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    Human encroachment into wildlife gut microbiomes

    1.Cunningham, A. A., Daszak, P. & Wood, J. L. N. One health, emerging infectious diseases and wildlife: two decades of progress? Philos. Trans. R. Soc. B Biol. Sci. 372, 20160167 (2017).2.Suzan, G., Esponda, F., Carrasco-Hernández, R. & Aguirre, A. A. in New Directions in Conservation Medicine: Applied Cases of Ecological Health (eds. Aguirre, A. A., Ostfeld, R. & Daszak, P.). 135–150 (Oxford University Press USA, 2012).3.Hussain, S., Ram, M. S., Kumar, A., Shivaji, S. & Umapathy, G. Human presence increases parasitic load in endangered lion-tailed macaques (Macaca silenus) in its fragmented rainforest habitats in Southern India. PLoS ONE 8, 1–8 (2013).
    Google Scholar 
    4.Junge, R. E., Barrett, M. A. & Yoder, A. D. Effects of anthropogenic disturbance on indri (Indri indri) health in Madagascar. Am. J. Primatol. 73, 632–642 (2011).PubMed 
    Article 

    Google Scholar 
    5.Friggens, M. M. & Beier, P. Anthropogenic disturbance and the risk of flea-borne disease transmission. Oecologia 164, 809–820 (2010).PubMed 
    Article 

    Google Scholar 
    6.Woodroffe, R. et al. Contact with domestic dogs increases pathogen exposure in endangered African wild dogs (Lycaon pictus). PLoS ONE 7, e30099 (2012).7.Crowl, T. A., Crist, T. O., Parmenter, R. R., Belovsky, G. & Lugo, A. E. The spread of invasive species and infectious disease as drivers of ecosystem change. Front. Ecol. Environ. 6, 238–246 (2008).Article 

    Google Scholar 
    8.Keesing, F., Holt, R. D. & Ostfeld, R. S. Effects of species diversity on disease risk. Ecol. Lett. 9, 485–498 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    9.Gámez-Virués, S. et al. Landscape simplification filters species traits and drives biotic homogenization. Nat. Commun. 6, 8568 (2015).10.Alberdi, A., Aizpurua, O., Bohmann, K., Zepeda-Mendoza, M. L. & Gilbert, M. T. P. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol. Evol. 31, 689–699 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

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

    Google Scholar 
    13.Brugman, S. et al. A comparative review on microbiota manipulation: lessons from fish, plants, livestock, and human research. Front. Nutr. 5, 1–15 (2018).Article 
    CAS 

    Google Scholar 
    14.Wasimuddin et al. Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats. ISME J. 12, 2883–2893 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    15.Wasimuddin et al. Adenovirus infection is associated with altered gut microbial communities in a non-human primate. Sci. Rep. 9, 1–12 (2019).CAS 
    Article 

    Google Scholar 
    16.Wilkins, L. J., Monga, M. & Miller, A. W. Defining dysbiosis for a cluster of chronic diseases. Sci. Rep. 9, 1–10 (2019).
    Google Scholar 
    17.Brüssow, H. Problems with the concept of gut microbiota dysbiosis. Microb. Biotechnol. 13, 423–434 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    18.Otto, S. P. Adaptation, speciation and extinction in the Anthropocene. Proc. R. Soc. B Biol. Sci. 285, 20182047 (2018).19.Amato, K. R. et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 7, 1344–1353 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    20.Ingala, M. R., Becker, D. J., Bak Holm, J., Kristiansen, K. & Simmons, N. B. Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats. Ecol. Evol. https://doi.org/10.1002/ece3.5228 (2019)21.Juan, P. A. S., Hendershot, J. N., Daily, G. C. & Fukami, T. Land-use change has host-specificinfluenc on avian gut microbiomes. ISME J. https://doi.org/10.1038/s41396-019-0535-4 (2019)22.Barelli, C. et al. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. Sci. Rep. 5, 14862 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.de Juan, S., Thrush, S. F. & Hewitt, J. E. Counting on β-diversity to safeguard the resilience of estuaries. PLoS ONE 8, 1–11 (2013).
    Google Scholar 
    24.Burnham, K. P. & Anderson, D. R. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach (Springer, 2002).25.Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-5. https://github.com/vegandevs/vegan (2019).26.Nakagawa, S. & Cuthill, I. C. Effect size, confidence interval and statistical significance: a practical guide for biologists. Biol. Rev. 82, 591–605 (2007).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    27.Cohen, J. Statistical Power Analysis for the Behavioral Sciences (Lawrence Erlbaum Associates, 1988).28.Gillingham, M. A. F. et al. Offspring microbiomes differ across breeding sites in a panmictic species. Front. Microbiol. 10, 35 (2019).29.Anderson, M. J. Distance-based tests for homogeneity of multivariate dispersions. Biometrics 62, 245–253 (2006).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Mandal, S. et al. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb. Ecol. Heal. Dis. 26, 1–7 (2015).
    Google Scholar 
    31.Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 669–673 (2020).Article 
    CAS 

    Google Scholar 
    32.Louca, S. & Doebeli, M. Efficient comparative phylogenetics on large trees. Bioinformatics 34, 1053–1055 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    33.Barbera, P. et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol. 68, 365–369 (2019).PubMed 
    Article 

    Google Scholar 
    34.Czech, L., Barbera, P. & Stamatakis, A. Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data. Bioinformatics 36, 3263–3265 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Nyhus, P. J. Human—wildlife conflict and coexistence. Annu. Rev. Environ. Resour. 41, 143–171 (2016).Article 

    Google Scholar 
    36.Foden, W. B. et al. Climate change vulnerability assessment of species. WIREs Clim. Chang. 10, 1–36 (2019).Article 

    Google Scholar 
    37.Beck, J. M. et al. Multicenter comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals. Am. J. Respir. Crit. Care Med. 192, 1335–1344 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    38.Pita, L., Rix, L., Slaby, B. M., Franke, A. & Hentschel, U. The sponge holobiont in a changing ocean: from microbes to ecosystems. Microbiome 6, 46 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    39.Rosado, P. M. et al. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 13, 921–936 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    40.Wang, L. et al. Corals and their microbiomes are differentially affected by exposure to elevated nutrients and a natural thermal anomaly. Front. Mar. Sci. 5, 1–16 (2018).Article 

    Google Scholar 
    41.Zaneveld, J. R., McMinds, R. & Thurber, R. V. Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat. Microbiol. 2, 17121 (2017).42.Rocca, J. D. et al. The Microbiome Stress Project: toward a global meta-analysis of environmental stressors and their effects on microbial communities. Front. Microbiol. 10, 3272 (2019).43.Gillingham, M. A. F. et al. Bioaccumulation of trace elements affects chick body condition and gut microbiome in greater flamingos. Sci. Total Environ. 761, 143250 (2020).44.Chase, J. M. Stochastic community assembly causes higher biodiversity in more productive environments. Science 328, 1388–1392 (2010).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    45.Jiménez, R. R., Alvarado, G., Estrella, J. & Sommer, S. Moving beyond the host: unraveling the skin microbiome of endangered Costa Rican amphibians. Front. Microbiol. 10, 1–18 (2019).Article 

    Google Scholar 
    46.Wang, J. et al. Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. ISME J. 7, 1310–1321 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    47.Chase, J. M. & Myers, J. A. Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. R. Soc. B Biol. Sci. 366, 2351–2363 (2011).Article 

    Google Scholar 
    48.Pound, K. L., Lawrence, G. B. & Passy, S. I. Beta diversity response to stress severity and heterogeneity in sensitive versus tolerant stream diatoms. Divers. Distrib. 25, 374–384 (2019).Article 

    Google Scholar 
    49.Zhou, J. & Ning, D. Stochastic Community Assembly: does it matter in microbial ecology? Microbiol. Mol. Biol. Rev. 81, 1–32 (2017).Article 

    Google Scholar 
    50.Nicholas, R. A. J. & Ayling, R. D. Mycoplasma bovis: disease, diagnosis, and control. Res. Vet. Sci. 74, 105–112 (2003).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    51.Ley, D. H. in Diseases of Poultry (eds. et al.) (Blackwell Publishing, 2008).52.Groebel, K., Hoelzle, K., Wittenbrink, M. M., Ziegler, U. & Hoelzle, L. E. Mycoplasma suis invades porcine erythrocytes. Infect. Immun. 77, 576–584 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.do Nascimento, N. C., Santos, A. P., Guimaraes, A. M. S., Sanmiguel, P. J. & Messick, J. B. Mycoplasma haemocanis—the canine hemoplasma and its feline counterpart in the genomic era. Vet. Res. 43, 66 (2012).54.Hardham, J. M. et al. Transfer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients. Int. J. Syst. Evol. Microbiol. 58, 103–109 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Kaakoush, N. O. Insights into the role of Erysipelotrichaceae in the human host. Front. Cell. Infect. Microbiol. 5, 1–4 (2015).Article 
    CAS 

    Google Scholar 
    56.Ormerod, K. L. et al. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome 4, 1–17 (2016).Article 

    Google Scholar 
    57.Herrmann, E. et al. RNA-based stable isotope probing suggests Allobaculum spp. as particularly active glucose assimilators in a complex murine microbiota cultured in vitro. Biomed Res. Int. 2017, 1829685 (2017).58.Greetham, H. L. et al. Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces. Anaerobe 10, 301–307 (2004).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    59.Silva, Y. P., Bernardi, A. & Frozza, R. L. The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front. Endocrinol. 11, 1–14 (2020).60.Wiegel, J., Tanner, R. & Rainey, F. A. in The Prokaryotes: Volume 4: Bacteria: Firmicutes, Cyanobacteria (eds. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H. & Stackebrandt, E.) 654–678 (Springer US, 2006).61.Tamanai-Shacoori, Z. et al. Roseburia spp.: a marker of health? Future Microbiol 12, 157–170 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    62.Freier, T. A., Beitz, D. C., Li, L. & Hartman, P. A. Characterization of Eubacterium coprostanoligenes sp. nov., a Cholesterol-Reducing Anaerobe. Int. J. Syst. Bacteriol. 44, 137–142 (1994).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    63.Venegas, D. P. et al. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front. Immunol. 10, 277 (2019).64.MetaCyc. MetaCyc Pathway: pyrimidine deoxyribonucleotides biosynthesis from CTP. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-7210&show-citations=T (2020).65.Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res. 46, D633–D639 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    66.MetaCyc. MetaCyc Pathway: poly(glycerol phosphate) wall teichoic acid biosynthesis. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TEICHOICACID-PWY (2020).67.Brown, S., Santa Maria, J. P. & Walker, S. Wall teichoic acids of gram-positive bacteria. Annu. Rev. Microbiol. 67, 313–336 (2013).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    68.MetaCyc. MetaCyc Pathway: L-lysine biosynthesis II. https://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-2941 (2020).69.Hutton, C. A., Perugini, M. A. & Gerrard, J. A. Inhibition of lysine biosynthesis: an evolving antibiotic strategy. Mol. Biosyst. 3, 458–465 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    70.Wanner, S. et al. Wall teichoic acids mediate increased virulence in Staphylococcus aureus. Nat. Microbiol. 2, 1–12 (2017).
    Google Scholar 
    71.MetaCyc. MetaCyc Pathway: formaldehyde assimilation II (assimilatory RuMP Cycle). https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-1861 (2020).72.Chen, N. H., Djoko, K. Y., Veyrier, F. J. & McEwan, A. G. Formaldehyde stress responses in bacterial pathogens. Front. Microbiol. 7, 1–17 (2016).
    Google Scholar 
    73.Tauseef, S. M., Premalatha, M., Abbasi, T. & Abbasi, S. A. Methane capture from livestock manure. J. Environ. Manag. 117, 187–207 (2013).CAS 
    Article 

    Google Scholar 
    74.Dale, V. H., Brown, S., Calderón, M. O., Montoya, A. S. & Martínez, R. E. Estimating baseline carbon emissions for the eastern Panama Canal watershed. Mitig. Adapt. Strateg. Glob. Chang 8, 323–348 (2003).Article 

    Google Scholar 
    75.Schmid, J. et al. Ecological drivers of Hepacivirus infection in a neotropical rodent inhabiting landscapes with various degrees of human environmental change. Oecologia https://doi.org/10.1007/s00442-018-4210-7 (2018)76.Adler, G. H. & Beatty, R. P. Changing reproductive rates in a neotropical forest rodent, Proechimys semispinosus. J. Anim. Ecol. 66, 472 (1997).Article 

    Google Scholar 
    77.Adler, G. H. Fruit and seed exploitation by Central American spiny rats, Proechimys semispinosus. Stud. Neotrop. Fauna Environ. 30, 237–244 (1995).78.Hoch, G. A. & Adler, G. H. Removal of black palm (Astrocaryum standleyanum) seeds by spiny rats (Proechimys semispinosus). J. Trop. Ecol. 13, 51–58 (1997).Article 

    Google Scholar 
    79.Endries, M. J. & Adler, G. H. Spacing patterns of a tropical forest rodent, the spiny rat (Proechimys semispinosus), in Panama. J. Zool. 265, 147–155 (2005).Article 

    Google Scholar 
    80.Adler, G. H. The island syndrome in isolated populations of a tropical forest rodent. Oecologia 108, 694–700 (1996).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    81.Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS 108, 4516–4522 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    82.Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    83.Menke, S. et al. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level. Front. Microbiol. 5, 526 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    84.Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

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

    Google Scholar 
    86.Callahan, B. J., Mcmurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    87.Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).Article 
    CAS 

    Google Scholar 
    88.Yilmaz, P. et al. The SILVA and ‘All-species Living Tree Project (LTP)’ taxonomic frameworks. Nucleic Acids Res. 42, 643–648 (2014).Article 
    CAS 

    Google Scholar 
    89.Glöckner, F. O. et al. 25 years of serving the community with ribosomal RNA gene reference databases and tools. J. Biotechnol. 261, 169–176 (2017).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    90.Pedregosa, F. et al. Scikit-learn: machine learning in python. J. Mach. Learn. Res. 12, 2825–2830 (2011).91.Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—āpproximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).92.Huson, D. H. & Scornavacca, C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067 (2012).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    93.R. Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing. http://www.r-project.org/index.html (2017).94.McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).95.Davis, N. M., Proctor, Di. M., Holmes, S. P., Relman, D. A. & Callahan, B. J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 1–14 (2018).Article 

    Google Scholar 
    96.Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379–423 (1948).Article 

    Google Scholar 
    97.Faith, D. P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61, 1–10 (1992).Article 

    Google Scholar 
    98.Bates, D., Mächler, M., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).99.Mcmurdie, P. J. & Holmes, S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10, e1003531 (2014).100.Kim, Y. S., Unno, T., Kim, B.-Y. & Park, M. Sex differences in gut microbiota. World J. Mens. Health 38, 48–60 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    101.Kolodny, O. et al. Coordinated change at the colony level in fruit bat fur microbiomes through time. Nat. Ecol. Evol. 3, 116–124 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    102.Kartzinel, T. R., Hsing, J. C., Musili, P. M., Brown, B. R. P. & Pringle, R. M. Covariation of diet and gut microbiome in African megafauna. Proc. Natl Acad. Sci. USA 116, 23588–23593 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    103.Zuur, A., Ieno, E. N., Walker, N., Saveliev, A. A. & Smith, G. M. Mixed Effects Models and Extensions in Ecology with R (Springer Science & Business Media, 2009).104.Nakagawa, S. & Schielzeth, H. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods Ecol. Evol. 4, 133–142 (2013).Article 

    Google Scholar 
    105.Brooks, M. E. et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R. J. 9, 378–400 (2017).Article 

    Google Scholar 
    106.Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    107.Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576–1585 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    108.Anderson, M. J. Permutational Multivariate Analysis of Variance (PERMANOVA). https://doi.org/10.1002/9781118445112.stat07841. (2017)109.Anderson, M. J. & Walsh, D. C. I. PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing? Ecol. Monogr. 83, 557–574 (2013).Article 

    Google Scholar 
    110.Li, H. et al. Pika population density is associated with the composition and diversity of gut microbiota. Front. Microbiol. 7, 1–9 (2016).
    Google Scholar 
    111.Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 1–18 (2017).Article 

    Google Scholar 
    112.Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).
    Google Scholar 
    113.Fackelmann, G. gfackelmann/human-encroachment-into-wildlife-gut-microbiomes: Release 1.0.0. https://doi.org/10.5281/zenodo.4725220. (2021) More

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    Social transmission in the wild can reduce predation pressure on novel prey signals

