DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

Comparative study of traditional and DNA-based methods for environmental impact assessment: A case study of marine aggregate extraction in the North Sea

Environmental impact assessments of marine aggregate extraction are traditionally conducted based on morphological characteristics of macrobenthos, which is time-consuming, labour-intensive and requires specific taxonomic expert knowledge. Bulk DNA metabarcoding is suggested as a promising alternative. This study compares the traditional morphological and the bulk DNA metabarcoding method to assess the impact of sand extraction activities on three sandbanks in the Belgian North Sea. Substantial differences in the detected species were observed between methods: Abundant and/or large macrobenthos species were detected by both methods, while small species or species with an exoskeleton were usually only detected by the morphological method. Taxa uniquely detected by bulk DNA metabarcoding could be explained by specimens identified at a higher taxonomic level by morphology, or by specimens with very low read numbers, probably representing species missed in the morphological sorting process, DNA traces on the specimens or false positives during PCR amplification efficiency. Despite the difference in detected species, comparable alpha and beta diversity patterns were observed by both methods, indicating that bulk DNA metabarcoding can effectively detect the overall ecological changes associated with sand extraction. We further demonstrate that bulk DNA metabarcoding reduces sample processing both in time (44 % faster) and cost (26 % cheaper) compared to the morphology-based identification. However, biomass quantification remains challenging for bulk DNA metabarcoding since of the ten most abundant genera, only two genera (Echinocardium and Ophelia) showed a significant positive correlation between biomass and read numbers. Additionally, bulk DNA metabarcoding does not provide information on life stages or size of the identified specimens. As such, our results underpin the complementary nature of both methods, wherein DNA-based analyses allow for rapid detection of community changes (as similar patterns in alpha and beta diversity and biotic index were observed), while morphology-based analyses provide additional information on e.g. secondary production (biomass) and size composition. We show how the strengths of both methods can be combined to assess the impact of sand extraction.

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.

eDNA metabarcoding reveals shifts in sediment eukaryote communities in a metal contaminated estuary

Metal contamination is a global issue impacting biodiversity in urbanised estuaries. Traditional methods to assess biodiversity are time consuming, costly and often exclude small or cryptic organisms due to difficulties with morphological identification. Metabarcoding approaches have been increasingly recognised for their utility in monitoring, however studies have focused on freshwater and marine systems despite the ecological significance of estuaries. We targeted estuarine eukaryote communities within the sediments of Australia's largest urbanised estuary, where a history of industrial activity has resulted in a metal contamination gradient. We identified specific eukaryote families with significant correlations with bioavailable metal concentrations, indicating sensitivity or tolerance to specific metals. While polychaete families Terebellidae and Syllidae demonstrated tolerance to the contamination gradient, members of the meio- and microfaunal communities including diatoms, dinoflagellates and nematodes displayed sensitivities. These may have high value as indicators but are frequently missed in traditional surveys due to sampling limitations.

Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition

The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.

Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment

The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.

eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects

Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.

Benthic infaunal assemblages adjacent to an ocean outfall in Australian marine waters: Impact assessment and identification of indicator taxa

An impact assessment of oceanic effluent releases from Belmont wastewater treatment works (WWTW) in Newcastle, Australia, was undertaken. Benthic infaunal assemblages in sandy sediments of ~25 m water depth were examined, at sites adjacent to the release point, and at increasing distances up to 2 km in both a NE and SW direction over five consecutive years (2016-2020). Localised impacts were evident for infaunal assemblages, with sites within 20 m of the outfall ("Impact" site types) exhibiting lower taxa richness and Shannon diversity, higher abundances of polychaetes and/or nematodes, higher polychaete ratios, and shifts in assemblage composition in comparison to sites at greater distances during some years. Taxa with increased localised abundances at the outfall were identified as indicators for monitoring impacts, including deposit-feeding polychaetes (Families Polygordiidae, Paraonidae and Dorvilleidae) and Phylum Nematoda. Future infaunal monitoring could include molecular tools and paired sediment analyses.

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.

Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos: the effect of technical replicates and pooled DNA extractions on species detection

DNA-based monitoring methods are potentially faster and cheaper compared to traditional morphological benthic identification. DNA metabarcoding involves various methodological choices which can introduce bias leading to a different outcome in biodiversity patterns. Therefore, it is important to harmonize DNA metabarcoding protocols to allow comparison across studies and this requires a good understanding of the effect of methodological choices on diversity estimates. This study investigated the impact of DNA and PCR replicates on the detection of macrobenthos species in locations with high, medium and low diversity. Our results show that two to three DNA replicates were needed in locations with a high and medium diversity to detect at least 80% of the species found in the six DNA replicates, while three to four replicates were needed in the location with low diversity. In contrast to general belief, larger body size or higher abundance of the species in a sample did not increase its detection prevalence among DNA replicates. However, rare species were less consistently detected across all DNA replicates of the location with high diversity compared to locations with less diversity. Our results further show that pooling of DNA replicates did not significantly alter diversity patterns, although a small number of rare species was lost. Finally, our results confirm high variation in species detection between PCR replicates, especially for the detection of rare species. These results contribute to create reliable, time and cost efficient metabarcoding protocols for the characterization of macrobenthos.

Suitability of a dual COI marker for marine zooplankton DNA metabarcoding

As DNA metabarcoding has become an emerging tool for surveying biodiversity, including its application in legally binding assessments, reliable and efficient barcodes are requested, especially for the highly diverse group of zooplankton. This study focuses on comparing the efficiency of two mitochondrial COI barcodes based on the internal primers mlCOIintF and mlCOIintR utilizing mesozooplankton samples collected in a Mediterranean lagoon. Our results indicate that after a slight adjustment, the mlCOIintR primer performs in combination with jdgLCO1490 (herein) very comparably to the much more widely used primer system mlCOIintF/jgHCO2198+dgHCO2198, in terms of level of taxonomic resolution, species detection and their relative abundance in terms of numbers of reads. As for some groups, like Ctenophora, this barcode is not suitable; a combination of them may be the best option to rely on the Folmer region in its entirety without the risk of losing information for a limited primer match.

Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.

Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments

Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost-effectiveness. Several programs have recently been developed which infer functional profiles from 16S rRNA gene data using hidden-state prediction (HSP) algorithms. These might offer an economic and scalable alternative to shotgun metagenomics. To date, HSP-based methods have seen limited use for benthic marine surveys and their performance in these environments remains unevaluated. In this study, 16S rRNA metabarcoding was applied to sediment samples collected at 0 and ≥1,200 m from Norwegian salmon farms, and three metabolic inference approaches (Paprica, Picrust2 and Tax4Fun2) evaluated against metagenomics and environmental data. While metabarcoding and metagenomics recovered a comparable functional diversity, the taxonomic composition differed between approaches, with genera richness up to 20× higher for metabarcoding. Comparisons between the sensitivity (highest true positive rates) and specificity (lowest true negative rates) of HSP-based programs in detecting functions found in metagenomic data ranged from 0.52 and 0.60 to 0.76 and 0.79, respectively. However, little correlation was observed between the relative abundance of their specific functions. Functional beta-diversity of HSP-based data was strongly associated with that of metagenomics (r ≥ 0.86 for Paprica and Tax4Fun2) and responded similarly to the impact of fish farm activities. Our results demonstrate that although HSP-based metabarcoding approaches provide a slightly different functional profile than metagenomics, partly due to recovering a distinct community, they represent a cost-effective and valuable tool for characterizing and assessing the effects of fish farming on benthic ecosystems.

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.

Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding

Traditional methods for algal biodiversity monitoring are costly and time inefficient because they rely on high-level taxonomic expertise to address species identity problems involving phenotypic plasticity and morphological convergence. These problems are exacerbated in regions such as the Gulf of Mexico, that has a limited history of phycological exploration, but that are economically important or threatened by numerous anthropogenic stressors. Given the high pace of disturbance to natural systems, there is a critical need for expedient and cost-effective tools for the study of benthic algal communities. Here we document the use of environmental DNA metabarcoding, using the partial LSU rDNA and 23S rDNA plastid molecular markers, to elucidate littoral algal diversity in the Northern Gulf of Mexico. We assigned 73.7% of algal OTUs to genus and 59.6% to species ranks. Our current study detected molecular signals for 35 algal/protist species with no previous reports in the Gulf of Mexico, thus providing an important, molecular-validated, baseline of species richness for this region. We also make several bioinformatic recommendations for the efficient use of high-throughput sequence data to assess biological communities.

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.

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.

Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering

Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time-consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular-based alternative to the morphology-based monitoring of streams using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulk material of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. In particular, we evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1-BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. In total, 140 taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the "best identity" criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed us to improve the match between biotic index values obtained with the bulk DNA versus morphology-based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.

Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity: A comparison of conventional and molecular tools

Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and is stocked for conservation management in England, but its impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicate their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and environmental DNA (eDNA) metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding and eDNA metabarcoding. Five 2 L water samples and 3 min sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e., ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.

Gap Analysis for DNA Barcode Reference Libraries for Aquatic Macroinvertebrate Species in the Apulia Region (Southeast of Italy)

The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more effective DNA barcode implementation effort and extensive use of the metabarcoding method. In this paper, a new combination of primers has revealed its experimental effectiveness at least on the species belonging to the three most represented taxa in the aquatic ecosystems of the Apulia region, highlighting the opportunity to develop combinations of primers useful at the regional level and the importance of studying DNA barcode gaps at the local/regional level. The DNA barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Acquatina di Frigole” in the Apulia region) and we sampled two macroinvertebrate species lacking DNA barcodes from “Aquatina di Frigole” NATURA 2000 Site IT9150003, Fabulina fabula and Tritia nitida, generated two new CO1 barcodes and added them to a DNA barcode reference library.

Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods

The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.

Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting

DNA-based identification through the use of metabarcoding has been proposed as the next step in the monitoring of biological communities, such as those assessed under the Water Framework Directive (WFD). Advances have been made in the field of metabarcoding, but challenges remain when using complex samples. Uneven biomass distributions, preferential amplification and reference database deficiencies can all lead to discrepancies between morphological and DNA-based taxa lists. The effects of different taxonomic groups on these issues remain understudied. By metabarcoding WFD monitoring samples, we analyzed six different taxonomic groups of freshwater organisms, both separately and combined. Identifications based on metabarcoding data were compared directly to morphological assessments performed under the WFD. The diversity of taxa for both morphological and DNA-based assessments was similar, although large differences were observed in some samples. The overlap between the two taxon lists was 56.8% on average across all taxa, and was highest for Crustacea, Heteroptera, and Coleoptera, and lowest for Annelida and Mollusca. Taxonomic sorting in six basic groups before DNA extraction and amplification improved taxon recovery by 46.5%. The impact on ecological quality ratio (EQR) scoring was considerable when replacing morphology with DNA-based identifications, but there was a high correlation when only replacing a single taxonomic group with molecular data. Different taxonomic groups provide their own challenges and benefits. Some groups might benefit from a more consistent and robust method of identification. Others present difficulties in molecular processing, due to uneven biomass distributions, large genetic diversity or shortcomings of the reference database. Sorting samples into basic taxonomic groups that require little taxonomic knowledge greatly improves the recovery of taxa with metabarcoding. Current standards for EQR monitoring may not be easily replaced completely with molecular strategies, but the effectiveness of molecular methods opens up the way for a paradigm shift in biomonitoring.

Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA

Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an as yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here, we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants environmental taxonomic units (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here, we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.

COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

Mixed community or environmental DNA marker gene sequencing has become a commonly used technique for biodiversity analyses in freshwater systems. Many cytochrome c oxidase subunit I (COI) primer sets are now available for such work. The purpose of this study is to test whether COI primer choice affects the recovery of arthropod richness, beta diversity, and recovery of target assemblages in the benthos kick-net samples typically used in freshwater biomonitoring. We examine six commonly used COI primer sets on samples collected from six freshwater sites. Biodiversity analyses show that richness is sensitive to primer choice and the combined use of multiple COI amplicons recovers higher richness. Thus, to recover maximum richness, multiple primer sets should be used with COI metabarcoding. In ordination analyses based on community dissimilarity, samples consistently cluster by site regardless of amplicon choice or PCR replicate. Thus, for broadscale community analyses, overall beta diversity patterns are robust to COI marker choice. Recovery of traditional freshwater bioindicator assemblages such as Ephemeroptera, Trichoptera, Plectoptera, and Chironomidae as well as Arthropoda site indicators were differentially detected by each amplicon tested. This work will help future biodiversity and biomonitoring studies develop not just standardized, but optimized workflows that either maximize taxon-detection or the selection of amplicons for water quality or Arthropoda site indicators.

Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach

Next-generation sequencing methods are increasingly used to identify eukaryotic, unicellular and multicellular symbiont communities within hosts. In this study, we analyzed the non-specific reads obtained during a metabarcoding survey of the bacterial communities associated to three different tissues collected from 13 wild Mediterranean teleost fish species. In total, 30 eukaryotic genera were identified as putative parasites of teleosts, associated to skin mucus, gills mucus and intestine: 2 ascomycetes, 4 arthropods, 2 cnidarians, 7 nematodes, 10 platyhelminthes, 4 apicomplexans, 1 ciliate as well as one order in dinoflagellates (Syndiniales). These results highlighted that (1) the metabarcoding approach was able to uncover a large spectrum of symbiotic organisms associated to the fish species studied, (2) symbionts not yet identified in several teleost species were putatively present, (3) the parasitic diversity differed markedly across host species and (4) in most cases, the distribution of known parasitic genera within tissues is in accordance with the literature. The current work illustrates the large insights that can be gained by making maximum use of data from a metabarcoding approach.

Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments

Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates.

Development of the cephalopod-specific universal primer set and its application for the metabarcoding analysis of planktonic cephalopods in Korean waters

Although spatiotemporal analysis of the cephalopod larvae provides the useful information for the effective management of their resources, it has been difficult mainly due to their low numbers in the mixed zooplankton net samples and difficulty in morphological identification. In order to analyze the planktonic cephalopods using next-generation sequencing (NGS), we have designed a cephalopod-specific universal (CPD) primer set targeting a region covering mitochondrial cytochrome b and ND6 genes based on the currently identified 36 complete cephalopod mitochondrial genome sequences in the GenBank database. The expected amplicon sizes by CPD primers were between 465 and 471 bp, which was applicable to the MiSeq system (Illumina, San Diego, CA, USA). NGS results of pooled DNAs from 8 months (including 739 zooplankton net samples) collected from Korean waters in 2016 showed the exclusive cephalopod sequences with little contaminant sequences supporting the specificity of CPD primer set. Total 47 representative cephalopod haplotypes (seven families and 10 genera) were obtained from 1,439,414 merged reads. Among the total analyzed haplotypes, Watasenia scintillans, Todarodes pacificus, and Sepiola birostrata were the most abundant species in Korean waters. Two “unidentified” clades in order Oegopsida were identified, which was showed less than 90% sequence identity but closely related to Enoploteuthidae and Idiosepiidae, respectively. Monthly changes in proportions of each haplotype were also identified, which may reflect its reproduction and spawning period. The larvae of W. scintillans was dominant from February to June, while high proportions of other cephalopod taxa were also identified from August to November. Only single haplotype was dominant in W. scintillans (Type 2) throughout the year, while two distinct haplotypes showed seasonal differences in T. pacificus.

Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment

One of the most common approaches for investigating the ecology of spatially complex environments is to examine a single biotic assemblage present, such as macroinvertebrates. Underlying this approach are assumptions that sampled and unsampled taxa respond similarly to environmental gradients and exhibit congruence across different sites. These assumptions were tested for five benthic groups of various sizes (archaea, bacteria, microbial eukaryotes/protists, meiofauna and macrofauna) in Plymouth Sound, a harbour with many different pollution sources. Sediments varied in granulometry, hydrocarbon and trace metal concentrations. Following variable reduction, canonical correspondence analysis did not identify any associations between sediment characteristics and assemblage composition of archaea or macrofauna. In contrast, variation in bacteria was associated with granulometry, trace metal variations and bioturbation (e.g. community bioturbation potential). Protists varied with granulometry, hydrocarbon and trace metal predictors. Meiofaunal variation was associated with hydrocarbon and bioturbation predictors. Taxon turnover between sites varied with only three out of 10 group pairs showing congruence (meiofauna-protists, meiofauna-macrofauna and protists-macrofauna). While our results support using eukaryotic taxa as proxies for others, the lack of congruence suggests caution should be applied to inferring wider indicator or functional interpretations from studies of a single biotic assemblage.

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Over 2.5 million COI sequences in GenBank and growing

The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. The number of COI records deposited to the NCBI nucleotide database has increased by a geometric average of 51% per year, from 8,137 records deposited in 2003 to a cumulative total of ~ 2.5 million by the end of 2017. About half of these records are fully identified to the species rank, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records, 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing reference sequences. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.