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    Pathways to engineering the phyllosphere microbiome for sustainable crop production

    Koskella, B. The phyllosphere. Curr. Biol. 30, R1143–R1146 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Lu, N. et al. Improved estimation of aboveground biomass in wheat from RGB imagery and point cloud data acquired with a low-cost unmanned aerial vehicle system. Plant Methods 15, 17 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Arye, G. C. & Harel, A. in Microbial Genomics in Sustainable Agroecosystems (eds Tripathi, V. et al.) 39–65 (Springer, 2020).Universal plant healthcare. Nat. Plants 6, 47 (2020).Fones, H. N. et al. Threats to global food security from emerging fungal and oomycete crop pathogens. Nat. Food 1, 332–342 (2020).Article 

    Google Scholar 
    Li, W., Deng, Y., Ning, Y., He, Z. & Wang, G. L. Exploiting broad-spectrum disease resistance in crops: from molecular dissection to breeding. Annu. Rev. Plant Biol. 71, 575–603 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Matsumoto, H. et al. Bacterial seed endophyte shapes disease resistance in rice. Nat. Plants 7, 60–72 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Thomazella, D. P. T. et al. Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. Proc. Natl Acad. Sci. USA 118, e2026152118 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Guo, Y. Molecular design for rice breeding. Nat. Food 2, 849–849 (2021).Article 

    Google Scholar 
    Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).Article 
    PubMed 

    Google Scholar 
    Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Carrion, V. J. et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366, 606–612 (2019).Article 
    CAS 
    PubMed 

    Google Scholar 
    Chialva, M., Lanfranco, L. & Bonfante, P. The plant microbiota: composition, functions, and engineering. Curr. Opin. Biotechnol. 73, 135–142 (2021).Article 
    PubMed 

    Google Scholar 
    Liu, H., Brettell, L. E. & Singh, B. Linking the phyllosphere microbiome to plant health. Trends Plant Sci. 25, 841–844 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Liu, H., Brettell, L. E., Qiu, Z. & Singh, B. K. Microbiome-mediated stress resistance in plants. Trends Plant Sci. 25, 733–743 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Xu, P. et al. Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens. J. Adv. Res. 39, 49–60 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, M. & Cernava, T. Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity. Environ. Sci. Ecotechnol. 4, 100061 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hegazi, N., Hartmann, A. & Ruppel, S. The plant microbiome: exploration of plant–microbe interactions for improving agricultural productivity. J. Adv. Res. 19, 1–2 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mittelviefhaus, M., Muller, D. B., Zambelli, T. & Vorholt, J. A. A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota. ISME J. 13, 1878–1882 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sapkota, R., Knorr, K., Jorgensen, L. N., O’Hanlon, K. A. & Nicolaisen, M. Host genotype is an important determinant of the cereal phyllosphere mycobiome. New Phytol. 207, 1134–1144 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bodenhausen, N., Bortfeld-Miller, M., Ackermann, M. & Vorholt, J. A. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet. 10, e1004283 (2014).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Horton, M. W. et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat. Commun. 5, 5320 (2014).Article 
    PubMed 

    Google Scholar 
    Wagner, M. R. et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat. Commun. 7, 12151 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Shakir, S., Zaidi, S. S., de Vries, F. T. & Mansoor, S. Plant genetic networks shaping phyllosphere microbial community. Trends Genet. 37, 306–316 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Xiong, C. et al. Plant developmental stage drives the differentiation in ecological role of the maize microbiome. Microbiome 9, 171 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Laforest-Lapointe, I., Paquette, A., Messier, C. & Kembel, S. W. Leaf bacterial diversity mediates plant diversity and ecosystem function relationships. Nature 546, 145–147 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Chen, T. et al. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pang, Z. et al. Linking plant secondary metabolites and plant microbiomes: a review. Front. Plant Sci. 12, 621276 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pfeilmeier, S. et al. The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves. Nat. Microbiol. 6, 852–864 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gupta, R. et al. Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues. ISME J. 16, 122–137 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Massoni, J. et al. Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species. ISME J. 14, 245–258 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Agler, M. T. et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, e1002352 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ren, G. et al. Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2 and soil temperature in a rice paddy. Plant Soil 392, 27–44 (2015).Article 
    CAS 

    Google Scholar 
    Meyer, K.M. et al. Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. ISME J. 16, 1376–1387 (2022).Article 
    PubMed 

    Google Scholar 
    Qiu, Y. et al. Warming and elevated ozone induce tradeoffs between fine roots and mycorrhizal fungi and stimulate organic carbon decomposition. Sci. Adv. 7, eabe9256 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Yu, H., Zhang, Y. & Tan, W. The “neighbor avoidance effect” of microplastics on bacterial and fungal diversity and communities in different soil horizons. Environ. Sci. Ecotechnol. 8, 100121 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, Q. et al. Interactive effects of ozone exposure and nitrogen addition on the rhizosphere bacterial community of poplar saplings. Sci. Total Environ. 754, 142134 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Zhang, H., Jiang, Q., Wang, J., Li, K. & Wang, F. Analysis on the impact of two winter precipitation episodes on PM2.5 in Beijing. Environ. Sci. Ecotechnol. 5, 100080 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Feng, Z. et al. Ozone pollution threatens the production of major staple crops in East Asia. Nat. Food 3, 47–56 (2022).Article 
    CAS 

    Google Scholar 
    Zhu, Y. G. et al. Impacts of global change on the phyllosphere microbiome. New Phytol. 234, 1977–1986 (2021).Article 

    Google Scholar 
    Sawada, H. et al. Elevated ozone deteriorates grain quality of japonica rice cv. Koshihikari, even if it does not cause yield reduction. Rice 9, 7 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Agathokleous, E. et al. Ozone affects plant, insect, and soil microbial communities: a threat to terrestrial ecosystems and biodiversity. Sci. Adv. 6, eabc1176 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mieczan, T. & Bartkowska, A. The effect of experimentally simulated climate warming on the microbiome of carnivorous plants—a microcosm experiment. Glob. Ecol. Conserv. 34, e02040 (2022).Article 

    Google Scholar 
    Liu, H. et al. Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens. New Phytol. 229, 2873–2885 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Gao, M. et al. Disease-induced changes in plant microbiome assembly and functional adaptation. Microbiome 9, 187 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Snelders, N. C. et al. Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins. Nat. Plants 6, 1365–1374 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Humphrey, P. T. & Whiteman, N. K. Insect herbivory reshapes a native leaf microbiome. Nat. Ecol. Evol. 4, 221–229 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Laforest-Lapointe, I., Messier, C. & Kembel, S. W. Tree leaf bacterial community structure and diversity differ along a gradient of urban intensity. mSystems 2, e00087–17 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Imperato, V. et al. Characterisation of the Carpinus betulus L. phyllomicrobiome in urban and forest areas. Front. Microbiol. 10, 1110 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Perreault, R. & Laforest-Lapointe, I. Plant–microbe interactions in the phyllosphere: facing challenges of the anthropocene. ISME J. 16, 339–345 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jain, A., Ranjan, S., Dasgupta, N. & Ramalingam, C. Nanomaterials in food and agriculture: an overview on their safety concerns and regulatory issues. Crit. Rev. Food Sci. Nutr. 58, 297–317 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Sillen, W. M. A. et al. Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis. Microbiome 8, 127 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Berg, G. & Cernava, T. The plant microbiota signature of the Anthropocene as a challenge for microbiome research. Microbiome 10, 54 (2022).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fan, X. et al. Microenvironmental interplay predominated by beneficial Aspergillus abates fungal pathogen incidence in paddy environment. Environ. Sci. Technol. 53, 13042–13052 (2019).Article 
    CAS 
    PubMed 

    Google Scholar 
    Chen, Y. et al. Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation. Nat. Commun. 9, 3429 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, M., Hashimoto, M. & Hashidoko, Y. Repression of tropolone production and induction of a Burkholderia plantarii pseudo-biofilm by carot-4-en-9,10-diol, a cell-to-cell signaling disrupter produced by Trichoderma virens. PLoS ONE 8, e78024 (2013).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. V., Jarmusch, A. K. & Dorrestein, P. C. Mass spectrometry-based metabolomics in microbiome investigations. Nat. Rev. Microbiol. 20, 143–160 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Matsumoto, H. et al. Reprogramming of phytopathogen transcriptome by a non-bactericidal pesticide residue alleviates its virulence in rice. Fundam. Res. 2, 198–207 (2022).Article 
    CAS 

    Google Scholar 
    Hou, S. et al. A microbiota–root–shoot circuit favours Arabidopsis growth over defence under suboptimal light. Nat. Plants 7, 1078–1092 (2021).Mathur, M., Nair, A. & Kadoo, N. Plant–pathogen interactions: microRNA-mediated trans-kingdom gene regulation in fungi and their host plants. Genomics 112, 3021–3035 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kaur, C. et al. Microbial methylglyoxal metabolism contributes towards growth promotion and stress tolerance in plants. Environ. Microbiol. 24, 2817–2836 (2021).Article 
    PubMed 

    Google Scholar 
    Castrillo, G. et al. Root microbiota drive direct integration of phosphate stress and immunity. Nature 543, 513–518 (2017).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Korenblum, E. et al. Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling. Proc. Natl Acad. Sci. USA 117, 3874–3883 (2020).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chisholm, S. T., Coaker, G., Day, B. & Staskawicz, B. J. Host–microbe interactions: shaping the evolution of the plant immune response. Cell 124, 803–814 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Jones, J. D. & Dangl, J. L. The plant immune system. Nature 444, 323–329 (2006).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Vogel, C., Bodenhausen, N., Gruissem, W. & Vorholt, J. A. The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health. New Phytol. 212, 192–207 (2016).Article 
    CAS 
    PubMed 

