen, B., Kristensen, K. & Christensen, B. T. Turnover of organic matter in differently textured soils: II. Microbial activity as influenced by soil water regimes. Geoderma 89, 199–218 (1999).ADS 
Article 

Google Scholar 
Rughöft, S. et al. Community composition and abundance of bacterial, archaeal and nitrifying populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa. Front. Microbiol. 7, 1638 (2016).
Google Scholar 
Xue, L. et al. Long term effects of management practice intensification on soil microbial community structure and co-occurrence network in a non-timber plantation. For. Ecol. Manag. 459, 117805 (2020).Article 

Google Scholar 
Naether, A. et al. Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest Soils. Appl. Environ. Microbiol. 78, 7398–7406 (2012).ADS 
CAS 
Article 

Google Scholar 
Fierer, N. et al. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342, 621–624 (2013).ADS 
CAS 
Article 

Google Scholar 
Fierer, N., Allen, A. S., Schimel, J. P. & Holden, P. A. Controls on microbial CO2 production: a comparison of surface and subsurface soil horizons. Glob. Change Biol. 9, 1322–1332 (2003).ADS 
Article 

Google Scholar 
Bergmann, G. T. et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol. Biochem. 43, 1450–1455 (2011).CAS 
Article 

Google Scholar 
Moreno-Espíndola, I. P. et al. The bacterial community structure and microbial activity in a traditional organic milpa farming system under different soil moisture conditions. Front. Microbiol. 9, 2737 (2018).Article 

Google Scholar 
Steven, B. et al. Resistance, resilience, and recovery of dryland soil bacterial communities across multiple disturbances. Front. Microbiol. 12, (2021).Elliott, E. T., Anderson, R. V., Coleman, D. C. & Cole, C. V. Habitable pore space and microbial trophic interactions. Oikos 35, 327–335 (1980).Article 

Google Scholar 
Bushby, H. V. A. & Marshall, K. C. Water status of rhizobia in relation to their susceptibility to desiccation and to their protection by montmorillonite. Microbiology 99, 19–27 (1977).
Google Scholar 
Bitton, G., Henis, Y. & Lahav, N. Influence of clay minerals, humic acid and bacterial capsular polysaccharide on the survival of Klebsiella aerogenes exposed to drying and heating in soils. Plant Soil 45, 65–74 (1976).Article 

Google Scholar 
Bastida, F. et al. Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes. ISME J. 15, 1–11 (2021).Article 

Google Scholar 
Hernandez, D. J., David, A. S., Menges, E. S., Searcy, C. A. & Afkhami, M. E. Environmental stress destabilizes microbial networks. ISME J. 15, 1–13 (2021).Article 

Google Scholar 
Jones, A. et al. (eds) Soil Atlas of Africa (European Commission. Publication Office of the European Union, 2013).
Google Scholar 
Mehlich, A. Mehlich 3 soil test extractant: a modification of Mehlich 2 extractant. Commun. Soil Sci. Plant Anal. 15, 1409–1416 (1984).CAS 
Article 

Google Scholar 
Hadas, A., Kautsky, L., Goek, M. & Erman Kara, E. Rates of decomposition of plant residues and available nitrogen in soil, related to residue composition through simulation of carbon and nitrogen turnover. Soil Biol. Biochem. 36, 255–266 (2004).CAS 
Article 

Google Scholar 
Sagova-Mareckova, M. et al. Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl. Environ. Microbiol. 74, 2902–2907 (2008).ADS 
CAS 
Article 

Google Scholar 
Miller, D. N., Bryant, J. E., Madsen, E. L. & Ghiorse, W. C. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65, 4715–4724 (1999).ADS 
CAS 
Article 

Google Scholar 
Schroeder, J., Kammann, L., Helfrich, M., Tebbe, C. C. & Poeplau, C. Impact of common sample pre-treatments on key soil microbial properties. Soil Biol. Biochem. 160, 108321 (2021).CAS 
Article 

Google Scholar 
Wang, F. et al. Air-drying and long time preservation of soil do not significantly impact microbial community composition and structure. Soil Biol. Biochem. 157, 108238 (2021).CAS 
Article 

Google Scholar 
Sirois, S. H. & Buckley, D. H. Factors governing extracellular DNA degradation dynamics in soil. Environ. Microbiol. Rep. 11, 173–184 (2019).CAS 
Article 

Google Scholar 
Carini, P. et al. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat. Microbiol. 2, 1–6 (2016).
Google Scholar 
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).CAS 
Article 

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

Google Scholar 
Mickan, B. S. et al. Soil disturbance and water stress interact to influence arbuscular mycorrhizal fungi, rhizosphere bacteria and potential for N and C cycling in an agricultural soil. Biol. Fertil. Soils 55, 53–66 (2019).CAS 
Article 

Google Scholar 
Lehman, C. L. & Tilman, D. Biodiversity, stability, and productivity in competitive communities. Am. Nat. 156, 534–552 (2000).Article 

Google Scholar  More

Fischer, R. et al. Accelerated forest fragmentation leads to critical increase in tropical forest edge area. Sci. Adv. 7, eabg7012 (2021).ADS 
CAS 
Article 

Google Scholar 
Newmark, W. D. & McNeally, P. B. Impact of habitat fragmentation on the spatial structure of the Eastern Arc forests in East Africa: Implications for biodiversity conservation. Biodivers. Conserv. 27, 1387–1402 (2018).Article 

Google Scholar 
Hall, J., Burgess, N. D., Lovett, J., Mbilinyi, B. & Gereau, R. E. Conservation implications of deforestation across an elevational gradient in the Eastern Arc Mountains, Tanzania. Biol. Conserv. 142, 2510–2521 (2009).Article 

Google Scholar 
Kuussaari, M. et al. Extinction debt: A challenge for biodiversity conservation. Trends Ecol. Evol. 24, 564–571 (2009).Article 

Google Scholar 
Gibson, L. et al. Near-complete extinction of native small mammal fauna 25 years after forest fragmentation. Science 341, 1508–1510 (2013).ADS 
CAS 
Article 

Google Scholar 
Burgess, N. D. et al. The biological importance of the Eastern Arc Mountains of Tanzania and Kenya. Biol. Conserv. 134, 209–231 (2007).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).ADS 
CAS 
Article 

Google Scholar 
Oates, J. F. et al. A new species of tree hyrax (Procaviidae: Dendrohyrax) from West Africa and the significance of the Niger-Volta interfluvium in mammalian biogeography. Zool. J. Linn. Soc. 194, 527–552 (2022).Article 

Google Scholar 
Bloomer, P. Extant hyrax diversity is vastly underestimated. Afrotherian. Conserv. 7, 11–16 (2009).
Google Scholar 
Roberts, D., Topp-Jørgensen, E. & Moyer, D. C. Dendrohyrax validus Eastern Tree Hyrax. In Mammals of Africa Vol. I (eds Kingdon, J. et al.) 158–161 (Bloomsbury, 2013).
Google Scholar 
Hoeck, H. Some thoughts on the distribution of the tree hyraxes (genus Dendrohyrax) in northern Tanzania. Afrotherian Conserv. 13, 47–49 (2017).
Google Scholar 
Rosti, H., Pihlström, H., Bearder, S., Pellikka, P. & Rikkinen, J. Vocalization analyses of nocturnal arboreal mammals of the Taita Hills, Kenya. Diversity 12, 473 (2020).Article 

Google Scholar 
Roberts, D. Geographic variation in the loud calls of tree hyrax – Dendrohyrax validus (True 1890) In the Eastern Arc Mountains, East Africa: taxonomic and conservation implications. (MSc thesis, University of Reading, 2001).True, F. W. Description of two new species of mammals from Mt. Kilima-Njaro, East Africa. Proc. US Nat. Mus. 13, 227–229 (1890).Article 

Google Scholar 
True, F. W. An annotated catalogue of the mammals collected by Dr. W. L. Abbott in the Kilma-Njaro region, East Africa. Proc. U. S. Nat. Mus. 15, 445–480 (1892).Article 

Google Scholar 
Kundaeli, J. N. Distribution of tree hyrax (Dendrohyrax validus validus True) on Mt Kilimanjaro, Tanzania. Afr. J. Ecol. 14, 253–264 (1976).Article 

Google Scholar 
Gaylard, A. & Kerley, G. I. H. Diet of tree hyraxes Dendrohyrax arboreus (Hyracoidea: Procaviidae) in the Eastern Cape, South Africa. J. Mammal. 78, 213–221 (1997).Article 

Google Scholar 
Milner, J. Relationships between the forest dwelling people of south-west Mau and tree hyrax, Dendrohyrax arboreus. J. East Afr. Nat. Hist. 83, 17–29 (1994).Article 

Google Scholar 
Milner, J. M. & Harris, S. Habitat use and ranging behaviour of tree hyrax, Dendrohyrax arboreus, in the Virunga Volcanoes, Rwanda. Afr. J. Ecol. 37, 281–294 (1999).Article 

Google Scholar 
Gaylard, A. & Kerley, G. I. H. Habitat assessment for a rare, arboreal forest mammal, the tree hyrax (Dendrohyrax arboreus). Afr. J. Ecol. 39, 205–212 (2001).Article 

