More stories

  • in

    Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development

    1.Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, et al. Cryptic species as a window on diversity and conservation. Trends Ecol Evol. 2007;22:148–55.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Tewksbury JJ, Anderson JGT, Bakker JD, Billo TJ, Dunwiddie PW, Groom MJ, et al. Natural history’s place in science and society. Bioscience. 2014;64:300–10.Article 

    Google Scholar 
    3.Leliaert F, Verbruggen H, Vanormelingen P, Steen F, López-Bautista JM, Zuccarello GC, et al. DNA-based species delimitation in algae. Eur J Phycol. 2014;49:179–96.Article 

    Google Scholar 
    4.Potter D, LaJeunesse TC, Saunders GW, Anderson RA. Convergent evolution masks extensive biodiversity among marine coccoid picoplankton. Biodivers Conserv. 1997;6:99–107.Article 

    Google Scholar 
    5.de Vargas C, Norris R, Zaninetti L, Gibb SW, Pawlowski J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc Natl Acad Sci USA. 1999;96:2864–8.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    6.John U, Litaker RW, Montresor M, Murray S, Brosnahan ML, Anderson DM. Formal revision of the alexandrium tamarense species complex (dinophyceae) taxonomy: the introduction of five species with emphasis on molecular-based (rDNA) classification. Protist. 2014;165:779–804.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    7.Hoppenrath M, Reñé A, Satta CT, Yamaguchi A, Leander BS. Morphology and molecular phylogeny of a new marine, sand-dwelling dinoflagellate genus, Pachena (Dinophyceae), with descriptions of three new species. J Phycol. 2020;56:798–817.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Sproles AE, Oakley CA, Krueger T, Grossman AR, Weis VM, Meibom A, et al. Sub-cellular imaging shows reduced photosynthetic carbon and increased nitrogen assimilation by the non-native endosymbiont Durusdinium trenchii in the model cnidarian Aiptasia. Environ Microbiol. 2020;22:3741–53.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    9.Hume BCC, Mejia-Restrepo A, Voolstra CR, Berumen ML. Fine-scale delineation of Symbiodiniaceae genotypes on a previously bleached central Red Sea reef system demonstrates a prevalence of coral host-specific associations. Coral Reefs. 2020;39:583–601.Article 

    Google Scholar 
    10.Gabay Y, Parkinson JE, Wilkinson SP, Weis VM, Davy SK. Inter-partner specificity limits the acquisition of thermotolerant symbionts in a model cnidarian-dinoflagellate symbiosis. ISME J. 2019;13:2489–99.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    11.Tivey TR, Parkinson JE, Weis VM. Host and symbiont cell cycle coordination is mediated by symbiotic state, nutrition, and partner identity in a model cnidarian-dinoflagellate symbiosis. MBio. 2020;11:1–17.Article 

    Google Scholar 
    12.Lawson CA, Possell M, Seymour JR, Raina JB, Suggett DJ. Coral endosymbionts (Symbiodiniaceae) emit species-specific volatilomes that shift when exposed to thermal stress. Sci Rep. 2019;9:1–11.
    Google Scholar 
    13.Reich HG, Rodriguez IB, LaJeunesse TC, Ho TY. Endosymbiotic dinoflagellates pump iron: differences in iron and other trace metal needs among the Symbiodiniaceae. Coral Reefs. 2020;39:915–27.Article 

    Google Scholar 
    14.de Queiroz A, Gatesy J. The supermatrix approach to systematics. Trends Ecol Evol. 2007;22:34–41.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.de Queiroz K. Species concepts and species delimitation. Syst Biol. 2007;56:879–86.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    16.Schönrogge K, Barr B, Wardlaw JC, Napper E, Gardner MG, Breen J, et al. When rare species become endangered: Cryptic speciation in myrmecophilous hoverflies. Biol J Linn Soc. 2002;75:291–300.Article 

    Google Scholar 
    17.Pettay DT, Wham DC, Pinzón JH, LaJeunesse TC. Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral. Mol Ecol. 2011;20:5197–212.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    18.Baums IB, Devlin-Durante MK, LaJeunesse TC. New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies. Mol Ecol. 2014;23:4203–15.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    19.Pinzón JH, LaJeunesse TC. Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology. Mol Ecol. 2011;20:311–25.PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    20.Sampayo EM, Dove S, LaJeunesse TC. Cohesive molecular genetic data delineate species diversity in the dinoflagellate genus Symbiodinium. Mol Ecol. 2009;18:500–19.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Lien AY, Fukami H, Yamashita Y, Lien Y, Fukami H, Yamashita Y. Symbiodinium Clade C dominates zooxanthellate corals (Scleractinia) in the temperate region of Japan. Zool Sci. 2012;29:173–80.Article 

    Google Scholar 
    22.LaJeunesse TC. ‘Species’ radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition. Mol Biol Evol. 2005;22:570–81.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    23.Wham DC, Carmichael M, LaJeunesse TC. Microsatellite loci for Symbiodinium goreaui and other Clade C Symbiodinium. Conserv Genet Resour. 2014;6:127–9.Article 

    Google Scholar 
    24.LaJeunesse TC, Pettay DT, Sampayo EM, Phongsuwan N, Borwn B, Obura DO, et al. Long standing environmental conditions, geographic isolation and host-symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus Symbiodinium. J Biogeogr. 2010;11:674–5.
    Google Scholar 
    25.Thornhill DJ, Lewis AM, Wham DC, LaJeunesse TC. Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts. Evolution. 2014;68:352–67.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.LaJeunesse TC, Bhagooli R, Hidaka M, DeVantier L, Done T, Schmidt GW, et al. Closely related Symbiodinium spp. differ in relative dominance in coral reef host communities across environmental, latitudinal and biogeographic gradients. Mar Ecol Prog Ser. 2004;284:147–61.Article 

    Google Scholar 
    27.Fitt WK, Gates RD, Hoegh-Guldberg O, Bythell JC, Jatkar A, Grottoli AG, et al. Response of two species of Indo-Pacific corals, Porites cylindrica and Stylophora pistillata, to short-term thermal stress: The host does matter in determining the tolerance of corals to bleaching. J Exp Mar Bio Ecol. 2009;373:102–10.Article 

    Google Scholar 
    28.Hume B, D’Angelo C, Burt J, Baker AC, Riegl B, Wiedenmann J. Corals from the Persian/Arabian Gulf as models for thermotolerant reef-builders: Prevalence of clade C3 Symbiodinium, host fluorescence and ex situ temperature tolerance. Mar Pollut Bull. 2013;72:313–22.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    29.Hoadley KD, Lewis AM, Wham DC, Pettay DT, Grasso C, Smith R, et al. Host – symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress. Sci Rep. 2019:9:1–15.30.Sampayo EM, Ridgway T, Bongaerts P, Hoegh-Guldberg O. Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type. Proc Natl Acad Sci USA. 2008;105:10444–9.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Lee SY, Jeong HJ, LaJeunesse TC. Cladocopium infistulum sp. nov. (Dinophyceae), a thermally tolerant dinoflagellate symbiotic with giant clams from the western Pacific Ocean. Phycologia. 2020;59:515–26.Article 

    Google Scholar 
    32.LaJeunesse TC, Wham DC, Pettay DT, Parkinson JE, Keshavmurthy S, Chen CA. Ecologically differentiated stress-tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species. Phycologia. 2014;53:305–19.Article 

    Google Scholar 
    33.Lewis AM, Chan AN, LaJeunesse TC. New species of closely related endosymbiotic dinoflagellates in the greater caribbean have niches corresponding to host coral phylogeny. J Eukaryot Microbiol. 2019;66:469–82.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    34.Veron JEN. Corals of the world. In: Stafford-Smith M, editor. Australian Institute of Marine Science; Townsville, Australia, 2000.35.Richmond RH. Energetics, competency, and long-distance dispersal of planula larvae of the coral Pocillopora damicornis. Mar Biol. 1987;93:527–33.Article 

    Google Scholar 
    36.Harrison PL, Wallace CC. A review of reproduction, larval dispersal and settlement of scleractinian corals. In: Dubinsky Z, editor. Ecosystems of the World 25 Coral Reefs; New York, NY, USA, 1990. p. 133–9637.Glynn PW. Coral reef bleaching: ecological perspectives. Coral Reefs. 1993;12:1–17.Article 

    Google Scholar 
    38.LaJeunesse TC, Smith R, Walther M, Pinzon J, Pettay DT, McGinley M, et al. Host-symbiont recombination versus natural selection in the response of coral-dinoflagellate symbioses to environmental disturbance. Proc R Soc B Biol Sci. 2010;277:2925–34.Article 

    Google Scholar 
    39.Stella JS, Pratchett MS, Hutchings PA, Jones GP. Coral-associated invertebrates: diversity, ecological importance and vulnerability to disturbance. Oceanogr Mar Biol Annu Rev. 2011;49:43–104.
    Google Scholar 
    40.Austin AD, Austin SA, Sale PF. Community structure of the fauna associated with the coral Pocillopora damicornis (L.) on the Great Barrier Reef. Mar Freshw Res. 1980;31:163–74.Article 

    Google Scholar 
    41.Glynn PW, Maté JL, Baker AC. Coral bleaching and mortality in Panama and Ecuador during the 1997 – 1998 El Niño – southern oscillation event: spatial/temporal patterns and comparisons with the 1982 – 1983 event. Bull Mar Sci. 2001;69:79–109.
    Google Scholar 
    42.Johnston EC, Forsman ZH, Flot J, Schmidt-Roach S, Pinzón H, Knapp ISS, et al. A genomic glance through the fog of plasticity and diversification in Pocillopora. Sci Rep. 2017;7:5991.43.Iglesias-Prieto R, Beltrán VH, LaJeunesse TC, Reyes-Bonilla H, Thomé PE. Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific. Proc R Soc B Biol Sci. 2004;271:1757–63.CAS 
    Article 

    Google Scholar 
    44.Bahr KD, Tran T, Jury CP, Toonen RJ. Abundance, size, and survival of recruits of the reef coral Pocillopora acuta under ocean warming and acidification. PLoS ONE. 2020;15:1–13.Article 
    CAS 

    Google Scholar 
    45.Flot JF, Tillier S. The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: The putative D-loop and a novel ORF of unknown function. Gene. 2007;401:80–7.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    46.LaJeunesse TC, Loh WKW, Van Woesik R, Schmidt GW, Fitt WK. Low symbiont diversity in southern Great Barrier Reef corals, relative to those of the Caribbean. Limnol Oceanogr. 2003;48:2046–54.Article 

    Google Scholar 
    47.Tonk L, Sampayo EM, LaJeunesse TC, Schrameyer V, Hoegh-Guldberg O. Symbiodinium (Dinophyceae) diversity in reef-invertebrates along an offshore to inshore reef gradient near Lizard Island, Great Barrier Reef. J Phycol. 2014;50:552–63.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Magalon H, Baudry E, Husté A, Adjeroud M, Veuille M. High genetic diversity of the symbiotic dinoflagellates in the coral Pocillopora meandrina from the South Pacific. Mar Biol. 2006;148:913–22.Article 

    Google Scholar 
    49.Pinzón JH, Sampayo E, Cox E, Chauka LJ, Chen CA, Voolstra CR, et al. Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia). J Biogeogr. 2013;40:1595–608.Article 

    Google Scholar 
    50.Silverstein RN, Correa AMS, LaJeunesse TC, Baker AC. Novel algal symbiont (Symbiodinium spp.) diversity in reef corals of Western Australia. Mar Ecol Prog Ser. 2011;422:63–75.Article 

    Google Scholar 
    51.Wham DC, LaJeunesse TC. Symbiodinium population genetics: testing for species boundaries and analysing samples with mixed genotypes. Mol Ecol. 2016;25:2699–712.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    52.Baums IB, Devlin-durante M, Laing BAA, Feingold J, Smith T, Bruckner A, et al. Marginal coral populations: the densest known aggregation of Pocillopora in the Galápagos Archipelago is of asexual origin. Front Mar Sci. 2014;1:1–11.Article 

    Google Scholar 
    53.McGinley MP, Aschaffenburg MD, Pettay DT, Smith RT, LaJeunesse TC, Warner ME. Symbiodinium spp. in colonies of eastern Pacific Pocillopora spp. are highly stable despite the prevalence of low-abundance background populations. Mar Ecol Prog Ser. 2012;462:1–7.Article 

    Google Scholar 
    54.Camp EF, Nitschke MR, Rodolfo-metalpa R, Gardner SG, Smith DJ, Zampighi M, et al. Reef-building corals thrive within hot-acidic and deoxygenated waters. Sci Rep. 2017;7:2434.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    55.LaJeunesse TC, Trench RK. Biogeography of two species of Symbiodinium (Freudenthal) inhabiting the intertidal sea anemone Anthopleura elegantissima (Brandt). Biol Bull. 2000;199:126–34.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    56.LaJeunesse TC. Investigating the biodiversity, ecology, and phylogeny of endosymbiotic dinoflagellates in the genus Symbiodinium using the its region: In search of a “species” level marker. J Phycol. 2001;880:866–80.Article 

    Google Scholar 
    57.Moore RB, Ferguson KM, Loh WKW, Hoegh-Guldberg O, Carter DA. Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium. Int J Syst Evol Microbiol. 2003;53:1725–34.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    58.LaJeunesse TC, Thornhill DJ. Improved resolution of reef-coral endosymbiont (Symbiodinium) species diversity, ecology, and evolution through psbA non-coding region genotyping. PLoS ONE. 2011;6:e29013.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    59.Swofford D. PAUP 4.0: Phylogenetic analysis using parsimony. Washington DC, USA: Smithson Inst.; 2014.60.Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, Höhna S, et al. Mrbayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539–42.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    61.Nylander JAA. MrModeltest v2. Uppsala, Sweden: Progr Distrib by author Evol Biol Centre, Uppsala Univ.; 2004.62.Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, et al. BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Comput Biol. 2014;10:1–6.Article 
    CAS 

    Google Scholar 
    63.Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018;67:901–4.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    64.Jackson JBC, O’Dea A. Timing of the oceanographic and biological isolation of the Caribbean sea from the tropical eastern pacific ocean. Bull Mar Sci. 2013;89:779–800.
    Google Scholar 
    65.Haug G, Tiedemann R. Effect of the formation of the Isthmus of Panama on Atlantic Ocean thermohaline circulation. Nature. 1998;394:1699–701.
    Google Scholar 
    66.O’Dea A, Lessios HA, Coates AG, Eytan RI, Restrepo-Moreno SA, Cione AL, et al. Formation of the Isthmus of Panama. Sci Adv. 2016;2:1–12.Article 

