eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications

• Published in: The Science of the total environment Vol. 649; pp. 1157 - 1170
• Main Authors: Coble, Ashley A., Flinders, Camille A., Homyack, Jessica A., Penaluna, Brooke E., Cronn, Richard C., Weitemier, Kevin
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.02.2019
• Subjects: Aquatic Organisms - chemistry; Biodiversity; DNA - analysis; Environment; Environmental DNA; Environmental Monitoring - methods; Forestry; Fresh Water; Hydrobiology - methods; Metagenomics; Pulp and paper; Environmental DNA; Metagenomics; Biodiversity; Pulp and paper
• ISSN: 0048-9697; 1879-1026
• DOI: 10.1016/j.scitotenv.2018.08.370

Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our objectives are to describe potential applications of eDNA across the wood products supply chain extending from regenerating forests, harvesting, and wood transport, to manufacturing facilities, and to review the current state of the science in this context. To meet our second objective, we summarize the taxa examined with targeted (PCR, qPCR or ddPCR) or metagenomic eDNA methods (eDNA metabarcoding), evaluate how estimated species richness compares between traditional field sampling and eDNA metabarcoding approaches, and compare the geographical representation of prior eDNA studies in freshwater ecosystems to global wood baskets. Potential applications of eDNA include evaluating the effects of forestry and forest manufacturing activities on aquatic biota, delineating fish-bearing versus non fish-bearing reaches, evaluating effectiveness of constructed road crossings for freshwater organism passage, and determining the presence of at-risk species. Studies using targeted eDNA approaches focused on fish, amphibians, and invertebrates, while metagenomic studies focused on fish, invertebrates, and microorganisms. Rare, threatened, or endangered species received the least attention in targeted eDNA research, but are arguably of greatest interest to sustainable forestry and forest manufacturing that seek to preserve freshwater biodiversity. Ultimately, using eDNA methods will enable forestry and forest manufacturing managers to have data-driven prioritization for conservation actions for all freshwater species. [Display omitted] •eDNA can evaluate management effects on biota or delineate fish-bearing streams.•eDNA can monitor wastewater treatment performance and evaluate effluent effects.•Fish and invertebrates are well-represented by targeted and metagenomic eDNA studies.•Sensitive species are least studied with eDNA, but are important to forestry.