Google Scholar 
Djossa, B., Zachee, B. & Sinzin, B. Activity patterns and habitat use of the western tree hyrax (Dendrohyrax dorsalis), within forest patches and implications for conservation. Ecotropica 18, 65–72 (2012).
Google Scholar 
Opperman, E. J., Cherry, M. I. & Makunga, N. P. Community harvesting of trees used as dens and for food by the tree hyrax (Dendrohyrax arboreus) in the Pirie forest, South Africa. Koedoe 60, a1481 (2018).
Cordeiro, N. J. et al. Notes on the ecology and status of some forest mammals in four Eastern Arc Mountains, Tanzania. J. East Afr. Nat. Hist. 94, 175–189 (2005).Article 

Google Scholar 
Koren, L. Vocalization as an indicator of individual quality in the rock hyrax. (PhD thesis, Tel-Aviv University, 2006).Koren, L., Mokady, O. & Geffen, E. Social status and cortisol levels in singing rock hyraxes. Horm. Behav. 54, 212–216 (2008).CAS 
Article 

Google Scholar 
Koren, L. & Geffen, E. Complex call in male rock hyrax (Procavia capensis): A multi-information distributing channel. Behav. Ecol. Sociobiol. 63, 581–590 (2009).Article 

Google Scholar 
Lawes, M. J., Mealin, P. E. & Piper, S. E. Patch occupancy and potential metapopulation dynamics of three forest mammals in fragmented Afromontane forest in South Africa. Conserv. Biol. 14, 1088–1098 (2000).Article 

Google Scholar 
Topp-Jørgensen, J. E., Marshal, A. R., Brink, H. & Pedersen, U. B. Quantifying the response of tree hyraxes (Dendrohyrax validus) to human disturbance in the Udzungwa Mountains, Tanzania. Trop. Conserv. Sci. 1, 63–74 (2008).Article 

Google Scholar 
Hill, A. P. et al. AudioMoth: Evaluation of a smart open acoustic device for monitoring biodiversity and the environment. Methods Ecol. Evol. 9, 1199–1211 (2018).Article 

Google Scholar 
Marques, T. A. et al. Estimating animal population density using passive acoustics. Biol. Rev. 88, 287–309 (2013).Article 

Google Scholar 
Pérez-Granados, C. & Traba, J. Estimating bird density using passive acoustic monitoring: A review of methods and suggestions for further research. Ibis 163, 765–783 (2021).Article 

Google Scholar 
Campos-Cerqueira, M. & Aide, T. M. Improving distribution data of threatened species by combining acoustic monitoring and occupancy modelling. Methods Ecol. Evol. 7, 1340–1348 (2016).Article 

Google Scholar 
McLean, K. A. et al. Movement patterns of three arboreal primates in a Neotropical moist forest explained by LiDAR-estimated canopy structure. Landsc. Ecol. 31, 1849–1862 (2016).Article 

Google Scholar 
Davies, A. B., Ancrenaz, M., Oram, F. & Asner, G. P. Canopy structure drives orangutan habitat selection in disturbed Bornean forests. Proc. Natl. Acad. Sci. USA 114, 8307–8312 (2017).CAS 
Article 

Google Scholar 
Singh, M., Cheyne, S. M. & Ehlers Smith, D. A. How conspecific primates use their habitats: Surviving in an anthropogenically-disturbed forest in Central Kalimantan, Indonesia. Ecol. Indic. 87, 167–177 (2018).Article 

Google Scholar 
Simonson, W. D., Allen, H. D. & Coomes, D. A. Applications of airborne lidar for the assessment of animal species diversity. Methods Ecol. Evol. 5, 719–729 (2014).Article 

Google Scholar 
Aerts, R. et al. Woody plant communities of isolated Afromontane cloud forests in Taita Hills, Kenya. Plant Ecol. 212, 639–649 (2011).Article 

Google Scholar 
Lovett, J. C., Wasser, S. K., Cambridge University Press. Biogeography and Ecology of the Rain Forests of Eastern Africa (Cambridge University Press, 2008).
Google Scholar 
Pellikka, P. K. E., Lötjönen, M., Siljander, M. & Lens, L. Airborne remote sensing of spatiotemporal change (1955–2004) in indigenous and exotic forest cover in the Taita Hills, Kenya. Int. J. Appl. Earth Obs. Geoinf. 11, 221–232 (2009).ADS 
Article 

Google Scholar 
Rovero, F. et al. Targeted vertebrate surveys enhance the faunal importance and improve explanatory models within the Eastern Arc Mountains of Kenya and Tanzania. Diversity Distrib. 20, 1438–1449 (2014).Article 

Google Scholar 
Rosti, H., Rikkinen, J., Pellikka, P., Bearder, S. & Mwamodenyi, J. M. Taita Mountain dwarf galago is extant in the Taita Hills of Kenya. Oryx 54, 152–153 (2020).Article 

Google Scholar 
Pihlström, H., Rosti, H., Lombo, B. & Pellikka, P. Domestic dog predation on white-tailed small-eared galago (Otolemur garnettii lasiotis) in the Taita Hills, Kenya. Afr. Primates 15, 31–38 (2021).
Google Scholar 
Etana, B. et al. Traditional shade coffee forest systems act as refuges for medium- and large-sized mammals as natural forest dwindles in Ethiopia. Biol. Conserv. 260, 109219 (2021).Article 

Google Scholar 
Hoeck, H., Rovero, F., Cordeiro, N., Butynski, T., Perkin, A. & Jones, T. Dendrohyrax validus. The IUCN Red List of Threatened Species (2015: e.T136599A21288090).Himberg, N. Traditionally protected forests’ role within transforming natural resource management regimes in Taita Hills, Kenya. (PhD thesis, University of Helsinki, 2011).Thijs, K. W., Roelen, I. & Musila, W. M. Field guide to the woody plants of Taita Hills, Kenya. J. East Afr. Nat. Hist. 102, 1–272 (2014).Article 

Google Scholar 
Yéboué, K. Y. et al. Genetic typing and in silico assignment of smoked and fresh bushmeat sold on markets and restaurants in west-central Côte d’Ivoire. Int. J. Genet. Mol. Biol. 13, 1–8 (2021).Article 

Google Scholar 
Brown, K. J. & Downs, C. T. Seasonal behavioural patterns of free-living rock hyrax (Procavia capensis). J. Zool. 265, 311–326 (2005).Article 

Google Scholar 
Brown, K. J. & Downs, C. T. Seasonal patterns in body temperature of free-living rock hyrax (Procavia capensis). Comp. Biochem. Physiol. Part A Mol. Integr. Physiol. 143, 42–49 (2006).Article 

Google Scholar 
Ilany, A., Barocas, A., Kam, M., Ilany, T. & Geffen, E. The energy cost of singing in wild rock hyrax males: Evidence for an index signal. Anim. Behav. 85, 995–1001 (2013).Article 

Google Scholar 
Demartsev, V. et al. Male hyraxes increase song complexity and duration in the presence of alert individuals. Behav. Ecol. 25, 1451–1458 (2014).Article 

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

Google Scholar 
Adhikari, H. et al. Determinants of aboveground biomass across an Afromontane landscape mosaic in Kenya. Remote Sens. 9, 827 (2017).ADS 
Article 

Google Scholar 
Heiskanen, J., Korhonen, L., Hietanen, J. & Pellikka, P. K. E. Use of airborne lidar for estimating canopy gap fraction and leaf area index of tropical montane forests. Int. J. Remote Sens. 36, 2569–2583 (2015).Article 

Google Scholar 
Roussel, J.-R. et al. lidR: An R package for analysis of Airborne Laser Scanning (ALS) data. Remote Sens. Environ. 251, 112061 (2020).ADS 
Article 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).
Google Scholar 
Brooks, M. E. et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J. 9, 378 (2017).Article 

Google Scholar 
Lüdecke, D., Ben-Shachar, M., Patil, I., Waggoner, P. & Makowski, D. Performance: An R package for assessment, comparison and testing of statistical models. JOSS 6, 3139 (2021).ADS 
Article 

Google Scholar 
Wickham, H. Ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).MATH 
Book 

Google Scholar 
Zuur, A. F., Savelʹev, A. A. & Ieno, E. N. Zero Inflated Models and Generalized Linear Mixed Models with R (Highland Statistics, 2012).
Google Scholar 
Campbell, H. The consequences of checking for zero-inflation and overdispersion in the analysis of count data. Methods Ecol. Evol. 12, 665–680 (2021).Article 

Google Scholar 
Zuur, A. F. & Ieno, E. N. A protocol for conducting and presenting results of regression-type analyses. Methods Ecol. Evol. 7, 636–645 (2016).Article 

Google Scholar 
Aho, K., Derryberry, D. & Peterson, T. Model selection for ecologists: The worldviews of AIC and BIC. Ecology 95, 631–636 (2014).Article 

Google Scholar  More

Rothstein, S. I. A model system for coevolution: Avian brood parasitism. Annu. Rev. Ecol. Syst. 21, 481–508 (1990).Article 

Google Scholar 
Feeney, W. E. et al. Brood parasitism and the evolution of cooperative breeding in birds. Science 342, 1506–1508 (2013).ADS 
CAS 
Article 

Google Scholar 
Brooke, M. de L. & Davies, N. B. Egg mimicry by cuckoos Cuculus canorus in relation to discrimination by hosts. Nature 335, 630–632 (1988).ADS 
Article 

Google Scholar 
Medina, I. & Langmore, N. E. The costs of avian brood parasitism explain variation in egg rejection behaviour in hosts. Biol. Let. 11, 20150296 (2015).Article 

