Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

Environmental gradients and optimal fixation time revealed with DNA metabarcoding of benthic sample fixative

Assessments of biodiversity and ecosystem status can benefit from DNA metabarcoding as a means to streamline sample processing and specimen identification. Moreover, processing the fixation medium instead of the precious material introduces straightforward protocols that allow subsequent focus on certain organisms detected among the preserved specimens. In this study, we present a proof of concept via the analysis of freshwater invertebrate samples from the Tatra Mountain lakes (Slovakia). Besides highlighting a match between the lake-specific environmental conditions and the results of our fixative DNA metabarcoding, we observed an option to fine-tune the fixation time: to prefer two weeks over a day or a month. This effect emerged from the presence/absence of individual taxa rather than from coarse per-sample records of taxonomic richness, demonstrating that metabarcoding studies-and efforts to optimize their protocols-can use the robust metrics to explore even subtle trends. We also provide evidence that fixative DNA might better capture large freshwater species than terrestrial or meiofauna.

Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates

Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.

Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries

Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.

TICI: a taxon-independent community index for eDNA-based ecological health assessment

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.

Coupling remote sensing and eDNA to monitor environmental impact: A pilot to quantify the environmental benefits of sustainable agriculture in the Brazilian Amazon

Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA) near São Félix do Xingu, in Pará, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORA's shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.

Comparative immune responses of blue mussel and zebra mussel haemocytes to simultaneous chemical and bacterial exposure

Biomonitoring at the scale of the aquatic continuum and based on biomarkers, requires various representative species and a knowledge of their sensitivity to contaminants. Mussel immunomarkers are established tools for evaluating immunotoxic stress, but little is known about the consequences of an immune activation by local microorganisms on their response to pollution. This study aims to compare the sensitivity of cellular immunomarkers in two mussel species from different environments, the marine mussel Mytilus edulis (blue mussel) and the freshwater mussel Dreissena polymorpha (zebra mussel), to chemical stressors combined with bacterial challenge. Haemocytes were exposed ex vivo to the contaminants (bisphenol A, caffeine, copper chloride, oestradiol, ionomycin) for 4 h. The chemical exposures were coupled with simultaneous bacterial challenges (Vibrio splendidus and Pseudomonas fluorescens) to trigger activation of the immune response. Cellular mortality, phagocytosis efficiency and phagocytosis avidity were then measured by flow cytometry. The two mussel species had different basal levels since D. polymorpha showed higher cell mortality than M. edulis (23.9 ± 11% and 5.5 ± 3% dead cells respectively), and lower phagocytosis efficiency (52.6 ± 12% and 62.2 ± 9%), but similar phagocytosis avidity (17.4 ± 5 and 13.4 ± 4 internalised beads). Both bacterial strains led to an increase in cellular mortality (+8.4% dead cells in D. polymorpha, +4.9% in M. edulis), as well an activation of phagocytosis (+9.2% of efficient cells in D. polymorpha, +6.2% efficient cells and +3 internalised beads per cell in M. edulis). All chemicals triggered an increase in haemocyte mortality and/or phagocytotic modulations, except for bisphenol A. The two species differed in the amplitude of their response. The addition of a bacterial challenge significantly altered cell responses to chemicals with synergetic and antagonistic variations compared to a single exposure, depending on the compound used and the mussel species. This work highlights the species-specific sensitivity of mussel immunomarkers to contaminants, with or without bacterial challenge, and the necessity of considering the presence of in natura non-pathogenic microorganisms for future in situ applications of immunomarkers.

