in

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities

  • 1.

    IPBES. Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science—Policy Platform on Biodiversity and Ecosystem Services (eds Brondizio, E. S. et al.) (IPBES Secretariat, 2019).

  • 2.

    Millennium Ecosystem Assessment. Ecosystems and Human Well-Being: Biodiversity Synthesis ed Ma (World Resources Institute, 2005). http://www.loc.gov/catdir/toc/ecip0512/2005013229.html. Accessed June 2019.

  • 3.

    Hooper, D. U. et al. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486(7401), 105 (2012).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 4.

    Vellend, M. et al. Homogenization of forest plant communities and weakening of species–environment relationships via agricultural land use. J. Ecol. 95(3), 565–573. https://doi.org/10.1111/j.1365-2745.2007.01233.x (2007).

    Article 

    Google Scholar 

  • 5.

    Karp, D. S. et al. Intensive agriculture erodes β-diversity at large scales. Ecol. Lett. 15(9), 963–970. https://doi.org/10.1111/j.1461-0248.2012.01815.x (2012).

    Article 
    PubMed 

    Google Scholar 

  • 6.

    Anderson, M. J. et al. Navigating the multiple meanings of β diversity: A roadmap for the practicing ecologist. Ecol. Lett. 14(1), 19–28. https://doi.org/10.1111/j.1461-0248.2010.01552.x (2011).

    ADS 
    Article 
    PubMed 

    Google Scholar 

  • 7.

    Socolar, J. B., Gilroy, J. J., Kunin, W. E. & Edwards, D. P. How should beta-diversity inform biodiversity conservation?. Trends Ecol. Evol. 31(1), 67–80. https://doi.org/10.1016/j.tree.2015.11.005 (2016).

    Article 
    PubMed 

    Google Scholar 

  • 8.

    Mori, A. S., Isbell, F. & Seidl, R. β-Diversity, community assembly, and ecosystem functioning. Trends Ecol. Evol. 33(7), 549–564 (2018).

    Article 

    Google Scholar 

  • 9.

    Vellend, M. Conceptual synthesis in community ecology. Q. Rev. Biol. 85(2), 183–206 (2010).

    Article 

    Google Scholar 

  • 10.

    Wang, S., Lamy, T., Hallett, L. M. & Loreau, M. Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: Linking theory to data. Ecography (Cop) 42(6), 1200–1211. https://doi.org/10.1111/ecog.04290 (2019).

    Article 

    Google Scholar 

  • 11.

    Olden, J. D. Biotic homogenization: A new research agenda for conservation biogeography. J. Biogeogr. 33(12), 2027–2039. https://doi.org/10.1111/j.1365-2699.2006.01572.x (2006).

    Article 

    Google Scholar 

  • 12.

    Loreau, M., Mouquet, N. & Gonzalez, A. Biodiversity as spatial insurance in heterogeneous landscapes. Proc. Natl. Acad. Sci. 100(22), 12765–12770 (2003).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 13.

    Harrison, S. Species Diversity, Spatial Scale, and Global Change (Sinauer Sunderland, 1993).

    Google Scholar 

  • 14.

    Sax, D. F. & Gaines, S. D. Species diversity: From global decreases to local increases. Trends Ecol. Evol. 18(11), 561–566 (2003).

    Article 

    Google Scholar 

  • 15.

    Hillebrand, H. & Matthiessen, B. Biodiversity in a complex world: Consolidation and progress in functional biodiversity research. Ecol. Lett. 12(12), 1405–1419 (2009).

    Article 

    Google Scholar 

  • 16.

    Magurran, A. E. & McGill, B. J. Biological Diversity: Frontiers in Measurement and Assessment (Oxford University Press, 2010).

    Google Scholar 

  • 17.

    Usseglio, P. Quantifying reef fishes: Bias in observational approaches. In Ecology of Fishes on Coral Reefs (ed Mora, C.) 270–273 (Cambridge University Press, 2015). https://www.cambridge.org/core/books/ecology-of-fishes-on-coral-reefs/quantifying-reef-fishes-bias-in-observational-approaches/660760F9E62CC61DEB48C8124AD44CDC. Accessed June 2019.

  • 18.

    Caldwell, Z. R., Zgliczynski, B. J., Williams, G. J. & Sandin, S. A. Reef Fish survey techniques: Assessing the potential for standardizing methodologies. PLoS One 11(4), e0153066. https://doi.org/10.1371/journal.pone.0153066 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 19.

