title: Is DNA barcoding actually cheaper and faster than traditional morphological methods: results from a survey of freshwater bioassessment efforts in the United States?
abstract: Taxonomic identification accounts for a substantial portion of cost associated with bioassessment programs across the United States. New analytical approaches, such as DNA barcoding have been promoted as a way to reduce monitoring costs and improve efficiency, yet this assumption has not been thoroughly evaluated. We address this question by comparing costs for traditional morphology-based bioassessment, the standard Sanger sequencing-based DNA barcoding approach, and emerging next-generation (NGS) molecular methods. Market demand for molecular approaches is also assessed through a survey of the level of freshwater bioassessment effort in the United States across multiple habitat types (lakes, streams, wetlands) and indicators (benthic invertebrates, fish, algae). All state and regional level programs administered by public agencies and reported via agency web sites were included in the survey. Costs were based on surveys of labs and programs willing to provide such information. More than 19,500 sites are sampled annually across the United States, with the majority of effort occurring in streams. Benthic invertebrates are the most commonly used indicator, but algae and fish comprise between 35% and 21% of total sampling effort, respectively. We estimate that between $104 and $193 million is spent annually on routine freshwater bioassessment in the United States. Approximately 30% of the bioassessment costs are comprised of the cost to conduct traditional morphology-based taxonomy. Current barcoding costs using Sanger sequencing are between 1.7 and 3.4 times as expensive as traditional taxonomic approaches, excluding the cost of field sampling (which is common to both approaches). However, the cost of NGS methods are comparable (or slightly less expensive) than traditional methods depending on the indicator. The promise of barcoding as a cheaper alternative to current practices is not yet realized, although molecular methods may provide other benefits, such as a faster sample processing and increased taxonomic resolution.
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, California, United States of America.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Stein
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, California, United States of America.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Martinez
authors.affiliation: Southern California Coastal Water Research Project, Costa Mesa, California, United States of America.
authors.forename: Sara
authors.initials: S
authors.lastname: Stiles
authors.affiliation: Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Miller
authors.affiliation: Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Evgeny V
authors.initials: EV
authors.lastname: Zakharov
mesh_terms: D000818:Animals; D044822:Biodiversity; D003362:Cost-Benefit Analysis; D058893:DNA Barcoding, Taxonomic / Q000191:economics / Q000379:methods; D004784:Environmental Monitoring / Q000191:economics / Q000379:methods; D005618:Fresh Water; D014481:United States
references.citation: PLoS One. 2011 Apr 13;6(4):e17497
references.pmid: 21533287
references.citation: Gigascience. 2013 Mar 27;2(1):4
references.pmid: 23587339
references.citation: Mol Ecol. 2012 Jun;21(11):2565-73
references.pmid: 22151771
references.citation: Proc Biol Sci. 2003 Feb 7;270(1512):313-21
references.pmid: 12614582
references.citation: Mol Ecol Resour. 2009 May;9 Suppl s1:27-34
references.pmid: 21564961
references.citation: Nat Biotechnol. 2012 May;30(5):434-9
references.pmid: 22522955
references.citation: Mol Ecol Notes. 2007 May 1;7(3):355-364
references.pmid: 18784790
references.citation: Syst Biol. 2006 Oct;55(5):844-7
references.pmid: 17060204
references.citation: Syst Biol. 2005 Oct;54(5):852-9
references.pmid: 16243770
references.citation: Mol Ecol Resour. 2009 May;9 Suppl s1:1-26
references.pmid: 21564960
references.citation: Sci Am. 2008 Oct;299(4):82-6, 88
references.pmid: 18847089
references.citation: Annu Rev Entomol. 2006;51:495-523
references.pmid: 16332221