More stories

  • in

    Catestatin selects for colonization of antimicrobial-resistant gut bacterial communities

    Kåhrström CT, Pariente N, Weiss U. Intestinal microbiota in health and disease. Nature 2016;535:47–47.Article 

    Google Scholar 
    El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, et al. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol. 2012;5:567–79.CAS 
    Article 

    Google Scholar 
    Okumura R, Takeda K. Roles of intestinal epithelial cells in the maintenance of gut homeostasis. Exp Mol Med. 2017;49:e338–e338.CAS 
    Article 

    Google Scholar 
    Mahata SK, O’Connor DT, Mahata M, Yoo SH, Taupenot L, Wu H, et al. Novel autocrine feedback control of catecholamine release. A discrete chromogranin a fragment is a noncompetitive nicotinic cholinergic antagonist. J Clin Invest. 1997;100:1623–33.CAS 
    Article 

    Google Scholar 
    Briolat J, Wu SD, Mahata SK, Gonthier B, Bagnard D, Chasserot-Golaz S, et al. New antimicrobial activity for the catecholamine release-inhibitory peptide from chromogranin A. Cell Mol Life Sci. 2005;62:377–85.CAS 
    Article 

    Google Scholar 
    Lugardon K, Raffner R, Goumon Y, Corti A, Delmas A, Bulet P, et al. Antibacterial and antifungal activities of vasostatin-1, the N-terminal fragment of chromogranin A. J Biol Chem. 2000;275:10745–53.CAS 
    Article 

    Google Scholar 
    Aslam R, Atindehou M, Lavaux T, Haïkel Y, Schneider F, Metz-Boutigue M-H. Chromogranin A-derived peptides are involved in innate immunity. Curr Med Chem. 2012;19:4115–23.CAS 
    Article 

    Google Scholar 
    El-Salhy M, Patcharatrakul T, Hatlebakk JG, Hausken T, Gilja OH, Gonlachanvit S. Chromogranin A cell density in the large intestine of Asian and European patients with irritable bowel syndrome. Scand J Gastroenterol. 2017;52:691–7.CAS 
    Article 

    Google Scholar 
    Bartolomucci A, Possenti R, Mahata SK, Fischer-Colbrie R, Loh YP, Salton SR. The extended granin family: structure, function, and biomedical implications. Endocr Rev. 2011;32:755–97.CAS 
    Article 

    Google Scholar 
    Mahata SK, Corti A. Chromogranin A and its fragments in cardiovascular, immunometabolic, and cancer regulation. Ann N Y Acad Sci. 2019;1455:34–58.CAS 
    Article 

    Google Scholar 
    Corti A, Marcucci F, Bachetti T. Circulating chromogranin A and its fragments as diagnostic and prognostic disease markers. Pflugers Archiv Eur J Physiol. 2018;470:199–210.Mahata SK, Mahata M, Fung MM, O’Connor DT. Catestatin: a multifunctional peptide from chromogranin A. Regul Pept. 2010;162:33–43.CAS 
    Article 

    Google Scholar 
    Ying W, Mahata S, Bandyopadhyay GK, Zhou Z, Wollam J, Vu J, et al. Catestatin inhibits obesity-induced macrophage infiltration and inflammation in the liver and suppresses hepatic glucose production, leading to improved insulin sensitivity. Diabetes. 2018;67:841–8.CAS 
    Article 

    Google Scholar 
    Mahata SK, Kiranmayi M, Mahapatra NR. Catestatin: a master regulator of cardiovascular functions. Curr Med Chem. 2018;25:1352–74.CAS 
    Article 

    Google Scholar 
    Muntjewerff EM, Tang K, Lutter L, Christoffersson G, Nicolasen MJT, Gao H, et al. Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides. Acta Physiol. 2021;232:e13655.Rabbi MF, Munyaka PM, Eissa N, Metz-Boutigue MH, Khafipour E, Ghia JE. Human catestatin alters gut microbiota composition in mice. Front Microbiol. 2017;7:1–12.Article 

    Google Scholar 
    Radek KA, Lopez-Garcia B, Hupe M, Niesman IR, Elias PM, Taupenot L, et al. The neuroendocrine peptide catestatin is a cutaneous antimicrobial and induced in the skin after injury. J Invest Dermatol. 2008;128:1525–34.CAS 
    Article 

    Google Scholar 
    Bevins CL, Salzman NH. Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis. Nat Rev Microbiol. 2011;9:356–68.CAS 
    Article 

    Google Scholar 
    Dupont A, Heinbockel L, Brandenburg K, Hornef MW. Antimicrobial peptides and the enteric mucus layer act in concert to protect the intestinal mucosa. Gut Microbes. 2014;5:761–5.Article 