    Study siteThe experiment was conducted at Madingley Wood, Cambridgeshire, UK (0◦3.2´E, 52◦12.9´N) during summer 2018. Madingley Wood is an established field site with an ongoing long-term study of the blue tit and great tit populations. During the autumn and winter birds are caught from feeding stations using mist nets and they are fitted with British Trust of Ornithology (BTO) ID rings. Since 2012, blue tits and great tits have been fitted with RFID tags (BTO Special Methods permit to HMR), which enables collecting data remotely about their foraging behavior and social relationships. The study site has 90 nest boxes that are monitored annually during the breeding season. In 2018 chicks (n = 325) fledged successfully from 45 nest boxes (blue tits = 21, great tits = 24) and they were all ringed and fitted with RFID tags when they were approximately 10 days old. Because new juvenile flocks were arriving at our study site throughout the summer, we also conducted several mist-netting and ringing sessions in July and August to maintain a high proportion of blue tits and great tits ringed and RFID tagged for the experiments (on average 89%, see below). The study protocol was approved by the Animal Users Committee at the Department of Zoology, University of Cambridge.Food itemsWe investigated birds’ foraging choices by offering them colored almond flakes at bird feeders that were distributed throughout the wood. Before beginning the experiments, we allowed the birds to become familiar with the food items by providing plain ‘control’ almonds (plain and not colored) in paired feeders (1.5 m apart) at three locations (approximately 170 m from each other). The feeders were surrounded with metal cages to exclude larger birds, and we placed plastic buckets under the feeders to collect any spilled almonds and minimize birds’ opportunities to forage from the ground. We introduced the feeders at the beginning of June when the nestlings had fledged and were beginning to forage independently, and continued to provide these plain almonds in between our learning experiments (Fig. 3c).In the learning experiments, almond flakes were dyed with non-toxic food dye (Classikool Concentrated Droplet Food Colouring). We used three different color pairs: green (Leaf Green) and red (Bright Red), purple (Lavender Purple) and blue (Royal Blue), and orange (Satsuma Orange) and yellow (Dandelion Yellow). Almond flakes were dyed by soaking them for approximately 20 min in a solution of 900 ml of water and 30 ml of food dye and then left to air dry for 48 h. In the avoidance learning experiments, we made half of the almond flakes unpalatable by soaking them for one hour in 67% solution of chloroquine phosphate, following previously established methods from avoidance learning studies with birds in captivity14,23,24,25. The food dye was added to the solution during the last 20 min.Red and green are common colors used by aposematic, or cryptic prey, respectively9. Therefore, we investigated whether blue tits and great tits had initial color biases towards these colors before starting the main experiment. Because we did not want the birds in our study population to have any experience of the colors before the main experiment, this pilot study was conducted in Newbury, which is 130 km from our main study site. Birds were simultaneously presented with two feeders containing red and green almonds (both palatable) for 30 min and the number of almonds of each color taken by blue tits or great tits was recorded using binoculars. The position of the feeders was switched after 15 min to control for any preferences for feeder location, and the test was repeated on 9 different days. We did not find any evidence that birds had initial color preferences (t-test: t = 0, df = 15.69, p = 1). For the other two learning experiments, we chose color pairs that were available as a food dye and as different from red and green in the visible spectrum as possible to avoid generalization across experiments. These color pairs (blue/purple and yellow/orange) had similar contrast ratios as green and red, based on their RGB values (measured from photographs, see Supplementary Information). Although avian and human vision is different, the discriminability of colors is likely to be similar51, and rapid avoidance learning in each experiment shows that all colors were easily distinguishable. This was the main requirement for testing social information use, and subtle differences in color pair discriminability should only introduce noise to our data but not influence our conclusions.Learning experiments with colored almondsWe conducted three avoidance learning experiments with different color pairs throughout the summer: red/green, blue/purple, and yellow/orange (unpalatable/palatable). In addition, we conducted a reversal-learning experiment with the blue/purple color pair by making both colors palatable after birds had acquired avoidance to blue almonds. Each experiment followed a similar protocol, in which birds were presented with colored almonds at the same three feeding stations where they were previously offered plain almonds. Each feeding station had two feeders, where one contained the palatable color and the other contained the unpalatable color (except in the reversal learning test when both colors were palatable). We switched the side of the feeders every day to make sure that birds learned to associate palatability with an almond color and not a feeder position. The feeders were filled at least once a day (or more often if necessary) to make sure that birds always had access to both colors. We continued each avoidance learning experiment until >90% of all recorded visits were to the feeder with palatable almonds, indicating that most birds in the population had learned to discriminate the colors. This took 7 days in the red/green experiment and 8 days in the other two color pairs (blue/purple and yellow/orange). The reversal learning experiment was finished after 9 days when 50% of the visits were to the previously unpalatable color (blue), indicating that most birds had reversed their learned avoidance towards it.Recording visits to feedersWe monitored visits to all feeders using RFID antennas and data loggers (Francis Scientific Instruments, Ltd) that scanned birds’ unique RFID tag codes when they landed on a perch attached to the feeder. During the learning experiments, each day we also recorded videos from all three feeding stations (using Go Pro Hero Action Camera and Canon Legria HF R66 Camcorder). From the videos, we monitored the proportion of blue tits and great tits that did not have RFID tags and were therefore not recorded when visiting the feeders. We calculated the estimated RFID tag coverage for each day of the experiments by watching at least 100 visits to the feeders from the videos (divided equally among the three feeding stations) and recording whether blue tits and great tits had an RFID tag or not. We realized that the number of untagged individuals was very high (approximately 50% of all visiting birds) when we started the experiment with the first color pair (red/green; see Supplementary Fig. 3). We, therefore, stopped the experiment after two days and caught birds from the feeding stations with mist nets to fit RFID tags to new individuals. To maintain a high number of individuals RFID tagged for the other color pairs, we conducted a mist netting session a day before starting each experiment, as well as 4–5 days after it. We always switched the feeders back to containing plain almonds during mist-netting sessions to ensure that this would not interfere with the learning experiments. Apart from the first two days of the red/green experiment, the RFID tag coverage was on average 89% throughout the experiments (varying between 80 and 95%, Supplementary Fig. 3).Birds were recorded every time that they visited the feeders, i.e., landed on the RFID antenna. However, it is possible that birds did not take the almond during every visit. To get an estimate of how often birds landed on the antenna without taking the almond, and whether this differed between palatable and unpalatable colors, we analyzed the visits to the feeders from the video recordings. We watched videos from the five first days of each experiment (i.e., different color pairs) and analyzed 60 visits to each color (divided approximately equally among the three feeding stations). We recorded whether the feeding event happened (birds ate the almond at the feeder or flew away with it) or whether birds left the feeder without sampling the almond. Because the number of visits to the unpalatable feeder was low during the last days of the avoidance learning experiments, we decided not to analyze avoidance learning videos after day five (but recorded visits from all days of the reversal learning experiment). We found that in avoidance learning experiments birds started to ‘reject’ unpalatable almonds after two days, i.e., they sometimes landed on the feeder but flew away without taking the almond (see Supplementary Fig. 4a). This change was not observed at palatable feeders where birds continued to consume almonds at a similar rate as at the beginning of the experiment (Supplementary Fig. 4a). In reversal learning, the proportion of visits that did not include a feeding event did not differ between purple and blue almonds: birds showed similar hesitation towards both colors at the beginning of the experiment, but this wariness decreased when the experiment progressed, with birds taking the almond during most of their visits (Supplementary Fig. 4b).Statistical analyses and model validationForaging choices in learning experimentsWe first analyzed how birds’ foraging choices changed during the learning experiments using generalized linear mixed-effects models with a binomial error distribution. The number of times an individual visited each feeder on each day of the experiment was used as a bounded response variable, and this was explained by species (blue tit/great tit), individuals’ age (juvenile/adult), and day of the experiment (continuous variable), as well as bird identity as a random effect. When analyzing avoidance learning, initial exploration of data suggested that results were similar across all three experiments, so we combined the experiments in the same model. To investigate whether learning curves differed between the species or age groups, the day of the experiment was included as a second-order polynomial term, and we started model selections with models that included a three-way interaction between species, age, and day2. Best-fitting models were selected based on Akaike’s information criterion (see Supplementary Tables 1 and 2).Social networkTo investigate if birds used social information in their foraging choices, we first constructed a social network of the bird population based on their visits to feeders outside of the learning experiments, i.e., when birds were presented with plain almonds (in total 92 days, see Supplementary Information for the robustness of analysis to exclusion of network data before or after the experiment). We used only these data as individuals were likely to vary in their hesitation to visit novel colored almonds. We used a Gaussian mixture model to detect the clusters of visits (‘gathering events’) at the feeders52 and then calculated association strengths between individuals based on how often they were observed in the same group (gambit of the group approach). These associations (network edges) were calculated using the simple ratio index, SRI35.$$frac{x}{x+{y}_{{mathrm{A}}}+{y}_{{mathrm{B}}}+{y}_{{{mathrm{AB}},}}}$$
    (2)
    where x is the number of samples where individuals A and B co-occurred in the same group, yA is the number of samples where only individual A was seen, yB is the number of samples where only individual B was seen, and yAB is the number of samples where both A and B were observed in the same sample but not together. Network associations, therefore, estimated the probability that two individuals were in the same group at a given time, with the values scaled between 0 (never observed in the same group) and 1 (always observed in the same group).Social information use during avoidance learning: model descriptionIf social avoidance learning was occurring, then the more birds observed negative responses of others feeding on the unpalatable feeder, the less likely they would be to choose the unpalatable feeder themselves. Thus, we expected the probability of bird j choosing the unpalatable option at time t to decrease with ({R}_{-,j}left(tright)) (the real number of negative feeding events observed by j prior to time t). Likewise, if appetitive social learning was occurring, then the more birds observed positive responses of others feeding on the palatable feeder, the more likely they would be to choose the palatable feeder themselves (rather than the unpalatable feeder). So, we also expected the probability of j choosing the unpalatable option at time t to decrease as ({R}_{+,j}left(tright),)(the real number of positive events observed by j prior to time t) increased.However, we could not test for an effect of ({R}_{-,j}left(tright)) and ({R}_{+,j}left(tright)) directly, since birds often ate the almond away from the feeder, and therefore the real number of observed feeding events could not be measured. Instead, we aimed to test for a pattern following the social network that is consistent with these social learning processes. We reasoned that the probability that one individual i, observes a specific feeding event by another individual j, was proportional to the network connection between them, aij (probability they are in the same feeding group at a given time). Therefore, in each avoidance learning experiment (i.e., different color pair), we calculated the expected number of negative feeding events observed, prior to each choice (occurring at time t) as$${O}_{-,i}left(tright)={sum }_{j}{N}_{-,j}left(tright){a}_{{ij}},$$
    (3)
    where ({N}_{-,j}left(tright)) was the number of times j had visited unpalatable almonds prior to time t (i ≠ j), and summation is across all birds in the network, and likewise for the expected number of positive feeding events:$${O}_{+,i}left(tright)={sum }_{j}{N}_{+,j}left(tright){a}_{{ij}},$$
    (4)
    where ({N}_{+,j}left(tright)) was the number of times j had visited palatable almonds prior to time t (i ≠ j).We analyzed whether the expected observations of positive and/or negative feeding events of others influenced the foraging choices in the avoidance learning experiments using generalized linear mixed-effects models with a binomial error distribution. We used each choice (i.e., visit a feeder) as a binary response variable (1 = unpalatable chosen, 0 = palatable chosen), with the probability that unpalatable feeder is chosen on feeding event E given by ({p}_{E}={p}_{-,{i}(E)}left({t}_{E}right)), where i(E) is the individual that fed during event E and ({t}_{E}) is the time at which event E occurred. We then modeled the probability of i choosing the unpalatable option at time t as:$${p}_{-,i}left(tright)={rm{logit}}left(alpha +{beta }_{{rm{asoc}}+}{N}_{+,i}left(tright)+{beta }_{{rm{asoc}}-}{N}_{-,i}left(tright)+{beta }_{{rm{soc}}+}{O}_{+,i}left(tright)+{beta }_{s{rm{oc}}-}{O}_{-,i}left(tright)+{{{{rm{B}}}}}_{i}right),$$
    (5)
    where ({N}_{+,i}left(tright)) is the number of times a choosing individual had visited the palatable feeder (positive personal information), ({N}_{-,i}left(tright)) is the number of times a choosing individual had visited the unpalatable feeder (negative personal information), ({O}_{+,i}left(tright)) is the expected number of observed positive (positive social information) and ({O}_{-,i}left(tright)) observed negative feeding events (negative social information). Bird identity was included as a random effect, ({{rm{{B}}}}_{i}) (age and species were later added as variables, see below). Parameters ({beta }_{{rm{asoc}}+}) and ({beta }_{{rm{asoc}}-}) are the effects of asocial learning about the palatable and unpalatable foods, ({beta }_{{rm{soc}}+}) is the effect of social learning about the palatable food, and ({beta }_{{rm{soc}}-})is the effect of social avoidance learning about the unpalatable food. Estimation of these parameters, with associated Wald tests and confidence intervals, allowed us to make inferences about which effects were operating and the size of these effects. To aid model fitting we standardized all predictor variables and then back-transformed the effects to the original scale (see Supplementary Tables 3–5 for the model outputs). To assess the importance of asocial and social effects, we also ran separate models that excluded either asocial or social parameters and compared them to the initial model in Eq. (5) using Akaike’s information criterion (see Supplementary Table 6). However, in most cases, this reduced model fit significantly, and we, therefore, kept all parameters in the final models.Our approach took ({O}_{-,{i}}left(tright)) as a measure of ({R}_{-,j}left(tright)), and ({O}_{+,{i}}left(tright)) as a measure of ({R}_{+,j}left(tright))-, which we termed the ‘expected’ number of observations of each type. Strictly speaking, ({O}_{-,{i}}left(tright)) and ({O}_{+,{i}}left(tright)) were upper limits on the expected number of observations, assuming that birds observed all feeding events in the groups in which they were present, whereas only an unknown proportion of such events (({p}_{o})) was observed. Therefore, the real expected number of negative/positive observations would be (Eleft({R}_{-,j}left(tright)right)={p}_{o}{O}_{-,{i}}left(tright)) and (Eleft({R}_{+,j}left(tright)right)={p}_{o}{O}_{+,{i}}left(tright)) respectively. Thus, the coefficient, ({beta }_{{rm{soc}}-}), for the effect of ({O}_{-,{i}}left(tright)) could be interpreted as ({beta }_{s{rm{oc}}-}={p}_{o}acute{{beta }_{{rm{soc}}-}}) where (acute{{beta }_{s{rm{oc}}-}}) is the effect per observation. Note that since ({p}_{o}le 1), and(,{beta }_{{rm{soc}}-}=acute{{beta }_{s{rm{oc}}-}}{p}_{o}), ({beta }_{s{rm{oc}}-}) is more likely to underestimate than overestimate the effect per observation of a negative feeding event. An analogous argument applies to the coefficient, ({beta }_{{rm{soc}}+}), for the effect of ({O}_{+,{i}}left(tright)).Social information use during avoidance learning: extension to test for species effectsAfter fitting the initial model shown in Eq. (5), we further broke down the model to test whether individuals were more likely to learn socially by observing conspecifics than heterospecifics. This was done by splitting the expected number of observed positive and negative feeding events to observations of conspecifics (({O}_{+{rm{C}},i}left(tright)), ({O}_{-{rm{C}},i}left(tright))) and heterospecifics (({O}_{+{rm{H}},i}left(tright)), ({O}_{-{rm{H}},i}left(tright))), and including these in the model as separate explanatory variables thus:$${p}_{-,i}(t)={rm{logit}}left(begin{array}{c}alpha +{beta }_{{rm{asoc}}+}{N}_{+,i}(t)+{beta }_{{rm{asoc}}-}{N}_{-,i}(t)\ +{beta }_{{rm{soc}},+{rm{H}}}{O}_{+{rm{H}},i}(t)+{beta }_{{rm{soc}},-{rm{H}}}{O}_{-{rm{H}},i}(t)\ +{beta }_{{rm{soc}},+{rm{C}}}{O}_{+{rm{C}},i}(t)+{beta }_{{rm{soc}},-{rm{C}}}{O}_{-{rm{C}},i}(t) \ +{{{{rm{B}}}}}_{i}end{array}right)$$
    (6a)
    with ({beta }_{{rm{soc}},-{rm{H}}}) and ({beta }_{{rm{soc}},-{rm{C}}}) giving the effect of a negative observation of a heterospecific and conspecific, respectively, whereas ({beta }_{{rm{soc}},+{rm{H}}}) and ({beta }_{{rm{soc}},+{rm{C}}}) give the effect of positive observation of a heterospecific and conspecific, respectively. In general –/+ subscripts refer to negative/positive feeding events and C/H subscripts to feeding events by conspecifics/heterospecifics. By re-parameterizing the model thus:$${p}_{-,i}left(tright)={rm{logit}}left(begin{array}{c}alpha +{beta }_{{rm{asoc}}+}{N}_{+,i}left(tright)+{beta }_{{rm{asoc}}-}{N}_{-,i}left(tright) \ +{beta }_{{rm{soc}},{rm{H}}+}{O}_{+,i}left(tright)+{beta }_{{rm{soc}},{rm{H}}-}{O}_{-,i}left(tright)\ +left({beta }_{{rm{soc}},{rm{C}}+}-{beta }_{{rm{soc}},{rm{H}}+}right){O}_{+{rm{C}},i}left(tright)+left({beta }_{{rm{soc}},{rm{C}}-}-{beta }_{{rm{soc}},{rm{H}}-}right){O}_{-{rm{C}},i}left(tright)\ +{{{{rm{B}}}}}_{i}end{array}right)$$
    (6b)
    we were able to test for a difference between observations of negative feeds by conspecifics and heterospecifics (left({beta }_{{rm{soc}},{rm{C}}-}-{beta }_{{rm{soc}},{rm{H}}-}right)) and between observations of positive feeds by conspecifics and heterospecifics (left({beta }_{{rm{soc}},{rm{C}}+}-{beta }_{{rm{soc}},{rm{H}}+}right)).For all experiments there was no evidence for a difference between ({beta }_{{rm{soc}},-{rm{H}}}) and ({beta }_{{rm{soc}},-{rm{C}}}) (yellow/orange: Z = 0.803, p = 0.42; red/green: Z = 0.065, p = 0.95; blue/purple: Z = 1.113, p = 0.27). However, there was some evidence of a difference between ({beta }_{{rm{soc}},+{rm{H}}}) and ({beta }_{{rm{soc}},+{rm{C}}}) in two of the three experiments (yellow/orange: Z = 1.359, p = 0.17; red/green: Z = 1.417, p = 0.16; blue/purple: Z = 0.729, p = 0.47). Consequently, we reduced the model down to:$${p}_{-,i}left(tright)={rm{logit}}left(begin{array}{c}alpha +{beta }_{{rm{asoc}}+}{N}_{+,i}left(tright)+{beta }_{{rm{asoc}}-}{N}_{-,i}left(tright)\ +{beta }_{{rm{soc}},-}{O}_{-,i}left(tright)+{beta }_{{rm{soc}},+{rm{H}}}{O}_{+{rm{H}},i}left(tright)+{beta }_{{rm{soc}},+{rm{C}}}{O}_{+{rm{C}},i}left(tright)\ +{{{{rm{B}}}}}_{i}end{array}right)$$
    (7)
    for further analysis, i.e., with different effects for observations of conspecific/heterospecific positive feeds, but not of negative feeds. We did this for all color combinations (including blue/purple) to allow comparison across experiments (see Table 1). The R code used to run these models can be found in Supplementary data53 in ‘GLMM models Orange Yellow final.r’.Social information use during avoidance learning: simulations to test for a network effectNext, we tested whether the social effects we detected followed the social network. When using a network-based diffusion analysis (NBDA43), researchers can compare a network model with one in which the network has homogeneous connections among all individuals, but we found this to be unreliable for our model. Instead, we used a simulation approach to generate a null distribution for the null hypothesis of homogeneous social effects, taking the size of the social effects from the fitted models. We ran 1000 simulations (using the same procedure described above) for all social effects that were found to be significant in each avoidance learning model (each color pair; see Table 1). The total number of expected observations was kept equal, but we homogenized the observation effect across all birds by replacing the probability of bird i observing a feed by bird j, previously ({a}_{{ij}}), with ({sum }_{i}{a}_{{ij}}/n), where n is the number of birds in the experiment, (i.e., all birds had the same probability of observing each feeding event). The model was fitted to the simulated data each time to extract the Z value (Wald test statistic) of the social effect of interest. The distribution of these values was then used as a null distribution to test whether our observed social effect differed from the effects that did not follow the social network. To this end, we calculated the proportion of simulations that yielded a Z value as extreme or more extreme than that observed (judged by distance in either direction from the mean of the null distribution). The R code used to run these simulations can be found in Supplementary data53 in ‘Simulations to test if network effects follow network Orange Yellow.r’.Social information use during avoidance learning: extension to test for age effectsWe then aimed to test whether each of the three social effects detected differed based on the age class of the observed individual (adult versus juveniles). We, therefore, split the negative expected observations ({O}_{-,i}left(tright)) into the expected observations of adults ({O}_{-{rm{A}},i}left(tright)) and juveniles ({O}_{-{rm{J}},i}left(tright)), each with its associated coefficient in the model ({beta }_{{rm{soc}},-{rm{A}}}) and ({beta }_{{rm{soc}},-{rm{J}}}). Likewise, we split positive observations of conspecifics as ({O}_{+{rm{CA}},i}left(tright)) and ({O}_{+{rm{CJ}},i}left(tright)) and positive observations of heterospecifics as ({O}_{+{rm{HA}},i}left(tright)) and ({O}_{+{rm{HJ}},i}left(tright)) to give the model:$${p}_{-,i}left(tright)={rm{logit}}left(begin{array}{c}alpha +{beta }_{{rm{asoc}}+}{N}_{+,i}left(tright)+{beta }_{{rm{asoc}}-}{N}_{-,i}left(tright)\ +{beta }_{{rm{soc}},-{rm{A}}}{O}_{-{rm{A}},i}left(tright)+{beta }_{{rm{soc}},-{rm{J}}}{O}_{-{rm{J}},i}left(tright)\ +{beta }_{{rm{soc}},+{rm{HA}}}{O}_{+{rm{HA}},i}left(tright)+{beta }_{{rm{soc}},+{rm{HJ}}}{O}_{+{rm{HJ}},i}left(tright)\ +{beta }_{{rm{soc}},+{rm{CA}}}{O}_{+{rm{CA}},i}left(tright)+{beta }_{{rm{soc}},+{rm{CJ}}}{O}_{+{rm{CJ}},i}left(tright)\ +{{{{rm{B}}}}}_{i}end{array}right)$$
    (8a)
    As before, –/+ subscripts refer to negative/positive feeding events, C/H subscripts to feeding events by conspecifics/heterospecifics, and A/J subscripts to feeding events by adults/juveniles. We also fitted a re-parameterized version allowing us to test for a difference between expected observations of adults and observations of juveniles for each of the three social effects:$${p}_{-,i}left(tright)={rm{logit}}left(begin{array}{c}alpha +{beta }_{{rm{asoc}}+}{N}_{+,i}left(tright)+{beta }_{{rm{asoc}}-}{N}_{-,i}left(tright)\ +{beta }_{{rm{soc}},-{rm{J}}}{O}_{-,i}left(tright)+left({{beta }_{{rm{soc}},-{rm{A}}}-beta }_{{rm{soc}},-{rm{J}}}right){O}_{-{rm{A}},i}left(tright)\ +{beta }_{{rm{soc}},+{rm{H}}}{O}_{+{rm{H}},i}left(tright)+left({{beta }_{{rm{soc}},+{rm{HA}}}-beta }_{{rm{soc}},+{rm{HJ}}}right){O}_{+{rm{JA}},i}left(tright)\ +{beta }_{{rm{soc}},+{rm{C}}}{O}_{+{rm{C}},i}left(tright)+left({{beta }_{{rm{soc}},+{rm{CA}}}-beta }_{{rm{soc}},+{rm{CJ}}}right){O}_{+{rm{CA}},i}left(tright)\ +{{{{rm{B}}}}}_{i}end{array}right)$$
    (8b)
    The R code used to run these models can be found in Supplementary data53 in ‘GLMM models Orange Yellow final.r’. The main results of each model are presented in Table 2 and full model outputs in Supplementary Tables 3–5.Social information use during reversal learningTo investigate social information use during reversal learning, we used the order of acquisition diffusion analysis (OADA), a variant of NBDA43, which explores the order in which individuals acquire a behavioral trait44. The rate of social transmission between two individuals is assumed to be linearly proportional to their network connection, and the spread of trait acquisition is therefore predicted to follow the network patterns if individuals are using social information. We used NBDA to investigate whether the order of individuals’ first visit to the previously unpalatable blue almonds (mimics) followed the network. We fitted several different models that included (i) only asocial learning, (ii) social transmission of information following a homogeneous network (equal associations among all individuals), or (iii) social transmission of information following our observed network. Models that included social transmission were further divided into models with equal or different transmission rates from adults and juveniles, and from conspecifics and heterospecifics, by constructing separate networks for each adult/juvenile and conspecific/heterospecific combination. To investigate whether asocial or social learning rates differed between blue tits and great tits, we included species as an individual-level variable. We then compared different social transmission models that assumed that species differed in both asocial and social learning rates, only in asocial or only in social learning rates, or that they did not differ in either (see Table 3). The best-supported model was selected using a model-averaging approach with Akaike’s information criterion corrected for small sample sizes. All analyses were conducted with the software R.3.6.154, using lme455, asnipe56, and NBDA57 packages.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