Google Scholar 
Langmore, N. E., Hunt, S. & Kilner, R. M. Escalation of a coevolutionary arms race through host rejection of brood parasitic young. Nature 422, 157–160 (2003).ADS 
CAS 
Article 

Google Scholar 
Grim, T. Experimental evidence for chick discrimination without recognition in a brood parasite host. Proc. R. Soc. B: Biol. Sci. 274, 373–381 (2007).Article 

Google Scholar 
Sato, N. J., Tokue, K., Noske, R. A., Mikami, O. K. & Ueda, K. Evicting cuckoo nestlings from the nest: A new anti-parasitism behaviour. Biol. Let. 6, 67–69. https://doi.org/10.1098/rsbl.2009.0540 (2010).Article 

Google Scholar 
Davies, N. & Brooke, M. de L. Cuckoos versus reed warblers: Adaptations and counteradaptations. Anim. Behav. 36, 262–284 (1988).Article 

Google Scholar 
Langmore, N. E. et al. Visual mimicry of host nestlings by cuckoos. Proc. R. Soc. B: Biol. Sci. 278, 2455–2463 (2011).Article 

Google Scholar 
Noh, H.-J., Gloag, R. & Langmore, N. E. True recognition of nestlings by hosts selects for mimetic cuckoo chicks. Proc. R. Soc. B: Bio. Sci. 285, 20180726 (2018).Article 

Google Scholar 
Spottiswoode, C. N. & Stevens, M. Host-parasite arms races and rapid changes in bird egg appearance. Am. Nat. 179, 633–648. https://doi.org/10.1086/665031 (2012).Article 

Google Scholar 
Taylor, C. J. & Langmore, N. E. How do brood-parasitic cuckoos reconcile conflicting environmental and host selection pressures on egg size investment?. Anim. Behav. 168, 89–96. https://doi.org/10.1016/j.anbehav.2020.08.003 (2020).Article 

Google Scholar 
Langmore, N. E., Maurer, G., Adcock, G. J. & Kilner, R. M. Socially acquired host-specific mimicry and the evolution of host races in Horsfield’s bronze-cuckoo Chalcites basalis. Evolution 62, 1689–1699 (2008).Article 

Google Scholar 
Noh, H. J., Jacomb, F., Gloag, R. & Langmore, N. E. Frontline defences against cuckoo parasitism in the large-billed gerygones. Anim. Behav. 174, 51–61. https://doi.org/10.1016/j.anbehav.2021.01.021 (2021).Article 

Google Scholar 
Langmore, N. E. & Kilner, R. M. Why do Horsfield’s bronze-cuckoo Chalcites basalis eggs mimic those of their hosts?. Behav. Ecol. Sociobiol. 63, 1127–1131. https://doi.org/10.1007/s00265-009-0759-9 (2009).Article 

Google Scholar 
Spottiswoode, C. N. & Stevens, M. How to evade a coevolving brood parasite: Egg discrimination versus egg variability as host defences. Proc. R. Soc. B: Biol. Sci. 278, 3566–3573. https://doi.org/10.1098/rspb.2011.0401 (2011).Article 

Google Scholar 
Yang, C., Wang, L., Liang, W. & Møller, A. P. Egg recognition as antiparasitism defence in hosts does not select for laying of matching eggs in parasitic cuckoos. Anim. Behav. 122, 177–181. https://doi.org/10.1016/j.anbehav.2016.10.018 (2016).Article 

Google Scholar 
Stevens, M. Bird brood parasitism. Curr. Biol. 23, R909–R913. https://doi.org/10.1016/j.cub.2013.08.025 (2013).MathSciNet 
CAS 
Article 

Google Scholar 
Feeney, W. E., Troscianko, J., Langmore, N. E. & Spottiswoode, C. N. Evidence for aggressive mimicry in an adult brood parasitic bird, and generalized defences in its host. Proc. R. Soc. B: Biol. Sci. 282, 20150795 (2015).Article 

Google Scholar 
Davies, N. B. & Welbergen, J. A. Cuckoo–hawk mimicry? An experimental test. Proc. R. Soc. B: Biol. Sci. 275, 1817–1822 (2008).CAS 
Article 

Google Scholar 
Brooker, L. C. & Brooker, M. G. Why are cuckoos host specific?. Oikos 57, 301–309. https://doi.org/10.2307/3565958 (1990).Article 

Google Scholar 
Langmore, N. E., Stevens, M., Maurer, G. & Kilner, R. M. Are dark cuckoo eggs cryptic in host nests?. Anim. Behav. 78, 461–468 (2009).Article 

Google Scholar 
Lack, D. L. Ecological Adaptations for Breeding in Birds (Methuen & Co., Ltd., 1968).
Google Scholar 
Spaw, C. D. & Rohwer, S. A comparative study of eggshell thickness in cowbirds and other passerines. The Condor 89, 307–318. https://doi.org/10.2307/1368483 (1987).Article 

Google Scholar 
Igic, B. et al. Alternative mechanisms of increased eggshell hardness of avian brood parasites relative to host species. J. R. Soc. Interface 8, 1654–1664. https://doi.org/10.1098/rsif.2011.0207 (2011).Article 

Google Scholar 
Brooker, M. G. & Brooker, L. C. Eggshell strength in cuckoos and cowbirds. Ibis 133, 406–413. https://doi.org/10.1111/j.1474-919X.1991.tb04589.x (1991).Article 

Google Scholar 
Maurer, G. et al. First light for avian embryos: eggshell thickness and pigmentation mediate variation in development and UV exposure in wild bird eggs. Funct. Ecol. 29, 209–218 (2015).Article 

Google Scholar 
Amos, A. & Rahn, H. Pores in avian eggshells: Gas conductance, gas exchange and embryonic growth rate. Respir. Physiol. 61, 1–20 (1985).Article 

Google Scholar 
Ar, A., Rahn, H. & Paganelli, C. V. The avian egg: Mass and strength. Condor 81, 331–337 (1979).Article 

Google Scholar 
Rahn, H. & Ar, A. Gas-exchange of the avian egg: Time, structure, and function. Am. Zool. 20, 477–484 (1980).Article 

Google Scholar 
Swynnerton, C. Rejections by birds of eggs unlike their own: With remarks on some of the cuckoo problems. Ibis 60, 127–154 (1918).Article 

Google Scholar 
López, A. V., Fiorini, V. D., Ellison, K. & Peer, B. D. Thick eggshells of brood parasitic cowbirds protect their eggs and damage host eggs during laying. Behav. Ecol. 29, 965–973 (2018).Article 

Google Scholar 
Wyllie, I. The Cuckoo (Batsford, 1981).
Google Scholar 
Yang, C. et al. Keeping eggs warm: Thermal and developmental advantages for parasitic cuckoos of laying unusually thick-shelled eggs. Sci. Nat. 105, 10 (2018).Article 

Google Scholar 
Davies, N. B. Cuckoos Cowbirds and other Cheats (T & A D Poyser, 2000).
Google Scholar 
Spottiswoode, C. N. The evolution of host-specific variation in cuckoo eggshell strength. J. Evol. Biol. 23, 1792–1799. https://doi.org/10.1111/j.1420-9101.2010.02010.x (2010).CAS 
Article 

Google Scholar 
Langmore, N. E. et al. The evolution of egg rejection by cuckoo hosts in Australia and Europe. Behav. Ecol. 16, 686–692. https://doi.org/10.1093/beheco/ari041 (2005).Article 

Google Scholar 
Rohwer, S., Spaw, C. D. & Røskaft, E. Costs to northern orioles of puncture-ejecting parasitic cowbird eggs from their nests. The Auk 106, 734–738 (1989).
Google Scholar 
Brooker, M. G., Brooker, L. C. & Rowley, I. Egg deposition by the bronze-cuckoos Chrysococcyx basalis and Chrysococcyx lucidus. Emu 88, 107–109. https://doi.org/10.1071/Mu9880107 (1988).Article 

Google Scholar 
McClelland, S. C. et al. Embryo movement is more frequent in avian brood parasites than birds with parental reproductive strategies. Proc. R. Soc B-Biol. Sci. https://doi.org/10.1098/rspb.2021.1137 (2021).Article 

Google Scholar 
Gosler, A. G. & Wilkin, T. A. Eggshell speckling in a passerine bird reveals chronic long-term decline in soil calcium. Bird Study 64, 195–204. https://doi.org/10.1080/00063657.2017.1314448 (2017).Article 

Google Scholar 
Lundholm, C. E. Inhibition of prostaglandin synthesis in eggshell gland mucosa as a mechanism for P, P’-DDE-induced eggshell thinning in birds: A comparison of ducks and domestic-fowls. Comp. Biochem. Phys. C 106, 389–394. https://doi.org/10.1016/0742-8413(93)90151-A (1993).Article 

Google Scholar 
Bitman, J., Cecil, H. C. & Fries, G. F. DDT-Induced inhibition of avian shell gland carbonic anhydrase: A mechanism for thin eggshells. Science 168, 594–596. https://doi.org/10.1126/science.168.3931.594 (1970).ADS 
CAS 
Article 

Google Scholar 
Ratcliffe, D. A. Changes attributable to pesticides in egg breakage frequency and eggshell thickness in some British birds. J. Appl. Ecol. 7, 67-+. https://doi.org/10.2307/2401613 (1970).Article 

