Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape

Metallomic mapping of gut and brain in heavy metal exposed earthworms: A novel paradigm in ecotoxicology

This study explored the uptake of lead in the epigeic earthworm Dendrobaena veneta exposed to 0, 1000, and 2500 μg Pb/g soil. The soil metal content was extracted using strong acid digestion and water leaching, and analysed by means of Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to estimate absolute and bioavailable concentrations of metals in the soil. The guts and heads of lead-exposed earthworms were processed into formalin-fixed and paraffin embedded sections for high-resolution multi-element metallomic imaging via Laser Ablation ICP-MS (LA-ICP-MS). Metallomic maps of phosphorus, zinc, and lead were produced at 15-μm resolution in the head and gut of D. veneta. Additional 4-μm resolution metallomic maps of the earthworm brains were taken, revealing the detailed localisation of metals in the brain. The Pb bioaccumulated in the chloragogenous tissues of the earthworm in a dose-dependent manner, making it possible to track the extent of soil contamination. The bioaccumulation of P and Zn in earthworm tissues was independent of Pb exposure concentration. This approach demonstrates the utility of LA-ICP-MS as a powerful approach for ecotoxicology and environmental risk assessments.

Differentiation and decreased genetic diversity in field contaminated oysters Crassostrea hongkongensis: Identification of selection signatures

The extent to which chemical contamination affects the population structure and genetic diversity of natural populations remains elusive. Here, we used the whole-genome resequencing and transcriptome to diagnose the effects of long-term exposure to multiple elevated chemical pollutants on the population differentiation and genetic diversity in oysters Crassostrea hongkongensis in a typically polluted Pearl River Estuary (PRE) of Southern China. Population structure revealed an obvious differentiation between the PRE oysters and those collected from a nearby clean Beihai (BH) individuals, while no significant differentiation was observed among individuals collected from the three pollution sites within PRE due to the high gene flow. The decreased genetic diversity in the PRE oysters reflected the long-term effects of chemical pollutants. Selective sweeps between BH and PRE oysters revealed that chemical defensome genes, including glutathione S-transferase, zinc transporter, were responsible for their differentiation, sharing common metabolic process of other pollutants. Combined with the genome-wide association analysis, 25 regions containing 77 genes were identified to be responsible for the direct selection regions of metals. Linkage disequilibrium blocks and haplotypes within these regions provided the biomarkers of permanent effects. Our results provide important insights to the genetic mechanisms underlying the rapid evolution under chemical contamination in marine bivalves.

Cryptic Species in Ecotoxicology

The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Perfluorooctanoic acid dominates the molecular-level effects of a mixture of equal masses of perfluorooctanoic acid and perfluorooctane sulfonic acid in earthworm

Per- and polyfluoroalkyl substances (PFAS) are an important class of emerging contaminants in the environment. Most studies on the impact of PFAS mixtures considered phenotypic endpoints, which may not adequately reflect the sublethal effects on organisms. To fill this knowledge gap, we investigated the subchronic impact of environmentally relevant concentrations of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS)-as individual compounds and a mixture (PFOS+PFOA)-on earthworm (Eisenia fetida), using phenotypic and molecular endpoints. PFAS decreased the survival (12.2-16.3%), biomass (9.0-9.8%), and reproduction (15.6-19.8%) of E. fetida after 28 d of exposure. The bioaccumulation of PFOS after 28 d increased (from 2790.7 ng/g-dw to 5224.9 ng/g-dw) while that of PFOA decreased (from 780.2 ng/g-dw to 280.5 ng/g-dw) when E. fetida was exposed to the mixture compared to the individual compounds. These bioaccumulation trends were partly attributed to changes in the soil distribution coefficient (K_d) of PFOS and PFOA when present in the mixture. Eighty percent of the (p and FDR < 0.05) altered metabolites after 28 d were similarly perturbed by both PFOA and PFOS+PFOA. The pathways dysregulated are related to the metabolism of amino acids, energy, and sulfur. We showed that PFOA dominates the molecular-level impact of the binary PFAS mixture.

