Detection Of Non-indigenous Species Research Articles

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.

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.

Non-Indigenous Species Dynamics in Time and Space within the Coastal Waters of The Netherlands

Information on temporal and spatial trends with regard to the introduction of non-indigenous species (NIS) is often sparsely available. These trends may potentially help improve the design and focus of monitoring programs, give insights into new pathways and hotspots, and facilitate horizon scanning. We provide an overview of 215 marine and brackish water NIS recorded in The Netherlands. Temporal trends over the most recent three decades for taxonomic groups, species origin, introduction vectors, and water systems were analysed. We attempt to explain the observed patterns and discuss factors that hamper their explanation. A shift in the region of origin from Pacific to W Atlantic can potentially be linked to legislation prohibiting Pacific oyster imports, whereas a subsequent shift backwards cannot. Case studies illustrate that NIS may not be first detected in the water systems where they were originally introduced. Additionally, it is shown that changes in allegedly native species’ distribution or seasonal pattern should be linked to an introduced cryptic NIS instead. We also discuss the shortcomings of monitoring programs that were originally not focused on NIS, the importance of naturalists’ observations, and the added value of a more recent network that is focused on NIS detection in the coastal waters of The Netherlands.

Detection and monitoring of invertebrate non-indigenous species through DNA metabarcoding in a recreational marina of the Northwest of Portugal

In marine and coastal ecosystems, the proliferation of non-indigenous species (NIS) is among the top causes of biodiversity loss. Thus, it is essential to prevent the entrance and proliferation of NIS by detecting their presence as early as possible at the most susceptible locations, such as ports and marinas. Molecular techniques, like DNA metabarcoding, may be faster and more effective in the early detection of NIS. Its high sensitivity allows the detection of species at any stage of their life cycle and when present at very low densities. However, the detection power can be affected by the methodologies employed through the DNA metabarcoding analytical chain. This study aimed to assess the seasonal effects, sampling method (hard and artificial substrates, zooplankton and eDNA) and genetic marker (COI and 18S) in the recovery of NIS through DNA metabarcoding. Sampling was conducted in 3 seasons (spring, autumn, and winter of 2020/2021) in the “Porto Atlântico” marina, which is located near a major commercial port of the North of Portugal (Leixões). Overall, 626 species were identified through DNA metabarcoding, with the dominance of Crustacea, Ascidiacea and Mollusca. The sampling method and season significantly affected the marine invertebrate species recorded, for both molecular markers, with a high proportion of species detected exclusively using one method (7 to 20%). Overall, 31 NIS were detected, 7 of which are considered invasive and 6 are presumed new records in mainland Portugal. Zooplankton sampling and winter were, respectively, the method and the season where the highest number of NIS was detected, but the maximum number was only attained when pooling the results from all sampling methods and seasons. Our study highlights that different sampling methods and genetic markers, over different seasons, are needed to detect NIS in marine habitats, since the number of species shared by these factors is low.

Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe

Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e. an ichthyological, hydrobiological and eDNA survey, whereby DNA was extracted from 500 ml surface water samples and amplified with two 16S rDNA primer assays targeting the fish and macroinvertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous benthic macroinvertebrates were detected by traditional surveys, while seven NISeDNA signals were picked up, including four fish, one aquatic and two benthic macroinvertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey might be attributed to: (i) preferential amplification of aquatic over benthic macroinvertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximise the probability of early detection of non-native organisms.

Biodiversity Studies for Sustainable Lagoon: Thermophilic and Tropical Fish Species vs. Endemic Commercial Species at Mellah Lagoon (Mediterranean, Algeria)

Lagoons play an important socio-economic role and represent a precious natural heritage at risk from fishing pressure and chemical and biological pollution. Our research focused on better understanding the discrimination of fish biodiversity, the detection of non-indigenous species, and the valorization of commercial indigenous species at Mellah lagoon (Algeria). Taxonomic characterization and barcoding for all fish species and Inkscape schematic drawings for the most common species are provided. A total of 20 families and 37 species were recorded. The thermophilic species Coris julis, Thalassoma pavo, and Aphanius fasciatus and tropical species such as Gambusia holbrooki and Parablennius pilicornis were identified. Numerous Mediterranean species of socio-economic importance are highlighted, and detailed information is summarized for the lagoon’s sustainability. This short-term evaluation goes hand in hand with long-term programs documenting the interaction between indigenous and non-indigenous species in the lagoon and will allow the development of a provisional relationship model for future studies. Thermophilic and tropical species patterns in the Mellah lagoon are presented. Taken together, we provide useful data that can guide future investigations and may become a potential management tool for achieving the Sustainable Development Goals and protecting species with large socio-economic roles from potential thermal stress impact.

Surveillance of non-indigenous invertebrate species through DNA metabarcoding in recreational marinas in the North and Center of Portugal

DNA metabarcoding has been widely used in biodiversity assessments as a complement to traditional morphology-based techniques. This technique is useful for the early detection and surveillance of non-indigenous species (NIS) in aquatic ecosystems. When introduced to new locations, NIS can establish, and become invasive, which may cause severe alterations to native ecosystems and biodiversity. As most introductions in coastal ecosystems occur by transport in ships (through ballast waters discharges and biofouling), ports and marinas are priority hubs for the early detection of NIS. The aim of this study was to survey marine invertebrate NIS in four marinas in the north and center of Portugal using (e)DNA metabarcoding and different sampling methodologies. We sampled four marinas in three locations in Portugal spanning a distance of ca. 150 km: one in Viana do Castelo (VC), one in Porto (L), inside the port of Leixões, and two in Aveiro (Av1: Costa Nova and Av2: Oudinot). Viana do Castelo, Porto, and Oudinot marinas are more sheltered, located near the coast, with a lower current flow, while Costa Nova marina is located inside a channel, more exposed to the passage of ships and to a higher current flow. Samples were taken of the organisms colonizing the marinas’ hard substrates (e.g., pontoons, buoys, ropes), as well as from water, for environmental DNA (eDNA) analysis, and zooplankton, collected using a 55-µm mesh net. We used two molecular markers: the mitochondrial cytochrome c oxidase gene (COI) and the small subunit ribosomal RNA gene (18S) to produce amplicon libraries for each sample, which were high throughput sequenced in an Illumina MiSeq platform. mBRAVE and SILVAngs were then used to process the sequence data and to generate species-level assignments for COI and 18S data, respectively. A total of 23 NIS was detected in this study: 13 using each molecular marker. Only 3 NIS were detected using both markers. The highest number of NIS was detected in the Av1 marina with COI (11), whereas in the other marinas this number ranged from 5-9 NIS depending on the molecular marker. Six NIS were common to all the marinas, amongst which Amphibalanus amphitrite and Amphibalanus eburneus, two invasive barnacle species and Eriocheir sinensis, the Chinese mitten crab, a very well-known species with invasive behavior that causes severe ecological and economic damages. Fifty percent of NIS belonged to the phyla Arthropoda: Crustacea and Chordata: Ascidiacea. The sampling method that registered the highest number of NIS (9) was the eDNA from water in Av1, using COI. Overall, 18S detected approximately 1,6 times higher numbers of OTUs (237-267), phyla (16-21) and species (179-210) than COI, and only 5-6% of species were detected using both markers. Regarding the type of sampling method, the zooplankton samples retrieved the highest number of phyla (20 in VC; COI: 12 and 18S: 20) and more species (40 to 155; COI: 90 and 18S: 155), namely from Mollusca and Annelida. Between the three methods, there were only 21 (COI) to 28% (18S) of shared species. Crustacea dominated most samples collected from hard substrates. As for marinas, VC had the highest number of recovered OTUs (267), phyla (21) and species (210), when analyzed with the 18S marker, and the lowest number of OTUs (94) and species (86) was recovered in Av1 with COI. Coincidently, this was also the marina with the highest number of NIS probably due to its more exposed location. These results show the efficiency of NIS detection using (e)DNA metabarcoding but reveal the need to employ different molecular markers and sampling methodologies to guarantee a more comprehensive surveillance and detection of NIS in these environments.

