Cowen R. The role of algal symbiosis in reefs through time. Palaios. 1988;3(2):221–7. https://doi.org/10.2307/3514532.
Article
Google Scholar
Baker AC. Flexibility and specificity in coral-algal symbiosis: diversity, ecology, and biogeography of Symbiodinium. Annu Rev Ecol Evol Syst. 2003;34(1):661–89. https://doi.org/10.1146/annurev.ecolsys.34.011802.132417.
Norris RD. Symbiosis as an evolutionary innovation in the radiation of Paleocene planktic foraminifera. Paleobiology. 1996;22(4):461–80. https://doi.org/10.1017/S0094837300016468.
Article
Google Scholar
Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, et al. Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef. BMC Evol Biol. 2013;13(1):205. https://doi.org/10.1186/1471-2148-13-205.
Muscatine L, Porter JW. Reef corals - mutualistic symbioses adapted to nutrient-poor environments. Bioscience. 1977;27(7):454–60. https://doi.org/10.2307/1297526.
Article
Google Scholar
Brown B. Coral bleaching: causes and consequences. Coral Reefs. 1997;16(1):S129–S38. https://doi.org/10.1007/s003380050249.
Article
Google Scholar
Chakravarti LJ, van Oppen MJH. Experimental evolution in coral photosymbionts as a tool to increase thermal tolerance. Front Mar Sci. 2018;5:227. https://doi.org/10.3389/fmars.2018.00227.
Article
Google Scholar
Howells EJ, Beltran VH, Larsen NW, Bay LK, Willis BL, van Oppen MJH. Coral thermal tolerance shaped by local adaptation of photosymbionts. Nat Clim Chang. 2012;2(2):116–20. https://doi.org/10.1038/nclimate1330.
Article
Google Scholar
Fay SA, Weber MX, Lipps JH. The distribution of Symbiodinium diversity within individual host foraminifera. Coral Reefs. 2009;28(3):717–26. https://doi.org/10.1007/s00338-009-0511-y.
Article
Google Scholar
Mieog JC, Olsen JL, Berkelmans R, Bleuler-Martinez SA, Willis BL, van Oppen MJH. The roles and interactions of symbiont, host and environment in defining coral fitness. Plos One. 2009;4(7):e6364. https://doi.org/10.1371/journal.pone.0006364.
Langer MR, Silk MT, Lipps JH. Global Ocean carbonate and carbon dioxide production; the role of reef foraminifera. J Foraminiferal Res. 1997;27(4):271–7. https://doi.org/10.2113/gsjfr.27.4.271.
Article
Google Scholar
Leutenegger S. Symbiosis in benthic foraminifera - specificity and host adaptations. J Foramin Res. 1984;14(1):16–35. https://doi.org/10.2113/gsjfr.14.1.16.
Article
Google Scholar
Boudagher-Fadel MK. Evolution and geological significance of larger benthic foraminifera. Wignall PB, editor. Amsterdam: Elsevier; 2008.
Google Scholar
Lee JJ, Hallock P. Algal symbiosis as the driving force in the evolution of larger Foraminifera. Ann N Y Acad Sci. 1987;503(1):330–47. https://doi.org/10.1111/j.1749-6632.1987.tb40619.x.
Hohenegger J. Depth coenoclines and environmental considerations of western pacific larger foraminifera. J Foramin Res. 2004;34(1):9–33. https://doi.org/10.2113/0340009.
Article
Google Scholar
Hallock P. Diversification in algal symbiont-bearing foraminifera: a response to oligotrophy? Rev Paléobiol. 1988;2:789–97.
Hallock P. Light dependence in Amphistegina. J Foraminifer Res. 1981;11(1):40–6. https://doi.org/10.2113/gsjfr.11.1.40.