Microplastic fibers influence Ag toxicity and bioaccumulation in Eisenia andrei but not in Enchytraeus crypticus

Microplastic fibers (MF) are released from synthetic textiles during washing and end up in the wastewater. Similarly, silver nanoparticles (AgNP), incorporated in textiles as antimicrobial agents, are released in washing machines, also reaching the wastewater treatment plants. Therefore, both MF and AgNP co-exist in the environment and enter the soil compartment mainly via the application of biosolids. Yet, the combined effect of MF and AgNP has not been studied. Here, we assessed the effects of polyester MF on the toxicity of AgNP and AgNO₃ to the earthworm Eisenia andrei and the enchytraeid Enchytraeus crypticus. The organisms were exposed to a range of concentration of AgNP (32, 100, 320, 1000, 3200 mg Ag/kg) and AgNO₃ (12.8, 32, 80, 200, 500 mg Ag/kg) in LUFA 2.2 soil in the absence or presence of MF (0.01% DW). Reproduction tests were conducted and the toxicity outcomes compared between soils with and without MF. The exposure to MF caused a decrease in the number of juveniles and changed the biochemical composition of earthworms. Moreover, the presence of MF increased the toxicity of AgNP to earthworm reproduction (EC50 = 165 mg Ag/kg) when compared to AgNP exposure alone (EC50 = 450 mg Ag/kg), but did not alter the toxicity of AgNO₃ (EC50 = 40 mg Ag/kg). For enchytraeids, no significant difference in Ag toxicity could be detected when MF was added to the soil for both AgNP and AgNO₃. Overall, Ag bioaccumulation was not affected by MF, except for a decrease in earthworm body concentration at the highest Ag soil concentration (3200 mg Ag/kg). Our results suggest that the presence of MF in the soil compartment may be a cause of concern, and that the joint exposure to Ag may be deleterious depending on the Ag form, organism, and endpoint. The present work provides the first evidence that a realistic MF concentration in soil lowers AgNP concentration necessary to provoke reproductive impairment in earthworms. The influence of MF on the risk assessment of AgNP should be considered.

Impact of soil metals on earthworm communities from the perspectives of earthworm ecotypes and metal bioaccumulation

The current study elucidates the impact of soil metal contamination on earthworm communities at the ecotype level. A total of 292 earthworms belonging to 13 species were collected in metal-contaminated soils from Wanshou (WSC), Daxing (DXC) and Lupu (LPC) plots (1.40-6.60, 29.4-126, 251-336 and 91.9-109 mg/kg for soil Cd, Cu, Zn and Pb, respectively) in Hunan Province, southern China. The results showed that the total earthworm density and biomass significantly decreased along the increasing metal-contaminated gradient while epigeic earthworms became more dominant than anecic and endogeic earthworms. Redundancy analysis (RDA) showed that soil pH, total nitrogen and Cd concentration were the primary factors influencing earthworm communities, explaining 33.7%, 29.1% and 26.7% of the total variance, respectively. In addition, epigeic earthworm Metaphire californica bioaccumulated more Cd (0.27-0.60 mmol/kg), while endogeic earthworm Amynthas hupeiensis and anecic earthworm Amynthas asacceus bioaccumulated more Cu (0.55-1.62 mmol/kg) and Zn (2.86-6.46 mmol/kg) from soil, respectively, which were related to their habit soils and showed the species-specific bioaccumulation features. Our study discovered the diverse responses of earthworm ecotypes to metal contamination and their specific features of metal bioaccumulation, provide insight for soil risk assessments and for biodiversity conservation from a niche partitioning perspective. CAPSULE: Earthworms of different ecotypes showed different responses to soil metal contamination and species-specific features of metal bioaccumulation.

Off-Target Stoichiometric Binding Identified from Toxicogenomics Explains Why Some Species Are More Sensitive than Others to a Widely Used Neonicotinoid

Neonicotinoids are currently licensed for use in 120 countries, making accurate nontarget species sensitivity predictions critical. Unfortunately, such predictions are fraught with uncertainty, as sensitivity is extrapolated from only a few test species and neonicotinoid sensitivities can differ greatly between closely related taxa. Combining classical toxicology with de novo toxicogenomics could greatly improve sensitivity predictions and identify unexpectedly susceptible species. We show that there is a >30-fold differential species sensitivity (DSS) for the neonicotinoid imidacloprid between five earthworm species, a critical nontarget taxon. This variation could not be explained by differential toxicokinetics. Furthermore, comparing key motif expression in subunit genes of the classical nicotinic acetylcholine receptor (nAChR) target predicts only minor differences in the ligand binding domains (LBDs). In contrast, predicted dissimilarities in LBDs do occur in the highly expressed but nonclassical targets, acetylcholine binding proteins (AChBPs). Critically, the predicted AChBP divergence is capable of explaining DSS. We propose that high expression levels of putative nonsynaptic AChBPs with high imidacloprid affinities reduce imidacloprid binding to critical nAChRs involved in vital synaptic neurotransmission. This study provides a clear example of how pragmatic interrogation of key motif expression in complex multisubunit receptors can predict observed DSS, thereby informing sensitivity predictions for essential nontarget species.

