Steven D. Gaines | Search USGS

USGS2026

Cost-efficient filtration and replication strategies match or exceed detection sensitivity for marine eDNA diversity at an intertidal site under a standardized laboratory workflow

Optimizing environmental DNA (eDNA) metabarcoding to maximize species detection while minimizing costs and effort remains a challenge, particularly in high-throughput workflows. In the marine intertidal zone off Point Conception, California, we compared eDNA richness accumulation between filtration approaches that differed in filter type and downstream processing, field and laboratory replicates, and independent and pooled polymerase chain reaction (PCR) replicates. Ten 10-cm 2 capsule filters and 10 5-cm 2 syringe disc filters were processed using a standardized laboratory workflow for 12S ribosomal ribonucleic acid (rRNA) (marine vertebrates) and 18S rRNA (metazoans and phytoplankton) metabarcoding, with 10 independent PCR replicates per filter. Because capsules generated larger lysate volumes than discs, the fixed extraction input volume under the standardized workflow resulted in less lysate being processed. A follow-up study pooled 10 PCR replicates for 12S rRNA. When comparing individual PCR replicates, individual filters, or all filters aggregated, discs detected greater marine vertebrate richness than capsules. Probabilistic models indicated that varying effective volume alone could produce similar richness accumulation patterns to those observed, though other filter characteristics were unaccounted for. Minimal differences in richness accumulation were detected between filters for 18S rRNA, and modeling indicated that this was not explained by higher initial copies of 18S rRNA. Meanwhile, vertebrate richness accumulation was similar when adding PCR replicates from the same sample or independent field samples across the short, relatively homogenous intertidal transect. Pooling PCR replicates had no detectable difference on richness compared to sequencing PCR replicates independently: a single pooled PCR replicate detected the same vertebrate richness as the sum of 10 independent PCR replicates. These results show that, under the standardized workflow and conditions tested here, eDNA programs may reduce costs and effort without detectable loss of richness by using filtration approaches aligned with extraction input and pooling technical replicates.

California↗

USGS2013

Managing bay and estuarine ecosystems for multiple services

Managers are moving from a model of managing individual sectors, human activities, or ecosystem services to an ecosystem-based management (EBM) approach which attempts to balance the range of services provided by ecosystems. Applying EBM is often difficult due to inherent tradeoffs in managing for different services. This challenge particularly holds for estuarine systems, which have been heavily altered in most regions and are often subject to intense management interventions. Estuarine managers can often choose among a range of management tactics to enhance a particular service; although some management actions will result in strong tradeoffs, others may enhance multiple services simultaneously. Management of estuarine ecosystems could be improved by distinguishing between optimal management actions for enhancing multiple services and those that have severe tradeoffs. This requires a framework that evaluates tradeoff scenarios and identifies management actions likely to benefit multiple services. We created a management action-services matrix as a first step towards assessing tradeoffs and providing managers with a decision support tool. We found that management actions that restored or enhanced natural vegetation (e.g., salt marsh and mangroves) and some shellfish (particularly oysters and oyster reef habitat) benefited multiple services. In contrast, management actions such as desalination, salt pond creation, sand mining, and large container shipping had large net negative effects on several of the other services considered in the matrix. Our framework provides resource managers a simple way to inform EBM decisions and can also be used as a first step in more sophisticated approaches that model service delivery.

Estuaries and Coasts↗