Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities

Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach

eDNA metabarcoding has been increasingly employed in the monitoring of marine invertebrate non-indigenous species (NIS), in particular using filtered seawater. However, comprehensive detection of all NIS may require a diversity of sampling substrates. To assess the effectiveness of 5 sample types (hard and artificial substrates, water, zooplankton) on the recovery of invertebrates' diversity, two marinas were monitored over three time points, using COI and 18S rRNA genes as DNA metabarcoding markers. We detected a total of 628 species and 23 NIS, with only up to 9% species and 17% of NIS detected by all sample types. Hard and artificial substrates were similar to each other but displayed the most significant difference in invertebrate recovery when compared to water eDNA and zooplankton. Five NIS are potential first records for Portugal. No NIS were detected in all sample types and seasons, highlighting the need for varied sampling approaches, and consideration of temporal variation for comprehensive marine NIS surveillance.

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.

VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages

Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.

Harnessing environmental DNA to reveal biogeographical patterns of non-indigenous species for improved co-governance of the marine environment in Aotearoa New Zealand

Aotearoa New Zealand's Northern region is a major gateway for the incursion and establishment of non-indigenous species (NIS) populations due to high numbers of recreational and commercial vessels. This region also holds a unique marine ecosystem, home to many taonga (treasured) species of cultural and economic importance. Regular surveillance, eradication plans and public information sharing are undertaken by local communities and governmental organizations to protect these ecosystems from the impact of NIS. Recently, considerable investments went into environmental DNA (eDNA) research, a promising approach for the early detection of NIS for complementing existing biosecurity systems. We applied eDNA metabarcoding for elucidating bioregional patterns of NIS distributions across a gradient from harbors (NIS hotspots) to open seas (spreading areas). Samples were collected during a research cruise sailing across three Aotearoa New Zealand harbors, Waitematā, Whangārei and Pēwhairangi (Bay of Islands), and their adjacent coastal waters. The small-ribosomal subunit (18S rRNA) and mitochondrial cytochrome c oxidase I (COI) genes were screened using the online Pest Alert Tool for automated detection of putative NIS sequences. Using a probabilistic modelling approach, location-dependent occupancies of NIS were investigated and related to the current information on species distribution from biosecurity surveillance programs. This study was collaboratively designed with Māori partners to initiate a model of co-governance within the existing science system.

Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches

Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.

Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment

Assessments of the ecological health of algal assemblages in streams typically focus on measures of their local diversity and classify individuals by morphotaxonomy. Such assemblages are often connected through various ecological processes, such as dispersal, and may be more accurately assessed as components of regional-, rather than local-scale assemblages. With recent declines in the costs of sequencing and computation, it has also become increasingly feasible to use metabarcoding to more accurately classify algal species and perform regional-scale bioassessments. Recently, zeta diversity has been explored as a novel method of constructing regional bioassessments for groups of streams. Here, we model the use of zeta diversity to investigate whether stream health can be determined by the landscape diversity of algal assemblages. We also compare the use of DNA metabarcoding and morphotaxonomy classifications in these zeta diversity-based bioassessments of regional stream health. From 96 stream samples in California, we used various orders of zeta diversity to construct models of biotic integrity for multiple assemblages of diatoms, as well as hybrid assemblages of diatoms in combination with soft-bodied algae, using taxonomy data generated with both DNA sequencing as well as traditional morphotaxonomic approaches. We compared our ability to evaluate the ecological health of streams with the performance of multiple algal indices of biological condition. Our zeta diversity-based models of regional biotic integrity were more strongly correlated with existing indices for algal assemblages classified using metabarcoding compared to morphotaxonomy. Metabarcoding for diatoms and hybrid algal assemblages involved rbcL and 18S V9 primers, respectively. Importantly, we also found that these algal assemblages, independent of the classification method, are more likely to be assembled under a process of niche differentiation rather than stochastically. Taken together, these results suggest the potential for zeta diversity patterns of algal assemblages classified using metabarcoding to inform stream bioassessments.