Chemicals with increasingly complex modes of action result in greater variation in sensitivity between earthworm species

The scale of variation in species sensitivity to toxicants has been theoretically linked to mode of action. Specifically, it has been proposed there will be greater variations for chemicals with a putative specific biological target than for toxicants with a non-specific narcotic mechanism. Here we test the hypothesis that mode of action is related to variation in sensitivity in a specifically designed experiment for species from a single ecologically important terrestrial taxa, namely earthworms. Earthworm toxicity tests were conducted with five species for four chemicals, providing a series of increasingly complex modes of action: a putative narcotic polycyclic aromatic hydrocarbon (fluoranthene), and three insecticides (chlorpyrifos, cypermethrin, imidacloprid) with known neuronal receptor targets. Across all the chemicals, the standard epigeic test species Eisenia fetida and Lumbricus rubellus, were generally among the two least sensitive, while the endogenic Aporrectodea caliginosa and Megascolecidae Amynthas gracilis were generally more sensitive (never being among the two least sensitive species). This indicates a potential for bias in the earthworm ecotoxicology literature, which is dominated by studies in epigeic Lumbricidae, but contains few endogeic or Megascolecidae data. Results confirmed the lowest range of variation in sensitivities for effects on reproduction was for fluoranthene (2.5 fold). All insecticides showed greater variation for species sensitivity (cypermethrin: 7.5 fold, chlorpyrifos: 10.3 fold, imidacloprid: 31.5 fold) consistent with the specific mechanisms of the pesticides. Difference in toxicodynamics, based on mode of action specificity and receptor complexity was reflected in the magnitude of sensitivity variation. However, measurements of tissue concentrations also indicated the potential importance of toxicokinetics in explaining species sensitivity variations for chlorpyrifos and cypermethrin.

Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview

Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.

Do Endemic Soil Fauna Species Deserve Extra Protection for Adverse Heavy Metal Conditions?

The concept of Ecotoxicological Species Sensitivity Distributions, as used in EU and US, to derive environmental standards for contaminants, starts from the assumption that by protecting the majority of species (95% confidence interval) all species will be protected. Nevertheless, 5% of the species outside the confidence interval might become harmed; half of it being the most sensitive for the particular compound tested. With respect to protection of rare endemic species it is not clear, however, if contamination is a driving factor for endemicity. The aim of this paper is to explore whether endemic and rare species deserve extra protection from adverse environmental conditions. To this end, a brief overview of the various forms of endemism, their relation to environmental stress factors and the distribution of endemic species is discussed. Further, the sensitivities of these species towards environmental stress factors are analysed, in order to conclude if and how endemic species could be better protected against environmental stress factors. This was achieved by specifically focusing on the potential impacts of metalliferous soils, mining, the treatment of mined soil and the storage of treated mine waste. It is concluded that at present there are some signals about specific sensitivities, but the database is much too small for a definite conclusion about adverse environmental factors as a threat to endemic species. The data gap has to be filled in with experimental tests with endemic species. This is hampered by the protection status of these endemic, rare species. Recommendations and derived activities are proposed to address this.

Genetic analysis in earthworm population from area contaminated with radionuclides and heavy metals

This study assessed the effects of environmental contamination by naturally occurring radionuclides and heavy metals on the genetic structure of a population of the earthworm Aporrectodea caliginosa. A. caliginosa were collected from four sites and characterized by amplified fragment length polymorphism (AFLP) analyses. No differences in genetic structure and diversity were found between sites that differed greatly in soil contamination levels of radionuclides and metals. However, when the genetic structure of the A. caliginosa population was analyzed without considering information about the sampling site, a complex intraspecific genetic structure was identified. At least three highly divergent lineages were found, in unequal proportions, of each genetically isolated group from each study site. No associations were found between the distribution of the detected genetic clusters and the geographical origin of the samples. Thus, no noticeable adaptive changes or signs of directional selection were detected, despite the long history of genotoxic waste disposal at the sampling site. These results suggest a combined effect of three factors on the genetic structure and diversity of A. caliginosa in soils: the complexity of the contaminant composition, the heterogeneous spatial distribution of the pollutants, and the complexity of the intraspecific genetic structures of A. caliginosa.

