Ecology

Yu, X. L., Ji, H., Wang, C. L. & Li, P. A survey of pharmacological effects of Fritillaria. Chin. Tradit. Herb. Drugs. 31, 313–315 (2000).
Google Scholar 
Wang, D. D. et al. Antitussive, expectorant and anti-inflammatory activities of four alkaloids isolated from bulbus of Fritillaria wabuensis. J. Ethnopharmacol. 139, 189 (2012).Article 
CAS 

Google Scholar 
Tan, S. F. et al. Evaluation on the effect of analgesia and expectorant of aconiti radix cocta in coordination with Fritillaria cirrhosa and Fritillaria thunbergii based on the uniform design method. China J. Chin. Mater. Med. 38, 2706–2713 (2013).
Google Scholar 
Chen, T. Z. & Zhang, M. Suitable technology for production and processing of Fritillaria cirrhosa (ed. Chen, T. Z. & Zhang, M.) 8 (China Medical Science Press, 2018).Chinese Pharmacopoeia Commission. Pharmacopoeia of the People’s Republic of China (ed. Zhao, Y. Y. et al.) (China Medical Science Press, 2015).Duan, B. Z. et al. A survey of resource science of Fritillaria taipaiensis. Mod. Chin. Med. 12, 12–14 (2010).
Google Scholar 
Duan, B. Z. et al. Regionalization for growing Fritillaria taipaiensis P Y Li by TCMGIS-II. World Sci. Technol/Modern Tradit. Chin. Med. Mater Med. 12, 486–488 (2012).
Google Scholar 
Jiang, S. Y., Sun, H. B., Qin, J. H., Zhu, W. T. & Sun, H. Functional production regionalization for Fritillariae Cirrhosae Bulbus based on growth and quality suitability assessment. China J. Chin. Mater. Med. 17, 3194–3201 (2016).
Google Scholar 
Gu, W. C., Mu, M. J., Yang, M., Guo, D. Q. & Zhou, N. Correlation analysis between bulb quality and rhizosphere soil factors of Fritillaria taibaiensis. Chin. J. Exp. Tradit. Med. Formulae. 26, 165–177 (2020).
Google Scholar 
Mu, M. J. et al. Correlation between rhizospheric microorganisms distribution and alkaloid content of Fritillaria taipaiensis. China J. Chin. Mater. Med. 11, 2231–2235 (2019).
Google Scholar 
Peng, R., Ma, P., Mo, R. Y. & Sun, N. X. Analysis of the bioactive components from different growth stages of Fritillaria taipaiensis PY Li. Acta Pharm. Sin. B. 3, 167–173 (2013).Article 

Google Scholar 
Zhou, X. J., Yang, Y. X., Hu, P., Zhang, M. & Xia, Y. L. Investigation on the resources of Fritillaria taipaiensis. J. Anhui Agric. Sci. 17, 84–85 (2015).CAS 

Google Scholar 
Wu, Z. Z. & Wu, C. S. Effects of different fertilization modes on the growth of Fritillaria taipaiensis. Agric. Eng. 6, 153–154 (2016).
Google Scholar 
Nannipieri, P., Kandeler, E., Ruggiero, P., Burns, R. G. & Dick, R. P. Enzymes in the environment: activity, ecology and applications (ed. Nannipieri, P.) (Marcel Dekker, 2002).Sparling, G. P. Biological indicators of soil health (ed. Sparling, G. P.) (CAB International, 1997).Alkorta, I. et al. Soil enzyme activities as biological indicators of soil health. Rev. Environ. Health. 18, 65–73 (2003).Article 

Google Scholar 
Lu, L. H. et al. Fungal networks in yield-invigorating and debilitating soils induced by prolonged potato monoculture. Soil. Biol. Biochem. 65, 186–194 (2013).Article 
CAS 

Google Scholar 
Sun, J., Zhang, Q., Zhou, J. & Wei, Q. P. Illumina amplicon sequencing of 16S rRNA Tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site. PLoS ONE 9, e111744 (2014).Article 
ADS 

Google Scholar 
Yao, H. Y., Jiao, X. D. & Wu, F. Z. Effects of continuous cucumber cropping and alternative rotations under protected cultivation on soil microbial community diversity. Plant. Soil. 284, 195–203 (2006).Article 
CAS 

Google Scholar 
Lee, S. A. et al. Diferent types of agricultural land use drive distinct soil bacterial communities. Sci. Rep. 10, 1–12 (2020).ADS 

Google Scholar 
Chen, M. et al. Soil eukaryotic microorganism succession as affected by continuous cropping of peanut-pathogenic and beneficial fungi were selected. PLoS ONE 7, e40659 (2012).Article 
ADS 
CAS 

Google Scholar 
Xiong, W. et al. The effect of long-term continuous cropping of black pepper on soil bacterial communities as determined by 454 pyrosequencing. PLoS ONE 10, e0136946 (2015).Article 

Google Scholar 
Zhang, Z. Y., Yang, W. X., Chen, Y. H. & Chen, X. J. Effects of consecutively monocultured Rehmannia glutinosa L. on diversity of fungal community in rhizospheric soil. J. Integr. Agric. 10, 1374–1384 (2011).
Google Scholar 
Zhou, X. & Wu, F. Dynamics of the diversity of fungal and Fusarium communities during continuous cropping of cucumber in the greenhouse. FEMS Microbiol. Ecol. 80, 469–478 (2012).Article 
CAS 

Google Scholar 
Mu, M. J. et al. Effect of growth years to the soil enzyme activities and heavy metal residue of Fritillaria taipaiensis P.Y. Li. Environ. Chem. 38, 1966–1972 (2019).CAS 

Google Scholar 
Zhou, N. et al. Rhizospheric Fungal diversities and soil biochemical factors of Fritillaria taipaiensis over five cultivation years. Horticulturae. 7(12), 560–574 (2021).Article 

Google Scholar 
Cai, L. T., Hu, Z. Y. & Luo, Z. Y. Extraction of total DNA of microbes from tobacco diseased-field soil by SDS-CTAB method. Acta Agric. Jiangxi. 23, 119–121 (2011).
Google Scholar 
Liang, Y. T. et al. Century long fertilization reduces stochasticity controlling grassland microbial community succession. Soil Biol. Biochem. 151, 128–142 (2020).Article 

Google Scholar 
Fudou, R. et al. Haliangicin, a novel antifungal metabolite produced by a marine myxobacterium. 2. Isolation and structural elucidation. J. Antibiot. 54(2), 153–156 (2001).Article 
CAS 

Google Scholar 
Lewin, G. R. et al. Cellulose-enriched microbial communities from leaf-cutter ant (Atta colombica) refuse dumps vary in taxonomic composition and degradation ability. PLoS ONE. 11(3), e0151840 (2016).Article 

Google Scholar 
Brewer, T. E., Handley, K. M., Carini, P., Gilbert, J. A. & Fierer, N. Genome reduction in an abundant and ubiquitous soil bacterium Candidatus Udaeobacter copiosus. Nat. Microbiol. 2, 16198 (2016).Article 
CAS 

Google Scholar 
Kalyuzhnaya, M. G., Hristova, K. R., Lidstrom, M. E. & Chistoserdova, L. Characterization of a novel methanol dehydrogenase in representatives of the Burkholderiales: Implication for environmental detection of methylotrophy and evidence for convergent evolution. J. Bacterial. 190, 3817–3823 (2008).Article 
CAS 

Google Scholar 
Banerjee, S. et al. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil. Biol. Biochem. 97, 188–198 (2016).Article 
CAS 

Google Scholar 
Yi, X. et al. Microbial community structures and important associations between soil nutrients and the responses of specific taxa to rice-frog cultivation. Front. Microbiol. 6(10), 1752 (2019).Article 

Google Scholar 
Makk, J. et al. Arenimonas subflava sp nov., isolated from a drinking water network, and emended description of the genus Arenimonas. Int. J. Syst. Evol. Microbiol. 65, 1915–1921 (2015).Article 
CAS 

Google Scholar 
Maki, K., Mitsuo, S., Masako, I., Shinji, S. & Yoshimi, B. Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 55(5), 2143–2147 (2005).Article 

Google Scholar 
Zhao, Y. C. et al. Variation of rhizosphere microbial community in continuous mono-maize seed production. Sci. Rep. 11, 1544 (2021).Article 
ADS 
CAS 

Google Scholar 
Liu, J. J. et al. High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China. Soil. Biol. Biochem. 70, 113–122 (2014).Article 
ADS 
CAS 

Google Scholar 
Yin, C. T. et al. Rhizosphere community selection reveals bacteria associated with reduced root disease. Microbiome. 9, 86–103 (2021).Article 
CAS 

Google Scholar 
Ren, H. Y. et al. Effect of two kinds of fertilizers on growth and rhizosphere soil properties of bayberry with decline disease. Plants. 10, 2386–2409 (2021).Article 
CAS 

Google Scholar 
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U. S. A. 103(3), 626–631 (2006).Article 
ADS 
CAS 

Google Scholar 
Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75(15), 5111–5120 (2009).Article 
ADS 
CAS 

Google Scholar 
Zhang, B., Liang, C., He, H. B. & Zhang, X. D. Variations in soil microbial communities and residues along an altitude gradient on the northern slope of changbai mountain, China. PLoS ONE. 8(6), e66184 (2013).Article 
ADS 
CAS 

Google Scholar 
Liu, Z. X. et al. Effects of continuous cropping years of soybean on the bacterial community structure in black soil. Acta Ecol. Sin. 39(12), 4337–4345 (2019).CAS 

Google Scholar 
Jekins, S. N. et al. Actinobacterial community dynamics in long term managed grasslands. Antonie Van Leeuwenhoek 95(4), 319–334 (2009).Article 

Google Scholar 
Lauber, C. L., Strickland, M. S., Bradford, M. & Fierer, N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40(9), 2407–2415 (2008).Article 
CAS 

Google Scholar 
Lu, K. H., Hu, Z. Y., Liang, J. J. & Zhu, J. Y. Characteristics of rhizosphere microbial community structure of two aquatic plants in eutrophic waters. China Environ. Sci. 30, 1508–1515 (2010).CAS 

Google Scholar 
Wang, J. J., Cao, B., Bai, C. C., Zhang, L. L. & Che, L. Potential distribution prediction and suitability evaluation of Fritillaria cirrhosa D. Don based on maxent modeling and GIS. Bull. Bot. Res. 34, 642–649 (2014).
Google Scholar 
Montazer, Z., Najafi, M. B. H. & Levin, B. D. Microbial degradation of low-density polyethylene and synthesis of polyhydroxyalkanoate polymers. Can. J. Microbiol. 65, 224–234 (2019).Article 
CAS 

Google Scholar 
Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classifification of soil bacteria. Ecology 88, 1354–1364 (2007).Article 

Google Scholar 
Lin, S., Zhuang, J. Q., Chen, T., Zhang, A. J. & Lin, W. X. Microbial diversity in rhizosphere soils of different planting year tea trees: An analysis with phospholipid fatty acid biomarkers. Chin. J. Ecol. 32, 64–71 (2013).CAS 

Google Scholar 
Bardgett, R. D., Lovell, R. D., Hobbs, P. J. & Jarvis, C. C. Seasonal changes in soil microbial communities along a fertility gradient of temperate grasslands. Soil Biol. Biochem. 31, 1021–1030 (1999).Article 
CAS 

Google Scholar 
Haynes, K. M., Preston, M. D., McLaughlin, J. W., Webster, K. & Basiliko, N. Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy. Can. J. Soil Sci. 95, 219–230 (2015).Article 
CAS 

Google Scholar 
Ye, W., Li, Y. C., Ye, M., Qian, Y. T. & Dai, W. S. Microbial biodiversity in rhizospheric soil of Torreya grandis ‘Merrillii’relative to cultivation history. Chin. J. Appl. Ecol. 29, 3783–3792 (2018).
Google Scholar 
Shen, Z. Z. et al. Induced soil microbial suppression of banana fusarium wilt disease using compost and biofertilizers to improve yield and quality. Eur. J. Soil Biol. 57, 1–8 (2013).Article 

Google Scholar 
Liu, C. et al. Soil bacterial communities of three types of plants from ecological restoration areas and plant-growth promotional benefits of Microbacterium invictum (strain X-18). Front. Microbiol. 13, 926037 (2022).Article 

Google Scholar 
Wang, L. X., Pang, X. Y., Li, N., Qi, K. & Yin, C. Effects of vegetation type, fine and coarse roots on soil microbial communities and enzyme activities in eastern tibetan plateau. Catena 194, 104694 (2020).Article 
CAS 

Google Scholar 
Su, Y. Z., Li, Y. L., Cui, J. Y. & Zhao, W. Z. Influences of continuous grazing and livestock exclusion on soil properties in a degraded sandy grassland, Inner Mongolia, Northern China. Catena 59(3), 267–278 (2005).Article 

Google Scholar 
Wallenstein, M. D., Mcmahon, S. K. & Schimel, J. P. Seasonal variation in enzyme activities and temperature sensitivities in arctic tundra soils. Glob. Chang. Biol. 15(7), 1631–1639 (2009).Article 
ADS 

Google Scholar 
Chang, W. H., Ma, W. W., Li, G., Xu, G. R. & Song, L. C. Temporal and spatial distribution characteristics of soil urease and protease activities in different degraded gradients of Gahai wetland. Soils. 54(3), 524–531 (2022).
Google Scholar 
Zhang, Y., Liu, C., Song, A., Jin, Z. J. & Li, Q. Relationship between soil physicochemical properties and soil enzyme activities in huixian karst wetland system based on canonica correspondence analysis. Carsol. Sin. 35(1), 11–18 (2016).
Google Scholar 
Zhang, Y., Ke, X., Zhang, G. C. & Guan, L. Z. Effects of acetochlor on soil urease kinetic characteristics. Plant Nutr. Fert. Sci. 18(4), 915–921 (2012).CAS 

Google Scholar 
Wang, H. Y., Ma, P. & Peng, R. Quantitative determination of peimisin and total alkaloids in Fritillaria taipaiensis of different growing stage. J. Chin. Med. Mater. 34, 1034–1037 (2011).
Google Scholar 
Gershenzon, J. Metabolic costs of terpenoid accumulation in high plants. J. Chem. Ecol. 20, 1281–1328 (1994).Article 
CAS 

Google Scholar 
Pramanik, M. H. R., Nagai, M., Asao, T. & Matsui, Y. Effect of temperature and hotoperiod on the phytotoxic root exudate of cucumber (Cucumis sativus) in hydroponic culture. J. Chem. Ecol. 28, 1953–1967 (2000).Article 

Google Scholar 
Bertin, C., Yang, X. & Weston, L. A. The role of root exudates and allelochemicals in rhizosphere. Plant Soil. 256, 67–83 (2003).Article 
CAS 

Google Scholar 
Zhang, Z. Y. & Lin, W. X. Continuous cropping obstacle and allelopathic autotoxicity of medicinal plants. Chin. J. Eco-Agric. 17, 189–196 (2019).Article 

Google Scholar 
Huang, Y. Q. et al. Effects of vanillic acid on seed germination, seedling growth and rhizosphere microflora of peanut. Sci. Agric. Sin. 9, 1735–1745 (2018).
Google Scholar  More

De Jesús-Crespo, R. & Ramírez, A. Effects of urbanisation on stream physicochemistry and macroinvertebrate assemblages in a tropical urban watershed in Puerto Rico. J. N. Am. Benthol. Soc. 30, 739. https://doi.org/10.1899/10-081.1 (2011).Article 

Google Scholar 
Start, D., Barbour, M. A. & Bonner, C. Urbanisation reshapes a food web. J. Anim. Ecol. 89(3), 808–816. https://doi.org/10.1111/1365-2656.131366 (2020).Article 