Microbial community shift on artificial biological reef structures (ABRs) deployed in the South China Sea

Many Artificial Reefs (ARs) have been used worldwide for marine habitat and coral reef restoration. However, the microbial community structure that colonize the ARs and their progressive development have been seldom investigated. In this study, the successive development of the microbial communities on environmentally friendly Artificial Biological Reef structures (ABRs)^R made of special concrete supported with bioactive materials collected from marine algal sources were studied. Three seasons (spring, summer and autumn), three coral reef localities and control models (SCE) without bioactive material and (NCE) made of normal cement were compared. The structure of the microbial pattern exhibited successive shifts from the natural environment to the ABRs supported with bioactive materials (ABAM). Cyanobacteria, Proteobacteria, and Planctomycetota were shown to be the most three dominant phyla. Their relative abundances pointedly increased on ABAM and SCE models compared to the environment. Amplicon Sequence Variant (ASV) Richness and Shannon index were obviously higher on ABAM models and showed significant positive relationship with that of macrobenthos than those on the controls and the natural reef (XR). Our results offer successful establishment of healthy microbial films on the ABR surfaces enhanced the restoration of macrobenthic community in the damaged coral reefs which better understands the ecological role of the ABRs.

Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository

Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.

Application of multi-region input-output analysis to examine biosecurity risks associated with the global shipping network

The vast majority of globally traded cargo is transported via maritime shipping. Whilst in port for loading and unloading, these ships can pick up local marine organisms with internal ballast water or as external biofouling assemblages and subsequently move these to destination far beyond their natural ranges. Over the past decades, this mechanism has led to the establishment of hundreds of non-indigenous species (NIS) around global coastlines. Marine NIS cause significant environmental, economic, cultural and human health impacts. Taking effective steps to preventing their dispersal and establishment is an enduring challenge for governments and conservation agencies around the world. Here we use international commodity trade data and a Nobel-Prize-winning economic analysis technique to develop a novel approach for assessing global marine NIS transfer risks. We show that by tracing the origins and destinations of seaborne trade connections, and the nature of the traded commodities, we can predict the strength of shipping vectors and associated marine biosecurity risks. We demonstrate the utility of our approach via a case-study, where we trace the spread of a hypothetical marine NIS from Japan and show the congruence of our model results with documented invasion histories from that region. Our study demonstrates that biosecurity risk can be assessed using established economic modelling frameworks on the basis of monetary transaction data alone, and without the need for detailed itineraries of the many thousand vessels making up the global commercial fleet. Novel, cost-effective tools are needed to mitigate biosecurity risks associated with maritime trade, and to meet conservation goals while enabling economic prosperity. The modelling framework presented here can be expanded to incorporate future risk factors, life-history traits of particular NIS of concern, and even adapted to simulate the dispersal of terrestrial pests or disease agents.

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.

Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates

DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency and incompleteness of databases. Here we assessed the efficiency of two different marker loci (COI and 18S) and three primer pairs in marine species detection through DNA metabarcoding of the macrozoobenthic communities colonizing three types of artificial substrates (slate, PVC and granite), sampled between 3 and 15 months of deployment. To accurately compare detection success between markers, we also compared the representativeness of the detected species in public databases and revised the reliability of the taxonomic assignments. Globally, we recorded extensive complementarity in the species detected by each marker, with 69% of the species exclusively detected by either 18S or COI. Individually, each of the three primer pairs recovered, at most, 52% of all species detected on the samples, showing also different abilities to amplify specific taxonomic groups. Most of the detected species have reliable reference sequences in their respective databases (82% for COI and 72% for 18S), meaning that when a species was detected by one marker and not by the other, it was most likely due to faulty amplification, and not by lack of matching sequences in the database. Overall, results showed the impact of marker and primer applied on species detection ability and indicated that, currently, if only a single marker or primer pair is employed in marine zoobenthos metabarcoding, a fair portion of the diversity may be overlooked.

Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters

Understanding the spread and distribution of Non-Indigenous Species (NIS) is key when implementing legislation to maintain good ecosystem health. Environmental DNA (eDNA) has shown great potential to detect aquatic organisms in a rapid and cost-effective way, however their applicability to new environments must be validated prior to their implementation. Here, we tested different field sampling methods in combination with eDNA metabarcoding to develop a tool to detect NIS. Large and small volumes of seawater were filtered, in addition to the collection of sediment and horizontal tow net samples at 12 locations across four distinct geographic areas in Ireland. The biggest dissimilarity in the species recovered was found between sediment and town net samples. Tow nets showed to be the most efficient. A total of 357 taxa were identified, including 16 NIS. Fine mesh tow nets were identified as the most cost-efficient for large-scale monitoring and surveillance of NIS.

Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach

Zooplankton plays a pivotal role in sustaining the majority of marine ecosystems. The distribution patterns and diversity of zooplankton provide key information for understanding the functioning of these ecosystems. Nevertheless, due to the numerous cryptic and sibling species and the lack of diagnostic characteristics for early developmental stages, the identification of the global-to-local patterns of zooplankton biodiversity and biogeography remains challenging in different research fields. The spatial and temporal changes in the zooplankton community in the open waters of the southern Gulf of Mexico were assessed using metabarcoding analysis of the V9 region of 18S rRNA and mitochondrial cytochrome oxidase c subunit I (COI). Additionally, a multiscale analysis was implemented to evaluate which environmental predictors may explain the variability in the structure of the zooplankton community. Our findings suggest that the synergistic effects of dissolved oxygen concentration, temperature, and longitude (intended as a proxy for still unidentified predictors) may explain both spatial and temporal zooplankton variability even with low contribution. Furthermore, the zooplankton distribution probably reflects the coexistence of three heterogeneous ecoregions and a bio-physical partitioning of the studied area. Finally, some taxa were either exclusive or predominant with either 18S or COI markers. This may suggest that comprehensive assessments of the zooplankton community may be more accurately met by the use of multilocus approaches.

The role of marinas in the establishment and spread of non-indigenous species in Baltic Sea fouling communities

The study included the sampling of 12 marinas across six areas of the Baltic Sea with settlement plates and scraping of submerged structures to assess the role of marinas in the spread of non-indigenous species (NIS) via biofouling. 15 NIS were detected in the marinas and secondary spread of previously introduced NIS was detected in five out of six sea areas. Salinity and sea area significantly affected the composition of the fouling assemblages. Settlement plates appeared as the more efficient sampling method over scraping, while the seasonal analyses revealed that the monitoring effort should span over the summer and early autumn in the south-eastern, central, and northern Baltic Sea. The present findings indicate that marinas contribute to the spread of non-indigenous fouling organisms, and there is an increasing demand for the monitoring of marinas and stricter regulations regarding the biofouling management of leisure boats in the Baltic Sea.

Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems

Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.

Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment

Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.

Poorer diversity but tougher species in old ballast water: Biosecurity challenges explored from visual and molecular techniques

Millions of tons of water cross the oceans inside ships' ballast tanks every day. Planktonic species hitch-hike with water and some may pose risks to ecosystems and economies if get released and establish outside their native range. We monitored ballast water in different trans-equatorial travels, visually and using molecular techniques, and found significant increases of potential nuisance taxa over travel duration, despite evident diversity depletion. Thus, less diverse but more resistant and potentially more harmful communities persist in ballast water over long voyages. If we consider the enormous volume transported every day, the persistence of resistant species in ballast water would be threating the global marine biodiversity. This should be taken into account when modeling and assessing the bioinvasion risks associated with the ballast water and transfer considered in the future research.

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores

Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.

Biopollution by Invasive Marine Non-Indigenous Species: A Review of Potential Adverse Ecological Effects in a Changing Climate

Biopollution by alien species is considered one of the main threats to environmental health. The marine environment, traditionally less studied than inland domains, has been the object of recent work that is reviewed here. Increasing scientific evidence has been accumulated worldwide on ecosystem deterioration induced by the development of massive non-indigenous population outbreaks in many coastal sites. Biopollution assessment procedures have been proposed, adopting criteria already used for xenochemical compounds, adjusting them to deal with alien species invasions. On the other hand, prevention and mitigation measures to reduce biopollution impact cannot always mimic the emission countermeasures that have been successfully applied for chemical pollutants. Nevertheless, in order to design comprehensive water-quality criteria, risk assessment and management strategies, based on scientific knowledge, have been developed in a similar way as for chemical pollution. The Mediterranean Sea is a well-known case of alien species invasion, mainly linked to the opening of the Suez Canal. Non-indigenous species have caused well-documented changes in many coastal ecosystems, favoured by concomitant changes induced by global warming and by the heavy load of nutrients and pollutants by various anthropogenic activities. Naval commercial traffic and leisure boats are among the most active vectors of spread for alien species inside the Mediterranean, and also towards other ocean regions. The scientific evidence gathered and summarized in this review suggests that effective management actions, under a precautionary approach, should be put in place in order to control introductions of species in new areas. These management measures are already established in international treaties and national legislations, but should be enforced to prevent the disruption of the dynamic ecological equilibria in the receiving environment and to control the direct adverse effects of alien species.

eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the "missing biomass") is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.