Genetic, epigenetic and microbiome characterisation of an earthworm species (Octolasion lacteum) along a radiation exposure gradient at Chernobyl

The effects of exposure to different levels of ionising radiation were assessed on the genetic, epigenetic and microbiome characteristics of the "hologenome" of earthworms collected at sites within the Chernobyl exclusion zone (CEZ). The earthworms Aporrectodea caliginosa (Savigny, 1826) and Octolasion lacteum (Örley, 1881) were the two species that were most frequently found at visited sites, however, only O. lacteum was present at sufficient number across different exposure levels to enable comparative hologenome analysis. The identification of morphotype O. lacteum as a probable single clade was established using a combination of mitochondrial (cytochrome oxidase I) and nuclear genome (Amplified Fragment Length Polymorphism (AFLP) using MspI loci). No clear site associated differences in population genetic structure was found between populations using the AFLP marker loci. Further, no relationship between ionising radiation exposure levels and the percentage of methylated loci or pattern of distribution of DNA methylation marks was found. Microbiome structure was clearly site dependent, with gut microbiome community structure and diversity being systematically associated with calculated site-specific earthworm dose rates. There was, however, also co-correlation between earthworm dose rates and other soil properties, notably soil pH; a property known to affect soil bacterial community structure. Such co-correlation means that it is not possible to attribute microbiome changes unequivocally to radionuclide exposure. A better understanding of the relationship between radionuclide exposure soil properties and their interactions on bacterial microbiome community response is, therefore, needed to establish whether these the observed microbiome changes are attributed directly to radiation exposure, other soil properties or to an interaction between multiple variables at sites within the CEZ.

The effect of the earthworm Lumbricus rubellus on the bioavailability of cadmium and lead to the springtail Folsomia candida in metal-polluted field soils

The bioavailability of metals can be influenced not only by soil properties but also by other species living at polluted sites. However, in laboratory experiments, usually only one test species is used to estimate bioavailability. In this study, a two-species approach was applied to assess the impact of the earthworm Lumbricus rubellus on the bioavailability of cadmium and lead to the springtail Folsomia candida using natural soils from a gradient of metal pollution. Earthworms were kept in half of the soil replicates for 4 weeks. Subsequently, the uptake and elimination kinetics of cadmium and lead in F. candida exposed for 21 days to the soils was determined. Earthworm activity affected soil properties but did not significantly affect metal uptake rate constants in springtails. The slightly higher uptake due to the presence of earthworms, which was consistent in all tested soils and for both metals, suggests that further research is needed on the role of species interactions in affecting metal bioavailability in soil.

Transcriptomic analysis confirms differences among nuclear genomes of cryptic earthworm lineages living in sympatry

BACKGROUND

Many earthworm species demonstrate significant cryptic diversity, with several highly diverged mitochondrial lineages found within most of the taxa studied to date. The status of differences between these lineages on the nuclear level is still unclear. Because of widespread polyploidy in earthworms, most studies were limited to two nuclear loci, the ribosomal and the histone clusters. Here we attempted to elucidate the status of a set of genetic lineages within Eisenia nordenskioldi nordenskioldi, an earthworm species from Northern Asia with high intraspecific diversity. We performed RNA-seq on an IonTorrent platform for five specimens of this species belonging to five genetic lineages, as well as two outgroups from the family Lumbricidae, the congenetic E. andrei, and Lumbricus rubellus.

RESULTS

We de novo assembled transcriptomes and constructed datasets of genes present in all seven specimens using broad (ProteinOrtho; 809 genes) and narrow (HaMStR; 203 genes) ortholog assignment. The majority of orthologs had identical amino acid sequences in all studied specimens, which we believe was due to strong bias towards the most conserved genes. However, for the rest of genes the differences among the lineages were lower than those between them and the congeneric E. andrei. Both datasets yielded phylogenetic trees with the same topology. E. n. nordenskioldi was found to be monophyletic. The differences on the genetic level had no concordance with geography, implying complex history of dispersal.

CONCLUSIONS

We found that genetic lineages of E. n. nordenskioldi are genetically distinct on nuclear level and probably diverged long ago. Current data implies that they might even represent distinct species within the E. nordenskioldi species complex.