Google Scholar 
Liu, Y. et al. Analysis of the influence paths of land use and landscape pattern on organic matter decomposition in river ecosystems: Focusing on microbial groups. Sci. Total Environ. 95(14), 106408. https://doi.org/10.1016/j.scitotenv.2022.152999 (2022).Article 
CAS 

Google Scholar 
Vörösmarty, C. J., Mcintyre, P. B., Gessner, M. O., Dudgeon, D. & Prusevich, A. Global threats to human water security and river biodiversity. Nature 467(7315), 555–561. https://doi.org/10.1038/nature09440 (2010).Article 
ADS 
CAS 

Google Scholar 
Weideman, E. A., Perold, V., Arnold, G. & Ryan, P. G. Quantifying changes in litter loads in urban stormwater runoff from Cape Town, South Africa, over the last two decades. Sci. Total Environ. 724, 138310. https://doi.org/10.1016/j.scitotenv.2020.138310 (2020).Article 
ADS 
CAS 

Google Scholar 
Charters, F. J., Cochrane, T. A. & O’Sullivan, A. D. The influence of urban surface type and characteristics on runoff water quality. Sci. Total Environ. 755, 142470. https://doi.org/10.1016/j.scitotenv.2020.142470 (2021).Article 
ADS 
CAS 

Google Scholar 
Espinoza-Toledo, A., Mendoza-Carranza, M., Castillo, M. M., Barba-Macías, E. & Capps, K. A. Taxonomic and functional responses of macroinvertebrates to riparian forest conversion in tropical streams. Sci. Total Environ. 757, 143972. https://doi.org/10.1016/j.scitotenv.2020.143972 (2021).Article 
ADS 
CAS 

Google Scholar 
Akamagwuna, C. F., Ntloko, P., Edegbene, A. O. & Odume, O. N. Are Ephemeroptera, Plecoptera and Trichoptera traits reliable indicators of semi- urban pollution in the Tsitsa River, Eastern Cape Province of South Africa ? Environ. Monit. Assess. 193, 1–15. https://doi.org/10.1007/s10661-021-09093-z (2021).Article 
CAS 

Google Scholar 
Edegbene, A. O., Odume, O. N., Arimoro, F. O. & Keke, U. N. Identifying and classifying macroinvertebrate indicator signature traits and ecological preferences along urban pollution gradient in the Niger Delta. Environ. Pollut. 281, 117076. https://doi.org/10.1016/j.envpol.2021.117076 (2021).Article 
CAS 

Google Scholar 
Odume, O. N. Searching for urban pollution signature and sensitive macroinvertebrate traits and ecological preferences in a river in the Eastern Cape of South Africa. Ecol. Indic. 108, 105759. https://doi.org/10.1016/j.ecolind.2019.105759 (2020).Article 
CAS 

Google Scholar 
World Bank Group. e-Conomy Africa 2020 Africa’s $180 billion Internet economy future. In E-Conomy Africa 2020 (2020).Petersen, C. R., Jovanovic, N. Z., Grenfell, M. C., Oberholster, P. J. & Cheng, P. Responses of aquatic communities to physical and chemical parameters in agriculturally impacted coastal river systems. Hydrobiologia 813(1), 157–175. https://doi.org/10.1007/s10750-018-3518-y (2018).Article 
CAS 

Google Scholar 
Zhao, Q., Guo, F., Zhang, Y., Yang, Z. & Ma, S. Effects of secondary salinisation on macroinvertebrate functional traits in surface mining-contaminated streams, and recovery potential. Sci. Total Environ. 640–641, 1088–1097. https://doi.org/10.1016/j.scitotenv.2018.05.347 (2018).Article 
ADS 
CAS 

Google Scholar 
Wang, Y. et al. Trophic structure in response to land use in subtropical streams. Ecol. Indic. 127, 107746. https://doi.org/10.1016/j.ecolind.2021.107746 (2021).Article 
CAS 

Google Scholar 
David, A. Landscapes and riverscapes: The influence of land use on stream ecosystems. Annu. Rev. Ecol. Evol. Syst. 35, 257–284. https://doi.org/10.1146/annurev.ecolsys.35.120202.110122 (2004).Article 

Google Scholar 
Monk, W. A., Wood, P. J., Hannah, D. M. & Wilson, D. A. Macroinvertebrate community response to inter-annual and regional river flow regime dynamics. River Res. Appl. 24(70), 988–1001 (2008).Article 

Google Scholar 
Fitzgerald, D. B., Winemiller, K. O., SabajPerez, M. H. & Sousa, L. M. Seasonal changes in the assembly mechanisms structuring tropical fish communities. Ecology 98, 21–31. https://doi.org/10.1002/ecy.1616 (2017).Article 

Google Scholar 
Rosenberg, D. M. & Resh, V. H. Freshwater Biomonitoring and Benthic Macroinvertebrates (Chapman and Hall, 1993).
Google Scholar 
Jiang, X., Xiong, J., Xie, Z. & Chen, Y. Longitudinal patterns of macroinvertebrate functional feeding groups in a Chinese river system: A test for river continuum concept (RCC). Quatern. Int. 244(2), 289–295. https://doi.org/10.1016/j.quaint.2010.08.015 (2011).Article 

Google Scholar 
Sun, L. Q. et al. Food web structure and ecosystem attributes of integrated multi-trophic aquaculture waters in Sanggou Bay. Aquac. Rep. 16, 100279. https://doi.org/10.1016/j.aqrep.2020.100279 (2020).Article 

Google Scholar 
Covich, A. P., Palmer, M. A. & Crowl, T. A. The role of benthic invertebrate species in freshwater ecosystems. Bioscience 49, 119–127 (1999).Article 

Google Scholar 
Hladyz, S., Kajsa, Å., Paul, S. G. & Guy, W. Impacts of an aggressive riparian invader on community structure and ecosystem functioning in stream food webs. J. Appl. Ecol. 48(2), 443–452. https://doi.org/10.1111/j.1365-2664.2010.01924.x (2011).Article 

Google Scholar 
Crowl, T. A. & Covich, A. P. Predator-induced life history shifts in a freshwater snail. Science 247, 949–951 (1990).Article 
ADS 
CAS 

Google Scholar 
Fierro, P. et al. Effects of local land-use on riparian vegetation, water quality, and the functional organisation of macroinvertebrate assemblages. Sci. Total Environ. 609, 724–734. https://doi.org/10.1016/j.scitotenv.2017.07.197 (2017).Article 
ADS 
CAS 

Google Scholar 
Lenat, D. R. & Barbour, M. T. Using benthic macroinvertebrate community structure for rapid, cost-effective, water quality monitoring: Rapid bioassessment. Biol. Monit. Aquat. Syst. 1, 187–215 (1994).
Google Scholar 
Edegbene, A., Arimoro, F. O. & Odume, O. N. How does urban pollution influence macroinvertebrate traits in forested riverine systems? Water 1, 2–17. https://doi.org/10.3390/w12113111 (2020).Article 

Google Scholar 
Walsh, C. J. et al. The urban stream syndrome: Current knowledge and the search for a cure. J. N. Am. Renthol. Soc. 24(3), 706–723. https://doi.org/10.1899/04-028.1 (2005).Article 

Google Scholar 
Bêche, L. A., Eric, P. M. & Vincent, H. R. Long-term seasonal variation in the biological traits of benthic-macroinvertebrates in two mediterranean-climate streams in California, USA. Freshw. Biol. 51(1), 56–75. https://doi.org/10.1111/j.1365-2427.2005.01473.x (2006).Article 

Google Scholar 
Sitati, A., Raburu, P. O., Yegon, M. J. & Masese, F. O. Land-use influence on the functional organization of Afrotropical macroinvertebrate assemblages. Limnologica 88, 125875. https://doi.org/10.1016/j.limno.2021.125875 (2021).Article 
CAS 

Google Scholar 
Álvarez-Cabria, M. J. & José, A. J. Spatial and seasonal variability of macroinvertebrate metrics: Do macroinvertebrate communities track river health? Ecol. Indic. 10(2), 370–379. https://doi.org/10.1016/j.ecolind.2009.06.018 (2010).Article 
CAS 

Google Scholar 
Masese, F. O. et al. Litter processing and shredder distribution as indicators of riparian and catchment influences on ecological health of tropical streams. Ecol. Indic. 46, 23–37. https://doi.org/10.1016/j.ecolind.2014.05.032 (2014).Article 

Google Scholar 
Merritt, R. & Cummins, K. An Introduction to the Aquatic Insects of North America 1996–862 (Kendall Hunt Publishing Co, 1995).
Google Scholar 
Merritt, R. W., Fenoglio, S. & Cummins, K. W. Promoting a functional macroinvertebrate approach in the biomonitoring of Italian lotic systems. J. Limnol. https://doi.org/10.4081/jlimnol.2016.1502 (2016).Article 

Google Scholar 
Edegbene, A.O., Akamagwuna, F.C., Arimoro, F.O., Akumabor, E.C. & Kaine, E.A. Effects of urban-agricultural land-use on Afrotropical macroinvertebrate functional feeding groups in selected rivers in the Niger Delta Region, Nigeria. Hydrobiologia 849, 4857–4869. https://doi.org/10.1007/s10750-022-05034-0 (2022).Article 
CAS 

Google Scholar 
Masese, F. O. et al. Macroinvertebrate functional feeding groups in Kenyan highland streams: Evidence for a diverse shredder guild. Freshw. Sci. 33(2), 435–450. https://doi.org/10.1086/675681 (2014).Article 

Google Scholar 
Moyo, S. & Richoux, N. B. Macroinvertebrate functional organisation along the longitudinal Gradient of an austral temperate river. Afr. Zool. 52(3), 125–136. https://doi.org/10.1080/15627020.2017.1354721 (2017).Article 

Google Scholar 
Vannote, R. L. et al. The river continuum concept. Can. J. Fish. Aquat. Sci. 37, 130–137 (1980).Article 

Google Scholar 
Ding, J. et al. Impacts of land use on surface water quality in a subtropical river basin: A case study of the Dongjiang River Basin, Southeastern China. Water 7(8), 4427–4445. https://doi.org/10.3390/w7084427 (2015).Article 
ADS 
CAS 

Google Scholar 
Miserendino, M. L. & Masi, C. I. The effects of land use on environmental features and functional organisation of macroinvertebrate communities in Patagonian low order streams. Ecol. Indic. 10(2), 311–319. https://doi.org/10.1016/j.ecolind.2009.06.008 (2010).Article 
CAS 

Google Scholar 
Solis, M., Arias, M., Fanelli, S., Bonetto, C. & Mugni, H. Agrochemicals’ effects on functional feeding groups of macroinvertebrates in Pampas streams. Ecol. Indic. 101, 373–379. https://doi.org/10.1016/j.ecolind.2019.01.036 (2019).Article 
CAS 

Google Scholar 
Mangadze, T., Wasserman, R., Froneman, W. & Dalu, T. Macroinvertebrate functional feeding group alterations in response to habitat degradation of headwater Austral streams. Sci. Total Environ. 695, 133910. https://doi.org/10.1016/j.scitotenv.2019.133910 (2019).Article 
ADS 
CAS 

Google Scholar 
Akamagwuna, F. C. & Odume, O. N. Ephemeroptera, Plecoptera and Trichoptera (EPT) functional feeding group responses to fine grain sediment stress in a river in the Eastern Cape, South Africa. Environ. Monit. Assess. 2, 1–11 (2020).
Google Scholar 
Iwegbue, C. M. A. et al. Polycyclic aromatic hydrocarbons (PAHs) in surficial sediments from selected rivers in the western Niger Delta of Nigeria: Spatial distribution, sources, and ecological and human health risks. Mar. Pollut. Bull. 167, 112351. https://doi.org/10.1016/j.marpolbul.2021.112351 (2021).Article 
CAS 

Google Scholar 
Arimoro, F. O., Abubakar, M. D., Obi-iyeke, G. E. & Keke, U. N. Environmental and sustainability indicators achieving sustainable river water quality for rural dwellers by prioritising the conservation of macroinvertebrates biodiversity in two Afrotropical streams. Environ. Sustain. Indic. 10, 100103. https://doi.org/10.1016/j.indic.2021.100103 (2021).Article 

Google Scholar 
Zabbey, N., Erondu, E. S. & Hart, A. I. Nigeria and the prospect of shrimp farming: Critical issues. Livestock Res. Rural Dev. 22, 11 (2010).
Google Scholar 
Edegbene, A. O., Arimoro, F. O. & Odume, O. N. Developing and applying a macroinvertebrate-based multimetric index for urban rivers in the Niger Delta, Nigeria. Ecol. Evol. 9(22), 12869–12885. https://doi.org/10.1002/ece3.5769 (2019).Article 

Google Scholar 
Iwegbue, C. M. A. et al. Distribution, sources and ecological risks of metals in surficial sediments of the Forcados River and its Estuary, Niger Delta, Nigeria. Environ. Earth Sci. 77(6), 1–18. https://doi.org/10.1007/s12665-018-7344-3 (2018).Article 
CAS 

Google Scholar 
Stoddard, J. L., Larsen, D. P., Hawkins, C. P., Johnson, R. K. & Norris, R. H. Setting expectations for the ecological condition of running waters: The concept of reference condition. Ecol. Appl. 16, 1267–1276 (2006).Article 

Google Scholar 
Whittier, T. R. et al. A structured approach for developing indices of biotic integrity: Three examples from streams and rivers in the western USA. Trans. Am. Fish. Soc. 136, 718–735 (2007).Article 

Google Scholar 
APHA. Standard Methods for the Examination of Water and Wastewater (American Public Health Association, 1995).
Google Scholar 
Dickens, C. W. & Graham, P. M. The South African scoring system (SASS) Version 5 rapid bioassessment method for Rivers. Afr. J. Aquat. Sci. 27(1), 1–10. https://doi.org/10.2989/16085914.2002.9626569 (2002).Article 

Google Scholar 
Day, J. A., & de Moor, I. J. Guides to the freshwater invertebrates of southern Africa. In Volume 6: Arachnida and Mollusca (Araneae, Water Mites and Mollusca). Water Research Commision, 6. WRC Report No. TT 182/02 (2002).De Moor, I. J., Day, J. A. & De Moor, F. C. Guides to the freshwater invertebrates of southern Africa. In Volume 8: Insecta II: Hemiptera, Megaloptera, Neuroptera, Trichoptera and Lepidoptera. Water Research Commision, 8 (2003).Merrit, R. W. et al. An Introduction to the Aquatic Insects of North America 4th edn. (Kendall Hunt Publishing Company, 2008).
Google Scholar 
Cummins, K. W., Merritt, R. W. & Andrade, P. C. N. The use of invertebrate functional groups to characterize ecosystem attributes in selected streams and rivers in South Brazil. Stud. Neotrop. Fauna Environ. 40(1), 69–89. https://doi.org/10.1080/01650520400025720 (2005).Article 

Google Scholar 
Palmer, C. G. Benthic Assemblage Structure, and the Feeding Biology of Sixteen Macro Invertebrate Taxa from the Buffalo River, Eastern Cape, South Africa. Rhodes University, Ph.D. thesis (1991).Palmer, C. G., Maart, B., Palmer, A. R. & O’keeffe, J. H. An assessment of macroinvertebrate functional feeding groups as water quality indicators in the Buffalo River, eastern Cape Province, South Africa. Hydrobiologia 318, 153–164 (1996).Article 

Google Scholar 
Palmer, C. G. & O’Keeffe, J. H. O. Feeding patterns of four macroinvertebrate taxa in the headwaters of the Buffalo River, Eastern Cape. Hydrobiologia 228, 157–173 (1992).Article 

Google Scholar 
Gayraud, S. & Michel, P. Influence of bed-sediment features on the interstitial habitat available for macroinvertebrates in 15 French streams. Int. Rev. Hydrobiol. 88(1), 77–93. https://doi.org/10.1002/iroh.200390007 (2003).Article 