    Google Scholar 
    Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant–pathogen interactions. Nat. Rev. Genet. 11, 539–548 (2010).Article 
    CAS 
    PubMed 

    Google Scholar 
    Stringlis, I. A. et al. Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists. Plant J. 93, 166–180 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    He, J. et al. A LysM receptor heteromer mediates perception of arbuscular mycorrhizal symbiotic signal in rice. Mol. Plant 12, 1561–1576 (2019).Article 
    CAS 
    PubMed 

    Google Scholar 
    Bozsoki, Z. et al. Ligand-recognizing motifs in plant LysM receptors are major determinants of specificity. Plant Sci. 369, 663–670 (2020).CAS 

    Google Scholar 
    Stringlis, I. A., Zhang, H., Pieterse, C. M. J., Bolton, M. D. & de Jonge, R. Microbial small molecules—weapons of plant subversion. Nat. Prod. Rep. 35, 410–433 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kong, H. G., Song, G. C., Sim, H. J. & Ryu, C. M. Achieving similar root microbiota composition in neighbouring plants through airborne signalling. ISME J. 15, 397–408 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Vacher, C. et al. The phyllosphere: microbial jungle at the plant–climate interface. Annu. Rev. Ecol. Evol. Syst. 47, 1–24 (2016).Article 

    Google Scholar 
    Thapa, S. & Prasanna, R. Prospecting the characteristics and significance of the phyllosphere microbiome. Ann. Microbiol. 68, 229–245 (2018).Article 
    CAS 

    Google Scholar 
    Vorholt, J. A., Vogel, C., Carlstrom, C. I. & Muller, D. B. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22, 142–155 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Chen, X., Wicaksono, W. A., Berg, G. & Cernava, T. Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide. Sci. Total Environ. 751, 141799 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Liu, Y. X. et al. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell 12, 315–330 (2021).Article 
    PubMed 

    Google Scholar 
    Hosokawa, M. et al. Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes. Biosens. Bioelectron. 67, 379–385 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kehe, J. et al. Massively parallel screening of synthetic microbial communities. Proc. Natl Acad. Sci. USA 116, 12804–12809 (2019).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, J. et al. High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat. Protoc. 16, 988–1012 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Grosskopf, T. & Soyer, O. S. Synthetic microbial communities. Curr. Opin. Microbiol. 18, 72–77 (2014).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vogel, C. M., Potthoff, D. B., Schafer, M., Barandun, N. & Vorholt, J. A. Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen. Nat. Microbiol. 6, 1537–1548 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Finkel, O. M. et al. A single bacterial genus maintains root growth in a complex microbiome. Nature 587, 103–108 (2020).Wagner, M. R. et al. Microbe-dependent heterosis in maize. Proc. Natl Acad. Sci. USA 118, e2021965118 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schafer, M., Vogel, C. M., Bortfeld-Miller, M., Mittelviefhaus, M. & Vorholt, J. A. Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships. Nat. Microbiol. 7, 856–867 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Han, B. & Huang, X. Sequencing-based genome-wide association study in rice. Curr. Opin. Plant Biol. 16, 133–138 (2013).Article 
    CAS 
    PubMed 

    Google Scholar 
    Roman-Reyna, V. et al. The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions. Cell Host Microbe https://doi.org/10.2139/ssrn.3382544 (2019).Deng, S. et al. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. ISME J. 15, 3181–3194 (2021).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wagner, M. R., Busby, P. E. & Balint-Kurti, P. Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance. New Phytol. 225, 2152–2165 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Wagner, M. R., Roberts, J. H., Balint-Kurti, P. & Holland, J. B. Heterosis of leaf and rhizosphere microbiomes in field-grown maize. New Phytol. 228, 1055–1069 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Nobori, T. et al. Transcriptome landscape of a bacterial pathogen under plant immunity. Proc. Natl Acad. Sci. USA 115, E3055–E3064 (2018).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Xu, L. et al. Holo-omics for deciphering plant–microbiome interactions. Microbiome 9, 69 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    French, E., Kaplan, I., Iyer-Pascuzzi, A., Nakatsu, C. H. & Enders, L. Emerging strategies for precision microbiome management in diverse agroecosystems. Nat. Plants 7, 256–267 (2021).Article 
    PubMed 

    Google Scholar 
    Lemmon, Z. H. et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants 4, 766–770 (2018).Article 
    CAS 
    PubMed 

    Google Scholar 
    Kamilaris, A. & Prenafeta-Boldú, F. X. Deep learning in agriculture: a survey. Comput. Electron. Agric. 147, 70–90 (2018).Article 

    Google Scholar 
    Zhou, L., Zhang, C., Liu, F., Qiu, Z. & He, Y. Application of deep learning in food: a review. Compr. Rev. Food Sci. Food Saf. 18, 1793–1811 (2019).Article 
    PubMed 

    Google Scholar 
    Moreno-Indias, I. et al. Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions. Front. Microbiol. 12, 635781 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Song, P., Wang, J., Guo, X., Yang, W. & Zhao, C. High-throughput phenotyping: breaking through the bottleneck in future crop breeding. Crop J. 9, 633–645 (2021).Article 

    Google Scholar  More

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    Algal sensitivity to nickel toxicity in response to phosphorus starvation

