Embedded in the interdisciplinary design of pelagic and benthic long-term observations at the Arctic long-term ecological research site HAUSGARTEN in Fram Strait (78 degrees 36,46 ' N-79 degrees 56,63 ' N 10 degrees 50,91 ' E-5 degrees 22,24 ' W; 250-5500 m), environmental DNA (eDNA)-based biodiversity studies span multiple habitats and trophic levels. These studies provide valuable insights into marine ecosystem functionality and carbon fluxes, including seasonal and interannual dynamics. Since 2009, eDNA studies of pelagic eukaryotic microbial communities have regularly been conducted. Recently, these studies have been expanded to cover the biodiversity of bacteria, archaea and metazoa such as zooplankton (including gelatinous taxa) and nekton (cephalopods and fish) alongside with microbial eukaryotes. The eDNA surveys have been coupled with measurements of physical and chemical properties, such as sea-ice coverage and water masses. By applying these approaches across spatial and trophic scales in a nested approach, we characterize the dynamics in biodiversity, its role in ecological processes, with a focus on current climate change. This is achieved by considering the complexity and interconnectivity of organisms, integrating information from different disciplines across scales and habitats, and focusing on functional processes including species composition. The resulting data improve our predictive capabilities for conservation and sustainable marine management in a rapidly changing Arctic. Here, we review the design of the first interdisciplinary Arctic eDNA long-term observatory and the results of more than ten years of method development and observations.

Taxonomic discussions often permeate the broader scientific community slowly, yet they may hold more relevance than typically assumed. In many zooplankton groups, identification issues arise from cryptic species complexes, increasingly revealed by molecular approaches, and from groups with high morphological similarity. These challenges can lead to substantial uncertainties in species-level identification, questioning whether the expected species are truly covered and whether those sharing names across ecosystems are indeed distinct entities. This review provides a condensed overview on identification challenges of key species in the ICES zooplankton time series from the North Atlantic and adjacent seas. Examples are given across all relevant groups, including copepods, gelatinous plankton, and meroplanktonic larvae. The high prevalence of challenging species complexes underscores the need to further explore the implications of an accurate species assignment for understanding what defines a species’ role in an ecosystem. This review highlights the dynamic nature of taxonomy, with species being split and cryptic species eventually becoming morphologically distinguishable. It provides examples showing that relying solely on molecular methods without deep taxonomic expertise poses significant risks. It also aims to serve as a starting point for delving deeper into the taxonomy of the ICES zooplankton time series.

Marine protected area (MPA) networks are important for supporting biodiversity, enhancing ecosystem resilience, and facilitating species recovery. For the effectiveness of conservation and restoration, functional connectivity plays a vital role. The dispersal, movement, and successful establishment of organisms between suitable habitats and MPAs ensure long-term sustainability of the populations. Despite its importance, functional connectivity is rarely integrated into restoration planning, which limits the effectiveness of species reintroductions, habitat connectivity, and adaptation to environmental changes. In this study, we applied an integrative approach combining molecular detections (environmental DNA [eDNA] and meroplankton metabarcoding) with biophysical modeling to explore the functional connectivity between two Natura 2000 MPAs in the North Sea: Borkum Reef Ground (BRG) and Sylt Outer Reef (SOR). We focused on the European flat oyster (Ostrea edulis), a reef-building species that once provided vast reef habitats but is now functionally extinct in the German Bight and is therefore the subject of recent restoration measures at BRG. Our results showed partial but informative correspondence between molecular detections of oyster genetic traces and the modeled larval pathways during the June-July 2022 sampling period. We further explored larval dispersal across entire spawning seasons in 2022 and 2023. Connectivity between BRG and SOR was highly dependent on larval drift depth. Surface-drifting larvae showed strong interannual variability, with 3% reaching SOR in 2022 when northwesterly winds dominated, increasing to 22% in 2023 under westerly and southwesterly winds. Larvae drifting at depth, however, exhibited near-zero connectivity, leading to high self-recruitment rates, with over 25% settling near the original restoration sites. Our results demonstrate that wind-driven currents are a key driver of interannual variability in larval retention and dispersal. Additionally, they highlight the role of biological traits, such as vertical positioning and pelagic larval duration, in shaping connectivity between MPAs and oyster restoration sites. These findings emphasize the need to integrate connectivity assessments into MPA management and the restoration planning of reef-building benthic species. The interdisciplinary approach presented here provides a quantitative framework for assessing connectivity under species- and site-specific conditions, offering a transferable tool to evaluate the restoration potential of other species and enhance the functional network between MPAs.