    Google Scholar 
    67.Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007;7:214.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    68.Bouckaert R, Heled J DensiTree 2: seeing trees through the forest. 2014. https://www.biorxiv.org/content/10.1101/012401v1.69.Bay LK, Howells EJ, van Oppen MJH. Isolation, characterisation and cross amplification of thirteen microsatellite loci for coral endo-symbiotic dinoflagellates (Symbiodinium clade C). Conserv Genet Resour. 2009;1:199–203.Article 

    Google Scholar 
    70.Peakall R, Smouse PE. GenALEx 6.5: genetic analysis in excel. population genetic software for teaching and research-an update. Bioinformatics. 2012;28:2537–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    71.Davies SW, Moreland KN, Wham DC, Kanke MR, Matz MV. Cladocopium community divergence in two Acropora coral hosts across multiple spatial scales. Mol Ecol. 2020;29:4559–72.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    72.Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012;4:359–61.Article 

    Google Scholar 
    73.Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, et al. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Commun Biol. 2018;1:95.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    74.Raymond M, Rousset F. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity. 1995:248–9.75.Rousset F. GENEPOP’007: A complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour. 2008;86:103–6.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    76.Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–59.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    77.van der Maaten L, Hinton G. Visualizing data using t-SNE. J Mach Learn Res. 2008;9:2579–605.
    Google Scholar 
    78.LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr Biol. 2018;28:2570–2580.e6.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    79.LaJeunesse TC, Bonilla HR, Warner ME, Wills M, Schmidt GW, Fitt WK. Specificity and stability in high latitude eastern Pacific coral-algal symbioses. Limnol Oceanogr. 2008;53:719–27.Article 

    Google Scholar 
    80.Ramsby BD, Hill MS, Thornhill DJ, Steenhuizen SF, Achlatis M, Lewis AM, et al. Sibling species of mutualistic Symbiodinium Clade G from bioeroding sponges in the western Pacific and western Atlantic oceans. J Phycol. 2017;53:951–60.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    81.Prada C, McIlroy SE, Beltrán DM, Valint DJ, Ford SA, Hellberg ME, et al. Cryptic diversity hides host and habitat specialization in a gorgonian-algal symbiosis. Mol Ecol. 2014;23:3330–40.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    82.Wham DC, Ning G, LaJeunesse TC. Symbiodinium glynnii sp. nov., a species of stress-tolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean. Phycologia. 2017;56:396–409.CAS 
    Article 

    Google Scholar 
    83.Mayr E. The growth of biological thought: Diversity, evolution, and inheritance. Cambridge, MA, USA: Belknap Press of Harvard University Press; 1982.84.Arnaud-Haond S, Duarte CM, Alberto F, Serrão EA. Standardizing methods to address clonality in population studies. Mol Ecol. 2007;16:5115–39.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    85.Jeong HJ, Lee SY, Kang NS, Yoo YD, Lim AS, Lee MJ, et al. Genetics and morphology characterize the dinoflagellate Symbiodinium voratum, n. sp., (dinophyceae) as the sole representative of Symbiodinium Clade E. J Eukaryot Microbiol. 2014;61:75–94.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    86.Blank RJ, Trench RK. Speciation and symbiotic dinoflagellates. Science. 1985;229:656–8.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    87.Suggett DJ, Moore CM, Hickman AE, Geider RJ. Interpretation of fast repetition rate (FRR) fluorescence: Signatures of phytoplankton community structure versus physiological state. Mar Ecol Prog Ser. 2009;376:1–19.Article 

    Google Scholar 
    88.Suggett DJ, Goyen S, Evenhuis C, Szabó M, Pettay DT, Warner ME, et al. Functional diversity of photobiological traits within the genus Symbiodinium appears to be governed by the interaction of cell size with cladal designation. New Phytol. 2015;208:370–81.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    89.Geider R, Piatt T, Raven J. Size dependence of growth and photosynthesis in diatoms: a synthesis. Mar Ecol Prog Ser. 1986;30:93–104.CAS 
    Article 

    Google Scholar 
    90.Finkel ZV. Light absorption and size scaling of light-limited metabolism in marine diatoms. Limnol Oceanogr. 2001;46:86–94.CAS 
    Article 

    Google Scholar 
    91.Irwin AJ, Finkel ZV, Schofield OME, Falkowski PG. Scaling-up from nutrient physiology to the size-structure of phytoplankton communities. J Plankton Res. 2006;28:459–71.Article 

    Google Scholar 
    92.Wu Y, Campbell DA, Irwin AJ, Suggett DJ, Finkel ZV. Ocean acidification enhances the growth rate of larger diatoms. Limnol Oceanogr. 2014;59:1027–34.CAS 
    Article 

    Google Scholar 
    93.Rowan R. Coral bleaching: thermal adaptation in reef coral symbionts. Nature. 2004;430:742.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    94.Berkelmans R, Van, Oppen MJH. The role of zooxanthellae in the thermal tolerance of corals: a “nugget of hope” for coral reefs in an era of climate change. Proc R Soc B Biol Sci. 2006;273:2305–12.Article 

    Google Scholar 
    95.Abrego D, Ulstrup KE, Willis BL, Van Oppen MJH. Species-specific interactions between algal endosymbionts and coral hosts define their bleaching response to heat and light stress. Proc R Soc B Biol Sci. 2008;275:2273–82.CAS 
    Article 

    Google Scholar 
    96.Schluter D. Evidence for ecological speciation and its alternative. Science. 2009;323:737–41.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    97.Hendry AP, Nosil P, Rieseberg LH. The speed of ecological speciation. Funct Ecol. 2007;21:455–64.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    98.Glynn PW, Gassman NJ, Eakin CM, Cortes J, Smith DB, Guzman HM. Reef coral reproduction in the eastern Pacific: Costa Rica, Panama, and Galapagos Islands (Ecuador). Mar Biol. 1991;109:355–68.Article 

    Google Scholar 
    99.Hirose M, Kinzie RA, Hidaka M. Early development of zooxanthella-containing eggs of the corals Pocillopora verrucosa and P. eydouxi with special reference to the distribution of zooxanthellae. Biol Bull. 2000;199:68–75.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    100.Chavez-Romo H. Sexual reproduction of the coral Pocillopora damicornis in the southern Gulf of California. Mex Cienc Mar. 2007;33:495–501.Article 

    Google Scholar 
    101.Russell SL, Chappell L, Sullivan W. A symbiont’s guide to the germline. 1st ed. In: Current topics in developmental biology. Vol 135. Amsterdam, The Netherlands: Elsevier Inc.; 2019. p. 351.102.LaJeunesse TC, Thornhill DJ, Cox EF, Stanton FG, Fitt WK, Schmidt GW. High diversity and host specificity observed among symbiotic dinoflagellates in reef coral communities from Hawaii. Coral Reefs. 2004;23:596–603.
    Google Scholar 
    103.Rowan ROB, Powers DA. A molecular genetic classification of zooxanthellae and the evolution of animal-algal symbioses. Science. 1991;251:1348–51.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    104.Zachos JC, Dickens GR, Zeebe RE. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature. 2008;451:279–83.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    105.LaJeunesse TC, Parkinson JE, Reimer JD. A genetics-based description of Symbiodinium minutum sp. nov. and S. psygmophilum sp. nov. (dinophyceae), two dinoflagellates symbiotic with cnidaria. J Phycol. 2012;48:1380–91.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    106.Pettay DT, LaJeunesse TC. Long-range dispersal and high-latitude environments influence the population structure of a “stress-tolerant” dinoflagellate endosymbiont. PLoS ONE. 2013;8:1–12.Article 
    CAS 

    Google Scholar 
    107.Wicks LC, Sampayo E, Gardner JPA, Davy SK. Local endemicity and high diversity characterise high-latitude coral- Symbiodinium partnerships. Coral Reefs. 2010;29:989–1003.Article 

    Google Scholar 
    108.Sampayo EM, Franceschinis L, Hoegh-Guldberg O, Dove S. Niche partitioning of closely related symbiotic dinoflagellates. Mol Ecol. 2007;16:3721–33.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    109.Thompson JN. The geographic mosaic of coevolution. Chicago, IL, USA: University of Chicago Press; 2005.110.Sampayo EM, Ridgway T, Franceschinis L, Roff G, Hoegh-Guldberg O, Dove S. Coral symbioses under prolonged environmental change: living near tolerance range limits. Sci Rep. 2016;6:36271.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    111.Janis CM. Tertiary mammal evolution in the context of changing climates, vegetation, and tectonic events. Annu Rev Ecol Syst. 1993;24:467–500.Article 

    Google Scholar 
    112.Willeit M, Ganopolski A, Calov R, Brovkin V. Mid-Pleistocene transition in glacial cycles explained by declining CO2 and regolith removal. Sci Adv. 2019;5:eaav7337.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    113.Palumbi SR, Barshis DJ, Traylor-Knowles N, Bay RA. Mechanisms of reef coral resistance to future climate change. Science. 2014;344:895–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    114.Pandolfi JM, Jackson JBC, Geister J. Geologically sudden extinction of two widespread late Pleistocene Caribbean reef corals. In: Evolutionary patterns: growth, form and tempo in the fossil record. Chicago, IL, USA: University of Chicago Press; 2001. p. 120–58.115.Toth LT, Aronson RB, Cobb KM, Cheng H, Edwards RL, Grothe PR, et al. Climatic and biotic thresholds of coral-reef shutdown. Nat Clim Chang. 2015;5:369–74.Article 

    Google Scholar 
    116.Baums IB, Baker AC, Davies SW, Grottoli AG, Kenkel CD, Kitchen SA, et al. Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic. Ecol Appl. 2019;29:1–23.Article 

    Google Scholar  More

  • in

    Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils

    1.Brilli M, Mengoni A, Fondi M, Bazzicalupo M, Liò P, Fani R. Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. BMC Bioinformatics. 2008;9:551.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    2.Dziewit L, Pyzik A, Szuplewska M, Matlakowska R, Mielnicki S, Wibberg D, et al. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. Front Microbiol. 2015;6:152.PubMed 
    PubMed Central 

    Google Scholar 
    3.Matyar F, Kaya A, Dinçer S. Antibacterial agents and heavy metal resistance in Gram-negative bacteria isolated from seawater, shrimp and sediment in Iskenderun Bay, Turkey. Sci Total Environ. 2008;407:279–85.CAS 
    PubMed 
    Article 

    Google Scholar 
    4.Dagan T, Artzy-Randrup Y, Martin W. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA. 2008;105:10039–44.CAS 
    PubMed 
    Article 

    Google Scholar 
    5.Heuer H, Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev. 2012;36:1083–104.CAS 
    PubMed 
    Article 

    Google Scholar 
    6.Morozova D, Möhlmann D, Wagner D. Survival of methanogenic archaea from Siberian permafrost under simulated Martian thermal conditions. Orig Life Evol Biosph. 2007;37:189–200.CAS 
    PubMed 
    Article 

    Google Scholar 
    7.Schimel J, Balser TC, Wallenstein M. Microbial stress-response physiology and its implications for ecosystem functioning. Ecology. 2007;88:1386–94.Article 

    Google Scholar 
    8.Margesin R, Miteva V. Diversity and ecology of psychrophilic microorganisms. Res Microbiol. 2011;162:346–61.PubMed 
    Article 

    Google Scholar 
    9.Dutta H, Dutta A. The microbial aspect of climate change. Energy, Ecol Environ. 2016;1:209–32.Article 

    Google Scholar 
    10.Leplae R, Lima-Mendez G, Toussaint A. A first global analysis of plasmid encoded proteins in the ACLAME database. FEMS Microbiol Rev. 2006;30:980–94.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.Couturier M, Bex F, Bergquist PL, Maas WK. Identification and classification of bacterial plasmids. Microbiol Rev. 1988;52:375–95.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    12.Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods. 2005;63:219–28.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    13.Johnson TJ, Wannemuehler YM, Johnson SJ, Logue CM, White DG, Doetkott C, et al. Plasmid replicon typing of commensal and pathogenic Escherichia coli isolates. Appl Environ Microbiol. 2007;73:1976–83.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    14.Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997;278:631–7.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Smalla K, Jechalke S, Top EM. Plasmid detection, characterization, and ecology. Microbiol Spectr. 2015;3:PLAS-0038-2014.16.Top EM, Holben WE, Forney LJ. Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol. 1995;61:1691–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    17.Sayler GS, Hooper SW, Layton AC, King JMH. Catabolic plasmids of environmental and ecological significance. Microb Ecol. 1990;19:1–20.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    18.Elsas JD, Bailey MJ. The ecology of transfer of mobile genetic elements. FEMS Microbiol Ecol. 2006;42:187–97.Article 

    Google Scholar 
    19.Barrón MD, La C, Merlin C, Guilloteau H, Montargès-Pelletier E, Bellanger X. Suspended materials in river waters differentially enrich class 1 integron- and IncP-1 plasmid-carrying bacteria in sediments. Front Microbiol. 2018;9:1443.Article 

    Google Scholar 
    20.Dziewit L, Bartosik D. Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. Front Microbiol. 2014;5:596.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    21.McCann CM, Christgen B, Roberts JA, Su JQ, Arnold KE, Gray ND, et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ Int. 2019;125:497–504.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Nesme J, Simonet P. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ Microbiol. 2015;17:913–30.PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    23.Sjölund M, Bonnedahl J, Hernandez J, Bengtsson S, Cederbrant G, Pinhassi J, et al. Dissemination of multidrug-resistant bacteria into the Arctic. Emerg Infect Dis. 2008;14:70–72.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    24.Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, et al. Functional characterization of bacteria isolated from ancient Arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS One. 2015;10:e0069533.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    25.Hernández J, González-Acuña D. Anthropogenic antibiotic resistance genes mobilization to the polar regions. Infect Ecol Epidemiol. 2016;6:32112.PubMed 
    PubMed Central 