Citizen Science and Biological Invasions: A Review

Biological invasions are among the most challenging ecological and conservation riddles of our times. Fortunately, citizen science projects became a valuable tool to detect non-indigenous species (NIS), document their spread, prevent dispersion, and eradicate localized populations. We evaluated the most undisputed definitions of citizen science and proposed that a combination of two of them is a better reflection of what citizen science has become. Thus, citizen science is any environmental and/or biological data collection and analysis, including data quality control, undertaken by members of the general public, as individuals or as organized groups of citizens, with the guidance and/or assistance of scientists toward solving environmental and/or community questions. With this review, we also assessed how citizen science has been advancing biological invasions research and its focus, by analyzing 126 peer-reviewed articles that used citizen science methods or data concerning NIS. Most of the articles studied terrestrial species (68%) and terrestrial plants were the most studied group (22.7%). Surprisingly, most first detection reports were of non-indigenous marine fish probably due to the constraints in accessing aquatic ecosystems which delays the detection of new NIS. Citizen science projects running over broad geographical areas are very cost-effective for the early detection of NIS, regardless of the studied environment. We also discuss the applicability and need to adapt the methods and approaches toward the studied ecosystem and species, but also the profile of the participating citizens, their motivations, level of engagement, or social status. We recommend authors to better acknowledge the work done by contributing citizens, and the putative limitations of data generated by citizen science projects. The outreach planning of citizen science projects is also evaluated, including the use of dedicated web platforms vs. pre-existent and disseminated web platforms, while discussing how such outreach actions can be maximized. Lastly, we present a framework that contextualizes the contributions of citizen science, scientific research, and regional and national stakeholders toward the integrated management of biological invasions.

Metabarcoding as a tool to enhance marine surveillance of nonindigenous species in tropical harbors: A case study in Tahiti

AbstractGlobalization has increased connectivity between countries enhancing the spread of marine nonindigenous species (NIS). The establishment of marine NIS shows substantial negative effects on the structure and functioning of the natural ecosystems by competing for habitats and resources. Ports are often hubs for the spread of NIS via commercial and recreational vessels. Prevention, detection, and mitigation efforts are required to avoid and manage the establishment of NIS in new ecosystems. In this study, metabarcoding approaches targeting the nuclear small‐subunit ribosomal RNA (18S rRNA) gene and mitochondrial cytochrome c oxidase I (COI) gene were used to investigate planktonic and sessile (i.e., biofouling) communities and NIS at four locations in Tahiti, including two marinas and one port with varying anthropogenic impacts, and a relatively pristine site (Manava) used as a control. ASV richness values showed significant differences (18S rRNA gene: p = .023; COI: p < .001) between locations in the plankton samples, with the control site (low impact) having the highest diversity for both genes. ASV richness was also significantly different among locations for the biofouling samples in the COI dataset (p = .002). Community composition differed between locations with spatial patterns appearing stronger for the plankton samples compared with the biofouling samples. Detection of NIS based on selected lists of globally invasive species revealed a wide diversity of potentially invasive taxa especially in the more anthropogenically impacted regions. The use of a multigene approach improved the detection of NIS. This study demonstrates the utility of using a metabarcoding approach to routinely monitor areas most at risk from NIS establishment in Tahiti and other coastal nations. These coastal nations are vulnerable to shipping‐mediated incursions, and baseline information is required for both native diversity and nonindigenous diversity.

A new approach to molecular biosurveillance of invasive species using DNA metabarcoding.