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    High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems

    1.Igwe, J. C. & Onyegbado, C. C. A review of palm oil mill effluent (pome) water treatment. Glob. J. Environ. Res. 1, 54–62 (2007).
    Google Scholar 
    2.World Wild Fund (WWF). Overview WWF Statement on the 2020 Palm Oil Buyers Scorecard. https://www.worldwildlife.org/industries/palm-oil (2020). Accessed 22 Feb 2021.3.CNUCED. Huile de palme. New York. https://www.surunctad.org/commodities (2016). Accessed 10 Jan 2020.4.Hassan, M. A., Njeshu, G., Raji, A., Zhengwuvi, L. & Salisu, J. Small-Scale Palm Oil Processing in West and Central Africa: Development and Challenges. J. Appl. Sci. Environ. Sust. 2, 102–114 (2016).
    Google Scholar 
    5.Bala, J. D., Lalung, J., Al-Gheethi, A. A. S., Kaizar, H. & Ismail, N. Reduction of organic load and biodegradation of palm oil mill effluent by aerobic indigenous mixed microbial consortium isolated from palm oil mill effluent (POME). Water Conserv. Sci. Eng. 3, 139. https://doi.org/10.1007/s41101-018-0043-9 (2018).Article 

    Google Scholar 
    6.Nwoko, O. C., Ogunyemi, S. & Nkwocha, E. E. Effect of pre-treatment of palm oil mill effluent (POME) and cassava mill effluent (CME) on the growth of tomato (Lycopersicum esculentum). J. Appl. Sci. Environ. 14, 67. https://doi.org/10.4314/JASEM.V14I1.56493 (2010).Article 

    Google Scholar 
    7.Singh, G., Huan, L. K., Leng, T. & Kow D. L. Oil Palm and the Environment: A Malaysian Perspective. (Kuala Lumpur,
    Malaysia, Malaysian Oil Palm Growers’ Council, 1999).8.Poku, K. Small-Scale Palm Oil Processing in Africa. Fao Agricultural Services Bulletin 148. http://www.fao.org/3/Y4355E/y4355e00.htm (2002) (ISSN 1010-1365). Accessed 22 Feb 2021.9.Ibekwe, A. M., Grieve, C. M. & Lyon, S. R. Characterization of microbial communities and composition in constructed dairy wetland wastewater effluent. Appl. Environ. Microbiol. 69, 5060. https://doi.org/10.1128/AEM.69.9.5060-5069.2003 (2003).CAS 
    Article 
    PubMed 

    Google Scholar 
    10.Sharuddin, S. S. et al. Bacterial community shift revealed Chromatiaceae and Alcaligenaceae as potential bioindicators in the receiving river due to palm oil mill effluent final discharge. Ecol. Indic. 82, 526–529. https://doi.org/10.1016/j.ecolind.2017.07.038 (2017).CAS 
    Article 

    Google Scholar 
    11.CIAPOL. Arrêté N°011264/MINEEF/CIAPOL/SDIIC du 04 Nov.2008 portant réglementation des rejets et emissions des installations classées pour la protection de l’environnement, 11 (2008).
    12.Soleimaninanadegani, M. & Manshad, S. Enhancement of biodegradation of palm oil mill effluents by local isolated microorganisms. Int. Sch. Res. Notices. 2014, Article ID 727049. https://doi.org/10.1155/2014/727049 (2014).Article 

    Google Scholar 
    13.Nwachukwu, J. N., Njoku, U. O., Agu, C. V., Okonkwo, C. C. & Obidiegwu, C. J. Impact of palm oil mill effluent (POME) contamination on soil enzyme activities and physicochemical properties. Res. J. Environ. Toxicol. 12, 34–41. https://doi.org/10.3923/rjet.2018.34.41 (2018).CAS 
    Article 

    Google Scholar 
    14.Hii, K. L., Yeap, S. P. & Mashitah, M. D. Cellulase production from palm oil mill effluent in Malaysia: Economical and technical perspectives. Eng. Life Sci. 12, 7–28. https://doi.org/10.1002/elsc.201000228 (2012).CAS 
    Article 

    Google Scholar 
    15.Ma, Q. et al. Identification of the microbial community composition and structure of coal-mine wastewater treatment plants. Microbiol. Res. 175, 1–5. https://doi.org/10.1016/j.micres.2014.12.013 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    16.Wang, X., Hu, M., Xia, Y., Wen, X. & Kun, D. K. Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Bioresour. Technol. 78, 7042–7047. https://doi.org/10.1128/AEM.01617-12 (2012).CAS 
    Article 

    Google Scholar 
    17.Wang, Z. et al. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing. PLoS One 9, e113603. https://doi.org/10.1371/journal.pone.0113603 (2014).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    18.Caporaso, J. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624. https://doi.org/10.1038/ismej.2012.8 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    19.Rana, S., Singh, L., Wahid, Z. & Liu, H. A recent overview of palm oil mill effluent management via bioreactor configurations. Curr. Pollut. Rep. 3, 254–267. https://doi.org/10.1007/s40726-017-0068-2 (2017).CAS 
    Article 

    Google Scholar 
    20.Vuono, D. C. et al. Disturbance and temporal partitioning of the activated sludge metacommunity. ISME J. 9, 425–435. https://doi.org/10.1038/ismej.2014.139 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    21.Jang, H. M., Kim, J. H., Ha, J. H. & Park, J. M. Bacterial and methanogenic archaeal communities during the single-stage anaerobic digestion of high-strength food wastewater. Bioresour. Technol. 165, 174–182. https://doi.org/10.1016/j.biortech.2014.02.028 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    22.Mohd-Nor, D. et al. Dynamics of microbial populations responsible for biodegradation during the full-scale treatment of palm oil mill effluent. Microbes Environ. 34, 121. https://doi.org/10.1264/jsme2.ME18104 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Sun, Z. et al. Identification and characterization of the dominant lactic acid bacteria from kurut: The naturally fermented yak milk in Qinghai, China. J. Gen. Appl. Microbiol. 56, 1–10. https://doi.org/10.2323/jgam.56.1 (2010).Article 
    PubMed 

    Google Scholar 
    24.Webster, N. S. & Taylor, M. W. Marine sponges and their microbial symbionts: Love and other relationships. Environ. Microbiol. 14, 335–346 (2012).CAS 
    Article 

    Google Scholar 
    25.Morrow, K. M., Fiore, C. L. & Lesser, M. P. Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient. Environ. Microbiol. 18, 2025–2038. https://doi.org/10.1111/1462-2920.13226 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    26.Parman, A., Isa, M. N. M., Farah, F. B., Noorbatcha, B. A. & Salleh, H. M. Comparative metagenomics analysis of palm oil mill effluent (pome) using three different bioinformatics pipelines. IIUM Eng. J. 20, 1–11. https://doi.org/10.31436/iiumej.v20i1.909 (2019).Article 

    Google Scholar 
    27.Mwaikono, K. S. et al. High-throughput sequencing of 16S rRNa gene reveals substantial bacterial diversity on the municipal dumpsite. BMC Microbiol. 16, 145. https://doi.org/10.1186/s12866-016-0758-8 (2016).Article 
    PubMed 

    Google Scholar 
    28.Silva-Bedoya, L. M., Sánchez-Pinzón, M. S., Cadavid-Restrepo, G. E. & Moreno-Herrera, C. X. Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms. Microbiol. Res. 192, 313. https://doi.org/10.1016/j.micres.2016.08.006 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    29.Lam, M. K. & Lee, K. T. Renewable and sustainable bioenergies production from palm oil mill effluent (POME): Win–win strategies toward better environmental protection. Biotechnol. Adv. 29, 124–141. https://doi.org/10.1016/j.biotechadv.2010.10.001 (2011).CAS 
    Article 
    PubMed 

    Google Scholar 
    30.Baharuddin, A. S., Wakisaka, M., Shirai, A.-A.Y.S., Abdul, R. & Hassan, M. A. Co-composting of empty fruit bunches and partially treated palm oil mill effluents in pilot scale. Int. J. Agric. Res. 4, 69–78. https://doi.org/10.3923/ijar.2009.69.78 (2009).CAS 
    Article 

    Google Scholar 
    31.Morikawa-Sakura, M. S. et al. Application of Lactobacillus plantarum ATCC 8014 for wastewater treatment in fisheries industry processing. Jpn. J. Water Treat. Biol. 49, 1–10. https://doi.org/10.2521/jswtb.49.1 (2013).Article 

    Google Scholar 
    32.Ren, Z., You, W., Wu, S., Poetsch, A. & Xu, C. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. Biotechnol. Biofuels 12, 183. https://doi.org/10.1186/s13068-019-1522-8 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    33.Lee, J. Z., Logan, A., Terry, S. & Spear, J. R. Microbial response to single-cell protein production and brewery wastewater treatment. Microb. Biotechnol. 8, 65. https://doi.org/10.1111/1751-7915.12128 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    34.Ye, L. & Zhang, T. Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl. Microbiol. Biotechnol. 97, 2681–2690 (2013).CAS 
    Article 