Google Scholar 
Bouwman, H., Govender, D., Underhill, L. & Polder, A. Chlorinated, brominated and fluorinated organic pollutants in African Penguin eggs: 30 years since the previous assessment. Chemosphere 126, 1–10. https://doi.org/10.1016/j.chemosphere.2014.12.071 (2015).ADS 
CAS 
Article 

Google Scholar 
Bleu, J., Agostini, S., Angelier, F. & Biard, C. Experimental increase in temperature affects eggshell thickness, and not egg mass, eggshell spottiness or egg composition in the great tit (Parus major). Gen. Comp. Endocr. 275, 73–81. https://doi.org/10.1016/j.ygcen.2019.02.004 (2019).CAS 
Article 

Google Scholar 
Picman, J. & Pribil, S. Is greater eggshell density an alternative mechanism by which parasitic cuckoos increase the strength of their eggs?. J. Ornithol. 138, 531–541. https://doi.org/10.1007/bf01651384 (1997).Article 

Google Scholar 
Lopez, A. V. et al. How to build a puncture- and breakage-resistant eggshell? Mechanical and structural analyses of avian brood parasites and their hosts. J. Exp. Biol. 224, jeb243016. https://doi.org/10.1242/jeb.243016 (2021).Article 

Google Scholar 
Soler, M., Rodriguez-Navarro, A. B., Perez-Contreras, T., Garcia-Ruiz, J. M. & Soler, J. J. Great spotted cuckoo eggshell microstructure characteristics can make eggs stronger. J. Avian Biol. 50, e02252. https://doi.org/10.1111/jav.02252 (2019).Article 

Google Scholar 
D’Alba, L. et al. Evolution of eggshell structure in relation to nesting ecology in non-avian reptiles. J. Morphol. 282, 1066–1079. https://doi.org/10.1002/jmor.21347 (2021).CAS 
Article 

Google Scholar 
Legendre, L. J. & Clarke, J. A. Shifts in eggshell thickness are related to changes in locomotor ecology in dinosaurs. Evolution 75, 1415–1430. https://doi.org/10.1111/evo.14245 (2021).Article 

Google Scholar 
Le Roy, N., Stapane, L., Gautron, J. & Hincke, M. T. Evolution of the avian eggshell biomineralization protein toolkit: New insights from multi-omics. Front. Genet. 12, 672433. https://doi.org/10.3389/fgene.2021.672433 (2021).CAS 
Article 

Google Scholar 
Medina, I. & Langmore, N. E. Batten down the thatches: Front-line defences in an apparently defenceless cuckoo host. Anim. Behav. 112, 195–201. https://doi.org/10.1016/j.anbehav.2015.12.006 (2016).Article 

Google Scholar 
Starling, M., Heinsohn, R., Cockburn, A. & Langmore, N. E. Cryptic gentes revealed in pallid cuckoos Cuculus pallidus using reflectance spectrophotometry. Proc. R. Soc. Lond. B 273, 1929–1934 (2006).CAS 

Google Scholar 
Abernathy, V. E., Troscianko, J. & Langmore, N. E. Egg mimicry by the Pacific koel: Mimicry of one host facilitates exploitation of other hosts with similar egg types. J. Avian Biol. 48, 1414–1424. https://doi.org/10.1111/jav.01530 (2017).Article 

Google Scholar 
Green, R. E. An evaluation of three indices of eggshell thickness. Ibis 142, 676–679. https://doi.org/10.1111/j.1474-919X.2000.tb04468.x (2000).Article 

Google Scholar 
Green, R. E. Long-term decline in the thickness of eggshells of thrushes, Turdus spp., in Britain. Proc. R. Soc. London. Ser. B: Biol. Sci. 265, 679–684. https://doi.org/10.1098/rspb.1998.0347 (1998).Article 

Google Scholar 
Igic, B. et al. Comparison of micrometer-and scanning electron microscope-based measurements of avian eggshell thickness. J. Field Ornithol. 81, 402–410 (2010).Article 

Google Scholar 
Maurer, G., Portugal, S. J. & Cassey, P. A comparison of indices and measured values of eggshell thickness of different shell regions using museum eggs of 230 European bird species. Ibis 154, 714–724 (2012).Article 

Google Scholar 
Becking, J. The ultrastructure of the avian eggshell. Ibis 117, 143–151 (1975).Article 

Google Scholar 
Birkhead, T. et al. New insights from old eggs–the shape and thickness of Great Auk Pinguinus impennis eggs. Ibis 162(4), 1345–1354 (2020).Article 

Google Scholar 
Riley, A., Sturrock, C., Mooney, S. & Luck, M. Quantification of eggshell microstructure using X-ray micro computed tomography. Br. Poult. Sci. 55, 311–320 (2014).CAS 
Article 

Google Scholar 
Kibala, L., Rozempolska-Rucinska, I., Kasperek, K., Zieba, G. & Lukaszewicz, M. Ultrasonic eggshell thickness measurement for selection of layers. Poult. Sci. 94, 2360–2363. https://doi.org/10.3382/ps/pev254 (2015).Article 

Google Scholar 
Khaliduzzaman, A. et al. A nondestructive eggshell thickness measurement technique using terahertz waves. Sci. Rep. 10, 1–5 (2020).Article 

Google Scholar 
Santolo, G. M. A new nondestructive method for measuring eggshell thickness using a non-ferrous material thickness gauge. Wilson J. Ornithol. 130, 502–509. https://doi.org/10.1676/17-035.1 (2018).Article 

Google Scholar 
Marini, M. A. et al. The five million bird eggs in the world’s museum collections are an invaluable and underused resource. Auk 137, ukaa036. https://doi.org/10.1093/auk/ukaa036 (2020).Article 

Google Scholar 
Brooker, M. G. & Brooker, L. C. Cuckoo hosts in Australia. Aust. Zool. Rev. 2, 1–67 (1989).
Google Scholar 
Higgins, P. J. Vol. Volume 4: Parrots to Dollarbird (Oxford University Press, 1999).
Google Scholar 
Higgins, P. J. & Peter, J. M. Vol. 6: Pardalotes to Shrike-Thrushes (Oxford University Press, 2002).
Google Scholar 
Higgins, P. J., Peter, J. M. & Cowling, S. J. Vol. 4: Parrots to Dollarbird (Oxford University Press, 2006).
Google Scholar 
Higgins, P. J., Peter, J. M. & Steele, W. K. Vol. 5: Tyrant-flycatchers to Chats (Oxford University Press, 2001).
Google Scholar 
Landstrom, M., Heinsohn, R. & Langmore, N. E. Clutch variation and egg rejection in three hosts of the pallid cuckoo Cuculus pallidus. Behaviour 147, 19–36. https://doi.org/10.1163/000579509X12483520922043 (2010).Article 

Google Scholar 
Abernathy, V. E., Johnson, L. E. & Langmore, N. E. An experimental test of defenses against avian brood parasitism in a recent host. Front. Ecol. Evol. 9, 244. https://doi.org/10.3389/fevo.2021.651733 (2021).Article 

Google Scholar 
Landstrom, M. T., Heinsohn, R. & Langmore, N. E. Does clutch variability differ between populations of cuckoo hosts in relation to the rate of parasitism?. Anim. Behav. 81, 307–312 (2011).Article 

Google Scholar 
Peterson, S. H. et al. Avian eggshell thickness in relation to egg morphometrics, embryonic development, and mercury contamination. Ecol. Evol. 10, 8715–8740. https://doi.org/10.1002/ece3.6570 (2020).Article 

Google Scholar 
Attard, M., Medina, I., Langmore, N. E. & Sherratt, E. Egg shape mimicry in parasitic cuckoos. J. Evol. Biol. 30, 2079–2084 (2017).CAS 
Article 

Google Scholar 
Birchard, G. F. & Deeming, D. C. Avian eggshell thickness: Scaling and maximum body mass in birds. J. Zool. 279, 95–101. https://doi.org/10.1111/j.1469-7998.2009.00596.x (2009).Article 

Google Scholar 
Orme, D. et al. The caper package: Comparative analysis of phylogenetics and evolution in R. R Packag. Vers. 5, 549–593 (2013).
Google Scholar 
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444–448. https://doi.org/10.1038/nature11631 (2012).ADS 
CAS 
Article 

Google Scholar 
Schliep, K. P. Phangorn: Phylogenetic analysis in R. Bioinformatics 27, 592–593. https://doi.org/10.1093/bioinformatics/btq706 (2011).CAS 
Article 

Google Scholar 
R Core Team. R: A language and environment for statistical computing, (2013). More

Desbruyères, D., Segonzac, M. & Bright, M. Handbook of deep-Sea Hydrothermal Vent Fauna 2nd edn. (Biologiezentrum, 2006).
Google Scholar 
Van Dover, C. L. The Ecology of Deep-Sea Hydrothermal Vents (Princeton University Press, 2000).Book 

Google Scholar 
Tarasov, V. G., Gebruk, A. V., Mironov, A. N. & Moskalev, L. I. Deep-sea and upper sublittoral hydrothermal vent communities: Two different phenomena?. Chem. Geol. 224, 5–39. https://doi.org/10.1016/j.chemgeo.2005.07.021 (2005).ADS 
CAS 
Article 

Google Scholar 
Lonsdale, P. Clustering of suspension-feeding macrobenthos near abyssal hydrothermal vents at oceanic spreading centers. Deep Sea Res. 24, 857–863. https://doi.org/10.1016/0146-6291(77)90478-7 (1977).ADS 
Article 