    Google Scholar 
    26.Tan L, Li L, Ashbolt N, Wang X, Cui Y, Zhu X, et al. Arctic antibiotic resistance gene contamination, a result of anthropogenic activities and natural origin. Sci Total Environ. 2018;621:1176–84.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    27.Wang F, Stedtfeld RD, Kim OS, Chai B, Yang L, Stedtfeld TM, et al. Influence of soil characteristics and proximity to antarctic research stations on abundance of antibiotic resistance genes in soils. Environ Sci Technol. 2016;50:12621–9.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    28.Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, et al. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep. 2018;8:1291.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    29.Liebner S, Harder J, Wagner D. Bacterial diversity and community structure in polygonal tundra soils from Samoylov Island, Lena Delta, Siberia. Int Microbiol. 2008;11:195–202.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Taş N, Prestat E, Wang S, Wu Y, Ulrich C, Kneafsey T, et al. Landscape topography structures the soil microbiome in Arctic polygonal tundra. Nat Commun. 2018;9:777.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    31.Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol. 1985;49:1–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    32.Muyzer G, De Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59:695–700.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Mizrahi-Man O, Davenport ER, Gilad Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One. 2013;8:e53608.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10.Article 

    Google Scholar 
    35.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 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    36.Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    37.Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:2584.Article 

    Google Scholar 
    38.Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    39.Hammer DAT, Ryan PD, Hammer Ø, Harper DAT. Past: paleontological statistics software package for education and data analysis. Palaeontol Electron. 2001;4:1–9.
    Google Scholar 
    40.Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    41.Krawczyk PS, Lipinski L, Dziembowski A. PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures. Nucleic Acids Res. 2018;46:e35.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    42.Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    43.Kahlke T, Ralph PJ. BASTA—taxonomic classification of sequences and sequence bins using last common ancestor estimations. Methods Ecol Evol. 2019;10:100–3.Article 

    Google Scholar 
    44.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    45.Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    46.Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. Third Int AAAI Conf Weblogs Soc Media. San Jose, California, USA. 2009.47.Jacomy M, Venturini T, Heymann S, Bastian M. ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software. PLoS One. 2014;9:e98679.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    48.McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013;57:3348–57.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    49.Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res. 2014;42:D737–43.CAS 
    PubMed 
    Article 

    Google Scholar 
    50.Caswell TA, Droettboom M, Hunter J, Lee A, Firing E, Stansby D, et al. matplotlib/matplotlib: REL: v3.1.1. 2019.51.Pham VHT, Kim J. Improvement for isolation of soil bacteria by using common culture media. J Pure Appl Microbiol. 2016;10:49–60.
    Google Scholar 
    52.Romaniuk K, Ciok A, Decewicz P, Uhrynowski W, Budzik K, Nieckarz M, et al. Insight into heavy metal resistome of soil psychrotolerant bacteria originating from King George Island (Antarctica). Polar Biol. 2018;41:1319–33.Article 

    Google Scholar 
    53.Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    54.Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, et al. Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol. 2005;71:2162–9.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    55.Stewart EJ. Growing unculturable bacteria. J Bacteriol. 2012;194:4151–60.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Ganzert L, Jurgens G, Munster U, Wagner D. Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints. FEMS Microbiol Ecol. 2007;59:476–88.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    57.Bajerski F, Ganzert L, Mangelsdorf K, Padur L, Lipski A, Wagner D. Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield. Int J Syst Evol Microbiol. 2013;63:2666–71.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    58.Filippidou S, Wunderlin T, Junier T, Jeanneret N, Dorador C, Molina V, et al. A combination of extreme environmental conditions favor the prevalence of endospore-forming Firmicutes. Front Microbiol. 2016;7:1707.PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    59.Kuramae EE, Yergeau E, Wong LC, Pijl AS, Veen JA, Kowalchuk GA. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol. 2012;79:12–24.CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    60.Filippidou S, Junier T, Wunderlin T, Lo CC, Li PE, Chain PS, et al. Under-detection of endospore-forming Firmicutes in metagenomic data. Comput Struct Biotechnol J. 2015;13:299–306.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    61.Dziewit L, Cegielski A, Romaniuk K, Uhrynowski W, Szych A, Niesiobedzki P, et al. Plasmid diversity in arctic strains of Psychrobacter spp. Extremophiles. 2013;17:433–44.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    62.Mindlin S, Petrenko A, Kurakov A, Beletsky A, Mardanov A, Petrova M. Resistance of permafrost and modern Acinetobacter lwoffiistrains to heavy metals and arsenic revealed by genome analysis. Biomed Res Int. 2016;2016:3970831.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    63.Moghadam MS, Albersmeier A, Winkler A, Cimmino L, Rise K, Hohmann-Marriott MF, et al. Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity. BMC Genomics. 2016;17:117.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    64.Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics. 2015;16:964.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    65.Carroll LM, Gaballa A, Guldimann C, Sullivan G, Henderson LO, Wiedmann M. Identification of novel mobilized colistin resistance gene mcr-9 in a multidrug-resistant, colistin-susceptible Salmonella enterica serotype Typhimurium isolate. MBio. 2019;10:e00853–19.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Bleich A, Fox JG. The mammalian microbiome and its importance in laboratory animal research. ILAR J. 2015;56:153–8.CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Grond K, Sandercock BK, Jumpponen A, Zeglin LH. The avian gut microbiota: community, physiology and function in wild birds. J Avian Biol. 2018;49:e01788.Article 

    Google Scholar 
    68.Anganova EV, Savchenkov MF, Stepanenko LA, Savilov ED. Microbiological monitoring of opportunistic Enterobacteriaceae of the Lena river. Gig Sanit. 2016;95:1124–8.69.Tignat-Perrier R, Dommergue A, Thollot A, Keuschnig C, Magand O, Vogel TM, et al. Global airborne microbial communities controlled by surrounding landscapes and wind conditions. Sci Rep. 2019;9:14441.PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    70.Mu C, Zhang F, Chen X, Ge S, Mu M, Jia L, et al. Carbon and mercury export from the Arctic rivers and response to permafrost degradation. Water Res. 2019;161:54–60.CAS 
    PubMed 
    Article 

    Google Scholar 
    71.Petrova M, Kurakov A, Shcherbatova N, Mindlin S. Genetic structure and biological properties of the first ancient multiresistance plasmid pKLH80 isolated from a permafrost bacterium. Microbiology. 2014;160:2253–63.CAS 
    PubMed 
    Article 

    Google Scholar 
    72.Afouda P, Dubourg G, Levasseur A, Fournier P-E, Delerce J, Mediannikov O, et al. Culturing ancient bacteria carrying resistance genes from permafrost and comparative genomics with modern isolates. Microorganisms. 2020;8:1522.CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar  More

  • in

    Overwintering fires in boreal forests

    1.Sedano, F. & Randerson, J. T. Multi-scale influence of vapor pressure deficit on fire ignition and spread in boreal forest ecosystems. Biogeosciences 11, 3739–3755 (2014).ADS 

    Google Scholar 
    2.Veraverbeke, S. et al. Lightning as a major driver of recent large fire years in North American boreal forests. Nat. Clim. Chang. 7, 529–534 (2017).ADS 

    Google Scholar 
    3.Calef, M. P., McGuire, A. D. & Chapin, F. S. Human influences on wildfire in Alaska from 1988 through 2005: an analysis of the spatial patterns of human impacts. Earth Interact. 12, 1–17 (2008).ADS 

    Google Scholar 
    4.McCarty, J. L., Smith, T. E. L. & Turetsky, M. R. Arctic fires re-emerging. Nat. Geosci. 13, 658–660 (2020).ADS 
    CAS 

    Google Scholar 
    5.Irannezhad, M., Liu, J., Ahmadi, B. & Chen, D. The dangers of Arctic zombie wildfires. Science 369, 1171 (2020).ADS 

    Google Scholar 
    6.Rein, G. in Fire Phenomena and the Earth System: An Interdisciplinary Guide to Fire Science (ed. Belcher, C. M.) 15–34 (Wiley-Blackwell, 2013).7.Post, E. et al. The polar regions in a 2 °C warmer world. Sci. Adv. 5, eaaw9883 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    8.Overland, J. E., Wang, M., Walsh, J. E. & Stroeve, J. C. Future Arctic climate changes: adaptation and mitigation time scales. Earth’s Future 2, 68–74 (2014).ADS 

    Google Scholar 
    9.Tarnocai, C. et al. Soil organic carbon pools in the northern circumpolar permafrost region. Glob. Biogeochem. Cycles 23, GB2023 (2009).ADS 

    Google Scholar 
    10.Walker, X. J. et al. Increasing wildfires threaten historic carbon sink of boreal forest soils. Nature 572, 520–523 (2019).ADS 
    CAS 

    Google Scholar 
    11.Turetsky, M. R. et al. Recent acceleration of biomass burning and carbon losses in Alaskan forests and peatlands. Nat. Geosci. 4, 27–31 (2011).ADS 
    CAS 

    Google Scholar 
    12.Walker, X. J. et al. Soil organic layer combustion in boreal black spruce and jack pine stands of the Northwest Territories, Canada. Int. J. Wildl. Fire 27, 125–134 (2018).
    Google Scholar 
    13.Turetsky, M. R. et al. Global vulnerability of peatlands to fire and carbon loss. Nat. Geosci. 8, 11–14 (2015).ADS 
    CAS 

    Google Scholar 
    14.Flannigan, M. D. et al. Fuel moisture sensitivity to temperature and precipitation: climate change implications. Clim. Change 134, 59–71 (2016).ADS 
    CAS 

    Google Scholar 
    15.Coops, N. C., Hermosilla, T., Wulder, M. A., White, J. C. & Bolton, D. K. A thirty year, fine-scale, characterization of area burned in Canadian forests shows evidence of regionally increasing trends in the last decade. PLoS One 13, e0197218 (2018).PubMed 
    PubMed Central 

    Google Scholar 
    16.USDA Forest Service, USFS-USDI and NASF. Large Fire Cost Reduction Action Plan https://www.fs.usda.gov/sites/default/files/media_wysiwyg/5100_largefirecostreductionaction_mar_03.pdf (2003).17.Podur, J. & Wotton, M. Will climate change overwhelm fire management capacity? Ecol. Modell. 221, 1301–1309 (2010).
    Google Scholar 
    18.Tymstra, C., Stocks, B. J., Cai, X. & Flannigan, M. D. Wildfire management in Canada: review, challenges and opportunities. Prog. Disaster Sci. 5, 100045 (2020); erratum 8, 100045 (2020).
    Google Scholar 
    19.Stocks, B. J. et al. Large forest fires in Canada, 1959–1997. J. Geophys. Res. 107, https://doi.org/10.1029/2001JD000484 (2002).20.Wiggins, E. B. et al. Evidence for a larger contribution of smoldering combustion to boreal forest fire emissions from tower observations in Alaska. Atmos. Chem. Phys. https://doi.org/10.5194/acp-2019-1067 (in the press).21.Rein, G., Garcia, J., Simeoni, A., Tihay, V. & Ferrat, L. Smouldering natural fires: comparison of burning dynamics in boreal peat and Mediterranean humus. WIT Trans. Ecol. Environ. 119, 183–192 (2008).
    Google Scholar 
    22.Baber, C. & McMaster, R. 2019 Alaska Statewide Annual Operating Plan. https://fire.ak.blm.gov/administration/asma.php (Alaska Statewide Master Agreement, 2019).23.Alaska Interagency Coordination Center. 2010 Alaska fire statistics. https://www.frames.gov/catalog/12055 (Wildland Fire Summary and Statistics Annual Report, 2010).24.Alaska Division of Forestry. State Forestry monitoring hot spots that overwintered from Deshka Landing Fire. https://akfireinfo.com/2020/04/10/state-forestry-monitoring-hot-spots-that-overwintered-from-deshka-landing-fire/ (2020).25.Giglio, L., Schroeder, W. & Justice, C. O. The collection 6 MODIS active fire detection algorithm and fire products. Remote Sens. Environ. 178, 31–41 (2016).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    26.Kasischke, E. S., Rupp, T. S. & Verbyla, D. L. in Alaska’s Changing Boreal Forest (eds Chapin, F. S. III, Oswood, M. et al.) 285–301 (Oxford Univ. Press, 2006).27.Westerling, A. L., Hidalgo, H. G., Cayan, D. R. & Swetnam, T. W. Warming and earlier spring increase western U.S. forest wildfire activity. Science 313, 940–943 (2006).ADS 
    CAS 

    Google Scholar 
    28.Painter, T. H. et al. Retrieval of subpixel snow covered area, grain size, and albedo from MODIS. Remote Sens. Environ. 113, 868–879 (2009).ADS 

    Google Scholar 
    29.Scholten, R. C., Jandt, R. R., Miller, E. A., Rogers, B. M. & Veraverbeke, S. ABoVE: Ignitions, burned area and emissions of fires in AK, YT, and NWT, 2001–2018. https://doi.org/10.3334/ORNLDAAC/1812 (2020).30.Xiao, J. & Zhuang, Q. Drought effects on large fire activity in Canadian and Alaskan forests. Environ. Res. Lett. 2, 044003 (2007).ADS 

    Google Scholar 
    31.Flannigan, M. D. et al. Global wildland fire season severity in the 21st century. For. Ecol. Manage. 294, 54–61 (2013).
    Google Scholar 
    32.Jolly, W. M. et al. Climate-induced variations in global wildfire danger from 1979 to 2013. Nat. Commun. 6, 7537 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    33.Adams, W. H. The Role of Fire in the Alaska Taiga. An Unsolved Problem (Bureau of Land Management, State Office, Anchorage, AK, 1974); preprint at https://scholarworks.alaska.edu/handle/11122/6675 (2016).34.Certini, G. Effects of fire on properties of forest soils: a review. Oecologia 143, 1–10 (2005).ADS 
    PubMed 

    Google Scholar 
    35.Kane, E. S., Kasischke, E. S., Valentine, D. W., Turetsky, M. R. & McGuire, A. D. Topographic influences on wildfire consumption of soil organic carbon in interior Alaska: implications for black carbon accumulation. J. Geophys. Res. Biogeosci. 112, 1–11 (2007).
    Google Scholar 
    36.Hoy, E. E., Turetsky, M. R. & Kasischke, E. S. More frequent burning increases vulnerability of Alaskan boreal black spruce forests. Environ. Res. Lett. 11, 095001 (2016).ADS 