Article
Google Scholar
Renema W. Terrestrial influence as a key driver of spatial variability in large benthic foraminiferal assemblage composition in the central indo-Pacific. Earth-Sci Rev. 2018;177:514–44. https://doi.org/10.1016/j.earscirev.2017.12.013.
Article
Google Scholar
Prazeres M, Renema W. Evolutionary significance of the microbial assemblages of large benthic foraminifera. Biol Rev. 2019;94(3):828–48. https://doi.org/10.1111/brv.12482.
Article
PubMed
Google Scholar
Barnes KH. Diversity and distribution of diatom endosymbionts in Amphistegina spp. (foraminifera) based on molecular and morphological techniques. St. Petersburg: University of South Florida; 2016.
Google Scholar
Pochon X, Garcia-Cuetos L, Baker AC, Castella E, Pawlowski J. One-year survey of a single Micronesian reef reveals extraordinarily rich diversity of Symbiodinium types in soritid foraminifera. Coral Reefs. 2007;26(4):867–82. https://doi.org/10.1007/s00338-007-0279-x.
Prazeres M, Ainsworth T, Roberts TE, Pandolfi JM, Leggat W. Symbiosis and microbiome flexibility in calcifying benthic foraminifera of the Great Barrier Reef. Microbiome. 2017;5(1):38. https://doi.org/10.1186/s40168-017-0257-7.
Holzmann M, Berney C, Hohenegger J. Molecular identification of diatom endosymbionts in nummulitid foraminifera. Symbiosis. 2006;42(2):93–101.
CAS
Google Scholar
Stuhr M, Meyer A, Reymond CE, Narayan GR, Rieder V, Rahnenfuhrer J, et al. Variable thermal stress tolerance of the reef-associated symbiont-bearing foraminifera Amphistegina linked to differences in symbiont type. Coral Reefs. 2018;37(3):811–24. https://doi.org/10.1007/s00338-018-1707-9.
Schmidt C, Morard R, Romero O, Kucera M. Diverse internal symbiont community in the endosymbiotic foraminifera Pararotalia calcariformata: implications for symbiont shuffling under thermal stress. Front Microbiol. 2018;9. https://doi.org/10.3389/fmicb.2018.02018.
Langer MR, Weinmann AE, Lotters S, Bernhard JM, Rodder D. Climate-driven range extension of Amphistegina (Protista, Foraminiferida): models of current and predicted future ranges. PLoS One. 2013;8(2):e54443. https://doi.org/10.1371/journal.pone.0054443.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weinmann AE, Rodder D, Lotters S, Langer MR. Traveling through time: the past, present and future biogeographic range of the invasive foraminifera Amphistegina spp. in the Mediterranean Sea. Mar Micropaleontol. 2013;105:30–9. https://doi.org/10.1016/j.marmicro.2013.10.002.
Prazeres M, Roberts TE, Pandolfi JM. Shifts in species abundance of large benthic foraminifera Amphistegina: the possible effects of tropical cyclone Ita. Coral Reefs. 2017;36(1):305–9. https://doi.org/10.1007/s00338-016-1497-x.
Narayan GR, Reymond CE, Stuhr M, Doo S, Schmidt C, Mann T, et al. Response of large benthic foraminifera to climate and local changes: implications for future carbonate production. Sedimentology. 2021. https://doi.org/10.1111/sed.12858.
Lee JJ. Algal symbiosis in larger foraminifera. Symbiosis. 2006;42(2):63–75.
Google Scholar
Stuhr M, Cameron LP, Blank-Landeshammer B, Reymond CE, Doo SS, Westphal H, et al. Divergent proteomic responses offer insights into resistant physiological responses of a reef-foraminifera to climate change scenarios. Oceans: Multidisciplinary Digital Publishing Institute; 2021.
Google Scholar
Silverstein RN, Correa AMS, Baker AC. Specificity is rarely absolute in coral-algal symbiosis: implications for coral response to climate change. P Roy Soc B-Biol Sci. 2012;279(1738):2609–18.