50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead

The essential key to routine molecular species identification (DNA barcoding/metabarcoding) is the existence of an error-free DNA barcode reference library providing full coverage of all species. Published studies generally state the need to produce more barcodes, and control their quality, but unfortunately, the number of barcoded species is still low. However, to initiate real progress, we need to know where the gaps lie, how big they are and why they persist. Our aims were to draw and understand the current state of knowledge regarding species diversity, distribution, and barcode coverage, and offer solutions for improvement. In this study, we used two groups of aquatic insects, beetles and true bugs. We have compiled and critically evaluated an essentially complete and up-to-date European list, containing 1527 species. The list served as a basis for the barcode gap analyses in the Barcode-of-Life-Data-System (BOLD) conducted in three subsequent years (2020-2022). The overall barcode coverage of the pan-European fauna was around 50 % in both groups. The lowest coverage was in the Mediterranean, the Balkans and South-eastern Europe. The coverage in each country depended significantly on the local diversity, the number of rare, endemic species and the similarity of its fauna to that of the most active barcoding European countries. Gap analyses showed a very small increase in species coverage (<1 % in European aquatic beetles) despite an ~25 % increase in the number of barcodes. Hence, it is clear that future barcoding campaigns must prioritise quality over quantity. To visibly improve reference libraries, we need to increase the involvement of taxonomic experts and focus on targeted studies and underexplored but biodiversity-rich areas.

Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions

The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference library for marine invertebrate NIS occurring in Europe. To do so, we compiled a list of NIS using three databases: the European Alien Species Information Network (EASIN), the Information System on Aquatic Non-indigenous and Cryptogenic Species (AquaNIS), and the World Register of Introduced Marine Species (WRiMS). For each species, we retrieved the available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from the Barcode of Life Data System (BOLD) and used the Barcode, Audit & Grade System (BAGS) to check congruence between morphospecies names and Barcode Index Numbers (BINs). From the 1249 species compiled, approximately 42% had records on BOLD, among which 56% were discordant. We further analyzed these cases to determine the causes of the discordances and attributed additional annotation tags. Of the 622 discordant BINs, after revision, 35% were successfully solved, which increased the number of NIS detected in metabarcoding datasets from 12 to 16. However, a fair number of BINs remained discordant. Reliability of reference barcode records is particularly critical in the case of NIS, where erroneous identification may trigger action or inaction when not required.

A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding

Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus

This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs diversity in the South Caucasus is far from comprehensive. For the studied 33 morpho-species, 289 barcodes were clustered into 40 BINs, from which unique BINs were defined for 12 species and five species were characterised with more than a single BIN. From the studied taxa, 60% were characterised larger than 2.2% sequence divergence indicating high genetic variation or cryptic diversity. Within our limited taxonomic coverage, we found one new species for the Republic of Georgia (Galbaschirazensis) and at least three undescribed species belonging to the genera Stagnicola, Segmentina and Anisus. Uniqueness and high molecular diversity of the studied species emphasise the need for further intensive morphological and molecular investigations of the South Caucasian freshwater molluscan fauna.

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments

Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.

A strategy for successful integration of DNA-based methods in aquatic monitoring

Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels.

To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work.

The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level.

This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.

Ichthyoplankton DNA metabarcoding: challenges and perspectives

DNA metabarcoding has been widely used to access and monitor species. However, several challenges remain open for its mainstream application in ecological studies, particularly when dealing with a quantitative approach. In a from the Cover article in this issue of Molecular Ecology, Mariac et al. (2021) report species-level ichthyoplankton dynamics for 97 fish species from two Amazon river basins using a clever quantitative metabarcoding approach employing a probe capture method. They clearly show that most species spawned during the floods, although ~20% also spawned mainly during the receding period and some other year-round, but interestingly, species from the same genus reproduced in distinct periods (i.e., inverse phenology). Opportunistically, Mariac et al. (2021) reported that during an intense hydrological anomaly, several species had a sharp reduction in spawning activity, demonstrating a quick response to environmental cues. This is an interesting result since the speed at which fish species can react to environmental changes, during the spawning period, is largely unknown. Thus, this study brings remarkable insights into basic life history information that is imperative for proposing strategies that could lead to a realistic framework for sustainable fisheries management practices and conservation, fundamental for an under-studied and threatened realm, such as the Amazon River basin.

Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (&gt;50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.

Global gap-analysis of amphipod barcode library

In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called 'gold-standard' gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as "white gaps". Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.

Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956

Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.

