Molecular barcoding of aquatic oligochaetes: implications for biomonitoring

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan

Among over 20,000 species of Annelida, only two branching species with a highly modified body-pattern are known until now: the Syllidae Syllis ramosa McIntosh, 1879, and Ramisyllis multicaudata Glasby et al. (Zoological Journal of the Linnean Society, 164, 481–497, 2012). Both have unusual ramified bodies with one head and multiple branches and live inside the canals of host sponges. Using an integrative approach (combining morphology, internal anatomy, ecology, phylogeny, genetic divergence, and the complete mitochondrial genome), we describe a new branching species from Japan, Ramisyllis kingghidorahi n. sp., inhabiting an undescribed species of Petrosia (Porifera: Demospongiae) from shallow waters. We compare the new species with its closest relative, R. multicaudata; emend the diagnosis of Ramisyllis; and discuss previous reports of S. ramosa. This study suggests a much higher diversity of branching syllids than currently known. Finally, we discuss possible explanations for the feeding behaviour in the new species in relation to its highly ciliated wall of the digestive tubes (especially at the distal branches and anus), and provide a hypothesis for the evolution of branching body patterns as the result of an adaptation to the host sponge labyrinthic canal system.

DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

Sokefun, Yadav S. Disentangling earthworm taxonomic stumbling blocks using molecular markers

Taxonomic classification of earthworms based on anatomical features has created several challenges for systematics and population genetics. This study examines the application of molecular markers, in particular mitochondrial cytochrome oxidase (COI), to facilitate discrimination of closely related earthworm species. Molecular markers have also provided insights into population genetics by aiding assessment of genetic diversity, lineage sorting, and genealogical distributions of populations for several species. Phylogeography—a study that evaluates the geographical distribution of these genealogical lineages and the role of historical processes in shaping their distribution—has also provided insights into ecology and biodiversity. Such studies are also essential to understand the distribution patterns of invasive earthworm species that have been introduced in non-native ecosystems globally. The negative consequences of these invasions on native species include competition for food resources and altered ecosystems. We anticipate that molecular markers such as COI and DNA barcoding offer potential solutions to disentangling taxonomic impediments in earthworms and advancing their systematics and population genetics. 

Ethanol eDNA Reveals Unique Community Composition of Aquatic Macroinvertebrates Compared to Bulk Tissue Metabarcoding in a Biomonitoring Sampling Scheme

Freshwater ecosystems provide essential ecosystem services and support biodiversity; however, their water quality and biological communities are influenced by adjacent agricultural land use. Aquatic macroinvertebrates are commonly used as bioindicators of stream conditions in freshwater biomonitoring programs. Sorting benthic samples for molecular identification is a time-consuming process, and this study investigates the potential of ethanol-collected environmental DNA (eDNA) for metabarcoding macroinvertebrates, especially for common bioindicator groups. The objective of this study was to compare macroinvertebrate composition between paired bulk tissue and ethanol eDNA samples, as eDNA could provide a less time-consuming and non-destructive method of sampling macroinvertebrates. We collected benthic samples from streams in Ontario, Canada, and found that community composition varied greatly between sampling methods and that few taxa were shared between paired tissue and ethanol samples, suggesting that ethanol eDNA is not an acceptable substitute. It is unclear why we did not detect all the organisms that were preserved in the ethanol, or the origin of the DNA we did detect. Furthermore, we also detected no difference in community composition for bioindicator taxa due to surrounding land use or water chemistry, suggesting sites were similar in ecological condition.

DNA metabarcoding improves the detection of multiple stressor responses of stream invertebrates to increased salinity, fine sediment deposition and reduced flow velocity

Worldwide, multiple stressors affect stream ecosystems and frequently lead to complex and non-linear biological responses. These combined stressor effects on ecologically diverse and functionally important macroinvertebrate communities are often difficult to assess, in particular species-specific responses across many species and effects of different stressors and stressor levels in concert. A central limitation in many studies is the taxonomic resolution applied for specimen identification. DNA metabarcoding can resolve taxonomy and provide greater insights into multiple stressor effects. This was detailed by results of a recent multiple stressor mesocosm experiment, where only for the dipteran family Chironomidae 183 Operational Taxonomic Units (OTUs) could be distinguished. Numerous OTUs showed very different response patterns to multiple stressors. In this study, we applied DNA metabarcoding to assess multiple stressor effects on all non-chironomid invertebrates from the same experiment. In the experiment, we applied three stressors (increased salinity, deposited fine sediment, reduced flow velocity) in a full-factorial design. We compared stressor responses inferred through DNA metabarcoding of the mitochondrial COI gene to responses based on morphotaxonomic taxa lists. We identified 435 OTUs, of which 122 OTUs were assigned to EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa. The most common 35 OTUs alone showed 15 different response patterns to the experimental manipulation, ranging from insensitivity to any applied stressor to sensitivity to single and multiple stressors. These response patterns even comprised differences within one family. The species-specific taxonomic resolution and the inferred response patterns to stressors highlights the potential of DNA metabarcoding in the context of multiple stressor research, even for well-known taxa such as EPT species.

Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy

The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R² = 0.86 and R² = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.

On the identity and phylogenetic position of Dero indica (Clitellata: Naididae)

The identity and validity of the freshwater worm Dero indica (Clitellata: Naididae; Naidinae) has been debated, and it has been suggested that it is likely to be identical with D. digitata. In this study we combine a newly generated COI sequence of D. indica with available sequences from GenBank, to estimate the phylogeny of Dero using both Bayesian Inference and Maximum Likelihood. The trees show that D. indica is well separated from D. digitata, instead it is closest to D. vaga, but with low support. Furthermore, the analyses confirm the close relationship between Dero and Branchiodrilus found in previous studies, and indicates the presence of cryptic species in D. furcata and D. digitata.

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.

Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators' communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017-2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.

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.

Fate and effects of sediment-associated triclosan in subtropical freshwater microcosms

Triclosan (TCS) is an antibacterial agent that is commonly used in personal care products. Because of its sediment-binding properties, TCS exposure presents a potential threat to sediment-dwelling aquatic organisms. Currently our knowledge of the fate and effects of sediment-associated TCS in aquatic systems is limited. To understand the impact of sediment-associated TCS, we used microcosms to assess effects of TCS exposure on a diverse range of organisms selected to mimic a subtropical community, with an exposure period of 28 days. We included the oligochaete freshwater worm Limnodrilus hoffmeisteri to evaluate the interaction between sediment-associated TCS and sediment-dwelling organisms, including potential loss of TCS from the sediment due to biological activity and bioaccumulation. Benthic macroinvertebrate presence significantly increased the TCS levels from 0.013 ± 0.007 μg/L to 0.613 ± 0.030 μg/L in the overlying water through biological activity, posing a potential additional risk to pelagic species, but it did not result in a significant reduction of the sediment concentration. Furthermore, worms accumulated TCS with estimated Biota-Sediment-Accumulation-Factors (BSAFs) ranging between 0.38-3.55. Other than for algae, TCS at environmental concentrations did not affect the survival of the introduced organisms, including the L. hoffmeisteri. Our results demonstrate that, although TCS at currently detected maximum concentration may not have observable toxic effects on the benthic macroinvertebrates in the short term, it can lead to bioaccumulation in worms.

A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy

The hyporheic zone, i.e. the ecotone between surface water and the groundwater, is a rarely studied freshwater ecosystem. Hyporheic taxa are often meiofaunal (<1 mm) in size and difficult to identify based on morphology. Metabarcoding approaches are promising for the study of these environments and taxa, but it is yet unclear if commonly applied metabarcoding primers and replication strategies can be used. In this study, we took sediment cores from two near natural upstream (NNU) and two ecologically improved downstream (EID) sites in the Boye catchment (Emscher River, Germany), metabarcoding their meiofaunal communities. We evaluated the usability of a commonly used, highly degenerate COI primer pair (BF2/BR2) and tested how sequencing three PCR replicates per sample and removing MOTUs present in only one out of three replicates impacts the inferred community composition. A total of 22,514 MOTUs were detected, of which only 263 were identified as Metazoa. Our results highlight the gaps in reference databases for meiofaunal taxa and the potential problems of using highly degenerate primers for studying samples containing a high number of non-metazoan taxa. Alpha diversity was higher in EID sites and showed higher community similarity when compared to NNU sites. Beta diversity analyses showed that removing MOTUs detected in only one out of three replicates per site greatly increased community similarity in samples. Sequencing three sample replicates and removing rare MOTUs is seen as a good compromise between retaining too many false-positives and introducing too many false-negatives. We conclude that metabarcoding hyporheic communities using highly degenerate COI primers can provide valuable first insights into the diversity of these ecosystems and highlight some potential application scenarios.