    Google Scholar 
    37.Miyanishi, K. & Johnson, E. A. Process and patterns of duff consumption in the mixedwood boreal forest. Can. J. For. Res. 32, 1285–1295 (2002).
    Google Scholar 
    38.Kasischke, E. S. & Turetsky, M. R. Recent changes in the fire regime across the North American boreal region — spatial and temporal patterns of burning across Canada and Alaska. Geophys. Res. Lett. 33, https://doi.org/10.1029/2006GL025677 (2006).39.Johnstone, J. F. et al. Factors shaping alternate successional trajectories in burned black spruce forests of Alaska. Ecosphere 11, https://doi.org/10.1002/ecs2.3129 (2020).40.Mekonnen, Z. A., Riley, W. J., Randerson, J. T., Grant, R. F. & Rogers, B. M. Expansion of high-latitude deciduous forests driven by interactions between climate warming and fire. Nat. Plants 5, 952–958 (2019).
    Google Scholar 
    41.Andreae, M. O. & Merlet, P. Emission of trace gases and aerosols from biomass burning. Glob. Biogeochem. Cycles 15, 955–966 (2001).ADS 
    CAS 

    Google Scholar 
    42.Dean, J. F. et al. Methane feedbacks to the global climate system in a warmer world. Rev. Geophys. 56, 207–250 (2018).ADS 

    Google Scholar 
    43.Beaudoin, A., Bernier, P. Y., Villemaire, P., Guindon, L. & Guo, X. J. Tracking forest attributes across Canada between 2001 and 2011 using a k nearest neighbors mapping approach applied to MODIS imagery. Can. J. For. Res. 48, 85–93 (2018).
    Google Scholar 
    44.Veraverbeke, S., Rogers, B. M. & Randerson, J. T. Daily burned area and carbon emissions from boreal fires in Alaska. Biogeosci. Discuss. 12, 3579–3601 (2015).ADS 
    CAS 

    Google Scholar 
    45.Kasischke, E. S. et al. Quantifying burned area for North American forests: implications for direct reduction of carbon stocks. J. Geophys. Res. Biogeosci. 116, 1–17 (2011).
    Google Scholar 
    46.Farukh, M. A. & Hayasaka, H. Active forest fire occurrences in severe lightning years in Alaska. J. Nat. Disaster Sci. 33, 71–84 (2012).
    Google Scholar 
    47.Burrows, W. R. & Kochtubajda, B. A decade of cloud-to-ground lightning in Canada: 1999-2008. Part 1: flash density and occurrence. Atmos.-Ocean 48, 177–194 (2010).
    Google Scholar 
    48.Bieniek, P. A. et al. Lightning variability in dynamically downscaled simulations of Alaska’s present and future summer climate. J. Appl. Meteorol. Climatol. 59, 1139–1152 (2020).ADS 

    Google Scholar 
    49.Kochtubajda, B. et al. Exceptional cloud-to-ground lightning during an unusually warm summer in Yukon, Canada. J. Geophys. Res. Atmos. 116, https://doi.org/10.1029/2011JD016080 (2011).50.Kochtubajda, B., Stewart, R. & Tropea, B. Lightning and weather associated with the extreme 2014 wildfire season in Canada’s Northwest Territories. In Proceedings of the 24th International Lightning Detection Conference 1–4 (VAISALA, 2016).51.Dowdy, A. J. & Mills, G. A. Atmospheric and fuel moisture characteristics associated with lightning-attributed fires. J. Appl. Meteorol. Climatol. 51, 2025–2037 (2012).ADS 

    Google Scholar 
    52.Larjavaara, M., Pennanen, J. & Tuomi, T. J. Lightning that ignites forest fires in Finland. Agric. For. Meteorol. 132, 171–180 (2005).ADS 

    Google Scholar 
    53.Duncan, B. W., Adrian, F. W. & Stolen, E. D. Isolating the lightning ignition regime from a contemporary background fire regime in east-central Florida, USA. Can. J. For. Res. 40, 286–297 (2010).
    Google Scholar 
    54.Veraverbeke, S. et al. Mapping the daily progression of large wildland fires using MODIS active fire data. Int. J. Wildl. Fire 23, 655–667 (2014).
    Google Scholar 
    55.Statistics Canada. Road Network File 2010. https://www150.statcan.gc.ca/n1/en/catalogue/92-500-X (2016).56.Government of Yukon. Corporate Spatial Warehouse. ftp://ftp.geomaticsyukon.ca/GeoYukon/Transportation/Roads_1M/ (2018).57.Rittger, K., Painter, T. H. & Dozier, J. Assessment of methods for mapping snow cover from MODIS. Adv. Water Resour. 51, 367–380 (2013).ADS 

    Google Scholar 
    58.Gallant, A. L., Binnian, E. F., Omernik, J. M. & Shasby, M. B. Ecoregions of Alaska (Professional Paper 1567, USGS, 1995).59.Canadian Council on Ecological Areas (CCEA). Canada ecozones. https://ccea-ccae.org/ecozones-downloads/ (2016).60.Mesinger, F. et al. North American regional reanalysis. Bull. Am. Meteorol. Soc. 87, 343–360 (2006).ADS 

    Google Scholar 
    61.Van Wagner, C. E. Development and Structure of the Canadian Fire Weather Index System. Forestry Technical Report Vol. 35 (Canadian Forestry Service Headquarters, Ottawa, 1987).62.York, A. D. & Jandt, R. R. Opportunities to Apply Remote Sensing in Boreal/Arctic Wildfire Management & Science: A Workshop Report www.frames.gov/catalog/57849 (University of Alaska, Fairbanks, 2019).63.Schroeder, W., Oliva, P., Giglio, L. & Csiszar, I. A. The New VIIRS 375m active fire detection data product: algorithm description and initial assessment. Remote Sens. Environ. 143, 85–96 (2014).ADS 

    Google Scholar 
    64.Welch, B. L. The significance of the difference between two means when the population variances are unequal. Biometrika 29, 350–362 (1938).MATH 

    Google Scholar 
    65.Welch, B. L. The generalization of ‘Student’s’ problem when several different population variances are involved. Biometrika 34, 28–35 (1947).MathSciNet 
    CAS 
    MATH 

    Google Scholar 
    66.Morin, P. et al. ArcticDEM; a publically available, high resolution elevation model of the Arctic. Geophys. Res. Abstr. 18, EGU2016-8396 (2016).
    Google Scholar 
    67.Porter, C. et al. ArcticDEM. https://doi.org/10.7910/DVN/OHHUKH (Harvard Dataverse, 2018).68.Dai, C., Durand, M., Howat, I. M., Altenau, E. H. & Pavelsky, T. M. Estimating river surface elevation from arcticDEM. Geophys. Res. Lett. 45, 3107–3114 (2018).ADS 

    Google Scholar 
    69.Hansen, M. C. et al. Global percent tree cover at a spatial resolution of 500 meters: first results of the MODIS vegetation continuous fields algorithm. Earth Interact. 7, 1–15 (2003).
    Google Scholar 
    70.Pettinari, M. L. & Chuvieco, E. Generation of a global fuel data set using the fuel characteristic classification system. Biogeosciences 13, 2061–2076 (2016).ADS 

    Google Scholar 
    71.Ottmar, R. D., Sandberg, D. V., Riccardi, C. L. & Prichard, S. J. An overview of the fuel characteristic classification system — quantifying, classifying, and creating fuelbeds for resource planning. Can. J. For. Res. 37, 2383–2393 (2007).
    Google Scholar 
    72.Riccardi, C. L. et al. The fuelbed: a key element of the fuel characteristic classification system. Can. J. For. Res. 37, 2394–2412 (2007).
    Google Scholar 
    73.Beaudoin, A., Bernier, P. Y., Villemaire, P., Guindon, L. & Guo, X. Species Composition, Forest Properties and Land Cover Types Across Canada’s Forests at 250m Resolution for 2001 and 2011. https://doi.org/10.23687/ec9e2659-1c29-4ddb-87a2-6aced147a990 (Natural Resources Canada, Canadian Forest Service, Laurentian Forest Centre, 2017).74.Hugelius, G. et al. The northern circumpolar soil carbon database: spatially distributed datasets of soil coverage and soil carbon storage in the northern permafrost regions. Earth Syst. Sci. Data 5, 3–13 (2013).ADS 

    Google Scholar  More

  • in

    Neogene hyperaridity in Arabia drove the directions of mammalian dispersal between Africa and Eurasia

    1.Prospero, J. M., Ginoux, P., Torres, O., Nicholson, S. E. & Gill, T. E. Environmental characterization of global sources of atmospheric soil dust identified with the Nimbus 7 Total Ozone Mapping Spectrometer (TOMS) absorbing aerosol product. Rev. Geophys. 40, 2-1–2-31 (2002).
    Google Scholar 
    2.Prospero, J. M. & Lamb, P. J. African droughts and dust transport to the Caribbean: climate change implications. Science 302, 1024–1027 (2003).CAS 

    Google Scholar 
    3.Jickells, T. et al. Global iron connections between desert dust, ocean biogeochemistry, and climate. science 308, 67–71 (2005).CAS 

    Google Scholar 
    4.Mahowald, N. M. et al. Atmospheric global dust cycle and iron inputs to the ocean. Glob. Biogeochem. Cycles 19, https://doi.org/10.1029/2004GB002402 (2005).5.Bristow, C. S., Hudson‐Edwards, K. A. & Chappell, A. Fertilizing the Amazon and equatorial Atlantic with West African dust. Geophys. Res. Lett. 37, https://doi.org/10.1029/2010GL043486 (2010).6.Rizzolo, J. A. et al. Soluble iron nutrients in Saharan dust over the central Amazon rainforest. Atmos. Chem. Phys. 17, 2673–2687 (2017).CAS 

    Google Scholar 
    7.Micheels, A., Eronen, J. & Mosbrugger, V. The Late Miocene climate response to a modern Sahara desert. Glob. Planet. Change 67, 193–204 (2009).
    Google Scholar 
    8.Lohmann, G., Butzin, M. & Bickert, T. Effect of vegetation on the Late Miocene ocean circulation. J. Mar. Sci. Eng. 3, 1311–1333 (2015).
    Google Scholar 
    9.Vinoj, V. et al. Short-term modulation of Indian summer monsoon rainfall by West Asian dust. Nat. Geosci. 7, 308–313 (2014).CAS 

    Google Scholar 
    10.Dave, P., Bhushan, M. & Venkataraman, C. Aerosols cause intraseasonal short-term suppression of Indian monsoon rainfall. Sci. Rep. 7, 1–12 (2017).CAS 

    Google Scholar 
    11.Besnard, G., de Casas, R., Christin, R. & Vargas, P.-A. P. Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: tertiary climatic shifts and lineage differentiation times. Ann. Bot. 104, 143–160 (2009).CAS 

    Google Scholar 
    12.Désamoré, A. et al. Out of Africa: north‐westwards Pleistocene expansions of the heather Erica arborea. J. Biogeogr. 38, 164–176 (2011).
    Google Scholar 
    13.Denk, T., Güner, H. T. & Grimm, G. W. From mesic to arid: Leaf epidermal features suggest preadaptation in Miocene dragon trees (Dracaena). Rev. Palaeobot. Palynol. 200, 211–228 (2014).
    Google Scholar 
    14.Mairal, M., Pokorny, L., Aldasoro, J. J., Alarcón, M. & Sanmartín, I. Ancient vicariance and climate‐driven extinction explain continental‐wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae). Mol. Ecol. 24, 1335–1354 (2015).CAS 

    Google Scholar 
    15.Douady, C. J. et al. The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews). Proc. Natl Acad. Sci. 100, 8325–8330 (2003).CAS 

    Google Scholar 
    16.Carranza, S., Arnold, E., Geniez, P., Roca, J. & Mateo, J. Radiation, multiple dispersal and parallelism in the skinks, Chalcides and Sphenops (Squamata: Scincidae), with comments on Scincus and Scincopus and the age of the Sahara Desert. Mol. Phylogenet. Evol. 46, 1071–1094 (2008).CAS 

    Google Scholar 
    17.Brito, J. C. et al. Unravelling biodiversity, evolution and threats to conservation in the Sahara‐Sahel. Biol. Rev. 89, 215–231 (2014).
    Google Scholar 
    18.Gonçalves, D. V. et al. The role of climatic cycles and trans-Saharan migration corridors in species diversification: biogeography of Psammophis schokari group in North Africa. Mol. Phylogenet. Evol. 118, 64–74 (2018).
    Google Scholar 
    19.Lado, S., Alves, P. C., Islam, M. Z., Brito, J. C. & Melo-Ferreira, J. The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography. Heredity 123, 634–646 (2019).CAS 

    Google Scholar 
    20.Moutinho, A. F. et al. Evolutionary history of two cryptic species of northern African jerboas. BMC Evolut. Biol. 20, 1–16 (2020).
    Google Scholar 
    21.Solounias, N., Plavcan, J., Quade, J. & Witmer, L. in The Evolution of Neogene Terrestrial Ecosystems in Europe (eds Rook, L. et al.) Ch. 22, 436–453 (Cambridge University Press, 1999).22.Thomas, H. Les bovidae (Artiodactyla: Mammalia) du miocene du sous-continent indien, de la peninsule arabique et de l’afrique: Biostratigraphie, biogeographie et ecologie. Palaeogeogr. Palaeoclimatol. Palaeoecol. 45, 251–299 (1984).
    Google Scholar 
    23.Bibi, F. Mio-Pliocene faunal exchanges and African biogeography: the record of fossil bovids. PLoS ONE 6, e16688 (2011).24.Bibi, F. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evolut. Biol. 13, 166 (2013).
    Google Scholar 
    25.Begun, D. R., Nargolwalla, M. C. & Kordos, L. European Miocene hominids and the origin of the African ape and human clade. Evolut. Anthropol. 21, 10–23 (2012).
    Google Scholar 
    26.Kaya, F. et al. The rise and fall of the Old World savannah fauna and the origins of the African savannah biome. Nat. Ecol. Evol. 2, 241–246 (2018).
    Google Scholar 
    27.Vrba, E. S. On the connections between paleoclimate and evolution. In Paleoclimate and evolution, with emphasis on human origins. (eds Vrba, E. S., Denton, G. H., Partridge, T. C. & Burckle, L. H.) p. 24–45 (Yale University Press, New Haven and Lopndon, 1995).28.Homke, S., Vergés, J., Garcés, M., Emami, H. & Karpuz, R. Magnetostratigraphy of Miocene–Pliocene Zagros foreland deposits in the front of the Push-e Kush arc (Lurestan Province, Iran). Earth Planet. Sci. Lett. 225, 397–410 (2004).CAS 