Non-indigenous species (NIS) reach every corner of the world, at times wreaking havoc on ecosystems and costing the global economy billions of dollars. A rapid and accurate biosurveillance tool tailored to a particular biogeographic region is needed to detect NIS when they are first introduced into an area as traditional detection methods are expensive and require specialized expertise. Metabarcoding of environmental and community DNA meets those biosurveillance requirements; a novel tool tailored to the Northwest Pacific Ocean is presented here using an approach that could revolutionize early detection of NIS. Eight newly designed genetic markers for multiple gene regions were implemented to meet the stringent taxonomic requirements for the detection of NIS across four major marine phyla. The tool was considered highly successful because it identified 12 known NIS in the study area and a further seven species representing potential new records. Overall community composition detected here was statistically different between substrate types; zooplankton sampling accounted for significantly higher species richness than filtered sea water in most cases, but this was dominated by mollusk and arthropod species. Both substrate types sampled were required to identify the wide taxonomic breadth of known NIS in the study area. Intensive sampling is known to be paramount for the detection of rare species, including new incursions of NIS, thus it is recommended to include diverse DNA sampling protocols based on species' life-history characteristics for broad detection capacity. Application of a metabarcoding-based molecular biosurveillance tool optimized for biogeographic regions enables rapid and accurate early detection across a wide taxonomic range to allow quick implementation of eradication or control efforts and potentially mitigate some of the devastating effects of NIS worldwide.

The potential of large rafting objects to spread Lessepsian invaders: the case of a detached buoy

A diverse and abundant fouling community dominated by Lessepsian non-indigenous species was identified on a 13.5-m-long steel buoy stranded on the Israeli coast but originating from Port Said, at the Mediterranean entrance of the Suez Canal, Egypt. The molluscan community was sampled quantitatively by scraping. Three quarters of the individuals and more than half of the species were non-indigenous. Among the latter, a mytilid bivalve, Gregariella cf. ehrenbergi, was first recorded in the Mediterranean Sea on the basis of these samples, suggesting that the full consideration of all potential vectors can contribute to non-indigenous species detection. Large floating objects in coastal waters, such as buoys, are particularly suitable for colonization by Lessepsian species because hard substrates, and artificial ones in particular, are highly susceptible to the establishment of non-indigenous species. Moreover, their size and persistence enable the development of abundant and mature fouling communities that can disseminate propagules as eggs and larvae over long distances and for extended periods if detached. This report highlights the potential for large rafting debris as a vector of the spread of non-indigenous biota within the Mediterranean Sea.

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

Marine infrastructure can favor the spread of non-indigenous marine biofouling species by providing a suitable habitat for them to proliferate. Cryptic organisms or those in early life stages can be difficult to distinguish by conventional morphological taxonomy. Molecular tools, such as metabarcoding, may improve their detection. In this study, the ability of morpho-taxonomy and metabarcoding (18S rRNA and COI) using three reference databases (PR2, BOLD and NCBI) to characterize biodiversity and detect non-indigenous species (NIS) in biofouling was compared on 60 passive samplers deployed over summer and winter in a New Zealand marina. Highest resolution of metazoan taxa was identified using 18S rRNA assigned to PR2. There were higher assignment rates to NCBI reference sequences, but poorer taxonomic identification. Using all methods, 48 potential NIS were identified. Metabarcoding detected the largest proportion of those NIS: 77% via 18S rRNA/PR2 and NCBI and 35% via COI/BOLD and NCBI. Morpho-taxonomy detected an additional 14% of all identified NIS comprising mainly of bryozoan taxa. The data highlight several on-going challenges, including: differential marker resolution, primer biases, incomplete sequence reference databases, and variations in bioinformatic pipelines. Combining morpho-taxonomy and molecular analysis methods will likely enhance the detection of NIS from complex biofouling.

