Abstract
Progressions accomplished in the field of molecular biology amid the most recent decade has changed the way in which we contemplate biodiversity on earth. Together with the accessibility of new molecular techniques like high-throughput sequencing (HTS), a prompt metamorphosis was attained in understanding the behaviour and biodiversity patterns of biological systems at a level never before possible. The DNA gathered from different environmental samples (named as environmental DNA or eDNA) when coupled with HTS offers a powerful tool by empowering the census of individual species on a global scale in real time. The applications of eDNA are transpiring in different domains, for example, trophic and community ecology (functional diversity, ecosystem dynamics and prey–predator interactions), biomonitoring, conservation biology (single and multi species detection, abundance estimates), invasion biology (early species detection, passive surveillance) and environmental assessment (detection of anthropogenic contamination, microbial source tracking). However, more empirical data is required to standardize the specific sampling procedures to achieve in the best possible way. Although the application of eDNA is intensifying swiftly at a global scale, there are still some knowledge gaps, especially with methods and applications. These procedures require some refinements and validations to diminish the burden of false positives/negatives. Considering these impediments, we mainly concentrated in pooling together the most recent outcome of research articles (2008–2019) available in eDNA analysis that converse about diverse ecosystems (freshwater, marine and terrestrial habitats). We likewise discussed developments and limitations that are generally concerned with eDNA exercise in the present review.
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References
Adams CI, Knapp M, Gemmell NJ, Jeunen G-J, Bunce M, Lamare MD, Taylor HR (2019) Beyond biodiversity: Can environmental DNA (eDNA) cut it as a population genetics tool? Genes 10(3):192
Adrian-Kalchhauser I, Burkhardt-Holm P (2016) An eDNA assay to monitor a globally invasive fish species from flowing freshwater. PLoS ONE 11(1):e0147558. https://doi.org/10.1371/journal.pone.0147558
Agersnap S, Larsen WB, Knudsen SW, Strand D, Thomsen PF, Hesselsøe M, Mortensen PB, Vrålstad T, Møller PR (2017) Monitoring of noble, signal and narrow-clawed crayfish using environmental DNA from freshwater samples. PLoS ONE 12(6):e0179261. https://doi.org/10.1371/journal.pone.0179261
Andruszkiewicz EA, Sassoubre LM, Boehm AB (2017) Persistence of marine fish environmental DNA and the influence of sunlight. PLoS ONE 12(9):e0185043. https://doi.org/10.1371/journal.pone.0185043
Apothéloz-Perret-Gentil L, Cordonier A, Straub F, Iseli J, Esling P, Pawlowski J (2017) Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring. Mol Ecol Resour 17(6):1231–1242. https://doi.org/10.1111/1755-0998.12668
Bailiff MD, Karl DM (1991) Dissolved and particulate DNA dynamics during a spring bloom in the Antarctic Peninsula region, 1986–1987. Deep Sea Res Part A Oceanogr Res Pap 38(8–9):1077–1095
Banchi E, Ametrano CG, Stanković D, Verardo P, Moretti O, Gabrielli F, Lazzarin S, Borney MF, Tassan F, Tretiach M (2018) DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy. PLoS ONE 13(3):e0194489
Barnes MA, Turner CR (2016) The ecology of environmental DNA and implications for conservation genetics. Conserv Genet 17(1):1–17. https://doi.org/10.1007/s10592-015-0775-4
Berry TE, Osterrieder SK, Murray DC, Coghlan ML, Richardson AJ, Grealy AK, Stat M, Bejder L, Bunce M (2017) DNA metabarcoding for diet analysis and biodiversity: a case study using the endangered Australian sea lion (Neophoca cinerea). Ecol Evol 7(14):5435–5453
Biggs J, Ewald N, Valentini A, Gaboriaud C, Dejean T, Griffiths RA, Foster J, Wilkinson JW, Arnell A, Brotherton P, Williams P, Dunn F (2015) Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biol Conserv 183:19–28. https://doi.org/10.1016/j.biocon.2014.11.029