Stress resistance for unraveling potential biopollutants. Insights from ballast water community analysis through DNA

In marine settings, anthropogenic disturbances and climate change increase the rate of biological invasions. Predicting still undescribed invasive alien species (IAS) is needed for preparing timely management responses. We tested a strategy for discovering new potential IAS using DNA in a trans-equatorial expedition onboard RV Polarstern. During one-month travel, species inside ballast water experienced oxygen depletion, warming, darkness and ammonium stress. Many organisms died but several phytoplankton and zooplankton survivors resisted and were detected through a robust combination of individual sampling, DNA barcoding and metabarcoding, new in ballast water studies. Ammonium was identified as an important influential factor to explain diversity changes in phytoplankton and zooplankton. Some species reproduced until the end of the travel. These species tolerant to travel stress could be targeted as potential IAS and prioritized for designing control measures. Introducing resistance to travel stress in biosecurity risk analysis would be recommended.

Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection

When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction 'hot-spot' in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. DNA extraction kits have been widely used and the 18S rRNA and the COI genes the most employed markers, but less than half of the studies targeted more than one marker loci. The Illumina MiSeq platform has been used in >50% of the publications. Current weaknesses include potential occurrence of false negatives due to the primer-biased or faulty DNA amplification and the incompleteness of reference libraries. This is particularly concerning in the case of NIS surveillance, where proficiency in species level detection is critical. Until these weaknesses are resolved, ideally NIS metabarcoding should be supported by complementary approaches, such as morphological analysis or more targeted molecular approaches (e.g. qPCR, ddPCR). Even so, metabarcoding has already proved to be a highly sensitive tool to detect small organisms or undifferentiated life stages across a wide taxonomic range. In addition, it also seems to be very effective in ballast water management and to improve the spatial and temporal sampling frequency of NIS surveillance in marine and coastal ecosystems. Although specific protocols may be required for species-specific NIS detection, for general monitoring it would be vital to settle on a standard protocol able to generate comparable results among surveillance campaigns and regions of the globe, seeking the best approach for detecting the broadest range of species, while minimizing the chances of a false positive or negative detection.

Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions

DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.

Monitoring of biofouling communities in a Portuguese port using a combined morphological and metabarcoding approach

Marine biofouling remains an unsolved problem with a serious economic impact on several marine associated industries and constitutes a major vector for the spread of non-indigenous species (NIS). The implementation of biofouling monitoring programs allows for better fouling management and also for the early identification of NIS. However, few monitoring studies have used recent methods, such as metabarcoding, that can significantly enhance the detection of those species. Here, we employed monthly monitoring of biofouling growth on stainless steel plates in the Atlantic Port of Leixões (Northern Portugal), over one year to test the effect of commercial anti-corrosion paint in the communities. Fouling organisms were identified by combining morpho-taxonomy identification with community DNA metabarcoding using multiple markers (16S rRNA, 18S rRNA, 23S rRNA, and COI genes). The dominant colonizers found at this location were hard foulers, namely barnacles and mussels, while other groups of organisms such as cnidarians, bryozoans, and ascidians were also abundant. Regarding the temporal dynamics of the fouling communities, there was a progressive increase in the colonization of cyanobacteria, green algae, and red algae during the sampled period with the replacement of less abundant groups. The tested anticorrosion paint demonstrated to have a significant prevention effect against the biofouling community resulting in a biomass reduction. Our study also reports, for the first time, 29 NIS in this port, substantiating the need for the implementation of recurring biofouling monitoring programs in ports and harbours.

Nuisance Algae in Ballast Water Facing International Conventions. Insights from DNA Metabarcoding in Ships Arriving in Bay of Biscay

Ballast water is one of the main vectors of transport of nuisance species among marine ports. Neither treatment nor interchange completely reduces the risk of ballast water containing DNA from harmful species, being a signal of potential threat. However, although there are some efficient treatments, they are not available on all ships and there might be some technological/economical constrains for their active and routine usage. Understanding what routes lead to a higher risk of contamination is important for designing targeted surveillance. We analysed ballast water from seven ships arriving in Gijon port (south Bay of Biscay, Spain). DNA metabarcoding was employed for identification of exotic species and harmful algae. One ship carried DNA of 20 risk species in the ballast water. Three ships contained DNA of only one risk species, and three ships had none. Seventy two algae species were found, 22.2% are exotic to the Bay of Biscay and 11.1% are catalogued as harmful. The results demonstrated the importance of continuous surveillance of ballast water.

The risks of using molecular biodiversity data for incidental detection of species of concern

Incidental detection of species of concern (e.g., invasive species, pathogens, threatened and endangered species) during biodiversity assessments based on high-throughput DNA sequencing holds significant risks in the absence of rigorous, fit-for-purpose data quality and reporting standards. Molecular biodiversity data are predominantly collected for ecological studies and thus are generated to common quality assurance standards. However, the detection of certain species of concern in these data would likely elicit interest from end users working in biosecurity or other surveillance contexts (e.g., pathogen detection in health-related fields), for which more stringent quality control standards are essential to ensure that data are suitable for informing decision-making and can withstand legal or political challenges. We suggest here that data quality and reporting criteria are urgently needed to enable clear identification of those studies that may be appropriately applied to surveillance contexts. In the interim, more pointed disclaimers on uncertainties associated with the detection and identification of species of concern may be warranted in published studies. This is not only to ensure the utility of molecular biodiversity data for consumers, but also to protect data generators from uncritical and potentially ill-advised application of their science in decision-making.

Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses

In this study, the evolution of ballast water (BW) assemblages across different trophic levels was characterized over a 21 day cross-latitudinal vessel transit using a combination of molecular methods. Triplicate BW samples were collected every second day and size-fractionated (<2.7, 10, >50 μm). Measurements of adenosine triphosphate (ATP) and metabarcoding of environmental nucleic acid (DNA and RNA) analyses, complemented by microscopy and flow cytometry, were performed on each sample. Measured ATP concentrations exhibited high variance between replicates and a strong negative trend in the large (≥50 μm) fraction over the voyage. In concert with microscopy, the metabarcoding data indicated a die-off of larger metazoans during the first week of study and gradual reductions in dinoflagellates and ochrophytes. The ATP and metabarcoding data signaled persistent or increased cellular activity of heterotrophic bacteria and protists in the BW, which was supported by flow cytometry. The metabarcoding showed the presence of active bacteria in all size fractions, suggesting that the sequential filtration approach does not ensure taxonomical differentiation, which has implications for BW quality assessment. Although our data show that ATP and metabarcoding have potential for indicative BW screening for BW compliance monitoring, further research and technological development is needed to improve representativeness of sampling and deliver the unequivocal response criteria required by the international Ballast Water Management Convention.

Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring

Nonindigenous species are introduced worldwide with ballast water (BW). To prevent further introductions, oceanic BW exchange and BW treatment systems are utilized, but their performance needs to be evaluated. To that aim, characterizing BW communities is essential but usually relies on exhaustive sampling and morphological taxonomic identification, which does not always allow fine-scale taxonomic resolution. Through the analysis of BW samples from 11 vessels arriving to the Chesapeake Bay (USA), we evaluated the potential of environmental DNA (eDNA) metabarcoding for BW monitoring by assessing whether the impact of BW management type could be identified, analyzing the influence of BW sampling access locations on communities, and comparing the accuracy of eDNA for taxonomic assignment and identification of nonindigenous taxa. We found that (1) different sampling access locations of the same tank resulted in different communities, (2) communities from treated and exchanged BW differ, (3) signals of source port and of ocean exchange are observed, (4) eDNA metabarcoding results in more diversity than morphological taxonomy, and (5) the nonindigenous copepod Oithona davisae, not reported before in the Chesapeake Bay, is detected. Overall, this study highlights the potential of eDNA metabarcoding for BW monitoring, but more comprehensive sampling will be needed to optimize the approach.