Alert calling in port areas: Marine litter as possible secondary dispersal vector for hitchhiking invasive species

Floating plastic debris, such as bottles and fishing gear, is a shelter for different species in the oceans. Litter may therefore help the spread of non-indigenous species (NIS). Here we have challenged the idea of using the abundance of marine litter present in a zone to estimate the risk of NIS introduction. To test this, a targeted sampling of plastic bottles and fishing gear (ropes and nets) was performed along 22 beaches from the Cantabrian coast where ports have been reported as a source of biological invasions. All items with attached organisms were collected and recorded. Genetic barcoding was used to ascertain the species and identify NIS. In total 17 species attached to plastic bottles and fishing gears were identified. Three of them, found on the two types of items, are catalogued as invasive species: Austrominius modestus; Magallana gigas; and, Amphibalanus amphitrite. Prevalence and mean intensity of non-indigenous biota on plastic bottles and fishing gear were not significantly different. The abundance of barnacles in litter was significantly correlated with that found from ports in the same region. The results suggest that ropes are able to transport different marine organisms and NIS as plastic bottles do. Monitoring biota on marine litter could serve as an additional tool for NIS detection.

Social networks allow early detection of non indigenous species

The red drum Sciaenops ocellatus is a large demersal fish that represents one of the top predators in estuarine environments of its native range. This species is commonly reared in aquaculture facilities, and it has already been reported as non indigenous from several countries. Here we report its first sighting in Italian waters, as well as the second documented occurrence for the Mediterranean Sea. The individual was landed in southern Sicily by artisanal fishery and this unusual observation was immediately shared on Facebook. The importance of considering social networks as tools for NIS detection is briefly discussed in light of the recognized difficulties to properly track biological introductions in the marine environment.

Predicting and mapping the risk of introduction of marine non-indigenous species into Great Britain and Ireland

Non-indigenous species (NIS) can have adverse environmental, economic and social impacts. Their management is now incorporated into key legislation, including the European Union (EU) Marine Strategy Framework Directive and the EU Regulation on the prevention and management of the introduction and spread of invasive alien species. Prevention of NIS introductions and the early detection of NIS following their introduction are recognised as the most effective approaches for reducing the potential impacts of NIS. This is true for most aquatic environments but especially so for the marine environment, where control and/or eradication are often not achievable. By assessing introduction vector activity, it is possible to identify coastal areas and specific locations where marine NIS may be more likely to be introduced. This study uses data relating to the activity of key introduction vectors; shipping, recreational boating and live animal aquaculture import, to estimate the relative risk of introduction of NIS around coastal regions of Great Britain and Ireland. Spatial analysis was used to create “heat” maps indicating coastal areas of increased relative risk of introduction of NIS by these vectors. The results of the present study will be crucial for the implementation of targeted vector management plans, supporting preventive strategies, and will facilitate a risk analyses of NIS threats to inform monitoring and surveillance programmes.

Is metabarcoding suitable for estuarine plankton monitoring? A comparative study with microscopy

Metabarcoding is becoming an increasingly valuable alternative approach to biodiversity assessment, due to the combination of extreme sensitivity and potential for the highest taxonomic resolution in a cost- and time-effective methodology. To evaluate the capacity of metabarcoding for estuarine plankton monitoring, a comparison between the results obtained with this approach were compared with those based on traditional taxonomic analysis (microscopy). Database incompleteness, one of the main limitations of metabarcoding, was somewhat overcome by the addition of DNA sequences for local species, which increased the taxonomic assignment success from 23.7 to 50.5 %. When the communities were studied along with environmental variables, similar spatial and temporal trends of taxonomic diversity were observed for metabarcoding and microscopic studies of zooplankton, but not for phytoplankton. This is most likely attributable to the lack of representative sequences for phytoplankton species in current databases. In addition, there was high correspondence in community composition when comparing abundances estimated from metabarcoding and microscopy, suggesting semiquantitative potential for metabarcoding. Furthermore, metabarcoding allowed the detection and identification of two non-indigenous species (NIS) found in the study area at abundances hardly detectable by microscopy. Overall, our results indicate that metabarcoding is a powerful approach with excellent possibilities for use in plankton monitoring, early detection of NIS and plankton biodiversity shifts.

Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

Introduction and spread of invasive non-indigenous species (NIS) has been clearly recognized as a growing global problem in marine and coastal ecosystems. Early detection of NIS has been recognized as one of the first priorities and effective ways in management programs. However, the detection of an array of rare NIS based on traditional morphological methods represents enormous technical challenges in the marine realm, as numerous poorly studied organisms may be small and/or have insufficient morphological distinctive features. The use of DNA-based approaches has largely increased the detection accuracy and efficiency. Owing to many obvious advantages such as the high capacity to detect extremely low-abundance species and low cost per sequence, high-throughput sequencing (HTS)-based methods have been popularly proposed for early detection of marine NIS. Although HTS-based approaches have been approved robust for the census of NIS in aquatic ecosystems, especially for those present at extremely low abundance, many factors in experimental design and data collection can cause errors including both false negatives and false positives. Here we identify factors responsible for both error types, discuss causes and consequences, and propose possible solutions when utilizing HTS for early detection of NIS in marine and coastal ecosystems.

Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes

Taxonomic and ecological studies of freshwater harpacticoid copepods are limited globally by the ability to easily and accurately identify specimens. Here, we test the use of the mitochondrial cytochrome c oxidase subunit I (COI) gene locus as a tool for assessing the diversity of freshwater Harpacticoida. We obtained sequences from New Zealand harpacticoid copepods, representing two families, five genera and nine species, including the non-indigenous Elaphoidella sewelli. All species were delineated by the COI gene. However, high intraspecific diversity was evident among populations of Elaphoidella bidens (>12%), and between North and South Island populations of Bryocamptus pygmaeus (>18%), potentially indicating the presence of morphologically cryptic taxa. We suggest that mitochondrial DNA (COI) sequences can provide a useful tool for the routine identification of freshwater harpacticoid copepods. Applications of these data will include assessing species diversity and biogeography as well as assisting with the detection of non-indigenous species.

Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

Marine biofilms are precursors for colonization by larger fouling organisms, including non-indigenous species (NIS). In this study, high-throughput sequencing (HTS) of 18S rRNA metabarcodes was used to investigate four sampling methods (modified syringe, sterilized sponge, underwater tape and sterilized swab) for characterizing eukaryotic communities in marine biofilms. PerspexTM plates were sampled in and out of water. DNA collected with tape did not amplify. Otherwise, there were no statistical differences in communities among the remaining three sampling devices or between the two environments. Sterilized sponges are recommended for ease of use underwater. In-depth HTS analysis identified diverse eukaryotic communities, dominated by Metazoa and Chromoalveolata. Among the latter, diatoms (Bacillariophyceae) were particularly abundant (33% of reads assigned to Chromalveolata). The NIS Ciona savignyi was detected in all samples. The application of HTS in marine biofilm surveillance could facilitate early detection of NIS, improving the probability of successful eradication.

Dose of truth—Monitoring marine non-indigenous species to serve legislative requirements

Non-indigenous species (NIS) are recognized as a global threat to biodiversity and monitoring their presence and impacts is considered a prerequisite for marine environmental management and sustainable development. However, monitoring for NIS seldom takes place except for a few baseline surveys. With the goal of serving the requirements of the EU Marine Strategy Framework Directive and the EU Regulation on the prevention and management of the introduction and spread of invasive alien species, the paper highlights the importance of early detection of NIS in dispersal hubs for a rapid management response, and of long-term monitoring for tracking the effects of NIS within recipient ecosystems, including coastal systems especially vulnerable to introductions. The conceptual framework also demonstrates the need for port monitoring, which should serve the above mentioned requirements but also provide the required information for implementation of the International Convention for the Control and Management of Ships Ballast Water and Sediments. Large scale monitoring of native, cryptogenic and NIS in natural and man-made habitats will collectively lead to meeting international requirements. Cost-efficient rapid assessments of target species may provide timely information for managers and policy-advisers focusing on particular NIS at particular localities, but this cannot replace long-term monitoring. To support legislative requirements, collected data should be verified and stored in a publicly accessible and routinely updated database/information system. Public involvement should be encouraged as part of monitoring programs where feasible.