Bista I, Carvalho GR, Walsh K, Seymour M, Hajibabaei M, Lallias D, Christmas M, Creer S (2017) Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat Commun 8:14087. https://doi.org/10.1038/ncomms14087
Bitok JK, Lemetre C, Ternei MA, Brady SF (2017) Identification of biosynthetic gene clusters from metagenomic libraries using PPTase complementation in a Streptomyces host. FEMS Microbiol Lett 364(16):fnx155. https://doi.org/10.1093/femsle/fnx155
Bovo S, Ribani A, Utzeri VJ, Schiavo G, Bertolini F, Fontanesi L (2018) Shotgun metagenomics of honey DNA: evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature. PLoS ONE 13(10):e0205575. https://doi.org/10.1371/journal.pone.0205575
Butchart SH, Walpole M, Collen B, Van Strien A, Scharlemann JP, Almond RE, Baillie JE, Bomhard B, Brown C, Bruno J (2010) Global biodiversity: indicators of recent declines. Science 28:1164–1168
Cannon MV, Hester J, Shalkhauser A, Chan ER, Logue K, Small ST, Serre D (2016) In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River. Sci Rep 6:22908. https://doi.org/10.1038/srep22908
Carraro L, Bertuzzo E, Mari L, Fontes I, Hartikainen H, Strepparava N, Schmidt-Posthaus H, Wahli T, Jokela J, Gatto M, Rinaldo A (2017) Integrated field, laboratory, and theoretical study of PKD spread in a Swiss prealpine river. Proc Natl Acad Sci 114(45):11992–11997. https://doi.org/10.1073/pnas.1713691114
Chang H, Guo J, Fu X, Liu Y, Wyckhuys K, Hou Y, Wu K (2018) Molecular-assisted pollen grain analysis reveals spatiotemporal origin of long-distance migrants of a Noctuid moth. Int J Mol Sci 19(2):567
Clare EL (2014) Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications. Evol Appl 7(9):1144–1157. https://doi.org/10.1111/eva.12225
Clusa L, Ardura A, Gower F, Miralles L, Tsartsianidou V, Zaiko A, Garcia-Vazquez E (2016) An easy phylogenetically informative method to trace the globally invasive potamopyrgus mud snail from river’s eDNA. PLoS ONE 11(10):e0162899. https://doi.org/10.1371/journal.pone.0162899
Clusa L, Miralles L, Basanta A, Escot C, García-Vázquez E (2017) eDNA for detection of five highly invasive molluscs. A case study in urban rivers from the Iberian Peninsula. PLOS ONE 12(11):e0188126. https://doi.org/10.1371/journal.pone.0188126
Cordier T, Esling P, Lejzerowicz F, Visco J, Ouadahi A, Martins C, Cedhagen T, Pawlowski J (2017) Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning. Environ Sci Technol 51(16):9118–9126. https://doi.org/10.1021/acs.est.7b01518
Cowart DA, Murphy KR, Cheng CHC (2018) Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula. Mar Genom 37:148–160. https://doi.org/10.1016/j.margen.2017.11.003
Cristescu ME (2014) From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol 29(10):566–571
Cristescu ME, Hebert PDN (2018) Uses and misuses of environmental DNA in biodiversity science and conservation. Annu Rev Ecol Evol Syst 49(1):209–230. https://doi.org/10.1146/annurev-ecolsys-110617-062306
Darling JA, Blum MJ (2007) DNA-based methods for monitoring invasive species: a review and prospectus. Biol Invasions 9(7):751–765. https://doi.org/10.1007/s10530-006-9079-4
Darling JA, Mahon AR (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environ Res 111(7):978–988. https://doi.org/10.1016/j.envres.2011.02.001
Davison PI, Créach V, Liang W-J, Andreou D, Britton JR, Copp GH (2016) Laboratory and field validation of a simple method for detecting four species of non-native freshwater fish using eDNA. J Fish Biol 89(3):1782–1793. https://doi.org/10.1111/jfb.13086
Davy CM, Kidd AG, Wilson CC (2015) Development and validation of environmental DNA (eDNA) markers for detection of freshwater turtles. PLoS ONE 10(7):e0130965. https://doi.org/10.1371/journal.pone.0130965
Deiner K, Walser J-C, Mächler E, Altermatt F (2015) Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol Conserv 183:53–63
