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DNA metabarcoding is an efficient method for measuring biodiversity, but the process of initiating long-term DNA-based monitoring programmes, or integrating with conventional programs, is only starting. In marine ecosystems, plankton surveys using the continuous plankton recorder (CPR) have characterized biodiversity along transects covering millions of kilometres with time-series spanning decades. We investigated the potential for use of metabarcoding in CPR surveys. Samples (n = 53) were collected in two Southern Ocean transects and metazoans identified using standard microscopic methods and by high-throughput sequencing of a cytochrome c oxidase subunit I marker. DNA increased the number of metazoan species identified and provided high-resolution taxonomy of groups problematic in conventional surveys (e.g., larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from large plankton such as krill masked the presence of smaller species. We investigated adding a fixed amount of exogenous DNA to samples as an internal control to allow determination of relative plankton biomass. Overall, the metabarcoding data represent a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing DNA metabarcoding from the current snapshot studies to the requirements of a long-term monitoring programme. Given the power and continually increasing efficiency of metabarcoding, it is almost certain this approach will play an important role in future plankton monitoring., (© 2017 Commonwealth of Australia. Molecular Ecology Resources © 2017 John Wiley & Sons Ltd.)

Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship‐based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan‐targeted cytochrome c oxidase I (COI) marker was used to characterize species‐level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non‐metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote‐targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity. [ABSTRACT FROM AUTHOR]

Species inventories and biodiversity assessments are critical to conservation. Yet cryptic species or recolonizing species can be challenging to detect. DNA metabarcoding provides an alternative tool to identify species that can be difficult to observe during field surveys. We test the efficacy of DNA analysis to identify burrowing petrel species in a rapidly changing landscape, on a remote sub‐Antarctic island following pest eradication. Discarded feathers and scats provided high quality DNA for species identification, assisting in detection of new species arrivals and new breeding sites across Macquarie Island. We highlight how DNA metabarcoding informs species inventories and is a valuable tool to complement seabird field surveys. [ABSTRACT FROM AUTHOR]