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

Genetic Variation and Phylogeography of Lumbriculus variegatus (Annelida: Clitellata: Lumbriculidae) Based on Mitochondrial Genes

Lumbriculus variegatus is a typical cold-water worm and is mainly distributed in the Tibetan Plateau and Northeast in China. The current study aimed to explore the genetic diversity and phylogeography of L. variegatus sampled from different geographical regions based on concatenated (COI + 16S rRNA, 879 bp) genes. Among 63 L. variegatus specimens, 29 haplotypes were identified with high haplotype diversity (h = 0.923) and nucleotide diversity (π = 0.062). The Bayesian phylogenetic analysis and Median-joining haplotype network revealed two lineages, or species, of L. variegatus. Taxa belonging to lineage I was mainly distributed in the Tibetan Plateau of China, North America, and Sweden, while lineage II composed taxa from Northeast China, southern China, and Sweden. The analysis of molecular variance indicated that the genetic difference was mainly due to differences between lineages. Neutrality tests showed that the overall L. variegatus have a stable population since the time of origin. Divergence time analysis suggested that L. variegatus originated from the Triassic period of Mesozoic in 235 MYA (95%HPD: 199–252 MYA), and the divergence between different lineages of L. variegatus began from the next 170 million years.

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.

Tasserkidriluscf.americanus (Clitellata, Naididae) - A new record from Slovakia confirms the dissimilarity between the European and North American populations

The main objective of this study is to present a new record of Tasserkidriluscf.americanus found in a channel near the Tešmak swamp in Slovakia (Central Europe) and to compare its morphological features and habitat requirements with those of populations occurring in North America and Europe. The new specimens are similar to those found in The Netherlands and Belgium, but dissimilar to previously reported North American material of T.americanus, reopening the question of whether the European form is a separate species. The European form has the penis sheaths approximately twice as long as and wider than the North American form and may inhabit slow-flowing or standing waters of a eutrophic character, which is in conflict with the current knowledge on the morphology and ecology of North American populations. Further investigation is necessary to solve the questions about the origin and taxonomic relationship of the European population to other populations.

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

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

Detection of Myxobolus cerebralis (Bivalvulida: Myxobolidae) in two non-Tubifex tubifex oligochaetes in the southeastern USA

Myxobolus cerebralis (Hofer, 1903), the etiological agent of salmonid whirling disease, reportedly matures in only the oligochaete 'Tubifex tubifex'. The concept of 'T. tubifex' is problematic because it is renowned as a species complex (or having 'strains'), and many sequences ascribed to this taxon in GenBank are misidentified or indicate several cryptic species. These facts cast doubt on the long-held notion that M. cerebralis is strictly host-specific to the single definitive host, T. tubifex. Herein, as part of an ongoing regional whirling disease monitoring project, oligochaetes (452 specimens) were collected from 31 riverine sites in western North Carolina (August through September 2015) and screened for infection by M. cerebralis. The species-specific nested PCR for M. cerebralis was positive for 8 oligochaete specimens from the French Broad River Basin (Mill Creek and Watauga River) and New River Basin (Big Horse Creek). We individually barcoded these M. cerebralis-positive oligochaete specimens using cytochrome oxidase 1 (CO1) primers and then conducted a Bayesian inference phylogenetic analysis. We identified 2 oligochaete genotypes: one sister to a clade comprising Limnodrilus udekemianus (Haplotaxida: Naididae) and another sister to Limnodrilus hoffmeisteri. This is the first detection of M. cerebralis from an oligochaete in the SE USA and the first detection of M. cerebralis from an oligochaete other than T. tubifex. These results suggest that other non-T. tubifex definitive hosts can harbor the pathogen and should be considered in the context of fish hatchery biosecurity and monitoring wild trout streams for M. cerebralis and whirling disease in the southeastern USA.