Coastlines are a mosaic of habitats, including rocky shores, sandy beaches, estuaries, and artificial substrata. Although modern microbialite pool formations were only recently discovered as an additional coastal habitat along the southern African coastline, they are now known to be surprisingly common to this region. These ecosystems function similarly to estuaries, where seawater and freshwater mix, but with groundwater as the freshwater source instead of river flow. Traditional community assessments from morphological identifications have revealed some similarities between the organisms inhabiting microbialite pools to those of nearby estuaries, but no systematic comparison has so far been undertaken. Here, we used molecular methods based on environmental DNA (eDNA) metabarcoding to characterise the eukaryote assemblages within and between three coastal southern African microbialite pools. We hypothesised that the three sites are taxonomically analogous to one another, which would support the existence of similar core ecological communities. Three genetic markers, one for metazoans (COI) and two for algae (rbcL and the V2+V3 regions of 18S rRNA) were targeted for metabarcoding. Our results show that the biodiversity of the pools was dominated by diatoms (particularly of the genera Navicula and Nitzschia) and, among the metazoans, by malacostracans, rotifers and nematodes. Although the three microbialite pools had similar broadscale community compositions at higher taxonomic levels (class and family), distinct community structure at lower taxonomic levels was observed, which may be a result of numerous opportunistic species being present in addition to the core organisms. The macroinvertebrate fauna of microbialite pools (e.g. peracarid crustaceans, polychaetes and insects) is well documented, although most are still missing from the DNA barcoding reference library. In contrast, the meiofauna (e.g. rotifers, nematodes and ostracods) is understudied. It remains unclear whether the two dominant diatom genera are the primary contributors to microbialite formation, or if other yet-undescribed species also contribute to the process. This study serves as an initial step in uncovering the hidden level of biodiversity within the unique microbialite ecosystems along the southern African coastline.

Biodiversity decline jeopardizes the foundation of natural ecosystems and human well-being, a concern that prompted major global agreements aiming to bend the curve towards a net positive biodiversity future. Still, the critical importance of safeguarding the diversity of life is far from receiving the attention it deserves, especially in marine settings. To understand (and overcome) the current limits of biodiversity mainstreaming, we integrate insights from the natural and social sciences to offer guidance on how to navigate the seemingly overwhelming complexity of this issue. We start by comparing biodiversity change to climate change to capture key distinctions in their multifaceted and context-dependent nature. Unlike climate change, the status and trends of biodiversity cannot be reduced to a single metric or target. Instead, effective biodiversity governance must focus on understanding how biodiversity is affected and how habitat extent, population size, or trends in composition capture these changes. The rise of molecular data promises to improve the representativeness of assessments and foster mechanistic understanding of the processes involved. Yet, it does not eliminate the need for effective communication of these issues to invoke meaningful action. Given its links to human well-being, biodiversity has a high chance of being engaging, but practitioners and scientists only marginally capitalize on the social, health, economic, and emotional values of their subject. Thus, we advocate for extending the assessment of biodiversity change and its functional consequences to include human values and emotions as an integral part of biodiversity reporting. Such a holistic framing, accounting for the complex spatial and temporal trajectories of biodiversity, will be vital in fostering more effective and inclusive conservation strategies.