Google Scholar 
Beketov, M. A. et al. SPEAR indicates pesticide effects in streams—Comparative use of species- and family-level biomonitoring data. Environ. Pollut. 157, 1841–1848. https://doi.org/10.1016/j.envpol.2009.01.021 (2009).Article 
CAS 

Google Scholar 
Anderson, M., Gorley, R. N. & Clarke, K. R. PERMANOVA + for PRIMER user manual. Primer-E Ltd 1(1), 218 (2008).
Google Scholar 
Dolédec, S., Chessel, D., ter Braak, C. J. F. & Champely, S. Matching species traits to environmental variables: A new three-table ordination method. Environ. Ecol. Stat. 3(2), 143–166. https://doi.org/10.1007/BF02427859 (1996).Article 

Google Scholar 
Juvigny-Khenafou, N. P. D. et al. Impacts of multiple anthropogenic stressors on stream macroinvertebrate community composition and functional diversity. Ecol. Evol. 11(1), 133–152. https://doi.org/10.1002/ece3.6979 (2021).Article 

Google Scholar 
Dray, P. S. et al. Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation. Ecology 95(1), 14–21 (2014).Article 

Google Scholar 
R Core Team, E. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).Lubanga, H. L., Manyala, J. O., Sitati, A., Yegon, M. J. & Masese, F. O. Spatial variability in water quality and macroinvertebrate assemblages across a disturbance gradient in the Mara River. Ecohydrol. Hydrobiol. https://doi.org/10.1016/j.ecohyd.2021.03.001 (2021).Article 

Google Scholar 
Arimoro, F. O. & Ikomi, R. B. Ecological integrity of upper Warri River, Niger Delta using aquatic insects as bioindicators. Ecol. Indic. 9(3), 455–461. https://doi.org/10.1016/j.ecolind.2008.06.006 (2009).Article 
CAS 

Google Scholar 
Arimoro, F. O., Odume, O. N., Uhunoma, S. I. & Edegbene, A. O. Anthropogenic impact on water chemistry and benthic macroinvertebrate associated changes in a southern Nigeria stream. Environ. Monit. Assess. 187(2), 1–14 (2015).Article 
CAS 

Google Scholar 
Keke, U. N. et al. Macroinvertebrate communities and physicochemical characteristics along an anthropogenic stress gradient in a southern Nigeria stream: Implications for ecological restoration. Environ. Sustain. Indic. https://doi.org/10.1016/j.indic.2021.100157 (2021).Article 

Google Scholar 
Edegbene, A. O. et al. A macroinvertebrate-based multimetric index for assessing ecological condition of forested stream sites draining Nigerian urbanizing landscapes. Sustainability 14, 11289. https://doi.org/10.3390/su141811289 (2022).Article 

Google Scholar 
Matemilola, S., Adedeji, O. H. & Enoguanbhor, E. C. Land use/land cover change in petroleum-producing regions of Nigeria. In The Political Ecology of Oil and Gas Activities in the Nigerian Aquatic Ecosystem (eds Matemilola, S. et al.) (Elsevier Inc., 2018).
Google Scholar 
Ukhurebor, K. E. et al. Environmental implications of petroleum spillages in the Niger Delta region of Nigeria: A review. J. Environ. Manag. 293, 112872. https://doi.org/10.1016/j.jenvman.2021.112872 (2021).Article 
CAS 

Google Scholar 
Masese, F. O. & Raburu, P. O. Improving the performance of the EPT Index to accommodate multiple stressors in Afrotropical streams. Afr. J. Aquat. Sci. 42(3), 219–233. https://doi.org/10.2989/16085914.2017.1392282 (2017).Article 

Google Scholar 
Akamagwuna, F. C. Application of Macroinvertebrate-Based Biomonitoring and Stable Isotopes for Assessing the Effects of Agricultural Land-Use on River Ecosystem Structure and Function in the Kat River, Eastern Cape, South Africa, 4 (Rhodes University, 2021).
Google Scholar 
Yang, F. et al. Application of stable isotopes to the bioaccumulation and trophic transfer of arsenic in aquatic organisms around a closed realgar mine. Sci. Total Environ. 726, 138550. https://doi.org/10.1016/j.scitotenv.2020.138550 (2020).Article 
ADS 
CAS 

Google Scholar 
Minaya, V., Mcclain, M. E., Moog, O., Omengo, F. & Singer, G. A. Scale-dependent effects of rural activities on benthic macroinvertebrates and physico-chemical characteristics in headwater streams of the Mara River, Kenya. Ecol. Indic. 32, 116–122. https://doi.org/10.1016/j.ecolind.2013.03.011 (2013).Article 
CAS 

Google Scholar 
Nelson Mwaijengo, G., Msigwa, A., Njau, K. N., Brendonck, L. & Vanschoenwinkel, B. Where does land use matter most? Contrasting land use effects on river quality at different spatial scales. Sci. Total Environ. 715, 134825. https://doi.org/10.1016/j.scitotenv.2019.134825 (2020).Article 
ADS 
CAS 

Google Scholar 
Moyo, S. & Richoux, N. B. The relative importance of autochthony along the longitudinal gradient of a small South African river influenced by agricultural activities. Food Webs 15, 1–12. https://doi.org/10.1016/j.fooweb.2018.e00082 (2018).Article 

Google Scholar 
Jones, I., Growns, I., Arnold, A., McCall, S. & Bowes, M. The effects of increased flow and fine sediment on hyporheic invertebrates and nutrients in stream mesocosms. Freshw. Biol. 60(4), 813–826. https://doi.org/10.1111/fwb.1253664 (2015).Article 
CAS 

Google Scholar 
Krynak, E. M. & Yates, A. G. Benthic invertebrates taxonomic and trait associations with land use intensively managed watershed: Implications for indicator identification. Ecol. Ind. 93, 1050–1059 (2018).Article 

Google Scholar 
Kuzmanovic, M. et al. Environmental stressors as driver of the trait composition of benthic macroinvertebrates assemblages in polluted Iberian rivers. Environ. Res. 156, 485–493 (2017).Article 
CAS 

Google Scholar 
Dalu, T. et al. Benthic diatom-based indices and isotopic biomonitoring of nitrogen pollution in a warm temperate Austral river system. Sci. Total Environ. 748, 142452. https://doi.org/10.1016/j.scitotenv.2020.142452 (2020).Article 
ADS 
CAS 

Google Scholar 
Tomanova, S., Goitia, E. & Helesˇic, J. H. Trophic levels and functional feeding groups of macroinvertebrates in neotropical streams. Hydrobiologia 556(3), 251–264. https://doi.org/10.1007/s10750-005-1255-5 (2006).Article 

Google Scholar 
da Conceição, A. A., Albertoni, E. F., Milesi, S. V. & Hepp, L. U. Influence of anthropic impacts on the functional structure of aquatic invertebrates in subtropical wetlands. Wetlands. https://doi.org/10.1007/s13157-020-01317-1 (2020).Article 

Google Scholar 
De, R. B. Effects of forest conversion on the assemblages’ structure of aquatic insects in subtropical regions. Rev. Bras. Entomol. 59(1), 43–49. https://doi.org/10.1016/j.rbe.2015.02.005 (2015).Article 
ADS 

Google Scholar 
Cheshire, K., Boyero, L. & Pearson, R. G. Food webs in tropical Austrian streams: Shredders are not scarce. Freshw. Biol. https://doi.org/10.1111/j.1365-2427.2005.01355-x (2005).Article 

Google Scholar 
Camacho, R., Boyero, L., Cornejo, A., Ibáñez, A. & Pearson, R. G. Local variation in shredder distribution can explain their oversight in tropical streams. Biotropica 41, 625–632 (2009).Article 

Google Scholar 
Boyero, L., Ramírez, A., Dudgeon, D. & Pearson, R. G. Are tropical streams really different? J. N. Am. Benthol. Soc. 28, 397–403 (2009).Article 

Google Scholar 
Ferreira, V. & Chauvet, E. Synergistic effects of water temperature and dissolved nutrients on litter decomposition and associated fungi. Glob. Change Biol. 17(1), 551–564. https://doi.org/10.1111/j.1365-2486.2010.02185.x (2011).Article 
ADS 

Google Scholar 
Whiles, M. R. & Wallace, J. B. Leaf litter decomposition and macroinvertebrate communities in headwater streams draining pine and hardwood catchments. Hydrobiologia 353, 107–119 (1997).Article 

Google Scholar 
Foucreau, N., Piscart, C., Puijalon, S. & Hervant, F. Effects of rising temperature on a functional process: Consumption and digestion of leaf litter by a freshwater shredder. Fundam. Appl. Limnol. 187(4), 295–306. https://doi.org/10.1127/fal/2016/0841 (2016).Article 

Google Scholar 
Poff, N. L. et al. Functional trait niches of North American lotic insects: Traits-based ecological applications in light of phylogenetic relationships. J. N. Am. Benthol. Soc. 25(4), 730–755 (2006).Article 

Google Scholar 
Menezes, S., Baird, D. J. & Soares, A. M. V. M. Beyond taxonomy: A review of macroinvertebrate trait-based community descriptors as tools for freshwater biomonitoring. J. Appl. Ecol. 47(4), 711–719. https://doi.org/10.1111/j.1365-2664.2010.01819.x (2010).Article 

Google Scholar 
Verberk, W. C. E. P., van Noordwijk, C. G. E. & Hildrew, A. G. Delivering on a promise: integrating species traits to transform descriptive community ecology into a predictive science. Freshw. Sci. 32(2), 531–547. https://doi.org/10.1899/12-092.1 (2013).Article 

Google Scholar 
Usseglio-Polatera, P., Bournaud, M., Richoux, P. & Tachet, H. Biomonitoring through biological traits of benthic macroinvertebrates: How to use species trait databases? Hydrobiologia 423, 153–162 (2000).Article 

Google Scholar 
Kneitel, J. & Chase, J. Trade-offs in community ecology: Linking spatial scales and species coexistence. Ecol. Lett. 7, 69–80 (2004).Article 

Google Scholar 
Pilière, A. F. H. et al. On the importance of trait interrelationships for understanding environmental responses of stream macroinvertebrates. Freshw. Biol. 61, 181–194. https://doi.org/10.1111/fwb.12690 (2016).Article 

Google Scholar  More

Baranova, M. Systematic anatomy of the leaf epidermis in the Magnoliaceae and some related families. Int. Assoc. Plant Taxon. (IAPT) 21, 447–469 (1972).
Google Scholar 
Suzuki, S., Kiyoshi, I., Saneyoshi, U., Yoshihiko, T. & Nobuhiro, T. Population differentiation and gene flow within ametapopulation of a threatened tree, Magnolia stellata (magnoliaceae). Am. J. Bot. 94, 128–136 (2007).Article 

Google Scholar 
Tan, M. et al. Study on seed germination and seedling growth of Magnolia officinalis in different habitats. J. Ecol. Rural Environ. 34, 910–916 (2018).
Google Scholar 
Zezhi, Y. et al. Study on population distribution and community structure of Magnolia sinostellata. Zhejiang For. Sci. Technol. 35, 47–52 (2015).
Google Scholar 
Yu, Q. et al. Light deficiency and waterlogging affect chlorophyll metabolism and photosynthesis in Magnolia sinostellata. Trees 33, 11–22. https://doi.org/10.1007/s00468-018-1753-5 (2018).Article 

Google Scholar 
Promis, A. & Allen, R. B. Tree seedlings respond to both light and soil nutrients in a Patagonian evergreen-deciduous forest. PLoS ONE 12, e0188686. https://doi.org/10.1371/journal.pone.0188686 (2017).Article 

Google Scholar 
Qin, Y. Effect of Light intensity and waterlogging on the physiology characteristic and the relative expression of genes in Magnolia sinostellata. 33, 11–22 (2018).
Chen, T. et al. Shade effects on peanut yield associate with physiological and expressional regulation on photosynthesis and sucrose metabolism. Int. J. Mol. Sci. https://doi.org/10.3390/ijms21155284 (2020).Article 

Google Scholar 
Yao, X. et al. Effect of shade on leaf photosynthetic capacity, light-intercepting, electron transfer and energy distribution of soybeans. Plant Growth Regul. 83, 409–416. https://doi.org/10.1007/s10725-017-0307-y (2017).Article 

Google Scholar 
Wu, Y., Gong, W. & Yang, W. Shade inhibits leaf size by controlling cell proliferation and enlargement in soybean. Sci. Rep. 7, 9259. https://doi.org/10.1038/s41598-017-10026-5 (2017).Article 
ADS 

Google Scholar 
Zhao, D., Hao, Z. & Tao, J. Effects of shade on plant growth and flower quality in the herbaceous peony (Paeonia lactiflora Pall.). Plant Physiol. Biochem. 61, 187–196. https://doi.org/10.1016/j.plaphy.2012.10.005 (2012).Article 

Google Scholar 
Tamaki, I. et al. Evaluation of a field experiment for the conservation of a Magnolia stellata stand using clear-cutting. Landscape Ecol. Eng. 14, 269–276. https://doi.org/10.1007/s11355-018-0348-z (2018).Article 

Google Scholar 
Jian, W. et al. Photosynthesis and chlorophyll fluorescence reaction to different shade stresses of weak light sensitive maize. Pak. J. Bot. 49, 1681–1688 (2017).
Google Scholar 
Quail, P. H. The phytochrome family dissection of functional roles and signalling pathways among family members. Philos. Trans. R. Soc. B 353, 1399–1403 (1998).Article 

Google Scholar 
Yang, F. et al. Effect of interactions between light intensity and red-to- far-red ratio on the photosynthesis of soybean leaves under shade condition. Environ. Exp. Bot. 150, 79–87. https://doi.org/10.1016/j.envexpbot.2018.03.008 (2018).Article 

Google Scholar 
Luesse, D. R., DeBlasio, S. L. & Hangarter, R. P. Integration of Phot1, Phot2, and PhyB signalling in light-induced chloroplast movements. J. Exp. Bot. 61, 4387–4397. https://doi.org/10.1093/jxb/erq242 (2010).Article 

Google Scholar 
Dinakar, C., Vishwakarma, A., Raghavendra, A. S. & Padmasree, K. Alternative oxidase pathway optimizes photosynthesis during osmotic and temperature stress by regulating cellular ROS, malate valve and antioxidative systems. Front. Plant Sci. 7, 68. https://doi.org/10.3389/fpls.2016.00068 (2016).Article 

Google Scholar 
Ruban, A. V. Light harvesting control in plants. FEBS Lett. 592, 3030–3039. https://doi.org/10.1002/1873-3468.13111 (2018).Article 

Google Scholar 
Wang, J. et al. Photosynthesis and chlorophyll fluorescence reaction to different shade stresses of weak light sensitive maize. Pak. J. Bo. 49, 1681–1688 (2017).
Google Scholar 
Yamori, W., Shikanai, T. & Makino, A. Photosystem I cyclic electron flow via chloroplast NADH dehydrogenase-like complex performs a physiological role for photosynthesis at low light. Sci. Rep. 5, 13908. https://doi.org/10.1038/srep13908 (2015).Article 
ADS 

Google Scholar 
Ng, J. & Mueller-Cajar, O. Rubisco activase remodels plant Rubisco via the large subunit N-terminus. bioRxiv https://doi.org/10.1101/2020.06.14.151407 (2020).Article 

Google Scholar 
Zhang, Y., Liu, N., Wang, W., Sun, J. & Zhu, L. Photosynthesis and related metabolic mechanism of promoted rice (Oryza sativa L.) growth by TiO2 nanoparticles. Front. Environ. Sci. Eng. https://doi.org/10.1007/s11783-020-1282-5 (2020).Article 

Google Scholar 
Suzuki, Y. & Makino, A. Translational downregulation of RBCL is operative in the coordinated expression of Rubisco genes in senescent leaves in rice. J. Exp. Bot. 64, 1145–1152. https://doi.org/10.1093/jxb/ers398 (2013).Article 