    Google Scholar 
    Tsukuda N, Yahagi K, Hara T, Watanabe Y, Matsumoto H, Mori H, et al. Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life. ISME J. 2021;15:2574–90.CAS 
    Article 

    Google Scholar 
    Nuri R, Shprung T, Shai Y. Defensive remodeling: How bacterial surface properties and biofilm formation promote resistance to antimicrobial peptides. Biochim Biophys Acta Biomembr. 2015;1848:3089–100.CAS 
    Article 

    Google Scholar 
    Jakobsson HE, Rodríguez‐Piñeiro AM, Schütte A, Ermund A, Boysen P, Bemark M, et al. The composition of the gut microbiota shapes the colon mucus barrier. EMBO Rep. 2015;16:164–77.CAS 
    Article 

    Google Scholar 
    Samantha A, Vrielink A. Lipid A Phosphoethanolamine Transferase: regulation, structure and immune response. J Mol Biol. 2020;432:5184–96.CAS 
    Article 

    Google Scholar 
    Gottesman S. Proteases and their targets in Escherichia coli. Annu Rev Genet. 1996;30:465–506.CAS 
    Article 

    Google Scholar 
    Mirsepasi-Lauridsen HC, Vallance BA, Krogfelt KA, Petersen AM. Escherichia coli pathobionts associated with inflammatory bowel disease. Clin Microbiol Rev. 2019;32:1–16.Article 

    Google Scholar 
    Nayfach S, Fischbach MA, Pollard KS. MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics. 2015;31:3368–70.CAS 
    Article 

    Google Scholar 
    Ying W, Tang K, Avolio E, Schilling JM, Pasqua T, Liu MA, et al. Immunosuppression of macrophages underlies the cardioprotective effects of CST (Catestatin). Hypertension. 2021;77:1670–82.CAS 
    Article 

    Google Scholar 
    Stojanov S, Berlec A, Štrukelj B. The influence of probiotics on the firmicutes/bacteroidetes ratio in the treatment of obesity and inflammatory bowel disease. Microorganisms. 2020;8:1–16.Article 

    Google Scholar 
    Indiani CMDSP, Rizzardi KF, Castelo PM, Ferraz LFC, Darrieux M, Parisotto TM. Childhood obesity and firmicutes/bacteroidetes ratio in the gut microbiota: a systematic review. Child Obes. 2018;14:501–9.Article 

    Google Scholar 
    Lam YY, Ha CWY, Campbell CR, Mitchell AJ, Dinudom A, Oscarsson J, et al. Increased gut permeability and microbiota change associate with mesenteric fat inflammation and metabolic dysfunction in diet-induced obese mice. PLoS One. 2012;7:1–10.
    Google Scholar 
    Herp S, Durai Raj AC, Salvado Silva M, Woelfel S, Stecher B. The human symbiont Mucispirillum schaedleri: causality in health and disease. Med Microbiol Immunol. 2021;210:173–9.Article 

    Google Scholar 
    Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A. The genus alistipes: gut bacteria with emerging implications to inflammation, cancer, and mental health. Front Immunol. 2020;11:1–15.Article 

    Google Scholar 
    Hiippala K, Barreto G, Burrello C, Diaz-Basabe A, Suutarinen M, Kainulainen V, et al. Novel Odoribacter splanchnicus strain and its outer membrane vesicles exert immunoregulatory effects in vitro. Front Microbiol. 2020;11:1–14.Article 

    Google Scholar 
    McPhee JB, Small CL, Reid-Yu SA, Brannon JR, Moual H LE, Coombes BK. Host defense peptide resistance contributes to colonization and maximal intestinal pathology by Crohn’s disease-associated adherent-invasive Escherichia coli. Infect Immun. 2014;82:3383–93.Article 

    Google Scholar 
    Xu Y, Wei W, Lei S, Lin J, Srinivas S, Feng Y. An evolutionarily conserved mechanism for intrinsic and transferable polymyxin resistance. MBio. 2018;9:1–18.Article 

    Google Scholar 
    Thomassin JL, Brannon JR, Gibbs BF, Gruenheid S, Le Moual H. OmpT outer membrane proteases of enterohemorrhagic and enteropathogenic Escherichia coli contribute differently to the degradation of human LL-37. Infect Immun. 2012;80:483–92.CAS 
    Article 

    Google Scholar 
    Desloges I, Taylor JA, Leclerc JM, Brannon JR, Portt A, Spencer JD, et al. Identification and characterization of OmpT-like proteases in uropathogenic Escherichia coli clinical isolates. Microbiologyopen. 2019;8:1–36.Article 