    Google Scholar 
    35.Stubbs, S., Mao, L., Waddington, R. J. & Embery, G. Hydrolytic and depolymerising enzyme activity of Prevotella intermedia and Prevotella nigrescens. Oral Dis. 2, 272. https://doi.org/10.1111/j.1601-0825.1996.tb00237.x (1996).CAS 
    Article 
    PubMed 

    Google Scholar 
    36.Komagata, K., Iino, T. & Yamada, Y. The family Acetobacteraceae. In The Prokaryotes (eds Rosenberg, E. et al.) 3–78 (Springer, 2014).Chapter 

    Google Scholar 
    37.Pires, J. F., Cardoso, L. S., Schwan, R. F. & Silva, C. F. Diversity of microbiota found in coffee processing wastewater treatment plant. World J. Microbiol. Biotechnol. 33, 211. https://doi.org/10.1007/s11274-017-2372-9 (2017).Article 
    PubMed 

    Google Scholar 
    38.Song, Z. Q., Wang, F. P. & Zhi, X. Y. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China. Environ. Microbiol. 15, 1160–1175 (2013).CAS 
    Article 

    Google Scholar 
    39.Li, J., Liu, R., Tao, Y. & Li, G. Archaea in wastewater treatment: Current research and emerging technology. Archaea 2018, 1. https://doi.org/10.1155/2018/6973294 (2018).CAS 
    Article 

    Google Scholar 
    40.Khan, M. A., Khan, S. T. & Sequeira, M. C. Comparative analysis of bacterial and archaeal population structure by illumina sequencing of 16S rRNA genes in three municipal anaerobic sludge digesters. Res. Sq. https://doi.org/10.21203/rs.3.rs-60183/v1 (2020).Article 

    Google Scholar 
    41.Mladenovska, Z., Dabrowski, S. & Ahring, B. K. Anaerobic digestion of manure and mixture of manure with lipids: Biogas reactor performance and microbial community analysis. Water Sci. Technol. 48, 271–278 (2013).Article 

    Google Scholar 
    42.Gerardi, M. H. Wastewater Bacteria (Wiley, 2006).Book 

    Google Scholar 
    43.Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414. https://doi.org/10.1111/1462-2920.13023 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    44.Andrews, S. FastQC: a quality control tool for high throughput sequence data (Online). https://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010). Accessed 15 Sept 2019.45.R Development Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2019). Accessed 8 Jan 2020.46.Callahan, B. J. et al. DADA2: High-resolution sample inference from illumina amplicon data. Nat. Methods 13, 581. https://doi.org/10.1038/nmeth.3869 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    47.Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, 590. https://doi.org/10.1093/nar/gks1219 (2012).CAS 
    Article 

    Google Scholar 
    48.Paradis, E., Julien, C. & Korbinian, S. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289. https://doi.org/10.1093/bioinformatics/btg412 (2004).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    49.McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, 61217. https://doi.org/10.1371/journal.pone.0061217 (2013).ADS 
    CAS 
    Article 

    Google Scholar 
    50.Oksanen, J. F. et al. vegan: Community Ecology Package. R package version 2.4-0. https://CRAN.R-project.org/package=vegan (2018). Accessed 8 Jan 2020.51.Lahti, L. & Sudarshan, S. Tools for microbiome analysis in R. Version 1.10.0. https://www.microbiome.github.com/microbiome (2017). Accessed 8 Jan 2020.52.Kenkel, N. C. & Orloci, L. Applying metric and nonmetric multidimensional scaling to ecological studies: Some new results. Ecology 67, 919. https://doi.org/10.2307/1939814 (1986).Article 

    Google Scholar 
    53.Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289–300 (1995).MathSciNet 
    MATH 

    Google Scholar  More

  • in

    Diversity increases yield but reduces harvest index in crop mixtures

    1.Weiner, J. Plant Reproductive Ecology: Patterns and Strategies (Oxford Univ. Press, 1988).2.Ashman, T. L. & Schoen, D. J. How long should flowers live? Nature 371, 788–791 (1994).CAS 
    Article 

    Google Scholar 
    3.Donald, C. M. The breeding of crop ideotypes. Euphytica 17, 385–403 (1968).Article 

    Google Scholar 
    4.Unkovich, M., Baldock, J. & Forbes, M. Variability in harvest index of grain crops and potential significance for carbon accounting: examples from Australian agriculture. Adv. Agron. 105, 173–219 (2010).Article 

    Google Scholar 
    5.Tamagno, S., Sadras, V. O., Ortez, O. A. & Ciampitti, I. A. Allometric analysis reveals enhanced reproductive allocation in historical set of soybean varieties. Field Crop Res. 248, 107717 (2020).Article 

    Google Scholar 
    6.Hector, A. et al. Plant diversity and productivity experiments in European grasslands. Science 286, 1123–1127 (1999).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    7.Grace, J. B. et al. Integrative modelling reveals mechanisms linking productivity and plant species richness. Nature 529, 390–393 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Huang, Y. et al. Impacts of species richness on productivity in a large-scale subtropical forest experiment. Science 362, 80–83 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    9.Letourneau, D. K. et al. Does plant diversity benefit agroecosystems? A synthetic review. Ecol. Appl. 21, 9–21 (2011).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    10.Li, C. et al. Syndromes of production in intercropping impact yield gains. Nat. Plants 6, 653–660 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.McConnaughay, K. D. M. & Coleman, J. S. Biomass allocation in plants: ontogeny or optimality? A test along three resource gradients. Ecology 80, 2581–2593 (1999).Article 

    Google Scholar 
    12.Bonser, S. P. & Aarssen, L. W. Allometry and plasticity of meristem allocation throughout development in Arabidopsis thaliana. J. Ecol. 89, 72–79 (2001).Article 

    Google Scholar 
    13.Reekie, E. G. & Bazzaz, F. A. Reproductive Allocation in Plants (Elsevier Academic Press, 2005).14.Wang, T. H., Zhou, D. W., Wang, P. & Zhang, H. X. Size-dependent reproductive effort in Amaranthus retroflexus: the influence of planting density and sowing date. Can. J. Bot. 84, 485–492 (2006).Article 

    Google Scholar 
    15.Gurr, G. M. et al. Multi-country evidence that crop diversification promotes ecological intensification of agriculture. Nat. Plants 2, 16014 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    16.Li, C. et al. Yield gain, complementarity and competitive dominance in intercropping in China: a meta-analysis of drivers of yield gain using additive partitioning. Eur. J. Agron. 113, 125987 (2020).CAS 
    Article 

    Google Scholar 
    17.Tilman, D. et al. Diversity and productivity in a long-term grassland experiment. Science 294, 843–845 (2001).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    18.Loreau, M. & Hector, A. Partitioning selection and complementarity in biodiversity experiments. Nature 412, 72–76 (2001).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    19.Li, L., Tilman, D., Lambers, H. & Zhang, F. S. Plant diversity and overyielding: insights from belowground facilitation of intercropping in agriculture. New Phytol. 203, 63–69 (2014).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    20.Brooker, R. W. et al. Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology. New Phytol. 206, 107–117 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Martin-Guay, M. O., Paquette, A., Dupras, J. & Rivest, D. The new green revolution: sustainable intensification of agriculture by intercropping. Sci. Total Environ. 615, 767–772 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Bazzaz, F. A., Chiariello, N. R., Coley, P. D. & Pitelka, L. F. Allocating resources to reproduction and defense. Bioscience 37, 58–67 (1987).Article 

    Google Scholar 
    23.Hartnett, D. C. Size-dependent allocation to sexual and vegetative reproduction in 4 clonal composites. Oecologia 84, 254–259 (1990).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    24.Vega, C. R. C., Sadras, V. O., Andrade, F. H. & Uhart, S. A. Reproductive allometry in soybean, maize and sunflower. Ann. Bot. 85, 461–468 (2000).Article 

    Google Scholar 
    25.Gifford, R. M., Thorne, J. H., Hitz, W. D. & Giaquinta, R. T. Crop productivity and photoassimilate partitioning. Science 225, 801–808 (1984).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.Andrade, F. H. et al. Kernel number determination in maize. Crop Sci. 39, 453–459 (1999).Article 

    Google Scholar 
    27.Milla, R., Osborne, C. P., Turcotte, M. M. & Violle, C. Plant domestication through an ecological lens. Trends Ecol. Evol. 30, 463–469 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    28.Niklas, K. J. Plant Allometry: The Scaling of Form and Process (Univ. of Chicago Press, 1994).29.Echarte, L. & Andrade, F. H. Harvest index stability of Argentinean maize hybrids released between 1965 and 1993. Field Crop Res. 82, 1–12 (2003).Article 

    Google Scholar 
    30.Weiner, J., Campbell, L. G., Pino, J. & Echarte, L. The allometry of reproduction within plant populations. J. Ecol. 97, 1220–1233 (2009).Article 

    Google Scholar 
    31.Sugiyama, S. & Bazzaz, F. A. Size dependence of reproductive allocation: the influence of resource availability, competition and genetic identity. Funct. Ecol. 12, 280–288 (1998).Article 

    Google Scholar 
    32.Weiner, J. Allocation, plasticity and allometry in plants. Perspect. Plant Ecol. 6, 207–215 (2004).Article 

    Google Scholar 
    33.Weiner, J. et al. Is reproductive allocation in Senecio vulgaris plastic? Botany 87, 475–481 (2009).Article 

    Google Scholar 
    34.Schmid, B. & Weiner, J. Plastic relationships between reproductive and vegetative mass in Solidago altissima. Evolution 47, 61–74 (1993).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    35.Schmid, B. & Pfisterer, A. B. Species vs community perspectives in biodiversity experiments. Oikos 100, 620–621 (2003).Article 

    Google Scholar 
    36.Lipowsky, A. et al. Plasticity of functional traits of forb species in response to biodiversity. Perspect. Plant Ecol. Evol. Syst. 17, 66–77 (2015).Article 

    Google Scholar 
    37.Abakumova, M., Zobel, K., Lepik, A. & Semchenko, M. Plasticity in plant functional traits is shaped by variability in neighbourhood species composition. New Phytol. 211, 455–463 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    38.Zhu, J. Q., van der Werf, W., Anten, N. P. R., Vos, J. & Evers, J. B. The contribution of phenotypic plasticity to complementary light capture in plant mixtures. New Phytol. 207, 1213–1222 (2015).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.Niklaus, P. A., Baruffol, M., He, J. S., Ma, K. P. & Schmid, B. Can niche plasticity promote biodiversity-productivity relationships through increased complementarity? Ecology 98, 1104–1116 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    40.Eziz, A. et al. Drought effect on plant biomass allocation: a meta-analysis. Ecol. Evol. 7, 11002–11010.41.Joshi, J. et al. Local adaptation enhances performance of common plant species. Ecol. Lett. 4, 536–544 (2001).Article 

    Google Scholar 
    42.Li, J. et al. Variations in maize dry matter, harvest index, and grain yield with plant density. Agron. J. 107, 829–834 (2015).Article 

    Google Scholar 
    43.Gou, F., van Ittersum, M. K., Wang, G. Y., van der Putten, P. E. L. & van der Werf, W. Yield and yield components of wheat and maize in wheat-maize intercropping in the Netherlands. Eur. J. Agron. 76, 17–27.44.Isbell, F. et al. Quantifying effects of biodiversity on ecosystem functioning across times and places. Ecol. Lett. 21, 763–778.45.Roscher, C. & Schumacher, J. Positive diversity effects on productivity in mixtures of arable weed species as related to density–size relationships. J. Plant Ecol. 9, 792–804 (2016).Article 

    Google Scholar 
    46.Roscher, C. et al. Overyielding in experimental grassland communities – irrespective of species pool or spatial scale. Ecol. Lett. 8, 419–429.47.Isbell, F. et al. High plant diversity is needed to maintain ecosystem services. Nature 477, 199–202 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Schmid, B., Baruffol, M., Wang, Z. & Niklaus, P. A. A guide to analyzing biodiversity experiments. J. Plant Ecol. 10, 91–110.49.Rosenthal, R. & Rosnow, R. L. Contrast Analysis: Focused Comparisons in the Analysis of Variance (Cambridge Univ. Press, 2010).50.Díaz-Sierra, R., Verwijmeren, M., Rietkerk, M., de Dios, V. R. & Baudena, M. A new family of standardized and symmetric indices for measuring the intensity and importance of plant neighbour effects. Methods Ecol. Evol. 8, 580–591 (2017).Article 

    Google Scholar 
    51.Poorter, H. & Garnier, E. in Handbook of Functional Plant Ecology (eds Pugnaire, F. I. & Valladares, F.) 81–120 (Marcel Dekker, 1999).52.Grime, J. P. Evidence for existence of 3 primary strategies in plants and its relevance to ecological and evolutionary theory. Am. Nat. 111, 1169–1194 (1977).Article 

    Google Scholar 
    53.Wilson, P. J., Thompson, K. & Hodgson, J. G. Specific leaf area and leaf dry matter content as alternative predictors of plant strategies. New Phytol. 143, 155–162 (1999).Article 

    Google Scholar 
    54.Poorter, H., Niinemets, U., Poorter, L., Wright, I. J. & Villar, R. Causes and consequences of variation in leaf mass per area (LMA): a meta-analysis. New Phytol. 182, 565–588 (2009).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Lavorel, S. & Grigulis, K. How fundamental plant functional trait relationships scale-up to trade-offs and synergies in ecosystem services. J. Ecol. 100, 128–140 (2012).Article 

    Google Scholar 
    56.Conti, G. & Díaz, S. Plant functional diversity and carbon storage – an empirical test in semi‐arid forest ecosystems. J. Ecol. 101, 18–28 (2013).CAS 
    Article 

    Google Scholar 
    57.R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019); https://www.r-project.org/58.Lüdecke, D. ggeffects: Tidy data frames of marginal effects from regression models. J. Open Source Softw. 3, 772 (2018).Article 

    Google Scholar 
    59.Lüdecke, D. sjPlot: data visualization for statistics in social science. Zenodo https://doi.org/10.5281/zenodo.1308157 (2018). More

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    Red light, green light: both signal ‘go’ to deadly algae

    Green and red lighting might be good for migratory birds and sea turtles, but could have undesirable effects if marine algae are present. Credit: Getty

    Ecology
    24 June 2021
    Red light, green light: both signal ‘go’ to deadly algae

    Artificial lighting thought to be more wildlife-friendly than white light could encourage algal blooms.

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    Green or red lights in seaside areas have been proposed as alternatives to white light to protect wildlife. But new experiments show that exposure to red or green light at night boosts the growth of some ocean algae — including species known to rob waters of oxygen.Little is known about the impact of artificial light on marine life, even though many brightly lit cities are coastal. To address that knowledge gap, Sofie Spatharis at the University of Glasgow, UK, and her colleagues exposed a mix of microscopic marine algae collected from Scottish waters to standard white light. They also exposed the mixture to red and green lights, which have been proposed to minimize impacts on sea turtles and migratory seabirds, respectively.The team found that all light colours enhanced growth of the microalgae mix. Red light had the most pronounced effect, doubling the number of cells produced. The proportions of species in the mixture also shifted: both red and green light especially favoured growth of harmful species in the Skeletonema genus, which form dense blooms that are deadly to fish.