    Effect of phosphorus starved cultures of Dunaliella tertiolecta on growth represented as optical density under stress of nickel ionsIn the case of normal culture, phosphorus starved control culture (without nickel stress), and phosphorus-starved treated cultures, data presented in Table 1 and graphed in figure (S1, Supplementary Data) clearly showed a progressive increase in optical density with increasing culturing period in case of normal culture, phosphorus-starved control culture, and phosphorus-starved treated cultures. Our findings are consistent with those of18 who found that in phosphorus starved cultures of three algae species, Microcystic aeruginosa, Chlorella pyrenoidesa, and Cyclotella sp., the biomass, specific growth rate, and Chl-a all declined significantly.The optical density achieved during the four periods of culturing was lower in phosphorus-depleted control cultures than in normal cultures (i.e., cultures contained phosphorus). When compared to a normal control (without nickel addition), the optical density was reduced by 9.1% after 4 days of culturing under phosphorus deprivation and by 10.0 percent after 8 days of culturing. In the case of 5 mg/L dissolved nickel, however, the obtained optical density values in phosphorus starved treatment cultures rose with the increase in culturing period during all culturing periods as compared to phosphorus-starved control (without nickel addition) cultures.At 10 mg/L dissolved nickel and after 4 days of culturing, the optical density although less than those in case of concentration 5 mg/L, yet it was higher than control (− P) but by increasing the culturing period more than 4 days, the optical density was less than control (− P). Our results are similar to those of19 who observed that the decrease in cell division rate signaled the onset of P-deficiency. The cultures that showed no significant increase in cell number for at least three consecutive days under the experimental conditions were considered P-depleted. In addition20, observed that the growth rate of Dunaliella prava was found to be dramatically lowered when phosphorus was limited. The content of chlorophyll fractions, total soluble carbohydrates, and proteins all fell considerably as a result of phosphorus restriction.The results concerning the effect of dissolved nickel on the growth of Dunaliella tertiolecta under conditions of phosphorus limitation show that phosphorus starved Dunaliella had lower growth as compared to the control (phosphorus-containing culture medium). These results are in agreement with those obtained by7 who reported that the optical density of Chlorella kessleri cell suspension decreased with phosphorus deficiency compared to control. Also21, found that Chlorella vulgaris cells grew 30–40% slower in phosphorus-starved cultures than in control cultures. Furthermore22, showed that diatoms were unable to thrive when phosphorus levels were insufficient. Diatom dominances were reduced to 45 and 55% in enclosures where phosphate was not provided23 observed that, under salt stress, Chlorella’s metabolic rate was substantially lower than Dunaliella’s.It can be concluded that when microorganisms are deprived of phosphorus, dissolved nickel uptake decreases, resulting in an increase in algal metabolism24. Also25, examined the effects of phosphorus and nitrogen starvation on the life cycle of Emiliania huxleyi (Haptophyta) and proved that various biochemical pathways’ metabolic load increased under P-starvation while it decreased under N-starvation.Effect of phosphorus starved cultures of Dunaliella tertiolecta on chlorophylls content under stress of nickel ionsTable 2 and figure (S2, Supplementary Data) show the sequences of change in the amount of chlorophylls a and b in phosphorus-depleted cultures of Dunaliella tertiolecta in response to various dissolved nickel concentrations. The results show that total chlorophyll content rose steadily until the end of the experiment under normal conditions (a control containing phosphorus). These results are in harmony with those obtained by24. The ratio between chlorophylls “a” and “b” remained nearly constant till the end of the 12th day. At the 16th day of culturing, the ratio decreased from 2.9:1 to 2.4:1. On the contrary, the total chlorophylls under control (in the absence of nickel element) in case of phosphorus-starved cultures showed a progressive increase up to the 12th day. At the 12th day the total chlorophylls in case of phosphorus-starved cultures decreased by 10.7% compared to the normal control. At the 16th day, the total chlorophylls in case of untreated phosphorus starved culture decreased by 20.8% compared to those obtained at normal control26. Reported that the chlorophyll content of Chlorella sorokiniana was significantly reduced due to a lack of nitrogen and phosphorus in the medium.Table 2 Effect of different concentrations of dissolved nickel (mg/L) on chlorophylls content (µg/ml) of Dunaliella tertiolecta under the stress of phosphorus starvation.Full size tableThe total chlorophyll content of Dunaliella tertiolecta in the phosphorus-starved cultures treated with 5 mg/L of dissolved nickel increased gradually until the 12th day, when the content of the total chlorophylls reached 2.11 µg/ml, i.e., higher than the phosphorus-starved control (− P) by 15.3%. At the 16th day, the total chlorophylls, although lower than those obtained at the 12th day, were still higher than the control (− P). At a concentration of 10 mg/L of dissolved nickel, slight increase in the content of total chlorophylls was recorded from the beginning to the end of the culturing period, i.e., from the 4th to the 16th day. At the other concentrations of dissolved nickel (15, 20, and 25 mg/L), a pronounced decrease in the total chlorophylls could be observed from the 4th to the 16th day of culturing compared to control (− P). Our results are going with an agreement with those obtained by27 who found that chlorophylls were inhibited maximum at higher dissolved nickel concentrations but activated at lower values. The normal ratio between chlorophylls “a” and “b” (3:1) was upset after the 8th day of culturing under concentrations 5, 10, and 15 mg/L of dissolved nickel. At 20 and 25 mg/L of dissolved nickel, this ratio was unstable from the beginning to the end of the experiment. The fact that dissolved nickel is extremely mobile and hence only absorbed to a minimal level may explain the sensitivity of the tested alga to nickel in response to phosphorus deficiency, and an increase in phosphorus concentration favors its absorption by microorganisms28. It can be concluded that when microorganisms are deprived of phosphorus, dissolved nickel uptake decreases, resulting in an increase in algal metabolism.Effect of different concentrations of dissolved nickel on photosynthesis (O2-evolution) of phosphorus starved cells of Dunaliella tertiolecta
    Data represented in Table 3 and graphed in figure (S3, Supplementary Data S3) showed that the effect of phosphorus limitation on the photosynthetic activity of Dunaliella tertiolecta in response to five different concentrations of dissolved nickel revealed that, under phosphorus limiting conditions, the amount of O2-evolution was lower than in untreated cultures (the control). The evolution of O2 after 4 days of culturing in case of phosphorus starved control decreased by 8.7% compared to normal control, while after 12 days it decreased by 30.4%. The rate of O2-evolution at different concentrations of dissolved nickel over 5 mg/L caused successive reductions in the O2-evolution of phosphorus starved cells. Application of 5 mg/L of dissolved nickel, the results cleared that the rate of O2-evolution increased under the effect of all tested concentrations till the end of the experiment. It is clear from our data that the rate of O2-evolution depended mainly on the concentration of the nickel element and the length of culturing period. The lower the rate of O2-evolution, the higher the element’s concentration, and the longer the culturing period. This coincided with the findings of7 who found that low phosphorus treatment causes Chlorella kessleri to lose its photosynthetic activity. In this regard, it was discovered that phosphorus deficiency resulted in a decrease in photosynthetic electron transport activity29 found that the O2-evolution of Chlamydomon reinhardtii declined by 75%. This decrease reflects damage of PSII and the generation of PSII QB-non reducing centers.Table 3 Effect of different concentrations of dissolved nickel (mg/L) on photosynthetic activity (O2-evolution calculated as µ mol O2 mg chl-1 h-1) on phosphorus supplemented and starved cells of Dunaliella tertiolecta.Full size tableAlso30 found that P- deficiency has been correlated with lower photosynthetic rates. In the case of the treated phosphorus-starved cultures with lower concentrations (5 mg/L) of dissolved nickel, the rate of photosynthesis increased when compared to the phosphorus-starved control, but was less than that of the normal control (without nickel treatment). On the contrary, it was found that, in the treated phosphorus-starved cultures at concentrations of 10, 15, 20 and 25 mg/L of the tested element, the rate of photosynthesis decreased from the beginning to the end of the experiment. With increasing concentration, duration of the culturing period, and kind of element, the condition of decrease in O2-evolution became more pronounced; the same results were also recorded by24. The stimulation of growth and photosynthesis in the presence of some concentrations of dissolved nickel under phosphorus-limiting conditions is observed by31 they report that in Cu2+ sensitive Scenedesmus acutus, intracellular polyphosphate plays a key role in shielding photosynthesis from Cu2+ toxicity but not in copper resistant species.Effect of different concentrations of dissolved nickel on respiration (O2-uptake) of phosphorus starved cells of Dunaliella tertiolectaData obtained in Table 4 and graphed in figure (S4, Supplementary Data S4) concerning the rate of respiration of Dunaliella tertiolecta under phosphorus-limiting conditions was higher than that of untreated phosphorus-starved (control) for a short period of time only, i.e., after 4 days, at concentrations 5, 10 and 15 mg/L of dissolved nickel, After 8 days of culturing, the rate of O2- uptake increased only at 5 mg/L of dissolved nickel, while at the other concentrations it decreased gradually with increasing the concentration of the element. This finding is consistent with the findings of23, who discovered that Dunaliella cells increased their O2 absorption and evolution rates in the presence of 2 M salt NaCl in the media. In terms of oxygen uptake rate, Dunaliella cells demonstrated an increase in salt concentrations. In 1.5 M NaCl, it increased significantly by 60–80%.Table 4 Effect of different concentrations of dissolved nickel (mg/L) on respiration activity (O2-uptake calculated as µ mol O2 h-1) on phosphorus supplemented and starved cells of Dunaliella tertiolecta.Full size tableConcerning the increase in respiration in P-depleted green alga species cultures5 suggested that Scenedesmus, for example, can utilize the energy stored in starch and lipids for active phosphorus uptake from lake sediments. This process is aided by an increase in phosphatase production32 and these cells’ ability to operate anaerobically33. When unicellular green algae or higher plants are exposed to P deficiency, the majority of newly fixed carbon appears to be allocated to the synthesis of non-phosphorylated storage polyglucans (i.e., starch) or sucrose, with less photosynthetic activity directed to respiratory metabolism and other biosynthesis pathways34. It can be concluded from the obtained results that, when the alga was cultivated under phosphorus deficiency and treated with varied amounts of dissolved nickel, the growth was the most sensitive characteristic, followed by photosynthesis, and then dark respiration. In the few comparative studies with several species of green algae, growth was more sensitive than the other physiological processes examined. Out of them35, reported that growth was more susceptible to phosphorus deficiency in Chlorella pyrenoidosa and Asterionella gracilis than photosynthesis and respiration (the least sensitive processes). Growth was also more sensitive than photosynthesis in Nitzschia closterium 36 . Another important fact reported by37 is that under low phosphorus conditions, Dunaliella parva accumulates lipids rather than carbohydrates. These findings imply that phosphorus stress may prevent starch and/or protein production, leading to an increase in carbon flux to lipids. More

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    Sap flow of sweet cherry reveals distinct effects of humidity and wind under rain covered and netted protected cropping systems

    Jensen, M. H. & Malter, A. J. Protected Agriculture—A Global Review. World Bank Technical Paper Number 253 (World Bank, 1995).
    Google Scholar 
    Meli, T., Riesen, W. & Widmer, A. Protection of sweet cherry hedgerows with polyethylene films. Acta Hortic. 155, 463–467 (1984).Article 

    Google Scholar 
    Janick, J. (ed.) Horticultural Reviews Vol. 30, 115–162 (Wiley, 2004).
    Google Scholar 
    Janke, R. R., Altamimi, M. E. & Khan, M. The use of high tunnels to produce fruit and vegetable crops in North America. Agric. Sci. 08, 692–715. https://doi.org/10.4236/as.2017.87052 (2017).Article 

    Google Scholar 
    Alarcon, J. J. et al. Sap flow as an indicator of transpiration and the water status of young apricot trees. Plant Soil 227, 77–85. https://doi.org/10.1023/A:1026520111166 (2000).Article 
    CAS 

    Google Scholar 
    Ferrara, G. & Flore, J. Comparison between different methods for measuring tranpiration in potted apple trees. Biol. Plant. 46, 41–47 (2003).Article 

    Google Scholar 
    Nicolás, E., Torrecillas, A., Amico, J. D. & Alarcón, J. J. Sap flow, gas exchange, and hydraulic conductance of young apricot trees growing under a shading net and different water supplies. J. Plant Physiol. 162, 439–447. https://doi.org/10.1016/j.jplph.2004.05.014 (2005).Article 
    CAS 

    Google Scholar 
    Green, S. & Romero, R. Can we improve heat-pulse to measure low and reverse flows. Acta Hortic. 951, 19–30 (2012).Article 

    Google Scholar 
    Noitsakis, B. & Nastis, A. S. Seasonal changes of water potential, stomatal conductance and transpiration in the leaf of cherry trees grown in shelter. CIHEAM 12, 267–270 (1995).
    Google Scholar 
    Lang, G. A. High tunnel tree fruit production: The final frontier. HortTechnology 19, 50–55 (2009).Article 

    Google Scholar 
    Lang, G. A. Tree fruit production in high tunnels: Current status and case study of sweet cherries. Acta Hortic. 987, 73–82 (2013).Article 

    Google Scholar 
    Meland, M., Frøynes, O. & Kaiser, C. High tunnel production systems improve yields and fruit size of sweet cherry. Acta Hortic. 1161, 117–124. https://doi.org/10.17660/ActaHortic.2017.1161.20 (2017).Article 

    Google Scholar 
    Cohen, S., Moreshet, S., Guillou, L. L., Simon, J.-C. & Cohen, M. Response of citrus trees to modified radiation regime in semi-arid conditions. J. Exp. Bot. 48, 35–44. https://doi.org/10.1093/jxb/48.1.35 (1997).Article 
    CAS 

    Google Scholar 
    Zeppel, M., Murray, B. R., Barton, C. & Eamus, D. Seasonal responses of xylem sap velocity to VPD and solar radiation during drought in a stand of native trees in temperate Australia. Funct. Plant Biol. 31, 461–470 (2004).Article 