    Worm, B. et al. Impacts of biodiversity loss on ocean ecosystem services. Science 314(5800), 787–790 (2006).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 20.

    Barbier, E. B. Marine ecosystem services. Curr. Biol. 27(11), R507–R510 (2017).

    CAS 
    Article 

    Google Scholar 

  • 21.

    Goodwin, K. D. et al. DNA sequencing as a tool to monitor marine ecological status. Front. Mar. Sci. 4, 107. https://doi.org/10.3389/fmars.2017.00107 (2017).

    Article 

    Google Scholar 

  • 22.

    Deiner, K. et al. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol. Ecol. 26(21), 5872–5895. https://doi.org/10.1111/mec.14350 (2017).

    Article 
    PubMed 

    Google Scholar 

  • 23.

    Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21(8), 2045–2050. https://doi.org/10.1111/j.1365-294X.2012.05470.x (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 24.

    Creer, S. et al. The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol. Evol. 7(9), 1008–1018. https://doi.org/10.1111/2041-210X.12574 (2016).

    Article 

    Google Scholar 

  • 25.

    Stat, M. et al. Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment. Sci. Rep. 7(1), 12240. https://doi.org/10.1038/s41598-017-12501-5 (2017).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 26.

    Bakker, J. et al. Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact. Sci. Rep. 7(1), 16886. https://doi.org/10.1038/s41598-017-17150-2 (2017).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Port, J. A. et al. Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Mol. Ecol. 25(2), 527–541. https://doi.org/10.1111/mec.13481 (2016).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 28.

    Andruszkiewicz, E. A. et al. Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS One 12(4), e0176343. https://doi.org/10.1371/journal.pone.0176343 (2017).

    MathSciNet 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 29.

    Yamamoto, S. et al. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci. Rep. 7, 40368. https://doi.org/10.1038/srep40368 (2017).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 30.

    O’Donnell, J. L. et al. Spatial distribution of environmental DNA in a nearshore marine habitat. PeerJ 5, e3044. https://doi.org/10.7717/peerj.3044 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 31.

    Jeunen, G.-J. et al. Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Mol. Ecol. Resour. 19(2), 426–438. https://doi.org/10.1111/1755-0998.12982 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 32.

    Stat, M. et al. Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conserv. Biol. 33(1), 196–205 (2019).

    Article 

    Google Scholar 

  • 33.

    West, K. M. et al. eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Mol. Ecol. 29(6), 1069–1086. https://doi.org/10.1111/mec.15382 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 34.

    Graham, H. M. Effects of local deforestation on the diversity and structure of Southern California giant kelp forest food webs. Ecosystems 7(4), 341–357. https://doi.org/10.1007/s10021-003-0245-6 (2004).

    Article 

    Google Scholar 

  • 35.

    Miller, R. J. et al. Giant kelp, Macrocystis pyrifera, increases faunal diversity through physical engineering. Proc R Soc B Biol Sci 285(1874), 20172571 (2018).

    Article 

    Google Scholar 

  • 36.

    Lamy, T. et al. Scale-specific drivers of kelp forest communities. Oecologia 186(1), 217–233 (2018).

    ADS 
    Article 

    Google Scholar 

  • 37.

    Vergés, A. et al. Long-term empirical evidence of ocean warming leading to tropicalization of fish communities, increased herbivory, and loss of kelp. Proc. Natl. Acad. Sci. 113(48), 13791–13796 (2016).

    Article 

    Google Scholar 

  • 38.

    Steneck, R. S. et al. Kelp forest ecosystems: Biodiversity, stability, resilience and future. Environ. Conserv. 29(04), 436–459 (2003).

    Article 

    Google Scholar 

  • 39.

    Nekola, J. C. & White, P. S. The distance decay of similarity in biogeography and ecology. J. Biogeogr. 26(4), 867–878. https://doi.org/10.1046/j.1365-2699.1999.00305.x (1999).

    Article 

    Google Scholar 

  • 40.

    Claisse, J. T. et al. Biogeographic patterns of communities across diverse marine ecosystems in southern California. Mar. Ecol. 39(S1), e12453. https://doi.org/10.1111/maec.12453 (2018).