EU directives (e.g. MSFD, Habitats Directive), along with OSPAR guidelines, mandate sustainable marine resource management across national borders. Benthic organisms are crucial for assessing marine ecosystem health, but their morphological identification is time-consuming and costly. High-throughput sequencing, particularly DNA metabarcoding, offers an alternative. However, DNA-based monitoring requires substantial investment in high-quality DNA reference libraries. The GEANS project (Genetic Tools for Ecosystem Health Assessment in the North Sea Region) aimed to develop efficient DNA-based tools for benthic biomonitoring. GEANS created a curated DNA reference library (COI) for species relevant to North Sea macrobenthos monitoring, using new sequences, non-public barcode sequences, and mined sequences from GenBank and BOLD. The library, stored in a dedicated BOLD project with photographs and metadata, includes DNA barcodes for 4005 specimens from 715 species, representing over 29% of North Sea macrobenthos species. Arthropoda is the most represented, while Bryozoa and Annelida have the lowest coverage. This DNA library is expected to facilitate fast, cost-effective environmental health assessments in the North Sea for public authorities and academics.

This study investigated the transport of European flat oyster (Ostrea edulis) larvae between two Marine Protected Areas in the North Sea: Borkum Reef Ground (BRG), where oysters were recently reintroduced, and Sylt Outer Reef (SOR). Additionally, we determined the source of oyster genetic material collected during cruises in 2022 between BRG and SOR. To achieve these goals, numerical simulations focusing on surface and depth-averaged water mass transport were conducted using the FESOM-C coastal ocean model with a forward/backward Lagrangian module. Surface drifter data were also analysed to examine surface transport and validate the model output. Our results indicate that typical summer wind conditions, along with tidal residual currents, support the transport of water masses and passive tracers from BRG to SOR. Surface water masses from BRG generally approach SOR from the south and west. However, BRG and SOR are usually connected over periods exceeding two weeks, even considering the fastest surface currents. Strong and persistent south-westerly winds, which are uncommon in summer, can accelerate this connection to under two weeks. Conversely, strong and persistent easterly or south-easterly winds, also rare in summer, can prevent some passive tracers originating from BRG from ever reaching SOR or the eastern North Sea. In the case of depth-averaged transport, significantly more time is required, with a minimum duration of eleven weeks to connect the domains. This connection could be facilitated by an intermediary habitat - as a stepping stone in the transition zone, if that provides suitable habitat for settlement and subsequent larval production.

Due to the high sensitivity of zooplankton to environmental fluctuations, monitoring their taxonomic composition, abundance and biomass is of high priority to identify changes in the ecosystem. Recent advances in imaging and molecular technologies promise to greatly accelerate the processing of samples to determine both the diversity and quantity of the zooplankton community. In our study, we analyzed the diversity and quantity of an epipelagic Arctic zooplankton community using multi-marker metabarcoding and imaging analysis (ZooScan). We identified a total of 11 phyla and 58 species in the northern Barents Sea and the Nansen Basin. Metabarcoding identified more taxa than image analysis, while imaging provided quantitative information on abundance and biomass. Multivariate analyses revealed overall the same significant environmental drivers (temperature and percentage of Polar Surface Water in the sampling depth layer) explaining the similarity and spatial distribution of the zooplankton community. For all approaches, similar spatial patterns of the zooplankton community were found. Abundance, biovolume and biomass decreased with increasing latitude within the analyzed regions. Based on this study, we recommend ZooScan image analysis in combination with COI metabarcoding for future monitoring of Arctic zooplankton diversity and quantification to ensure the detection of changes in both aspects of these communities.