Deiner K, Fronhofer EA, Mächler E, Walser J-C, Altermatt F (2016) Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nat Commun 7:12544. https://doi.org/10.1038/ncomms12544
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L (2017) Environmental DNA metabarcoding: transforming how we survey animal and plant communities. Mol Ecol 26(21):5872–5895. https://doi.org/10.1111/mec.14350
Der Sarkissian C, Pichereau V, Dupont C, Ilsøe PC, Perrigault M, Butler P, Chauvaud L, Eiriksson J, Scourse J, Paillard C (2017) Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol Ecol Resour 17(5):835–853
DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Bunce M (2019) Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ 7:e6379. https://doi.org/10.7717/peerj.6379
Dirzo R, Young HS, Galetti M, Ceballos G, Isaac NJB, Collen B (2014) Defaunation in the anthropocene. Science 345(6195):401–406. https://doi.org/10.1126/science.1251817
Djurhuus A, Pitz K, Sawaya NA, Rojas-Márquez J, Michaud B, Montes E, Muller-Karger F, Breitbart M (2018) Evaluation of marine zooplankton community structure through environmental DNA metabarcoding. Limnol Oceanogr Methods 16(4):209–221. https://doi.org/10.1002/lom3.10237
Dunker KJ, Sepulveda AJ, Massengill RL, Olsen JB, Russ OL, Wenburg JK, Antonovich A (2016) Potential of environmental DNA to evaluate northern pike (Esox lucius) eradication efforts: an experimental test and case study. PLoS ONE 11(9):e0162277. https://doi.org/10.1371/journal.pone.0162277
Erickson RA, Rees CB, Coulter AA, Merkes CM, McCalla SG, Touzinsky KF, Walleser L, Goforth RR, Amberg JJ (2016) Detecting the movement and spawning activity of bigheaded carps with environmental DNA. Mol Ecol Resour 16(4):957–965. https://doi.org/10.1111/1755-0998.12533
Ficetola GF, Taberlet P, Coissac E (2016) How to limit false positives in environmental DNA and metabarcoding? Mol Ecol Resour 16(3):604–607. https://doi.org/10.1111/1755-0998.12508
Flaviani F, Schroeder DC, Balestreri C, Schroeder JL, Moore K, Paszkiewicz K, Pfaff MC, Rybicki EP (2017) A pelagic microbiome (viruses to protists) from a small cup of seawater. Viruses 9(3):47
Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert MTP (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7(8):e41781. https://doi.org/10.1371/journal.pone.0041781
Forsström T, Vasemägi A (2016) Can environmental DNA (eDNA) be used for detection and monitoring of introduced crab species in the Baltic Sea? Mar Pollut Bull 109(1):350–355. https://doi.org/10.1016/j.marpolbul.2016.05.054
Forster D, Filker S, Kochems R, Breiner HW, Cordier T, Pawlowski J, Stoeck T (2018) A comparison of different ciliate metabarcode genes as bioindicators for environmental impact assessments of salmon aquaculture. J Eukaryot Microbiol 66:294–308
Freeland JR (2016) The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA. Genome 60(4):358–374
Friedberg EC (2003) DNA damage and repair. Nature 421(6921):436–440. https://doi.org/10.1038/nature01408
Galan M, Pons J-B, Tournayre O, Pierre É, Leuchtmann M, Pontier D, Charbonnel N (2018) Metabarcoding for the parallel identification of several hundred predators and their prey: application to bat species diet analysis. Mol Ecol Resour 18(3):474–489. https://doi.org/10.1111/1755-0998.12749
Gall SC, Thompson RC (2015) The impact of debris on marine life. Mar Pollut Bull 92(1):170–179. https://doi.org/10.1016/j.marpolbul.2014.12.041
Gellie NJC, Mills JG, Breed MF, Lowe AJ (2017) Revegetation rewilds the soil bacterial microbiome of an old field. Mol Ecol 26(11):2895–2904. https://doi.org/10.1111/mec.14081
Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Spear SF, McKee A, Oyler-McCance SJ, Cornman RS, Laramie MB, Mahon AR, Lance RF, Pilliod DS, Strickler KM, Waits LP, Fremier AK, Takahara T, Herder JE, Taberlet P (2016) Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods Ecol Evol 7(11):1299–1307. https://doi.org/10.1111/2041-210x.12595