    Google Scholar 
    Bonada, M., Buesa, I., Moran, M. A. & Sadras, V. O. Interactive effects of warming and water deficit on Shiraz vine transpiration in the Barossa Valley, Australia. OENO One 52, 189–202. https://doi.org/10.20870/oeno-one.2018.52.2.2141 (2018).Article 
    CAS 

    Google Scholar 
    Wang, K. Y., Kellomaki, S., Zha, T. & Peltola, H. Annual and seasonal variation of sap flow and conductance of pine trees grown in elevated carbon dioxide and temperature. J. Exp. Bot. 56, 155–165. https://doi.org/10.1093/jxb/eri013 (2005).Article 
    CAS 

    Google Scholar 
    Laplace, S., Chu, C. & Kume, S. Wind speed response of sap flow in five subtropical trees based on wind tunnel experiments. Br. J. Environ. Clim. Change 3, 160–171. https://doi.org/10.9734/BJECC/2013/3842 (2013).Article 

    Google Scholar 
    Kellomäki, S. & Wang, K. Y. Sap flow in Scots pine growing under conditions of year-round carbon dioxide enrichment and temperature elevation. Plant, Cell Environ. 21, 969–981. https://doi.org/10.1046/j.1365-3040.1998.00352.x (2002).Article 

    Google Scholar 
    Urban, J., Ingwers, M., McGuire, M. A. & Teskey, R. O. Stomatal conductance increases with rising temperature. Plant Signal. Behav. 12, 3–6. https://doi.org/10.1080/15592324.2017.1356534 (2017).Article 
    CAS 

    Google Scholar 
    Wu, J. et al. Nocturnal sap flow is mainly caused by stem refilling rather than nocturnal transpiration for Acer truncatum in urban environment. Urban For. Urban Green. 56, 126800. https://doi.org/10.1016/j.ufug.2020.126800 (2020).Article 

    Google Scholar 
    Chen, Y.-J. et al. Time lags between crown and basal sap flows in tropical lianas and co-occurring trees. Tree Physiol. 36, 736–747. https://doi.org/10.1093/treephys/tpv103 (2015).Article 

    Google Scholar 
    Marshall, D. C. Measurment of sap flow in conifers by heat transport. Plant Physiol. 33, 385–396 (1958).Article 
    CAS 

    Google Scholar 
    Swanson, R. H. & Whitfield, W. A. A numerical analysis of heat pulse velocity theory and practice. J. Exp. Bot. 32, 221–239 (1981).Article 

    Google Scholar 
    Green, S., Clothier, B. & Jardine, B. Theory and practical application of heat pulse to measure sap flow. Am. Soc. Agron. 95, 1371–1379 (2003).Article 

    Google Scholar 
    Goodwin, I., Cornwall, D. & Green, S. R. Pear transpiration and basal crop coefficients estimated by sap flow. Acta Hortic. 951, 183–190. https://doi.org/10.17660/ActaHortic.2012.951.22 (2012).Article 

    Google Scholar 
    Fernandez, J. E. et al. Heat-pulse measurements of sap flow in olives for automating irrigation, tests, root flow and diagnostics of water stress. Agric. Water Manag. 51, 99–123 (2001).Article 

    Google Scholar 
    Green, S. R. & Clothier, B. Water use of kiwifruit vines and apple trees by the heat-pulse technique. J. Exp. Bot. 39, 115–123 (1988).Article 

    Google Scholar 
    Green, S. R. et al. Measurement of sap flow in young apple trees using the average gradient heat-pulse method. Acta Hortic. 1222, 173–178. https://doi.org/10.17660/ActaHortic.2018.1222.35 (2018).Article 

    Google Scholar 
    Green, S., Clothier, B. & Perie, E. A re-analysis of heat pulse theory across a wide range of sap flows. Acta Hortic. 846, 95–104 (2009).Article 

    Google Scholar 
    Allen, R. G., Pereira, L. S., Raes, D. & Smith, M. Crop Evapotranspiration Guidelines for Computing Crop Water Requirements, FAO Irrigation and Drainage Paper 56 300 (FAO, 1998).
    Google Scholar 
    R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2010).Hastie, T. & Tibshirani, R. Generalized Additive Models (Chapman and Hall/CRC, 1990).MATH 

    Google Scholar 
    Akaike, H. A new look at the statistical model identification. IEEE Trans. Autom. Control 19, 716–723. https://doi.org/10.1109/TAC.1974.1100705 (1974).Article 
    MathSciNet 
    MATH 

    Google Scholar 
    Sams, C. E. & Flore, J. A. The influence of leaf age, leaf position on the shoot, and environmental variables on net photosynthetic rate of sour cherry (Prunus cerasus L. ’Montmorency’). J. Am. Soc. Hortic. Sci. 107, 339–344 (1982).Article 

    Google Scholar 
    Wallberg, B. N. & Sagredo, K. X. Vegetative and reproductive development of “Lapins” sweet cherry trees under rain protective cropping. Int. Soc. Hortic. Sci. 1058, 411–417 (2014).
    Google Scholar 
    Lang, G. A. Growing sweet cherries under plastic covers and tunnels: Physiological aspects and practical considerations. Acta Hortic. 1020, 303–312. https://doi.org/10.17660/ActaHortic.2014.1020.43 (2014).Article 

    Google Scholar 
    Goodwin, I., McClymont, L., Turpin, S. & Darbyshire, R. Effectiveness of netting in decreasing fruit surface temperature and sunburn damage of red-blushed pear. N. Z. J. Crop. Hortic. Sci. 46, 334–345. https://doi.org/10.1080/01140671.2018.1432492 (2018).Article 
    CAS 

    Google Scholar 
    Mika, A., Buler, Z., Wójcik, K. & Konopacka, D. Influence of the plastic cover on the protection of sweet cherry fruit against cracking, on the microclimate under cover and fruit quality. J. Hortic. Res. 27, 31–38. https://doi.org/10.2478/johr-2019-0018 (2019).Article 
    CAS 

    Google Scholar 
    Blanco, V., Zoffoli, J. P. & Ayala, M. High tunnel cultivation of sweet cherry (Prunus avium L.): Physiological and production variables. Sci. Hortic. 251, 108–117. https://doi.org/10.1016/j.scienta.2019.02.023 (2019).Article 

    Google Scholar 
    Sams, C. E. & Flore, J. A. Net photosynthetic rate of sour cherry (Prunus cerasus L. ‘Montmorency’) during the growing season with particular reference to fruiting. Photosynth. Res. 4, 307–316. https://doi.org/10.1007/BF00054139 (1983).Article 

    Google Scholar 
    Lange, O. L., Schulze, E. D., Evenari, M., Kappen, L. & Buschbom, U. The temperature-related photosynthesis capacity of plants under desert conditions. Oecologia 17, 97–110. https://doi.org/10.1007/BF00346273 (1974).Article 
    CAS 

    Google Scholar 
    Beckman, T. G., Perry, R. L. & Flore, J. A. Short-term flooding affects gas exchange characteristics of containerized sour cherry trees. HortScience 27, 1297. https://doi.org/10.21273/hortsci.27.12.1297 (1992).Article 

    Google Scholar 
    Lei, H., Zhi-Shan, Z. & Xin-Rong, L. Sap flow of Artemisia ordosica and the influence of environmental factors in a revegetated desert area: Tengger Desert, China. Hydrol. Processes 24, 1248–1253. https://doi.org/10.1002/hyp.7584 (2010).Article 

    Google Scholar 
    Juhász, A., Hrotko, K. & Tokei, L. Air and Water Components of the Environment, 76–82.Ravi, S. & D’Odorico, P. A field-scale analysis of the dependence of wind erosion threshold velocity on air humidity. Geophys. Res. Lett. 32, 023675. https://doi.org/10.1029/2005gl023675 (2005).Article 

    Google Scholar 
    Holmes, M. & Farrell, D. South African Avocado Growers Association Yearbook Vol. 16, 59–64 (1993).Jones, H. G. Plants and Microclimate: A quantitative Approach to Environmental Plant Physiology 3rd edn. (Cambridge University Press, 2014).
    Google Scholar 
    Juhász, Á., Sepsi, P., Nagy, Z., Tőkei, L. & Hrotkó, K. Water consumption of sweet cherry trees estimated by sap flow measurement. Sci. Hortic. 164, 41–49. https://doi.org/10.1016/j.scienta.2013.08.022 (2013).Article 

    Google Scholar 
    Gussakovsky, E. E., Salomon, E., Ratner, K., Shahak, Y. & Driesenaar, A. R. J. Photoinhibition (light stress) in citrus leaves. Acta Hortic. 349, 139–143 (1993).Article 

    Google Scholar 
    Grappadelli, L. C. & Lakso, A. N. Is maximizing orchard light interception always the best choice? Acta Hortic. 732, 507–518. https://doi.org/10.17660/ActaHortic.2007.732.77 (2007).Article 

    Google Scholar  More

  • in

    Vegetation assessments under the influence of environmental variables from the Yakhtangay Hill of the Hindu-Himalayan range, North Western Pakistan

    Khan, M. et al. Plant species and communities assessment in interaction with edaphic and topographic factors; an ecological study of the mount Eelum District Swat Pakistan. Saudi J. Biol. Sci. 24(4), 778–786 (2017).Article 

    Google Scholar 
    Ur Rahman, A. et al. Impact of multiple environmental factors on species abundance in various forest layers using an integrative modeling approach. Global Ecol. Conserv. 29, e01712 (2021).Article 