    Google Scholar 
    29.Alavi, M. Tectonics of the Zagros orogenic belt of Iran: new data and interpretations. Tectonophysics 229, 211–238 (1994).
    Google Scholar 
    30.Berberian, M. Master “blind” thrust faults hidden under the Zagros folds: active basement tectonics and surface morphotectonics. Tectonophysics 241, 193–224 (1995).
    Google Scholar 
    31.Mather, A., Stokes, M., Pirrie, D. & Hartley, R. Generation, transport and preservation of armoured mudballs in an ephemeral gully system. Geomorphology 100, 104–119 (2008).
    Google Scholar 
    32.Bachmann, G. H. & Wang, Y. Armoured mud balls as a result of ephemeral fluvial flood in a humid climate: modern example from Guizhou Province, South China. J. Palaeogeogr. 3, 410–418 (2014).
    Google Scholar 
    33.Vicente, A., Expósito, M., Sanjuan, J. & Martín-Closas, C. Small sized charophyte gyrogonites in the Maastrichtian of Coll de Nargó, Eastern Pyrenees: an adaptation to temporary floodplain ponds. Cretac. Research 57, 443–456 (2016).
    Google Scholar 
    34.Fakhari, M. D., Axen, G. J., Horton, B. K., Hassanzadeh, J. & Amini, A. Revised age of proximal deposits in the Zagros foreland basin and implications for Cenozoic evolution of the High Zagros. Tectonophysics 451, 170–185 (2008).
    Google Scholar 
    35.Emami, H. et al. Structure of the Mountain Front Flexure along the Anaran anticline in the Pusht-e Kuh Arc (NW Zagros, Iran): insights from sand box models. Geol. Soc. Lond. Spec. Publ. 330, 155–178 (2010).36.Ewing, S. A. et al. A threshold in soil formation at Earth’s arid–hyperarid transition. Geochim. Cosmochim. Acta 70, 5293–5322 (2006).CAS 

    Google Scholar 
    37.Rosenthal, E., Magaritz, M., Ronen, D. & Roded, R. Origin of nitrates in the Negev Desert, Israel. Appl. Geochem 2, 347–354 (1987).CAS 

    Google Scholar 
    38.Michalski, G., Böhlke, J. & Thiemens, M. Long term atmospheric deposition as the source of nitrate and other salts in the Atacama Desert, Chile: new evidence from mass-independent oxygen isotopic compositions. Geochim. Cosmochim. Acta 68, 4023–4038 (2004).CAS 

    Google Scholar 
    39.Mouthereau, F., Lacombe, O. & Vergés, J. Building the Zagros collisional orogen: timing, strain distribution and the dynamics of Arabia/Eurasia plate convergence. Tectonophysics 532, 27–60 (2012).
    Google Scholar 
    40.Reynolds, R. L. et al. Dust emission from wet and dry playas in the Mojave Desert, USA. Earth Surf. Process. Landf. 32, 1811–1827 (2007).
    Google Scholar 
    41.Cosentino, D. et al. Refining the Mediterranean “Messinian gap” with high-precision U-Pb zircon geochronology, central and northern Italy. Geology 41, 323–326 (2013).CAS 

    Google Scholar 
    42.Lisiecki, L. E. & Raymo, M. E. A Pliocene‐Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20, https://doi.org/10.1029/2004PA001071 (2005).43.Tan, N. et al. Exploring the MIS M2 glaciation occurring during a warm and high atmospheric CO2 Pliocene background climate. Earth Planet. Sci. Lett. 472, 266–276 (2017).CAS 

    Google Scholar 
    44.Miller, K. G. et al. High tide of the warm Pliocene: Implications of global sea level for Antarctic deglaciation. Geology 40, 407–410 (2012).CAS 

    Google Scholar 
    45.Ohneiser, C. et al. Antarctic glacio-eustatic contributions to late Miocene Mediterranean desiccation and reflooding. Nat. Commun. 6, 1–10 (2015).
    Google Scholar 
    46.Haywood, A. M., Dowsett, H. J. & Dolan, A. M. Integrating geological archives and climate models for the mid-Pliocene warm period. Nat. Commun. 7, 1–14 (2016).
    Google Scholar 
    47.Manzi, V. et al. Age refinement of the Messinian salinity crisis onset in the Mediterranean. Terra Nova 25, 315–322 (2013).
    Google Scholar 
    48.Ryan, W. B. Decoding the Mediterranean salinity crisis. Sedimentology 56, 95–136 (2009).
    Google Scholar 
    49.Roveri, M. et al. The Messinian Salinity Crisis: past and future of a great challenge for marine sciences. Mar. Geol. 352, 25–58 (2014).
    Google Scholar 
    50.Madof, A. S., Bertoni, C. & Lofi, J. Discovery of vast fluvial deposits provides evidence for drawdown during the late Miocene Messinian salinity crisis. Geology 47, 171–174 (2019).CAS 

    Google Scholar 
    51.Krijgsman, W., Stoica, M., Vasiliev, I. & Popov, V. Rise and fall of the Paratethys Sea during the Messinian Salinity Crisis. Earth Planet. Sci. Lett. 290, 183–191 (2010).CAS 

    Google Scholar 
    52.van Baak, C. G. et al. Paratethys response to the Messinian salinity crisis. Earth Sci. Rev. 172, 193–223 (2017).
    Google Scholar 
    53.Böhme, M., Ilg, A. & Winklhofer, M. Late Miocene “washhouse” climate in Europe. Earth Planet. Sci. Lett. 275, 393–401 (2008).
    Google Scholar 
    54.Schuster, M. et al. The age of the Sahara desert. Science 311, 821–821 (2006).CAS 

    Google Scholar 
    55.Böhme, M. et al. Messinian age and savannah environment of the possible hominin Graecopithecus from Europe. PLoS ONE 12, e0177347 (2017).56.Böhme, M., Van Baak, C. G., Prieto, J., Winklhofer, M. & Spassov, N. Late Miocene stratigraphy, palaeoclimate and evolution of the Sandanski Basin (Bulgaria) and the chronology of the Pikermian faunal changes. Glob. Planet. Change 170, 1–19 (2018).
    Google Scholar 
    57.Alijani, B. & Harman, J. R. Synoptic climatology of precipitation in Iran. Ann. Assoc. Am. Geogr. 75, 404–416 (1985).
    Google Scholar 
    58.Perșoiu, A., Ionita, M. & Weiss, H. Atmospheric blocking induced by the strengthened Siberian High led to drying in west Asia during the 4.2 ka BP event—a hypothesis. Clim. Past 15, 781–793 (2019).
    Google Scholar 
    59.Ramstein, G., Fluteau, F., Besse, J. & Joussaume, S. Effect of orogeny, plate motion and land–sea distribution on Eurasian climate change over the past 30 million years. Nature 386, 788–795 (1997).CAS 

    Google Scholar 
    60.Zhongshi, Z., Wang, H., Guo, Z. & Jiang, D. What triggers the transition of palaeoenvironmental patterns in China, the Tibetan Plateau uplift or the Paratethys Sea retreat? Palaeogeogr. Palaeoclimatol. Palaeoecol. 245, 317–331 (2007).
    Google Scholar 
    61.Najafi, M. S., Sarraf, B., Zarrin, A. & Rasouli, A. Climatology of atmospheric circulation patterns of Arabian dust in western Iran. Environ. Monit. Assess. 189, 473 (2017).
    Google Scholar 
    62.van Baak, C. G., Stoica, M., Grothe, A., Aliyeva, E. & Krijgsman, W. Mediterranean-Paratethys connectivity during the Messinian salinity crisis: the Pontian of Azerbaijan. Glob. Planet. Change 141, 63–81 (2016).
    Google Scholar 
    63.Naidina, O. D. & Richards, K. The Akchagylian stage (late Pliocene-early Pleistocene) in the North Caspian region: Pollen evidence for vegetation and climate change in the Urals-Emba region. Quat. Int. 540, 22–37 (2020).
    Google Scholar 
    64.Burls, N. J. & Fedorov, A. V. Wetter subtropics in a warmer world: contrasting past and future hydrological cycles. Proc. Natl Acad. Sci. 114, 12888–12893 (2017).CAS 

    Google Scholar 
    65.Colleoni, F., Cherchi, A., Masina, S. & Brierley, C. M. Impact of global SST gradients on the Mediterranean runoff changes across the Plio‐Pleistocene transition. Paleoceanography 30, 751–767 (2015).
    Google Scholar 
    66.Holbourn, A. E. et al. Late Miocene climate cooling and intensification of southeast Asian winter monsoon. Nat. Commun. 9, 1–13 (2018).CAS 

    Google Scholar 
    67.White, S. & Ravelo, A. Dampened El Niño in the early Pliocene warm period. Geophys. Res. Lett. 47, e2019GL085504 (2020).
    Google Scholar 
    68.Tozuka, T., Endo, S. & Yamagata, T. Anomalous Walker circulations associated with two flavors of the Indian Ocean Dipole. Geophys. Res. Lett. 43, 5378–5384 (2016).
    Google Scholar 
    69.Annamalai, H., Okajima, H. & Watanabe, M. Possible impact of the Indian Ocean SST on the Northern Hemisphere circulation during El Niño. J. Clim. 20, 3164–3189 (2007).
    Google Scholar 
    70.Nazemosadat, M., Samani, N., Barry, D. & Molaii Niko, M. ENSO forcing on climate change in Iran: precipitation analysis. Iran. J. Sci. Technol. Trans. B 30, 555–565 (2006).
    Google Scholar 
    71.Trauth, M. H. et al. High-and low-latitude forcing of Plio-Pleistocene East African climate and human evolution. J. Hum. Evol. 53, 475–486 (2007).
    Google Scholar 
    72.Blumenthal, S. A. et al. Aridity and hominin environments. Proc. Natl Acad. Sci. 114, 7331–7336 (2017).CAS 

    Google Scholar 
    73.Lebatard, A.-E. et al. Application of the authigenic 10Be/9Be dating method to continental sediments: reconstruction of the Mio-Pleistocene sedimentary sequence in the early hominid fossiliferous areas of the northern Chad Basin. Earth Planet. Sci. Lett. 297, 57–70 (2010).CAS 

    Google Scholar 
    74.Tiedemann, R., et al. Proc. ODP, Sci. Results. 241–277.75.Hilgen, F. et al. Integrated stratigraphy and astrochronology of the Messinian GSSP at Oued Akrech (Atlantic Morocco). Earth Planet. Sci. Lett. 182, 237–251 (2000).CAS 

    Google Scholar 
    76.Dupont, L. M. & Leroy, S. A. Steps Toward Drier Climatic Conditions in Northwestern Africa during the Upper Pliocene. Paleoclimate and Evolution with Emphasis on Human Origins 289–298 (Yale University Press, 1995)77.Darwin, C. & Bynum, W. F. The Origin of Species by Means of Natural Selection: Or, the Preservation of favored Races in the Struggle for Life (Penguin Harmondsworth, 2009).78.Herbert, T. D. et al. Late Miocene global cooling and the rise of modern ecosystems. Nat. Geosci. 9, 843–847 (2016).CAS 

    Google Scholar 
    79.Gradstein, F. M., Ogg, J. G., Schmitz, M. B. & Ogg, G. M. The Geologic Time Scale 2012. (Elsevier, 2012).80.Epp, T. et al. Vegetation canopy effects on total and dissolved Cl, Br, F and I concentrations in soil and their fate along the hydrological flow path. Sci. Total Environ. 712, 135473 (2020).CAS 

    Google Scholar 
    81.Dietze, E. & Dietze, M. Grain-size distribution unmixing using the R package EMMAgeo. E&G-Quat. Sci. J. 68, 29–46 (2019).
    Google Scholar 
    82.Andò, S. Gravimetric separation of heavy minerals in sediments and rocks. Minerals 10, 273 (2020).
    Google Scholar 
    83.Al-Juboury, A. I. & Al-Miamary, F. A. Geochemical variations in heavy minerals as provenance indications: application to the Tigris river sand, northern Iraq. J. Mediter. Earth Sci. 1, 33–45 (2009).
    Google Scholar 
    84.Garzanti, E. et al. The Euphrates-Tigris-Karun river system: Provenance, recycling and dispersal of quartz-poor foreland-basin sediments in arid climate. Earth Sci. Rev. 162, 107–128 (2016).CAS 

    Google Scholar 
    85.Philip, G. Mineralogy of the Recent sediments of Tigris and Euphrates rivers and some of the older detrital deposits. J. Sediment. Res. 38, 35–44 (1968).
    Google Scholar 
    86.Skoček, V. & Saadallah, A. Grain-size distribution, carbonate content and heavy minerals in eolian sands, southern desert, Iraq. Sediment. Geol. 8, 29–46 (1972).
    Google Scholar 
    87.Popov, S., Antipov, M., Zastrozhnov, A., Kurina, E. & Pinchuk, T. Sea-level fluctuations on the northern shelf of the Eastern Paratethys in the Oligocene-Neogene. Stratigr. Geol. Correl. 18, 200–224 (2010).
    Google Scholar 
    88.Krijgsman, W. et al. Quaternary time scales for the Pontocaspian domain: interbasinal connectivity and faunal evolution. Earth Sci. Rev. 188, 1–40 (2019).
    Google Scholar 
    89.van Baak, C. G. et al. Messinian events in the Black Sea. Terra Nova 27, 433–441 (2015).
    Google Scholar 
    90.Green, T., Abdullayev, N., Hossack, J., Riley, G. & Roberts, A. M. Sedimentation and Subsidence in the South Caspian Basin, Azerbaijan vol. 312 (Geological Society, London, Special Publications, 2009) 241–260 (2009).91.Abdullayev, N. R., Riley, G. W. & Bowman, A. P. Regional controls on lacustrine sandstone reservoirs: the Pliocene of the South Caspian Basin. (2012).92.Trubikhin, V. Paleomagnetic data for the Pontian. Chronostratigraphie und Neostratotypen–Pontien. Chronostratigraphie und Neostratotypen, Zagreb–Beograd. 76–79 (1989).93.Van Baak, C. G. et al. A magnetostratigraphic time frame for Plio-Pleistocene transgressions in the South Caspian Basin, Azerbaijan. Glob. Planet. Change 103, 119–134 (2013).
    Google Scholar 
    94.Davis, S. N., Fabryka-Martin, J. T. & Wolfsberg, L. E. Variations of bromide in potable ground water in the United States. Ground Water 42, 902–909 (2004).CAS 

