Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.

[1]  L. Blau Inland Fisheries Management In North America , 2016 .

[2]  Kristine Bohmann,et al.  Tag jumps illuminated – reducing sequence‐to‐sample misidentifications in metabarcoding studies , 2015, Molecular ecology resources.

[3]  D. Chapman,et al.  Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix. , 2015 .

[4]  C. Turner,et al.  Fish environmental DNA is more concentrated in aquatic sediments than surface water , 2015 .

[5]  K. Peay,et al.  Parsing ecological signal from noise in next generation amplicon sequencing. , 2015, The New phytologist.

[6]  Eske Willerslev,et al.  Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity , 2015 .

[7]  B. Letcher,et al.  Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams , 2015, Molecular ecology resources.

[8]  D. Lodge,et al.  The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol–chloroform–isoamyl alcohol DNA extraction , 2014, Molecular ecology resources.

[9]  M. Kondoh,et al.  The Release Rate of Environmental DNA from Juvenile and Adult Fish , 2014, PloS one.

[10]  Helen C. Rees,et al.  REVIEW: The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology , 2014 .

[11]  Douglas W. Yu,et al.  Environmental DNA for wildlife biology and biodiversity monitoring. , 2014, Trends in ecology & evolution.

[12]  Mehrdad Hajibabaei,et al.  Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics , 2014, Proceedings of the National Academy of Sciences.

[13]  D. Lodge,et al.  Particle size distribution and optimal capture of aqueous macrobial eDNA , 2014, bioRxiv.

[14]  Jesse A. Port,et al.  Using Environmental DNA to Census Marine Fishes in a Large Mesocosm , 2014, PloS one.

[15]  W. L. Chadderton,et al.  Environmental conditions influence eDNA persistence in aquatic systems. , 2014, Environmental science & technology.

[16]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[17]  A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust , 2013, Microbial Ecology.

[18]  B. Deagle,et al.  Quantifying sequence proportions in a DNA‐based diet study using Ion Torrent amplicon sequencing: which counts count? , 2013, Molecular ecology resources.

[19]  Robert S. Arkle,et al.  Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples , 2013 .

[20]  David M Erceg-Hurn,et al.  Robust Statistical Estimation , 2013 .

[21]  H. Doi,et al.  Using Environmental DNA to Estimate the Distribution of an Invasive Fish Species in Ponds , 2013, PloS one.

[22]  Eske Willerslev,et al.  Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples , 2012, PloS one.

[23]  C. Wiuf,et al.  Monitoring endangered freshwater biodiversity using environmental DNA. , 2012, Molecular ecology.

[24]  Z. Kawabata,et al.  Estimation of Fish Biomass Using Environmental DNA , 2012, PloS one.

[25]  P. Taberlet,et al.  Environmental DNA , 2012, Molecular ecology.

[26]  James Haile,et al.  DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches , 2011, PloS one.

[27]  Alain Viari,et al.  ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis , 2011, Nucleic acids research.

[28]  J. Weber,et al.  DNA Extraction Columns Contaminated with Murine Sequences , 2011, PloS one.

[29]  François Pompanon,et al.  Persistence of Environmental DNA in Freshwater Ecosystems , 2011, PloS one.

[30]  Asif U. Tamuri,et al.  PCR Master Mixes Harbour Murine DNA Sequences. Caveat Emptor! , 2011, PloS one.

[31]  W. L. Chadderton,et al.  “Sight‐unseen” detection of rare aquatic species using environmental DNA , 2011 .

[32]  D. Dudgeon Prospects for sustaining freshwater biodiversity in the 21st century: linking ecosystem structure and function , 2010 .

[33]  T. Bruns,et al.  Quantifying microbial communities with 454 pyrosequencing: does read abundance count? , 2010, Molecular ecology.

[34]  Thierry Grange,et al.  An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications , 2010, PloS one.

[35]  R. Giblin-Davis,et al.  Reproducibility of read numbers in high‐throughput sequencing analysis of nematode community composition and structure , 2009, Molecular ecology resources.

[36]  Gordon Luikart,et al.  Advancing ecological understandings through technological transformations in noninvasive genetics , 2009, Molecular ecology resources.

[37]  David W. Willis,et al.  Standard Methods for Sampling North American Freshwater Fishes , 2009 .

[38]  P. Taberlet,et al.  Species detection using environmental DNA from water samples , 2008, Biology Letters.

[39]  G. Allen,et al.  Freshwater Ecoregions of the World: A New Map of Biogeographic Units for Freshwater Biodiversity Conservation , 2008 .

[40]  Mary Dawood,et al.  Sampling rare populations. , 2008, Nurse researcher.

[41]  K. Brander Global fish production and climate change , 2007, Proceedings of the National Academy of Sciences.

[42]  W. Tian,et al.  Two universal primer sets for species identification among vertebrates , 2007, International Journal of Legal Medicine.

[43]  Darryl I. MacKenzie,et al.  Designing occupancy studies: general advice and allocating survey effort , 2005 .

[44]  D. Lodge,et al.  Scenarios of freshwater fish extinctions from climate change and water withdrawal , 2005 .

[45]  Sara M. Handy,et al.  Improved quantitative real‐time PCR assays for enumeration of harmful algal species in field samples using an exogenous DNA reference standard , 2005 .

[46]  J. Nichols,et al.  IMPROVING INFERENCES IN POPULATION STUDIES OF RARE SPECIES THAT ARE DETECTED IMPERFECTLY , 2005 .

[47]  B. Young,et al.  Status and Trends of Amphibian Declines and Extinctions Worldwide , 2004, Science.

[48]  R. Swihart,et al.  Absent or undetected? Effects of non-detection of species occurrence on wildlife-habitat models , 2004 .

[49]  S. Hawkins,et al.  Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments , 2004 .

[50]  M. Bruton Have fishes had their chips? The dilemma of threatened fishes , 1995, Environmental Biology of Fishes.

[51]  T. Reynoldson,et al.  Bioassessment of Freshwater Ecosystems , 2004 .

[52]  A. Magurran,et al.  Explaining the excess of rare species in natural species abundance distributions , 2003, Nature.

[53]  Daniel Jameson,et al.  OGRe: a relational database for comparative analysis of mitochondrial genomes , 2003, Nucleic Acids Res..

[54]  Olaf Lenzmann,et al.  Status and Trends , 1991 .

[55]  James T. Peterson,et al.  An approach to estimate probability of presence and richness of fish species , 2001 .

[56]  R. Nielsen Statistical tests of selective neutrality in the age of genomics , 2001, Heredity.

[57]  David P. Larsen,et al.  Rare species in multivariate analysis for bioassessment: some considerations , 2001, Journal of the North American Benthological Society.

[58]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .

[59]  P. Hübner,et al.  Mitochondrial DNA enrichment for species identification and evolutionary analysis , 1998 .

[60]  J. Herskowitz,et al.  Proceedings of the National Academy of Sciences, USA , 1996, Current Biology.

[61]  Christopher C. Kohler,et al.  Inland Fisheries Management in North America , 1993 .

[62]  A M Prince,et al.  PCR: how to kill unwanted DNA. , 1992, BioTechniques.

[63]  V. Yohai HIGH BREAKDOWN-POINT AND HIGH EFFICIENCY ROBUST ESTIMATES FOR REGRESSION , 1987 .

[64]  C. B. Williams Ecology. (Book Reviews: Patterns in the Balance of Nature. And related problems in quantitative ecology) , 1966 .