The power of metabarcoding: Can we improve bioassessment and biodiversity surveys of stream macroinvertebrate communities?

Most stream bioassessment and biodiversity surveys are currently based on morphological identification of communities. However, DNA metabarcoding is emerging as a fast and cost-effective alternative for species identification. We compared both methods in a survey of benthic macroinvertebrate communities across 36 stream sites in northern Finland. We identified 291 taxa of which 62% were identified only by DNA metabarcoding. DNA metabarcoding produced extensive species level inventories for groups (Oligochaeta, Chironomidae, Simuliidae, Limoniidae and Limnephilidae), for which morphological identification was not feasible due to the high level of expertise needed. Metabarcoding also provided more insightful taxonomic information on the occurrence of three red-listed vulnerable or data deficient species, the discovery of two likely cryptic and potentially new species to Finland and species information of insect genera at an early larval stage that could not be separated morphologically. However, it systematically failed to reliably detect the occurrence of gastropods that were easily identified morphologically. The impact of mining on community structure could only be shown using DNA metabarcoding data which suggests that the finer taxonomic detail can improve detection of subtle impacts. Both methods generally exhibited similar strength of community-environment relationships, but DNA metabarcoding showed better performance with presence/absence data than with relative DNA sequence abundances. Our results suggest that DNA metabarcoding holds a promise for future anthropogenic impact assessments, although, in our case, the performance did not improve much from the morphological species identification. The key advantage of DNA metabarcoding lies in efficient biodiversity surveys, taxonomical studies and applications in conservation biology.

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.

Cyprus' diatom diversity and the association of environmental and anthropogenic influences for ecological assessment of rivers using DNA metabarcoding

Human activities are the leading cause of environmental impairments. Appropriate biomonitoring of ecosystems is needed to assess these activities effectively. In freshwater ecosystems, periphytic and epilithic biofilms have diatom assemblages. These assemblages respond rapidly to environmental changes, making diatoms valuable bioindicators. For this reason, freshwater biomonitoring programs are currently using diatoms (e.g., Water Framework Directive). In the past ten years, DNA metabarcoding coupled with next-generation sequencing and bioinformatics represents a complementary approach for diatom biomonitoring. In this study, this approach is used for the first time in Cyprus by considering the association of environmental and anthropogenic pressures to diatom assemblages. Statistical analysis was then applied to identify the environmental (i.e., river types, geo-morphological) and anthropogenic (i.e., physicochemical, human land-use pressures) variables' role in the observed diatom diversity. Results indicate differences in diatom assemblages between intermittent and perennial rivers. Achnanthidium minutissimum was more abundant in intermittent rivers; whereas Amphora pediculus and Planothidium caputium in perennial ones. Additionally, we could demonstrate the correlation between nutrients (e.g., nitrogen, phosphorus), stations' local characteristics (e.g., elevation), and land use activities on the observed differences in diatom diversity. Finally, we conclude that multi-stressors and anthropogenic pressures together as multiple stressors have a significant statistical relationship to the observed diatom diversity and play a pivotal role in determining Cyprus' rivers' ecological status.

Coverage and quality of DNA barcode references for Central and Northern European Odonata

Background

Dragonflies and damselflies (Odonata) are important components in biomonitoring due to their amphibiotic lifecycle and specific habitat requirements. They are charismatic and popular insects, but can be challenging to identify despite large size and often distinct coloration, especially the immature stages. DNA-based assessment tools rely on validated DNA barcode reference libraries evaluated in a supraregional context to minimize taxonomic incongruence and identification mismatches.

Methods

This study reports on findings from the analysis of the most comprehensive DNA barcode dataset for Central European Odonata to date, with 103 out of 145 recorded European species included and publicly deposited in the Barcode of Life Data System (BOLD). The complete dataset includes 697 specimens (548 adults, 108 larvae) from 274 localities in 16 countries with a geographic emphasis on Central Europe. We used BOLD to generate sequence divergence metrics and to examine the taxonomic composition of the DNA barcode clusters within the dataset and in comparison with all data on BOLD.