Google Scholar 
Sun, J. et al. Low light stress down-regulated rubisco gene expression and photosynthetic capacity during cucumber (Cucumis sativus L.) leaf development. J. Integr. Agric. 13, 997–1007. https://doi.org/10.1016/s2095-3119(13)60670-x (2014).Article 

Google Scholar 
Wu, H. Y., Liu, L. A., Shi, L., Zhang, W. F. & Jiang, C. D. Photosynthetic acclimation during low-light-induced leaf senescence in post-anthesis maize plants. Photosynth. Res. 150, 313–326. https://doi.org/10.1007/s11120-021-00851-1 (2021).Article 

Google Scholar 
Zou, D., Gao, K. & Chen, W. Photosynthetic carbon acquisition in Sargassum henslowianum (Fucales, Phaeophyta), with special reference to the comparison between the vegetative and reproductive tissues. Photosynth. Res. 107, 159–168. https://doi.org/10.1007/s11120-010-9612-2 (2011).Article 

Google Scholar 
Wu, Z.-F. et al. Effects of low light stress on rubisco activity and the ultrastructure of chloroplast in functional leaves of peanut. Chin. J. Plant Ecol. 38, 740–748. https://doi.org/10.3724/SP.J.1258.2014.00069 (2014).Article 

Google Scholar 
Valladares, F. et al. The greater seedling high-light tolerance of Quercus robur over Fagus sylvatica is linked to a greater physiological plasticity. Trees 16, 395–403. https://doi.org/10.1007/s00468-002-0184-4 (2002).Article 

Google Scholar 
Rojas-Gonzalez, J. A. et al. Disruption of both chloroplastic and cytosolic FBPase genes results in a dwarf phenotype and important starch and metabolite changes in Arabidopsis thaliana. J. Exp. Bot. 66, 2673–2689. https://doi.org/10.1093/jxb/erv062 (2015).Article 

Google Scholar 
Lowe, H., Hobmeier, K., Moos, M., Kremling, A. & Pfluger-Grau, K. Photoautotrophic production of polyhydroxyalkanoates in a synthetic mixed culture of Synechococcus elongatus cscB and Pseudomonas putida cscAB. Biotechnol. Biofuels 10, 190. https://doi.org/10.1186/s13068-017-0875-0 (2017).Article 

Google Scholar 
Wang, B. et al. Photosynthesis, sucrose metabolism, and starch accumulation in two NILs of winter wheat. Photosynth. Res. 126, 363–373. https://doi.org/10.1007/s11120-015-0126-9 (2015).Article 

Google Scholar 
Myers, J. A. & Kitajima, K. Carbohydrate storage enhances seedling shade and stress tolerance in a neotropical forest. J. Ecol. 95, 383–395. https://doi.org/10.1111/j.1365-2745.2006.01207.x (2007).Article 

Google Scholar 
Lestari, D. P. & Nichols, J. D. Seedlings of subtropical rainforest species from similar successional guild show different photosynthetic and morphological responses to varying light levels. Tree Physiol. 37, 186–198. https://doi.org/10.1093/treephys/tpw088 (2017).Article 

Google Scholar 
Wu, M., Li, Z. & Wang, J. Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plant Solidago canadensis. Ecol. Evol. 10, 4391–4406. https://doi.org/10.1002/ece3.6206 (2020).Article 

Google Scholar 
Miao, Z. Q. et al. HOMEOBOX PROTEIN52 mediates the crosstalk between ethylene and auxin signaling during primary root elongation by modulating auxin transport-related gene expression. Plant Cell 30, 2761–2778. https://doi.org/10.1105/tpc.18.00584 (2018).Article 

Google Scholar 
Liu, B. et al. A domestication-associated gene, CsLH, encodes a phytochrome B protein that regulates hypocotyl elongation in cucumber. Mol. Hortic. https://doi.org/10.1186/s43897-021-00005-w (2021).Article 

Google Scholar 
Sun, W. et al. Mediator subunit MED25 physically interacts with phytochrome interacting factor4 to regulate shade-induced hypocotyl elongation in tomato. Plant Physiol. 184, 1549–1562. https://doi.org/10.1104/pp.20.00587 (2020).Article 

Google Scholar 
Bawa, G. et al. Gibberellins and auxin regulate soybean hypocotyl elongation under low light and high-temperature interaction. Physiol. Plant 170, 345–356. https://doi.org/10.1111/ppl.13158 (2020).Article 

Google Scholar 
Potter, T. I., Rood, S. B. & Zanewich, K. P. Light intensity, gibberellin content and the resolution of shoot growth in Brassica. Planta 207, 505–511 (1999).Article 

Google Scholar 
Ballare, C. L., Scopel, A. L. & San, R. A. Foraging for light photosensory ecology and agricultural implications. Plant Cell Environ. 20, 820–825 (1997).Article 

Google Scholar 
Hope, E., Gracie, A., Carins-Murphy, M. R., Hudson, C. & Baxter, L. Opium poppy capsule growth and alkaloid production is constrained by shade during early floral development. Ann. Appl. Biol. 176, 296–307 (2020).Article 

Google Scholar 
Lu, D. et al. Light deficiency inhibits growth by affecting photosynthesis efficiency as well as JA and ethylene signaling in endangered plant Magnolia sinostellata. Plants https://doi.org/10.3390/plants10112261 (2021).Article 

Google Scholar 
Lin, W., Guo, X., Pan, X. & Li, Z. Chlorophyll composition, chlorophyll fluorescence, and grain yield change in esl mutant rice. Int. J. Mol. Sci. https://doi.org/10.3390/ijms19102945 (2018).Article 

Google Scholar 
Sano, S. et al. Stress responses of shade-treated tea leaves to high light exposure after removal of shading. Plants (Basel) https://doi.org/10.3390/plants9030302 (2020).Article 

Google Scholar 
Liu, D. L. et al. Genetic map construction and QTL analysis of leaf-related traits in soybean under monoculture and relay intercropping. Sci. Rep. 9, 2716. https://doi.org/10.1038/s41598-019-39110-8 (2019).Article 
ADS 

Google Scholar 
Sekhar, S. et al. Comparative transcriptome profiling of low light tolerant and sensitive rice varieties induced by low light stress at active tillering stage. Sci. Rep. 9, 5753. https://doi.org/10.1038/s41598-019-42170-5 (2019).Article 
ADS 

Google Scholar 
Wegener, F., Beyschlag, W. & Werner, C. High intraspecific ability to adjust both carbon uptake and allocation under light and nutrient reduction in Halimium halimifolium L. Front. Plant Sci. 6, 609. https://doi.org/10.3389/fpls.2015.00609 (2015).Article 

Google Scholar 
Liu, B. et al. A HY5-COL3-COL13 regulatory chain for controlling hypocotyl elongation in Arabidopsis. Plant Cell Environ. 44, 130–142. https://doi.org/10.1111/pce.13899 (2021).Article 

Google Scholar 
Cookson, S. J. & Granier, C. A dynamic analysis of the shade-induced plasticity in Arabidopsis thaliana rosette leaf development reveals new components of the shade-adaptative response. Ann. Bot. 97, 443–452. https://doi.org/10.1093/aob/mcj047 (2006).Article 

Google Scholar 
Zhong, X. M., Shi, Z. S., Li, F. H. & Huang, H. J. Photosynthesis and chlorophyll fluorescence of infertile and fertile stalks of paired near-isogenic lines in maize (Zea mays L.) under shade conditions. Photosynthetica 52, 597–603. https://doi.org/10.1007/s11099-014-0071-4 (2014).Article 

Google Scholar 
Kittiwongwattana, C. Differential effects of synthetic media on long-term growth, starch accumulation and transcription of ADP-glucosepyrophosphorylase subunit genes in Landoltia punctata. Sci. Rep. 9, 15310. https://doi.org/10.1038/s41598-019-51677-w (2019).Article 
ADS 

Google Scholar 
Sagadevan, G. M. et al. Physiological and molecular insights into drought tolerance. Afr. J. Biotechnol. 1, 28–38 (2002).Article 

Google Scholar 
Xiaotao, D. et al. Effects of cytokinin on photosynthetic gas exchange, chlorophyll fluorescence parameters, antioxidative system and carbohydrate accumulation in cucumber (Cucumis sativus L.) under low light. Acta Physiologiae Plant. 35, 1427–1438. https://doi.org/10.1007/s11738-012-1182-9 (2012).Article 

Google Scholar 
Sofo, A., Dichio, B., Montanaro, G. & Xiloyannis, C. Photosynthetic performance and light response of two olive cultivars under different water and light regimes. Photosynthetica 47, 602–608 (2009).Article 

Google Scholar 
Zhou, Y., Zhu, J., Shao, L. & Guo, M. Current advances in acteoside biosynthesis pathway elucidation and biosynthesis. Fitoterapia 142, 104495. https://doi.org/10.1016/j.fitote.2020.104495 (2020).Article 

Google Scholar 
Huang, P. et al. Overexpression of L-type lectin-like protein kinase 1 confers pathogen resistance and regulates salinity response in Arabidopsis thaliana. Plant Sci. 203–204, 98–106. https://doi.org/10.1016/j.plantsci.2012.12.019 (2013).Article 

Google Scholar 
Vorontsov, I. I. et al. Crystal structure of an apo form of Shigella flexneri ArsH protein with an NADPH-dependent FMN reductase activity. Protein Sci. 16, 2483–2490. https://doi.org/10.1110/ps.073029607 (2007).Article 

Google Scholar 
Guo, M. et al. Proteomic and phosphoproteomic analyses of NaCl stress-responsive proteins in Arabidopsis roots. J. Plant Interact. 9, 396–401. https://doi.org/10.1080/17429145.2013.845262 (2013).Article 

Google Scholar 
Smith, C. et al. Alterations in the mitochondrial alternative NAD(P)H Dehydrogenase NDB4 lead to changes in mitochondrial electron transport chain composition, plant growth and response to oxidative stress. Plant Cell Physiol. 52, 1222–1237. https://doi.org/10.1093/pcp/pcr073 (2011).Article 

Google Scholar 
Johnson, K. L., Jones, B. J., Bacic, A. & Schultz, C. J. The fasciclin-like arabinogalactan proteins of Arabidopsis. A multigene family of putative cell adhesion molecules. Plant Physiol. 133, 1911–1925. https://doi.org/10.1104/pp.103.031237 (2003).Article 

Google Scholar 
Merz, D. et al. T-DNA alleles of the receptor kinase THESEUS1 with opposing effects on cell wall integrity signaling. J. Exp. Bot. 68, 4583–4593. https://doi.org/10.1093/jxb/erx263 (2017).Article 

Google Scholar 
Figueiredo, J., Silva, M. S. & Figueiredo, A. Subtilisin-like proteases in plant defence: The past, the present and beyond. Mol. Plant Pathol. 19, 1017–1028. https://doi.org/10.1111/mpp.12567 (2018).Article 

Google Scholar 
Sintupachee, S., Promden, W., Ngamrojanavanich, N., Sitthithaworn, W. & De-Eknamkul, W. Functional expression of a putative geraniol 8-hydroxylase by reconstitution of bacterially expressed plant CYP76F45 and NADPH-cytochrome P450 reductase CPR I from Croton stellatopilosus Ohba. Phytochemistry 118, 204–215. https://doi.org/10.1016/j.phytochem.2015.08.005 (2015).Article 

Google Scholar 
Chen, Y. et al. Enzymatic reaction-related protein degradation and proteinaceous amino acid metabolism during the black tea (Camellia sinensis) manufacturing process. Foods https://doi.org/10.3390/foods9010066 (2020).Smidansky, E. D. et al. Expression of a modified ADP-glucose pyrophosphorylase large subunit in wheat seeds stimulates photosynthesis and carbon metabolism. Planta 225, 965–976. https://doi.org/10.1007/s00425-006-0400-3 (2007).Article 

Google Scholar 
Mathur, S., Jain, L. & Jajoo, A. Photosynthetic efficiency in sun and shade plants. Photosynthetica https://doi.org/10.1007/s11099-018-0767-y (2018).Article 

Google Scholar 
Huang, W., Zhang, S. B. & Liu, T. Moderate photoinhibition of photosystem II significantly affects linear electron flow in the shade-demanding plant panax notoginseng. Front. Plant Sci. 9, 637. https://doi.org/10.3389/fpls.2018.00637 (2018).Article 

Google Scholar 
Li, Q. et al. Quantitative trait locus (QTLs) mapping for quality traits of wheat based on high density genetic map combined with bulked segregant analysis RNA-seq (BSR-Seq) indicates that the basic 7S globulin gene is related to falling number. Front. Plant Sci. 11, 600788. https://doi.org/10.3389/fpls.2020.600788 (2020).Article 

Google Scholar 
Hashempour, A., Ghasemnezhad, M., Sohani, M. M., Ghazvini, R. F. & Abedi, A. Effects of freezing stress on the expression of fatty acid desaturase (FAD2, FAD6 and FAD7) and beta-glucosidase (BGLC) genes in tolerant and sensitive olive cultivars. Russ. J. Plant Physiol. 66, 214–222. https://doi.org/10.1134/s1021443719020079 (2019).Article 

Google Scholar 
Limami, M. A., Sun, L.-Y., Douat, C., Helgeson, J. & Tepfer, D. Natural genetic transformation by__Agrobacterium rhizogenes. Plant Physiol. 118, 543–550 (1998).Article 

Google Scholar 
Devlin, P. F., Yanovsky, M. J. & Kay, S. A. A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol. 133, 1617–1629. https://doi.org/10.1104/pp.103.034397 (2003).Article 

Google Scholar 
Lorenzo, C. D. et al. Shade delays flowering in Medicago sativa. Plant J. 99, 7–22. https://doi.org/10.1111/tpj.14333 (2019).Article 

Google Scholar 
Rezazadeh, A., Harkess, R. & Telmadarrehei, T. The effect of light intensity and temperature on flowering and morphology of potted red firespike. Horticulturae https://doi.org/10.3390/horticulturae4040036 (2018).Article 

Google Scholar 
Guo, C. et al. OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice. J. Integr. Plant Biol. 58, 492–502. https://doi.org/10.1111/jipb.12376 (2016).Article 

Google Scholar 
Kapolas, G. et al. APRF1 promotes flowering under long days in Arabidopsis thaliana. Plant Sci. 253, 141–153. https://doi.org/10.1016/j.plantsci.2016.09.015 (2016).Article 

Google Scholar 
Walla, A. et al. An Acyl-CoA N-Acyltransferase regulates meristem phase change and plant architecture in barley. Plant Physiol. 183, 1088–1109. https://doi.org/10.1104/pp.20.00087 (2020).Article 
ADS 

Google Scholar 
Goto, M. K. A. S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).Article 