    MathSciNet 
    Article 

    Google Scholar 

  • 41.

    Jerde, C. L., Wilson, E. A. & Dressler, T. L. Measuring global fish species richness with eDNA metabarcoding. Mol. Ecol. Resour. 19(1), 19–22. https://doi.org/10.1111/1755-0998.12929 (2019).

    Article 
    PubMed 

    Google Scholar 

  • 42.

    Sigsgaard, E. E. et al. Seawater environmental DNA reflects seasonality of a coastal fish community. Mar. Biol. 164(6), 128. https://doi.org/10.1007/s00227-017-3147-4 (2017).

    CAS 
    Article 

    Google Scholar 

  • 43.

    Nickols, K. J., Wilson White, J., Largier, J. L. & Gaylord, B. Marine population connectivity: Reconciling large-scale dispersal and high self-retention. Am. Nat. 185(2), 196–211. https://doi.org/10.1086/679503 (2015).

    Article 
    PubMed 

    Google Scholar 

  • 44.

    Nickols, K. J., Gaylord, B. & Largier, J. L. The coastal boundary layer: Predictable current structure decreases alongshore transport and alters scales of dispersal. Mar. Ecol. Prog. Ser. 464, 17–35 (2012).

    ADS 
    Article 

    Google Scholar 

  • 45.

    Sassoubre, L. M., Yamahara, K. M., Gardner, L. D., Block, B. A. & Boehm, A. B. Quantification of environmental DNA (eDNA) shedding and decay rates for three marine fish. Environ. Sci. Technol. 50(19), 10456–10464. https://doi.org/10.1021/acs.est.6b03114 (2016).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 46.

    Collins, R. A. et al. Persistence of environmental DNA in marine systems. Commun. Biol. 1(1), 185. https://doi.org/10.1038/s42003-018-0192-6 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 47.

    Andruszkiewicz Allan, E., Zhang, W. G., Lavery, C. A. & Govindarajan, F. A. Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes. Environ. DNA 3(2), 492–514. https://doi.org/10.1002/edn3.141 (2021).

    Article 

    Google Scholar 

  • 48.

    Hansen, B. K., Bekkevold, D., Clausen, L. W. & Nielsen, E. E. The sceptical optimist: Challenges and perspectives for the application of environmental DNA in marine fisheries. Fish Fish. 19(5), 751–768. https://doi.org/10.1111/faf.12286 (2018).

    Article 

    Google Scholar 

  • 49.

    Weltz, K. et al. Application of environmental DNA to detect an endangered marine skate species in the wild. PLoS One 12(6), e0178124. https://doi.org/10.1371/journal.pone.0178124 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 50.

    Fram, J. P. et al. Physical pathways and utilization of nitrate supply to the giant kelp, Macrocystis pyrifera. Limnol. Oceanogr. 53(4), 1589–1603. https://doi.org/10.4319/lo.2008.53.4.1589 (2008).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 51.

    Jackson, G. A. & Winant, C. D. Effect of a kelp forest on coastal currents. Cont. Shelf. Res. 2(1), 75–80 (1983).

    ADS 
    Article 

    Google Scholar 

  • 52.

    Grant, W. D. & Madsen, O. S. The continental-shelf bottom boundary layer. Annu. Rev. Fluid Mech. 18(1), 265–305. https://doi.org/10.1146/annurev.fl.18.010186.001405 (1986).

    ADS 
    MathSciNet 
    Article 
    MATH 

    Google Scholar 

  • 53.

    Leary, P. R. et al. “Internal tide pools” prolong kelp forest hypoxic events. Limnol. Oceanogr. 62(6), 2864–2878. https://doi.org/10.1002/lno.10716 (2017).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 54.

    Gaylord, B. et al. Spatial patterns of flow and their modification within and around a giant kelp forest. Limnol. Oceanogr. 52(5), 1838–1852 (2007).

    ADS 
    Article 

    Google Scholar 

  • 55.

    Lafferty, K. D., Benesh, K. C., Mahon, A. R., Jerde, C. L. & Lowe, C. G. Detecting Southern California’s white sharks with environmental DNA. Front. Mar. Sci. 5, 355. https://doi.org/10.3389/fmars.2018.00355 (2018).

    Article 

    Google Scholar 

  • 56.

    Miya, M. et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2(7), 150088 (2015).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 57.

