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.
Highlights
Bioassessment has become a cornerstone of environmental monitoring over the past 30 years
Our cost estimates are similar to the $5 per sample costs reported by Cameron et al [18] and the $3–$7.50 per sample for plants reported by [19], both of which included the cost of PCR, purification, and sequencing
These costs do not include the upfront cost of building a local reference library of fully vouchered specimens with barcodes, which may or may not be necessary depending on the type of bioassessment metrics used
Summary
Bioassessment has become a cornerstone of environmental monitoring over the past 30 years. Most states in the U.S use bioassessment to support State water quality assessment programs, to comply with Federal mandates and (to a lesser extent) as a regulatory tool to assess compliance with biological objectives or criteria [3]. Regulatory programs are developing biologically based standards, objectives or criteria that use biological indices as a basis for permit compliance, restoration success, or stressor remediation. The increased application of bioassessment has translated to an increased need for local capacity for taxonomic identification and interpretation. This need is complicated by the fact that sufficient numbers of trained taxonomists are rarely available and experience, quality, and level of taxonomic resolution varies considerably across states and programs [5]
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