    Google Scholar 
    95.Davis, S. N., Whittemore, D. O. & Fabryka-Martin, J. Uses of chloride/bromide ratios in studies of potable water. Ground Water 36, 338–350 (1998).CAS 

    Google Scholar 
    96.Alcalá, F. J. & Custodio, E. Using the Cl/Br ratio as a tracer to identify the origin of salinity in aquifers in Spain and Portugal. J. Hydrol. 359, 189–207 (2008).
    Google Scholar 
    97.Dickson, A. & Goyet, C. Handbook of Methods for the Analysis of the Various Parameters of the Carbon Dioxide System in Sea Water 166–187 (ORNL/CDIAC-74, U. S. Department of Energy, 1994).98.Tan, H., Ma, H., Li, B., Zhang, X. & Xiao, Y. Strontium and boron isotopic constraint on the marine origin of the Khammuane potash deposits in southeastern Laos. Chin. Sci. Bull. 55, 3181–3188 (2010).CAS 

    Google Scholar 
    99.Turk, L., Davis, S. & Bingham, C. Hydrogeology of lacustrine sediments, Bonneville Salt Flats, Utah. Econ. Geol. 68, 65–78 (1973).CAS 

    Google Scholar 
    100.Sun, S. et al. Bromine content and Br/Cl molar ratio of halite in a core from Laos: implications for origin and environmental changes. Carbon. Evaporites 34, 1107–1115 (2019).CAS 

    Google Scholar 
    101.Fomba, K. W. et al. Long-term chemical characterization of tropical and marine aerosols at the CVAO: field studies (2007 to 2011). Atmos. Chem. Phys 14, 3917–3971 (2014).
    Google Scholar 
    102.Manö, S. & Andreae, M. O. Emission of methyl bromide from biomass burning. Science 263, 1255–1257 (1994).
    Google Scholar 
    103.Goni, I., Fellman, E. & Edmunds, W. Rainfall geochemistry in the Sahel region of northern Nigeria. Atmos. Environ. 35, 4331–4339 (2001).CAS 

    Google Scholar 
    104.Horst, A. et al. Stable bromine isotopic composition of methyl bromide released from plant matter. Geochim. Cosmochim. Acta 125, 186–195 (2014).CAS 

    Google Scholar 
    105.Helder, R. The absorption of labelled chloride and bromide ions by young intact barley plants. Acta Bot. Neerl. 13, 488–506 (1965).
    Google Scholar 
    106.Bowen, H. J. M. Environmental Chemistry of the Elements (Academic Press, 1979).107.Gerritse, R. G. & George, R. J. The role of soil organic matter in the geochemical cycling of chloride and bromide. J. Hydrol. 101, 83–95 (1988).CAS 

    Google Scholar 
    108.Wishkerman, A. et al. Abiotic methyl bromide formation from vegetation, and its strong dependence on temperature. Environ. Sci. Technol. 42, 6837–6842 (2008).CAS 

    Google Scholar 
    109.Delany, A. C., Pollock, W. H. & Shedlovsky, J. P. Tropospheric aerosol—relative contribution of marine and continental components. J. Geophys. Res. 78, 6249–6265 (1973).CAS 

    Google Scholar 
    110.Pérez-Fodich, A. et al. Climate change and tectonic uplift triggered the formation of the Atacama Desert’s giant nitrate deposits. Geology 42, 251–254 (2014).
    Google Scholar 
    111.Reich, M. & Bao, H. M. Nitrate deposits of the Atacama Desert: a marker of long-term hyperaridity. Elements 14, 251–256 (2018).CAS 

    Google Scholar 
    112.Erickson, D. J. III & Duce, R. A. On the global flux of atmospheric sea salt. J. Geophys. Res. 93, 14079–14088 (1988).
    Google Scholar 
    113.Murphy, D. M. et al. The distribution of sea-salt aerosol in the global troposphere. Atmos. Chem. Phys. 19, https://doi.org/10.5194/acp-19-4093-2019 (2019).114.Walvoord, M. A. et al. A reservoir of nitrate beneath desert soils. Science 302, 1021–1024 (2003).CAS 

    Google Scholar 
    115.Graham, R. C., Hirmas, D. R., Wood, Y. A. & Amrhein, C. Large near-surface nitrate pools in soils capped by desert pavement in the Mojave Desert, California. Geology 36, 259–262 (2008).CAS 

    Google Scholar 
    116.Voigt, C., Klipsch, S., Herwartz, D., Chong, G. & Staubwasser, M. The spatial distribution of soluble salts in the surface soil of the Atacama Desert and their relationship to hyperaridity. Glob. Planet. Change 184, 103077 (2020).
    Google Scholar 
    117.Böhlke, J., Ericksen, G. & Revesz, K. Stable isotope evidence for an atmospheric origin of desert nitrate deposits in northern Chile and southern California, USA. chemical. Chem. Geol. 136, 135–152 (1997).
    Google Scholar 
    118.Jin, Z., Zhu, Y., Li, X., Dong, Y. & An, Z. Soil N retention and nitrate leaching in three types of dunes in the Mu Us desert of China. Sci. Rep. 5, 14222 (2015).CAS 

    Google Scholar 
    119.Ericksen, G. E., Hosterman, J. W. & Amand, P. S. Chemistry, mineralogy and origin of the clay-hill nitrate deposits, Amargosa River valley, Death Valley region, California, USA. Chem. Geol. 67, 85–102 (1988).CAS 

    Google Scholar 
    120.Qin, Y. et al. Massive atmospheric nitrate accumulation in a continental interior desert, northwestern China. Geology 40, 623–626 (2012).CAS 

    Google Scholar 
    121.Lybrand, R. A. et al. Nitrate, perchlorate, and iodate co-occur in coastal and inland deserts on Earth. Chemical. Geology 442, 174–186 (2016).CAS 

    Google Scholar 
    122.Wood, G. in American Association of Stratigraphic Palynologists Foundation vol. 1 29–50 (1996).123.Wallace, A. The Geographical Distribution of Animals Vol. I & II (Harper and Brothers, 1876).124.Wessel, P. & Luis, J. F. The GMT/MATLAB Toolbox. Geochem. Geophys. Geosyst. 18, 811–823 (2017).
    Google Scholar 
    125.Amante, C. & Eakins, B. ETOPO1 Global Relief Model Converted to PanMap Layer Format (NOAA-National Geophysical Data Center, 2009).126.Flint, A. L., Flint, L. E., Curtis, J. A. & Buesch, D. C. A preliminary water balance model for the Tigris and Euphrates river system. US Geological Survey, Water Budget Report (2011). More

  • in

    Low annual temperature likely prevents the Holarctic amphipod Gammarus lacustris from invading Lake Baikal

    This study aimed to investigate species-specific thermal adaptations of two endemic amphipod species differing in their thermal tolerance and one widespread Holarctic species by comparing long-term responses to cold and warm temperatures beyond their respective preference temperatures. We hypothesize that the Holarctic G. lacustris is limited at the extreme low temperature (i.e. 1.5 °C) preventing this species from establishing a stable population in Lake Baikal, whereas the Baikal endemic amphipods possessing specific thermal adaptations to maintain a high energy metabolism in winter at low temperatures.To test this hypothesis, we measured metabolic markers in long-term acclimated animals exposed to four different temperatures (i.e., 1.5 °C, 6 °C, 12 °C and 15 °C) including the respective preference temperature of each species. More specifically , we studied key metabolic enzyme activities, such as citrate synthase and cytochrome c and oxidase, to estimate aerobic energy production and lactate dehydrogenase as an indicator of anaerobic glycolysis. To better understand the metabolic output of these enzymes we studied metabolite contents such as ATP, lactate, and glycogen. Finally, we investigated activities of three antioxidant enzymes to evaluate the level of cellular stress. Overall, we could demonstrate significant differences of several markers between all three species and their responsiveness to temperature. Common patterns and their implications for the performance of the species in their habitats are discussed in the following.Metabolic properties at optimal temperaturesLong-term acclimation to the preferred (= optimal) temperatures allows maintaining homeostasis and avoids any stress related to the non-optimal thermal conditions. At these optimal temperatures, the aerobic scopes of the species should be at their maxima meaning that maximum excess oxygen is available to fuel processes above maintenance to support e.g., growth and reproduction7,27.Here, we found differences in the capacities of aerobic metabolism, levels of energy equivalents and energy stores between the three species, as indicated by the higher activity of cytochrome c oxidase, ATP and glycogen levels in G. lacustris compared to the two Baikal species. This is in line with our previous findings about routine metabolic rates, measured as oxygen consumption in the studied species21.Constantly low temperatures led to decreased cellular ATP levels and activities of cytochrome c oxidase in Baikal endemics, thereby indicating a reduced rate of basal metabolism. The same trend was observed in Antarctic fish compared to temperate and tropical fish species27,28.However, the activity of another marker of aerobic metabolism—citrate synthase—is similar among the three species. The higher citrate synthase/cytochrome c oxidase ratio in Baikal species compared to G. lacustris may be attributed to the prevalence of lipid over glucose metabolism in Baikal species29. Significantly higher levels of glycogen in G. lacustris support this assumption.Here, we studied one thermally tolerant Baikal endemic species, E. cyaneus, and one cold-stenothermal species, E. verrucosus. Previous studies on the molecular evolution of thermal tolerance revealed significant structural and functional differences in heat shock proteins (Hsp70), a universal molecular protection system24. Significant differences in routine metabolic rate and lethal temperatures were also shown21, supporting both endemic species’ thermal classification. The present results widen our mechanistic understanding of thermotolerance in Baikal amphipods. Particularly, when acclimated to their preferred temperatures, the two Baikal species showed some differences in metabolic fuel usage. Higher glucose, glycogen and lactate levels correspond to a more enhanced glucose metabolism, which may be required to maintain higher metabolic activity of the thermotolerant species E. cyaneus. However, capacities of cytochrome c oxidase and citrate synthase activities are similar, as well as the ATP level, which indicates similar rates of oxygen metabolism under optimal thermal condition in these two species.Oxygen metabolism is tightly connected with the antioxidative defense against reactive oxygen species (ROS) as they are natural byproducts of aerobic metabolism. Therefore, we studied the activity of three antioxidative enzymes. Our results indicate that despite higher aerobic capacities and presumably higher metabolic rates in G. lacustris compared to the two Baikal species, the activities of catalase and glutathione S-transferase were comparable and for peroxidase even higher in the cold stenothermal E. verrucosus than in G. lacustris (Fig. 2). Similarly, Abele and Puntarulo24,30 showed that the basic levels of superoxide dismutase activity in polar mollusks are higher than in temperate ones. Increased ROS generation in cells of ectothermic animals may occur due to higher oxygen solubility in cold water and biological fluids31,32. Thus, higher peroxidase level in E. verrucosus is likely an adaptation to the low temperatures with its high dissolved oxygen content in Baikal water.Glutathione S-transferase activities were found to be higher in both thermotolerant species—G. lacustris and E. cyaneus. Besides protecting against ROS, this enzyme has multiple functions, including xenobiotic detoxification33. Thus, its higher activity may be related to the enhanced tolerance level to various environmental factors in both species besides temperature.Thermal exposure to lower than the preferred temperaturesWe hypothesized that Baikal species have metabolic adaptations to cold temperatures that allow an active lifestyle in the cold. Thus, we expected cold compensation mechanisms (i.e., increased enzyme activities due to higher densities of mitochondria in cold stenotherms). Our results indicate that this is the case only for E. cyaneus (Baikal endemic, thermotolerant), as it showed increased cytochrome c oxidase activities at 1.5 °C. As the citrate synthase activity and ATP level remained unchanged, compensation of the respiratory chain seems to be sufficient to support stable energy production at low temperatures and an alteration of the mitochondrial ultrastructure, i.e., increased cristae density (cytochrome c oxidase) relative to the matrix (citrate synthase) may be involved in cold acclimation.E. cyaneus represents the rather small summer-reproducing complex among Baikal endemic amphipods. Despite its relatively high thermotolerance24, this species is actively moving under the ice cover in winter. In our experiments, animals of this species expressed high locomotor and feeding activity at all exposure temperatures, including 1.5 °C. Our results unravel the metabolic adaptation providing this rather wide thermotolerance window of this species. Already at 6 °C, glycogen started to accumulate, which also reoccurred at 1.5 °C. Glycogen accumulation is a well-known strategy of overwintering ectotherms known as cold hardiness, especially in those surviving in frozen habitats under oxygen-limited conditions34. Similar, we found an accumulation of glycogen above the control level in the Holarctic G. lacustris when exposed to 12 and 6 °C. However, at 1.5 °C the level of glycogen in this species was below the control level, indicating reduced glycogenesis possibly due to metabolic depression in the cold.Instead, E. cyaneus can maintain a high level of glycogenesis at 1.5 °C, and therefore accumulate glycogen in winter, despite its lower metabolic rate compared to G. lacustris. Surprisingly, at 6 °C we found a strong increase in lactate dehydrogenase activity in E. cyaneus, which was not followed by a significant accumulation of lactate or significant depletion of ATP indicating the absence of functional anaerobiosis. This unpredicted reaction of lactate dehydrogenase in this species at 6 °C, which is the Baikal littoral zone’s annual average temperature, requires further studies.Exposure to 1.5 °C and 6 °C caused decreased catalase and peroxidase activities and decreased lactate levels in E. cyaneus, which would be in line with a reduced metabolic rate, following the Q10 rule. Thus, our results indicate that E. cyaneus can maintain a high level of aerobic metabolism within a wide thermal range including the common winter temperature—1.5 °C. Although E. cyaneus is one of the most thermotolerant Baikal amphipod species, differences to the closely-related thermotolerant Holarctic G. lacustris became apparent as the latter failed to maintain high ATP and lactate levels at the lowest exposure temperature likely due to lacking compensation (citrate synthase, cytochrome c oxidase) or even inactivation of enzyme functions (including lactate dehydrogenase). This reduced energy state may likely contribute to the low locomotor activity of G. lacustris at the lowest exposure temperature.Surprisingly, no cold compensation in any of the studied parameters was found for the cold-loving Baikal endemic species E. verrucosus. This species belongs to the winter-reproducing complex, which is most common in the littoral zone. The absence in cold compensation of this species indicates that at 1.5 °C its energy metabolism remains on its physiological maximum.The absence of glycogen accumulation at low temperatures in this species can be explained by the food availability during winter in Lake Baikal’s littoral zone. Presumably, the existing amount of winter nutrition is sufficient for E. verrucosus to maintain maximum aerobic capacities and energy metabolism. The high nutrition allows the species to breed, develop eggs and release juveniles, which occurs during the seasons with lowest annual temperatures. Another explanation can be the usage of lipids instead of carbohydrates as energy source in winter. The lower amount of glycogen and free glucose than in the thermotolerant congener E. cyaneus, supports this hypothesis.Thus, despite the relatively similar aerobic capacities of the thermotolerant E. cyaneus and the winter-reproducing cold stenothermal E. verrucosus at their respective preference temperatures, the latter species shows a different metabolic fuel use, that allows E. verrucosus to maintain its maximum metabolic rate at 1.5 °C.We hypothesized that the Holarctic G. lacustris has disadvantages compared to the two Baikal species regarding energy metabolism at low temperatures. Gammarus lacustris is eurythermal and often overwinters in small ponds, which are nearly completely frozen in winter35. However, it has been shown that temperatures below its optimal range cause decreased respiration rates and activity possibly resulting in torpor21,35. Our observations confirmed these assumptions as at 1.5 °C individuals of G. lacustris significantly decreased their locomotor and feeding activities. The assumption that G. lacustris shows metabolic depression at 6 °C and 1.5 °C is supported by the decreased ATP, lactate, and lactate dehydrogenase activity levels. Moreover, only for this species we observed mortality at 1.5 °C, which indicates that this experimental thermal condition is stressful. This is supported by the increase in catalase activity over the control level and the elevated level of peroxidase activity at 1.5 °C, while at 12 °C and 6 °C, the capacity for this enzyme was decreased compared to the control (following the Q10 rule). In this case, exposure to 1.5 °C could cause cellular damages resulting in the development of oxidative stress. Preparation for such extreme temperatures for G. lacustris like requires enough time to accumulate cryoprotectors25 and adjust the metabolism in its natural habitat. Besides, we observed the accumulation of glycogen, like in the thermotolerant E. cyaneus. For G. lacustris, accumulation of glycogen for the wintertime is essential, as it is often overwintering in nearly completely frozen ponds and therefore experiences periods of hypoxia23. Glycogen can be metabolized via anaerobic glycolysis, in contrast to lipid storages, which require oxygen for their metabolizations34. In comparison to E. cyaneus, accumulation of glycogen over the control level in G. lacustris occurs already at 12 °C, indicating the lower thermal threshold of the zone of preferred temperatures for this species22, but this accumulation disappeared at the lowest temperature indicating that G. lacustris follows a different strategy for winter survival than cold hardiness34.Thermal exposure to higher than the preferred temperaturesPrevious studies indicated that 15 °C is the critical thermal threshold for large adults of the stenothermal E. verrucosus, and it was observed that most of these individuals start to migrate to deeper littoral zones when the temperature in the Baikal littoral surpass about 11 °C21. Thus, E. verrucosus is behaviorally adapted to escape deleterious temperatures. When exposed to gradual temperature increase, individuals of E. verrucosus showed accumulation of lactate and heat shock proteins at temperatures exceeding 12 °C22,24. Our results complement these previous findings, as lactate levels were significantly higher than the control lactate levels at 12 °C. At 15 °C, increases of lactate dehydrogenase capacities were detected, which may foster a higher turnover and remobilization of lactate at this temperature compared to 12 °C, as lactate level did not further increase. As shown earlier lactate dehydrogenase was the only metabolic enzyme exhibited similar kinetic and regulatory properties as the other two amphipod species (following simple Q10 rules)23. The results here confirm the need of E. verrucosus to keep higher anaerobic capacities and turnover rates at the upper limit of the thermal window, where functional hypoxia may appear7,27.In the more thermotolerant E. cyaneus, exposure to 15 °C caused increases of ATP, lactate, and both peroxidase and catalase activities. Increases of both ATP and lactate likely indicate the enhancement of the cellular respiration rather than the onset of anaerobiosis. Activation of peroxidase and catalase may indicate both the development of cellular stress and the general increase in metabolic rate following the Q10 rule. The last explanation is more likely, as antioxidant enzyme activities, lactate and ATP content gradually increased with rising temperature. As E. cyaneus is a sedentary species, that occupies a rather narrow zone of the upper littoral, such a metabolic plasticity can serve as a specific adaptation to its thermal niche. Opposite, for the migrating E. verrucosus, behavioral responses are more important when temperatures gradually increase. More