    Proc. R. Soc. B (2021)

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    Random population fluctuations bias the Living Planet Index

    1.Mace, G. M. et al. Aiming higher to bend the curve of biodiversity loss. Nat. Sustain. 1, 448–451 (2018).Article 

    Google Scholar 
    2.Leclère, D. et al. Bending the curve of terrestrial biodiversity needs an integrated strategy. Nature 585, 551–556 (2020).PubMed 

    Google Scholar 
    3.Updated Zero Draft of the Post-2020 Global Biodiversity Framework (Convention on Biological Diversity, 2020); https://www.cbd.int/doc/c/3064/749a/0f65ac7f9def86707f4eaefa/post2020-prep-02-01-en.pdf4.Pereira, H. M. et al. Essential biodiversity variables. Science 339, 277–278 (2013).CAS 
    Article 

    Google Scholar 
    5.Loh, J. et al. The Living Planet Index: using species population time series to track trends in biodiversity. Philos. Trans. R. Soc. B 360, 289–295 (2005).Article 

    Google Scholar 
    6.Collen, B. et al. Monitoring change in vertebrate abundance: the Living Planet Index. Conserv. Biol. 23, 317–327 (2009).Article 

    Google Scholar 
    7.McRae, L., Deinet, S. & Freeman, R. The diversity-weighted Living Planet Index: controlling for taxonomic bias in a global biodiversity indicator. PLoS ONE 12, e0169156 (2017).Article 

    Google Scholar 
    8.Almond, R.E.A., Grooten M. & Petersen, T. (eds) Living Planet Report 2020—Bending the Curve of Biodiversity Loss (WWF, 2020).9.Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019).10.Global Biodiversity Outlook 5 (Convention on Biological Diversity, 2020).11.Jaspers, A. Can a single index track the state of global biodiversity? Biol. Conserv. 246, 108524 (2020).Article 

    Google Scholar 
    12.Leung, B. et al. Clustered versus catastrophic global vertebrate declines. Nature 588, 267–271 (2020).CAS 
    Article 

    Google Scholar 
    13.Buckland, S. T., Studeny, A. C., Magurran, A. E., Illian, J. & Newson, S. E. The geometric mean of relative abundance indices: a biodiversity measure with a difference. Ecosphere 2, 100 (2011).14.de Valpine, P. & Hastings, A. Fitting population models incorporating process noise and observation error. Ecol. Monogr. 72, 57–76.15.Daskalova, G. N., Myers-Smith, I. H. & Godlee, J. L. Rare and common vertebrates span a wide spectrum of population trends. Nat. Commun. 11, 4394 (2020).CAS 
    Article 

    Google Scholar 
    16.Living Planet Report 2020. Technical Supplement: Living Planet Index (WWF, 2020); https://f.hubspotusercontent20.net/hubfs/4783129/LPR/PDFs/ENGLISH%20-%20TECH%20SUPPLIMENT.pdf17.Vellend, M. Conceptual synthesis in community ecology. Quart. Rev. Biol. 85, 183–206 (2010).Article 

    Google Scholar 
    18.Vellend, M. et al. Assessing the relative importance of neutral stochasticity in ecological communities. Oikos 123, 1420–1430 (2014).Article 

    Google Scholar 
    19.Lande, R. Risks of population extinction from demographic and environmental stochasticity and random catastrophes. Am. Nat. 142, 911–927 (1993).Article 

    Google Scholar 
    20.Gravel, D., Guichard, F. & Hochberg, M. E. Species coexistence in a variable world. Ecol. Lett. 14, 828–839 (2011).Article 

    Google Scholar 
    21.Kotze, D. J., O’Hara, R. B. & Lehvävirta, S. Dealing with varying detection probability, unequal sample sizes and clumped distributions in count data. PLoS ONE 7, e40923 (2012).CAS 
    Article 

    Google Scholar 
    22.Kellner, K. F. & Swihart, R. K. Accounting for imperfect detection in ecology: a quantitative review. PLoS ONE 9, e111436 (2014).Article 

    Google Scholar 
    23.Di Fonzo, M., Collen, B. & Mace, G. M. A new method for identifying rapid decline dynamics in wild vertebrate populations. Ecol. Evol. 3, 2378–2391 (2013).Article 

    Google Scholar 
    24.Maxwell, S. L. et al. Being smart about SMART environmental targets. Science 347, 1075–1076 (2015).CAS 
    Article 

    Google Scholar 
    25.Butchart, S. H. M., Di Marco, M. & Watson, J. E. M. Formulating SMART commitments on biodiversity: lessons from the Aichi Targets. Conserv Lett. 9, 457–468 (2016).Article 

    Google Scholar 
    26.Green, E. J. et al. Relating characteristics of global biodiversity targets to reported progress. Conserv. Biol. 33, 1360–1369 (2019).Article 

    Google Scholar 
    27.Dornelas, M. et al. A balance of winners and losers in the Anthropocene. Ecol. Lett. 22, 847–854 (2019).Article 

    Google Scholar 
    28.Fournier, A. M. V., White, E. R. & Heard, S. B. Site‐selection bias and apparent population declines in long‐term studies. Conserv. Biol. 33, 1370–1379 (2019).Article 

    Google Scholar 
    29.Pauly, D. Anecdotes and the shifting baseline syndrome of fisheries. Trends Ecol. Evol. 10, 430 (1995).CAS 
    Article 

    Google Scholar 
    30.Papworth, S. K., Rist, J., Coad, L. & Milner-Gulland, E. J. Evidence for shifting baseline syndrome in conservation. Conserv Lett. 2, 93–100 (2009).
    Google Scholar 
    31.Barnosky, A. D. et al. Approaching a state shift in Earth’s biosphere. Nature 486, 52–58 (2012).CAS 
    Article 

    Google Scholar 
    32.Nicholson, E. et al. Scenarios and models to support global conservation targets. Trends Ecol. Evol. 34, 57–68 (2019).Article 

    Google Scholar 
    33.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 (2021).Article 

    Google Scholar 
    34.van Strien, A. J. et al. Modest recovery of biodiversity in a western European country: The Living Planet Index for the Netherlands. Biol. Conserv. 200, 44–50 (2016).Article 

    Google Scholar 
    35.Wauchope, H. S., Amano, T., Sutherland, W. J. & Johnston, A. When can we trust population trends? A method for quantifying the effects of sampling interval and duration. Methods Ecol. Evol. 10, 2067–2078 (2019).Article 

    Google Scholar 
    36.Wauchope, H. S. et al. Evaluating impact using time-series data. Trends Ecol. Evol. https://doi.org/10.1016/j.tree.2020.11.001 (2020).37.R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).38.Buschke, F. T. Biodiversity trajectories and the time needed to achieve no net loss through averted-loss biodiversity offsets. Ecol. Model 352, 54–57 (2017).Article 

    Google Scholar  More

  • in

    Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen

    1.De’Ath G, Fabricius KE, Sweatman H, Puotinen M. The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proc Natl Acad Sci U.S.A. 2012;109:17995–9.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Randall CJ, van Woesik R. Contemporary white-band disease in Caribbean corals driven by climate change. Nat Clim Chang. 2015;5:375–9.Article 

    Google Scholar 
    3.Maynard J, van Hooidonk R, Eakin CM, Puotinen M, Garren M, Williams G, et al. Projections of climate conditions that increase coral disease susceptibility and pathogen abundance and virulence. Nat Clim Chang. 2015;5:688–95.Article 

    Google Scholar 
    4.Cziesielski MJ, Schmidt-Roach S, Aranda M. The past, present, and future of coral heat stress studies. Ecol Evol. 2019;9:10055–66.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    5.Bourne D, Iida Y, Uthicke S, Smith-Keune C. Changes in coral-associated microbial communities during a bleaching event. ISME J. 2008;2:350–63.CAS 
    PubMed 
    Article 

    Google Scholar 
    6.van de Water JAJM, Chaib De Mares M, Dixon GB, Raina JB, Willis BL, Bourne DG, et al. Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef-building coral. Mol Ecol. 2018;27:1065–80.PubMed 
    Article 
    CAS 

    Google Scholar 
    7.Sussman M, Mieog JC, Doyle J, Victor S, Willis BL, Bourne DG. Vibrio zinc-metalloprotease causes photoinactivation of coral endosymbionts and coral tissue lesions. PLoS ONE. 2009;4:1–14.8.Ben-Haim Y, Zicherman-Keren M, Rosenberg E. Temperature-regulated bleaching and lysis of the coral Pocillopora damicornis by the novel pathogen Vibrio coralliilyticus. Appl Environ Microbiol. 2003;69:4236–41.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Garren M, Son K, Raina J-B, Rusconi R, Menolascina F, Shapiro OH, et al. A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals. ISME J. 2014;8:999–1007.CAS 
    PubMed 
    Article 

    Google Scholar 
    10.Garren M, Son K, Tout J, Seymour JR, Stocker R. Temperature-induced behavioral switches in a bacterial coral pathogen. ISME J. 2016;10:1363–72.CAS 
    PubMed 
    Article 

    Google Scholar 
    11.Barbara GM, Mitchell JG. Marine bacterial organisation around point-like sources of amino acids. FEMS Microbiol Ecol. 2003;43:99–109.CAS 
    PubMed 
    Article 

    Google Scholar 
    12.Seymour JR, Marcos, Stocker R. Resource patch formation and exploitation throughout the marine microbial food web. Am Nat. 2009;173:E15–29.CAS 
    PubMed 
    Article 

    Google Scholar 
    13.Son K, Menolascina F, Stocker R. Speed-dependent chemotactic precision in marine bacteria. Proc Natl Acad Sci U.S.A. 2016;113:8624–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    14.Meron D, Efrony R, Johnson WR, Schaefer AL, Morris PJ, Rosenberg E, et al. Role of Flagella in virulence of the coral pathogen Vibrio coralliilyticus. Appl Environ Microbiol. 2009;75:5704–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    15.Ushijima B, Häse CC. Influence of chemotaxis and swimming patterns on the virulence of the coral pathogen Vibrio coralliilyticus. J Bacteriol. 2018;200:1–16.Article 

    Google Scholar 
    16.Crossland CJ, Barnes DJ, Borowitzka MA. Diurnal lipid and mucus production in the staghorn coral Acropora acuminata. Mar Biol. 1980;60:81–90.17.Davies PS. The role of zooxanthellae in the nutritional energy requirements of Pocillopora eydouxi. Coral Reefs. 1984;2:181–6.18.Rix L, de Goeij JM, Mueller CE, Struck U, Middelburg JJ, van Duyl FC, et al. Coral mucus fuels the sponge loop in warm-and cold-water coral reef ecosystems. Sci Rep. 2016;6:1–11.Article 
    CAS 

    Google Scholar 
    19.Naumann MS, Haas A, Struck U, Mayr C, El-Zibdah M, Wild C. Organic matter release by dominant hermatypic corals of the Northern Red Sea. Coral Reefs. 2010;29:649–59.Article 

    Google Scholar 
    20.Wild C, Huettel M, Klueter A, Kremb SG, Rasheed MYM, Jørgensen BB. Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature. 2004;428:66–70.CAS 
    PubMed 
    Article 

    Google Scholar 
    21.Bythell JC, Wild C. Biology and ecology of coral mucus release. J Exp Mar Bio Ecol. 2011;408:88–93.Article 

    Google Scholar 
    22.Bakshani CR, Morales-Garcia AL, Althaus M, Wilcox MD, Pearson JP, Bythell JC, et al. Evolutionary conservation of the antimicrobial function of mucus: a first defence against infection. NPJ Biofilms Microbiomes. 2018;14:1–12.
    Google Scholar 
    23.Gibbin E, Gavish A, Krueger T, Kramarsky-Winter E, Shapiro O, Guiet R, et al. Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral. ISME J. 2019;13:989–1003.24.Gavish AR, Shapiro OH, Kramarsky-Winter E, Vardi A. Microscale tracking of coral-vibrio interactions. ISME Communications. 2021;1:1–18.25.Shapiro OH, Fernandez VI, Garren M, Guasto JS, Debaillon-Vesque FP, Kramarsky-Winter E, et al. Vortical ciliary flows actively enhance mass transport in reef corals. Proc Natl Acad Sci U.S.A. 2014;111:13391–6.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    26.Seymour JR, Ahmed T, Stocker R. A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches. Limnol Oceanogr Methods. 2008;6:477–88.CAS 
    Article 

    Google Scholar 
    27.Penn K, Wang J, Fernando SC, Thompson JR. Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacterial bloom. ISME J. 2014;8:1866–78.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    28.Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.Article 
    CAS 

    Google Scholar 
    29.Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:1–12.30.Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U.S.A. 2005;102:15545–50.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    31.Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267–73.CAS 
    PubMed 
    Article 

    Google Scholar 
    32.Schneider WR, Doetsch RN. Effect of viscosity on bacterial motility. J Bacteriol. 1974;117:696–701.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Martinez VA, Schwarz-Linek J, Reufer M, Wilson LG, Morozov AN, Poon WCK. Flagellated bacterial motility in polymer solutions. Proc Natl Acad Sci U.S.A. 2014;111:17771–6.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Kimes NE, Grim CJ, Johnson WR, Hasan NA, Tall BD, Kothary MH, et al. Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. ISME J. 2012;6:835–46.CAS 
    PubMed 
    Article 

    Google Scholar 
    35.Kojima S, Yamamoto K, Kawagishi I, Homma M. The polar flagellar motor of Vibrio cholerae is driven by an Na+ motive force. J Bacteriol. 1999;181:1927–30.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Sowa Y, Hotta H, Homma M, Ishijima A. Torque-speed relationship of the Na+-driven flagellar motor of Vibrio alginolyticus. J Mol Biol. 2003;327:1043–51.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    37.Milo R, Phillips R. Cell biology by the numbers. 1st ed. New York, NY: Garland Science; 2016.38.Crossland CJ. In situ release of mucus and DOC-lipid from the corals Acropora variabilis and Stylophora pistillata in different light regimes. Coral Reefs. 1987;6:35–42.CAS 
    Article 

    Google Scholar 
    39.Wild C, Woyt H, Huettel M. Influence of coral mucus on nutrient fluxes in carbonate sands. Mar Ecol Prog Ser. 2005;287:87–98.40.Ducklow HW, Mitchell R. Composition of mucus released by coral reef coelenterates. Limnol Oceanogr. 1979;24:706–14.CAS 
    Article 

    Google Scholar 
    41.Meikle P, Richards GN, Yellowlees D. Structural determination of the oligosaccharide side chains from a glycoprotein isolated from the mucus of the coral Acropora formosa. J Biol Chem. 1987;262:16941–7.CAS 
    PubMed 
    Article 

    Google Scholar 
    42.Coddeville B, Maes E, Ferrier-Pagès C, Guerardel Y. Glycan profiling of gel forming mucus layer from the scleractinian symbiotic coral Oculina arbuscula. Biomacromolecules. 2011;12:2064–73.CAS 
    PubMed 
    Article 

    Google Scholar 
    43.Hasegawa H, Häse CC. TetR-type transcriptional regulator VtpR functions as a global regulator in Vibrio tubiashii. Appl Environ Microbiol. 2009;75:7602–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Ball AS, Chaparian RR, van Kessel JC. Quorum sensing gene regulation by LuxR/HapR master regulators in Vibrios. J Bacteriol. 2017;199:1–13.45.Rutherford ST, Van Kessel JC, Shao Y, Bassler BL. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. Genes Dev. 2011;25:397–408.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    46.Hammer BK, Bassler BL. Quorum sensing controls biofilm formation in Vibrio cholerae. Mol Microbiol. 2003;50:101–4.CAS 
    PubMed 
    Article 

    Google Scholar 
    47.Waters CM, Lu W, Rabinowitz JD, Bassler BL. Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic Di-GMP levels and repression of vpsT. J Bacteriol. 2008;190:2527–36.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    48.Burger AH. Quorum Sensing in the Hawai’ian Coral Pathogen Vibrio coralliilyticus strain OCN008. University of Hawaii at Manoa; 2017.49.Yildiz FH, Schoolnik GK. Vibrio cholerae O1 El Tor: identification of a gene cluster required for the rugose colony type, exopolysaccharide production, chlorine resistance, and biofilm formation. Proc Natl Acad Sci U.S.A. 1999;96:4028–33.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    50.Fong JCN, Syed KA, Klose KE, Yildiz FH. Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis. Microbiology. 2010;156:2757–69.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    51.Fong JCN, Karplus K, Schoolnik GK, Yildiz FH. Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae. J Bacteriol. 2006;188:1049–59.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    52.Fong JCN, Yildiz FH. The rbmBCDEF gene cluster modulates development of rugose colony morphology and biofilm formation in Vibrio cholerae. J Bacteriol. 2007;189:2319–30.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    53.DiRita VJ, Mekalanos JJ. Periplasmic interaction between two membrane regulatory proteins, ToxR and ToxS, results in signal transduction and transcriptional activation. Cell. 1991;64:29–37.CAS 
    PubMed 
    Article 

    Google Scholar 
    54.Almagro-Moreno S, Root MZ, Taylor RK. Role of ToxS in the proteolytic cascade of virulence regulator ToxR in Vibrio cholerae. Mol Microbiol. 2015;98:963–76.CAS 
    PubMed 
    Article 

    Google Scholar 
    55.Lee SE, Ryu PY, Kim SY, Kim YR, Koh JT, Kim OJ, et al. Production of Vibrio vulnificus hemolysin in vivo and its pathogenic significance. Biochem Biophys Res Commun. 2004;324:86–91.56.Senoh M, Okita Y, Shinoda S, Miyoshi S. The crucial amino acid residue related to inactivation of Vibrio vulnificus hemolysin. Micro Pathog. 2008;44:78–83.CAS 
    Article 

    Google Scholar 
    57.Bröms JE, Ishikawa T, Wai SN, Sjöstedt A. A functional VipA-VipB interaction is required for the type VI secretion system activity of Vibrio cholerae O1 strain A1552. BMC Microbiol. 2013;13:1–12.Article 
    CAS 

    Google Scholar 
    58.Vizcaino MI, Johnson WR, Kimes NE, Williams K, Torralba M, Nelson KE, et al. Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral. Micro Ecol. 2010;59:646–57.Article 

    Google Scholar 
    59.Ritchie KB. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar Ecol Prog Ser. 2006;322:1–14.CAS 
    Article 

    Google Scholar 
    60.Nissimov J, Rosenberg E, Munn CB. Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica. FEMS Microbiol Lett. 2009;292:210–5.CAS 
    PubMed 
    Article 

    Google Scholar 
    61.Shnit-Orland M, Kushmaro A. Coral mucus-associated bacteria: a possible first line of defense. FEMS Microbiol Ecol. 2009;67:371–80.CAS 
    PubMed 
    Article 