Google Scholar 
Reid, W. D. et al. Spatial differences in East Scotia Ridge hydrothermal vent food webs: Influences of chemistry, microbiology and predation on trophodynamics. PLoS One 8, e65553. https://doi.org/10.1371/journal.pone.006555 (2013).ADS 
CAS 
Article 

Google Scholar 
Levin, L. A. et al. Hydrothermal vents and methane seeps: Rethinking the sphere of influence. Front. Mar. Sci. 3, 72. https://doi.org/10.3389/fmars.2016.00072 (2016).ADS 
Article 

Google Scholar 
Mullineaux, L. S. et al. Exploring the ecology of deep-sea hydrothermal vents in a metacommunity framework. Front. Mar. Sci. 5, 49. https://doi.org/10.3389/fmars.2018.00049 (2018).Article 

Google Scholar 
Tarasov, V. G. Effects of shallow-water hydrothermal venting on biological communities of coastal marine ecosystems of the western Pacific. Adv. Mar. Biol. 50, 267–421. https://doi.org/10.1016/S0065-2881(05)50004-X (2006).CAS 
Article 

Google Scholar 
Dando, P. R. Biological communities at marine shallow-water vent and seep sites. In The Vent and Seep Biota (ed. Kiel, S.) 333–378 (Springer, 2010).Chapter 

Google Scholar 
Couto, R. P., Rodriguesa, A. S. & Neto, A. I. Shallow-water hydrothermal vents in the Azores (Portugal). J. Integr. Coast. Zone Manage. 15, 495–505. https://doi.org/10.5894/rgci584 (2015).Article 

Google Scholar 
Bellec, L. et al. Microbial communities of the shallow-water hydrothermal vent near Naples, Italy, and chemosynthetic symbionts associated with a free-living marine nematode. Front. Microbiol. 11, 2023. https://doi.org/10.3389/fmicb.2020.02023 (2020).Article 

Google Scholar 
Chan, B. K. K. et al. Community structure of macrobiota and environmental parameters in shallow water hydrothermal vents off Kueishan Island, Taiwan. PLoS One 11, e0148675. https://doi.org/10.1371/journal.pone.0148675 (2016).CAS 
Article 

Google Scholar 
Donnarumma, L. et al. Environmental and benthic community patterns of the shallow hydrothermal area of Secca Delle Fumose (Baia, Naples, Italy). Front. Mar. Sci. 6, 685. https://doi.org/10.3389/fmars.2019.00685 (2019).Article 

Google Scholar 
Southward, A. J. et al. On the biology of submarine caves with sulphur springs: Appraisal of 13C/12C ratios as a guide to trophic relations. J. Mar. Biol. Ass. UK 76, 265–285. https://doi.org/10.1017/S002531540003054X (1996).CAS 
Article 

Google Scholar 
Southward, A. J. et al. Behaviour and feeding of the Nassariid gastropod Cyclope neritea, abundant at hydrothermal brine seeps off Milos (Aegean Sea). J. Mar. Biol. Ass. UK 77, 753–771. https://doi.org/10.1017/S0025315400036171 (1997).Article 

Google Scholar 
Chang, N. N. et al. Trophic structure and energy flow in a shallow-water hydrothermal vent: Insights from a stable isotope approach. PLoS One 13, e0204753. https://doi.org/10.1371/journal.pone.0204753 (2018).CAS 
Article 

Google Scholar 
Trager, G. C. & DeNiro, M. J. Chemoautotrophic sulphur bacteria as a food source for mollusks at intertidal hydrothermal vents: Evidence from stable isotopes. Veliger 33, 359–362 (1990).
Google Scholar 
Kharlamenko, V. I., Zhukova, N. V., Khotimchenko, S. V., Svetashev, V. I. & Kamenev, G. M. Fatty acids as markers of food sources in a shallow-water hydrothermal ecosystem (Kraternaya Bight, Yankich Island, Kurile Islands). Mar. Ecol. Progr. Ser. 120, 231–241. https://doi.org/10.3354/meps120231 (1995).ADS 
CAS 
Article 

Google Scholar 
Chen, C. T. A. et al. Investigation into extremely acidic hydrothermal fluids off Kueishantao Islet, Taiwan. Acta. Oceanol. Sin. 24, 125–133 (2005).CAS 

Google Scholar 
Wang, T. W., Chan, T. Y. & Chan, B. K. K. Trophic relationships of hydrothermal vent and non-vent communities in the upper sublittoral and upper bathyal zones off Kueishan Island, Taiwan: A combined morphological, gut content analysis and stable isotope approach. Mar. Biol. 161, 2447–2463. https://doi.org/10.1007/s00227-014-2479-6 (2014).Article 

Google Scholar 
Chen, C., Chan, T. Y. & Chan, B. K. K. Molluscan diversity in shallow water hydrothermal vents off Kueishan Island, Taiwan. Mar. Biodivers. 48, 709–714. https://doi.org/10.1007/s12526-017-0804-2 (2017).Article 

Google Scholar 
Lebrato, M. et al. Earthquake and typhoon trigger unprecedented transient shifts in shallow hydrothermal vents biogeochemistry. Sci. Rep. 9, 16926. https://doi.org/10.1038/s41598-019-53314-y (2019).ADS 
CAS 
Article 

Google Scholar 
Lin, Y.-S. et al. Intense but variable autotrophic activity in a rapidly flushed shallow-water hydrothermal plume (Kueishantao Islet, Taiwan). Geobiology 19, 87–101. https://doi.org/10.1111/gbi.12418 (2021).CAS 
Article 

Google Scholar 
Jeng, M. S., Ng, N. K. & Ng, P. K. L. Hydrothermal vent crabs feast on sea ‘snow’. Nature 432, 969. https://doi.org/10.1038/432969a (2004).ADS 
CAS 
Article 

Google Scholar 
Ho, T. W., Hwang, J. S., Cheung, M. K., Kwan, H. S. & Wong, C. K. Dietary analysis on the shallow-water hydrothermal vent crab Xenograpsus testudinatus using Illumina sequencing. Mar. Biol. 162, 1787–1798. https://doi.org/10.1007/s00227-015-2711-z (2015).CAS 
Article 

Google Scholar 
Yang, S. H. et al. Bacterial community associated with organs of shallow hydrothermal vent crab Xenograpsus testudinatus near Kueishan Island, Taiwan. PLoS One 11, e0150597. https://doi.org/10.1371/journal.pone.0150597 (2016).CAS 
Article 

Google Scholar 
Wu, J.-Y. et al. Isotopic niche differentiation in benthic consumers from shallow-water hydrothermal vents and nearby non-vent rocky reefs in northeastern Taiwan. Prog. Oceanogr. 195, 102596. https://doi.org/10.1016/j.pocean.2021.102596 (2021).Article 

Google Scholar 
Collin, R. Calyptraeidae from the northeast Pacific (Gastropoda: Caenogastropoda). Zoosymposia 13, 28. https://doi.org/10.11646/zoosymposia.13.1.12 (2019).Article 

Google Scholar 
Phillips, B. T. Beyond the vent: New perspectives on hydrothermal plumes and pelagic biology. Deep-Sea Res. II: Top. Stud. Oceanogr. 137, 480–485. https://doi.org/10.1016/j.dsr2.2016.10.005 (2017).ADS 
CAS 
Article 

Google Scholar 
Portail, M. et al. Food-web complexity across hydrothermal vents on the Azores triple junction. Deep-Sea Res. I: Oceanogr. Res. Pap. 131, 101–120. https://doi.org/10.1016/j.dsr.2017.11.010 (2018).ADS 
CAS 
Article 

Google Scholar 
Nomaki, H. et al. Nutritional sources of meio- and macrofauna at hydrothermal vents and adjacent areas: Natural-abundance radiocarbon and stable isotope analyses. Mar. Ecol. Prog. Ser. 622, 49–65. https://doi.org/10.1016/j.dsr.2017.11.010 (2019).ADS 
CAS 
Article 

Google Scholar 
Alfaro-Lucas, J. M. et al. High environmental stress and productivity increase functional diversity along a deep-sea hydrothermal vent gradient. Ecology 101, e03144. https://doi.org/10.1002/ecy.3144 (2020).CAS 
Article 

Google Scholar 
Stock, B. C. et al. Analyzing mixing systems using a new generation of Bayesian tracer mixing models. PeerJ 6, e5096. https://doi.org/10.7717/peerj.5096 (2018).Article 

Google Scholar 
Michener, R. H. & Kaufman, L. Stable isotope ratios as tracers in marine food webs: An update. In Stable Isotopes in Ecology and Environmental Science (eds Michener, R. & Lajtha, K.) 238–283 (Blackwell Pub, 2007). https://doi.org/10.1002/9780470691854.ch9.Chapter 

Google Scholar 
Montoya, J. P. Natural abundance of 15N in marine planktonic ecosystems. In Stable Isotopes in Ecology and Environmental Science (eds Michener, R. & Lajtha, K.) 176–201 (Blackwell Pub, 2007). https://doi.org/10.1002/9780470691854.ch7.Chapter 

Google Scholar 
Dietl, G. P. First report of cannibalism in Triplofusus giganteus (Gastropoda: Fasciolariidae). Bull. Mar. Sci. 73, 757–761 (2003).ADS 

