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

Contamination acts as a genotype-dependent barrier to gene flow, causing genetic erosion and fine-grained population subdivision in Mussels from the Strait of Istanbul

This study provides evidence of fine-grained genetic structuring in Mediterranean mussels (Mytilus galloprovincialis) from the Strait of Istanbul, caused by barriers to gene flow via contaminant-mediated selection. In this study, mitochondrial D-loop sequences were analyzed in mussels from 8 localities, all less than 30 kilometers apart, with differing contaminant loads. The results were: 1) Intra-population genetic differentiation (ΦST) between sites with high and low contaminant loads was high (up to 0.459), even at distances of only a few kilometers. 2) Genetic diversity was negatively correlated with the contaminant load ("genetic erosion"). 3) There was evidence of selection, based on haplotype frequencies and neutrality tests (Tajima's D), with purifying selection at the most contaminated site and balancing selection at the least contaminated. 4) Genetic distance was not correlated with geographic distance (no isolation-by-distance), but was correlated with contaminant load at each site. 5) Population dendrograms and Bayesian estimators of migration indicated that gene flow between sites was affected by contamination. For the dendrograms of the sampling sites, the clades clustered according to contaminant load more than geographic distance. Overall, these results suggest that 1) contamination may serve as a genotype-dependent dispersal barrier (i.e., contamination may not affect total number of migrants, just the relative proportions of the haplotypes in the established immigrants), leading strong population differentiation over short distances, and 2) genetic erosion may occur by a combination of selection and altered patterns of haplotype-specific gene flow. These effects may be more pronounced in the Strait of Istanbul than in other locations because of the riverine nature and strong, uni-directional current of the strait.

Multigenerational effects of TiO2 rutile nanoparticles on earthworms

Nanoparticles have gained considerable attention as one of the pollutants released into the environment through consumer products. This study describes the sub-chronic and generational effects of TiO2 (rutile) nanoparticles on earthworms over a 252-day duration, with exposure ranging from 0.1 to 1000 mg kg-1. Results indicate that sub-chronic exposure (28 days) of TiO2 nanoparticles did not cause notable adverse effects on the weight, reproduction, and tissue accumulation in parent earthworms. However, the F1 generation displayed remarkable growth and maturity retardation during their early developmental stages, even at lower nano-TiO2 (rutile). Significant impacts on the reproduction of the F1 generation were observed solely at the highest concentration (1000 mg kg-1), which is predicted to be below the highest exposure scenario. Moreover, long-term (252 days) exposure resulted in considerable bioaccumulation of Ti metal in the F1 generation of E. fetida. This study uncovers the negative effects of TiO2 rutile nanoparticles on earthworms across two generations, with pronounced effects on the growth, maturity, and bioaccumulation in the F1 generation compared to the parent generation. These findings suggest the potential induction of toxic effects by TiO2 rutile nanoparticles, emphasizing the sensitivity of juvenile parameters over adult parameters in toxicity assessments. Furthermore, the study highlights the urgent need for comprehensive evaluations of the longer-term toxicity of nanoparticles on terrestrial organisms. Implementing multigenerational studies will contribute significantly to a better understanding of nanoparticle ecotoxicity on environmental organisms.

Evidence for the metal resistance of earthworm Eisenia fetida across generations (F1 and F2) under laboratory metal exposure

Environmental stressors are persistent but most toxicological studies always evaluate the risk via short-term acute toxicity, while continuous toxicity and biological resistance across generations are relatively unknown. Here, earthworm Eisenia fetida was laboratory-reared and exposed to historically contaminated soils with an increasing metal gradient (CK, LM and HM), to investigate cross-generation toxicity and resistance of F1 and F2 worms. The results elucidated that biomass and juvenile hatching rate of F2 E. fetida showed maximum decreases of 20.8% and 38.5% than those of F1, which indicated severer toxicity of earthworm offspring. However, metal bioaccumulation in F2 E. fetida showed maximum increases of 150%, 49.2%, 19.7% and 25.5% than F1 for Cd, Cu, Zn and Pb, respectively. F2 E. fetida suffered less oxidative stress because the activities of superoxide dismutase (SOD), peroxidase (POD), glutathione (GSH), and malondialdehyde (MDA) contents were basically lower than that of F1. Meanwhile, the detoxification genes of metallothionein and heat shock protein 70 in F2 E. fetida showed maximum of 296% and 78.9% up-regulations, respectively, which suggested greater metal resistance of F2 E. fetida. This study confirmed the cross-generation toxicity and resistance of earthworms, which provides novel insights to reveal specific contaminant risks from longer lifecycles. CAPSULE: Earthworms under cross-generation exposure can develop metal resistance despite suffering worse toxicity effects.