Grey EK, Bernatchez L, Cassey P, Deiner K, Deveney M, Howland KL, Lacoursière-Roussel A, Leong SCY, Li Y, Olds B, Pfrender ME, Prowse TAA, Renshaw MA, Lodge DM (2018) Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys. Sci Rep 8(1):8843. https://doi.org/10.1038/s41598-018-27048-2
Guardiola M, Wangensteen OS, Taberlet P, Coissac E, Uriz MJ, Turon X (2016) Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 4:e2807. https://doi.org/10.7717/peerj.2807
Guillera-Arroita G, Lahoz-Monfort JJ, van Rooyen AR, Weeks AR, Tingley R (2017) Dealing with false-positive and false-negative errors about species occurrence at multiple levels. Methods Ecol Evol 8(9):1081–1091. https://doi.org/10.1111/2041-210x.12743
Guo X, Yang Y, Lu D, Niu Z, Feng J, Chen Y, Tou F, Garner E, Xu J, Liu M, Hochella MF (2018) Biofilms as a sink for antibiotic resistance genes (ARGs) in the Yangtze Estuary. Water Res 129:277–286. https://doi.org/10.1016/j.watres.2017.11.029
Gustavson MS, Collins PC, Finarelli JA, Egan D, Conchuir RO, Wightman GD, King JJ, Gauthier DT, Whelan K, Carlsson JE, Carlsson J (2015) An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water. J Fish Biol 87(5):1254–1262. https://doi.org/10.1111/jfb.12781
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685. https://doi.org/10.1128/mmbr.68.4.669-685.2004
Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107(1):1–8. https://doi.org/10.1016/j.ygeno.2015.11.003
Henne A, Schmitz RA, Bömeke M, Gottschalk G, Daniel R (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol 66(7):3113–3116
Hooper DU, Adair EC, Cardinale BJ, Byrnes JEK, Hungate BA, Matulich KL, Gonzalez A, Duffy JE, Gamfeldt L, O’Connor MI (2012) A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486:105. https://doi.org/10.1038/nature11118
Hunter ME, Oyler-McCance SJ, Dorazio RM, Fike JA, Smith BJ, Hunter CT, Reed RN, Hart KM (2015) Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons. PLoS ONE 10(4):e0121655. https://doi.org/10.1371/journal.pone.0121655
Jeunen G-J, Knapp M, Spencer HG, Lamare MD, Taylor HR, Stat M, Bunce M, Gemmell NJ (2018) Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.12982
Katz M, Hover BM, Brady SF (2016) Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 43(2):129–141. https://doi.org/10.1007/s10295-015-1706-6
Keeley N, Wood SA, Pochon X (2018) Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment. Ecol Ind 85:1044–1057
Keller A, Danner N, Grimmer G, Ankenbrand M, Von Der Ohe K, Von Der Ohe W, Rost S, Härtel S, Steffan-Dewenter I (2015) Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples. Plant Biol 17(2):558–566
Kelly RP, Port JA, Yamahara KM, Crowder LB (2014a) Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE 9(1):e86175. https://doi.org/10.1371/journal.pone.0086175
Kelly RP, Port JA, Yamahara KM, Martone RG, Lowell N, Thomsen PF, Mach ME, Bennett M, Prahler E, Caldwell MR (2014b) Harnessing DNA to improve environmental management. Science 344(6191):1455–1456
Kelly RP, O’Donnell JL, Lowell NC, Shelton AO, Samhouri JF, Hennessey SM, Feist BE, Williams GD (2016) Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 4:e2444. https://doi.org/10.7717/peerj.2444
Khaliq I, Hardy GESJ, White D, Burgess TI (2018) eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems. FEMS Microbiol Ecol 94(5):fiy048. https://doi.org/10.1093/femsec/fiy048
Kim P, Kim D, Yoon TJ, Shin S (2018) Early detection of marine invasive species, Bugula neritina (Bryozoa: Cheilostomatida), using species-specific primers and environmental DNA analysis in Korea. Mar Environ Res 139:1–10. https://doi.org/10.1016/j.marenvres.2018.04.015
Klymus KE, Marshall NT, Stepien CA (2017) Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes. PLoS ONE 12(5):e0177643. https://doi.org/10.1371/journal.pone.0177643
Lacoursière-Roussel A, Côté G, Leclerc V, Bernatchez L (2016) Quantifying relative fish abundance with eDNA: a promising tool for fisheries management. J Appl Ecol 53(4):1148–1157