Google Scholar  More

Research site descriptionA 3-year stationary field experiment was conducted at the Yuanziqu experimental station of the Bayannur Academy of Agricultural and Animal Husbandry Sciences (40° 90′ N, 107° 17′ E), Linhe, Inner Mongolia, China, from 2019 to 2021. The site has a continental monsoon climate typical of the northern mid-temperate zone, with a mean annual temperature from 3.7  to  7.6 °C, and the potential evaporation is 2200–2400 mm15. The total precipitation during the wheat growth period (March–July) was 66 mm, 110 mm and 47 mm in 2019, 2020, and 2021, respectively. Daily air temperature and precipitation during the field trial period are presented in Fig. 1.Figure 1Daily maximum temperature, daily minimum temperature and precipitation during the growth period (March–July) of spring wheat from 2019 to 2021 in the field experiment at Linhe, Inner Mongolia, China.Full size imageThe soil at the experimental site is a silt loam. The major physical and chemical properties of the 0–20 cm soil layer at the experimental site in 2019 were as follows: a bulk density of 1.48 g cm−3, pH 8.3, organic matter content of 15.49 g kg−1, total N concentration of 1.20 g kg−1, nitrate (NO3− N) concentration of 3.98 mg N kg−1, Olsen-P concentration of 32.3 mg P kg−1 and available K concentration of 180.0 mg K kg−1.Experimental design and field managementA local popular spring wheat (Triticum aestivum L.) cultivar, Yongliang No. 4, was used in the trials. The sowing dates were 20 March, 16 March and 13 March in 2019, 2020 and 2021, respectively; the harvest dates were 15 July, 15 July and 5 July in 2019, 2020 and 2021, respectively. A total of 375 kg ha−1 wheat seeds were sown at a depth of 5 cm.Five fertilization treatments were set in the three consecutive experimental years, including the control (CK), farmer practice (FP) and three balanced fertilization treatments (BF1, BF2 and BF3), as presented in Table 1. The P and K fertilizers as single superphosphate and K2SO4 were basal dressed, respectively. Both basal- and top-dressing of N fertilizer as urea were applied as shown in the research program. The basal applications occurred during sowing, and the remaining N fertilizer was top-dressed at the tillering stage (Table 1). The experimental plot was 10 m × 7 m with 13 cm row spacing and a buffer zone of 1 m between plots. The plots were laid out in a completely randomized block design with three replications.Table 1 Fertilization regimes of the different treatments in the 2019–2021 field trial.Full size tableEvery plot was ridged around its border to ensure the uniformity of irrigation. Flood irrigation from Yellow River water was performed according to the local policy and farmer practices. Irrigation water (30 mm) was applied at the tillering, jointing, heading and grain filling stages of spring wheat in 2019–2021. Disease, weed, and pest control, as well as other management, were performed according to local standard methods.Sampling and sample analysisThree 50 cm-long rows of spring wheat plants were selected randomly and pulled from each plot, from which 10 large, middle and small seedlings were picked out during each sampling effort. Then, the roots were cut off from the junction between the root and the stem, two plant parts (leaves and stems) before the heading stage, three plant parts (leaves, stems and spikes) at the heading stage, and four plant parts (leaves, stems, glumes and grains) at the grain filling stages and maturity were separated and pooled. The samples were dried for 30 min at 105 °C and then at 80 °C in an oven (DHG-9070A, China) until they reached a constant weight; the dry weight was then measured.The N concentrations in leaves, stems, spikes and grains of spring wheat were measured with three replications depending on the crop stage, following the Kjeldahl procedure using an element analyzer (Vario El cube, Elementar, Germany).Three soil cores containing 0–100 cm of soil were taken from each plot using an auger at the harvest of spring wheat each year. The soil samples of each 20 cm layer were collected separately and sealed immediately in a marked plastic bag. The extracts were immediately measured for nitrate-N concentration as described by Dai et al. (2015) with a continuous flow analyzer (SKALAR SAN++, Netherlands)16. The soil nitrate-N concentration was expressed on the basis of the oven-dried soil.Grain yield was evaluated at maturity by selecting two 2 m2 (avoiding border rows) randomly and harvested. A fresh weight of ∼ 1 kg of grain from each plot was weighed in the field, and the water content from each plot was oven dried for the calculation. The actual yield was adjusted by a grain water content of 13%17. Grains per spike, 1000-grain weight and spike number were determined at three 50-cm sites sampled randomly from each plot.Calculation methodsTo clarify the effect of nitrate residue in the soil under balanced fertilization, the amount of soil nitrate-N (AN, kg N ha−1) in each layer was expressed as:$${text{AN}} = left( {{text{Ti}};*;{text{Di}};*;{text{Ci}}} right)/10$$
where Ti is the soil layer thickness (cm), Di is the soil bulk density (g cm−3), Ci is the soil nitrate concentration (mg N kg−1) of the corresponding layer, and 10 is the conversion coefficient16. The AN of 0–20, 20–40, 40–60, 60–80 and 80–100 cm soil layers were recorded and measured, respectively.Nitrogen accumulation in the vegetative organs and their distribution into the grain were investigated. Based on the dry weight and corresponding measured N concentration in the different organs, apparent N translocation (TA, kg ha−1) and apparent N translocation efficiency (TR, %) were calculated as proposed by Cox et al.18 as follows:$$begin{aligned} {text{TA}} & {text{ = H}}_{{text{N}}} – {text{M}}_{{text{N}}} \ {text{TR}} & = {text{TA/H}}_{{text{N}}} *100 \ end{aligned}$$
where HN is the N assimilation in leaves or stems prior to anthesis (kg ha−1), MN is the N assimilation in leaves or stems at maturity (kg ha−1).Two parameters of nitrogen use efficiency of spring wheat, nitrogen fertilizer partial productivity (PFPN, kg/kg) and agronomic nitrogen efficiency (NAEN, kg kg−1) were determined using the following formulas:$$begin{aligned} {text{PFP}}_{{text{N}}} & = {text{ Y}}_{N; , fertilizer} /{text{N}}_{rate} \ {text{NAE}}_{{text{N}}} & = , left( {{text{Y}}_{{N;fertilizer , {-}}} {text{Y}}_{blank} } right)/{text{N}}_{rate} \ end{aligned}$$
where YN fertilizer is the grain yield of the plot with dressed N fertilizer (kg ha−1), Yblank is the grain yield of the plot without dressed N fertilizer (kg ha−1), and Nrate is the N rate of the dressed fertilizer plot (kg ha−1). Three measurements for each treatment was recorded and calculated.Two key indicators were chosen to evaluate the risk of N losses as described by Li et al. (2020)7, including N surplus (kg N per hectare per year, Nsur) and N input (kg N per hectare per year, Ninput). The N surplus was used to evaluate the risk of N losses and the N input to guide farmers’ fertilization practices directly. The detailed calculation is as follows:$$begin{aligned} {text{N}}_{{{text{sur}}}} & = {text{ N}}_{{{text{fer}}}} + {text{ N}}_{{{text{dep}}}} + {text{ N}}_{{{text{fix}}}} – {text{ N}}_{{{text{har}}}} \ {text{N}}_{{{text{input}}}} & = {text{ N}}_{{{text{har}}}} + {text{ N}}_{{{text{sur}}}} + {text{ soil N change in stock }};;;( approx 0{text{ in long run}}) \ end{aligned}$$
where Nfer, Ndep and Nfix represent N from fertilizer, atmospheric deposition and biological fixed N, respectively. Seed N was negligible as it was present in a very small amount compared to the fertilization input19. The total N deposition of spring wheat field and biological N fixation were adopted according to Li et al. (2020). Nhar refers to the harvested N in spring wheat.Economic analysisThe inputs into local spring wheat production included chemical fertilizer, irrigated water, agricultural chemicals, seed, mechanical effort and labor costs, while income was obtained from the grain and wheat straw. The net income was determined from the difference between the total output and total input. The irrigated water, agricultural chemicals, seed, mechanical effort and labor costs were the same for the different treatments. The prices of the input and output materials were determined according to the average local market prices, and fluctuations were not considered among years.Statistical analysesThe results were analyzed using SPSS software (version 19.0; SPSS Inc., Chicago, IL, USA). Analysis of variance (ANOVA) and the least significant difference (LSD) test were used, and a P value of 0.05 was considered significant. More

Smith, K. F., Sax, D. F. & Lafferty, K. D. Evidence for the role of infectious disease in species extinction and endangerment. Conserv. Biol. 20, 1349–1357 (2006).Article 

Google Scholar 
Daszak, P., Cunningham, A. A. & Hyatt, A. D. Emerging infectious diseases of wildlife—Threats to biodiversity and human health. Science 287, 443–449 (2000).Article 
ADS 

Google Scholar 
Pedersen, A. B., Jones, K. E., Nunn, C. L. & Altizer, S. Infectious diseases and extinction risk in wild mammals. Conserv. Biol. 21, 1269–1279 (2007).Article 

Google Scholar 
Kołodziej-Sobocińska, M. Factors affecting the spread of parasites in populations of wild European terrestrial mammals. Mamm. Res. 64, 301–318 (2019).Article 

Google Scholar 
Borowik, T., Ratkiewicz, M., Maślanko, W., Duda, N. & Kowalczyk, R. Too hot to handle: Summer space use shift in a cold-adapted ungulate at the edge of its range. Landsc. Ecol. 35, 1341–1351 (2020).Article 

Google Scholar 
Demiaszkiewicz, A. W. et al. The Nematodes Thelazia gulosa Railiet and Henry, 1910 and Thelazia skrjabini Erschov, 1928 as a cause of blindness in European Bison (Bison bonasus) in Poland. Acta Parasitol. 65, 963–968 (2020).Article 

Google Scholar 
Anderson, R. C. (ed.) Nematode Parasites of Vertebrates. Their Development and Transmission (CAB International, 1992).
Google Scholar 
Otranto, D. & Traversa, D. Thelazia eyeworm: An original endo- and ecto-parasitic nematode. Trends Parasitol. 21, 1–4 (2005).Article 

Google Scholar 
Bradbury, R. S. et al. A second case of human conjunctival infestation with Thelazia gulosa and a review of T. gulosa in North America. Clin. Infect. Dis. 70, 518–520 (2020).
Google Scholar 
Lyons, E. T., Drudge, J. H. & Tolliver, S. C. Thelazia lacrymalis in horses in Kentucky and observations on the face fly (Musca autumnalis) as a probable intermediate host. J. Parasitol. 62, 877–880 (1976).Article 

Google Scholar 
Giangaspero, A., Traversa, D. & Otranto, D. Ecology of Thelazia spp. in cattle and their vectors in Italy. Parasitologia 46, 257–259 (2004).
Google Scholar 
Kostyra, J. The clinical picture and treatment of bovine thelaziosis (Przebieg i leczenie telazjozy u bydła, in Polish). Med. Weter. 16, 584–587 (1960).
Google Scholar 
Rosłan, J. Badania nad telazjozą bydła w Polsce. Wiad. Parazyt. 11, 73–79 (1965).
Google Scholar 
Kozakiewicz, B. Bovine thelaziosis in Żuławy (Telazjoza bydła na Żuławach, in Polish). Med. Weter. 27, 241–243 (1971).
Google Scholar 
Samojlik, T. (ed.) European Bison. The Nature Monograph (Springer, 2013).
Google Scholar 
Raczyński, J. (ed.) European Bison Pedigree Book (Księga rodowodowa żubrów, in Polish) 1–82 (Białowieski Park Narodowy, 2019).
Google Scholar 
Pucek, Z. et al. (eds) European Bison. Status Survey and Conservation Action Plan (IUCN/SSC Action Plans for the Conservation of Biological Diversity, 2004).
Google Scholar 
Buchmann, K., Christiansen, L.-L., Kania, P. W. & Thamsborg, S. M. Introduced European bison (Bison bonasus) in a confined forest district: A ten year parasitological survey. Int. J. Parasitol. Parasites Wildl. 18, 292–299 (2022).Article 

Google Scholar 
Giangaspero, A., Otranto, D., Vovlas, N. & Puccini, V. Thelazia gulosa Railliet & Henry, 1910 and T. skrjabini Erschow, 1928 infection in southern Europe (Italy). Parasite 7, 327–329 (2000).Article 

Google Scholar 
Klësov, M. D. Contribution to the question of the biology of two nematodes of the genus Thelazia Bosc, 1819, parasites of the eyes of cattle. Dokl. Akad. Nauk SSSR 75, 591–594 (1950).
Google Scholar 
Arbuckle, J. B. & Khalil, L. F. A survey of Thelazia worms in the eyelids of British cattle. Vet. Rec. 102, 207–210 (1978).Article 

Google Scholar 
Tweedle, D. M., Fox, M. T., Gibbons, L. M. & Tennant, K. V. Change in the prevalence of Thelazia species in bovine eyes in England. Vet. Rec. 157, 555–556 (2005).Article 

Google Scholar 
Kolstrup, N. Thelazia skrjabini in Danish cattle. Nord. Vet. Med. 26, 459–462 (1974).
Google Scholar 
Deak, G., Ionică, A. M., Oros, N. V., Gherman, C. M. & Mihalca, A. D. Thelazia rhodesi in a dairy farm in Romania and successful treatment using eprinomectin. Parasitol. Int. 80, 102183 (2021).Article 

Google Scholar 
Dróżdż, J. A study on helminth and helminthiases in bison, Bison bonasus (L.) in Poland. Acta Parasitol. Pol. 9, 55–96 (1961).
Google Scholar 
Dróżdż, J., Demiaszkiewicz, A. W. & Lachowicz, J. The helminth fauna of free-ranging European bison, Bison bonasus (L.). Acta Parasitol. Pol. 34, 117–124 (1989).
Google Scholar 
Otranto, D., Tarsitano, E., Traversa, D., De Luca, F. & Giangaspero, A. Molecular epidemiological survey on the vectors of Thelazia gulosa, Thelazia rhodesi and Thelazia skrjabini (Spirurida: Thelaziidae). Parasitology 127, 365–373 (2003).Article 

Google Scholar 
Viney, M. E. & Graham, A. L. Patterns and processes in parasite co-infection. Adv. Parasitol. 82, 321–369 (2013).Article 

Google Scholar 
Demiaszkiewicz, A. W. & Kaczor, S. Thelaziasis in European bison in Bieszczady—A case report. Życie Weter. 90, 108–110 (2015).
Google Scholar 
Thompson, R. C. Parasite zoonoses and wildlife: One health, spillover and human activity. Int. J. Parasitol. 43, 1079–1088 (2013).Article 

Google Scholar 
Naem, S. Thelazia rhodesi (Spirurida, Thelaziidae), bovine eyeworm: Morphological study by scanning electron microscopy. Parasitol. Res. 100, 855–860 (2007).Article 

Google Scholar 
Krasińska, M. & Krasiński, Z. A. Composition, group size, and spatial distribution of European bison bulls in Białowieża Forest. Acta Theriol. 40, 1–21 (1995).Article 

Google Scholar 
Krasińska, M., Krasiński, Z. A. & Bunevich, A. N. Factors affecting the variability in home range size and distribution in European bison in the Polish and Belarussian parts of the Białowieża Forest. Acta Theriol. 45, 321–334 (2000).Article 

Google Scholar 
Lloyd, S. Effect of pregnancy and lactation upon infection. Vet. Immunol. Immunopathol. 4, 153–176 (1983).Article 

Google Scholar 
Martin, L. B., Weil, Z. M. & Nelson, R. J. Seasonal changes in vertebrate immune activity: Mediation by physiological trade-offs. Philos. Trans. R. Soc. Lond. B Biol Sci. 363, 321–339 (2008).Article 

Google Scholar 
Muturi, K. N. et al. The effect of dietary polyunsaturated fatty acids (PUFA) on infection with the nematodes Ostertagia ostertagi and Cooperia oncophora in calves. Vet. Parasitol. 129, 273–283 (2005).Article 

Google Scholar 
Krasnov, B. R. & Matthee, S. Spatial variation in gender-biased parasitism: Host-related, parasite-related and environment-related effects. Parasitology 137, 1527–1536 (2010).Article 

Google Scholar 
Dunn, A. M. (ed.) Veterinary Helminthology (William Heinemann Medical Books, 1978).
Google Scholar 
Khedri, J., Radfar, M. H., Borji, H. & Azizzadeh, M. Epidemiological survey of bovine thelaziosis in southeastern of Iran. Iran. J. Parasitol. 11, 221–225 (2016).
Google Scholar 
Draber-Mońko, A. Synanthropic Calyptrata in selected habitats in Poland. Wiad. Parazytol. 32, 411–418 (1986).
Google Scholar 
Draber-Mońko, A. Dipterans of the families Muscidae (Muscinae) and Scathophagidae (Diptera, Calyptrata) of the Świętokrzyski Region. Fragmenta Faunistica 36, 205–233 (1993).Article 