Marine protected area (MPA) networks are fundamental for restoring and conserving ecosystem functions like biodiversity and general ecosystem health. Ideally, the effects of local conservation measures are not limited to one particular MPA alone but influence and connect regions beyond, or even other MPAs, through the spreading, replenishment and potential recovery of populations and communities. Connectivity defines, in a probabilistic sense, the functional linkage exchange between individual MPAs or key regions, and it depends on the features of the selected tracers (including the specific biological traits of target organisms), but it is also to a large degree determined by the hydrodynamic circulation patterns in the area. For the German Bight (south-eastern North Sea), we are focusing in particular on potential spillover from a restoration site for the European flat oyster (Ostrea edulis) through the spread of planktonic life stages. The circulation regimes are determined mainly by tidal and wind forcings. The prevailing wind-driven surface circulation in the area is cyclonic, influenced by frequent south-westerly to westerly winds. However, winds from other directions, for instance from the North-West, have the potential to modify and even reverse this circulation pattern. Wind intensity and directions have a clear seasonal variability, with higher magnitudes in winter and lower in summer, but also exhibit a significant interannual variability driven by the strength and location of high and low mean sea level atmospheric pressure centres. Moreover, winds from the East are relatively rare compared to the other patterns but can be extremely persistent (up to hundreds of hours) and thus affect the hydrodynamics and, hence, the connectivity between the MPAs. In this study, we catalogued the wind events according to their typical duration and magnitude using 10m eastward and northwards components retrieved from ERA5 reanalysis data and characterized them according to their seasonality and interannual variability. The results can be used to define realistic atmospheric scenarios to numerically simulate the sea dynamics in the southern North Sea and, consequently, assess the connectivity among different sites, including established MPAs. These efforts are crucial for a proper planning of conservation and restoration measures in the German Bight, which is one of the most exploited marine regions in the world.

Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1,246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.

Marine metazoan biodiversity is accretively being explored through environmental DNA (eDNA) metabarcoding of seawater. However, knowledge gaps in the use of eDNA to study changes in diversity resulting from changing abiotic conditions still do exist. In order to address these gaps, we analyzed patterns of marine invertebrate biodiversity based on eDNA from water and sediment samples along a decreasing salinity gradient from the North Sea toward the Baltic Sea. eDNA was collected from surface (SW) and bottom (BW) water, and from the uppermost sediment layer (SE). To supplement the eDNA approach, we conducted parallel zooplankton (ZP) metabarcoding and morphological identification. DNA was extracted from eDNA and ZP samples, amplified using two universal primers that target of the mitochondrial cytochrome c oxidase subunit 1 (COI) and the nuclear ribosomal 18S rRNA genes, and paired-end sequenced on Illumina Miseq. Metabarcoding detected 279 metazoan species (from 16 phyla) of which > 87% are known from the study area or adjacent regions. Communities identified in SW eDNA were a subset of communities identified in ZP metabarcoding. BW eDNA had additional benthic (mainly bivalve) species. Communities identified in SE eDNA were distinct from those in water eDNA and ZP metabarcoding, and mainly represented by in- and meiofauna. Out of all approaches, only ZP metabarcoding uncovered the expected decrease in species richness toward brackish conditions. Neither salinity nor spatial distance had a significant effect on species composition. All approaches revealed regional differences of which SE eDNA was least informative. The detection of holoplanktonic species from SE eDNA provided evidence for sinking of eDNA particles, dead organisms or the presence of resting eggs. Our study confirms the value of metabarcoding to identify the North Sea and Baltic Sea invertebrates and underscores the importance of combining multiple approaches to understand invertebrate biodiversity and its change in the marine realm.

Morphological identification of cnidarian species can be difficult throughout all life stages due to the lack of distinct morphological characters. Moreover, in some cnidarian taxa genetic markers are not fully informative, and in these cases combinations of different markers or additional morphological verifications may be required. Proteomic fingerprinting based on MALDI-TOF mass spectra was previously shown to provide reliable species identification in different metazoans including some cnidarian taxa. For the first time, we tested the method across four cnidarian classes (Staurozoa, Scyphozoa, Anthozoa, Hydrozoa) and included different scyphozoan life-history stages (polyp, ephyra, medusa) in our dataset. Our results revealed reliable species identification based on MALDI-TOF mass spectra across all taxa with species-specific clusters for all 23 analysed species. In addition, proteomic fingerprinting was successful for distinguishing developmental stages, still by retaining a species specific signal. Furthermore, we identified the impact of different salinities in different regions (North Sea and Baltic Sea) on proteomic fingerprints to be negligible. In conclusion, the effects of environmental factors and developmental stages on proteomic fingerprints seem to be low in cnidarians. This would allow using reference libraries built up entirely of adult or cultured cnidarian specimens for the identification of their juvenile stages or specimens from different geographic regions in future biodiversity assessment studies.

Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1-C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods.