    Google Scholar 
    62.Rypien KL, Ward JR, Azam F. Antagonistic interactions among coral-associated bacteria. Environ Microbiol. 2010;12:28–39.CAS 
    PubMed 
    Article 

    Google Scholar 
    63.Alagely A, Krediet CJ, Ritchie KB, Teplitski M. Signaling-mediated cross-talk modulates swarming and biofilm formation in a coral pathogen Serratia marcescens. ISME J. 2011;5:1609–20.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    64.Stocker R, Seymour JR, Samadani A, Hunt DE, Polz MF. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proc Natl Acad Sci U.S.A. 2008;105:4209–14.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    65.Polz MF, Hunt DE, Preheim SP, Weinreich DM. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc B Biol Sci. 2006;361:2009–21.Article 

    Google Scholar 
    66.Taylor JR, Stocker R. Trade-offs of chemotactic foraging in turbulent water. Science. 2012;338:675–9.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    67.Krediet CJ, Ritchie KB, Cohen M, Lipp EK, Patterson Sutherland K, Teplitski M. Utilization of mucus from the coral Acropora palmata by the pathogen Serratia marcescens and by environmental and coral commensal bacteria. Appl Environ Microbiol. 2009;75:3851–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    68.Krediet CJ, Ritchie KB, Alagely A, Teplitski M. Members of native coral microbiota inhibit glycosidases and thwart colonization of coral mucus by an opportunistic pathogen. ISME J. 2013;7:980–90.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    69.Packer HL, Armitage JP. The chemokinetic and chemotactic behavior of Rhodobacter sphaeroides: two independent responses. J Bacteriol. 1994;176:206–12.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    70.Deepika D, Karmakar R, Tirumkudulu MS, Venkatesh KV. Variation in swimming speed of Escherichia coli in response to attractant. Arch Microbiol. 2015;197:211–22.CAS 
    PubMed 
    Article 

    Google Scholar 
    71.Zhulin IB, Armitage JP. Motility, chemokinesis, and methylation-independent chemotaxis in Azospirillum brasilense. J Bacteriol. 1993;175:952–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    72.Ramos HC, Rumbo M, Sirard J-C. Bacterial flagellins: mediators of pathogenicity and host immune responses in mucosa. Trends Microbiol. 2004;12:509–17.CAS 
    PubMed 
    Article 

    Google Scholar 
    73.Reed KC, Muller EM, van Woesik R. Coral immunology and resistance to disease. Dis Aquat Organ. 2010;90:85–92.CAS 
    PubMed 
    Article 

    Google Scholar 
    74.Ushijima B, Videau P, Poscablo D, Stengel JW, Beurmann S, Burger AH, et al. Mutation of the toxR or mshA genes from Vibrio coralliilyticus strain OCN014 reduces infection of the coral Acropora cytherea. Environ Microbiol. 2016;18:4055–67.CAS 
    PubMed 
    Article 

    Google Scholar 
    75.Ushijima B, Richards GP, Watson MA, Schubiger CB, Häse CC. Factors affecting infection of corals and larval oysters by Vibrio coralliilyticus. PLoS ONE. 2018;13:e0199475.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    76.Peterson KM, Mekalanos JJ. Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. Infect Immun. 1988;56:2822–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    77.Provenzano D, Klose KE. Altered expression of the ToxR-regulated porins OmpU and OmpT diminishes Vibrio cholerae bile resistance, virulence factor expression, and intestinal colonization. Proc Natl Acad Sci U.S.A. 2000;97:10220–4.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Waters CM, Bassler BL. The Vibrio harveyi quorum-sensing system uses shared regulatory components to discriminate between multiple autoinducers. Genes Dev. 2006;20:2754–67.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    79.Mukherjee S, Bassler BL. Bacterial quorum sensing in complex and dynamically changing environments. Nat Rev Microbiol. 2019;17:371–82.80.Sikora AE, Zielke RA, Lawrence DA, Andrews PC, Sandkvist M. Proteomic analysis of the Vibrio cholerae type II secretome reveals new proteins, including three related serine proteases. J Biol Chem. 2011;286:16555–66.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    81.Korotkov KV, Sandkvist M, Hol WGJ. The type II secretion system: biogenesis, molecular architecture and mechanism. Nat Rev Microbiol. 2012;10:336–51.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    82.Stathopoulos C, Hendrixson DR, Thanassi DG, Hultgren SJ, St. Geme III JW, Curtiss III R. Secretion of virulence determinants by the general secretory pathway in Gram-negative pathogens: an evolving story. Microbes Infect. 2000;2:1061–72.83.Hood RD, Singh P, Hsu FS, Güvener T, Carl MA, Trinidad RRS, et al. A Type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe. 2010;7:25–37.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    84.Zheng J, Ho B, Mekalanos JJ. Genetic analysis of anti-amoebae and anti-bacterial activities of the Type VI secretion system in Vibrio cholerae. PLoS ONE. 2011;6:e23876.85.MacIntyre DL, Miyata ST, Kitaoka M, Pukatzki S. The Vibrio cholerae type VI secretion system displays antimicrobial properties. Proc Natl Acad Sci U.S.A. 2010;107:19520–4.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    86.Lee SH, Hava DL, Waldor MK, Camilli A. Regulation and temporal expression patterns of Vibrio cholerae virulence genes during infection. Cell. 1999;99:625–34.87.Pennetzdorfer N, Lembke M, Pressler K, Matson JS, Reidl J, Schild S. Regulated proteolysis in Vibrio cholerae allowing rapid adaptation to stress conditions. Front Cell Infect Microbiol. 2019;9:1–9.Article 
    CAS 

    Google Scholar 
    88.Liu R, Chen H, Zhang R, Zhou Z, Hou Z, Gao D, et al. Comparative transcriptome analysis of Vibrio splendidus JZ6 reveals the mechanism of its pathogenicity at low temperatures. Appl Environ Microbiol. 2016;82:2050–61.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    89.Hughes TP, Anderson KD, Connolly SR, Heron SF, Kerry JT, Lough JM, et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science. 2018;359:80–3.90.Vezzulli L, Previati M, Pruzzo C, Marchese A, Bourne DG, Cerrano C, et al. Vibrio infections triggering mass mortality events in a warming Mediterranean Sea. Environ Microbiol. 2010;12:2007–19.91.Zaneveld JR, Burkepile DE, Shantz AA, Pritchard CE, McMinds R, Payet JP, et al. Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales. Nat Commun. 2016;7:1–12.Article 
    CAS 

    Google Scholar  More

  • in

    The global distribution and environmental drivers of aboveground versus belowground plant biomass

    1.Erb, K. H. et al. Unexpectedly large impact of forest management and grazing on global vegetation biomass. Nature 553, 73–76 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    2.Luyssaert, S. et al. Old-growth forests as global carbon sinks. Nature 455, 213–215 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    3.Drake, J. B. et al. Above-ground biomass estimation in closed canopy Neotropical forests using lidar remote sensing: factors affecting the generality of relationships. Glob. Ecol. Biogeogr. 12, 147–159 (2003).Article 

    Google Scholar 
    4.Lefsky, M. A. et al. Lidar remote sensing of above-ground biomass in three biomes. Glob. Ecol. Biogeogr. 11, 393–399 (2002).Article 

    Google Scholar 
    5.Duncanson, L. et al. The importance of consistent global forest aboveground biomass product validation. Surv. Geophys. 40, 979–999 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Spawn, S. A., Sullivan, C. C., Lark, T. J. & Gibbs, H. K. Harmonized global maps of above and belowground biomass carbon density in the year 2010. Sci. Data 7, 112 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    7.Ottaviani, G. et al. The neglected belowground dimension of plant dominance. Trends Ecol. Evol. 35, 763–766 (2020).PubMed 
    Article 

    Google Scholar 
    8.Jackson, L. E., Burger, M. & Cavagnaro, T. R. Roots, nitrogen transformations, and ecosystem services. Annu. Rev. Plant Biol. 59, 341–363 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    9.Gill, R. A. & Jackson, R. B. Global patterns of root turnover for terrestrial ecosystems. New Phytol. 147, 13–31 (2000).Article 

    Google Scholar 
    10.Robinson, D. Implications of a large global root biomass for carbon sink estimates and for soil carbon dynamics. Proc. R. Soc. Lond. B 274, 2753–2759 (2007).CAS 

    Google Scholar 
    11.Bardgett, R. D., Mommer, L. & De Vries, F. T. Going underground: root traits as drivers of ecosystem processes. Trends Ecol. Evol. 29, 692–699 (2014).PubMed 
    Article 

    Google Scholar 
    12.Ribeiro, S. C. et al. Above- and belowground biomass in a Brazilian Cerrado. For. Ecol. Manage. 262, 491–499 (2011).Article 

    Google Scholar 
    13.Mokany, K., Raison, R. J. & Prokushkin, A. S. Critical analysis of root:shoot ratios in terrestrial biomes. Glob. Chang. Biol. 12, 84–96 (2006).Article 

    Google Scholar 
    14.Saatchi, S. S. et al. Benchmark map of forest carbon stocks in tropical regions across three continents. Proc. Natl Acad. Sci. USA 108, 9899–9904 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    15.Ruesch, A. S. & Gibbs, H. H. K. New IPCC Tier-1 Global Biomass Carbon Map for the Year 2000 (Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, 2008).16.Chen, J. L. & Reynolds, J. F. A coordination model of whole-plant carbon allocation in relation to water stress. Ann. Bot. 80, 45–55 (1997).CAS 
    Article 

    Google Scholar 
    17.Franklin, O. et al. Modeling carbon allocation in trees: a search for principles. Tree Physiol. 32, 648–666 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    18.Bloom, A. J., Chapin, F. S. & Mooney, H. A. Resource limitation in plants—an economic analogy. Annu. Rev. Ecol. Syst. 16, 363–392 (1985).Article 

    Google Scholar 
    19.Poorter, H. et al. Biomass allocation to leaves, stems and roots: meta-analyses of interspecific variation and environmental control. New Phytol. 193, 30–50 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    20.Reich, P. in Plant Roots: The Hidden Half (eds. Waisel, Y. et al.) 205–220 (Marcel Dekker, 2006).21.Ledo, A. et al. Tree size and climatic water deficit control root to shoot ratio in individual trees globally. New Phytol. 217, 8–11 (2018).PubMed 
    Article 

    Google Scholar 
    22.Qi, Y., Wei, W., Chen, C. & Chen, L. Plant root-shoot biomass allocation over diverse biomes: a global synthesis. Glob. Ecol. Conserv. 18, e00606 (2019).Article 

    Google Scholar 
    23.Reich, P. B. et al. Temperature drives global patterns in forest biomass distribution in leaves, stems, and roots. Proc. Natl Acad. Sci. USA 111, 13721–13726 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    24.De Frenne, P. et al. Latitudinal gradients as natural laboratories to infer species’ responses to temperature. J. Ecol. 101, 784–795 (2013).Article 

    Google Scholar 
    25.Luo, Y. Terrestrial carbon-cycle feedback to climate warming. Annu. Rev. Ecol. Evol. Syst. 38, 683–712 (2007).Article 

    Google Scholar 
    26.Jackson, R. B. et al. A global analysis of root distributions for terrestrial biomes. Oecologia 108, 389–411 (1996).CAS 
    PubMed 
    Article 

    Google Scholar 
    27.Malhi, Y., Doughty, C. & Galbraith, D. The allocation of ecosystem net primary productivity in tropical forests. Philos. Trans. R. Soc. Lond. B 366, 3225–3245 (2011).CAS 
    Article 

    Google Scholar 
    28.Roberts, D. R. et al. Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure. Ecography 40, 913–929 (2017).Article 

    Google Scholar 
    29.Cairns, M. A., Brown, S., Helmer, E. H. & Baumgardner, G. A. Root biomass allocation in the world’s upland forests. Oecologia 111, 1–11 (1997).PubMed 
    Article 

    Google Scholar 
    30.McCarthy, M. C. & Enquist, B. J. Consistency between an allometric approach and optimal partitioning theory in global patterns of plant biomass allocation. Funct. Ecol. 21, 713–720 (2007).Article 

    Google Scholar 
    31.Barton, C. V. M. & Montagu, K. D. Effect of spacing and water availability on root:shoot ratio in Eucalyptus camaldulensis. For. Ecol. Manage. 221, 52–62 (2006).Article 

    Google Scholar 
    32.Enquist, B. J. & Niklas, K. J. Global allocation rules for patterns of biomass partitioning in seed plants. Science 295, 1517–1520 (2002).CAS 
    PubMed 
    Article 

    Google Scholar 
    33.Goward, S. N., Tucker, C. J. & Dye, D. G. North American vegetation patterns observed with the NOAA-7 advanced very high resolution radiometer. Vegetatio 64, 3–14 (1985).Article 

    Google Scholar 
    34.Manzoni, S., Jackson, R. B., Trofymow, J. A. & Porporato, A. The global stoichiometry of litter nitrogen mineralization. Science 321, 684–686 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    35.Kaiser, C., Franklin, O., Dieckmann, U. & Richter, A. Microbial community dynamics alleviate stoichiometric constraints during litter decay. Ecol. Lett. 17, 680–690 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Jiao, F., Shi, X. R., Han, F. P. & Yuan, Z. Y. Increasing aridity, temperature and soil pH induce soil C-N-P imbalance in grasslands. Sci. Rep. 6, 19601 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    37.Sitch, S. et al. Recent trends and drivers of regional sources and sinks of carbon dioxide. Biogeosciences 12, 653–679 (2015).Article 

    Google Scholar 
    38.De Deyn, G. B., Cornelissen, J. H. C. & Bardgett, R. D. Plant functional traits and soil carbon sequestration in contrasting biomes. Ecol. Lett. 11, 516–531 (2008).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    39.Tjoelker, M. G., Craine, J. M., Wedin, D., Reich, P. B. & Tilman, D. Linking leaf and root trait syndromes among 39 grassland and savannah species. New Phytol. 167, 493–508 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    40.Personeni, E. & Loiseau, P. How does the nature of living and dead roots affect the residence time of carbon in the root litter continuum? Plant Soil 267, 129–141 (2004).CAS 
    Article 

    Google Scholar 
    41.Tuanmu, M. N. & Jetz, W. A global 1-km consensus land-cover product for biodiversity and ecosystem modelling. Glob. Ecol. Biogeogr. 23, 1031–1045 (2014).Article 

    Google Scholar 
    42.Pan, Y., Birdsey, R. A., Phillips, O. L. & Jackson, R. B. The structure, distribution, and biomass of the world’s forests. Annu. Rev. Ecol. Evol. Syst. 44, 593–622 (2013).Article 

    Google Scholar 
    43.Jackson, R. B., Mooney, H. A. & Schulze, E. D. A global budget for fine root biomass, surface area, and nutrient contents. Proc. Natl Acad. Sci. USA 94, 7362–7366 (1997).CAS 
    PubMed 
    Article 

    Google Scholar 
    44.Genet, H., Bréda, N. & Dufrêne, E. Age-related variation in carbon allocation at tree and stand scales in beech (Fagus sylvatica L.) and sessile oak (Quercus petraea (Matt.) Liebl.) using a chronosequence approach. Tree Physiol. 30, 177–192 (2009).PubMed 
    Article 

    Google Scholar 
    45.De Castro, E. A. & Kauffman, J. B. Ecosystem structure in the Brazilian Cerrado: a vegetation gradient of aboveground biomass, root mass and consumption by fire. J. Trop. Ecol. 14, 263–283 (1998).Article 

    Google Scholar 
    46.Ding, B. & Sun, J. Study on biomass of Korean pine plantation in east mountain areas of northeast China. Bull. Bot. Res. 9, 149–157 (1989).
    Google Scholar 
    47.Ding, B., Liu, S. & Cai, T. Studies on biological productivity of artificial forests of Dahurian larches. Chin. J. Plant Ecol. 14, 226–236 (1990).
    Google Scholar 
    48.Ding, B. & Sun, J. Accumulation and distribution of productivity and nutrient element in natural Manchurian ash. J. Northeast For. Univ. 4, 1–9 (1989).
    Google Scholar 
    49.Dossa, E. L., Fernandes, E. C. M., Reid, W. S. & Ezui, K. Above- and belowground biomass, nutrient and carbon stocks contrasting an open-grown and a shaded coffee plantation. Agrofor. Syst. 72, 103–115 (2008).Article 

    Google Scholar 
    50.Epron, D. et al. Do changes in carbon allocation account for the growth response to potassium and sodium applications in tropical Eucalyptus plantations? Tree Physiol. 32, 667–679 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    51.Fonseca, W., Rey Benayas, J. M. & Alice, F. E. Carbon accumulation in the biomass and soil of different aged secondary forests in the humid tropics of Costa Rica. For. Ecol. Manage. 262, 1400–1408 (2011).Article 

    Google Scholar 
    52.Goodman, R. C. et al. Amazon palm biomass and allometry. For. Ecol. Manage. 310, 994–1004 (2013).Article 