BBI: an R package for the computation of Benthic Biotic Indices from composition data

The monitoring of impacts of anthropic activities in marine environments, such as aquaculture, oil-drilling platforms or deep-sea mining, relies on Benthic Biotic Indices (BBI). Several indices have been formalised to reduce the multivariate composition data into a single continuous value that is ascribed to a discrete ecological quality status. Such composition data is traditionally obtained from macrofaunal inventories, which is time-consuming and expertise-demanding. Important efforts are ongoing towards using High-Throughput Sequencing of environmental DNA (eDNA metabarcoding) to replace or complement morpho-taxonomic surveys for routine biomonitoring. The computation of BBI from such composition data is usually being undertaken by practitioners with excel spreadsheets or through custom script. Hence, the updating of reference morpho-taxonomic tables and cross studies comparison could be hampered. Here we introduce the R package BBI for the computation of BBI from composition data, either obtained from traditional morpho-taxonomic inventories or from metabarcoding data. Its aim is to provide an open-source, transparent and centralised method to compute BBI for routine biomonitoring.

Genetic diversity of marine oligochaetous clitellates in selected areas of the South Atlantic as revealed by DNA barcoding

Marine oligochaetous clitellates are poorly investigated in the South Atlantic Ocean, especially along the east coast of South America. Closely related species are often difficult to distinguish based on morphology. The lack of specialists and modern identification guides have been pointed out as the main reasons for the scarcity of studies in the South Atlantic Ocean as a whole. To increase the knowledge of this group in the South Atlantic, the genetic diversity of a sample of marine oligochaetous clitellates from Brazil, South Africa and Antarctica was assessed by the Automatic Barcode Gap Discovery (ABGD) and the generalised mixed Yule coalescent (GMYC) approaches. In total, 80 cytochrome c oxidase subunit I (COI) sequences were obtained, each with ~658bp, estimated to represent 32 distinct putative species. ABGD established a barcoding gap between 3% and 14% divergence for uncorrected p-distances and the estimates of GMYC were largely concordant. All the clusters or putative species were genetically associated with previously known species or genera. This study thus confirms the adequacy of the COI barcoding approach combined with a genetic divergence threshold at the order of 10% for marine oligochaetous clitellates.

New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)

Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.

Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database

Introduction

Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation.

Methods

We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful.

Results

We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species.

Discussion

Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.

Taxonomy of North European Lumbricillus (Clitellata, Enchytraeidae)

Lumbricillus is a genus of clitellate worms with about 80 described species that inhabit marine and limnic habitats. This study follows a recent analysis of the phylogeny of the genus based on 24 species of Lumbricillus collected mainly in Norway and Sweden. We provide the illustrated taxonomic descriptions of all these species and describe two of them as new; Lumbricillus latithecatussp. n. and L. scandicussp. n. Using the recent phylogeny, we informally divide Lumbricillus into five distinct morphological groups, into which we also tentatively place the Lumbricillus species not included in this study. Furthermore, we establish Claparedrilusgen. n., with the type species C. semifuscoidessp. n., and transfer Pachydrilus semifuscus Claparède, 1861 (previously referred to Lumbricillus) into said genus.

DNA barcoding of formalin-fixed aquatic oligochaetes for biomonitoring

BACKGROUND

Oligochaetes are valuable bioindicators of the quality of watercourse and lake sediments. The morphological identification of aquatic oligochaetes is difficult, prompting the development of new molecular oligochaete indices based on DNA barcoding and Next-generation sequencing of sorted specimens. In general, the samples for DNA barcoding are fixed in absolute ethanol. However, in the case of aquatic oligochaetes, this medium is not appropriate as it can induce a modification of specimen abundances and of the composition of communities. Therefore, we investigated the possibility to amplify and sequence aquatic oligochaetes fixed in formalin for a short time. We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of the cytochrome c oxydase I (COI) gene on tissue fragments fixed in formalin for different periods of time (from 1 h to 1 week) and in ethanol.

RESULTS

The large majority of aquatic oligochaete specimens fixed in formalin for up to 1 week could be successfully amplified and all obtained sequences were of high quality. The amplification and sequencing success rate of formalin-fixed samples and ethanol-fixed samples was similar. These results suggest that formalin fixation of aquatic oligochaete tissues for a short time does not cause serious damages to DNA and inhibit PCR amplification.

CONCLUSION

The possibility to fix aquatic oligochaetes with formalin before genetic analyses is very promising for diversity monitoring, for construction of a comprehensive DNA barcode library and for development of an index based on Next-generation sequencing analysis of samples composed of sorted specimens.

Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities

Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities.