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Environmental DNA signatures distinguish between tsunami and storm deposition in overwash sand

  • 1.

    Nicholls, R. J. et al. in Climate Change 2007: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (eds Parry, M. L., Canziani, O. F., Palutikof, J. P., van der Linden, P. J. & Hanson, C. E.) Ch. 6 (Cambridge University Press, 2007).

  • 2.

    Gordon, M. et al. in Global Assessment Report on Disaster Risk Reduction Ch. 3 (UNDRR, 2019).

  • 3.

    Dominey-Howes, D. Documentary and geological records of tsunamis in the Aegean Sea region of Greece and their potential value to risk assessment and disaster management. Nat. Hazards 25, 195–224 (2002).

    Article 

    Google Scholar 

  • 4.

    Switzer, A. D., Yu, F., Gouramanis, C., Soria, J. & Pham, T. D. Integrated different records to assess coastal hazards at multi-century timescales. J. Coastal Res. 70, 723–728 (2014).

    Article 

    Google Scholar 

  • 5.

    Jankaew, K. et al. Medieval forewarning of the 2004 Indian Ocean tsunami in Thailand. Nature 455, 1228–1231 (2008).

    CAS 
    Article 

    Google Scholar 

  • 6.

    Liu, K. B. & Fearn, M. L. Reconstruction of prehistoric landfall frequencies of catastrophic hurricanes in northwestern Florida from lake sediment records. Quaternary Res. 54, 238–245 (2000).

    Article 

    Google Scholar 

  • 7.

    Donnelly, J. P. & Woodruff, J. D. Intense hurricane activity over the past 5,000 years controlled by El Nino and the West African monsoon. Nature 447, 465–468 (2007).

    CAS 
    Article 

    Google Scholar 

  • 8.

    Nanayama, F. et al. Unusually large earthquakes inferred from tsunami deposits along the Kuril trench. Nature 424, 660–663 (2003).

    CAS 
    Article 

    Google Scholar 

  • 9.

    Gouramanis, C. et al. High-frequency coastal overwash deposits from Phra Thong Island, Thailand. Sci. Rep. 7, 1–9 (2017).

    Article 

    Google Scholar 

  • 10.

    Nanayama, F. et al. differences between the 1993 Hokkaido-nansei-oki tsunami and the 1959 Miyakojima typhoon at Taisei, southwestern Hokkaido, northern Japan. Sediment. Geol. 135, 255–264 (2000).

    Article 

    Google Scholar 

  • 11.

    Morton, R. A., Gelfenbaum, G. & Jaffe, B. E. Physical criteria for distinguishing sandy tsunami and storm deposits using modern examples. Sediment. Geol. 200, 184–207 (2007).

    Article 

    Google Scholar 

  • 12.

    Marriner, N. et al. Tsunamis in the geological record: Making waves with a cautionary tale from the Mediterranean. Sci. Adv. 3, e1700485 (2017).

    Article 

    Google Scholar 

  • 13.

    Vött, A. et al. Returning to facts: response to the refusal of tsunami traces in the ancient harbour of Lechaion (Gulf of Corinth, Greece) by ‘non-catastrophists’ – Reaffirmed evidence of harbour destruction by historical earthquakes and tsunamis in AD 69–79 and the 6th cent. AD and a preceding pre-historical event in the early 8th cent. BC. Zeitschriff Geomorphologie 61, 275–302 (2018).

  • 14.

    Shanmugam, G. The tsunamite problem. J. Sediment. Res. 76, 718–730 (2006).

    Article 

    Google Scholar 

  • 15.

    Chagué-Goff, C., Chan, J. C. H., Goff, J. & Gadd, P. Late Holocene record of environmental changes, cyclones and tsunamis in a coastal lake, Mangaia, Cook Islands. Isl. Arc 25, 333–349 (2016).

    Article 

    Google Scholar 

  • 16.

    Pham, D. T. et al. Elemental and mineralogical analysis of marine and coastal sediments from Phra Thong Island, Thailand: Insights into the provenance of coastal hazard deposits. Mar. Geol. 385, 274–292 (2017).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Sawai, Y. et al. Diatom assemblages in tsunami deposits associated with the 2004 Indian Ocean Tsunami at Phra Thong Island, Thailand. Mar. Micropaleontol. 73, 70–79 (2009).

    Article 

    Google Scholar 

  • 18.

    Pilarczyk, J. E. et al. Microfossils from coastal environments as indicators of paleo-earthquakes, tsunamis and storms. Palaeogrogr. Palaeocl. 413, 144–157 (2017).

    Article 

    Google Scholar 

  • 19.

    Gouramanis C. in Geological Records of Tsunamis and other Extreme Waves (eds Engel, M., Pilarczyk, J., May, S. M., Brill, D. & Garrett, E.) Ch. 13 (Elsevier, 2020).

  • 20.

    Goff, J., Chagué-Goff, C., Nichol, S., Jaffe, B. & Dominey-Howes, D. Progress in palaeotsunami research. Sediment. Geol. 243, 70–88 (2012).

    Article 

    Google Scholar 

  • 21.

    Asano, R. et al. Changes in bacterial communities in seawater-flooded soil in the four years after the 2011 Tohoku tsunami in Japan. J. Mar. Sci. Eng. 8, 76 (2020).

    Article 

    Google Scholar 

  • 22.

    Atwater, B. F. et al. Extreme waves in the British Virgin Islands during the last centuries before 1500 CE. Geosphere 13, 301–368 (2017).

    Article 

    Google Scholar 

  • 23.

    Jentsch, A. & White, P. A theory of pulse dynamics and disturbance in ecology. Ecology 100, e02734 (2019).

    Article 

    Google Scholar 

  • 24.

    Ramesh, S., Jayaprakashvel, M. & Mathivanan, N. Microbial status in seawater and coastal sediment during pre- and post-tsunami periods in the Bay of Bengal, India. Mar. Ecol. 27, 198–203 (2006).

    Article 

    Google Scholar 

  • 25.

    Nayak, A. K. et al. Post tsunami changes in soil properties of Andaman Islands, India. Environ. Monit. Assess. 170, 185–193 (2010).

    CAS 
    Article 

    Google Scholar 

  • 26.

    Godson, P. S., Chandrasekar, N., Kumar, S. K. & Vimi, P. V. Microbial diversity in coastal sediments during pre- and post-tsunami periods in the south east coast of India. Front. Biol. 9, 161–167 (2014).

    Article 

    Google Scholar 

  • 27.

    Hiraoka, S. et al. Genomic and metagenomics analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. BMC Genomics 17, 1–13 (2016).

    Article 
    CAS 

    Google Scholar 

  • 28.

    Asano, R. et al. Seawater inundation from the 2011 Tohoku Tsunami continues to strongly affect soil bacterial communities 1 year later. Microb. Ecol. 66, 639–646 (2013).

    CAS 
    Article 

    Google Scholar 

  • 29.

    Somboonna, N. et al. Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials. PLoS ONE 9, e94236 (2014).

    Article 
    CAS 

    Google Scholar 

  • 30.

    Tas, N. et al. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J 8, 1904–1919 (2014).

    CAS 
    Article 

    Google Scholar 

  • 31.

    Dooley, S. R. & Treseder, K. K. The effect of fire on microbial biomass: a meta-analysis of field studies. Biogeochemistry 109, 49–61 (2012).

    Article 

    Google Scholar 

  • 32.

    Kawagucci, S. et al. Disturbance of deep-sea environments induced by the M9. 0 Tohoku Earthquake. Sci. Rep. 2, 1–7 (2012).

    Article 
    CAS 

    Google Scholar 

  • 33.

    Morimura, S., Zeng, X., Noboru, N. & Hosono, T. Changes to the microbial communities within groundwater in response to a large crustal earthquake in Kumamoto, southern Japan. J. Hydrol. 581, 124341 (2020).

    Article 

    Google Scholar 

  • 34.

    Olsen, G. J., Lane, D. J., Giovannoni, S. J. & Pace, N. R. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365 (1986).

    CAS 
    Article 

    Google Scholar 

  • 35.

    Handelsman, J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol. Biol. R 68, 669–685 (2004).

    CAS 
    Article 

    Google Scholar 

  • 36.

    Szczuciński, W. et al. Ancient sedimentary DNA reveals past tsunami deposits. Mar. Geol. 381, 29–33 (2016).

    Article 
    CAS 

    Google Scholar 

  • 37.

    Nealson, K. H. Sediment bacteria: who’s there, what are they doing, and what’s new? Annu. Rev. Earth Pl. Sc 25, 403–434 (1997).

    CAS 
    Article 

    Google Scholar 

  • 38.

    Srinivasalu, S., Karthikeyan, A., Switzer, A. D. & Gouramanis, C. Sedimentological characteristics of tsunami and storm deposits: a modern analogue from Southeast Indian Coast. In Paper Presented at the AOGS-AGU Join Assembly, Singapore, 13–17 September 2012 (2012)

  • 39.

    Switzer, A. D., Srinivasalu, S., Thangadurai, N. & Mohan, V. R. Bedding structures in Indian tsunami deposits provide clues to the dynamics of tsunami inundation. Geol. Soc. Spec. Publ. 361, 61–77 (2012).

    Article 

    Google Scholar 

  • 40.

    Gouramanis, C. et al. Same Same, but different: sedimentological comparison of recent storm and Tsunami deposits from the south-eastern coastline of India. In Paper presented in AGU Fall Meeting (NH21A-3811), San Francisco, California, 15 – 19 December 2014 (2014).

  • 41.

    Fisher, R. A., Corbet, A. S. & Williams, C. B. The relation between the number of species and the number of individuals in a random sample of animal population. J. Anim. Ecol. 12, 42–58 (1943).

    Article 

    Google Scholar 

  • 42.

    Hurlbert, S. H. The nonconcept of species diversity: a critique and alternative parameters. Ecology 52, 577–586 (1971).

    Article 

    Google Scholar 

  • 43.

    Xu, X. et al. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems. Sci. Rep. 5, 1–8 (2020).

    Google Scholar 

  • 44.