    Google Scholar 
    53.Greenland, D. J. & Kowal, J. M. L. Nutrient content of the moist tropical forest of Ghana. Plant Soil 12, 154–173 (1960).CAS 
    Article 

    Google Scholar 
    54.He, Y. et al. Carbon storage capacity of monoculture and mixed-species plantations in subtropical China. For. Ecol. Manage. 295, 193–198 (2013).Article 

    Google Scholar 
    55.Aiba, M. & Nakashizuka, T. Variation in juvenile survival and related physiological traits among dipterocarp species co‐existing in a Bornean forest. J. Veg. Sci. 18, 379–388 (2007).Article 

    Google Scholar 
    56.Jha, K. K. Carbon storage and sequestration rate assessment and allometric model development in young teak plantations of tropical moist deciduous forest, India. J. For. Res. 26, 589–604 (2015).CAS 
    Article 

    Google Scholar 
    57.Kalita, R. M., Das, A. K. & Nath, A. J. Allometric equations for estimating above- and belowground biomass in Tea (Camellia sinensis (L.) O. Kuntze) agroforestry system of Barak Valley, Assam, northeast India. Biomass Bioenergy 83, 42–49 (2015).Article 

    Google Scholar 
    58.Kenzo, T. et al. Development of allometric relationships for accurate estimation of above- and below-ground biomass in tropical secondary forests in Sarawak, Malaysia. J. Trop. Ecol. 25, 371–386 (2009).Article 

    Google Scholar 
    59.Kenzo, T. et al. Allometric equations for accurate estimation of above-ground biomass in logged-over tropical rainforests in Sarawak, Malaysia. J. For. Res. 14, 365–372 (2009).CAS 
    Article 

    Google Scholar 
    60.Kraenzel, M., Castillo, A., Moore, T. & Potvin, C. Carbon storage of harvest-age teak (Tectona grandis) plantations, Panama. For. Ecol. Manage. 173, 213–225 (2003).Article 

    Google Scholar 
    61.Kuyah, S., Dietz, J., Muthuri, C., van Noordwijk, M. & Neufeldt, H. Allometry and partitioning of above- and below-ground biomass in farmed eucalyptus species dominant in Western Kenyan agricultural landscapes. Biomass Bioenergy 55, 276–284 (2013).Article 

    Google Scholar 
    62.Liu, S., Cai, Y. & Cai, T. in Long-term Research on Forest Ecosystems (ed. Zhou, X.) 419–427 (Northeast Forestry Univ. Press, 1991).63.Luo, T. et al. Root biomass along subtropical to alpine gradients: global implication from Tibetan transect studies. For. Ecol. Manage. 206, 349–363 (2005).Article 

    Google Scholar 
    64.Markesteijn, L. & Poorter, L. Seedling root morphology and biomass allocation of 62 tropical tree species in relation to drought- and shade-tolerance. J. Ecol. 97, 311–325 (2009).Article 

    Google Scholar 
    65.McNicol, I. M. et al. Development of allometric models for above and belowground biomass in swidden cultivation fallows of northern Laos. For. Ecol. Manage. 357, 104–116 (2015).Article 

    Google Scholar 
    66.Aiba, M. & Nakashizuka, T. Sapling structure and regeneration strategy in 18 Shorea species co-occurring in a tropical rainforest. Ann. Bot. 96, 313–321 (2005).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Menaut, J. C. & Cesar, J. Structure and primary productivity of Lamto savannas, Ivory Coast. Ecology 60, 1197–1210 (1979).Article 

    Google Scholar 
    68.Morais, V. A. et al. Estoques de carbono e biomassa de um fragmento de cerradão em Minas Gerais, Brasil. Cerne 19, 237–245 (2013).Article 

    Google Scholar 
    69.Mugasha, W. A. et al. Allometric models for prediction of above- and belowground biomass of trees in the miombo woodlands of Tanzania. For. Ecol. Manage. 310, 87–101 (2013).Article 

    Google Scholar 
    70.Návar, J. Plasticity of biomass component allocation patterns in semiarid Tamaulipan thornscrub and dry temperate pine species of northeastern Mexico. Polibotánica 31, 121–141 (2011).
    Google Scholar 
    71.Njana, M. A., Eid, T., Zahabu, E. & Malimbwi, R. Procedures for quantification of belowground biomass of three mangrove tree species. Wetl. Ecol. Manage. 23, 749–764 (2015).Article 

    Google Scholar 
    72.Nogueira Junior, L. R., Engel, V. L., Parrotta, J. A., de Melo, A. C. G. & Ré, D. S. Equações alométricas para estimativa da biomassa arbórea em plantios mistos com espécies nativas na restauração da Mata Atlântica. Biota Neotrop. 14, 1–9 (2014).Article 

    Google Scholar 
    73.Peichl, M. & Arain, M. A. Above- and belowground ecosystem biomass and carbon pools in an age-sequence of temperate pine plantation forests. Agric. For. Meteorol. 140, e20130084 (2006).Article 

    Google Scholar 
    74.Battles, J. J. et al. Vegetation composition, structure, and biomass of two unpolluted watersheds in the Cordillera de Piuchué, Chiloé Island, Chile. Plant Ecol. 158, 5–19 (2002).Article 

    Google Scholar 
    75.Ryan, C. M., Williams, M. & Grace, J. Above- and belowground carbon stocks in a miombo woodland landscape of Mozambique. Biotropica 43, 423–432 (2011).Article 

    Google Scholar 
    76.Saint-André, L. et al. Age-related equations for above- and below-ground biomass of a Eucalyptus hybrid in Congo. For. Ecol. Manage. 205, 199–214 (2005).Article 

    Google Scholar 
    77.Aryal, D. R., De Jong, B. H. J., Ochoa-Gaona, S., Esparza-Olguin, L. & Mendoza-Vega, J. Carbon stocks and changes in tropical secondary forests of southern Mexico. Agric. Ecosyst. Environ. 195, 220–230 (2014).Article 

    Google Scholar 
    78.Schepaschenko, D. et al. A dataset of forest biomass structure for Eurasia. Sci. Data 4, 170070 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    79.Schroth, G., D’Angelo, S. A., Teixeira, W. G., Haag, D. & Lieberei, R. Conversion of secondary forest into agroforestry and monoculture plantations in Amazonia: consequences for biomass, litter and soil carbon stocks after 7 years. For. Ecol. Manage. 163, 131–150 (2002).Article 

    Google Scholar 
    80.Schulze, E. D. et al. Rooting depth, water availability, and vegetation cover along an aridity gradient in Patagonia. Oecologia 108, 503–511 (1996).Article 

    Google Scholar 
    81.Stolbovoi, V. & McCallum, I. Land resources of Russia [CD] (International Institute for Applied Systems Analysis and the Russian Academy of Science, 2002); http://www.iiasa.ac.at/Research/FOR/russia_cd/guide.htm82.Wang, L. et al. Biomass allocation patterns across China’s terrestrial biomes. PLoS ONE 9, e93566 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    83.Wauters, J. B., Coudert, S., Grallien, E., Jonard, M. & Ponette, Q. Carbon stock in rubber tree plantations in Western Ghana and Mato Grosso (Brazil). For. Ecol. Manage. 255, 2347–2361 (2008).Article 

    Google Scholar 
    84.Williams-Linera, G. Biomass and nutrient content in two successional stages of tropical wet forest in Uxpanapa, Mexico. Biotropica 15, 275–284 (1983).Article 

    Google Scholar 
    85.Xu, Y. et al. Improving allometry models to estimate the above- and belowground biomass of subtropical forest, China. Ecosphere 6, 289 (2015).Article 

    Google Scholar 
    86.Youkhana, A. H. & Idol, T. W. Allometric models for predicting above- and belowground biomass of Leucaena-KX2 in a shaded coffee agroecosystem in Hawaii. Agrofor. Syst. 83, 331–345 (2011).Article 

    Google Scholar 
    87.Zhang, H. et al. Biogeographical patterns of biomass allocation in leaves, stems, and roots in China’s forests. Sci. Rep. 5, 15997 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    88.Castellanos, J., Maass, M. & Kummerow, J. Root biomass of a dry deciduous tropical forest in Mexico. Plant Soil 131, 225–228 (1991).Article 

    Google Scholar 
    89.Zheng, Z., Feng, Z., Cao, M., Li, Z. & Zhang, J. Forest structure and biomass of a tropical seasonal rain forest in Xishuangbanna, southwest China. Biotropica 38, 318–327 (2006).Article 

    Google Scholar 
    90.Návar, J. Root stock biomass and productivity assessments of reforested pine stands in northern Mexico. For. Ecol. Manage. 338, 139–147 (2015).Article 

    Google Scholar 
    91.Wang, X., Fang, J. & Zhu, B. Forest biomass and root–shoot allocation in northeast China. For. Ecol. Manage. 255, 4007–4020 (2008).Article 

    Google Scholar 
    92.Chen, D. K., Zhou, X. F., Zhao, H. X., Wang, Y. H. & Jing, Y. Y. Study on the structure, function and succession of the four types in natural secondary forest. J. Northeast For. Univ. 2, 1–20 (1982).
    Google Scholar 
    93.Chidumayo, E. N. Estimating tree biomass and changes in root biomass following clear-cutting of Brachystegia-Julbernardia (miombo) woodland in central Zambia. Environ. Conserv. 41, 54–63 (2014).Article 

    Google Scholar 
    94.Coll, L., Potvin, C., Messier, C. & Delagrange, S. Root architecture and allocation patterns of eight native tropical species with different successional status used in open-grown mixed plantations in Panama. Trees 22, 585–596 (2008).Article 

    Google Scholar 
    95.Das, D. K. & Chaturvedi, O. P. Structure and function of Populus deltoides agroforestry systems in eastern India: 1. dry matter dynamics. Agrofor. Syst. 65, 215–221 (2005).Article 

    Google Scholar 
    96.Ni, J. Estimating net primary productivity of grasslands from field biomass measurements in temperate northern China. Plant Ecol. 174, 217–234 (2011).Article 

    Google Scholar 
    97.Olson, R. et al. NPP Multi-Biome: Summary Data from Intensive Studies at 125 Sites, 1936–2006 (ORNL DAAC, accessed 19 June 2019); https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=135298.Perez, C. A. & Frangi, J. L. Grassland biomass dynamics along an altitudinal gradient in the pampa. J. Range Manage. 53, 518–528 (2007).Article 

    Google Scholar 
    99.Perez-Quezada, J. F. F., Delpiano, C. A. A., Snyder, K. A. A., Johnson, D. A. A. & Franck, N. Carbon pools in an arid shrubland in Chile under natural and afforested conditions. J. Arid Environ. 75, 29–37 (2011).Article 

    Google Scholar 
    100.Pornon, A., Boutin, M. & Lamaze, T. Contribution of plant species to the high N retention capacity of a subalpine meadow undergoing elevated N deposition and warming. Environ. Pollut. 245, 235–242 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    101.Ramakrishnan, P. S. & Ram, S. C. Vegetation, biomass and productivity of seral grasslands of Cherrapunji in north-east India. Vegetatio 74, 47–53 (1988).Article 

    Google Scholar 
    102.Shaver, G. R., Laundre, J. A., Giblin, A. E. & Nadelhoffer, K. J. Changes in live plant biomass, primary production, and species composition along a riverside toposequence in Arctic Alaska, USA. Arct. Alp. Res. 28, 363–379 (2006).Article 

    Google Scholar 
    103.Smith, J. M. B. & Klinger, L. F. Aboveground:belowground phytomass ratios in Venezuelan paramo vegetation and their significance. Arct. Alp. Res. 17, 189–198 (2006).Article 

    Google Scholar 
    104.Sun, J. et al. Effects of grazing regimes on plant traits and soil nutrients in an alpine steppe, northern Tibetan Plateau. PLoS ONE 9, e108821 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    105.Wang, P. et al. Belowground plant biomass allocation in tundra ecosystems and its relationship with temperature. Environ. Res. Lett. 11, 055003 (2016).Article 
    CAS 

    Google Scholar 
    106.Yang, Y., Fang, J., Ji, C. & Han, W. Above- and belowground biomass allocation in Tibetan grasslands. J. Veg. Sci. 20, 177–184 (2009).Article 

    Google Scholar 
    107.Yang, Y., Fang, J., Ma, W., Guo, D. & Mohammat, A. Large-scale pattern of biomass partitioning across China’s grasslands. Glob. Ecol. Biogeogr. 19, 268–277 (2010).Article 

    Google Scholar 
    108.Geng, H. L., Wang, Y. H., Wang, F. Y. & Jia, B. R. The dynamics of root-shoot ratio and its environmental effective factors of recovering Leymus chinensis steppe vegetation in Inner Mongolia, China. Acta Ecol. Sin. 28, 4629–4634 (2008).Article 

    Google Scholar 
    109.Hui, D. & Jackson, R. B. Geographical and interannual variability in biomass partitioning in grassland ecosystems: a synthesis of field data. New Phytol. 169, 85–93 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    110.Jouquet, P., Tavernier, V., Abbadie, L. & Lepage, M. Nests of subterranean fungus-growing termites (Isoptera, Macrotermitinae) as nutrient patches for grasses in savannah ecosystems. Afr. J. Ecol. 43, 191–196 (2005).Article 

    Google Scholar 
    111.Leonid, U. et al. Impact of climate and grazing on biomass components of eastern Russia typical steppe. J. Integr. Agric. 13, 1183–1192 (2014).Article 

    Google Scholar 
    112.Lucash, M. S., Farnsworth, B. & Winner, W. E. Response of sagebrush steppe species to elevated CO2 and soil temperature. West. N. Am. Nat. 65, 80–86 (2005).
    Google Scholar 
    113.Luo, W. et al. Patterns of plant biomass allocation in temperate grasslands across a 2500-km transect in northern China. PLoS ONE 8, e71749 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    114.Barbour, M. G. Desert dogma reexamined: root/shoot productivity and plant spacing. Am. Midl. Nat. 89, 41–57 (1973).Article 

    Google Scholar 
    115.Becker, P., Sharbini, N. & Yahya, R. Root architecture and root:shoot allocation of shrubs and saplings in two lowland tropical forests: implications for life-form composition. Biotropica 31, 93–101 (1999).
    Google Scholar 
    116.Becker, P. & Castillo, A. Root architecture of shrubs and saplings in the understory of a tropical moist forest in lowland Panama. Biotropica 22, 242–249 (1990).Article 

    Google Scholar 
    117.Beier, C. et al. Carbon and nitrogen balances for six shrublands across Europe. Glob. Biogeochem. Cycles 23, GB4008 (2009).Article 
    CAS 

    Google Scholar 
    118.Bhatt, Y. D., Rawat, Y. S. & Singh, S. P. Changes in ecosystem functioning after replacement of forest by Lantana shrubland in Kumaun Himalaya. J. Veg. Sci. 5, 67–70 (1994).Article 

    Google Scholar 
    119.Caldwell, M. M., White, R. S., Moore, R. T. & Camp, L. B. Carbon balance, productivity, and water use of cold-winter desert shrub communities dominated by C3 and C4 species. Oecologia 29, 275–300 (1977).PubMed 
    Article 

    Google Scholar 
    120.De Viñas, I. C. R. et al. Biomass of root and shoot systems of Quercus coccifera shrublands in eastern Spain. Ann. For. Sci. 57, 803–810 (2000).Article 

    Google Scholar 
    121.Caravaca, F., Figueroa, D., Alguacil, M. M. & Roldán, A. Application of composted urban residue enhanced the performance of afforested shrub species in a degraded semiarid land. Bioresour. Technol. 90, 65–70 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    122.Caravaca, F., Figueroa, D., Azcón-Aguilar, C., Barea, J. M. & Roldán, A. Medium-term effects of mycorrhizal inoculation and composted municipal waste addition on the establishment of two Mediterranean shrub species under semiarid field conditions. Agric. Ecosyst. Environ. 97, 95–105 (2003).Article 

    Google Scholar 
    123.Carrasco, L., Azcón, R., Kohler, J., Roldán, A. & Caravaca, F. Comparative effects of native filamentous and arbuscular mycorrhizal fungi in the establishment of an autochthonous, leguminous shrub growing in a metal-contaminated soil. Sci. Total Environ. 409, 1205–1209 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    124.Carrillo-Garcia, Á., Bashan, Y. & Bethlenfalvay, G. J. Resource-island soils and the survival of the giant cactus, cardon, of Baja California Sur. Plant Soil 218, 207–214 (2000).CAS 
    Article 

    Google Scholar 
    125.Carrión-Prieto, P. et al. Mediterranean shrublands as carbon sinks for climate change mitigation: new root-to-shoot ratios. Carbon Manage. 8, 67–77 (2017).Article 
    CAS 

    Google Scholar 
    126.Deng, L., Han, Q. S., Zhang, C., Tang, Z. S. & Shangguan, Z. P. Above-ground and below-ground ecosystem biomass accumulation and carbon sequestration with Caragana korshinskii Kom plantation development. Land Degrad. Dev. 28, 906–917 (2017).Article 