Google Scholar 
Nosal, P., Kowal, J., Węglarz, A. & Wyrobisz-Papiewska, A. The occurrence and diversity of flies (Diptera) related to ruminant farming in southern Poland. Ann. Parasitol. 65, 357–363 (2019).
Google Scholar 
Cotuțiu, V. D. et al. Thelazia lacrymalis in horses from Romania: Epidemiology, morphology and phylogenetic analysis. Parasites Vectors 15, 425 (2022).Article 

Google Scholar 
Nowosad, M. Outlines of climate of the Bieszczady National Park and its buffer zone in the light of previous studies. Roczniki Bieszczadzkie 4, 163–183 (1995).
Google Scholar 
Guindon, S. & Gascuel, O. A. Simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003).Article 

Google Scholar 
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: More models, new heuristics and parallel computing. Nat. Methods 9, 77 (2012).Article 

Google Scholar 
Altman, D. G. et al. (eds) Statistics with Confidence 2nd edn, 46–47 (BMJ Books, 2000).
Google Scholar  More

Gentry, A. Mammal Species of the World. A Taxonomic and Geographic Reference. 2005. Don E. Wilson & DeeAnn M. Reeder (Eds.). Ed. 3, 2 Vols., 2142 Pp. Johns Hopkins University Press, Baltimore. ISBN 0-8018-8221-4. A Nomenclatural Review. The Bulletin of zoological nomenclature. 2006, 63, 215–219.Dickman, C. R. Rodent-ecosystem relationships: A review. Ecologically-based management of rodent pests. ACIAR Monogr. 59, 113–133 (1999).
Google Scholar 
Tobin, M., Fall, M. W. Pest control: Rodents. In Pest Control: Rodents, Encyclopedia of Life Support Systems (EOLSS) (2005).Meerburg, B. G., Singleton, G. R. & Kijlstra, A. Rodent-borne diseases and their risks for public health. Crit. Rev. Microbiol. 35, 221–270. https://doi.org/10.1080/10408410902989837 (2009).Article 

Google Scholar 
Kalfayan, B. H. Leptospira Icterohaemorrhagiae in rats of Beirut. Trans. R. Soc. Trop. Med. Hyg. 40, 895–900. https://doi.org/10.1016/0035-9203(47)90045-X (1947).Article 

Google Scholar 
Jackson, W. B. Evaluation of rodent depredations to crops and stored products1. EPPO Bull. 7, 439–458. https://doi.org/10.1111/j.1365-2338.1977.tb02743.x (1977).Article 

Google Scholar 
Stejskal, V., Hubert, J., Aulicky, R. & Kucerova, Z. Overview of present and past and pest-associated risks in stored food and feed products: European perspective. J. Stored Prod. Res. 64, 122–132. https://doi.org/10.1016/j.jspr.2014.12.006 (2015).Article 

Google Scholar 
Jacob, J., Buckle, A. Use of anticoagulant rodenticides in different applications around the world. In Anticoagulant Rodenticides and Wildlife 11–43. https://doi.org/10.1007/978-3-319-64377-9_2Puckett, E. E. et al. Global population divergence and admixture of the brown rat (Rattus Norvegicus). Proc. R. Soc. B Biol. Sci. 283, 20161762. https://doi.org/10.1098/rspb.2016.1762 (2016).Article 

Google Scholar 
Barzman, M. et al. Eight principles of integrated pest management. Agron. Sustain. Dev. 35, 1199–1215. https://doi.org/10.1007/s13593-015-0327-9 (2015).Article 

Google Scholar 
Chellappan, M. Rodents. in Polyphagous Pests of Crops (ed. Omkar) 457–532 (Springer: Singapore, 2021) ISBN 9789811580758.Prakash, I. in Rodent Pest Management (CRC Press, 2018) ISBN 978-1351-08490-1.Hadler, M. R., Buckle, A. P. Forty five years of anticoagulant rodenticides-past, present and future trends. In: Proceedings of the 15th Vertebrate Pest Conference 149–155 (1992).Watt, B. E., Proudfoot, A. T., Bradberry, S. M. & Vale, J. A. Anticoagulant rodenticides. Toxicol. Rev. 24, 259–269. https://doi.org/10.2165/00139709-200524040-00005 (2005).Article 

Google Scholar 
Matagrin, B. et al. New insights into the catalytic mechanism of vitamin K epoxide reductase (VKORC1)—The catalytic properties of the major mutations of RVKORC1 explain the biological cost associated to mutations. FEBS Open Bio 3, 144–150. https://doi.org/10.1016/j.fob.2013.02.001 (2013).Article 

Google Scholar 
RRAC Rodenticide Resistance Action Group Available online: http://guide.rrac.info/resistancemaps/resistance-maps/. Information correct as off 09. (Accessed on 7 April 2021).McGee, C. F., McGilloway, D. A. & Buckle, A. P. Anticoagulant rodenticides and resistance development in rodent pest species—A comprehensive review. J. Stored Prod. Res. 88, 101688. https://doi.org/10.1016/j.jspr.2020.101688 (2020).Article 

Google Scholar 
Tie, J.-K., Nicchitta, C., von Heijne, G. & Stafford, D. W. Membrane topology mapping of vitamin K epoxide reductase by in vitro translation/cotranslocation*. J. Biol. Chem. 280, 16410–16416. https://doi.org/10.1074/jbc.M500765200 (2005).Article 

Google Scholar 
Goulois, J., Lambert, V., Legros, L., Benoit, E. & Lattard, V. Adaptative evolution of the Vkorc1 gene in mus musculus domesticus is influenced by the selective pressure of anticoagulant rodenticides. Ecol. Evol. 7, 2767–2776. https://doi.org/10.1002/ece3.2829 (2017).Article 

Google Scholar 
Pelz, H.-J. The genetic basis of resistance to anticoagulants in rodents. Genetics 170, 1839–1847. https://doi.org/10.1534/genetics.104.040360 (2005).Article 

Google Scholar 
Rost, S. et al. Novel mutations in the VKORC1 gene of wild rats and mice—A response to 50 years of selection pressure by warfarin?. BMC Genet. 10, 4. https://doi.org/10.1186/1471-2156-10-4 (2009).Article 

Google Scholar 
Çetintürk, D., Yiğit, N., Çolak, E., Duman, T., Gül, N., Saygılı Yiğit, F. First Report for Anticoagulant Rodenticide Resistance in Turkish Norway Rat. Jan 5 (2018).Gérard, J., Nehmé, C. Lebanon. A geography of contrasts. Méditerranée. Revue géographique des pays méditerranéens/J. Mediterr. Geogra. (2020).Haktanir, K., Karaca, A., Omar, S. M. The prospects of the impact of desertification on Turkey, Lebanon, Syria and Iraq. In Proceedings of the Environmental Challenges in the Mediterranean 2000–2050 (ed. Marquina, A.) 139–154 (Springer Netherlands, Dordrecht, 2004).Bradley, C. A. & Altizer, S. Urbanization and the ecology of wildlife diseases. Trends Ecol. Evol. 22, 95–102. https://doi.org/10.1016/j.tree.2006.11.001 (2007).Article 

Google Scholar 
Lewis, R., Lewis, J. & Atallah, S. A review of Lebanese Mammals Lagomorpha and Rodentia*. J. Zool. 153, 45–70. https://doi.org/10.1111/j.1469-7998.1967.tb05030.x (1967).Article 

Google Scholar 
Bate, D. M. A. XIV—Note on small Mammals from the Lebanon Mountains, Syria. Ann. Mag. Nat. Hist. 12, 141–158. https://doi.org/10.1080/00222934508527500 (1945).Article 

Google Scholar 
Sprenger, A., Lebanon, A. R. Small Mammal Survey Report (Dec 2001–Mar 2002). 5.Boukhdoud, L., Saliba, C., Kahale, R. & Kharrat, M. B. D. Tracking Mammals in a Lebanese protected area using environmental DNA-based approach. Environ. DNA https://doi.org/10.1002/edn3.183 (2021).Article 

Google Scholar 
Bou Dagher Kharrat, M., Kahale, R., Saliba, C., Boukhdoud, L. Mammals at first sight: Discover lebanese wild mammals (2019).Khater, C., El-Hajj, R. in Terrestrial Biodiversity in Lebanon 141–169 (2012).Nader, M. R., El Indary, S., Abi Salloum, B. & Abou Dagher, M. Combining non-invasive methods for the rapid assessment of Mammalian richness in a transect-quadrat survey scheme—Case study of the Horsh Ehden nature reserve, North Lebanon. Zookeys 119, 63–71. https://doi.org/10.3897/zookeys.119.1040 (2011).Article 

Google Scholar 
Kersten, A. M. P. Rodents and insectivores from the palaeolithic Rock Shelter of Ksar ’Akil (Lebanon) and their palaeoecological implications. Paléorient 18, 27–45. https://doi.org/10.3406/paleo.1992.4561 (1992).Article 

Google Scholar 
Amr, Z. S., Abi-Said, M. R. & Shehab, A. H. Diet of the Barn Owl (Tyto Alba ) from Chaddra-Akkar Northern Lebanon. JJBS 7, 109–112. https://doi.org/10.12816/0008223 (2014).Article 

Google Scholar 
Abi-Said, Mounir R. in A Baseline Survey of the Mammals in Jabal Moussa Nature Reserve (JMNR) (2009).Kryštufek, B., Abi-Said, M. & Hladnik, M. The Iranian vole microtus Irani occurs in Lebanon (Mammalia: Rodentia). Zool. Middle East 59, 101–106. https://doi.org/10.1080/09397140.2013.810863 (2013).Article 

Google Scholar 
Inc, G.I., Berger, D.S. in Leptospirosis: Global Status: 2020 Ed (GIDEON Informatics Inc, 2020) ISBN 978-1-4988-2877-2.Iacucci, A. et al. VKORC1 mutation in European populations of Rattus Norvegicus with first data for italy and the report of a new amino acid substitution. Hystrix It. J. Mamm. 29, 95–99. https://doi.org/10.4404/hystrix-00055-2018 (2018).Article 

Google Scholar 
Backhans, A. et al. Occurrence of pathogens in wild rodents caught on Swedish pig and chicken farms. Epidemiol. Infect. 141, 1885–1891. https://doi.org/10.1017/S0950268812002609 (2013).Article 

Google Scholar 
Franssen, F., Swart, A., van Knapen, F. & van der Giessen, J. Helminth Parasites in black rats (Rattus Rattus) and brown rats (Rattus Norvegicus) from different environments in the Netherlands. Infect. Ecol. Epidemiol. 6, 31413. https://doi.org/10.3402/iee.v6.31413 (2016).Article 

Google Scholar 
Umali, D. V., Lapuz, R. R. S. P., Suzuki, T., Shirota, K. & Katoh, H. Transmission and shedding patterns of salmonella in naturally infected captive wild roof rats (Rattus Rattus) from a salmonella-contaminated layer farm. Avian Dis. 56, 288–294. https://doi.org/10.1637/9911-090411-Reg.1 (2012).Article 

Google Scholar 
Heiberg, A.-C. Anticoagulant resistance: A relevant issue in sewer rat (Rattus Norvegicus) control?. Pest Manag. Sci. 65, 444–449. https://doi.org/10.1002/ps.1709 (2009).Article 

Google Scholar 
Mohammadi, Z., Darvish, J., Ghorbani, F., Mostafavi, E. First Record of the Caucasus Field Mouse Apodemus Ponticus Sviridenko, 1936 (Rodentia Muridae) from Iran. 7.Albaba, I. The terrestrial mammals of palestine: A preliminary checklist. Int. J. Fauna Biol. Stud. 3(4), 28–35 (2016).
Google Scholar 
Brooks, J. E. & Jackson, W. B. A review of commensal rodents and their control. CRC Crit. Rev. Environ. Control 3, 405–453. https://doi.org/10.1080/10643387309381607 (1973).Article 

Google Scholar 
Abou Zeid, M. I., Jammoul, A. M., Melki, K. C., Jawdah, Y. A. & Awad, M. K. Suggested policy and legislation reforms to reduce deleterious effect of pesticides in Lebanon. Heliyon 6, e05524. https://doi.org/10.1016/j.heliyon.2020.e05524 (2020).Article 

Google Scholar 
Buckle, A., Prescott, C. Anticoagulants and risk mitigation. In Anticoagulant Rodenticides and Wildlife (eds. van den Brink, N. W., Elliott, J. E., Shore, R. F., Rattner, B. A.) 319–355 (Springer International Publishing, Cham, 2018) ISBN 978-3-319-64377-9.Berny, P., Esther, A., Jacob, J., Prescott, C. Development of resistance to anticoagulant rodenticides in rodents. In Anticoagulant Rodenticides and Wildlife (eds. van den Brink, N. W., Elliott, J. E., Shore, R. F., Rattner, B. A.) (Springer International Publishing, Cham, 2018) 259–286 ISBN 978-3-319-64377-9.Abil Khalil, R. et al. Seasonal diet-based resistance to anticoagulant rodenticides in the fossorial water vole (Arvicola Amphibius). Environ. Res. 200, 111422 (2021).Article 

Google Scholar 
Ma, X. et al. Low warfarin resistance frequency in Norway rats in Two cities in China after 30 years of usage of anticoagulant rodenticides. Pest Manag. Sci. 74, 2555–2560. https://doi.org/10.1002/ps.5040 (2018).Article 

Google Scholar 
Prescott, C., Buckle, A., Gibbings, G., Allan, E. & Stuart, A. Anticoagulant resistance in Norway rats (Rattus Norvegicus Berk.) in Kent—A VKORC1 single nucleotide polymorphism, tyrosine139phenylalanine, New to the UK. Int. J. Pest Manag. 57, 61–65. https://doi.org/10.1080/09670874.2010.523124 (2011).Article 

Google Scholar 
Cowan, P. E. et al. Vkorc1 sequencing suggests anticoagulant resistance in rats in New Zealand. Pest Manag. Sci. 73, 262–266. https://doi.org/10.1002/ps.4304 (2017).Article 

Google Scholar 
Pelz, H.-J. et al. Distribution and Frequency of VKORC1 sequence variants conferring resistance to anticoagulants in mus musculus. Pest. Manag. Sci. 68, 254–259. https://doi.org/10.1002/ps.2254 (2012).Article 

Google Scholar 
Mooney, J. et al. VKORC1 sequence variants associated with resistance to anticoagulant rodenticides in irish populations of Rattus Norvegicus and mus musculus domesticus. Sci. Rep. 8, 4535. https://doi.org/10.1038/s41598-018-22815-7 (2018).Article 
ADS 

Google Scholar 
Šćepović, T. et al. VKOR variant and sex are the main influencing factors on bromadiolone tolerance of the house mouse (Mus Musculus L.). Pest Manag. Sci. 72, 574–579. https://doi.org/10.1002/ps.4027 (2016).Article 

Google Scholar 
Greaves, J. H., Redfern, R. & Anasuya, B. Inheritance of resistance to warfarin in Rattus Rattus L. J. Stored Prod. Res. 12, 225–228. https://doi.org/10.1016/0022-474X(76)90037-0 (1976).Article 

Google Scholar 
Leung, L.K.-P. & Clark, N. M. Bait avoidance and habitat use by the roof rat, Rattus Rattus, in a Piggery. Int. Biodeterior. Biodegrad. 55, 77–84. https://doi.org/10.1016/j.ibiod.2004.07.004 (2005).Article 

Google Scholar 
Takeda, K. et al. Novel revelation of warfarin resistant mechanism in roof rats (Rattus Rattus) using pharmacokinetic/pharmacodynamic analysis. Pestic. Biochem. Physiol. 134, 1–7. https://doi.org/10.1016/j.pestbp.2016.04.004 (2016).Article 