  • in

    Global effects of land-use intensity on local pollinator biodiversity

    1.Potts, S. G. et al. Global pollinator declines: trends, impacts and drivers. Trends Ecol. Evol. 25, 345–353 (2010).Article 

    Google Scholar 
    2.Steffan-Dewenter, I. & Westphal, C. The interplay of pollinator diversity, pollination services and landscape change. J. Appl. Ecol. 45, 737–741 (2007).Article 

    Google Scholar 
    3.Woodcock, B. A. et al. Impacts of neonicotinoid use on long-term population changes in wild bees in England. Nat. Commun. 7, 12459 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    4.Winfree, R., Bartomeus, I. & Cariveau, D. P. Native pollinators in anthropogenic habitats. Annu. Rev. Ecol. Evol. Syst. 42, 1–22 (2011).Article 

    Google Scholar 
    5.Soroye, P., Newbold, T. & Kerr, J. Climate change contributes to widespread declines among bumble bees across continents. Science 367, 685–688 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    6.IPBES (2017). The Assessment Report on Pollinators, Pollination and Food Production. Bonn.7.Biesmeijer, J. C. et al. Parallel declines in pollinators and insect-pollinated plants in Britain and the Netherlands. Science 313, 351–354 (2006).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    8.Embury-Dennis, T. The Independent. 19 October. (2017) http://www.independent.co.uk/news/science/flying-insects-numbers-drop-ecological-armageddon-75-per-cent-plummet-a8008406.html. Accessed 03 Dec 2020.9.Sánchez-Bayo, F. & Wyckhuys, K. A. G. Worldwide decline of the entomofauna: a review of its drivers. Biol. Conserv. 232, 8–27 (2019).Article 

    Google Scholar 
    10.Martin, E. A. et al. The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agroecosystem services across Europe. Ecol. Lett. 22, 1083–1094 (2019).PubMed 
    Article 

    Google Scholar 
    11.Powney, G. D. et al. Widespread losses of pollinating insects in Britain. Nat. Commun. 10, 1–6 (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    12.Lister, B. C. & Garcia, A. Climate-driven declines in arthropod abundance restructure a rainforest food web. Proc. Natl Acad. Sci. USA 115, E10397–E10406. (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    13.Hallmann, C. A. et al. More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLOS ONE 12, e0185809 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    14.Ollerton, J. Pollinator diversity: distribution, ecological function, and conservation. Annu. Rev. Ecol. Evol. Syst. 48, 353–376 (2017).Article 

    Google Scholar 
    15.Saunders, M. E., Janes, J. K. & O’hanlon, J. C. Moving on from the insect apocalypse narrative: engaging with evidence-based insect conservation. BioScience 70, 80–89 (2020).Article 

    Google Scholar 
    16.De Palma, A. et al. Predicting bee community responses to land-use changes: effects of geographic and taxonomic biases. Sci. Rep. 6, 31153 (2016).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    17.Kunin, W. E. Robust evidence of declines in insect abundance and biodiversity. Nature 574, 641–642 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    18.Macgregor, C. J. et al. Moth biomass increases and decreases over 50 years in Britain. Nat. Ecol. Evol. 3, 1645–1649 (2019).PubMed 
    Article 

    Google Scholar 
    19.Millard, J. W., Freeman, R. & Newbold, T. Text‐analysis reveals taxonomic and geographic disparities in animal pollination literature. Ecography 43, 44–59 (2020).Article 

    Google Scholar 
    20.Klein, A.-M. et al. Importance of pollinators in changing landscapes for world crops. Proc. R. Soc. Lond. Ser. B 274, 303–313 (2007).
    Google Scholar 
    21.European Commission. EU Pollinators Initiative (European Commission, Brussels, 2018).22.Food and Agriculture Organization. The International Pollinator Initiative plan of action 2018-2030 (FAO, Rome, 2018).23.Secretariat of the Convention on Biological Diversity. Zero Draft of the Post-2020 Global Biodiversity Framework (CBD, Montreal, 2020).24.Ellis, E. C. & Ramankutty, N. Putting people in the map: anthropogenic biomes of the world. Front. Ecol. Environ. 6, 439–447 (2008).Article 

    Google Scholar 
    25.Le B. Hooke, R., Martín-Duque, J. F. and Pedraza, J. Land transformation by humans: a review. GSA Today 22, 4–10 (2012).26.Donald, P. F., Green, R. E. & Heath, M. F. Agricultural intensifcation and the collapse of Europe’s farmland bird populations. Proc. R. Soc. Lond. B. 268, 25–29 (2001).Article 

    Google Scholar 
    27.Benton, T. G. et al. Linking agricultural practice to insect and bird populations: a historical study over three decades. J. Appl. Ecol. 39, 673–687 (2002).Article 

    Google Scholar 
    28.Benton, T. G., Vickery, J. A. & Wilson, J. D. Farmland biodiversity: is habitat heterogeneity the key? Trends Ecol. Evol. 18, 182–188 (2003).Article 

    Google Scholar 
    29.Tscharntke, T. et al. Contribution of small habitat fragments to conservation of insect communities of grassland–cropland landscapes. Ecol. Appl. 12, 354–363 (2002).
    Google Scholar 
    30.Kennedy, C. M. et al. A global quantitative synthesis of local and landscape effects on wild bee pollinators in agroecosystems. Ecol. Lett. 16, 584–599 (2013).PubMed 
    Article 

    Google Scholar 
    31.Ricketts, T. H. et al. Landscape effects on crop pollination services: are there general patterns? Ecol. Lett. 11, 499–515 (2008).PubMed 
    Article 

    Google Scholar 
    32.Klein, A.-M., Steffan-Dewenter, I. & Tscharntke, T. Fruit set of highland coffee increases with the diversity of pollinating bees. Proc. R. Soc. Lond. Biol. Sci. 270, 955–961 (2003).Article 

    Google Scholar 
    33.Xiao, Y. et al. The diverse effects of habitat fragmentation on plant–pollinator interactions. Plant Ecol. 217, 857–868 (2016).Article 

    Google Scholar 
    34.Goulson, D. An overview of the environmental risks posed by neonicotinoid insecticides. J. Appl. Ecol. 50, 977–987 (2013).Article 

    Google Scholar 
    35.Pisa, L. W. et al. Effects of neonicotinoids and fipronil on non-target invertebrates. Environ. Sci. Pollut. Res. 22, 68–102 (2015).CAS 
    Article 

    Google Scholar 
    36.Sánchez-Bayo, F. & Goka, K. Pesticide residues and bees—a risk assessment. PLoS One. 9, e94482 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    37.Pilling, E. D. & Jepson, P. C. Synergism between EBI fungicides and a pyrethroid insecticide in the honeybee (Apis mellifera). Pestic. Sci. 39, 293–297 (1993).CAS 
    Article 

    Google Scholar 
    38.Crall, J. D. et al. Neonicotinoid exposure disrupts bumblebee nest behavior, social networks, and thermoregulation. Science 362, 683–686 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    39.Schmuck, R., Stadler, T. & Schmidt, H.-W. Field relevance of a synergistic effect observed in the laboratory between an EBI fungicide and a chloronicotinyl insecticide in the honeybee (Apis mellifera L, Hymenoptera). Pest Manag. Sci. 59, 279–286 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    40.Morandin, L. A. & Winston, M. L. Wild bee abundance and seed production in conventional, organic, and genetically modified canola. Ecol. Appl. 15, 871–881 (2005).Article 

    Google Scholar 
    41.Ridding, L. E. et al. Long-term change in calcareous grassland vegetation and drivers over three time periods between 1970 and 2016. Plant Ecol. 221, 377–394 (2020).Article 

    Google Scholar 
    42.Goulson, D., Lye, G. C. & Darvill, B. Decline and conservation of bumble bees. Annu. Rev. Entomol. 53, 191–208 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    43.Michener, C. D. The Bees of the World (Johns Hopkins University Press 2007).44.Deans, A. M. et al. Hoverfly (Syrphidae) communities respond to varying structural retention after harvesting in Canadian peatland black spruce forests. Environ. Entomol. 36, 308–318 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    45.Kuussaari, M. et al. Determinants of local species richness of diurnal Lepidoptera in boreal agricultural landscapes. Agric. Ecosyst. Environ. 122, 366–376 (2007).Article 

    Google Scholar 
    46.Tscharntke, T. et al. Landscape constraints on functional diversity of birds and insects in tropical agroecosystems. Ecology 89, 944–951 (2008).PubMed 
    Article 

    Google Scholar 
    47.Hall, D. M. et al. The city as a refuge for insect pollinators. Conserv. Biol. 31, 24–29 (2017).PubMed 
    Article 

    Google Scholar 
    48.Öckinger, E. et al. Life-history traits predict species responses to habitat area and isolation: a cross-continental synthesis. Ecol. Lett. 13, 969–979 (2010).PubMed 

    Google Scholar 
    49.Burivalova, Z. et al. Avian responses to selective logging shaped by species traits and logging practices. Proc. R. Soc. B 282, 20150164 (2015).PubMed 
    Article 

    Google Scholar 
    50.Montero-Castaño, A. & Vilà, M. Impact of landscape alteration and invasions on pollinators: a meta-analysis. J. Ecol. 100, 884–893 (2012).Article 

    Google Scholar 
    51.De Palma, A. et al. Ecological traits affect the sensitivity of bees to land-use pressures in European agricultural landscapes. J. Appl. Ecol. 52, 1567–1577 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    52.Aguirre-Gutiérrez, J. et al. Functional traits help to explain half-century long shifts in pollinator distributions. Sci. Rep. 6, 1–13. (2016).Article 
    CAS 