    Google Scholar 
    127.Perkins, S. R. & Owens, M. K. Growth and biomass allocation of shrub and grass seedlings in response to predicted changes in precipitation seasonality. Plant Ecol. 168, 107–120 (2003).Article 

    Google Scholar 
    128.Gargaglione, V., Peri, P. L. & Rubio, G. Allometric relations for biomass partitioning of Nothofagus antarctica trees of different crown classes over a site quality gradient. For. Ecol. Manage. 259, 1118–1126 (2010).Article 

    Google Scholar 
    129.Hao, H. M. et al. Effects of shrub patch size succession on plant diversity and soil water content in the water-wind erosion crisscross region on the Loess Plateau. Catena 144, 177–183 (2016).Article 

    Google Scholar 
    130.Herwitz, S. R. & Olsvig-Whittaker, L. Preferential upslope growth of Zygophyllum dumosum Boiss. (Zygophyllaceae) roots into bedrock fissures in the northern Negev desert. J. Biogeogr. 16, 457–460 (1989).Article 

    Google Scholar 
    131.Hoffmann, A. & Kummerow, J. Root studies in the Chilean matorral. Oecologia 32, 57–69 (1978).PubMed 
    Article 

    Google Scholar 
    132.Holl, K. D. Effects of above- and below-ground competition of shrubs and grass on Calophyllum brasiliense (Camb.) seedling growth in abandoned tropical pasture. For. Ecol. Manage. 109, 187–195 (1998).Article 

    Google Scholar 
    133.Hollister, R. D. & Flaherty, K. J. Above- and below-ground plant biomass response to experimental warming in northern Alaska. Appl. Veg. Sci. 13, 378–387 (2010).
    Google Scholar 
    134.Kizito, F. et al. Seasonal soil water variation and root patterns between two semi-arid shrubs co-existing with pearl millet in Senegal, West Africa. J. Arid Environ. 67, 436–455 (2006).Article 

    Google Scholar 
    135.Kummerow, J., Krause, D. & Jow, W. Root systems of chaparral shrubs. Oecologia 29, 163–177 (1977).PubMed 
    Article 

    Google Scholar 
    136.León, M. F., Squeo, F. A., Gutiérrez, J. R. & Holmgren, M. Rapid root extension during water pulses enhances establishment of shrub seedlings in the Atacama Desert. J. Veg. Sci. 22, 120–129 (2011).Article 

    Google Scholar 
    137.Li, C. P. & Xiao, C. W. Above- and belowground biomass of Artemisia ordosica communities in three contrasting habitats of the Mu Us Desert, northern China. J. Arid Environ. 70, 195–207 (2007).Article 

    Google Scholar 
    138.Liang, Y. M., Hazlett, D. L. & Lauenroth, W. K. Biomass dynamics and water use efficiencies of five plant communities in the shortgrass steppe. Oecologia 80, 148–153 (1989).CAS 
    PubMed 
    Article 

    Google Scholar 
    139.Zan, Q., Wang, Y., Liao, B. & Zheng, D. Biomass and net productivity of Sonneratia apetala, S. caseolaris mangrove man-made forest. Wuhan Bot. Res. 19, 391–396 (2001).
    Google Scholar 
    140.Liao, B., Zheng, D. & Zheng, S. Studies on the biomass of Sonneratia caseolaris stand. For. Res. 3, 47–54 (1990).
    Google Scholar 
    141.Lufafa, A. et al. Allometric relationships and peak-season community biomass stocks of native shrubs in Senegal’s Peanut Basin. J. Arid Environ. 73, 260–266 (2009).Article 

    Google Scholar 
    142.Lusk, C. H. Leaf area and growth of juvenile temperate evergreens in low light: species of contrasting shade tolerance change rank during ontogeny. Funct. Ecol. 18, 820–828 (2004).Article 

    Google Scholar 
    143.Marsh, A. S., Arnone, J. A., Bormann, B. T. & Gordon, J. C. The role of Equisetum in nutrient cycling in an Alaskan shrub wetland. J. Ecol. 88, 999–1011 (2000).Article 

    Google Scholar 
    144.Martínez, F. et al. Belowground structure and production in a Mediterranean sand dune shrub community. Plant Soil 201, 209–216 (1998).Article 

    Google Scholar 
    145.Marziliano, P. A. et al. Estimating belowground biomass and root/shoot ratio of Phillyrea latifolia L. in the Mediterranean forest landscapes. Ann. For. Sci. 72, 585–593 (2015).Article 

    Google Scholar 
    146.Mauchamp, A., Montaña, C., Lepart, J., Rambal, S. & Montana, C. Ecotone dependent recruitment of a desert shrub, Flourensia cernua, in vegetation stripes. Oikos 68, 107–116 (1993).Article 

    Google Scholar 
    147.Mendoza-Ponce, A. & Galicia, L. Aboveground and belowground biomass and carbon pools in highland temperate forest landscape in central Mexico. Forestry 83, 497–506 (2010).Article 

    Google Scholar 
    148.Miller, P. C. & Ng, E. Root:shoot biomass ratios in shrubs in southern California and central Chile. Madrono 24, 215–223 (1977).
    Google Scholar 
    149.Mooney, H. A. & Rundel, P. W. Nutrient relations of the evergreen shrub, Adenostoma fasciculatum, in the California chaparral. Bot. Gaz. 140, 109–113 (1979).CAS 
    Article 

    Google Scholar 
    150.Moro, M. J., Pugnaire, F. I., Haase, P. & Puigdefábregas, J. Effect of the canopy of Retama sphaerocarpa on its understorey in a semiarid environment. Funct. Ecol. 11, 425–431 (1997).Article 

    Google Scholar 
    151.Negreiros, D., Fernandes, G. W., Silveira, F. A. O. & Chalub, C. Seedling growth and biomass allocation of endemic and threatened shrubs of rupestrian fields. Acta Oecol. 35, 301–310 (2009).Article 

    Google Scholar 
    152.Nie, X., Yang, Y., Yang, L. & Zhou, G. Above- and belowground biomass allocation in shrub biomes across the northeast Tibetan Plateau. PLoS ONE 11, e0154251 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    153.Nobel, P. S., Quero, E. & Linares, H. Root versus shoot biomass: responses to water, nitrogen, and phosphorus applications for Agave lechuguilla. Bot. Gaz. 150, 411–416 (1989).Article 

    Google Scholar 
    154.Pacaldo, R. S., Volk, T. A. & Briggs, R. D. Greenhouse gas potentials of shrub willow biomass crops based on below- and aboveground biomass inventory along a 19-year chronosequence. Bioenergy Res. 6, 252–262 (2013).CAS 
    Article 

    Google Scholar 
    155.Padilla, F. M., Miranda, J. D., Jorquera, M. J. & Pugnaire, F. I. Variability in amount and frequency of water supply affects roots but not growth of arid shrubs. Plant Ecol. 204, 261–270 (2009).Article 

    Google Scholar 
    156.Portsmuth, A., Niinemets, Ü., Truus, L. & Pensa, M. Biomass allocation and growth rates in Pinus sylvestris are interactively modified by nitrogen and phosphorus availabilities and by tree size and age. Can. J. For. Res. 35, 2346–2359 (2005).CAS 
    Article 

    Google Scholar 
    157.Roth, G. A., Whitford, W. G. & Steinberger, Y. Jackrabbit (Lepus californicus) herbivory changes dominance in desertified Chihuahuan Desert ecosystems. J. Arid Environ. 70, 418–426 (2007).Article 

    Google Scholar 
    158.Ruiz-Peinado, R., Moreno, G., Juarez, E., Montero, G. & Roig, S. The contribution of two common shrub species to aboveground and belowground carbon stock in Iberian dehesas. J. Arid Environ. 91, 22–30 (2013).Article 

    Google Scholar 
    159.Rundel, P. W. Biomass, productivity, and nutrient allocation in subalpine shrublands and meadows of the Emerald Lake Basin, Sequoia National Park, California. Arct. Antarct. Alp. Res. 47, 115–123 (2015).Article 

    Google Scholar 
    160.Millikin, C. S. & Bledsoe, C. S. Biomass and distribution of fine and coarse roots from blue oak (Quercus douglasii) trees in the northern Sierra Nevada foothills of California. Plant Soil 214, 27–38 (1999).CAS 
    Article 

    Google Scholar 
    161.Saura-Mas, S. & Lloret, F. Adult root structure of Mediterranean shrubs: relationship with post-fire regenerative syndrome. Plant Biol. 16, 147–154 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    162.Schenk, H. J. & Mahall, B. E. Positive and negative plant interactions contribute to a north-south-patterned association between two desert shrub species. Oecologia 132, 402–410 (2002).PubMed 
    Article 

    Google Scholar 
    163.Silva, J. S., Rego, F. C. & Martins-Loução, M. A. Belowground traits of Mediterranean woody plants in a Portuguese shrubland. Ecol. Mediterr. 28, 5–13 (2002).Article 

    Google Scholar 
    164.Simões, M. P., Madeira, M. & Gazarini, L. Biomass and nutrient dynamics in Mediterranean seasonal dimorphic shrubs: strategies to face environmental constraints. Plant Biosyst. 146, 500–510 (2012).
    Google Scholar 
    165.Tao, Y., Zhang, Y. M. & Downing, A. Similarity and difference in vegetation structure of three desert shrub communities under the same temperate climate but with different microhabitats. Bot. Stud. 54, 59 (2013).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    166.Toscano, S., Scuderi, D., Giuffrida, F. & Romano, D. Responses of Mediterranean ornamental shrubs to drought stress and recovery. Sci. Hortic. 178, 145–153 (2014).Article 

    Google Scholar 
    167.Trubat, R., Cortina, J. & Vilagrosa, A. Nutrient deprivation improves field performance of woody seedlings in a degraded semi-arid shrubland. Ecol. Eng. 37, 1164–1173 (2011).Article 

    Google Scholar 
    168.Van Wijk, M. T., Williams, M., Gough, L., Hobbie, S. E. & Shaver, G. R. Luxury consumption of soil nutrients: a possible competitive strategy in above-ground and below-ground biomass allocation and root morphology for slow-growing arctic vegetation? J. Ecol. 91, 664–676 (2003).Article 

    Google Scholar 
    169.Walker, L. R., Clarkson, B. D., Silvester, W. B. & Clarkson, B. R. Colonization dynamics and facilitative impacts of a nitrogen-fixing shrub in primary succession. J. Veg. Sci. 14, 277–290 (2003).Article 

    Google Scholar 
    170.Wang, B. & Yang, X. S. Comparison of biomass and species diversity of four typical zonal vegetations. J. Fujian Coll. For. 29, 345–350 (2009).
    Google Scholar 
    171.Wang, M. & Li, H. Quantitative study on the soil water dynamics of various forest plantations in the Loess Plateau region in northwestern Shanxi. Acta Ecol. Sin. 2, 178–184 (1995).
    Google Scholar 
    172.Wang, P. et al. Seasonal changes and vertical distribution of root standing biomass of graminoids and shrubs at a Siberian tundra site. Plant Soil 407, 55–65 (2016).CAS 
    Article 

    Google Scholar 
    173.Whittaker, R. H. & Woodwell, G. M. Dimension and production relations of trees and shrubs in the Brookhaven Forest, New York. J. Ecol. 56, 1–25 (1968).Article 

    Google Scholar 
    174.Xu, H., Li, Y., Xu, G. & Zou, T. Ecophysiological response and morphological adjustment of two Central Asian desert shrubs towards variation in summer precipitation. Plant Cell Environ. 30, 399–409 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    175.Yan, Z. Biomass and its allocation in a 28-year-old Castanopsis kawakamii plantation. J. Fujian Coll. For. 2, 114–118 (1996).
    Google Scholar 
    176.Gong, Y. et al. Carbon storage and vertical distribution in three shrubland communities in Gurbantünggüt Desert, Uygur Autonomous Region of Xinjiang, northwest China. Chin. Geogr. Sci. 22, 541–549 (2012).Article 

    Google Scholar 
    177.Yu, Y., Shi, D., Qiuyi, J., He, L. & Cheng, G. On the biomass of secondary Schima superba forest in Hangzhou. J. Zhejiang For. Coll. 2, 157–161 (1993).
    Google Scholar 
    178.Kato, T. et al. Carbon dioxide exchange between the atmosphere and an alpine meadow ecosystem on the Qinghai-Tibetan Plateau, China. Agric. Meteorol. 124, 121–134 (2004).Article 

    Google Scholar 
    179.Li, Z., Zhu, Q. & Li, J. A comparison of photosynthetic carbon sequestration of four shrubs in Ningxia. Pratacultural Sci. 29, 352–357 (2012).CAS 

    Google Scholar 
    180.Zhu, X., Shi, Q. & Li, Y. A preliminary study on the Qinghai’s treasure house of the forest biomass and shrubs. Sci. Technol. Qinghai Agric. For. 1, 15–20 (1993).
    Google Scholar 
    181.Liao, B. & Zheng, D. Study on the forest biomass and productivity of olive wood. For. Res. 4, 22–29 (1991).
    Google Scholar 
    182.Liu, B., Liu, Z., Lü, X., Maestre, F. T. & Wang, L. Sand burial compensates for the negative effects of erosion on the dune-building shrub Artemisia wudanica. Plant Soil 374, 263–273 (2014).CAS 
    Article 

    Google Scholar 
    183.Alguacil, M. M., Hernández, J. A., Caravaca, F., Portillo, B. & Roldán, A. Antioxidant enzyme activities in shoots from three mycorrhizal shrub species afforested in a degraded semi-arid soil. Physiol. Plant. 118, 562–570 (2003).CAS 
    Article 

    Google Scholar 
    184.Axe, M. S., Grange, I. D. & Conway, J. S. Carbon storage in hedge biomass—a case study of actively managed hedges in England. Agric. Ecosyst. Environ. 250, 81–88 (2017).Article 

    Google Scholar 
    185.van den Hoogen, J. et al. Soil nematode abundance and functional group composition at a global scale. Nature 572, 194–198 (2019).PubMed 
    Article 
    CAS 

    Google Scholar 
    186.Erin, L. et al. h2o: R Interface for the ‘H2O’ Scalable Machine Learning Platform. R package v.3.32.0.2 (2020); https://github.com/h2oai/h2o-3187.Sagi, O. & Rokach, L. Ensemble learning: a survey. WIREs Data Min. Knowl. Discov. 8, e1249 (2018).
    Google Scholar 
    188.R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019).189.Gorelick, N. et al. Google Earth Engine: planetary-scale geospatial analysis for everyone. Remote Sens. Environ. 202, 18–27 (2017).Article 

    Google Scholar 
    190.Heiberger, R. M. HH: Statistical Analysis and Data Display: Heiberger and Holland (2020).191.Hothorn, T. & Zeileis, A. partykit: A modular toolkit for recursive partytioning in R. J. Mach. Learn. Res. 16, 3905–3909 (2015).
    Google Scholar 
    192.Borkovec, M. & Madin, N. ggparty: ‘ggplot’ visualizations for the ‘partykit’ package (2019).193.Dormann, C. F. Effects of incorporating spatial autocorrelation into the analysis of species distribution data. Glob. Ecol. Biogeogr. 16, 129–138 (2007).Article 

    Google Scholar 
    194.Hutchinson, M., Xu, T., Houlder, D., Nix, H. & McMahon, J. ANUCLIM 6.0 User’s Guide (Australian National Univ., 2009).195.Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    196.Global Aridity and PET database (CGIAR-CSI, accessed 15 May 2018); http://www.cgiarcsi.community/data/global-aridity-and-pet-database197.CIESIN Gridded Population of the World, version 4 (GPWv4): Population Density Adjusted to Match 2015 Revision UN WPP Country Totals (NASA SEDAC, 2018); https://doi.org/10.7927/H4HX19NJ198.Venter, O. et al. Global terrestrial human footprint maps for 1993 and 2009. Sci. Data 3, 160067 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    199.SoilGrids (ISRIC, accessed 15 May 2018); https://www.soilgrids.org200.Entekhabi, D. et al. The soil moisture active passive (SMAP) mission. Proc. IEEE 98, 704–716 (2010).Article 

    Google Scholar 
    201.Fan, Y., Li, H. & Miguez-Macho, G. Global patterns of groundwater table depth. Science 339, 940–943 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    202.Batjes, N. H. Harmonized soil property values for broad-scale modelling (WISE30sec) with estimates of global soil carbon stocks. Geoderma 269, 61–68 (2016).CAS 
    Article 

    Google Scholar 
    203.Schaaf, C. & Wang, Z. MCD43A1 MODIS/Terra+Aqua BRDF/Albedo Model Parameters Daily L3 Global – 500m V006 (NASA LP DAAC, 2015); https://doi.org/10.5067/MODIS/MCD43A1C.006204.Didan, K. MOD13Q1 MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V006 (NASA LP DAAC, 2015).205.Crowther, T. W. et al. Mapping tree density at a global scale. Nature 525, 201–205 (2015).CAS 
    PubMed 
    Article 

    Google Scholar  More