Google Scholar 
Song, Y. et al. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice., adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. Curr Biol 21, 1296–1301. https://doi.org/10.1016/j.cub.2011.06.043 (2011).Article 

Google Scholar 
Aplin, K. P., Brown, P. R., Jacob, J., Krebs, C. J. & Singleton, G. R. Field methods for rodent studies in Asia and the Indo-Pacific (No. 435-2016-33720) (2003).Irwin, D. M., Kocher, T. D. & Wilson, A. C. Evolution of the cytochrome b gene of Mammals. J. Mol. Evol. 32, 128–144. https://doi.org/10.1007/BF02515385 (1991).Article 
ADS 

Google Scholar 
Pagès, M. et al. Revisiting the taxonomy of the rattini tribe: A phylogeny-based delimitation of species boundaries. BMC Evol. Biol. 10, 184. https://doi.org/10.1186/1471-2148-10-184 (2010).Article 

Google Scholar 
Bradley, R. D. & Baker, E. J. A test of the genetic species concept: Cytochrome-b sequences and mammals. J. Mammal. 82, 960–973 (2001).Article 

Google Scholar 
Hall, T. A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95–98 (1999).
Google Scholar 
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. GenBank. Nucleic Acids Res. 37, D26–D31. https://doi.org/10.1093/nar/gkn723 (2009).Article 

Google Scholar  More

McCauley, D. J., Pinsky, M. L., Palumbi, S. R., Estes, J. A. & Warner, R. R. Marine defaunation: Animal loss in the global ocean. Science 347(6219), 1255641 (2015).Article 

Google Scholar 
Webb, T. J. & Mindel, B. L. Global patterns of extinction risk in marine and non-marine systems. Curr. Biol. 25(4), 506–511 (2015).Article 
CAS 

Google Scholar 
Pinsky, M. L. & Fredston, A. A stark future for ocean life. Science 376(6592), 452–453 (2022).Article 
ADS 
CAS 

Google Scholar 
Bell, J. J., Bennett, H. M., Rovellini, A. & Webster, N. S. Sponges to be winners under near-future climate scenarios. Bioscience 68(12), 955–968 (2018).Article 

Google Scholar 
Dulvy, N. K. et al. Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Curr. Biol. 31(21), 4773-4787.e8 (2021).Article 
CAS 

Google Scholar 
Penn, J. L. & Deutsch, C. Avoiding ocean mass extinction from climate warming. Science 376(6592), 524–526 (2022).Article 
ADS 
CAS 

Google Scholar 
Hubbard, D. M., Dugan, J. E., Schooler, N. K. & Viola, S. M. Local extirpations and regional declines of endemic upper beach invertebrates in southern California. Estuar. Coast. Shelf Sci. 150(Part A), 67–75 (2014).Article 
ADS 

Google Scholar 
Poquita-Du, R. C. et al. Last species standing: loss of Pocilloporidae corals associated with coastal urbanization in a tropical city state. Mar. Biodivers. 49, 1727–1741 (2019).Article 

Google Scholar 
Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).Article 
ADS 
CAS 

Google Scholar 
Bellwood, D. R. et al. Coral reef conservation in the Anthropocene: Confronting spatial mismatches and prioritizing functions. Biol. Conserv. 236, 604–615 (2019).Article 

Google Scholar 
Bell, et al. Global conservation status of sponges. Conserv. Biol. 29(1), 42–53 (2015).Article 

Google Scholar 
Kelmo, F., Bell, J. J. & Attrill, M. J. Tolerance of sponge assemblages to temperature anomalies: Resilience and proliferation of sponges following the 1997–8 El-Niño southern oscillation. PLoS ONE 8(10), e76441 (2013).Article 
ADS 
CAS 

Google Scholar 
Micaroni, V. et al. Adaptive strategies of sponges to deoxygenated oceans. Glob. Change Biol. 28(6), 1972–1989 (2022).Article 

Google Scholar 
Di Camillo, C. G., Bartolucci, I., Cerrano, C. & Bavestrello, G. Sponge disease in the Adriatic Sea. Mar. Ecol. 34(1), 62–71 (2013).Article 
ADS 

Google Scholar 
Pérez, T. & Vacelet, J. Effect of climatic and anthropogenic disturbances on sponge fisheries. In The Mediterranean Sea (eds Goffredo, S. & Dubinsky, Z.) 577–587 (Springer, 2014).Chapter 

Google Scholar 
Ereskovsky, A., Ozerov, D. A., Pantyulin, A. N. & Tzetlin, A. B. Mass mortality event of White Sea sponges as the result of high temperature in summer 2018. Polar Biol. 42, 2313–2318 (2019).Article 

Google Scholar 
Lesser, M. P. & Slattery, M. Will coral reef sponges be winners in the Anthropocene?. Glob. Change Biol. 26(6), 3202–3211 (2020).Article 
ADS 

Google Scholar 
Stevenson, A. et al. Warming and acidification threaten glass sponge Aphrocallistes vastus pumping and reef formation. Sci. Rep. 10, 8176 (2020).Article 
ADS 
CAS 

Google Scholar 
Beepat, S. S., Davy, S. K., Woods, L. & Bell, J. J. Short-term responses of tropical lagoon sponges to elevated temperature and nitrate. Mar. Environ. Res. 157, 104922 (2020).Article 
CAS 

Google Scholar 
Shore, A. et al. On a reef far, far away: Anthropogenic impacts following extreme storms affect sponge health and bacterial communities. Front. Mar. Sci. 8, 608036 (2021).Article 

Google Scholar 
de Voogd et al. World Porifera Database https://www.marinespecies.org/porifera/ (2022).Wulff, J. L. Assessing and monitoring coral reef sponges: Why and how?. Bull. Mar. Sci. 69(2), 831–846 (2001).ADS 

Google Scholar 
Bell, J. J. The functional roles of marine sponges. Estuar. Coast. Shelf Sci. 79(3), 341–353 (2008).Article 
ADS 

Google Scholar 
Folkers, M. & Rombouts, T. Sponges revealed: a synthesis of their overlooked ecological functions within aquatic ecosystems. In YOUMARES 9—The Oceans: Our Research, Our Future (eds Jungblut, S. et al.) 181–194 (Springer, 2019).
Google Scholar 
Pawlik, J. R. & McMurray, S. E. The emerging ecological and biogeochemical importance of sponges on coral reefs. Ann. Rev. Mar. Sci. 12, 315–337 (2020).Article 

Google Scholar 
Sawangwong, P. et al. Secondary metabolites from a marine sponge Cliona patera. Biochem. Syst. Ecol. 36(5), 493–496 (2008).Article 
CAS 

Google Scholar 
Zhang, H. et al. Bioactive secondary metabolites from the marine sponge genus Agelas. Mar. Drugs 15(11), 351 (2017).Article 

Google Scholar 
He, Q., Miao, S., Ni, N., Man, Y. & Gong, K. A review of the secondary metabolites from the marine sponges of the genus Aaptos. Nat. Prod. Commun. 15(9), 1–12 (2020).CAS 

Google Scholar 
Ho, et al. Assessing the diversity and biomedical potential of microbes associated with the Neptune’s Cup sponge, Cliona patera. Front. Microbiol. 12, 631445 (2021).Article 

Google Scholar 
Pronzato, R. Mediterranean sponge fauna: A biological, historical and cultural heritage. Biogeographia 24(1), 91–99 (2003).
Google Scholar 
DiBattista, J. D. et al. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci. Rep. 10, 8365 (2020).Article 
ADS 
CAS 

Google Scholar 
Halpern, B. S. et al. A global map of human impact on marine ecosystems. Science 319(5865), 948–952 (2008).Article 
ADS 
CAS 

Google Scholar 
Vosmaer, G. C. J. Poterion a boring sponge. K. Ned. Akad. Wet. Proc. 11, 37–41 (1908).
Google Scholar 
Lim, S. C., Tun, K. & Goh, E. Rediscovery of the Neptune’s Cup sponge in Singapore: Cliona or Poterion? Contributions to Marine Science 2012, 49–56 (2012).Low, M. E. Y. The date of publication of Cliona patera (Hardwicke), the ‘sponge plant from the shores of Singapore’ (Porifera: Hadromerida: Clionaidae). Nat. Singap. 5, 223–227 (2012).
Google Scholar 
Knight, K. Super-rare giant sponge discovered in seahorse hotspot. Fauna & Floral International https://www.fauna-flora.org/news/super-rare-sponge-discovered-seahorse-hotspot/ (2018).The State of Queensland (Queensland Museum). Cliona patera. Queensland Museum Network https://collections.qm.qld.gov.au/objects/73638/cliona-patera (2012–2022).Heath, D. J. Simultaneous hermaphroditism; Cost and benefit. J. Theor. Biol. 64, 363–373 (1977).Article 
ADS 
CAS 

Google Scholar 
André, C. & Lindegarth, M. Fertilization efficiency and gamete viability of a sessile, free-spawning bivalve, Cerastoderma edule. Ophelia 43(3), 215–227 (1995).Article 

Google Scholar 
Bayer, S. R. et al. Fertilization success in scallop aggregations: Reconciling model predictions and field measurements of density effects. Ecosphere 9(8), e02359 (2018).Article 

Google Scholar 
Yund, P. O. How severe is sperm limitation in natural populations of marine free-spawners?. Trends Ecol. Evol. 15(1), 10–13 (2000).Article 
CAS 

Google Scholar 
Frankham, R. Relationship of genetic variation to population size in wildlife. Conserv. Biol. 10(6), 1500–1508 (1996).Article 

Google Scholar 
Lim, S. C. Porifera. Singapore Red Data Book. https://www.nparks.gov.sg/biodiversity/wildlife-in-singapore/species-list/sponge (2022).Quek, Z. B. R., Chang, J. J. M., Ip, Y. C. A., Chan, Y. K. S. & Huang, D. Mitogenomes reveal alternative initiation codons and lineage-specific gene order conservation in echinoderms. Mol. Biol. Evol. 38(3), 981–985 (2021).Article 
CAS 

Google Scholar 
Wörheide, G., Nichols, S. A. & Goldberg, J. Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): Implications for phylogenetic studies. Mol. Phylogenet. Evol. 33(3), 816–830 (2004).Article 

Google Scholar 
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17), i884–i890 (2018).Article 

Google Scholar 
Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477 (2012).Article 
MathSciNet 
CAS 

Google Scholar 
Hahn, C., Bachmann, L. & Chevreux, B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads: A baiting and iterative mapping approach. Nucleic Acids Res. 41(13), e129 (2013).Article 
CAS 

Google Scholar 
Donath, A. et al. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res. 47(20), 10543–10552 (2019).Article 
CAS 

Google Scholar 
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30(4), 772–780 (2013).Article 
CAS 

Google Scholar 
Darriba, D. et al. ModelTest-NG: A new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37(1), 291–294 (2020).Article 
MathSciNet 
CAS 

Google Scholar 
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35(21), 4453–4455 (2019).Article 
CAS 

Google Scholar 
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6), 1547–1549 (2018).Article 
CAS 

Google Scholar 
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9(7), 671–675 (2012).Article 
CAS 

Google Scholar 
Xavier, J. R. et al. Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae). Mol. Phylogenet. Evol. 56(1), 13–20 (2010).Article 
CAS 

Google Scholar 
de Paula, T. S., Zilberberg, C., Hajdu, E. & Lôbo-Hajdua, G. Morphology and molecules on opposite sides of the diversity gradient: Four cryptic species of the Cliona celata (Porifera, Demospongiae) complex in South America revealed by mitochondrial and nuclear markers. Mol. Phylogenet. Evol. 62(1), 529–541 (2012).Article 

Google Scholar 
Plese, B. et al. Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology. Mol Phylogenet Evol 155, 107011 (2021).Article 

Google Scholar 
Lavrov, D. V., Adamski, M., Chevaldonné, P. & Adamska, M. Extensive mitochondrial mRNA editing and unusual mitochondrial genome organization in calcaronean sponges. Curr. Biol. 26(1), 86–92 (2016).Article 
CAS 

Google Scholar 
Lavrov, D. V. & Pett, W. Animal mitochondrial DNA as we do not know it: mt-genome organization and evolution in nonbilaterian lineages. Genome Biol. Evol. 8(9), 2896–2913 (2016).Article 
CAS 

Google Scholar 
Haen, K. M., Pett, W. & Lavrov, D. V. Eight new mtDNA sequences of glass sponges reveal an extensive usage of + 1 frameshifting in mitochondrial translation. Gene 535(2), 336–344 (2014).Article 
CAS 

Google Scholar 
Shearer, T. L., van Oppen, M. J. H., Romano, S. L. & Wörheide, G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11(12), 2475–2487 (2002).Article 
CAS 

Google Scholar 
Lavrov, D. V., Forget, L., Kelly, M. & Lang, B. F. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol. Biol. Evol. 22(5), 1231–1239 (2005).Article 
CAS 

Google Scholar 
Huang, D., Meier, R., Todd, P. A. & Chou, L. M. Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J. Mol. Evol. 66(2), 167–174 (2008).Article 
ADS 
CAS 

Google Scholar 
Wörheide, G. Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific. Mar. Biol. 148, 907–912 (2006).Article 

Google Scholar 
León-Pech, M. G., Cruz-Barraza, J. A., Carballo, J. L., Calderon-Aguilera, L. E. & Rocha-Olivares, A. Pervasive genetic structure at different geographic scales in the coral-excavating sponge Cliona vermifera (Hancock, 1867) in the Mexican Pacific. Coral Reefs 34, 887–897 (2015).Article 
ADS 

Google Scholar 
Yang, Q., Franco, C. M. M., Sorokin, S. J. & Zhang, W. Development of a multilocus-based approach for sponge (phylum Porifera) identification: Refinement and limitations. Sci. Rep. 7, 41422 (2017).Article 
ADS 
CAS 

Google Scholar 
Wörheide, G., Epp, L. S. & Macis, L. Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): Founder effects, vicariance, or both?. BMC Evol. Biol. 8, 24 (2008).Article 

Google Scholar 
Lai, S., Loke, L. H. L., Hilton, M. J., Bouma, T. J. & Todd, P. A. The effects of urbanisation on coastal habitats and the potential for ecological engineering: A Singapore case study. Ocean Coast. Manag. 103, 78–85 (2015).Article 

Google Scholar 
Kuempel, C. D. et al. Identifying management opportunities to combat climate, land, and marine threats across less climate exposed coral reefs. Conserv. Biol. 36(3), e13856 (2022).Article 

Google Scholar 
Neo, M. L. et al. Giant clams (Bivalvia: Cardiidae: Tridacninae): A comprehensive update of species and their distribution, current threats and conservation status. In Oceanography and Marine Biology: An Annual Review Vol. 55 (eds Hawkins, S. J. et al.) 87–388 (CRC Press, 2017).Chapter 

Google Scholar 
Orlando, L. et al. Ancient DNA analysis. Nat. Rev. Methods Prim. 1, 14 (2021).Article 
CAS 

Google Scholar 
Cárdenas, P. & Moore, J. A. First records of Geodia demosponges from the New England seamounts, an opportunity to test the use of DNA mini-barcodes on museum specimens. Mar. Biodiv. 49, 163–174 (2019).Article 

Google Scholar 
Erpenbeck, D. et al. Minimalist barcodes for sponges: A case study classifying African freshwater Spongillida. Genome 62(1), 1–10 (2019).Article 

Google Scholar 
Chang, D. & Shapiro, B. Using ancient DNA and coalescent-based methods to infer extinction. Biol. Lett. 12(2), 20150822 (2016).Article 

Google Scholar 
Pacioni, C. et al. Genetic diversity loss in a biodiversity hotspot: Ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Mol. Ecol. 24(23), 5813–5828 (2015).Article 
CAS 

Google Scholar 
Lombal, A. J. et al. Using ancient DNA to quantify losses of genetic and species diversity in seabirds: A case study of Pterodroma petrels from a Pacific island. Biodivers. Conserv. 29, 2361–2375 (2020).Article 