Interoceanic canals can facilitate biological invasions as they connectthe world’s oceans and dissolve dispersal barriers between bioregions.As a consequence, multiple opportunities for biotic exchange arise andthe resulting establishment of migrant species often causes adverseecological and economic impacts. The Panama Canal is a key region forbiotic exchange as it connects the Pacific and Atlantic Oceans inCentral America. In this study, we used two complementary methods(environmental DNA (eDNA) and gillnetting) to survey fish communities inthis unique waterway. Using COI (cytochrome oxidase subunit I)metabarcoding, we detected a total of 142 taxa, including evidence forthe presence of sixteen Atlantic and eight Pacific marine fish insidedifferent sections of the Canal. Of these, ten are potentially newrecords of marine taxa detected in the freshwater segment of the Canal.Molecular data did not capture all species caught with gillnets, butgenerally provided a more complete image of the fish fauna. Diversityindices based on eDNA surveys revealed significant differences acrossdifferent sections of the Canal reflecting in part the prevailingenvironmental conditions. The observed increase in the presence ofmarine fish species in the Canal indicates a growing potential forinteroceanic exchange of fishes across the Isthmus. Monitoring usingeDNA is a rapid and efficient way to assess potential changes in thefishes of this important waterway.

Marine community diversity surveys require a reliable assessment to estimate ecosystem functions and their dynamics. For these, non-invasive environmental DNA (eDNA) metabarcoding is increasingly applied in zoological studies to complement or even replace traditional morphological identification methods. However, uncertainties remain about the accuracy of the diversity detected with eDNA to capture the actual diversity in the field. Here, we validate the reliability of eDNA metabarcoding in identifying metazoan biodiversity in highly dynamic marine waters of the North Sea. We analyzed biodiversity from water (eDNA) and zooplankton samples with cytochrome c oxidase subunit 1 (COI) and 18S rRNA (18S) metabarcoding at Helgoland Roads and validated the optimal molecular resolution by morphological and molecular zooplankton identification (metabarcoding) with the result of merely a few false-negative detections. eDNA and zooplankton metabarcoding resolved 354 species from all major and in total 16 metazoan phyla. This molecular genetic species inventory overlapped by 95.9% (COI) and 81.9% (18S) with published inventories of local, morphologically identified species, among them neozoa and rediscovered species. Even though half of all species were detected by both eDNA and zooplankton metabarcoding, the methods differed significantly in their detected diversity. eDNA metabarcoding performed very well in cnidarians and annelids, whereas zooplankton metabarcoding identified higher numbers of fish and malacostraca. Species assemblages significantly differed between the individual sampling events and the cumulative number of identified species increased steadily over the sampling period and did not reach saturation. About a third of the species were detected only once while a core community of 22 species was identified continuously. Our study confirms eDNA metabarcoding to be a powerful tool to identify and analyze North Sea fauna in highly dynamic waters and we recommend investing in high sampling efforts by repetitive sampling and replication using at least 0.45 mu m filters to increase filtration volume. By using an integrated morphological and genetic approach, we validated eDNA and zooplankton metabarcoding as a holistic approach to reliably identify marine metazoan fauna in highly dynamic waters of the North Sea. COI metabarcoding outperformed 18S V4 metabarcoding in terms of the number of detected species. Albeit high sampling efforts, we identified a third of all species only once during our sampling campaign, and with each sampling event, we detected additional species with no evidence of saturation in the cumulative number of species.image

We analysed the robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS (matrix-assisted laser desorption ionization time of flight mass spectrometry) data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to the species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity, that is identification was based on complex pattern-differences rather than on presence of single markers. Proteomic distance was not consistently related to phylogenetic distance. A species-gap in proteome composition appeared at 0.7 Euclidean distance when using only specimens from the same sample. When other regions or seasons were included, intraspecific variability increased, resulting in overlaps of intra and inter-specific distance. Highest intraspecific distances (>0.7) were observed between specimens from brackish and marine habitats (i.e., salinity probably affects proteomic patterns). When testing library sensitivity of the RF model to regionality, strong misidentification was only detected between two congener pairs. Still, the choice of reference library may have an impact on identification of closely related species and should be tested before routine application. We envisage high relevance of this time- and cost-efficient method for future zooplankton monitoring as it provides not only in-depth taxonomic resolution for counted specimens but also add-on information, such as on developmental stage or environmental conditions.