    Google Scholar 
    Arneth, A., Uncertain future for vegetation cover. Nature 524(7563), 44–45.Goldsmith, F., Description and analysis of vegetation. Methods Plant Ecol. (1976).Rahman, I. U. et al. First insights into the floristic diversity, biological spectra and phenology of Manoor Valley Pakistan. Pak. J. Bot 50(3), 1113–1124 (2018).
    Google Scholar 
    Khan, S.M., Plant communities and vegetation ecosystem services in the Naran Valley, Western Himalaya, 2012, University of Leicester.Haq, F., Ahmad, H. & Iqbal, Z. Vegetation description and phytoclimatic gradients of subtropical forests of Nandiar Khuwar catchment District Battagram. Pak. J. Bot 47(4), 1399–1405 (2015).
    Google Scholar 
    Iqbal, M. et al. A novel approach to phytosociological classification of weeds flora of an agro-ecological system through Cluster, two way cluster and indicator species analyses. Ecol. Ind. 84, 590–606 (2018).Article 

    Google Scholar 
    Shaw, M. R. et al. Grassland responses to global environmental changes suppressed by elevated CO2. Science 298(5600), 1987–1990 (2002).Article 

    Google Scholar 
    Drenovsky, R.E., Effects of mineral nutrient deficiencies on plant performance in the desert shrubs Chrysothamnus nauseosus ssp. consimilis and Sarcobatus vermiculatus2002: University of California, Davis.Iqbal, M. et al. Vegetation classification of the Margalla Foothills, Islamabad under the influence of edaphic factors and anthropogenic activities using modern ecological tools. Pak. J. Bot 53(5), 1831–1843 (2021).Article 

    Google Scholar 
    Bai, Y. et al. Landscape-level dynamics of grassland-forest transitions in British Columbia. J. Range Manag. 57(1), 66–75 (2004).Article 

    Google Scholar 
    Zhao, T. et al. Retrievals of soil moisture and vegetation optical depth using a multi-channel collaborative algorithm. Remote Sens. Environ. 257, 112321 (2021).Article 

    Google Scholar 
    Austin, M., Chapter 2: Vegetation and environment: discontinuities and continuities. IN VAN DER MAAREL, E.(Ed.) Végétation ecology. Etats‐Unis, 2005, Blackwell Publishing.Peña-Claros, M. et al. Soil effects on forest structure and diversity in a moist and a dry tropical forest. Biotropica 44(3), 276–283 (2012).Article 

    Google Scholar 
    Miao, R. et al. Effects of long-term grazing exclusion on plant and soil properties vary with position in dune systems in the Horqin Sandy Land. CATENA 209, 105860 (2022).Article 

    Google Scholar 
    Abbas, Z. et al. Plant communities and anthropo-natural threats in the Shigar valley,(Central Karakorum) Baltistan-Pakistan. Pak. J. Bot. 52, 987–994 (2020).Article 

    Google Scholar 
    Anwar, S., et al., Plant diversity and communities pattern with special emphasis on the indicator species of a dry temperate forest: A case study from Liakot area of the Hindu Kush mountains, Pakistan. Trop. Ecol. 1–16 (2022).Mumshad, M. et al. Phyto-ecological studies and distribution pattern of plant species and communities of Dhirkot, Azad Jammu and Kashmir, Pakistan. PLoS ONE 16(10), e0257493 (2021).Article 

    Google Scholar 
    Baldeck, C. A. et al. Soil resources and topography shape local tree community structure in tropical forests. Proc. R. Soc. B Biol. Sci. 280(1753), 20122532 (2013).Article 

    Google Scholar 
    Guerra, T. N. F. et al. Influence of edge and topography on the vegetation in an Atlantic Forest remnant in northeastern Brazil. J. For. Res. 18(2), 200–208 (2013).Article 

    Google Scholar 
    Townsend, A. R., Asner, G. P. & Cleveland, C. C. The biogeochemical heterogeneity of tropical forests. Trends Ecol. Evol. 23(8), 424–431 (2008).Article 

    Google Scholar 
    Becknell, J. M. & Powers, J. S. Stand age and soils as drivers of plant functional traits and aboveground biomass in secondary tropical dry forest. Can. J. For. Res. 44(6), 604–613 (2014).Article 

    Google Scholar 
    Geri, F., Rocchini, D. & Chiarucci, A. Landscape metrics and topographical determinants of large-scale forest dynamics in a Mediterranean landscape. Landsc. Urban Plan. 95(1–2), 46–53 (2010).Article 

    Google Scholar 
    Lomolino, M. V. Elevation gradients of species-density: historical and prospective views. Glob. Ecol. Biogeogr. 10(1), 3–13 (2001).Article 

    Google Scholar 
    Zhang, K. et al. An integrated flood risk assessment approach based on coupled hydrological-hydraulic modeling and bottom-up hazard vulnerability analysis. Environ. Model. Softw. 148, 105279 (2022).Article 

    Google Scholar 
    Liu, Y. et al. A hybrid runoff generation modelling framework based on spatial combination of three runoff generation schemes for semi-humid and semi-arid watersheds. J. Hydrol. 590, 125440 (2020).Article 

    Google Scholar 
    Mir, A. Y. et al. Ethnopharmacology and phenology of high-altitude medicinal plants in Kashmir Northern Himalaya. Ethnobot. Res. Appl. 22, 1–15 (2021).
    Google Scholar 
    Vetaas, O. R. & Grytnes, J. A. Distribution of vascular plant species richness and endemic richness along the Himalayan elevation gradient in Nepal. Glob. Ecol. Biogeogr. 11(4), 291–301 (2002).Article 

    Google Scholar 
    Li, W. et al. Fine root biomass and morphology in a temperate forest are influenced more by the nitrogen treatment approach than the rate. Ecol. Ind. 130, 108031 (2021).Article 

    Google Scholar 
    Su, N. et al. Landscape context determines soil fungal diversity in a fragmented habitat. CATENA 213, 106163 (2022).Article 

    Google Scholar 
    Yang, Y., et al., Nitrogen fertilization weakens the linkage between soil carbon and microbial diversity: a global meta‐analysis. Global Change Biol. (2022).Ahmad, Z. et al. Weed species composition and distribution pattern in the maize crop under the influence of edaphic factors and farming practices: A case study from Mardan Pakistan. Saudi J. Biol. Sci. 23(6), 741–748 (2016).Article 

    Google Scholar 
    Rahman, A. U. et al. Ecological assessment of plant communities and associated edaphic and topographic variables in the Peochar Valley of the Hindu Kush mountains. Mt. Res. Dev. 36(3), 332–341 (2016).Article 

    Google Scholar 
    Ashton, P. S. A contribution of rain forest research to evolutionary theory. Ann. Mo. Bot. Gard. 64(4), 694–705 (1977).Article 

    Google Scholar 
    Yang, Y. et al. Negative effects of multiple global change factors on soil microbial diversity. Soil Biol. Biochem. 156, 108229 (2021).Article 

    Google Scholar 
    Pärtel, M. Local plant diversity patterns and evolutionary history at the regional scale. Ecology 83(9), 2361–2366 (2002).Article 

    Google Scholar 
    Taylor, D.R., Aarssen, L.W., & Loehle, C. On the relationship between r/K selection and environmental carrying capacity: A new habitat templet for plant life history strategies. Oikos 239–250 (1990).Knapp, A. K. et al. Rainfall variability, carbon cycling, and plant species diversity in a mesic grassland. Science 298(5601), 2202–2205 (2002).Article 

    Google Scholar 
    Zscheischler, J. et al. Short-term favorable weather conditions are an important control of interannual variability in carbon and water fluxes. J. Geophys. Res. Biogeosci. 121(8), 2186–2198 (2016).Article 

    Google Scholar 
    Gao, C. et al. Simulation and design of joint distribution of rainfall and tide level in Wuchengxiyu Region China. Urban Clim. 40, 101005 (2021).Article 

    Google Scholar 
    Wang, S. et al. Exploring the utility of radar and satellite-sensed precipitation and their dynamic bias correction for integrated prediction of flood and landslide hazards. J. Hydrol. 603, 126964 (2021).Article 

    Google Scholar 
    Zhang, K. et al. The sensitivity of North American terrestrial carbon fluxes to spatial and temporal variation in soil moisture: An analysis using radar-derived estimates of root-zone soil moisture. J. Geophys. Res. Biogeosci. 124(11), 3208–3231 (2019).Article 

    Google Scholar 
    Yang, Y. et al. Increasing contribution of microbial residues to soil organic carbon in grassland restoration chronosequence. Soil Biol. Biochem. 170, 108688 (2022).Article 

    Google Scholar 
    Li, J. et al. Differential mechanisms drive species loss under artificial shade and fertilization in the Alpine Meadow of the Tibetan Plateau. Front. Plant Sci. 13, 832473–832473 (2022).Article 

    Google Scholar 
    Fischer, C. et al. How do earthworms, soil texture and plant composition affect infiltration along an experimental plant diversity gradient in grassland?. PLoS ONE 9(6), e98987 (2014).Article 

    Google Scholar 
    Zhao, T. et al. Soil moisture experiment in the Luan River supporting new satellite mission opportunities. Remote Sens. Environ. 240, 111680 (2020).Article 

    Google Scholar 
    Marandi, A., Polikarpus, M. & Jõeleht, A. A new approach for describing the relationship between electrical conductivity and major anion concentration in natural waters. Appl. Geochem. 38, 103–109 (2013).Article 

    Google Scholar 
    Xu, J. et al. Modeling of coupled transfer of water, heat and solute in saline loess considering sodium sulfate crystallization. Cold Reg. Sci. Technol. 189, 103335 (2021).Article 

    Google Scholar 
    Chen, X. et al. Spatiotemporal characteristics and attribution of dry/wet conditions in the Weihe River Basin within a typical monsoon transition zone of East Asia over the recent 547 years. Environ. Model. Softw. 143, 105116 (2021).Article 