    Google Scholar 
    McCarter JD, Stephens D, Shoemaker K, Rosenberg S, Kirsch JF, Georgiou G. Substrate specificity of the Escherichia coli outer membrane protease OmpT. J Bacteriol. 2004;186:5919–25.CAS 
    Article 

    Google Scholar 
    Kulkarni HM, Nagaraj R, Jagannadham MV. Protective role of E. coli outer membrane vesicles against antibiotics. Microbiol Res. 2015;181:1–7.CAS 
    Article 

    Google Scholar 
    Muntjewerff EM, Dunkel G, Nicolasen MJT, Mahata SK, van den Bogaart G. Catestatin as a Target for Treatment of Inflammatory Diseases. Front Immunol. 2018;9:2199.Santella RM. Approaches to DNA/RNA extraction and whole genome amplification: table 1. Cancer Epidemiol Biomark Prev. 2006;15:1585–7.CAS 
    Article 

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

    Google Scholar 
    R Core Team. R: a language and environment for statistical computing. Vienna, Austria; 2019. https://www.r-project.org/.Lahti L, Shetty S. microbiome R package. http://microbiome.github.io.McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.Paulson JN, Colin Stine O, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200–2.CAS 
    Article 

    Google Scholar 
    Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.Article 

    Google Scholar 
    Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;38:685–8.CAS 
    Article 

    Google Scholar 
    Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123–4.CAS 
    Article 

    Google Scholar 
    Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, et al. The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe. 2022;30:124–138.e8.CAS 
    Article 

    Google Scholar 
    Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.CAS 
    Article 

    Google Scholar 
    Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.Article 

    Google Scholar 
    Menardo F, Loiseau C, Brites D, Coscolla M, Gygli SM, Rutaihwa LK, et al. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinforma. 2018;19:1–8.Article 

    Google Scholar 
    Haider SR, Reid HJ, Sharp BL. Tricine-SDS-PAGE. In: Kurien B., Scofield R. editors. Protein electrophoresis. Methods in Molecular Biology (Methods and Protocols). Totowa, NJ: Humana Press; 2012. p. 81–91.Schägger H. Tricine-SDS-PAGE. Nat Protoc. 2006;1:16–22.Article 

    Google Scholar 
    Zoetendal EG, Booijink CCGM, Klaassens ES, Heilig HGHJ, Kleerebezem M, Smidt H, et al. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat Protoc. 2006;1:954–9.CAS 
    Article 

    Google Scholar 
    Zhou K, Zhou L, Lim Q, Zou R, Stephanopoulos G, Too HP. Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR. BMC Mol Biol. 2011;12:18.CAS 
    Article 

    Google Scholar 
    Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods. 2001;25:402–8.CAS 
    Article 

    Google Scholar  More

  • in

    Punishment institutions selected and sustained through voting and learning

    Henrich, J. et al. Costly punishment across human societies. Science https://doi.org/10.1126/science.1127333 (2006).Ostrom, E. Governing the Commons: The Evolution of Institutions for Collective Action (Cambridge University Press, 1990).Ostrom, E., Walker, J. & Gardner, R. Covenants with and without a sword: self-governance is possible. Am. Polit. Sci. Rev. 86, 404–417 (1992).Article 

    Google Scholar 
    Fehr, E. & Gächter, S. Cooperation and punishment in public goods experiments. Am. Econ. Rev. 90, 980–994 (2000).Article 

    Google Scholar 
    Dreber, A., Rand, D. G., Fudenberg, D. & Nowak, M. A. Winners don’t punish. Nature https://doi.org/10.1038/nature06723 (2008).Rand, D. G., Ohtsuki, H. & Nowak, M. A. Direct reciprocity with costly punishment: generous tit-for-tat prevails. J. Theor. Biol. https://doi.org/10.1016/j.jtbi.2008.09.015 (2009).Ohtsuki, H., Iwasa, Y. & Nowak, M. A. Indirect reciprocity provides only a narrow margin of efficiency for costly punishment. Nature https://doi.org/10.1038/nature07601 (2009).Sethi, R. & Somanathan, E. Understanding reciprocity. J. Econ. Behav. Organ. 50, 1–27 (2003).Article 