Microsatellite polymorphism of Trifolium pratense population at the conditions of radioactive and chemical contamination of soil (Komi republic, Russia)

There is no clear understanding of microevolutionary changes in natural populations of plants and animals due to anthropogenic contamination of the environment with toxicants and mutagens. But such data are necessary to forecast long-term effects of human activity. In this research, we studied genetic polymorphism in T. pratense sampled from seven sites varying in radioactive and chemical soil contamination in the vicinity of Vodny settlement (Komi, Russia). Analysis of five SSR loci was shown to be similar in a whole (N), mean (N_a) and effective (N_e) numbers of alleles, heterozygosity indexes (H_o and H_e), and the Shannon index (I). Difference in the private allele numbers was registered: the most contaminated site has 5 and others from 0 up 2 private alleles. No difference was found in the genetic structure of T. pratense population growing at the conditions of radioactive and chemical contamination. The Bayesian analysis provided evidence of a single cluster (K = 1) due to a similar genetic structure of samples, while AMOVA results demonstrated a high variability within individuals (75%) and a low variability (1%) among groups of T. pratense from sites that differ in the contamination level. Thus, the long-term radioactive and heavy metal contamination of soil did not result in significant microevolutionary changes in T. pratense population.

Mining and Planetary Health: A GeoHealth-Led Special Collection

Mining is a vital part of the global economy, but unmanaged releases of mine wastes can affect the health of humans, ecosystems, water, soil and Earth surface environments (e.g., rivers and estuaries). New technological developments and multidisciplinary collaborations are leading to new insights into the relationship between mining and the health of the Earth. In recognition of the importance of this topic, GeoHealth is leading in the creation of a special collection of papers on the theme of Mining and Planetary Health, to summarize the current state of knowledge, outline topics for urgent action and further research, and highlight positive efforts in environmental and health protection. Submissions are invited from researchers investigating the impacts of mining at the intersection of the Earth and environmental sciences and human, ecosystem, and planetary health.

Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites

BACKGROUND

Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes. Furthermore, the occurrence of L. rubellus lineages across the UK allows for inferences of mechanisms associated with drivers of speciation and local adaptation.

RESULTS

Using RADseq, we were able to define population structure between the two lineages through the use of draft genomes for each, demonstrating an absence of admixture between lineages and that populations over extensive geographic distances form discrete populations. Between the two British lineages, we were able to provide evidence for selection near to genes associated with epigenetic and morphological functions, as well as near a gene encoding a pheromone. Earthworms inhabiting highly contaminated soils bare close genomic resemblance to those from proximal control soils. We were able to define a number of SNPs that largely segregate populations and are indicative of genes that are likely under selection for managing metal toxicity. This includes calcium and phosphate-handling mechanisms linked to lead and arsenic contaminants, respectively, while we also observed evidence for glutathione-related mechanisms, including metallothionein, across multiple populations. Population genomic end points demonstrate no consistent reduction in nucleotide diversity, or increase in inbreeding coefficient, relative to history of exposure.

CONCLUSIONS

Though we can clearly define lineage membership using genomic markers, as well as population structure between geographic localities, it is difficult to resolve markers that segregate entirely between populations in response to soil metal concentrations. This may represent a highly variable series of traits in response to the heterogenous nature of the soil environment, but ultimately demonstrates the maintenance of lineage-specific genetic variation among local populations. L. rubellus appears to provide an exemplary system for exploring drivers for speciation, with a continuum of lineages coexisting across continental Europe, while distinct lineages exist in isolation throughout the UK.

Preliminary evidence of differences in cadmium tolerance in metal-free stocks of the standard earthworm test species Eisenia andrei (Oligochaeta)

To test whether metal-tolerant and metal-sensitive earthworm specimens could be an inherent part of metal-free earthworm populations, (i) we used DNA barcoding to identify and categorize earthworms from 8 populations of the standard test species Eisenia andrei, and (ii) the earthworms carrying three of the identified COI haplotypes (named Hap1, hap3 and Hap3) were paired up and exposed to Cd in order to assess the difference in Cd sensitivity between the breeding pairs. A total of six breeding pairs were exposed to 0, 25, 50 and 100 mg Cd/kg for 4 weeks at 20 °C. The survival of the breeding pairs, their change in biomass and cocoon production were assessed. For all of the endpoints assessed, the results indicated that couple 6 (Hap3 × Hap3) was the most sensitive breeding pair whereas couple 4 (Hap1 × Hap3) was the least sensitive one. The analysis of Cd tissue contents revealed that with increasing Cd concentration, Cp6 (Hap3 × Hap3) could accumulate significantly more Cd than any other breeding pair (p ≤ 0.01). Our findings indicate that E. andrei may harbour intrinsically Cd-tolerant and Cd-sensitive individuals and that this may be due to individual differences in Cd accumulation kinetics. In the context of ecotoxicological testing, our results underline the importance of using genetically diverse populations in laboratory testing to prevent generating flawed data from genetically homogeneous laboratory stocks. Although we do not regard the present mitochondrial haplotypes as proxy for possibly nuclear encoded traits, we discuss the necessity of a standardised earthworm barcoding protocol that could help not only to confirm the taxonomy of laboratory earthworm stocks but also to select genetically diverse stocks suitable for laboratory testing.