Google Scholar 
Ruzicka, R. & Gleason, D. F. Sponge community structure and anti-predator defenses on temperate reefs of the South Atlantic Bight. J. Exp. Mar. Biol. Ecol. 380(1–2), 36–46 (2009).Article 

Google Scholar 
Loh, T. L. & Pawlik, J. R. Chemical defenses and resource trade-offs structure sponge communities on Caribbean coral reefs. Proc. Natl. Acad. Sci. U.S.A. 111(11), 4151–4156 (2014).Article 
ADS 
CAS 

Google Scholar 
Wulff, J. L. Targeted predator defenses of sponges shape community organization and tropical marine ecosystem function. Ecol. Monogr. 91(2), e01438 (2021).Article 

Google Scholar 
Coppock, A. G., Kingsford, M. J., Battershill, C. N. & Jones, G. P. Significance of fish–sponge interactions in coral reef ecosystems. Coral Reefs 41, 1285–1308 (2022).Article 

Google Scholar 
Baumbach, D. S., Zhang, R., Hayes, C. T., Wright, M. K. & Dunbar, S. G. Strategic foraging: Understanding hawksbill (Eretmochelys imbricata) prey item energy values and distribution within a marine protected area. Mar. Ecol. 00, e12703 (2022).CAS 

Google Scholar 
Guida, V. G. Sponge predation in the oyster reef community as demonstrated with Cliona celata Grant. J. Exp. Mar. Biol. Ecol. 25(2), 109–122 (1976).Article 

Google Scholar 
Verdín, P. C. J., Carballo, J. L. & Camacho, M. L. A qualitative assessment of sponge-feeding organisms from the Mexican Pacific coast. Open Mar. Biol. J. 4, 39–46 (2010).Article 

Google Scholar 
Márquez, J. C. & Zea, S. Parrotfish mediation in coral mortality and bioerosion by the encrusting, excavating sponge Cliona tenuis. Mar. Ecol. 33(4), 417–426 (2012).Article 
ADS 

Google Scholar 
González-Rivero, M., Ferrari, R., Schönberg, C. H. L. & Mumby, P. J. Impacts of macroalgal competition and parrotfish predation on the growth of a common bioeroding sponge. Mar. Ecol. Prog. Ser. 444, 133–142 (2012).Article 
ADS 

Google Scholar 
von Brandis, R. G., Mortimer, J. A., Reilly, B. K., van Soest, R. W. M. & Branch, G. M. Diet composition of hawksbill turtles (Eretmochelys imbricata) in the Republic of Seychelles. Western Indian Ocean J. Mar. Sci. 13(1), 81–91 (2014).
Google Scholar 
Mortimer, C., Dunn, M., Haris, A., Jompa, J. & Bell, J. Estimates of sponge consumption rates on an Indo-Pacific reef. Mar. Ecol. Prog. Ser. 672, 123–140 (2021).Article 
ADS 
CAS 

Google Scholar 
Hoppe, W. F. Growth, regeneration and predation in three species of large coral reef sponges. Mar. Ecol. Prog. Ser. 50(12), 117–125 (1988).Article 
ADS 

Google Scholar 
Bell, J. J. Regeneration rates of a sublittoral demosponge. J. Mar. Biol. Assoc. U.K. 82(1), 169–170 (2002).Article 

Google Scholar 
Wu, Y.-C. et al. Opisthobranch grazing results in mobilisation of spherulous cells and re-allocation of secondary metabolites in the sponge Aplysina aerophoba. Sci. Rep. 10, 21934 (2020).Article 
ADS 
CAS 

Google Scholar 
Wu, Y.-C., Franzenburg, S., Ribes, M. & Pita, L. Wounding response in Porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer. Sci. Rep. 12, 1307 (2022).Article 
ADS 
CAS 

Google Scholar 
González-Rivero, M. et al. Life-history traits of a common Caribbean coral-excavating sponge, Cliona tenuis (Porifera: Hadromerida). J. Nat. Hist. 47(45–46), 1–20 (2013).
Google Scholar 
Chaves-Fonnegra, A., Maldonado, M., Blackwelder, P. & Lopez, J. V. Asynchronous reproduction and multi-spawning in the coral-excavating sponge Cliona delitrix. J. Mar. Biol. Assoc. U.K. 96(2), 515–528 (2015).Article 

Google Scholar 
Bautista-Guerrero, E., Carballo, J. L. & Maldonado, M. Abundance and reproductive patterns of the excavating sponge Cliona vermifera: A threat to Pacific coral reefs?. Coral Reefs 33, 259–266 (2014).Article 
ADS 

Google Scholar 
Piscitelli, M., Corriero, G., Gaino, E. & Uriz, M.-J. Reproductive cycles of the sympatric excavating sponges Cliona celata and Cliona viridis in the Mediterranean Sea. Invertebr. Biol. 130(1), 1–10 (2011).Article 

Google Scholar 
Chaves-Fonnegra, A., Feldheim, K. A., Secord, J. & Lopez, J. V. Population structure and dispersal of the coral-excavating sponge Cliona delitrix. Mol. Ecol. 24(7), 1447–1466 (2015).Article 

Google Scholar 
Zilberberg, C., Maldonado, M. & Solé-Cava, A. Assessment of the relative contribution of asexual propagation in a population of the coral-excavating sponge Cliona delitrix from the Bahamas. Coral Reefs 25, 297–301 (2006).Article 
ADS 

Google Scholar 
Wulff, J. L. Effects of a hurricane on survival and orientation of large erect coral reef sponges. Coral Reefs 14, 55–61 (1995).Article 
ADS 

Google Scholar 
Wilkinson, C. R. & Thompson, J. E. Experimental sponge transplantation provides information on reproduction by fragmentation. Proc. 8th Int. Coral Reef Symp. 2, 1417–1420 (1997).CAS 

Google Scholar 
da Silva, R. et al. Assessing the conservation potential of fish and corals in aquariums globally. J. Nat. Conserv. 48, 1–11 (2019).Article 

Google Scholar 
Neumann, A. C. Observations on coastal erosion in Bermuda and measurements of the boring rate of the sponge, Cliona lampa. Limnol. Oceanogr. 11(1), 92–108 (1966).Article 
ADS 

Google Scholar 
Rosell, D. & Uriz, M. J. Do associated zooxanthellae and the nature of the substratum affect survival, attachment and growth of Cliona viridis (Porifera: Hadromerida)? An experimental approach. Mar. Biol. 114, 503–507 (1992).Article 

Google Scholar 
Ramsby, B. D., Hoogenboom, M. O., Smith, H. A., Whalan, S. & Webster, N. S. The bioeroding sponge Cliona orientalis will not tolerate future projected ocean warming. Sci. Rep. 8, 8302 (2018).Article 
ADS 

Google Scholar  More

Peixoto, R. S., Harkins, D. M. & Nelson, K. E. Advances in microbiome research for animal health. Annu. Rev. Anim. Biosci. 9, 289–311 (2021).Article 

Google Scholar 
Amato, K. R. et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 7, 1344 (2013).Article 

Google Scholar 
West, A. G. et al. The microbiome in threatened species conservation. Biol. Conserv. 229, 85–98 (2019).Article 

Google Scholar 
Robinson, J. M., Mills, J. G. & Breed, M. F. Walking ecosystems in microbiome-inspired green infrastructure: An ecological perspective on enhancing personal and planetary health. Challenges 9, 40 (2018).Article 

Google Scholar 
Mills, J. G. et al. Urban habitat restoration provides a human health benefit through microbiome rewilding: The Microbiome Rewilding Hypothesis. Restor. Ecol. 25, 866–872 (2017).Article 

Google Scholar 
Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B 286, 20182448 (2019).Article 

Google Scholar 
Dallas, J. W. & Warne, R. W. Captivity and animal microbiomes: Potential roles of microbiota for influencing animal conservation. Microb. Ecol. https://doi.org/10.1007/s00248-022-01991-0 (2022).Article 

Google Scholar 
Bornbusch, S. L. et al. Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota. Anim. Microbiome 4, 1–19 (2022).Article 

Google Scholar 
Greene, L. K. et al. Gut microbiota of frugo-folivorous sifakas across environments. Anim. Microbiome 3, 39 (2021).Article 

Google Scholar 
McKenzie, V. J. et al. The effects of captivity on the mammalian gut microbiome. Integr. Comp. Biol. 57, 690–704 (2017).Article 

Google Scholar 
Bornbusch, S. L. & Drea, C. M. Antibiotic resistance genes in lemur gut and soil microbiota along a gradient of anthropogenic disturbance. Front. Ecol. Evol. 9, 514 (2021).Article 

Google Scholar 
Hyde, E. R. et al. The oral and skin microbiomes of captive komodo dragons are significantly shared with their habitat. mSystems 1, e00046-e116 (2016).Article 

Google Scholar 
LaFleur, M., Clarke, T. A., Reuter, K. E. & Schaefer, M. S. Illegal trade of wild-captured Lemur catta within Madagascar. Folia Primatol. 90, 199–214 (2019).Article 

Google Scholar 
Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).Article 

Google Scholar 
Choo, J. M., Leong, L. E. & Rogers, G. B. Sample storage conditions significantly influence faecal microbiome profiles. Sci. Rep. 5, 16350 (2015).Article 
ADS 

Google Scholar 
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).Article 

Google Scholar 
Hasan, N. A. et al. Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS ONE 9, e97699 (2014).Article 
ADS 

Google Scholar 
Bornbusch, S. L. et al. Stable and transient structural variation in lemur vaginal, labial and axillary microbiomes: Patterns by species, body site, ovarian hormones and forest access. FEMS Microbiol. Ecol. 96, fiaa090 (2020).Article 

Google Scholar 
Bolyen, E. et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ 37, 852–857 (2018).
Google Scholar 
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581 (2016).Article 

Google Scholar 
Trosvik, P., Rueness, E. K., de Muinck, E. J., Moges, A. & Mekonnen, A. Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys. Sci. Rep. 8, 1–10 (2018).Article 

Google Scholar 
Wills, M. O. et al. Host species and captivity distinguish the microbiome compositions of a diverse zoo-resident non-human primate population. Diversity 14, 715 (2022).Article 

Google Scholar 
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).Article 

Google Scholar 
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).Article 
ADS 

Google Scholar 
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).Article 

Google Scholar 
Yarza, P. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12, 635 (2014).Article 

Google Scholar 
Aitchison, J. The statistical analysis of compositional data. J. R. Stat. Soc. Ser. B 44, 139–160 (1982).MathSciNet 
MATH 

Google Scholar 
Quinn, T. P., Erb, I., Richardson, M. F. & Crowley, T. M. Understanding sequencing data as compositions: An outlook and review. Bioinformatics 34, 2870–2878 (2018).Article 

Google Scholar 
Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: And this is not optional. Front. Microbiol. 8, 2224 (2017).Article 

Google Scholar 
Ottesen, A. et al. Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak. BMC Microbiol. 16, 1–11 (2016).Article 

Google Scholar 
Lax, S. et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345, 1048–1052 (2014).Article 
ADS 

Google Scholar 
Shenhav, L. et al. FEAST: Fast expectation-maximization for microbial source tracking. Nat. Methods 16, 627 (2019).Article 

Google Scholar 
Barelli, C. et al. The gut microbiota communities of wild arboreal and ground-feeding tropical primates are affected differently by habitat disturbance. mSystems 5, e00061 (2020).Article 

Google Scholar 
Frankel, J. S., Mallott, E. K., Hopper, L. M., Ross, S. R. & Amato, K. R. The effect of captivity on the primate gut microbiome varies with host dietary niche. Am. J. Primatol. 81, e23061 (2019).Article 

Google Scholar 
Bornbusch, S. L. et al. Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts. Anim. Microbiome 3, 65 (2021).Article 

Google Scholar 
Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576–587 (2019).Article 

Google Scholar 
Bornbusch, S. L. et al. A comparative study of gut microbiomes in captive nocturnal strepsirrhines. Am. J. Primatol. 81, e22986 (2019).Article 

Google Scholar 
Nishida, A. H. & Ochman, H. A great-ape view of the gut microbiome. Nat. Rev. Genet. 20, 195–206 (2019).Article 

Google Scholar 
Nagpal, R. et al. Gut microbiome composition in non-human primates consuming a Western or Mediterranean diet. Front. Nutr. 5, 28 (2018).Article 

Google Scholar 
Deng, H. et al. Bacteroides fragilis prevents Clostridium difficile infection in a mouse model by restoring gut barrier and microbiome regulation. Front. Microbiol. 9, 2976 (2018).Article 

Google Scholar 
Wang, C. et al. Roles of intestinal bacteroides in human health and diseases. Crit. Rev. Food Sci. Nutr. 61, 3518–3536 (2021).Article 

Google Scholar 
Townsend, G. E. et al. Dietary sugar silences a colonization factor in a mammalian gut symbiont. Proc. Natl. Acad. Sci. USA 116, 233–238 (2019).Article 
ADS 

Google Scholar 
LaFleur, M. et al. Drug-resistant tuberculosis in pet ring-tailed lemur, Madagascar. Emerg. Infect. Dis. 27, 977 (2021).Article 

Google Scholar 
Gálvez, E. J. C. et al. Distinct polysaccharide utilization determines interspecies competition between intestinal Prevotella spp. Cell Host Microbe 28, 838–852 (2020).Article 

Google Scholar 
Costea, P. I. et al. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3, 8–16 (2018).Article 

Google Scholar 
Roager, H. M., Licht, T. R., Poulsen, S. K., Larsen, T. M. & Bahl, M. I. Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet. Appl. Environ. Microbiol. 80, 1142–1149 (2014).Article 
ADS 

Google Scholar 
Hjorth, M. F. et al. Pretreatment Prevotella-to-Bacteroides ratio and markers of glucose metabolism as prognostic markers for dietary weight loss maintenance. Eur. J. Clin. Nutr. 74, 338–347 (2020).Article 

Google Scholar 
Hjorth, M. F. et al. Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. Int. J. Obes. 42, 580–583 (2018).Article 

Google Scholar 
DeMartino, P. & Cockburn, D. W. Resistant starch: Impact on the gut microbiome and health. Curr. Opin. Biotechnol. 61, 66–71 (2020).Article 

Google Scholar 
Wang, K. et al. Diet with a high proportion of rice alters profiles and potential function of digesta-associated microbiota in the ileum of goats. Animals 10, 1261 (2020).Article 

Google Scholar 
Greene, L. K., McKenney, E. A., O’Connell, T. M. & Drea, C. M. The critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas. Sci. Rep. 8, 14482 (2018).Article 
ADS 

Google Scholar 
Allen, H. K. et al. Call of the wild: Antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).Article 

Google Scholar 
Daszak, P., Cunningham, A. A. & Hyatt, A. D. Anthropogenic environmental change and the emergence of infectious diseases in wildlife. Acta Trop. 78, 103–116 (2001).Article 

Google Scholar 
Shapira, M. Gut microbiotas and host evolution: Scaling up symbiosis. Trends Ecol. Evol. 31, 539–549 (2016).Article 

Google Scholar 
Sbihi, H. et al. Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy 74, 2103–2115 (2019).Article 

Google Scholar 
Bendiks, M. & Kopp, M. V. The relationship between advances in understanding the microbiome and the maturing hygiene hypothesis. Curr. Allergy Asthma Rep. 13, 487–494 (2013).Article 

Google Scholar 
Alexandre-Silva, G. M. et al. The hygiene hypothesis at a glance: Early exposures, immune mechanism and novel therapies. Acta Trop. 188, 16–26 (2018).Article 

Google Scholar 
Yao, R. et al. The, “wildness” of the giant panda gut microbiome and its relevance to effective translocation. Glob. Ecol. Conserv. 18, e00644 (2019).Article 

Google Scholar  More