    Google Scholar 
    Ali, G., Siddique, S. & Suliman, M. Effect of canopy cover on natural regeneration of pinus wallichiana in moist temperate forest of Yakh Tangay, District Shangla Swat Pakistan. FUUAST J. Biol. 8(2), 193–201 (2018).
    Google Scholar 
    Zhang, K. et al. Characteristics and influencing factors of rainfall-induced landslide and debris flow hazards in Shaanxi Province, China. Nat. Hazard. 19(1), 93–105 (2019).Article 

    Google Scholar 
    Khan, W. et al. Vegetation mapping and multivariate approach to indicator species of a forest ecosystem: A case study from the Thandiani sub Forests Division (TsFD) in the Western Himalayas. Ecol. Ind. 71, 336–351 (2016).Article 

    Google Scholar 
    Iqbal, J. & Ahmed, M. Vegetation description of some pine forests of Shangla district of Khyber Pakhtunkhwa Pakistan: A preliminary study. FUUAST J. Biol. 4(1), 83–88 (2014).
    Google Scholar 
    Sparrow, B. D. et al. A vegetation and soil survey method for surveillance monitoring of rangeland environments. Front. Ecol. Evol. 8, 157 (2020).Article 

    Google Scholar 
    Esri, R., ArcGIS desktop: release 10. Environmental Systems Research Institute, CA (2011).Salzer, D., & Willoughby, J. Standardize this! The futility of attempting to apply a standard quadrat size and shape to rare plant monitoring. in Proceedings of the symposium of the North Coast Chapter of the California Native Plant Society: the ecology and management of rare plants of northwestern California. Arcata, CA. Sacramento, CA: The California Native Plant Society (2004).Bano, S. et al. Eco-Floristic studies of native plants of the Beer Hills along the Indus River in the districts Haripur and Abbottabad Pakistan. Saudi J. Biol. Sci. 25(4), 801–810 (2018).Article 

    Google Scholar 
    Perveen, A. & Qaiser, M. Pollen flora of Pakistan–XXXI Betulaceae. Pak. J. Bot. 31, 243–246 (1999).
    Google Scholar 
    Raunkiaer, C., The life forms of plants and statistical plant geography; being the collected papers of C. Raunkiaer. The life forms of plants and statistical plant geography; being the collected papers of C. Raunkiaer. (1934).Hussain, S.S., Pakistan manual of plant ecology1984: National Book Foundation.Kamran, S. et al. The role of graveyards in species conservation and beta diversity: A vegetation appraisal of sacred habitats from Bannu Pakistan. J. For. Res. 31(4), 1147–1158 (2020).Article 

    Google Scholar 
    Manan, F. et al. Environmental determinants of plant associations and evaluation of the conservation status of Parrotiopsis jacquemontiana in Dir, the Hindu Kush Range of Mountains. Trop. Ecol. 61(4), 509–526 (2020).Article 

    Google Scholar 
    Tfaily, M. M. et al. Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry. Anal. Chim. Acta 972, 54–61 (2017).Article 

    Google Scholar 
    Chaney, R., Slonim, S., & Slonim, S. Determination of calcium carbonate content in soils, in Geotechnical properties, behavior, and performance of calcareous soils1982, ASTM International.McCune, B., & Mefford, M. PC-ORD, Multivariate analysis of ecological data, Version 5 for Windows edition. MjM Software Design, Gleneden Beach, Oregon USA (2005).Lepš, J., & Šmilauer, P. Multivariate analysis of ecological data using CANOCO2003: Cambridge university press.Xie, W. et al. A novel hybrid method for landslide susceptibility mapping-based geodetector and machine learning cluster: A case of Xiaojin county, China. ISPRS Int. J. Geo Inf. 10(2), 93 (2021).Article 

    Google Scholar 
    Li, L., Lei, Y. & Pan, D. Economic and environmental evaluation of coal production in China and policy implications. Nat. Hazards 77(2), 1125–1141 (2015).Article 

    Google Scholar 
    Team, R.C., R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/ (2013).Anwar, S. et al. Floristic composition and ecological gradient analyses of the Liakot Forests in the Kalam region of District Swat Pakistan. J. For. Res. 30(4), 1407–1416 (2019).Article 

    Google Scholar 
    Haq, S. M. et al. Exploring and understanding the floristic richness, life-form, leaf-size spectra and phenology of plants in protected forests: A case study of Dachigam National Park in Himalaya Asia. Acta Ecol. Sin. 41(5), 479–490 (2021).Article 

    Google Scholar 
    Ilyas, M. et al. A Preliminary checklist of the vascular flora of Kabal Valley, Swat Pakistan. Pak. J. Bot 45(2), 605–615 (2013).
    Google Scholar 
    Amjad, M. S. et al. Floristic composition, biological spectrum and phenological pattern of vegetation in the subtropical forest of Kotli District, AJK Pakistan. Pure Appl. Biol. (PAB) 6(2), 426–447 (2017).
    Google Scholar 
    Shaheen, H. et al. Species diversity, community structure, and distribution patterns in western Himalayan alpine pastures of Kashmir Pakistan. Mount. Res. Dev. 31(2), 153–159 (2011).Article 

    Google Scholar 
    Abbas, Z. et al. Ethnobotany of the balti community, tormik valley, karakorum range, baltistan, pakistan. J. Ethnobiol. Ethnomed. 12(1), 1–16 (2016).Article 

    Google Scholar 
    Ahmed, M. et al. Phytosociology and structure of Himalayan forests from different climatic zones of Pakistan. Pak. J. Bot. 38(2), 361 (2006).MathSciNet 

    Google Scholar 
    Shehzadi, S. et al. Floristic compositions along an 18-Km long transect in Ayubia National Park District Abbottabad Pakistan. Pak. J. Bot. 41(5), 2115–2127 (2009).
    Google Scholar 
    Khan, W., et al., Life forms, leaf size spectra and diversity indices of plant species grown in the Thandiani forests, district Abbottabad, Khyber Pakhtunkhwa, Pakistan. Saudi J. Biol. Sci.Kharkwal, G. et al. Phytodiversity and growth form in relation to altitudinal gradient in the Central Himalayan (Kumaun) region of India. Curr. Sci. 1, 873–878 (2005).
    Google Scholar 
    Bennie, J. et al. Slope, aspect and climate: Spatially explicit and implicit models of topographic microclimate in chalk grassland. Ecol. Model. 216(1), 47–59 (2008).Article 

    Google Scholar 
    Choudhary, K. & Nama, K. S. Phyto-diversity of Mukundara hills national park of Kota district, Rajasthan India. Adv. Appl. Sci. Res. 5(1), 18–23 (2014).
    Google Scholar 
    Shimwell, D.W., Description and classification of vegetation (1971).Malik, Z.H., Comparative study of vegetation of GungaChotti and Bedori Hills, Distric Bagh, Azad Jammu and Kashmir with special reference to range conditions, 2005, University of Peshawar, Pakistan.Khan, W. et al. Life forms, leaf size spectra, regeneration capacity and diversity of plant species grown in the Thandiani forests, district Abbottabad, Khyber Pakhtunkhwa Pakistan. Saudi J. Biol. Sci. 25(1), 94–100 (2018).Article 

    Google Scholar 
    Grytnes, J. A. & Vetaas, O. R. Species richness and altitude: A comparison between null models and interpolated plant species richness along the Himalayan altitudinal gradient Nepal. Am. Nat. 159(3), 294–304 (2002).Article 

    Google Scholar 
    Majid, A., Khan, M. & Calixto, E. Ecological assessment of plant communities along the edaphic and topographic gradients of biha valley, District Swat Pakistan. Appl. Ecol. Environ. Res. 16(5), 5611–5631 (2018).Article 

    Google Scholar 
    Khan, S.M., et al., Vegetation dynamics in the Western Himalayas, diversity indices and climate change. Sci. Tech. Dev. 31(3), 232–243 (2012).Khan, S. M. et al. Identifying plant species and communities across environmental gradients in the Western Himalayas: Method development and conservation use. Eco. Inform. 14, 99–103 (2013).Article 

    Google Scholar 
    Shaheen, H. & Shinwari, Z. K. Phyto diversity and endemic richness of Karambar lake vegetation from Chitral Hindukush-Himalayas. Pak. J. Bot 44(1), 17–21 (2012).
    Google Scholar 
    Wana, D., Plant communities and diversity along altitudinal gradients from Lake Abaya to Chencha Highlands, 2002, MA Thesis, School of Graduate Studies, Addis Ababa University. Addis Ababa.Canfora, L. et al. Is soil microbial diversity affected by soil and groundwater salinity? Evidences from a coastal system in central Italy. Environ. Monit. Assess. 189(7), 1–15 (2017).Article 

    Google Scholar 
    Liu, S., et al., The distribution characteristics and human health risks of high-fluorine groundwater in coastal plain: A case study in Southern Laizhou Bay, China. Front. Environ. Sci. 568 (2022).Niu, Y. et al. Vegetation distribution along mountain environmental gradient predicts shifts in plant community response to climate change in alpine meadow on the Tibetan Plateau. Sci. Total Environ. 650, 505–514 (2019).Article 

    Google Scholar 
    Nadal-Romero, E. et al. Effects of slope angle and aspect on plant cover and species richness in a humid Mediterranean badland. Earth Surf. Proc. Land. 39(13), 1705–1716 (2014).Article 

    Google Scholar  More

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    Phytoplankton in the middle