Hybridization relics complicate barcode-based identification of species in earthworms

Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation.

Evaluating the impact of a fluoropolymer plant on a river macrobenthic community by a combined chemical, ecological and genetic approach

Effect-based monitoring is a recommended approach suggested in European Guidelines to assess the response of ecosystem affected by a pollution source, considering the effects at community, population, individual but also at suborganism level. A combined chemical, ecological and genetic approach was applied in order to assess the impact of a fluoropolymer plant on the macrobenthic community of the Northern Italian river Bormida (Piedmont region). The macrobenthic community living downstream of the industrial discharge was chronically exposed to a mixture of perfluoroalkyl substances (PFAS), with perfluorooctanoic acid as the main compound, at concentrations up to several μgL(-1). Ecological assessment proved that the downstream community was not substantially different from that living upstream of the pollution source. The impact on community is not quantifiable with the traditional monitoring methods used for ecological classification under European regulation because macrobenthic communities showed only slight differences in their structure. In order to highlight effects on genetic variability of the native population, a subcellular analysis by using the AFLP (Amplified Fragment Length Polymorphism) genetic technique was applied to genotype of individuals of a selected species (Hydropsyche modesta, Trichoptera) collected in the two sampling sites. Percentage of variation between the two populations was 6.8%, a threshold compatible with a genetic drift induced in the downstream population. The genetic study carried out in field identified a significant divergence between exposed and non-exposed populations, but at present it is not possible to associate this divergence to a specific effect induced by PFAS.

Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated

Background

The accurate delimitation of species is essential to numerous areas of biological research. An unbiased assessment of the diversity, including the cryptic diversity, is of particular importance for the below ground fauna, a major component of global biodiversity. On the British Isles, the epigeic earthworm Lumbricus rubellus, which is a sentinel species in soil ecotoxicology, consists of two cryptic taxa that are differentiated in both the nuclear and the mitochondrial (mtDNA) genomes. Recently, several deeply divergent mtDNA lineages were detected in mainland Europe, but whether these earthworms also constitute cryptic species remains unclear. This information is important from an evolutionary perspective, but it is also essential for the interpretation and the design of ecotoxicological projects. In this study, we used genome-wide RADseq data to assess the reproductive isolation of the divergent mitochondrial lineages of L. rubellus that occur in sympatry in multiple localities in Central Europe.

Results

We identified five divergent (up to 16 % net p-distance) mitochondrial lineages of L. rubellus in sympatry. Because the clustering of the RADseq data was according to the population of origin and not the mtDNA lineage, reproductive isolation among the mtDNA lineages was not likely. Although each population contained multiple mtDNA lineages, subdivisions within the populations were not observed for the nuclear genome. The lack of fixed differences and sharing of the overwhelming majority of nuclear polymorphisms between localities, indicated that the populations did not constitute allopatric species. The nucleotide diversity within the populations was high, 0.7–0.8 %.

Conclusions

The deeply divergent mtDNA sympatric lineages of L. rubellus in Central Europe were not reproductively isolated groups. The earthworm L. rubellus, which is represented by several mtDNA lineages in continental Europe, apparently is a single highly polymorphic species rather than a complex of several cryptic species. This study demonstrated the critical importance of the use of multilocus nuclear data for the unbiased assessment of cryptic diversity and for the delimitation of species in soil invertebrates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0488-9) contains supplementary material, which is available to authorized users.

Genome-wide genetic diversity of rove beetle populations along a metal pollution gradient

To what extent chemical contamination affects genetic diversity of wild populations remains an open question in ecotoxicology. Here we used a genome-wide approach (615 nuclear RADseq loci containing 3017 SNPs) and a mtDNA fragment (ATP6) to analyze the effect of long-term exposure to elevated concentrations of metals (Cd, Pb, Zn) on genetic diversity in rove beetle (Staphylinus erythropterus) populations living along a pollution gradient in Poland. In total, 96 individuals collected from six sites at increasing distance from the source of pollution were analyzed. We found weak differentiation between populations suggesting extensive gene flow. The highest genetic diversity was observed in a population inhabiting the polluted site with the highest metal availability. This may suggest increased mutation rates, possibly in relation to elevated oxidative stress levels. The polluted site could also act as an ecological sink receiving numerous migrants from neighboring populations. Despite higher genetic diversity at the most polluted site, there was no correlation between the genetic diversity and metal pollution or other soil properties. We did not find a clear genomic signature of local adaptation to metal pollution. Like in some other cases of metal tolerance in soil invertebrates, high mobility may counteract possible effects of local selective forces associated with soil pollution.