Results

Over 88% of the species included can be readily identified using their DNA barcodes and the reference dataset provided. Considering the complete European dataset, unambiguous identification is hampered in 12 species due to weak mitochondrial differentiation and partial haplotype sharing. However, considering the known species distributions only two groups of five species possibly co-occur, leading to an unambiguous identification of more than 95% of the analysed Odonata via DNA barcoding in real applications. The cases of small interspecific genetic distances and the observed deep intraspecific variation in Cordulia aenea (Linnaeus, 1758) are discussed in detail and the corresponding taxa in the public reference database are highlighted. They should be considered in future applications of DNA barcoding and metabarcoding and represent interesting evolutionary biological questions, which call for in depth analyses of the involved taxa throughout their distribution ranges.

Deep learning and computer vision will transform entomology

Most animal species on Earth are insects, and recent reports suggest that their abundance is in drastic decline. Although these reports come from a wide range of insect taxa and regions, the evidence to assess the extent of the phenomenon is sparse. Insect populations are challenging to study, and most monitoring methods are labor intensive and inefficient. Advances in computer vision and deep learning provide potential new solutions to this global challenge. Cameras and other sensors can effectively, continuously, and noninvasively perform entomological observations throughout diurnal and seasonal cycles. The physical appearance of specimens can also be captured by automated imaging in the laboratory. When trained on these data, deep learning models can provide estimates of insect abundance, biomass, and diversity. Further, deep learning models can quantify variation in phenotypic traits, behavior, and interactions. Here, we connect recent developments in deep learning and computer vision to the urgent demand for more cost-efficient monitoring of insects and other invertebrates. We present examples of sensor-based monitoring of insects. We show how deep learning tools can be applied to exceptionally large datasets to derive ecological information and discuss the challenges that lie ahead for the implementation of such solutions in entomology. We identify four focal areas, which will facilitate this transformation: 1) validation of image-based taxonomic identification; 2) generation of sufficient training data; 3) development of public, curated reference databases; and 4) solutions to integrate deep learning and molecular tools.

A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring

Environmental genomics is a promising field for monitoring biodiversity in a timely fashion. Efforts have increasingly been dedicated to the use of bacteria DNA derived data to develop biotic indices for benthic monitoring. However, a substantial debate exists about whether bacteria-derived data using DNA metabarcoding should follow, for example, a taxonomy-based or a taxonomy-free approach to marine bioassessments. Here, we showcase the value of DNA-based monitoring using the impact of fish farming as an example of anthropogenic disturbances in coastal areas and compare the performance of taxonomy-based and taxonomy-free approaches in detecting environmental alterations. We analysed samples collected near to the farm cages and along distance gradients from two aquaculture installations, and at control sites, to evaluate the effect of this activity on bacterial assemblages. Using the putative response of bacterial taxa to stress we calculated the taxonomy-based biotic index microgAMBI. The distribution of individual amplicon sequence variants (ASVs), as a function of a gradient in sediment acid volatile sulphides, was then used to derive a taxonomy-free bacterial biotic index specific for this data set using a de novo approach based on quantile regression splines. Our results show that microgAMBI revealed a organically enriched environment along the gradient. However, the de novo biotic index outperformed microgAMBI by providing a higher discriminatory power in detecting changes in abiotic factors directly related to fish production, whilst allowing the identification of new ASVs bioindicators. The de novo strategy applied here represents a robust method to define new bioindicators in regions or habitats where no previous information about the response of bacteria to environmental stressors exists.

Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance

The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.