    Marine phytoplankton both follow and actively influence the environment they inhabit. Unpacking the complex ecological and biogeochemical roles of these tiny organisms can help reveal the workings of the Earth system.
    Phytoplankton are the workers of an ocean-spanning factory converting sunlight and raw nutrients into organic matter. These little organisms — the foundation of the marine ecosystem — feed into a myriad of biogeochemical cycles, the balance of which help control the distribution of carbon on the Earth surface and ultimately the overall climate state. As papers in this issue of Nature Geoscience show, phytoplankton are far from passive actors in the global web of biogeochemical cycles. The functioning of phytoplankton is not just a matter for biologists, but is also important for geoscientists seeking to understand the Earth system more broadly.Phytoplankton are concentrated where local nutrient and sea surface temperatures are optimal, factors which aren’t always static in time. Prominent temperature fluctuations, from seasonal to daily cycles, are reflected in phytoplankton biomass, with cascading effects on other parts of marine ecosystems, such as economically-important fisheries. In an Article in this issue, Keerthi et al., show that phytoplankton biomass, tracked by satellite measurements of chlorophyll for relatively small ( More

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    Sewage surveillance of antibiotic resistance holds both opportunities and challenges

    Huijbers, P. M. C., Flach, C.-F. & Larsson, D. G. J. A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance. Environ. Int. 130, 104880 (2019).Article 

    Google Scholar 
    Aarestrup, F. M. & Woolhouse, M. E. J. Using sewage for surveillance of antimicrobial resistance. Science 367, 630–632 (2020).Article 

    Google Scholar 
    European Commission. Proposal for a revised Urban Wastewater Treatment Directive. European Commission https://environment.ec.europa.eu/publications/proposal-revised-urban-wastewater-treatment-directive_en (2022).US Centres for Disease Control and Prevention. COVID-19 impacts on environment (e.g., water, soil) and sanitation: addressing antimicrobials and antimicrobial resistant threats in the environment. US Centres for Disease Control and Prevention https://www.cdc.gov/drugresistance/pdf/covid19/COVID19-Impacts-AR-Environment-Sanitation-508.pdf (2021).Flach, C.-F., Hutinel, M., Razavi, M., Åhrén, C. & Larsson, D. G. J. Monitoring of hospital sewage shows both promise and limitations as an early-warning system for carbapenemase-producing Enterobacterales in a low-prevalence setting. Water Res. 200, 117261 (2021).Article 

    Google Scholar 
    Larsson, D. G. J. & Flach, C.-F. Antibiotic resistance in the environment. Nat. Rev. Microbiol. 20, 257–269 (2022).Article 

    Google Scholar 
    Newton, R. J. et al. Sewage reflects the microbiomes of human populations. mBio 6, e02574 (2015).Article 

    Google Scholar 
    Huijbers, P. M. C., Larsson, D. G. J. & Flach, C. F. Surveillance of antibiotic resistant Escherichia coli in human populations through urban wastewater in ten European countries. Environ. Pollut. 261, 114200 (2020).Article 

    Google Scholar 
    Laxminarayan, R. & Macauley, M. K. The Value of Infromation: Methodological Frontiers and New Applications in Environment and Health 1st edn (Springer Dordrecht, 2012).Munk, P. et al. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat. Commun. 13, 7251 (2022).Article 

    Google Scholar  More

  • in

    Rare and declining bird species benefit most from designating protected areas for conservation in the UK

    Johnson, C. N. et al. Biodiversity losses and conservation responses in the Anthropocene. Science 356, 270–275 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Rockström, J. et al. A safe operating space for humanity. Nature 461, 472–475 (2009).Article 
    PubMed 

    Google Scholar 
    Maxwell, S. L. et al. Area-based conservation in the twenty-first century. Nature 586, 217–227 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Schulze, K. et al. An assessment of threats to terrestrial protected areas. Conserv. Lett. 11, e12435 (2018).Article 

    Google Scholar 
    Bingham, H. C. et al. (eds). Protected Planet Report 2020 (UNEP-WCMC & IUCN, 2021); https://livereport.protectedplanet.net/Buchanan, G. M., Butchart, S. H., Chandler, G. & Gregory, R. D. Assessment of national-level progress towards elements of the Aichi Biodiversity Targets. Ecol. Indic. 116, 106497 (2020).Article 

    Google Scholar 
    Xu, H. et al. Ensuring effective implementation of the post-2020 global biodiversity targets. Nat. Ecol. Evol. 5, 411–418 (2021).Article 
    PubMed 

    Google Scholar 
    Report of the Open-ended Working Group on the Post-2020 Global Biodiversity Framework on Its Third Meeting (CBD Secretariat, 2022); https://www.cbd.int/conferences/post2020/wg2020-03/documentsRodrigues, A. S. & Cazalis, V. The multifaceted challenge of evaluating protected area effectiveness. Nat. Commun. 11, 5147 (2020).Article 
    PubMed Central 
    CAS 
    PubMed 

    Google Scholar 
    Geldmann, J., Manica, A., Burgess, N. D., Coad, L. & Balmford, A. A global-level assessment of the effectiveness of protected areas at resisting anthropogenic pressures. Proc. Natl Acad. Sci. USA 116, 23209–23215 (2019).Article 
    PubMed Central 
    CAS 
    PubMed 

    Google Scholar 
    Starnes, T. et al. The extent and effectiveness of protected areas in the UK. Glob. Ecol. Conserv. 30, e01745 (2021).Article 

    Google Scholar 
    Kremen, C. et al. Aligning conservation priorities across taxa in Madagascar with high-resolution planning tools. Science 320, 222–226 (2008).Article 
    CAS 
    PubMed 

    Google Scholar 
    Cazalis, V. et al. Mismatch between bird species sensitivity and the protection of intact habitats across the Americas. Ecol. Lett. 24, 2394–2405 (2021).Article 
    PubMed 

    Google Scholar 
    Venter, O. et al. Targeting global protected area expansion for imperiled biodiversity. PLoS Biol. 12, e1001891 (2014).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    Gamero, A. et al. Tracking progress toward EU biodiversity strategy targets: EU policy effects in preserving its common farmland birds. Conserv. Lett. 10, 395–402 (2017).Article 

    Google Scholar 
    Pellissier, V. et al. Effects of Natura 2000 on nontarget bird and butterfly species based on citizen science data. Conserv. Biol. 34, 666–676 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    Princé, K., Rouveyrol, P., Pellissier, V., Touroult, J. & Jiguet, F. Long-term effectiveness of Natura 2000 network to protect biodiversity: a hint of optimism for common birds. Biol. Conserv. 253, 108871 (2021).Article 

    Google Scholar 
    Cunningham, C. A., Thomas, C. D., Morecroft, M. D., Crick, H. Q. P. & Beale, C. M. The effectiveness of the protected area network of Great Britain. Biol. Conserv. 257, 109146 (2021).Article 

    Google Scholar 
    Duckworth, G. D. & Altwegg, R. Effectiveness of protected areas for bird conservation depends on guild. Divers. Distrib. 24, 1083–1091 (2018).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    Rada, S. et al. Protected areas do not mitigate biodiversity declines: a case study on butterflies. Divers. Distrib. 25, 217–224 (2019).Article 

    Google Scholar 
    Terraube, J., Van Doninck, J., Helle, P., & Cabeza, M. Assessing the effectiveness of a national protected area network for carnivore conservation. Nat. Commun. 11, 2957 (2020).Article 
    PubMed Central 
    CAS 
    PubMed 

    Google Scholar 
    Lenoir, J. et al. Species better track the shifting isotherms in the oceans than on land. Nat. Ecol. Evol. 4, 1044–1059 (2020).Article 
    PubMed 

    Google Scholar 
    van Teeffelen, A., Meller, L., van Minnen, J., Vermaat, J. & Cabeza, M. How climate proof is the European Union’s biodiversity policy? Regional Environ. Change 15, 997–1010 (2015).Article 

    Google Scholar 
    Thomas, C. D. & Gillingham, P. K. The performance of protected areas for biodiversity under climate change. Biol. J. Linn. Soc. Lond. 115, 718–730 (2015).Article 

    Google Scholar 
    Gillingham, P. K. et al. The effectiveness of protected areas in the conservation of species with changing geographical ranges. Biol. J. Linn. Soc. Lond. 115, 707–717 (2015).Article 

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

    Google Scholar 
    Stokstad, E. Species? Climate? Cost? Ambitious goal means trade-offs. Science 371, 555 (2021).Article 
    CAS 
    PubMed 

    Google Scholar 
    Brlík, V. et al. Long-term and large-scale multispecies dataset tracking population changes of common European breeding birds. Sci. Data 8, 21 (2021).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    Stanbury, A. et al. The status of bird populations: the fifth Birds of Conservation Concern in the United Kingdom, Channel Islands and Isle of Man and second IUCN Red List assessment of extinction risk for Great Britain. Br. Birds 114, 723–747 (2021).
    Google Scholar 
    Dudley, N. (ed). Guidelines for Applying Protected Area Management Categories (IUCN, 2008).Deguignet, M. et al. Measuring the extent of overlaps in protected area designations. PLoS ONE 12, e0188681 (2017).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    JNCC. Common Standards Monitoring: Introduction to the Guidance Manual (JNCC Resource Hub, 2004).Hayhow, D. B. et al. State of Nature 2019 (RSPB, 2019).Schleicher, J. et al. Statistical matching for conservation science. Conserv. Biol. 34, 538–549 (2019).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    Waldron, A. et al. Protecting 30% of the Planet for Nature: Costs, Benefits and Economic Implications (Campaign for Nature, 2020); https://helda.helsinki.fi/handle/10138/326470Franks, S. E., Roodbergen, M., Teunissen, W., Carrington Cotton, A. & Pearce‐Higgins, J. W. Evaluating the effectiveness of conservation measures for European grassland‐breeding waders. Ecol. Evol. 8, 10555–10568 (2018).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    Pearce-Higgins, J. W. et al. Site-based adaptation reduces the negative effects of weather upon a southern range margin Welsh black grouse Tetrao tetrix population that is vulnerable to climate change. Clim. Change 153, 253–265 (2019).Article 