Identifying biochemical phenotypic differences between cryptic species

Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.

Toxicokinetics of metals in the earthworm Lumbricus rubellus exposed to natural polluted soils--relevance of laboratory tests to the field situation

The aim of this study was to estimate the bioavailability of essential (Zn, Cu) and non-essential metals (Cd, Pb) to the earthworm Lumbricus rubellus exposed to soils originating from a gradient of metal pollution in Southern Poland. Metal uptake and elimination kinetics were determined and related to soils properties. Experimental results were compared with tissue metal concentrations observed in earthworms from the studied transect. Cd and Pb were intensively accumulated by the earthworms, with very slow or no elimination. Their uptake rate constants, based on 0.01 M CaCl2-extractable concentrations in the soils, increased with soil pH. Internal concentrations of Cu and Zn were maintained by the earthworms at a stable level, suggesting efficient regulation of these metals by the animals. The estimated uptake and elimination kinetics parameters enabled fairly accurate prediction of metal concentrations reached within a life span of L. rubellus in nature.

Living on a volcano's edge: genetic isolation of an extremophile terrestrial metazoan

Communities of organisms inhabiting extreme terrestrial environments provide a unique opportunity to study evolutionary forces that drive population structure and genetic diversity under the combined challenges posed by multiple geogenic stressors. High abundance of an invasive pantropical earthworm (and the absence of indigenous lumbricid species) in the Furnas geothermal field (Sao Miguel Island, Azores) indicates its remarkable tolerance to high soil temperature, exceptionally high carbon dioxide and low oxygen levels, and elevated metal bioavailability, conditions which are lethal for the majority of terrestrial metazoans. Mitochondrial and nuclear markers were used to analyze the relationship between populations living inside and outside the geothermal field. Results showed that Pontoscolex corethrurus (Annelida, Oligochaeta, Glossoscolecidae) to be a genetically heterogeneous complex within the Sao Miguel landscape and is probably differentiated into cryptic species. The population exposed to the hostile soil conditions within the volcanic caldera possesses the lowest within-population mitochondrial diversity but an unexpectedly high degree of nuclear variability with several loci evidencing positive selection, parameters indicative of a genetically unique population only distantly related to conspecifics living outside the caldera. In conclusion, P. corethrurus inhabiting active volcanic soil is a discrete extremophile population that has evolved by tolerating a mixture of non-anthropogenic chemical and physical stressors.

Assessing ecotoxicity and uptake of metals and metalloids in relation to two different earthworm species (Eiseina hortensis and Lumbricus terrestris)

Due to diffuse atmospheric fallouts of process particles enriched by metals and metalloids, polluted soils concern large areas at the global scale. Useful tools to assess ecotoxicity induced by these polluted soils are therefore needed. Earthworms are currently used as biotest, however the influence of specie and earthworm behaviour, soil characteristics are poorly highlighted. Our aim was therefore to assess the toxicity of various polluted soils with process particles enriches by metals and metalloids (Pb, Cd, Cu, Zn, As and Sb) collected from a lead recycling facility on two earthworm species belonging to different ecological types and thus likely to have contrasted behavioural responses (Eiseina hortensis and Lumbricus terrestris). The combination of behavioural factors measurements (cast production and biomass) and physico-chemical parameters such as metal absorption, bioaccumulation by earthworms and their localization in invertebrate tissues provided a valuable indication of pollutant bioavailability and ecotoxicity. Soil characteristics influenced ecotoxicity and metal uptake by earthworms, as well as their soil bioturbation.

Life-history effects of arsenic toxicity in clades of the earthworm Lumbricus rubellus

Exposures of Lumbricus rubellus to a series of arsenic concentrations in soil were used to assess life-stage (juvenile, adult) and genotype specific sensitivities, to calculate population growth rate (λ) and to assess patterns of As accumulation. Significant mortality was seen in juveniles at 125 mg/kg As, while growth and maturation was affected from 36 mg/kg and above. In adults, cocoon production at the highest concentration (125 mg/kg) was significantly reduced. Phylogenetic analysis was performed by comparison of mitochondrial sequences to establish genotypic variation among juveniles. Three clades with more than 7.5% divergent were described, with 70% of earthworms belonging to a single clade. Date of and mass at maturation was significantly different between clades, but clades were not differentially As sensitive. Parameter λ was reduced at 36 mg/kg As and was negative at 125 mg/kg As, suggesting impacts and population stability and potential extinction at environmentally relevant concentrations.