Compressed raw sequencing data generated from eDNA collected from the Panama Canal.

Accurate and reliable biodiversity estimates of marine zooplankton are a prerequisite to understand how changes in diversity can affect whole ecosystems. Species identification in the deep sea is significantly impeded by high numbers of new species and decreasing numbers of taxonomic experts, hampering any assessment of biodiversity. We used in parallel morphological, genetic, and proteomic characteristics of specimens of calanoid copepods from the abyssal South Atlantic to test if proteomic fingerprinting can accelerate estimating biodiversity. We cross‐validated the respective molecular discrimination methods with morphological identifications to establish COI and proteomic reference libraries, as they are a pre‐requisite to assign taxonomic information to the identified molecular species clusters. Due to the high number of new species only 37% of the individuals could be assigned to species or genus level morphologically. COI sequencing was successful for 70% of the specimens analysed, while proteomic fingerprinting was successful for all specimens examined. Predicted species richness based on morphological and molecular methods was 42 morphospecies, 56 molecular operational taxonomic units (MOTUs) and 79 proteomic operational taxonomic units (POTUs), respectively. Species diversity was predicted based on proteomic profiles using hierarchical cluster analysis followed by application of the variance ratio criterion for identification of species clusters. It was comparable to species diversity calculated based on COI sequence distances. Less than 7% of specimens were misidentified by proteomic profiles when compared with COI derived MOTUs, indicating that unsupervised machine learning using solely proteomic data could be used for quickly assessing species diversity.

Shipping corridors can be hotspots for biological invasions as they connect the world’s oceans and dissolve dispersal barriers between these aquatic systems. As a consequence, multiple opportunities for biotic exchange arise and the resulting establishment of non-native species often causes adverse ecological and economic impacts. In this study, a combined effort of traditional gillnetting and eDNA-based surveys was implemented to characterize the fish community of the Panama Canal, which is a key region for biotic exchange as it connects the Pacific and Atlantic Oceans in Central America. The Canal was recently expanded and new lock systems installed potentially providing novel opportunities for fish to enter the Canal. Using COI metabarcoding, we detected a total of 142 taxa, including thirteen potentially new records for the freshwater part of the Canal. Furthermore, we found evidence for the presence of 16 Atlantic and 10 Pacific non-native marine fish inside different sections of the Canal. Identifications based on molecular data did not cover all species caught with gillnets, but generally provided a more complete image of the fish fauna. Diversity indices based on eDNA surveys revealed significant differences across different sections of the Canal reflecting in part the prevailing environmental conditions. The observed changes in the fish community may be attributed to the recent expansion of the lock systems, which facilitates species migration directly by enlarging the canal entrances on either side of the Isthmus and indirectly by allowing more salt water to enter the Canal and thus increasing the overall salinity. Given the potential ecological and socio-economic consequences of non-native species crossing the Canal and establishing in the ocean basins on either end, it seems advisable to evaluate limiting salt water intrusion as well as implementing additional barriers to species dispersal (acoustic/electric/chemical deterrents) as a precautionary measure.

An accurate identification of species and communities is a prerequisite for analysing and recording biodiversity and community shifts. In the context of marine biodiversity conservation and management, this review outlines past, present and forward-looking perspectives on identifying and recording planktonic diversity by illustrating the transition from traditional species identification based on morphological diagnostic characters to full molecular genetic identification of marine assemblages. In this process, the article presents the methodological advancements by discussing progress and critical aspects of the crossover from traditional to novel and future molecular genetic identifications and it outlines the advantages of integrative approaches using the strengths of both morphological and molecular techniques to identify species and assemblages. We demonstrate this process of identifying and recording marine biodiversity on pelagic copepods as model taxon. Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms of biodiversity and ecosystem functioning. Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.