    Google Scholar 
    Bowles, S. & Gintis, H. A Cooperative Species (Princeton Univ. Press, 2011).Hauert, C., Traulsen, A., Brandt, H., Nowak, M. A. & Sigmund, K. Via freedom to coercion: the emergence of costly punishment. Science https://doi.org/10.1126/science.1141588 (2007).Brandt, H., Hauert, C. & Sigmund, K. Punishment and reputation in spatial public goods games. Proc. R. Soc. B https://doi.org/10.1098/rspb.2003.2336 (2003).Helbing, D., Szolnoki, A., Perc, M. & Szabó, G. Evolutionary establishment of moral and double moral standards through spatial interactions. PLoS Comput. Biol. https://doi.org/10.1371/journal.pcbi.1000758 (2010).Helbing, D., Szolnoki, A., Perc, M. & Szabó, G. Punish, but not too hard: how costly punishment spreads in the spatial public goods game. New J. Phys. https://doi.org/10.1088/1367-2630/12/8/083005 (2010).Perc, M. & Szolnoki, A. Self-organization of punishment in structured populations. New J. Phys. https://doi.org/10.1088/1367-2630/14/4/043013 (2012).Boyd, R., Gintis, H. & Bowles, S. Coordinated punishment of defectors sustains cooperation and can proliferate when rare. Science https://doi.org/10.1126/science.1183665 (2010).Sigmund, K., De Silva, H., Traulsen, A. & Hauert, C. Social learning promotes institutions for governing the commons. Nature 466, 861–863 (2010).CAS 
    Article 

    Google Scholar 
    Hilbe, C., Traulsen, A., Röhl, T. & Milinski, M. Democratic decisions establish stable authorities that overcome the paradox of second-order punishment. Proc. Natl Acad. Sci. USA 111, 752–756 (2014).CAS 
    Article 

    Google Scholar 
    Murphy, B. The Punisher’s Brain: The Evolution of Judge and Jury. By Hoffman, Morris B. Pp. xi, 359. Cambridge/NY, Cambridge University Press, 2014, £21.99/$30.00. Heythrop J. https://doi.org/10.1111/heyj.12249_81 (2015).Gruter, M. & Masters, R. D. Ostracism as a social and biological phenomenon: an introduction. Ethol. Sociobiolo. https://doi.org/10.1016/0162-3095(86)90043-9 (1986).Molleman, L., Kölle, F., Starmer, C. & Gächter, S. People prefer coordinated punishment in cooperative interactions. Nat. Hum. Behav. https://doi.org/10.1038/s41562-019-0707-2 (2019).Szolnoki, A., Szabó, G. & Perc, M. Phase diagrams for the spatial public goods game with pool punishment. Phys. Rev. E https://doi.org/10.1103/PhysRevE.83.036101 (2011).Ostrom, E. Collective action and the evolution of social norms. J. Econ. Perspect. 14, 137–158 (2000).Article 

    Google Scholar 
    Platteau, J.-P. Institutions, Social Norms, and Economic Development Vol. 1 (Psychology Press, 2000).van den Bergh, J. C. J. M., Ferrer-i-Carbonell, A. & Munda, G. Alternative models of individual behaviour and implications for environmental policy. Ecol. Econ. 32, 43–61 (2000).Article 

    Google Scholar 
    Traulsen, A., Nowak, M. A. & Pacheco, J. M. Stochastic dynamics of invasion and fixation. Phys. Rev. E 74, 11909 (2006).Article 

    Google Scholar 
    Dequech, D. Institutions, social norms, and decision-theoretic norms. J. Econ. Behav. Organ. 72, 70–78 (2009).Article 

    Google Scholar 
    Dunn, S. P. Bounded rationality is not fundamental uncertainty: a post Keynesian perspective. J. Post Keynes. Econ. 23, 567–587 (2001).Article 

    Google Scholar 
    Levin, S. The trouble of discounting tomorrow. Solutions 3, 20–24 (2012).
    Google Scholar 
    Alford, R. P. The proliferation of international courts and tribunals: international adjudication in ascendance. In Proc. Annual Meeting of the American Society of International Law Vol. 94, 160–165 (Cambridge University Press, 2000).Dunn, L. A. Containing Nuclear Proliferation (International Institute for Strategic Studies, 1991).Potoski, M. Green clubs in building block climate change regimes. Climatic Change 144, 53–63 (2017).Article 

    Google Scholar 
    Trzyna, T. C., Margold, E. & Osborn, J. K. World Directory of Environmental Organizations: A Handbook of National and International Organizations and Programs—Governmental and Non-governmental—Concerned with Protecting the Earth’s Resources Vol. 5 (Earthscan, 1996).Dixit, A. & Levin, S. in The Theory of Externalities and Public Goods: Essays in Memory of Richard C. Cornes (eds Buchholz, W. and Rübbelke, D.) 127–143 (Springer, 2017); https://doi.org/10.1007/978-3-319-49442-5_7Vasconcelos, V. V., Santos, F. C. & Pacheco, J. M. A bottom-up institutional approach to cooperative governance of risky commons. Nat. Clim. Change 3, 797–801 (2013).Article 

    Google Scholar 
    Vasconcelos, V. V., Santos, F. C. & Pacheco, J. M. Cooperation dynamics of polycentric climate governance. Math. Model. Methods Appl. Sci. 25, 2503–2517 (2015).Article 