Lacoursière-Roussel A, Howland K, Normandeau E, Grey EK, Archambault P, Deiner K, Lodge DM, Hernandez C, Leduc N, Bernatchez L (2018) eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol Evol 8(16):7763–7777. https://doi.org/10.1002/ece3.4213
Laroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, Pochon X (2017) Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5:e3347. https://doi.org/10.7717/peerj.3347
Lasken RS, McLean JS (2014) Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15(9):577
Lemetre C, Maniko J, Charlop-Powers Z, Sparrow B, Lowe AJ, Brady SF (2017) Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale. Proc Natl Acad Sci 114(44):11615–11620. https://doi.org/10.1073/pnas.1710262114
Levi T, Allen JM, Bell D, Joyce J, Russell JR, Tallmon DA, Vulstek SC, Yang C, Yu DW (2018) Environmental DNA for the enumeration and management of Pacific salmon. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.12987
Li F, Peng Y, Fang W, Altermatt F, Xie Y, Yang J, Zhang X (2018) Application of environmental DNA metabarcoding for predicting anthropogenic pollution in rivers. Environ Sci Technol 52(20):11708–11719
Lim NKM, Tay YC, Srivathsan A, Tan JWT, Kwik JTB, Baloğlu B, Meier R, Yeo DCJ (2016) Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities. R Soc Open Sci 3(11):160635. https://doi.org/10.1098/rsos.160635
Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362(6422):709–715
Linnarsson S (2010) Recent advances in DNA sequencing methods—general principles of sample preparation. Exp Cell Res 316(8):1339–1343. https://doi.org/10.1016/j.yexcr.2010.02.036
Liu D, Nishida M, Takahashi T, Asakawa S (2018) Transcription of mcrA gene decreases upon prolonged non-flooding period in a methanogenic archaeal community of a paddy-upland rotational field soil. Microb Ecol 75(3):751–760. https://doi.org/10.1007/s00248-017-1063-2
Mächler E, Deiner K, Steinmann P, Altermatt F (2014) Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species. Freshw Sci 33(4):1174–1183
Madison JT, Holley RW (1965) The presence of 5,6-dihydrouridylic acid in yeast “soluble” ribonucleic acid. Biochem Biophys Res Commun 18(2):153–157
Matsuhashi S, Doi H, Fujiwara A, Watanabe S, Minamoto T (2016) Evaluation of the environmental DNA method for estimating distribution and biomass of submerged aquatic plants. PLoS ONE 11(6):e0156217. https://doi.org/10.1371/journal.pone.0156217
Mauvisseau Q, Burian A, Gibson C, Brys R, Ramsey A, Sweet M (2019) Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches. Sci Rep 9(1):580
Mohiuddin M, Schellhorn H (2015) Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis. Front Microbiol. https://doi.org/10.3389/fmicb.2015.00960
Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microbiol Methods 7(2–3):57–66
Oh S-Y, Fong JJ, Park MS, Chang L, Lim YW (2014) Identifying airborne fungi in Seoul, Korea using metagenomics. J Microbiol 52(6):465–472
Pace NR (1985) Analyzing natural microbial populations by rRNA sequences. ASM News 51:4–12
Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P (2015) Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Mol Ecol 24(7):1485–1498. https://doi.org/10.1111/mec.13136
Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW (2017) Ancient plant DNA in lake sediments. New Phytol 214(3):924–942. https://doi.org/10.1111/nph.14470
Parro V, Moreno-Paz M, González-Toril E (2007) Analysis of environmental transcriptomes by DNA microarrays. Environ Microbiol 9(2):453–464
Parsons KM, Everett M, Dahlheim M, Park L (2018) Water, water everywhere: environmental DNA can unlock population structure in elusive marine species. R Soc Open Sci 5(8):180537. https://doi.org/10.1098/rsos.180537
Paul JH, Kellogg CA, Jiang SC (1996) Viruses and DNA in marine environments. In: Colwell RR, Simidu U, Ohwada K (eds) Microbial diversity in time and space. Springer, Boston, pp 115–124. https://doi.org/10.1007/978-0-585-34046-3_14