Google Scholar
Prazeres M, Uthicke S, Pandolfi JM. Influence of local habitat on the physiological responses of large benthic foraminifera to temperature and nutrient stress. Sci Rep. 2016;6(1):21936. https://doi.org/10.1038/srep21936.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmidt C, Morard R, Almogi-Labin A, Weinmann AE, Titelboim D, Abramovich S, et al. Recent invasion of the symbiont-bearing foraminifera Pararotalia into the eastern Mediterranean facilitated by the ongoing warming trend. PLoS One. 2015;10(8):e0132917. https://doi.org/10.1371/journal.pone.0132917.
Lee JJ. Diatoms as endosymbionts. In: Seckbach J, Kociolek P (editors) The diatom world: Springer, Dordrecht; 2011. p. 437–64.
Lee JJ, McEnergy M, Ter Kuile B, Erez J, Roetger R, Rockwell R, et al. Identification and distribution of endosymbiotic diatoms in larger foraminifera. Micropaleontology. 1989;35(4):353–66. https://doi.org/10.2307/1485677.
Article
Google Scholar
Akther S, Suzuki J, Pokhrel P, Okada T, Imamura M, Enomoto T, et al. Behavior of eukaryotic symbionts in large benthic foraminifers Calcarina gaudichaudii and Baculogypsina sphaerulata under exposure to wastewater. Environ Pollut. 2020;265(Part A):114971. https://doi.org/10.1016/j.envpol.2020.114971.
Roth MS. The engine of the reef: photobiology of the coral–algal symbiosis. Front Microbiol. 2014;5:422. https://doi.org/10.3389/fmicb.2014.00422.
van Oppen MJ, Palstra FP, Piquet AM-T, Miller DJ. Patterns of coral–dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host–symbiont selectivity. Proc R Soc Lond Ser B Biol Sci. 2001;268(1478):1759–67. https://doi.org/10.1098/rspb.2001.1733.
Garcia-Cuetos L, Pochon X, Pawlowski J. Molecular evidence for host–symbiont specificity in soritid foraminifera. Protist. 2005;156(4):399–412. https://doi.org/10.1016/j.protis.2005.08.003.
Article
CAS
PubMed
Google Scholar
Momigliano P, Uthicke S. Symbiosis in a giant protist (Marginopora vertebralis, Soritinae): flexibility in symbiotic partnerships along a natural temperature gradient. Mar Ecol Prog Ser. 2013;491:33–46. https://doi.org/10.3354/meps10465.
Article
Google Scholar
Lee J, Sang K, Ter Kuile B, Strauss E, Lee P, Faber W. Nutritional and related experiments on laboratory maintenance of three species of symbiont-bearing, large foraminifera. Mar Biol. 1991;109(3):417–25. https://doi.org/10.1007/BF01313507.
Article
Google Scholar
Ter Kuile B, Erez J. The size and function of the internal inorganic carbon pool of the foraminifer Amphistegina lobifera. Mar Biol. 1988;99(4):481–7. https://doi.org/10.1007/BF00392555.
Uthicke S, Nobes K. Benthic Foraminifera as ecological indicators for water quality on the Great Barrier Reef. Estuar Coast Shelf Sci. 2008;78(4):763–73. https://doi.org/10.1016/j.ecss.2008.02.014.
Schmidt C, Morard R, Prazeres M, Barak H, Kucera M. Retention of high thermal tolerance in the invasive foraminifera Amphistegina lobifera from the eastern Mediterranean and the Gulf of Aqaba. Mar Biol. 2016;163(11):228. https://doi.org/10.1007/s00227-016-2998-4.
Article
Google Scholar
Uthicke S, Altenrath C. Water column nutrients control growth and C: N ratios of symbiont-bearing benthic foraminifera on the Great Barrier Reef, Australia. Limnol Oceanogr. 2010;55(4):1681–96. https://doi.org/10.4319/lo.2010.55.4.1681.