    Google Scholar 
    Ostrom, E. Beyond markets and states: polycentric governance of complex economic systems. Am. Econ. Rev. 100, 641–672 (2010).Article 

    Google Scholar 
    Vasconcelos, V. V., Hannam, P. M., Levin, S. A. & Pacheco, J. M. Coalition-structured governance improves cooperation to provide public goods. Sci. Rep. 10, 9194 (2020).CAS 
    Article 

    Google Scholar 
    Nyborg, K. et al. Social norms as solutions. Science 354, 42–43 (2016).CAS 
    Article 

    Google Scholar 
    Hannam, P. M., Vasconcelos, V. V., Levin, S. A. & Pacheco, J. M. Incomplete cooperation and co-benefits: deepening climate cooperation with a proliferation of small agreements. Climatic Change 144, 65–79 (2017).Article 

    Google Scholar 
    Markussen, T., Putterman, L. & Tyran, J.-R. Self-organization for collective action: an experimental study of voting on sanction regimes. Rev. Econ. Stud. 81, 301–324 (2014).Article 

    Google Scholar 
    Gürerk, Ö., Irlenbusch, B. & Rockenbach, B. The competitive advantage of sanctioning institutions. Science 312, 108–111 (2006).Article 

    Google Scholar 
    Dannenberg, A. & Gallier, C. The choice of institutions to solve cooperation problems: a survey of experimental research. Exp. Econ. https://doi.org/10.1007/s10683-019-09629-8 (2019).Bühren, C. & Dannenberg, A. The demand for punishment to promote cooperation among like-minded people. Eur. Econ. Rev. 138, 103862 (2021).Radzvilavicius, A. L., Kessinger, T. A. & Plotkin, J. B. Adherence to public institutions that foster cooperation. Nat. Commun. 12, 3567 (2021).CAS 
    Article 

    Google Scholar  More

  • in

    Sexual morph specialisation in a trioecious nematode balances opposing selective forces

    Darwin, C. The Effects of Cross and Self Fertilisation in the Vegetable Kingdom (D. Appleton and Company, 1877).
    Google Scholar 
    Charlesworth, D. Androdioecy and the evolution of dioecy. Biol. J. Linn Soc. 22, 333–348 (1984).Article 

    Google Scholar 
    Charlesworth, D., Morgan, M. T. & Charlesworth, B. Inbreeding depression, genetic load, and the evolution of outcrossing rates in a multilocus system with no linkage. Evolution 44, 1469–1489 (1990).CAS 
    Article 

    Google Scholar 
    Lande, R. & Schemske, D. W. The evolution of self-fertilization and inbreeding depression in plants. I. Genetic models. Evolution 39, 24–40 (1985).
    Google Scholar 
    Weeks, S. C. When males and hermaphrodites coexist: a review of androdioecy in animals. Integr. Comp. Biol. 46, 449–464 (2006).Article 

    Google Scholar 
    Pannell, J. The maintenance of gynodioecy and androdioecy in a metapopulation. Evolution 51, 10–20 (1997).Article 

    Google Scholar 
    Wolf, D. E. & Takebayashi, N. Pollen limitation and the evolution of androdioecy from dioecy. Am. Nat. 163, 122–137 (2004).Article 

    Google Scholar 
    Charlesworth, D. Theories of the evolution of dioecy. In Gender and Sexual Dimorphism in Flowering Plants (eds Geber, M. A. et al.) 33–60 (Springer, Berlin, 1999). https://doi.org/10.1007/978-3-662-03908-3_2.Chapter 

    Google Scholar 
    Denver, D. R., Clark, K. A. & Raboin, M. J. Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species. Mol. Phylogenetics Evol. 61, 584–592 (2011).CAS 
    Article 

    Google Scholar 
    Pires-daSilva, A. Evolution of the control of sexual identity in nematodes. Semin. Cell Dev. Biol. 18, 362–370 (2007).Article 

    Google Scholar 
    Kanzaki, N. et al. Description of two three-gendered nematode species in the new genus Auanema (Rhabditina) that are models for reproductive mode evolution. Sci. Rep. 7, 11135 (2017).ADS 
    Article 

    Google Scholar 
    Tandonnet, S. et al. Sex- and gamete-specific patterns of X chromosome segregation in a trioecious nematode. Curr. Biol. 28, 93-99.e3 (2018).CAS 
    Article 

    Google Scholar 
    Chaudhuri, J. et al. Mating dynamics in a nematode with three sexes and its evolutionary implications. Sci. Rep. 5, 17676 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    Félix, M.-A. Alternative morphs and plasticity of vulval development in a rhabditid nematode species. Dev. Genes Evol. 214, 55–63 (2004).Article 