    Hyde, J. R. & Vetter, R. D. The origin, evolution, and diversification of rockfishes of the genus Sebastes (Cuvier). Mol. Phylogenet. Evol. 44(2), 790–811 (2007).

    CAS 
    Article 

    Google Scholar 

  • 58.

    Min, M. A., Barber, P. H. & Gold, Z. MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes). bioRxiv. (2020). http://biorxiv.org/content/early/2020/10/30/2020.10.29.360859.abstract. Accessed January 2021.

  • 59.

    Gold, Z., Sprague, J., Kushner, D. J., Zerecero Marin, E. & Barber, P. H. eDNA metabarcoding as a biomonitoring tool for marine protected areas. PLoS One 16(2), e0238557. https://doi.org/10.1371/journal.pone.0238557 (2021).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 60.

    Civade, R. et al. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS One 11(6), e0157366 (2016).

    Article 

    Google Scholar 

  • 61.

    Berry, T. E. et al. Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events. PLoS Genet. 15(2), e1007943. https://doi.org/10.1371/journal.pgen.1007943 (2019).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 62.

    Ausubel, J. H., Stoeckle, M. Y. & Gaffney, P. Final Report of the 1st US National Conference on Marine Environmental DNA (eDNA). (2019).

  • 63.

    Reed, D. C. SBC LTER: Reef: Annual time series of biomass for kelp forest species, ongoing since 2000. Environ. Data Initiat. https://doi.org/10.6073/pasta/23965abf42954f345cfd6642fe3c4810 (2018).

  • 64.

    O’Donnell, J. L., Kelly, R. P., Lowell, N. C. & Port, J. A. Indexed PCR primers induce template-specific bias in large-scale DNA sequencing studies. PLoS One 11(3), e0148698 (2016).

    Article 

    Google Scholar 

  • 65.

    Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30(5), 614–620 (2014).

    CAS 
    Article 

    Google Scholar 

  • 66.

    Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).

    Article 

    Google Scholar 

  • 67.

    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17(1), 10–12 (2011).

    Article 

    Google Scholar 

  • 68.

    Mahé, F., Rognes, T., Quince, C., de Vargas, C. & Dunthorn, M. Swarm: Robust and fast clustering method for amplicon-based studies. PeerJ 2, e593 (2014).

    Article 

    Google Scholar 

  • 69.

    Huson, D. H. et al. MEGAN community edition—interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12(6), 1–12 (2016).

    Article 

    Google Scholar 

  • 70.

    McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8(4), e61217. https://doi.org/10.1371/journal.pone.0061217 (2013).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 71.

    Crist, T. O., Veech, J. A., Gering, J. C. & Summerville, K. S. Partitioning species diversity across landscapes and regions: A hierarchical analysis of alpha, beta, and gamma diversity. Am. Nat. 162(6), 734–743 (2003).

    Article 

    Google Scholar 

  • 72.

    Muggeo, V. M. R. Estimating regression models with unknown break-points. Stat. Med. 22(19), 3055–3071 (2003).

    Article 

    Google Scholar 

  • 73.

    Legendre, P., Borcard, D. & Roberts, D. W. Variation partitioning involving orthogonal spatial eigenfunction submodels. Ecology 93(5), 1234–1240. https://doi.org/10.1890/11-2028.1 (2012).

    Article 
    PubMed 

    Google Scholar 

  • 74.

    Silva, A. R., Dias, C. T. S., Cecon, P. R. & Rêgo, E. R. An alternative procedure for performing a power analysis of Mantel’s test. J. Appl. Stat. 42(9), 1984–1992. https://doi.org/10.1080/02664763.2015.1014894 (2015).

    MathSciNet 
    Article 
    MATH 

    Google Scholar 

  • 75.

    Dufrêne, M. & Legendre, P. Species assemblages and indicator species: The need for a flexible asymetrical approach. Ecol. Monogr. 67(3), 345–366 (1997).

    Google Scholar 

  • 76.

    Team, R. C. R: A language and environment for statistical computing. (2018). https://www.r-project.org/. Accessed June 2018.

  • 77.

    Oksanen, J. et al. Package ‘vegan.’ Community Ecol Packag version:2. (2015).


  • Source: Ecology - nature.com

    Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics

    Long term relationship between farming damselfish, predators, competitors and benthic habitat on coral reefs of Moorea Island