On the Diversity of Phyllodocida (Annelida: Errantia), with a Focus on Glyceridae, Goniadidae, Nephtyidae, Polynoidae, Sphaerodoridae, Syllidae, and the Holoplanktonic Families

Phyllodocida is a clade of errantiate annelids characterized by having ventral sensory palps, anterior enlarged cirri, axial muscular proboscis, compound chaetae (if present) with a single ligament, and of lacking dorsolateral folds. Members of most families date back to the Carboniferous, although the earliest fossil was dated from the Devonian. Phyllodocida holds 27 well-established and morphologically homogenous clades ranked as families, gathering more than 4600 currently accepted nominal species. Among them, Syllidae and Polynoidae are the most specious polychaete groups. Species of Phyllodocida are mainly found in the marine benthos, although a few inhabit freshwater, terrestrial and planktonic environments, and occur from intertidal to deep waters in all oceans. In this review, we (1) explore the current knowledge on species diversity trends (based on traditional species concept and molecular data), phylogeny, ecology, and geographic distribution for the whole group, (2) try to identify the main knowledge gaps, and (3) focus on selected families: Alciopidae, Goniadidae, Glyceridae, Iospilidae, Lopadorrhynchidae, Polynoidae, Pontodoridae, Nephtyidae, Sphaerodoridae, Syllidae, Tomopteridae, Typhloscolecidae, and Yndolaciidae. The highest species richness is concentrated in European, North American, and Australian continental shelves (reflecting a strong sampling bias). While most data come from shallow coastal and surface environments most world oceans are clearly under-studied. The overall trends indicate that new descriptions are constantly added through time and that less than 10% of the known species have molecular barcode information available.

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.

Application of propylene glycol in DNA-based studies of invertebrates

High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion.

The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects.

When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable.

Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit.

Adding DNA barcoding to stream monitoring protocols - What's the additional value and congruence between morphological and molecular identification approaches?

Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.

Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.

Decision-making and best practices for taxonomy-free environmental DNA metabarcoding in biomonitoring using Hill numbers

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km² river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.

Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia

In this study, we provide a first estimation of the molecular diversity of the freshwater fishes of Georgia. In addition to field collections, we integrated DNA barcode data obtained from recent works and public databases (BOLD and NCBI GenBank). Currently, the DNA barcode reference library for freshwater fishes of Georgia comprises 352 DNA barcodes for 50 species, 36 genera and 15 families (52% of total Georgian freshwater fish diversity), from which 162 DNA barcodes belonging to 41 species were newly generated as part of this study. A total of 22 species are reported from the Caspian Sea basin and 31 from the Black Sea basin. Amongst the studied taxa, seven species were found with large interspecific divergences (> 2%) while 11 species were found to share DNA barcodes within our dataset. In the course of the study, we found the first evidence of the existence of Gymnocephaluscernua (Linnaeus, 1758) and also confirm the second occurrence of invasive Rhinogobiuslindbergi (Berg, 1933) in Georgia. Based on the evaluation of currently-available barcode data for Georgian fishes, we highlighted major gaps and research needs to further progress DNA-based biodiversity studies in Georgia. Though this study lays a solid base for DNA, based biodiversity assessment and monitoring approaches, further efforts within the recently started CaBOL (Caucasus Barcode Of Life) project are needed to obtain reference data for the species still lacking DNA barcodes.

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.

DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage

Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.

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.

Water Microbiota in Greenhouses With Soilless Cultures of Tomato by Metabarcoding and Culture-Dependent Approaches

Water supply, in hydroponic greenhouses, can originate from groundwater, surface water or rainwater stored in open tanks. To limit contamination of water supply, several methods have been used including active and passive methods such as slow filtration techniques which consist in passing the nutrient solutions slowly through filters. The purpose of this study was to describe the microbiota associated with water sampled before entering greenhouses and in recirculating nutrient solutions, either before or after running through a biofiltration system. Metabarcoding analysis revealed that water ecosystems were unique niches for diverse bacterial and fungal communities. Microbial composition varied greatly across storage conditions (groundwater vs. rainwater) and among greenhouses, suggesting that water microbiota is site- and storage-condition-specific. Nonetheless, we found that microbiota structure in open-stored water (either coming from ground or rain) shared a higher degree of similarity than with water directly pumped out of the ground. Open-stored waters were characterized by predominant taxa, notably those involved in aerobic chemoheterotrophy, such as the Sphingomonadaceae and Hyphomicrobiaceae families. Water directly collected from the ground showed the lowest levels of fungal and bacterial richness while also characterized by a significantly higher level of bacterial equitability and an enrichment in taxa involved in N-cycling. Slow filtration allowed reducing cultivable bacterial loads as well Pythium spp. and Fusarium oxysporum propagules, based on culture-dependent results, without compromising microbiota richness and diversity. Although compositional structure was similar following biofiltration, significant differences in bacterial (but not fungal) taxa abundance were reported, with primarily an enrichment of Chelativorans, Mycobacterium, and Gemmata as well as a depletion of Rhodobacter, Aminobacter, and Ellin329. The exact mechanisms by which such taxa would be favored at the expense of other remained unknown. Besides the accurate description of microbiota found in water at both taxonomical and predicted functional levels, our study allowed comparing the water microbiota between various storage system and following biofiltration. Although preliminary, our results provide a first insight into the potential microbial diversity, which can increase ecosystem functionality.