    Google Scholar 
    Shakes, D. C., Neva, B. J., Huynh, H., Chaudhuri, J. & Pires-daSilva, A. Asymmetric spermatocyte division as a mechanism for controlling sex ratios. Nat. Commun. 2, 157 (2011).ADS 
    Article 

    Google Scholar 
    Winter, E. S. et al. Cytoskeletal variations in an asymmetric cell division support diversity in nematode sperm size and sex ratios. Development 144, 3253–3263 (2017).CAS 

    Google Scholar 
    Robles, P. et al. Parental energy-sensing pathways control intergenerational offspring sex determination in the nematode Auanema freiburgensis. BMC Biol. 19, 102 (2021).CAS 
    Article 

    Google Scholar 
    Zuco, G. et al. Sensory neurons control heritable adaptation to stress through germline reprogramming. bioRxiv 406033 (2018) https://doi.org/10.1101/406033.Colegrave, N., Kaltz, O. & Bell, G. The ecology and genetics of fitness in chlamydomonas. VIII. The dynamics of adaptation to novel environments after a single episode of sex. Evolution 56, 14–21 (2002).Article 

    Google Scholar 
    Goddard, M. R., Godfray, H. C. J. & Burt, A. Sex increases the efficacy of natural selection in experimental yeast populations. Nature 434, 636–640 (2005).ADS 
    CAS 
    Article 

    Google Scholar 
    Gray, J. C. & Goddard, M. R. Sex enhances adaptation by unlinking beneficial from detrimental mutations in experimental yeast populations. BMC Evol. Biol. 12, 43 (2012).Article 

    Google Scholar 
    Poon, A. & Chao, L. Drift increases the advantage of sex in RNA bacteriophage ⌽6. Genetics 166, 19 (2004).Article 

    Google Scholar 
    Stewart, A. D. & Phillips, P. C. Selection and maintenance of androdioecy in Caenorhabditis elegans. Genetics 160, 975–982 (2002).Article 

    Google Scholar 
    Stiernagle, T. Maintenance of C. elegans. WormBook: The Online Review of C. elegans Biology (WormBook, 2006).Avery, L. The genetics of feeding in Caenorhabditis elegans. Genetics 133, 897–917 (1993).CAS 
    Article 

    Google Scholar 
    Bargmann, C. I. & Horvitz, H. R. Control of larval development by chemosensory neurons in Caenorhabditis elegans. Science 251, 1243–1246 (1991).ADS 
    CAS 
    Article 

    Google Scholar 
    Lenth, R. V. Emmeans: estimated marginal means, aka least-squares means (2021).Lipton, J., Kleemann, G., Ghosh, R., Lints, R. & Emmons, S. W. Mate searching in Caenorhabditis elegans: a genetic model for sex drive in a simple invertebrate. J. Neurosci. 24, 7427–7434 (2004).CAS 
    Article 

    Google Scholar 
    Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    Pino, E. C., Webster, C. M., Carr, C. E. & Soukas, A. A. Biochemical and high throughput microscopic assessment of fat mass in Caenorhabditis elegans. J. Vis. Exp. https://doi.org/10.3791/50180 (2013).Article 

    Google Scholar 
    Hakim, A. et al. WorMachine: machine learning-based phenotypic analysis tool for worms. BMC Biol. 16, 8 (2018).Article 

    Google Scholar 
    Motola, D. L. et al. Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans. Cell 124, 1209–1223 (2006).CAS 
    Article 

    Google Scholar 
    Ogawa, A., Streit, A., Antebi, A. & Sommer, R. J. A conserved endocrine mechanism controls the formation of dauer and infective larvae in nematodes. Curr. Biol. 19, 67–71 (2009).CAS 
    Article 

    Google Scholar 
    Wang, Z. et al. Identification of the nuclear receptor DAF-12 as a therapeutic target in parasitic nematodes. Proc. Natl. Acad. Sci. 106, 9138–9143 (2009).ADS 
    CAS 
    Article 

    Google Scholar 
    Hu, P. Dauer. WormBook: The C. elegans Research Community (2007).Chaudhuri, J., Kache, V. & Pires-daSilva, A. Regulation of sexual plasticity in a nematode that produces males, females, and hermaphrodites. Curr. Biol. 21, 1548–1551 (2011).CAS 
    Article 

    Google Scholar 
    Luciani, G. M. et al. Dafadine inhibits DAF-9 to promote dauer formation and longevity of Caenorhabditis elegans. Nat. Chem. Biol. 7, 891–893 (2011).CAS 
    Article 

    Google Scholar 
    Adams, S., Pathak, P., Shao, H., Lok, J. B. & Pires-daSilva, A. Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems. Sci. Rep. 9, 483 (2019).ADS 
    Article 