The Foreign Oligochaete Species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: Morphological and Molecular Characterization and Environmental Influences on Its Distribution

Simple Summary

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900), originating from North America, has been mentioned in Europe for some decades and was recently found in Swiss lakes. Here, we report its repartition and abundance in Lake Geneva based on morphological and eDNA surveys and study its ecology and invasive potential in this lake. We also provide an identification key of this species and two closely related species and describe the phylogenetic position of Q. multisetosus within several Tubificinae lineages based on the cytochrome c oxidase marker. Our results showed that this species was restricted to an area close to the outlet of a wastewater treatment plant and to a combined sewer overflow, was highly tolerant to organic matter pollution and had a limited capacity to disseminate in this lake. Even if the trophic status (oligo-mesotrophic) of Lake Geneva seems unfavorable for the development of this species, we recommend continuing monitoring its presence in this lake in the future, as the current warming of waters could contribute to its expansion.

Abstract

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it can be considered as potentially invasive. This species was recently discovered in Lake Geneva (Switzerland/France) and three other Swiss lakes. The aims of the present work are to report its repartition and abundance in Lake Geneva, to study its ecology and to determine its invasive potential in this lake. We also provide an identification key for correctly differentiating Q. multisetosus from the closely related species Spirosperma ferox Eisen, 1879 and Embolocephalus velutinus (Grube, 1879), and study the phylogenetic position of Q. multisetosus within several Tubificinae lineages based on the cytochrome c oxidase (COI) marker. Twenty-eight sites have been monitored since 2009 in Lake Geneva. In several sites, the COI sequence corresponding to this species was also searched for in sediment samples using high-throughput sequencing. In addition, we examined specimens collected in this lake before 2009 likely to belong to Q. multisetosus and to have been misidentified. We found that Q. multisetosus was only present in the lake downstream of a wastewater treatment plant and a combined sewer overflow in the Vidy Bay (near Lausanne) and at a site located nearby. These results confirmed the high tolerance of this species to organic matter pollution. Q. multisetosus was already present in this location in 1974 (misidentified as Spirosperma ferox), which suggests that Q. multisetosus has a limited capacity to disseminate in this lake. However, we recommend continuing monitoring its presence in Lake Geneva in the future, especially in the context of warming of waters that could contribute to the expansion of this species.

Effect Thresholds of Metals in Stream Sediments Based on In Situ Oligochaete Communities

Aquatic oligochaetes, comprising a large number of species showing various degrees of resistance to chemical pollution, are recognized as valuable bioindicators of sediments’ quality. In the Geneva area (Switzerland), oligochaete tools were previously tested for assessing the biological quality of stream sediments, and effect thresholds of combined metals (quotients) in sediments were defined. The aims of the present study were to update this previous work with new data acquired in different cantons of Switzerland and to establish effect thresholds on oligochaete communities for individual metals and for combined metals. The oligochaete metrics “Oligochaete index of sediment bioindication (IOBS)”, “oligochaete density” and “percentage of tubificids without hair setae” proved pertinent for assessing the effects of metals and organic matter in sediments. We established a threshold effect level (TELoligo) and probable effect level (PELoligo) for eight metals in sediments (Cr, Ni, Zn, Cu, Pb, Cd, Hg and As) as well as a probable effect level for these metals combined (mPELoligo-Q). These thresholds could be used directly to screen for alteration of in situ communities restricted to sediments and/or for establishing sediment quality standards based on a combination of different biological and ecotoxicological tools.

High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.

Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices

Introduction

Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species.

Methods

We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol.

Results

The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates.

Discussion

Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices.

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.

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.

The Swiss Ecotox Centre: bridging the gap between research and application

The Swiss Centre for Applied Ecotoxicology (Ecotox Centre) was created in recognition of the urgent societal need to provide expertise, education and tools for assessing the risks and effects of anthropogenic chemicals in the environment. Founded in 2008, the Ecotox Centre conducts applied, practice-oriented research in the areas of aquatic (water and sediment) and terrestrial (with focus on soil) ecotoxicology, and provides further education and consulting services to its stakeholders. To date, its most important activities focus on (1) the validation and standardization of bioassays for use in monitoring of water, sediment or soil quality and (2) the development of tools for retrospective risk assessment, including approaches to assess mixture risk.