Google Scholar 
Cumplido, M., Pappalardo, P., Fernandez, M., Averbuj, A. & Bigatti, G. Embryonic development, feeding and intracapsular oxygen availability in Trophon geversianus (Gastropoda: Muricudae). J. Molluscan. Stud. 77, 429–436. https://doi.org/10.1093/mollus/eyr025 (2011).Article 

Google Scholar 
Modica, M. V. & Holford, M. The neogastropoda: Evolutionary innovations of predatory marine snails with remarkable pharmacological potential. In Evolutionary Biology—Concepts, Molecular and Morphological Evolution (ed. Pontarotti, P.) 249–270 (Springer, 2010).Chapter 

Google Scholar 
Sebens, K. P. Recruitment and habitat selection in the intertidal sea anemones, Anthopleura elegantissima (Brandt) and A. xanthogrammica (Brandt). J. Exp. Mar. Biol. Ecol. 59, 103–124. https://doi.org/10.1016/0022-0981(82)90110-1 (1982).Article 

Google Scholar 
Naumann, M. S., Orejas, C., Wild, C. & Ferrier-Pages, C. First evidence for zooplankton feeding sustaining key physiological processes in a scleractinian cold-water coral. J. Exp. Mar. Biol. Ecol. 214, 3570–3576. https://doi.org/10.1242/jeb.061390 (2011).CAS 
Article 

Google Scholar 
Dodds, L. A., Roberts, J. M., Taylor, A. C. & Marubini, F. Metabolic tolerance of the cold-water coral Lophelia pertusa (Scleractinia) to temperature and dissolved oxygen change. J. Exp. Mar. Biol. Ecol. 349, 205–214. https://doi.org/10.1016/j.jembe.2007.05.013 (2007).CAS 
Article 

Google Scholar 
Quesada, A. J., Acuña, F. H. & Cortés, J. Diet of the sea anemone Anthopleura nigrescens: Composition and variation between daytime and nighttime high tides. Zool. Stud. 53, 26. https://doi.org/10.1186/s40555-014-0026-2 (2014).Article 

Google Scholar 
Ferrier-Pagès, C., Witting, J., Tambutté, E. & Sebens, K. P. Effect of natural zooplankton feeding on the tissue and skeletal growth of the scleractinian coral Stylophora pistillata. Coral Reefs 22, 229–240. https://doi.org/10.1007/s00338-003-0312-7 (2003).Article 

Google Scholar 
Teece, M. A., Estes, B., Gelsleichter, E. & Lirman, D. Heterotrophic and autotrophic assimilation of fatty acids by two scleractinian corals, Montastraea faveolata and Porites astreoides. Limnol. Oceanogr. 56, 1285–1296. https://doi.org/10.4319/lo.2011.56.4.1285 (2011).ADS 
CAS 
Article 

Google Scholar 
Pawlik, J. R. & Deignan, L. K. Cowries graze verongid sponges on Caribbean reefs. Coral Reefs 34, 663. https://doi.org/10.1007/s00338-015-1279-x (2015).ADS 
Article 

Google Scholar 
Chan, B. K. K., Shao, K. T., Shao, Y. T. & Chang, Y. W. A simplified, economical, and robust light trap for capturing benthic and pelagic zooplankton. J. Exp. Mar. Biol. Ecol. 482, 25–32. https://doi.org/10.1016/j.jembe.2016.04.003 (2016).Article 

Google Scholar 
Viozzi, M. F., Martinex del Rio, C. & Williner, V. Tissue-specific isotopic incorporation turnover rates and trophic discrimination factors in the freshwater shrimp Macrobrachium borellii (Crustacea: Decapoda: Palaemonidae). Zool. Stud. 60, 28. https://doi.org/10.6620/ZS.2021.60-28 (2021).CAS 
Article 

Google Scholar 
Tixier, P. et al. Importance of toothfish in the diet of generalist subantarctic killer whales: Implications for fisheries interactions. Mar. Ecol. Prog. Ser. 613, 197–210. https://doi.org/10.3354/meps12894 (2019).ADS 
CAS 
Article 

Google Scholar 
Nolan, E. T., Roberts, C. G. & Britton, R. J. Predicting the contributions of novel marine prey resources from angling and anadromy to the diet of a freshwater apex predator. Freshw. Biol. 64, 1542–1554. https://doi.org/10.1111/fwb.13326 (2019).Article 

Google Scholar 
Stock, B. C. & Semmens, B. X. MixSIAR GUI user manual. Version 3.1. 716. https://doi.org/10.5281/zenodo.561 (2016).R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org (2019).McCutchan, J. H. Jr., Lewis, W. M. Jr., Kendall, C. & McGrath, C. C. Variation in trophic shift for stable isotope ratios of carbon, nitrogen and sulfur. Oikos 102, 378–390. https://doi.org/10.1034/j.1600-0706.2003.12098.x (2003).CAS 
Article 

Google Scholar 
Gelman, A. Analysis of variance—why it is more important than ever. Ann. Stat. 33, 1–53. https://doi.org/10.1214/009053604000001048 (2005).MathSciNet 
Article 
MATH 

Google Scholar 
Gelman, A., Carlin, J. B., Stern, H. S. & Rubin, D. B. Bayesian Data Analysis (CRC Press, 2014).MATH 

Google Scholar 
Jackson, A. L., Parnell, A. C., Inger, R. & Bearhop, S. Comparing isotopic niche widths among and within communities: SIBER—Stable Isotope Bayesian Ellipses in R. J. Anim. Ecol. 80, 595–602. https://doi.org/10.1111/j.1365-2656.2011.01806.x (2011).Article 

Google Scholar  More

Feng, T. et al. Modeling soil erosion using a spatially distributed model in a karst catchment of northwest Guangxi, China. Earth Surf. Process. Landf. 39, 1005 (2015).
Google Scholar 
Bodoque, J. M. et al. Source of error and uncertainty in sheet erosion rates estimated from dendrogeomorphology. Earth Surf. Process. Landf. 40(9), 1146–1157 (2015).ADS 
Article 

Google Scholar 
Larney, F. J. et al. Erosion–productivity–soil amendment relationships for wheat over 16 years. Soil Tillage Res. 103(1), 73–83 (2009).Article 

Google Scholar 
Xiao, H. et al. Response of soil detachment rate to the hydraulic parameters of concentrated flow on steep loessial slopes on the Loess Plateau of China. Hydrol. Process. 31(14), 2613–2621 (2017).ADS 
Article 

Google Scholar 
Wei, W. et al. Effect of rainfall variation and landscape change on runoff and sediment yield from a loess hilly catchment in China. Environ. Earth Sci. 73(3), 1005–1016 (2015).Article 

Google Scholar 
Yu, F. A. et al. Effects of surface coal mining and land reclamation on soil properties: A review. Earth-Sci. Rev. 191, 12–25 (2019).Article 

Google Scholar 
Valmis, S., Dimoyiannis, D. & Danalatos, N. G. Assessing interrill erosion rate from soil aggregate instability index, rainfall intensity and slope angle on cultivated soils in central Greece. Soil Tillage Res. 80(1–2), 139–147 (2005).Article 

Google Scholar 
Qz, A. et al. Plot-based experimental study of raindrop detachment, interrill wash and erosion-limiting degree on a clayey loessal soil. J. Hydrol. 575, 1280–1287 (2019).Article 

Google Scholar 
Dongdong, W. et al. Sheet erosion rates and erosion control on steep rangelands in loess regions: Sheet erosion rates and erosion control on steep rangelands. Earth Surf. Process. Landf. 43, 146 (2018).
Google Scholar 
Mohammad, A. G. & Adam, M. A. The impact of vegetative cover type on runoff and soil erosion under different land uses. Catena 81(2), 97–103 (2010).Article 

Google Scholar 
Shin, J. Y. et al. Spatial and temporal variations in rainfall erosivity and erosivity density in South Korea. Catena. 176, 125–144 (2019).Article 

Google Scholar 
Wang, D. et al. Characterisation of soil erosion and overland flow on vegetation-growing slopes in fragile ecological regions: A review. J. Environ. Manag. 285, 1400 (2021).
Google Scholar 
Li, Z. W. et al. Rill erodibility as influenced by soil and land use in a small watershed of the Loess Plateau, China. Biosyst. Eng. 129, 248–257 (2015).Article 

Google Scholar 
Yu, L. et al. Hydrological responses and soil erosion potential of abandoned cropland in the loess plateau, China. Geomorphology 138(1), 404–414 (2012).ADS 
Article 

Google Scholar 
Nearing, M. A., Bradford, J. M. & Parker, S. C. Soil detachment by shallow flow at low slopes. Soil Sci. Soc. Am. J. 55(2), 351–357 (1991).Article 

Google Scholar 
Prosser, I. P. & Rustomji, P. Sediment transport capacity relations for overland flow. Prog. Phys. Geogr. 24, 179–193 (2000).Article 

Google Scholar 
Yang, C. T. Minimum unit stream power and fluvial hydraulics. J. Hydraul. Div. 102(7), 769–784 (1976).
Google Scholar 
Zhao, Z. X. & He, J. J. Hydraulics 2nd edn, 193–198 (Springer, 2010).
Google Scholar 
Zhang, M. et al. The response of soil microbial communities to soil erodibility depends on the plant and soil properties in semiarid regions. Land Degrad. Dev. 7, 14005 (2021).
Google Scholar 
Zhang, K. L. et al. Soil erodibility and its estimation for agricultural soils in China. Acta Pedol. Sin. 72(6), 1002–1011 (2008).
Google Scholar 
Long, S. et al. Soil surface roughness change and its effect on runoff and erosion on the Loess Plateau of China. J. Arid Land. 6(4), 400–409 (2014).Article 