Utility of bioassays (lettuce, red clover, red fescue, Microtox, MetSTICK, Hyalella, bait lamina) in ecological risk screening of acid metal (Zn) contaminated soil

The objective of this study was to assess selected bioassays and ecological screening tools for their suitability in a weight of evidence risk screening process of acidic metal contaminated soil. Intact soil cores were used for the tests, which minimizes changes in pH and metal bioavailability that may result from homogenization and drying of the soil. Soil cores were spiked with ZnCl(2) or CaCl(2). Leachate collected from the soil cores was used to account for the exposure pathways through pore water and groundwater. Tests assessed included MetSTICK in soil cores and Microtox in soil leachate, lettuce (Lactuca sativa), red fescue (Festuca rubra) and red clover (Trifolium pratense) in the soil cores and lettuce and red clover in soil leachate, Hyallella azteca in soil leachate, and an ecological soil function test using Bait Lamina in soil cores. Microtox, H. azteca, lettuce and red fescue showed higher sensitivity to low pH than to Zn concentrations and are therefore not recommended as tests on intact acidic soil cores and soil leachate. The Bait Lamina test appeared sensitive to pH levels below 3.7 but should be investigated further as a screening tool in less acidic soils. Among the bioassays, the MetSTICK and the T. pratense bioassays in soil cores were the most sensitive to Zn, with the lowest nominal NOEC of 200 and 400mg Zn/kg d.w., respectively. These bioassays were also tolerant of low pH, which make them suitable for assessing hazards of metal contaminated acid soils.

The effect of metal pollution on the population genetic structure of brown trout (Salmo trutta L.) residing in the River Hayle, Cornwall, UK

The River Hayle in south-west England is impacted with metals and can be divided into three regions depending on the copper and zinc concentrations: a low-metal upper section; a highly-contaminated middle section and a moderately contaminated lower section. Hayle river water is toxic to metal-naive brown trout, but brown trout are found in the upper and lower regions. The study aimed to evaluate the population genetic structure of River Hayle brown trout and to determine if the highly-contaminated section acts as a chemical barrier to migration. Population genetic analysis indicated that metals were not a barrier to gene flow within the river, but there was a high level of differentiation observed between fish sampled at two sites in the upper region, despite being separated by only 1 km. The metal tolerance trait exhibited by this brown trout population may represent an important component of the species genetic diversity in this region.

Characteristics of immune-competent amoebocytes non-invasively retrieved from populations of the sentinel earthworm Lumbricus rubellus (Annelida; Oligochaeta; Lumbricidae) inhabiting metal polluted field soils

Lumbricus rubellus is a cosmopolitan earthworm devoid of riboflavin-storing eleocytes; its immune competent coelomocytes are predominantly amoebocytes. Our aim was to determine whether amoebocyte cytometrics in L. rubellus are robust biomarkers for innate immunological responses to environmental pollutants. Investigations were conducted on populations inhabiting three unpolluted and five metalliferous (mainly Pb+Zn+Cd) habitats in the UK and Poland. Inter-population differences in worm mass and amoebocyte numbers did not consistently reflect soil or tissue metal concentrations. Flow cytometry indicated that autofluorescence of the amoebocytes differs between cells from the unpolluted and metal-polluted worms, and pinocytosis of neutral red by amoebocytes was lower (especially at 15 versus 60 min incubation) in worms from the polluted Poland site compared with the reference population. To conclude, amoebocyte cytometrics and functionality are potentially useful for environmental diagnostics; deployment is contingent on better understanding potential confounders.

Transcriptomic underpinning of toxicant-mediated physiological function alterations in three terrestrial invertebrate taxa: a review

Diverse anthropogenic activities often lead to the accumulation of inorganic and organic residues in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organisation throughout the continuum from the molecular-genetic to ecological and community levels. To date, the relationship between changes at the molecular (mRNA expression) and biochemical/physiological levels evoked by exposures to chemical compounds has been partially established in a limited number of terrestrial invertebrate species. Recently, the advent of a family of transcriptomic tools (e.g. Real-time PCR, Subtractive Suppressive Hybridization, Expressed Sequence Tag sequencing, pyro-sequencing technologies, Microarray chips), together with supporting informatic and statistical procedures, have permitted the robust analyses of global gene expression changes within an ecotoxicological context. This review focuses on how transcriptomics is enlightening our understanding of the molecular-genetic responses of three contrasting terrestrial macroinvertebrate taxa (nematodes, earthworms, and springtails) to inorganics, organics, and agrochemicals.