    Legendre, P. & Anderson, M. J. Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol. Monogr. 69, 1–24 (1999).

    Article 

    Google Scholar 

  • 45.

    Ranjard, L. et al. Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity. Nat. Commun. 4, 1–10 (2013).

    Article 
    CAS 

    Google Scholar 

  • 46.

    Shanmugam, G. Process-sedimentological challenges in distinguishing paleo-tsunami deposits. Nat. Hazards 63, 5–30 (2012).

    Article 

    Google Scholar 

  • 47.

    Szczuciński, W. et al. Sediment sources and sedimentation processes of 2011 Tohoku-oki tsunami deposits on the Sendai Plain, Japan – Insights from diatoms, nannoliths and grain size distribution. Sediment. Geol. 282, 40–56 (2012).

    Article 

    Google Scholar 

  • 48.

    Costa, P. J. M. et al. The application of microtextural and heavy mineral analysis to discriminate between storm and tsunami deposits. Geol. Soc. Spec. Publ. 456, 167–190 (2018).

    Article 

    Google Scholar 

  • 49.

    Dominey-Howes, D., Dawson, A. & Smith, D. Late Holocene coastal tectonics at Falasarna, western Crete: a sedimentary study. Geol. Soc. Spec. Publ. 146, 343–352 (1999).

    Article 

    Google Scholar 

  • 50.

    Switzer, A. D. & Jones, B. G. Large-scale washover sedimentation in a freshwater lagoon from the southeast Australian coast: sea-level change, tsunami or exceptionally large storm? Holocene 18, 787–803 (2008).

    Article 

    Google Scholar 

  • 51.

    Waring, B. & Hawkes, C. V. Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient. FEMS Microbiol. Ecol. 94, fiy001 (2018).

  • 52.

    Chénard, C. et al. Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters. Sci. Rep. 9, 1–13 (2019).

    Article 
    CAS 

    Google Scholar 

  • 53.

    Saxena, G. et al. Metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway. mSystems 3, e00136–17 (2018).

  • 54.

    Hadziavdic, K. et al. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PloS ONE 9, e87624 (2014).

    Article 
    CAS 

    Google Scholar 

  • 55.

    Mariadassou, M., Pichon, S. & Ebert, D. Microbial ecosystems are dominated by specialist taxa. Ecol. Lett. 18, 974–982 (2015).

    Article 

    Google Scholar 

  • 56.

    Sheth, A., Sanyal, S., Jaiswal, A. & Gandhi, P. Effects of the December 2004 India Ocean Tsunami on the Indian mainland. Earthq. Spectra 22, S435–S473 (2006).

    Article 

    Google Scholar 

  • 57.

    Blot, S. J. & Pye, K. GRADISTAT: a grain size distribution and statistics package for the analysis of unconsolidated sediments. Earth Surf. Proc. Land. 26, 1237–1248 (2001).

    Article 

    Google Scholar 

  • 58.

    Folk, R. L. & Ward, W. C. Brazos river bar: a study in the significance of grain size parameter. J. Sediment. Res. 27, 3–26 (1957).

    Article 

    Google Scholar 

  • 59.

    Sambrook, J., Russell, D., & Sambrook, J. in The Condensed Protocols from Molecular Cloning: A Laboratory Manual (eds Sambrook, J. & Russell, D. W.) (Cold Spring Harbor Laboratory Press, 2006).

  • 60.

    Wilkins, D., Van Sebille, E., Rintoul, S. R., Lauro, F. M. & Cavicchioli, R. Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects. Nat. Commun. 4, 1–7 (2013).

    Article 
    CAS 

    Google Scholar 

  • 61.

    Allen, M. A. & Cavicchioli, R. Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data. Sci. Rep. 7, 1–16 (2017).

    Article 
    CAS 

    Google Scholar 

  • 62.

    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet 17, 10–12 (2011).

    Article 

    Google Scholar 

  • 63.

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

    CAS 
    Article 

    Google Scholar 

  • 64.

    Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J 11, 2639–2643 (2017).

    Article 

    Google Scholar 

  • 65.

    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

    CAS 
    Article 

    Google Scholar 

  • 66.

    Guillou, L. et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41, D597–D604 (2012).

    Article 
    CAS 

    Google Scholar 

  • 67.

    R Core Team. R: A language and environment for statistical computing. R https://www.R-project.org/ (2017).

  • 68.

    Oksanen, J. et al. vegan: Community Ecology Package. Vienna: R Foundation for Statistical Computing.[Google Scholar]. (2016).

  • 69.

    Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral. Ecol. 26, 32–46 (2001).

    Google Scholar 

  • 70.

    Anderson, M. & Ter Braa, C. Permutation tests for multi-factorial analysis of variance. J. Stat. Comput. Sim. 73, 85–113 (2003).

    Article 

    Google Scholar 

  • 71.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).

    Article 
    CAS 

    Google Scholar 

  • 72.

    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B: Met. 57, 289–300 (1995).

    Google Scholar 

  • 73.

    Murtagh, F. & Legendre, P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? J. Classif. 31, 274–295 (2014).

    Article 

    Google Scholar 


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