    Google Scholar 
    Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).CAS 
    Article 

    Google Scholar 
    Grabherr, M. G. et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol. 29, 644–652 (2011).CAS 
    Article 

    Google Scholar 
    Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat. Protoc. 8, 1494 (2013).CAS 
    Article 

    Google Scholar 
    Schmieder, R. & Edwards, R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6, e17288 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    Huang, Y., Niu, B., Gao, Y., Fu, L. & Li, W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26, 680–682 (2010).CAS 
    Article 

    Google Scholar 
    Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12, 323 (2011).CAS 
    Article 

    Google Scholar 
    Bendtsen, J. D., Nielsen, H., von Heijne, G. & Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783–795 (2004).Article 

    Google Scholar 
    Bryant, D. M. et al. A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Rep. 18, 762–776 (2017).CAS 
    Article 

    Google Scholar 
    Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucl. Acids Res. 39, W29–W37 (2011).CAS 
    Article 

    Google Scholar 
    Andersen, C. L., Jensen, J. L. & Ørntoft, T. F. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 64, 5245–5250 (2004).CAS 
    Article 

    Google Scholar 
    McGhee, J. D. The C. elegans intestine. WormBook: The Online Review of C. elegans Biology [Internet] (WormBook, 2007).Mullaney, B. C. & Ashrafi, K. C. elegans fat storage and metabolic regulation. Biochim. Biophys. Acta (BBA) Mol. Cell Biol. Lipids 1791, 474–478 (2009).CAS 

    Google Scholar 
    O’Rourke, E. J., Soukas, A. A., Carr, C. E. & Ruvkun, G. C. elegans major fats are stored in vesicles distinct from lysosome-related organelles. Cell Metab. 10, 430–435 (2009).Article 

    Google Scholar 
    Mak, H. Y. Lipid droplets as fat storage organelles in Caenorhabditis elegans. J. Lipid Res. 53, 28–33 (2012).CAS 
    Article 

    Google Scholar 
    Kroetz, S. M., Srinivasan, J., Yaghoobian, J., Sternberg, P. W. & Hong, R. L. The cGMP signaling pathway affects feeding behavior in the necromenic nematode Pristionchus pacificus. BMC Proc. 6, P27 (2012).Article 

    Google Scholar 
    Edgar, L. G. & McGhee, J. D. Embryonic expression of a gut-specific esterase in Caenorhabditis elegans. Dev. Biol. 114, 109–118 (1986).CAS 
    Article 

    Google Scholar 
    Barr, M. M. & Sternberg, P. W. A polycystic kidney-disease gene homologue required for male mating behaviour in C. elegans. Nature 401, 386 (1999).ADS 
    CAS 

    Google Scholar 
    Bendesky, A., Tsunozaki, M., Rockman, M. V., Kruglyak, L. & Bargmann, C. I. Catecholamine receptor polymorphisms affect decision-making in C. elegans. Nature 472, 313–318 (2011).ADS 
    CAS 
    Article 

    Google Scholar 
    Garrison, J. L. et al. Oxytocin/vasopressin-related peptides have an ancient role in reproductive behavior. Science 338, 540–543 (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    Joo, H.-J. et al. Contribution of the peroxisomal acox gene to the dynamic balance of daumone production in Caenorhabditis elegans. J. Biol. Chem. 285, 29319–29325 (2010).CAS 
    Article 

    Google Scholar 
    Yassin, L. et al. Characterization of the DEG-3/DES-2 receptor: a nicotinic acetylcholine receptor that mutates to cause neuronal degeneration. Mol. Cell. Neurosci. 17, 589–599 (2001).CAS 
    Article 

    Google Scholar 
    Zhang, X., Wang, Y., Perez, D. H., Lipinski, R. A. J. & Butcher, R. A. Acyl-CoA oxidases fine-tune the production of ascaroside pheromones with specific side chain lengths. ACS Chem. Biol. https://doi.org/10.1021/acschembio.7b01021 (2018).Article 

    Google Scholar 
    Borne, F., Kasimatis, K. R. & Phillips, P. C. Quantifying male and female pheromone-based mate choice in Caenorhabditis nematodes using a novel microfluidic technique. PLoS ONE 87, 511 (2017).
    Google Scholar 
    Choe, A. et al. Sex-specific mating pheromones in the nematode Panagrellus redivivus. Proc. Natl. Acad. Sci. 109, 20949–20954 (2012).ADS 
    CAS 
    Article 

    Google Scholar 
    Duggal, C. L. Sex attraction in the free-living nematode panagrellus redivivus. Nematologica 24, 213–221 (1978).Article 

    Google Scholar 
    Andersson, M. Sexual Selection Vol. 72 (Princeton University Press, 1994).Book 