    Google Scholar 
    53.Shuler, R. E., Roulston, T. H. & Farris, G. E. Farming practices influence wild pollinator populations on squash and pumpkin. J. Economic Entomol. 98, 790–795 (2005).Article 

    Google Scholar 
    54.Cusser, S., Neff, J. L. & Jha, S. Land-use history drives contemporary pollinator community similarity. Landsc. Ecol. 33, 1335–1351 (2018).Article 

    Google Scholar 
    55.Balmford, A. Extinction filters and current resilience: the significance of past selection pressures for conservation biology. Trends Ecol. Evol. 1, 193–196 (1996).Article 

    Google Scholar 
    56.Høye, T., Post, E., Schmidt, N., Trøjelsgaard, K. & Forchhammer, M. C. Shorter flowering seasons and declining abundance of flower visitors in a warmer Arctic. Nat. Clim. Change 3, 759–763 (2013).ADS 
    Article 

    Google Scholar 
    57.Barlow, J. et al. The future of hyperdiverse tropical ecosystems. Nature 559, 517–526 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    58.Williams, J. J., Bates, A. E. & Newbold, T. Human‐dominated land uses favour species affiliated with more extreme climates, especially in the tropics. Ecography 43, 391–405 (2020).Article 

    Google Scholar 
    59.Deutsch, C. A. et al. Impacts of climate warming on terrestrial ectotherms across latitude. Proc. Natl Acad. Sci. USA 105, 6668–6672 (2008).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    60.Blowes, S. A. et al. The geography of biodiversity change in marine and terrestrial assemblages. Science 366, 339–345 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    61.Newbold, T., Oppenheimer, P., Etard, A. & Williams, J. J. Tropical and Mediterranean biodiversity is disproportionately sensitive to land-use and climate change. Nat. Ecol. Evol. 4, 1630–1638 (2020).PubMed 
    Article 

    Google Scholar 
    62.Hudson, L. N. et al. The database of the PREDICTS (Projecting Responses of Ecological Diversity in Changing Terrestrial Systems) project. Ecol. Evolution 7, 145–188 (2017).Article 

    Google Scholar 
    63.Clough, Y. et al. Density of insect-pollinated grassland plants decreases with increasing surrounding land-use intensity. Ecol. Lett. 17, 1168–1177 (2014).PubMed 
    Article 

    Google Scholar 
    64.Lazaro, A., Tscheulin, T., Devalez, J., Nakas, G. & Petanidou, T. Effects of grazing intensity on pollinator abundance and diversity, and on pollination services. Ecol. Entomol. 41, 400–412 (2016).Article 

    Google Scholar 
    65.Baldock, K. C. R. et al. A systems approach reveals urban pollinator hotspots and conservation opportunities. Nat. Ecol. Evol. 3, 363–373 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Ollerton, J., Tarrant, S. & Winfree, R. How many flowering plants are pollinated by animals? Oikos 120, 321–326 (2011).Article 

    Google Scholar 
    67.Hurtt, G. C. et al. Harmonization of land-use scenarios for the period 1500–2100: 600 years of global gridded annual land-use transitions, wood harvest, and resulting secondary lands. Clim. Change 109, 117–161 (2011).ADS 
    Article 

    Google Scholar 
    68.Outhwaite, C. L. et al. Complex long-term biodiversity change among invertebrates, bryophytes and lichens. Nat. Ecol. Evol. 4, 384–392 (2020).PubMed 
    Article 

    Google Scholar 
    69.Rader, R. et al. The winners and losers of land use intensification: Pollinator community disassembly is non-random and alters functional diversity. Diversity Distrib. 20, 908–917 (2014).Article 

    Google Scholar 
    70.Woodcock, B. A. et al. Meta-analysis reveals that pollinator functional diversity and abundance enhance crop pollination and yield. Nat. Commun. 10, 1–10. (2019).ADS 
    CAS 
    Article 

    Google Scholar 
    71.Tscharntke, T. et al. Landscape perspectives on agricultural intensification and biodiversity–ecosystem service management. Ecol. Lett. 8, 857–874 (2005).Article 

    Google Scholar 
    72.DeFries, R. & Rosenzweig, C. Toward a whole-landscape approach for sustainable land use in the tropics. Proc. Natl Acad. Sci. USA 107, 19627–19632 (2010).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    73.Seibold, S. et al. Arthropod decline in grasslands and forests is associated with landscape-level drivers. Nature 574, 671–674 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    74.Weiner, C. N. et al. Land use intensity in grasslands: changes in biodiversity, species composition and specialisation in flower visitor networks. Basic Appl. Ecol. 12, 292–299 (2011).Article 

    Google Scholar 
    75.Parker, W. E. & Howard, J. J. The biology and management of wireworms (Agriotes spp.) on potato with particular reference to the UK. Agric. For. Entomol. 3, 85–98 (2001).Article 

    Google Scholar 
    76.Jauker, F. et al. Pollinator dispersal in an agricultural matrix: opposing responses of wild bees and hoverflies to landscape structure and distance from main habitat. Landsc. Ecol. 24, 547–555 (2009).Article 

    Google Scholar 
    77.Haenke, S. et al. Increasing syrphid fly diversity and density in sown flower strips within simple vs. complex landscapes. J. Appl. Ecol. 46, 1106–1114 (2009).Article 

    Google Scholar 
    78.Speight, M. C. D. Species Accounts of European Syrphidae, 2017. Syrph Net. Database Eur. Syrphidae (Diptera) 97, 1–294 (2017).
    Google Scholar 
    79.Easton, A. H. & Goulson, D. The neonicotinoid insecticide imidacloprid repels pollinating flies and beetles at field-realistic concentrations. PLoS One 8, e54819 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    80.Maggi, F. et al. PEST-CHEMGRIDS, global gridded maps of the top 20 crop-specific pesticide application rates from 2015 to 2025. Sci. Data 6, 1–20. (2019).CAS 
    Article 

    Google Scholar 
    81.Henle, K., Davies, K. F., Kleyer, M., Margules, C. & Settele, J. Predictors of species sensitivity to fragmentation. Biodivers. Conserv. 13, 207–251 (2004).Article 

    Google Scholar 
    82.Watanabe, M. E. Pollination worries rise as honey bees decline. Science 265, 1170 (1994).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    83.Kevan, P. G. Blueberry crops in Nova Scotia and New Brunswick—pesticides and crop reductions. Can. J. Agric. Econ. 25, 61–64 (1977).Article 

    Google Scholar 
    84.Garibaldi, L. A. et al. Wild pollinators enhance fruit set of crops regardless of honey bee abundance. Science 340, 1608–1611 (2013).ADS 
    Article 
    CAS 

    Google Scholar 
    85.Ollerton J. Pollinators & Pollination: Nature and Society (Pelagic Publishing, Exeter, 2021).86.Purvis, A. et al. Modelling and projecting the response of local terrestrial biodiversity worldwide to land use and related pressures: the PREDICTS project. Adv. Ecol. Res. 58, 201–241 (2018).Article 

    Google Scholar 
    87.Brittain, C. A. et al. Impacts of a pesticide on pollinator species richness at different spatial scales. Basic Appl. Ecol. 11, 106–115 (2010).CAS 
    Article 

    Google Scholar 
    88.Melidonis, C. A. & Peter, C. I. Diurnal pollination, primarily by a single species of rodent, documented in Protea foliosa using modified camera traps. South Afr. J. Bot. 97, 9–15 (2015).Article 

    Google Scholar 
    89.Ollerton, J. & Liede, S. Pollination systems in the Asclepiadaceae: a survey and preliminary analysis. Biol. J. Linn. Soc. 62, 593–610 (1997).Article 

    Google Scholar 
    90.Dutton, E. M. & Frederickson, M. E. Why ant pollination is rare: new evidence and implications of the antibiotic hypothesis. Arthropod-Plant Interact. 6, 561–569 (2012).Article 

    Google Scholar 
    91.Dukas, R. & Morse, D. H. Crab spiders affect flower visitation by bees. Oikos 101, 157–163 (2003).Article 

    Google Scholar 
    92.Myers, S. A., Donnellan, S. & Kleindorfer, S. Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland honeyeater (Phylidonyris novaehollandiae). Ecol. Evol. 2, 2397–2412 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    93.Newbold, T. et al. Global effects of land use on local terrestrial biodiversity. Nature 520, 45–50 (2015).ADS 
    CAS 
    Article 

    Google Scholar 
    94.Chao, A., Chazdon, R. L., Colwell, R. K. & Shen, T. J. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8, 148–159 (2005).Article 

    Google Scholar 
    95.Rigby, R. A., Stasinopoulos, D. M. & Akantziliotou, C. A framework for modelling overdispersed count data, including the Poisson-shifted generalized inverse Gaussian distribution. Comput. Stat. Data Anal. 53, 381–393 (2008).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    96.Hansen, M. C. et al. High-resolution global maps of 21st-century forest cover change. Science 342, 850–853 (2013).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    97.Mueller, N. D. et al. Closing yield gaps through nutrient and water management. Nature 490, 254–257 (2012).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    98.West, P. C. et al. Leverage points for improving global food security and the environment. Science 345, 325–328 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    99.Millard, J. et al. Global_effects_of_land-use_intensity_on_local_pollinator-biodiversity (Version v1.0.0). Zenodo https://doi.org/10.5281/zenodo.4593493 (2021). More

  • in

    Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees

    1.Moran NA, McCutcheon JP, Nakabachi A. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. 2008;42:165–90.CAS 
    Article 

    Google Scholar 
    2.Bourguignon T, Lo N, Dietrich C, Roisin Y, Brune A, Evans TA, et al. Rampant host switching shaped the termite gut microbiome. Curr Biol. 2018;28:649–54.CAS 
    Article 

    Google Scholar 
    3.Matsuura Y, Moriyama M, Łukasik P, Vanderpool D, Tanahashi M, Meng X. Recurrent symbiont recruitment from fungal parasites in cicadas. Proc Natl Acad Sci USA. 2018;115:E5970–9.CAS 
    Article 

    Google Scholar 
    4.Chong RA, Moran NA. Evolutionary loss and replacement of Buchnera, the obligate endosymbiont of aphids. ISME J. 2018;12:898–908.CAS 
    Article 

    Google Scholar 
    5.Bennett GM, Moran NA. Heritable symbiosis: the advantages and perils of an evolutionary rabbit hole. Proc Natl Acad Sci USA. 2015;112:10169–76.CAS 
    Article 

    Google Scholar 
    6.Sudakaran S, Kost C, Kaltenpoth M. Symbiont acquisition and replacement as a source of ecological innovation. Trends Microbiol. 2017;25:1–16.Article 

    Google Scholar 
    7.Martinson VG, Danforth BN, Minckley RL, Rueppell O, Tingek S, Moran NA. A simple and distinctive microbiota associated with honey bees and bumble bees. Mol Ecol. 2011;20:619–28.Article 

    Google Scholar 
    8.Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, et al. Dynamic microbiome evolution in social bees. Sci Adv. 2017;3:1–17.Article 

    Google Scholar 
    9.Kwong WK, Moran NA. Gut microbial communities of social bees. Nat Rev Microbiol. 2016;14:374–84.CAS 
    Article 

    Google Scholar 
    10.Rothman JA, Leger L, Graystock P, Russell K, McFrederick QS. The bumble bee microbiome increases survival of bees exposed to selenate toxicity. Environ Microbiol. 2019;21:3417–29.CAS 
    Article 

    Google Scholar 
    11.Koch H, Schmid-Hempel P. Socially transmitted gut microbiota protect bumble bees against an intestinal parasite. Proc Natl Acad Sci USA. 2011;108:19288–92.CAS 
    Article 

    Google Scholar 
    12.Zheng H, Powell JE, Steele MI, Dietrich C, Moran NA. Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proc Natl Acad Sci USA. 2017;114:4775–80.CAS 
    Article 

    Google Scholar 
    13.Mockler BK, Kwong WK, Moran NA, Koch H. Microbiome structure influences infection by the parasite Crithidia bombi in bumble bees. Appl Environ Microbiol. 2018;84:1–11.CAS 
    Article 

    Google Scholar 
    14.Giannini TCG, Boff S, Cordeiro GD, Cartonalo EA Jr, Veiga AK, Imperatriz-Fonseca VL, et al. Crop pollinators in Brazil: a review of reported interactions. Apidologie. 2015;46:209–23.Article 

    Google Scholar 
    15.Koch H, Abrol DP, Li J, Schmid-Hempel P. Diversity and evolutionary patterns of bacterial gut associates of corbiculate bees. Mol Ecol. 2013;22:2028–44.CAS 
    Article 

    Google Scholar 
    16.Leonhardt SD, Kaltenpoth M. Microbial communities of three sympatric Australian stingless bee species. PLoS One. 2014;9:1–6.Article 

    Google Scholar 
    17.Díaz S, de Souza Urbano S, Caesar L, Blochtein B, Sattler A, Zuge V, et al. Report on the microbiota of Melipona quadrifasciata affected by a recurrent disease. J Invertebr Pathol. 2017;143:35–39.Article 

    Google Scholar 
    18.Teixeira ACP, Marini MM, Nicoli JR, Antonini Y, Martins RP, Lachance M-A, et al. Starmerella meliponinorum sp. nov., a novel ascomycetous yeast species associated with stingless bees. Int J Syst Evol Microbiol. 2003;53:339–43.Article 

    Google Scholar 
    19.Paludo CR, Menezes C, Silva-Junior EA, Vollet-Neto A, Andrade-Dominguez A, Pishchany G, et al. Stingless bee larvae require fungal steroid to pupate. Sci Rep. 2018;8:1–10.CAS 
    Article 

    Google Scholar 
    20.Ramírez SR, Nieh JC, Quental TB, Roubik DW, Imperatriz-Fonseca VL, Pierce NE. A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae). Mol Phylogenet Evol. 2010;56:519–25.Article 

    Google Scholar  More

  • in

    Retraction Note: Tree growth in sync

    AffiliationsEnergy and Resources Group, UC Berkeley and Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USALara M. KueppersAuthorsLara M. KueppersCorresponding authorCorrespondence to
    Lara M. Kueppers. More