A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay

Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost-prohibitive to increase the scale of monitoring programmes. Metabarcoding of environmental DNA has clear potential to overcome many of the problems associated with traditional monitoring, with prokaryotes and other microorganisms showing particular promise as bioindicators. However, due to the limited knowledge regarding the ecological roles and responses of environmental microorganisms to different types of pressure, the use of de novo approaches is necessary. Here, we use two such approaches for the prediction of multiple impacts present in estuaries and coastal areas of the Bay of Biscay based on microbial communities. The first (Random Forests) is a machine learning method while the second (Threshold Indicator Taxa Analysis and quantile regression splines) is based on de novo identification of bioindicators. Our results show that both methods overlap considerably in the indicator taxa identified, but less for sequence variants. Both methods also perform well in spite of the complexity of the studied ecosystem, providing predictive models with strong correlation to reference values and fair to good agreement with ecological status groups. The ability to predict several specific types of pressure is especially appealing. The cross-validated models and biotic indices developed can be directly applied to predict the environmental status of estuaries in the same geographical region, although more work is needed to evaluate and improve them for use in new regions or habitats.

Are Environmental DNA Methods Ready for Aquatic Invasive Species Management?

Multiple studies have demonstrated environmental (e)DNA detections of rare and invasive species. However, invasive species managers struggle with using eDNA results because detections might not indicate species presence. We evaluated whether eDNA methods have matured to a point where they can be widely applied to aquatic invasive species management. We have found that eDNA methods meet legal standards for being admissible as evidence in most courts, suggesting eDNA method reliability is not the problem. Rather, we suggest the interface between results and management needs attention since there are few tools for integrating uncertainty into decision-making. Solutions include decision-support trees based on molecular best practices that integrate the temporal and spatial trends in eDNA positives relative to human risk tolerance.

Application of deep learning in aquatic bioassessment: Towards automated identification of non-biting midges

Morphological species identification is often a difficult, expensive, and time-consuming process which hinders the ability for reliable biomonitoring of aquatic ecosystems. An alternative approach is to automate the whole process, accelerating the identification process. Here, we demonstrate an automatic machine-based identification approach for non-biting midges (Diptera: Chironomidae) using Convolutional Neural Networks (CNNs) as a means of increasing taxonomic resolution of biomonitoring data at a minimal cost. Chironomidae were used to build the automatic identifier, as a family of insects that are abundant and ecologically important, yet difficult and time-consuming to accurately identify. The approach was tested with 10 morphologically very similar species from the same genus or subfamilies, comprising 1846 specimens from the South Morava river basin, Serbia. Three CNN models were built utilizing either species, genus, or subfamily data. After training the artificial neural network, images that the network had not seen during the training phase achieved an accuracy of 99.5% for species-level identification, while at the genus and subfamily level all images were correctly assigned (100% accuracy). Gradient-weighted Class Activation Mapping (Grad-CAM) visualized the mentum, ventromental plates, mandibles, submentum, and postoccipital margin to be morphologically important features for CNN classification. Thus, the CNN approach was a highly accurate solution for chironomid identification of aquatic macroinvertebrates opening a new avenue for implementation of artificial intelligence and deep learning methodology in the biomonitoring world. This approach also provides a means to overcome the gap in bioassessment for developing countries where widespread use techniques for routine monitoring are currently limited.

Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data

Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules “organic pollution” (i.e., the saprobic index) and “general degradation” (a multimetric index) as well as their underlying metrics.

In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from ‘good’ to ‘moderate’ (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.

Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation: lessons from the UK diatom metabarcoding exercise

Development of effective metabarcoding-based tools for ecological assessment requires more than just detailed knowledge of ecology and molecular genetics. There is also a need to understand the context within which they will be used, and for the organisation that uses it to understand the techniques involved and, more especially, how the data that are produced differs from that generated by traditional ecological methods. Lessons learnt during the development of a metabarcoding tool for phytobenthos in the UK are set out in this paper. This attempted to develop a molecular “mirror” of the existing light microscopy-based approach to ecological assessment. Although this conservative approach does not exploit the full potential of metabarcoding data, it does mean that benchmarks exist against which performance and data can be judged. However, the pace of developments within molecular ecology means that regulators will need to find ways of incorporating new scientific insights whilst, at the same time, ensuring a stable regulatory regime. Installation of a metabarcoding technique within a regulatory organisation, in other words, is more than a transaction in which one approach is switched for another. A deeper transformation of the organisation is required.

Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.

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.

Taming the Wild West of Molecular Tools Application in Aquatic Research and Biomonitoring

Modern high-throughput sequencing technologies are becoming a game changer in many fields of aquatic research and biomonitoring. To unfold their full potential, however, the independent development of approaches has to be streamlined. This discussion must be fuelled by stakeholders and practitioners and, scientific results collaboratively filtered to identify the most promising avenues. Furthermore, aspects such as time, budget, skills and the application context have to be considered, finally communicating good practice strategies to target audiences.

Since 2016, the EU COST Action DNAqua-Net is taming the wild west of molecular tools application in aquatic research and biomonitoring. After nucleating available knowledge by the formation of a highly international and transdisciplinary network of scientists, stakeholders, practitioners and enterprises, fields of high methodological diversity were identified. Relevant aspects are currently ground truthed, thereby reducing the plethora of pipelines, parameters and protocols to a subset of good practices or standardisations. To effectively bridge the science-application interface, the very same network is exploited for the dissemination of results (Leese et al. 2018).

The internal working group structure of DNAqua-Net is used to provide an overview of existing methodological fields of diversity in DNA-based aquatic biomonitoring:

WG1 -DNA Barcode References: Different marker systems are targeted for the same organism group. Even in case the same molecular marker is investigated, different primer pairs are frequently applied for DNA metabarcoding. Both aspects challenge the further development of high-quality and complete DNA barcode reference libraries (Weigand et al. 2019).

WG2 -Biotic Indices &amp; Metrics: Index systems are developed from molecular data in various ways: from the estimation of species' biomass (as a proxy for abundance) from sequence reads, to the correlation of presence/absence data of molecular operational taxonomic units (MOTUs) with environmental parameters (Pawlowski et al. 2018).

WG3 -Field &amp; Lab Protocols: Using environmental DNA (eDNA) metabarcoding as an example, diverse sampling techniques based on varying water volumes, different filter systems and collection devices as well as a multitude of laboratory protocols for PCR, replication and sequencing are considered.

WG4 -Data Analysis &amp; Storage: During the process of MOTU identification, varying threshold values and conceptually different pipelines are used, potentially impacting the final list of MOTUs or species retrieved. Furthermore, routine storage concepts for big biodiversity data are only in development and some sample types (e.g. eDNA) have no sophisticated metadata descriptions.

WG5 -Implementation Strategy &amp; Legal Issues: The working group picks up collaboratively filtered good practice strategies and generates room for discussions at the science-policy interface (Hering et al. 2018). The CEN working group WG28 "DNA methods" has been initiated and the development of standardisations is fostered.