Pereira HM, Leadley PW, Proença V, Alkemade R, Scharlemann JPW, Fernandez-Manjarrés JF, Araújo MB, Balvanera P, Biggs R, Cheung WWL, Chini L, Cooper HD, Gilman EL, Guénette S, Hurtt GC, Huntington HP, Mace GM, Oberdorff T, Revenga C, Rodrigues P, Scholes RJ, Sumaila UR, Walpole M (2010) Scenarios for global biodiversity in the 21st century. Science 330(6010):1496–1501. https://doi.org/10.1126/science.1196624
Pikitch EK (2018) A tool for finding rare marine species. Science 360(6394):1180–1182. https://doi.org/10.1126/science.aao3787
Pochon X, Zaiko A, Fletcher LM, Laroche O, Wood SA (2017) Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS ONE 12(11):e0187636. https://doi.org/10.1371/journal.pone.0187636
Prosser CM, Hedgpeth BM (2018) Effects of bioturbation on environmental DNA migration through soil media. PLoS ONE 13(4):e0196430. https://doi.org/10.1371/journal.pone.0196430
Ramírez GA, Jørgensen SL, Zhao R, D’Hondt S (2018) Minimal influence of extracellular DNA on molecular surveys of marine sedimentary communities. Front Microbiol. https://doi.org/10.3389/fmicb.2018.02969
Rees HC, Bishop K, Middleditch DJ, Patmore JRM, Maddison BC, Gough KC (2014a) The application of eDNA for monitoring of the Great Crested Newt in the UK. Ecol Evol 4(21):4023–4032. https://doi.org/10.1002/ece3.1272
Rees HC, Maddison BC, Middleditch DJ, Patmore JR, Gough KC (2014b) The detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J Appl Ecol 51(5):1450–1459
Rees HC, Baker CA, Gardner DS, Maddison BC, Gough KC (2017) The detection of great crested newts year round via environmental DNA analysis. BMC Res Notes 10(1):327. https://doi.org/10.1186/s13104-017-2657-y
Roussel J-M, Paillisson J-M, Tréguier A, Petit E (2015) The downside of eDNA as a survey tool in water bodies. J Appl Ecol 52(4):823–826. https://doi.org/10.1111/1365-2664.12428
Ruppert KM, Kline RJ, Rahman MS (2019) Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 17:e00547
Sansom BJ, Sassoubre LM (2017) Environmental DNA (eDNA) shedding and decay rates to model freshwater mussel eDNA transport in a river. Environ Sci Technol 51(24):14244–14253. https://doi.org/10.1021/acs.est.7b05199
Sassoubre LM, Yamahara KM, Gardner LD, Block BA, Boehm AB (2016) 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
Sawaya NA, Djurhuus A, Closek CJ, Hepner M, Olesin E, Visser L, Kelble C, Hubbard K, Breitbart M (2019) Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding. Ecol Evol 9(3):1029–1040. https://doi.org/10.1002/ece3.4742
Schmidt TM, DeLong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173(14):4371–4378. https://doi.org/10.1128/jb.173.14.4371-4378.1991
Shaw JLA, Clarke LJ, Wedderburn SD, Barnes TC, Weyrich LS, Cooper A (2016) Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biol Conserv 197:131–138. https://doi.org/10.1016/j.biocon.2016.03.010
Shaw JLA, Weyrich LS, Hallegraeff G, Cooper A (2019) Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments. Mol Ecol. https://doi.org/10.1111/mec.15055
Shogren AJ, Tank JL, Andruszkiewicz E, Olds B, Mahon AR, Jerde CL, Bolster D (2017) Controls on eDNA movement in streams: transport, retention, and resuspension. Sci Rep 7(1):5065. https://doi.org/10.1038/s41598-017-05223-1
Simpson TJS, Dias PJ, Snow M, Muñoz J, Berry T (2017) Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context. Mol Ecol Resour 17(3):443–453. https://doi.org/10.1111/1755-0998.12581
Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, Sønstebø JH, Ims RA, Yoccoz NG (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zool 6(1):16
Song JW, Small MJ, Casman EA (2017) Making sense of the noise: the effect of hydrology on silver carp eDNA detection in the Chicago area waterway system. Sci Total Environ 605–606:713–720. https://doi.org/10.1016/j.scitotenv.2017.06.255
Stat M, Huggett MJ, Bernasconi R, DiBattista JD, Berry TE, Newman SJ, Harvey ES, Bunce M (2017) 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