Article
CAS
Google Scholar
Larsen AR. Phylogentic and paleobiogeographical trends in the foraminiferal genus Amphistegina. Revista Espanola de Micropaleontolgia. 1978;10(2):217–43.
Google Scholar
Larsen AR. Studies of recent Amphistegina, taxonomy and some ecological aspects. Israel J Earth Sci. 1976;25(1):1–26.
Google Scholar
Manning MM, Gates RD. Diversity in populations of free-living Symbiodinium from a Caribbean and Pacific reef. Limnol Oceanogr. 2008;53(5):1853–61. https://doi.org/10.4319/lo.2008.53.5.1853.
Caruso A, Cosentino C. The first colonization of the genus Amphistegina and other exotic benthic foraminifera of the Pelagian Islands and South-Eastern Sicily (Central Mediterranean Sea). Mar Micropaleontol. 2014;111:38–52. https://doi.org/10.1016/j.marmicro.2014.05.002.
Article
Google Scholar
Dunnington D. ggspatial: Spatial Data Framework for ggplot2. R package version 1.1.4; 2020.
Google Scholar
South A. rnaturalearthdata: World Vector Map Data from Natural Earth Used in ‘rnaturalearth’. R package version 0.1.0; 2017.
Google Scholar
Förderer M, Rodder D, Langer MR. Patterns of species richness and the center of diversity in modern indo-Pacific larger foraminifera. Sci Rep. 2018;8(1):8189. https://doi.org/10.1038/s41598-018-26598-9.
Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One. 2014;9(2):e87624. https://doi.org/10.1371/journal.pone.0087624.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31. https://doi.org/10.1111/j.1365-294X.2009.04480.x.
Article
CAS
PubMed
Google Scholar
Team RC. R: a language and environment for statistical computing. R Foundation for Statistical Computing: Vienna; 2018.
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3. https://doi.org/10.1038/nmeth.3869.
Article
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 2; referees: 3 approved]. F1000 Research. 2016;5:1492. https://doi.org/10.12688/f1000research.8986.2.
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(D1):D590–D6.
Article
CAS
PubMed
Google Scholar
Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics. 2015;16(1):322. https://doi.org/10.1186/s12859-015-0749-z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schliep KP. Phangorn: phylogenetic analysis in R. Bioinformatics. 2011;27(4):592–3. https://doi.org/10.1093/bioinformatics/btq706.
Article
CAS
PubMed
Google Scholar
McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Plos One. 2013;8(4):e61217. https://doi.org/10.1371/journal.pone.0061217.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. R package version 2.5–1. 2017.
Google Scholar
Lahti L, Shetty S, Blake T, Salojarvi J. Tools for microbiome analysis in R. Version 1.1.10012; 2017.
Google Scholar
Chao A. Nonparametric estimation of the number of classes in a population. Scand J Stat. 1984;11(4):265–70.
Simpson EH. Measurement of diversity. Nature. 1949;163(4148):688.
Article
Google Scholar
Andersen KS, Kirkegaard RH, Karst SM, Albertsen M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. bioRxiv; 2018.
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leigh JW, Bryant D. POPART: full-feature software for haplotype network construction. Methods Ecol Evol. 2015;6(9):1110–6. https://doi.org/10.1111/2041-210X.12410.
Article
Google Scholar
Bandelt H-J, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999;16(1):37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036.
Article
CAS
PubMed
Google Scholar
Glez-Peña D, Gómez-Blanco D, Reboiro-Jato M, Fdez-Riverola F, Posada D. ALTER: program-oriented format conversion of DNA and protein alignments. Nucleic Acids Res. 2010;38(suppl_2):W14–W8. https://doi.org/10.1093/nar/gkq321.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–W9. https://doi.org/10.1093/nar/gkz239.
Article
CAS
PubMed
PubMed Central
Google Scholar