Google Scholar 
Zhang, Y. W. et al. Changes in soil water holding capacity and water availability following vegetation restoration on the Chinese Loess Plateau. Sci. Rep. 11(1), 1000 (2021).Article 

Google Scholar 
Liu, J. et al. Sediment transport capacity and its response to hydraulic parameters in experimental rill flow on steep slope. J. Soil Water Conserv. 70, 36–44 (2018).
Google Scholar 
Vargas-Luna, A., Crosato, A. & Uijttewaal, W. S. J. Effects of vegetation on flow and sediment transport: comparative analyses and validation of predicting models. Earth Surf. Process. Landf. 40(2), 157–176 (2015).ADS 
Article 

Google Scholar 
Wang, J. G. et al. Particle size and shape variation of Ultisol aggregates affected by abrasion under different transport distances in overland flow. Catena 123, 153–162 (2014).CAS 
Article 

Google Scholar 
Wang, D. et al. Modeling soil detachment capacity by rill flow using hydraulic parameters. J. Hydrol. 535, 473–479 (2016).ADS 
Article 

Google Scholar 
Zhang, B. J. et al. Soil resistance to flowing water erosion of seven typical plant communities on steep gully slopes on the Loess Plateau of China. Catena. 173, 375–383 (2019).Article 

Google Scholar 
Maïga-Yaleu, S. B. et al. Impact of sheet erosion mechanisms on organic carbon losses from crusted soils in the Sahel. Catena 126, 60–67 (2015).Article 

Google Scholar 
Mo, M. et al. Water and sediment runoff and soil moisture response to grass cover in sloping citrus land, Southern China. Soil Water Res. 14(1), 1004 (2018).
Google Scholar 
Jin, F. et al. Effects of vegetation and climate on the changes of soil erosion in the Loess Plateau of China. Sci. Total Enviro. 773, 10078 (2021).Article 

Google Scholar 
Yu, M. et al. Impact of land-use changes on soil hydraulic properties of Calcaric Regosols on the Loess Plateau, NW China. J. Plant Nutr. Soil Sci. 178(3), 486–498 (2018).Article 

Google Scholar 
Liu, W. Isotopic indicators of carbon and nitrogen cycles in river catchments during soil erosion in the arid loess plateau of china. Chem. Geol. 296–297, 66–72 (2012).ADS 
CAS 
Article 

Google Scholar 
Cheng, M. & Shaoshan, A. N. Response of soil nitrogen, phosphorous and organic matter to vegetation succession on the Loess Plateau of China. J. Arid Land. 7(2), 216–223 (2015).Article 

Google Scholar 
Zhang, G. H. et al. Influence of vegetation parameters on runoff and sediment characteristics in patterned Artemisia capillaris plots. J. Arid Land. 2, 1440 (2014).
Google Scholar 
Hao, H. X. et al. Vegetation restoration and fine roots promote soil infiltrability in heavy-textured soils. Soil Tillage Res. 198, 104542 (2020).Article 

Google Scholar 
Chen, Y. et al. Soil enzyme activities of typical plant communities after vegetation restoration on the Loess Plateau, China. China Appl. Soil Ecol. 170, 104292 (2020).Article 

Google Scholar 
Mga, B. et al. Revegetation induced change in soil erodibility as influenced by slope situation on the Loess Plateau. Sci. Total Environ. 2, 158 (2021).
Google Scholar 
Ma, L. et al. Effects of earthworm (Metaphire guillelmi) density on soil macropore and soil water content in typical Anthrosol soil. Agric. Ecosyst. Environ. 311(5), 107338 (2021).Article 

Google Scholar 
Chen, Y. et al. Soil enzyme activities of typical plant communities after vegetation restoration on the Loess Plateau, China. China Appl. Soil Ecol. 170, 104292 (2020).Article 

Google Scholar 
Xu, W. et al. Strengthening protected areas for biodiversity and ecosystem services in China. Proc. Natl. Acad. Sci. USA 114(7), 1601 (2017).CAS 
Article 

Google Scholar 
Ran, Q., Wang, F. & Gao, J. The effect of storm movement on infiltration, runoff and soil erosion in a semi-arid catchment. Hydrol. Process. 6, 7600 (2020).
Google Scholar  More

Cullen-Unsworth, L. C. et al. Seagrass meadows globally as a coupled social-ecological system: Implications for human wellbeing. Mar. Pollut. Bull. 83, 387–397 (2014).CAS 
Article 

Google Scholar 
Ondiviela, B. et al. The role of seagrasses in coastal protection in a changing climate. Coast. Eng. 87, 158–168 (2014).Article 

Google Scholar 
Campagne, C. S., Salles, J.-M., Boissery, P. & Deter, J. The seagrass Posidonia oceanica: ecosystem services identification and economic evaluation of goods and benefits. Mar. Pollut. Bull. 97, 391–400 (2015).CAS 
Article 

Google Scholar 
Boudouresque, C. F., Mayot, N. & Pergent, G. The outstanding traits of the functioning of the Posidonia oceanica seagrass ecosystem. Biol. Mar. Medit. 13, 109–113 (2006).
Google Scholar 
Duarte, C. M., Kennedy, H., Marbà, N. & Hendriks, I. Assessing the capacity of seagrass meadows for carbon burial: Current limitations and future strategies. Ocean Coast. Manag. 83, 32–38 (2013).Article 

Google Scholar 
Barrón, C., Duarte, C. M., Frankignoulle, M. & Borges, A. V. Organic carbon metabolism and carbonate dynamics in a mediterranean seagrass (Posidonia oceanica) Meadow. Estuar. Coasts 29, 417–426 (2006).Article 

Google Scholar 
Marbà, N., Díaz-Almela, E. & Duarte, C. M. Mediterranean seagrass (Posidonia oceanica) loss between 1842 and 2009. Biol. Conserv. 176, 183–190 (2014).Article 

Google Scholar 
Chefaoui, R. M., Duarte, C. M. & Serrão, E. A. Dramatic loss of seagrass habitat under projected climate change in the Mediterranean Sea. Glob. Chang. Biol. 24, 4919–4928 (2018).ADS 
Article 

Google Scholar 
Marbà, N. & Duarte, C. M. Mediterranean warming triggers seagrass (Posidonia oceanica) shoot mortality. Glob. Chang. Biol. 16, 2366–2375 (2010).ADS 
Article 

Google Scholar 
Lovelock, C. E. et al. Assessing the risk of carbon dioxide emissions from blue carbon ecosystems. Front Ecol Env. 15, 257–265 (2017).Article 

Google Scholar 
Kroeker, K. J. et al. Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming. Glob. Chang. Biol. 19, 1884–1896 (2013).ADS 
Article 

Google Scholar 
Zunino, S., Libralato, S., Canu, D. M., Prato, G. & Solidoro, C. Impact of ocean acidification on ecosystem functioning and services in habitat-forming species and marine ecosystems. Ecosystems https://doi.org/10.1007/s10021-021-0060 (2021).Article 

Google Scholar 
Riebesell, U. et al. Reduced calcification of marine plankton in response to increased atmospheric CO2. Nature 407, 364–367 (2000).ADS 
CAS 
Article 

Google Scholar 
Doney, S. C., Fabry, V. J., Feely, R. A. & Kleypas, J. A. Ocean acidification: the other CO2 problem. Annu. Rev. Mar. Sci. 1, 169–192 (2009).ADS 
Article 

Google Scholar 
Koch, M., Bowes, G., Ross, C. & Zhang, X.-H. Climate change and ocean acidification effects on seagrasses and marine macroalgae. Glob. Chang. Biol. 19, 103–132 (2013).ADS 
Article 

Google Scholar 
Zimmerman, R. C. et al. Experimental impacts of climate warming and ocean carbonation on eelgrass Zostera marina. Mar. Ecol. Prog. Ser. 566, 1–15 (2017).ADS 
CAS 
Article 

Google Scholar 
Egea, L. G., Jimé Nez-Ramos, R., Herná Ndez, I., Bouma, T. J. & Brun, F. G. Effects of ocean acidification and hydrodynamic conditions on carbon metabolism and dissolved organic carbon (DOC) fluxes in seagrass populations. PLoS ONE https://doi.org/10.1371/journal.pone.0192402 (2018).Article 

Google Scholar 
Jiang, Z. J., Huang, X.-P. & Zhang, J.-P. Effects of CO 2 enrichment on photosynthesis, growth, and biochemical composition of seagrass thalassia hemprichii (ehrenb.) aschers. J. Integr. Plant Biol. 52, 904–913 (2010).CAS 
Article 

Google Scholar 
Apostolaki, E. T., Vizzini, S., Hendriks, I. E. & Olsen, Y. S. Seagrass ecosystem response to long-term high CO2 in a Mediterranean volcanic vent. Mar. Environ. Res. 99, 9–15 (2014).CAS 
Article 

Google Scholar 
Hendriks, I. E. et al. Photosynthetic activity buffers ocean acidification in seagrass meadows. Biogeosciences 11, 333–346 (2014).ADS 
Article 

Google Scholar 
Bergstrom, E., Silva, J., Martins, C. & Horta, P. Seagrass can mitigate negative ocean acidification effects on calcifying algae. Sci. Rep. 9(1), 1–11 (2019).CAS 
Article 