    Google Scholar 
    Jellesmark, S. et al. A counterfactual approach to measure the impact of wet grassland conservation on U.K. breeding bird populations. Conserv. Biol. 35, 1575–1585 (2021).Article 
    PubMed 

    Google Scholar 
    Morrison, C. A. et al. Covariation in population trends and demography reveals targets for conservation action. Proc. Biol. Sci. 288, 20202955 (2021).PubMed Central 
    PubMed 

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

    Google Scholar 
    Martay, B. et al. Monitoring landscape-scale environmental changes with citizen scientists: Twenty years of land use change in Great Britain. J. Nat. Conserv. 44, 33–42 (2018).Article 

    Google Scholar 
    Sullivan, M. J. P., Newson, S. E. & Pearce‐Higgins, J. W. Changing densities of generalist species underlie apparent homogenization of UK bird communities. Ibis 158, 645–655 (2016).Article 

    Google Scholar 
    Wauchope, H. S. et al. Evaluating impact using time-series data. Trends Ecol. Evol. 36, 196–205 (2021).Article 
    PubMed 

    Google Scholar 
    Devictor, V. et al. Differences in the climatic debts of birds and butterflies at a continental scale. Nat. Clim. Change 2, 121–124 (2012).Article 

    Google Scholar 
    Lehikoinen, P., Santangeli, A., Jaatinen, K., Rajasärkkä, A. & Lehikoinen, A. Protected areas act as a buffer against detrimental effects of climate change—evidence from large‐scale, long‐term abundance data. Glob. Change Biol. 25, 304–313 (2019).Article 

    Google Scholar 
    Gaüzère, P., Jiguet, F. & Devictor, V. Can protected areas mitigate the impacts of climate change on bird’s species and communities? Diversity Distrib. 22, 625–637 (2016).Article 

    Google Scholar 
    Neate‐Clegg, M. H. C., Jones, S. E. I., Burdekin, O., Jocque, M. & Şekercioğlu, Ç. H. Elevational changes in the avian community of a Mesoamerican cloud forest park. Biotropica 50, 805–815 (2018).Article 

    Google Scholar 
    Oliver, T. H. et al. Large extents of intensive land use limit community reorganization during climate warming. Glob. Change Biol. 23, 2272–2283 (2017).Article 

    Google Scholar 
    Hiley, J. R., Bradbury, R. B., Holling, M. & Thomas, C. D. Protected areas act as establishment centres for species colonizing the UK. Proc. Biol. Sci. 280, 20122310 (2013).PubMed Central 
    PubMed 

    Google Scholar 
    Thomas, C. D. et al. Protected areas facilitate species’ range expansions. Proc. Natl Acad. Sci. USA 109, 14063–14068 (2012).Article 
    PubMed Central 
    CAS 
    PubMed 

    Google Scholar 
    Grace, M. K. et al. Testing a global standard for quantifying species recovery and assessing conservation impact. Conserv. Biol. 35, 1833–1849 (2021).Article 
    PubMed 

    Google Scholar 
    Gibbons, D. W., Reid, J. B. & Chapman, R. A. The New Atlas of Breeding Birds in Britain & Ireland 1988–1991 (T. & A. D. Poyser, 1993).Balmer, D. E. et al. Bird Atlas 2007–11: the Breeding and Wintering Birds of Britain and Ireland (BTO, 2013).Gillings, S. et al. Breeding and wintering bird distributions in Britain and Ireland from citizen science bird atlases. Glob. Ecol. Biogeogr. 28, 866–874 (2019).Article 

    Google Scholar 
    Freeman, S. N., Noble, D. G., Newson, S. E. & Baillie, S. R. Modelling population changes using data from different surveys: the Common Birds Census and the Breeding Bird Survey. Bird Study 54, 61–72 (2007).Article 

    Google Scholar 
    Robinson, R. A., Julliard, R. & Saracco, J. F. Constant effort: studying avian population processes using standardised ringing. Ring. Migr. 24, 199–204 (2009).Article 

    Google Scholar 
    Cave, V. M., Freeman, S. N., Brooks, S. P., King, R. & Balmer, D. E. in Modeling Demographic Processes in Marked Populations, 949–963 (Springer, 2009).Rowland, C. S. et al. Land Cover Map 2015 (1km Percentage Aggregate Class, GB) (eds Thomson, D. L. et al) (Environmental Information Data Centre, 2017); https://doi.org/10.5285/7115bc48-3ab0-475d-84ae-fd3126c20984Rowland, C. S. et al. Land Cover Map 2015 (1km Percentage Aggregate Class, N. Ireland) (Environmental Information Data Centre, 2017); https://doi.org/10.5285/362feaea-0ccf-4a45-b11f-980c6b89a858ASTER Global Digital Elevation Model V003 (dataset). NASA EOSDIS Land Processes DAAC (NASA/METI/AIST/Japan Space Systems and U.S./Japan ASTER Science Team, 2019); https://doi.org/10.5067/ASTER/ASTGTM.003Schiavina, M., Freire, S. & MacManus, K. GHS-SMOD R2019A – GHS Settlement Layers, Updated and Refined REGIO Model 2014 in Application to GHS-BUILT R2018A and GHS-POP R2019A, Multitemporal (1975-1990-2000-2015) (European Commission Joint Research Centre, 2019); https://doi.org/10.2905/42E8BE89-54FF-464E-BE7B-BF9E64DA5218Robinson, R. A. BirdFacts: Profiles of Birds Occurring in Britain & Ireland (BTO, 2005).Gibbons, D. W. et al. Bird species of conservation concern in the United Kingdom, Channel Islands and Isle of Man: revising the Red Data List. RSPB Conserv. Rev. 10, 7–18 (1996).
    Google Scholar 
    Stone, B. H. et al. Population estimates of birds in Britain and in the United Kingdom. Br. Birds 90, 1–22 (1997).
    Google Scholar 
    Woodward, I. et al. Population estimates of birds in Great Britain and the United Kingdom. Br. Birds 113, 69–104 (2020).
    Google Scholar 
    R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/Joppa, L. N. & Pfaff, A. High and far: biases in the location of protected areas. PLoS ONE 4, e8273 (2009).Article 
    PubMed Central 
    PubMed 

    Google Scholar 
    Bull, J. W., Strange, N., Smith, R. J. & Gordon, A. Reconciling multiple counterfactuals when evaluating biodiversity conservation impact in social‐ecological systems. Conserv. Biol. 35, 510–521 (2020).Article 
    PubMed 

    Google Scholar 
    Jellesmark, S. et al. Assessing the global impact of targeted conservation actions on species abundance. Preprint at bioRxiv https://doi.org/10.1101/2022.01.14.476374 (2022).Wauchope, H. S. et al. Protected areas have a mixed impact on waterbirds but management helps. Nature 605, 103–107 (2022).Article 
    CAS 
    PubMed 

    Google Scholar 
    Ho, D. E., Imai, K., King, G. & Stuart, E. A. MatchIt: nonparametric preprocessing for parametric causal inference. J. Stat. Softw. 42, 1–28 (2011).Article 

    Google Scholar 
    Wood, S. N. Generalized Additive Models: an Introduction with R 2nd edn (Chapman and Hall/CRC, 2017).Hartig, F. DHARMa: Residual diagnostics for hierarchical (multi-level/mixed) regression models. R package v.0.4.4 (2021); https://CRAN.R-project.org/package=DHARMaJetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444–448 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Hadfield, J. D. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J. Stat. Softw. 33, 1–22 (2010).Article 

    Google Scholar 
    Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).Article 
    CAS 
    PubMed 

    Google Scholar 
    Johnston, A. et al. Species traits explain variation in detectability of UK birds. Bird Study 61, 340–350 (2014).Article 

    Google Scholar 
    Hill, M. O. Diversity and evenness: a unifying notation and its consequences. Ecology 54, 427–432 (1973).Article 

    Google Scholar 
    Ho, D. E., Imai, K., King, G. & Stuart, E. A. Matching as nonparametric preprocessing for reducing model dependence in parametric causal inference. Political Anal. 15, 199–236 (2007).Article 

    Google Scholar 
    Julliard, R., Clavel, J., Devictor, V., Jiguet, F. & Couvet, D. Spatial segregation of specialists and generalists in bird communities. Ecol. Lett. 9, 1237–1244 (2006).Article 
    PubMed 

    Google Scholar 
    Devictor, V., Julliard, R., Couvet, D. & Jiguet, F. Birds are tracking climate warming, but not fast enough. Proc. Biol. Sci. 275, 2743–2748 (2008).PubMed Central 
    PubMed 

    Google Scholar  More

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    10 startling images of nature in crisis — and the struggle to save it

    Global statistics on declining biodiversity can give the impression that every population of every species is in a downward spiral. In fact, many populations are stable or growing, while a small number of species faces truly existential challenges. These photos capture some specific crises. They are images of threats unfolding, of desperate attempts at species defence and of the beautiful living world that is at stake.
    The 15th United Nations Biodiversity Conference, COP15, opens in Montreal, Canada, on 7 December. At the meeting, delegates will attempt to agree on goals for stabilizing species’ declines by 2030 and reverse them by mid-century. The current draft framework agreement promises nothing less than a “transformation in society’s relationship with biodiversity”.
    Help for the kelp. Tasmania’s forests of giant kelp (Macrocystis pyrifera) are dying as climate change shifts ocean currents, bringing warm water to the east coast of the temperate Australian island. The kelp forests host an entire ecosystem, including abalone and crayfish — both economically important species and part of local food culture. Now, researchers at the Institute for Marine and Antarctic Studies in Hobart are breeding kelp plants that can tolerate warmer conditions, and replanting them along the coast — a trial for what they hope will become a landscape-scale restoration. More