Suchan T, Talavera G, Sáez L, Ronikier M, Vila R (2019) Pollen metabarcoding as a tool for tracking long-distance insect migrations. Mol Ecol Resour 19(1):149–162
Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012) Environmental DNA. Mol Ecol 21(8):1789–1793. https://doi.org/10.1111/j.1365-294X.2012.05542.x
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44(14):6614–6624. https://doi.org/10.1093/nar/gkw569
Tessler M, Brugler MR, DeSalle R, Hersch R, Velho LFM, Segovia BT, Lansac-Toha FA, Lemke MJ (2017) A global eDNA comparison of freshwater bacterioplankton assemblages focusing on large-river floodplain lakes of Brazil. Microb Ecol 73(1):61–74. https://doi.org/10.1007/s00248-016-0834-5
Thomsen PF, Sigsgaard EE (2019) Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods. Ecol Evol 9(4):1665–1679. https://doi.org/10.1002/ece3.4809
Thomsen PF, Willerslev E (2015) Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18. https://doi.org/10.1016/j.biocon.2014.11.019
Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21(11):2565–2573. https://doi.org/10.1111/j.1365-294X.2011.05418.x
Turner CR, Barnes MA, Xu CC, Jones SE, Jerde CL, Lodge DM (2014) Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods Ecol Evol 5(7):676–684
Ushio M, Murata K, Sado T, Nishiumi I, Takeshita M, Iwasaki W, Miya M (2018) Demonstration of the potential of environmental DNA as a tool for the detection of avian species. Sci Rep 8(1):4493. https://doi.org/10.1038/s41598-018-22817-5
Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, Bellemain E, Besnard A, Coissac E, Boyer F, Gaboriaud C, Jean P, Poulet N, Roset N, Copp GH, Geniez P, Pont D, Argillier C, Baudoin J-M, Peroux T, Crivelli AJ, Olivier A, Acqueberge M, Le Brun M, Møller PR, Willerslev E, Dejean T (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol 25(4):929–942. https://doi.org/10.1111/mec.13428
Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30(9):418–426
Wakelin SA, Cave VM, Dignam BE, D’Ath C, Tourna M, Condron LM, Zhou J, Van Nostrand JD, O’Callaghan M (2016) Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture. N Z J Agric Res 59(4):333–350. https://doi.org/10.1080/00288233.2016.1209529
Watson JD, Crick FH (1953) Molecular structure of nucleic acids. Nature 171(4356):737–738
Weltz K, Lyle JM, Ovenden J, Morgan JAT, Moreno DA, Semmens JM (2017) 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
Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE 8(3):e59520
Wilcox TM, McKelvey KS, Young MK, Lowe WH, Schwartz MK (2015) Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis). Conserv Genet Resour 7(3):639–641
Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221–271
Won N-I, Kim K-H, Kang JH, Park SR, Lee HJ (2017) Exploring the impacts of anthropogenic disturbance on seawater and sediment microbial communities in korean coastal waters using metagenomics analysis. Int J Environ Res Public Health 14(2):130
Xie Y, Zhang X, Yang J, Kim S, Hong S, Giesy JP, Yim UH, Shim WJ, Yu H, Khim JS (2018) eDNA-based bioassessment of coastal sediments impacted by an oil spill. Environ Pollut 238:739–748
Yang J, Jeppe K, Pettigrove V, Zhang X (2018) Environmental DNA metabarcoding supporting community assessment of environmental stressors in a field-based sediment microcosm study. Environ Sci Technol 52(24):14469–14479. https://doi.org/10.1021/acs.est.8b04903
Zallen DT (2003) Despite Franklin’s work, Wilkins earned his Nobel. Nature 425:15. https://doi.org/10.1038/425015b
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Garlapati, D., Charankumar, B., Ramu, K. et al. A review on the applications and recent advances in environmental DNA (eDNA) metagenomics. Rev Environ Sci Biotechnol 18, 389–411 (2019). https://doi.org/10.1007/s11157-019-09501-4
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DOI: https://doi.org/10.1007/s11157-019-09501-4