    Google Scholar 
    Bateman, A. J. Intra-sexual selection in Drosophila. Heredity 2, 349–368 (1948).CAS 
    Article 

    Google Scholar 
    Kvarnemo, C. & Simmons, L. W. Polyandry as a mediator of sexual selection before and after mating. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20120042 (2013).Article 

    Google Scholar 
    Parker, G. A. & Birkhead, T. R. Polyandry: the history of a revolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20120335 (2013).Article 

    Google Scholar 
    Rhainds, M. Female mating failures in insects. Entomol. Exp. Appl. 136, 211–226 (2010).Article 

    Google Scholar 
    Hammond, K. A. Adaptation of the maternal intestine during lactation. J. Mammary Gland Biol. Neoplasia 2, 243–252 (1997).CAS 
    Article 

    Google Scholar 
    Speakman, J. R. The physiological costs of reproduction in small mammals. Philos. Trans. R. Soc. B Biol. Sci. 363, 375–398 (2008).Article 

    Google Scholar 
    Reiff, T. et al. Endocrine remodelling of the adult intestine sustains reproduction in Drosophila. Elife 4, e06930 (2015).Article 

    Google Scholar 
    Kaliszewicz, A. Interference of asexual and sexual reproduction in the green hydra. Ecol. Res. 26, 147–152 (2011).Article 

    Google Scholar 
    Oyarzún, P. A., Nuñez, J. J., Toro, J. E. & Gardner, J. P. A. Trioecy in the Marine Mussel Semimytilus algosus (Mollusca, Bivalvia): stable sex ratios across 22 degrees of a latitudinal gradient. Front. Mar. Sci. 7, 348 (2020).Article 

    Google Scholar 
    Armoza-Zvuloni, R., Kramarsky-Winter, E., Loya, Y., Schlesinger, A. & Rosenfeld, H. Trioecy, a unique breeding strategy in the sea anemone aiptasia diaphana and its association with sex steroids. Biol. Reprod. 90, 122 (2014).Article 

    Google Scholar 
    Greene, J. S. et al. Balancing selection shapes density-dependent foraging behaviour. Nature. 539(7628), 254–258. https://doi.org/10.1038/nature19848 (2016).ADS 
    CAS 
    Article 

    Google Scholar 
    Kieninger, M. R. et al. The Nuclear Hormone Receptor NHR-40 Acts Downstream of the Sulfatase EUD-1 as Part of a Developmental Plasticity Switch in Pristionchus.Curr Biol 26(16), 2174–2179. https://doi.org/10.1016/j.cub.2016.06.018 (2016).Therrien, M., Rouleau, G. A., Dion, P. A., Parker, J. A. & Dupuy, D. Deletion of C9ORF72 Results in Motor Neuron Degeneration and Stress Sensitivity in C. elegans. PLoS ONE 8(12), e83450. https://doi.org/10.1371/journal.pone.0083450 (2013).Lee, B. H., Liu, J., Wong, D., Srinivasan, S., Ashrafi, K. & Kim, S. K. Hyperactive Neuroendocrine Secretion Causes Size Feeding and Metabolic Defects of C. elegans Bardet-Biedl Syndrome Mutants. PLoS Biol 9(12), e1001219. https://doi.org/10.1371/journal.pbio.1001219 (2011).CAS 
    Article 

    Google Scholar 
    Li, C. & Kim, K. Family of FLP Peptides in Caenorhabditis elegans and Related Nematodes. Front Endocrinol. https://doi.org/10.3389/fendo.2014.00150 (2014). Buntschuh, I. et al. FLP-1 neuropeptides modulate sensory and motor circuits in the nematode Caenorhabditis elegans. PLoS ONE 13(1), e0189320. https://doi.org/10.1371/journal.pone.0189320 (2018).Topalidou, I. et al. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. PLOS Genet 12(5), e1006074. https://doi.org/10.1371/journal.pgen.1006074 (2016).Maman, M. et al. A Neuronal GPCR is Critical for the Induction of the Heat Shock Response in the Nematode C. elegans. J Neurosci 33(14), 6102–6111. https://doi.org/10.1523/JNEUROSCI.4023-12.2013 (2013). More

  • in

    Local neural-network-weighted models for occurrence and number of down wood in natural forest ecosystem

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Google Scholar  More

  • in

    The coral reef-dwelling Peneroplis spp. shows calcification recovery to ocean acidification conditions

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Google Scholar  More

  • in

    Responses of CO2 emissions and soil microbial community structures to organic amendment in two contrasting soils in Zambia

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Google Scholar  More

  • in

    The role of epiphytes in seagrass productivity under ocean acidification

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Google Scholar  More