Google Scholar 
Hernán, G. et al. Seagrass (Posidonia oceanica) seedlings in a high-CO 2 world: from physiology to herbivory. Sci. Rep. 6(1), 1–12 (2016).MathSciNet 
Article 

Google Scholar 
Cox, T. E. et al. Effects of ocean acidification on Posidonia oceanica epiphytic community and shoot productivity. J. Ecol. 103, 1594–1609 (2015).CAS 
Article 

Google Scholar 
Cox, T. E. et al. Effects of in situ CO2 enrichment on structural characteristics, photosynthesis, and growth of the Mediterranean seagrass Posidonia oceanica. Biogeosciences 13, 2179–2194 (2016).ADS 
Article 

Google Scholar 
Hall-Spencer, J. M. et al. Volcanic carbon dioxide vents show ecosystem effects of ocean acidification. Nature 454(7200), 96–99 (2008).ADS 
CAS 
Article 

Google Scholar 
Mecca, S., Casoli, E., Ardizzone, G. & Gambi, M. C. Effects of ocean acidification on phenology and epiphytes of the seagrass Posidonia oceanica at two CO2 vent systems of Ischia (Italy). Mediterr. Mar. Sci. 21, 70–83 (2020).Article 

Google Scholar 
Ugarelli, K., Chakrabarti, S., Laas, P. & Stingl, U. The seagrass holobiont and its microbiome. Microorganisms 5(4), 81 (2017).Article 

Google Scholar 
Tarquinio, F., Hyndes, G. A., Laverock, B., Koenders, A. & Säwström, C. The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning. FEMS Microbiol. Lett. 366, 1–15 (2019).Article 

Google Scholar 
Brodersen, K. E. & Kühl, M. Effects of Epiphytes on the Seagrass Phyllosphere. Front. Mar. Sci. 9, 1–10 (2022).Article 

Google Scholar 
Seymour, J. R., Laverock, B., Nielsen, D. A., M., T.-T. S. & Macreadie, P. I. The Microbiology of Seagrasses. in Seagrasses of Australia 343–392 (Springer International Publishing, 2018). https://doi.org/10.1007/978-3-319-71354-0Ruocco, N. et al. First evidence of Halomicronema metazoicum (Cyanobacteria) free-living on Posidonia oceanica leaves. PLoS ONE 13(10), e0204954 (2018).Article 

Google Scholar 
Kohn, T. et al. The microbiome of posidonia oceanica seagrass leaves can be dominated by planctomycetes. Front. Microbiol 11, 1458 (2020).Article 

Google Scholar 
Casola, E., Scardi, M., Mazzella, L. & Fresi, E. Structure of the epiphytic community of posidonia oceanica leaves in a shallow meadow. Mar. Ecol. 8, 285–296 (1987).ADS 
Article 

Google Scholar 
Martin, S. et al. Effects of naturally acidified seawater on seagrass calcareous epibionts. Biol. Lett 4, 689–692 (2008).Article 

Google Scholar 
Foo, S. A., Byrne, M., Ricevuto, E. & Gambi, M. C. The carbon dioxide vents of Ischia, Italy, a natural system to assess impacts of ocean acidification on marine ecosystems: an overview of research and comparisons with other vent systems. Oceanogr. Mar. Biol. 56, 237–310 (2018).
Google Scholar 
Olivé, I., Silva, J., Costa, M. M. & Santos, R. Estimating seagrass community metabolism using benthic chambers: the effect of incubation time. Estuaries Coasts 39, 138–144 (2016).Article 

Google Scholar 
Barrón, C. & Duarte, C. M. Dissolved organic matter release in a Posidonia oceanica meadow. Mar. Ecol. Prog. Ser. 374, 75–84 (2009).ADS 
Article 

Google Scholar 
Langsrud, Ø. ANOVA for unbalanced data: Use Type II instead of Type III sums of squares. Stat. Comput. 13, 163–167 (2003).MathSciNet 
Article 

Google Scholar 
RStudio Team. RStudio. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. (2021).Donnarumma, L., Lombardi, C., Cocito, S. & Gambi, M. C. Settlement pattern of Posidonia oceanica epibionts along a gradient of ocean acidification: an approach with mimics. Mediterr. Mar. Sci. 15, 498–509 (2014).Article 

Google Scholar 
Gravili, C., Cozzoli, F. & Gambi, M. C. Epiphytic hydroids on Posidonia oceanica seagrass meadows are winner organisms under future ocean acidification conditions: evidence from a CO2 vent system (Ischia Island, Italy). Eur. Zool. J. 88, 472–486 (2021).CAS 
Article 

Google Scholar 
Rodolfo-Metalpa, R., Lombardi, C., Cocito, S., Hall-Spencer, J. M. & Gambi, M. C. Effects of ocean acidification and high temperatures on the bryozoan Myriapora truncata at natural CO2 vents. Mar. Ecol. 31, 447–456 (2010).CAS 

Google Scholar 
Wear, D. J., Sullivan, M. J., Moore, A. D. & Millie, D. F. Effects of water-column enrichment on the production dynamics of three seagrass species and their epiphytic algae. Mar. Ecol. Prog. Ser. 179, 201–213 (1999).ADS 
Article 

Google Scholar 
Hasegawa, N., Hori, M. & Mukai, H. Seasonal shifts in seagrass bed primary producers in a cold-temperate estuary: Dynamics of eelgrass Zostera marina and associated epiphytic algae. Aquat. Bot. 86, 337–345 (2007).Article 

Google Scholar 
Piazzi, L., Balata, D. & Ceccherelli, G. Epiphyte assemblages of the Mediterranean seagrass Posidonia oceanica: an overview. Mar. Ecol. 37, 3–41 (2016).ADS 
Article 

Google Scholar 
Celdrán, D., Espinosa, E., Sánchez-Amat, A. & Marín, A. Effects of epibiotic bacteria on leaf growth and epiphytes of the seagrass Posidonia oceanica. Mar. Ecol. Prog. Ser. 456, 21–27 (2012).ADS 
Article 

Google Scholar 
Brodersen, K. E., Koren, K., Revsbech, N. P. & Kühl, M. Strong leaf surface basification and CO2 limitation of seagrass induced by epiphytic biofilm microenvironments. Plant Cell Environ. 43, 174–187 (2020).CAS 
Article 

Google Scholar 
Noisette, F., Depetris, A., Kühl, M. & Brodersen, K. E. Flow and epiphyte growth effects on the thermal, optical and chemical microenvironment in the leaf phyllosphere of seagrass (Zostera marina). J. R. Soc. Interface 17(171), 20200485 (2020).Article 

Google Scholar 
Costa, M. M. et al. Epiphytes modulate posidonia oceanica photosynthetic production, energetic balance, antioxidant mechanisms, and oxidative damage. Front. Mar. Sci. 2, 111 (2015).Article 

Google Scholar 
Guilini, K. et al. Response of Posidonia oceanica seagrass and its epibiont communities to ocean acidification. PLoS ONE 12(8), e0181531 (2017).Article 

Google Scholar 
Palacios, S. L. & Zimmerman, R. C. Response of eelgrass Zostera marina to CO2 enrichment: possible impacts of climate change and potential for remediation of coastal habitats. Mar. Ecol. Prog. Ser. 344, 1–13 (2007).ADS 
Article 

Google Scholar 
Scartazza, A. et al. Carbon and nitrogen allocation strategy in Posidonia oceanica is altered by seawater acidification. Sci. Total Environ. 607, 954–964 (2017).ADS 
Article 

Google Scholar 
Hansen, A. B., Pedersen, A. S., Kühl, M. & Brodersen, K. E. Temperature Effects on Leaf and Epiphyte Photosynthesis, Bicarbonate Use and Diel O 2 Budgets of the Seagrass Zostera marina L. Front. Mar. Sci. 9, (2022).Burnell, O. W., Russell, B. D., Irving, A. D. & Connell, S. D. Seagrass response to CO2 contingent on epiphytic algae: indirect effects can overwhelm direct effects. Oecologia 1, 871–882 (2014).ADS 
Article 

Google Scholar 
Mabrouk, L., Hamza, A., Brahim, B. & Bradai, M.-N. Variability in the structure of epiphyte assemblages on leaves and rhizomes of Posidonia oceanica in relation to human disturbances in a seagrass meadow off Tunisia. Aquat. Bot. 108, 33–40 (2013).Article 

Google Scholar 
Garrard, S. L. et al. Indirect effects may buffer negative responses of seagrass invertebrate communities to ocean acidification. J. Exp. Mar. Bio. Ecol. 461, 31–38 (2014).Article 

Google Scholar 
Touchette, B. W. & Burkholder, J. A. M. Review of nitrogen and phosphorus metabolism in seagrasses. J. Exp. Mar. Bio. Ecol. 250, 133–167 (2000).CAS 
Article 

Google Scholar 
Borg, J. A., Rowden, A. A., Attrill, M. J., Schembri, P. J. & Jones, M. B. Wanted dead or alive: high diversity of macroinvertebrates associated with living and ‘dead’ Posidonia oceanica matte. Mar. Biol. 149, 667–677 (2006).Article 

Google Scholar 
Teixidó, N. et al. Functional biodiversity loss along natural CO 2 gradients. Nat. Commun. 9(1), 1–9 (2018).Article 

Google Scholar  More