Polymorphic microsatellite markers demonstrate hybridization and interspecific gene flow between lumbricid earthworm species, Eisenia andrei and E. fetida

The lumbricid earthworms Eisenia andrei (Ea) and E. fetida (Ef) have been used as model organisms for studies on hybridization. Previously they have been identified by species specific sequences of the mitochondrial COI gene of maternal origin ('a' or 'f') and the nuclear 28S gene of maternal/paternal origin ('A' or 'F'). In experimental crosses, these hermaphroditic species produce progeny of genotypes Ea (aAA), Ef (fFF) and hybrids (aAF and fFA) originating by self-fertilization or cross-fertilization. To facilitate studies on new aspects of the breeding biology and hybridization of earthworms, polymorphic microsatellite markers were developed based on 12 Ea and 12 Ef specimens and validated on DNA samples extracted from 24 genotyped specimens (aAA, fFF, aAF and fFA) from three laboratory-raised families and 10 of them were applied in the present study. The results indicate that microsatellite markers are valuable tools for tracking interspecific gene flow between these species.

Metagenomic sequencing reveals detoxifying and tolerant functional genes in predominant bacteria assist Metaphire guillelmi adapt to soil vanadium exposure

Due to extensive vanadium (V) mining and processing, an increasing amount of V has accumulated in soil, which poses a threat to public health. Consequently, we used earthworm (Metaphire guillelmi) incubation trials in V-contaminated soil (0-300 mg kg^-1) to explore the response of soil indigenous bacteria and earthworm intestinal bacteria to V stress. Metagenomic analysis revealed that V exposure changed the bacterial composition in the soil and the worm gut. However, although the core species varied between soil and worm gut, the two systems shared the predominant bacteria, including Staphylococcus, Nocardioides, Streptococcus, and Nitrosopumilales. Two functional genotypes were detected in the shared core species, i.e., reductive genes and resistant genes. The reductive genes mainly consisted of those involved in glutathione, cysteine, methionine, sulfur, and nitrogen metabolisms. The resistant genes included those encoding the oxidation damage repair system, the outer membrane protein, the antioxidant enzyme system, the metal-binding, and the heavy-metal efflux. Therefore, the shared core species exert a comprehensive strategy to survive V stress involving the alliance of heavy metal detoxifying and tolerant genes. This study provides novel information about the detoxification mechanisms of bacterial populations in soil and worm gut to survive V stress.

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.

The Effects of In Vivo Exposure to Copper Oxide Nanoparticles on the Gut Microbiome, Host Immunity, and Susceptibility to a Bacterial Infection in Earthworms

Nanomaterials (NMs) can interact with the innate immunity of organisms. It remains, however, unclear whether these interactions can compromise the immune functioning of the host when faced with a disease threat. Co-exposure with pathogens is thus a powerful approach to assess the immuno-safety of NMs. In this paper, we studied the impacts of in vivo exposure to a biocidal NM on the gut microbiome, host immune responses, and susceptibility of the host to a bacterial challenge in an earthworm. Eisenia fetida were exposed to CuO-nanoparticles in soil for 28 days, after which the earthworms were challenged with the soil bacterium Bacillus subtilis. Immune responses were monitored by measuring mRNA levels of known earthworm immune genes. Effects of treatments on the gut microbiome were also assessed to link microbiome changes to immune responses. Treatments caused a shift in the earthworm gut microbiome. Despite these effects, no impacts of treatment on the expression of earthworm immune markers were recorded. The methodological approach applied in this paper provides a useful framework for improved assessment of immuno-safety of NMs. In addition, we highlight the need to investigate time as a factor in earthworm immune responses to NM exposure.

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.

Use of integrated biomarker response for studying the resistance strategy of the earthworm Metaphire californica in Cd-contaminated field soils in Hunan Province, South China

Research was conducted to study the response and detoxification mechanisms of earthworms collected from Cd-contaminated areas in Hunan Province, South China. Metaphire californica, the dominant earthworm species in fields, referred as earthworm-A and -B that collected from low- (0.81 mg kg^-1) and high-Cd soil (13.3 mg kg^-1), respectively, for exchanging incubation in laboratory. The results showed that earthworm-A gradually accumulated higher Cd when exposed in the high-Cd soil, whereas Cd concentration of earthworm-B decreased after being transferred to low-Cd soil (albeit BAF_Cd >20). The integrated biomarker response index was calculated with the biomarkers of antioxidant systems (e.g., superoxide dismutase (SOD), peroxidase (POD), glutathione (GSH), glutathione peroxidase (GPx), glutathione-S transferase (GST), and malondialdehyde (MDA)) and energy index (e.g., protein and glycogen) in M. californica. GSH, GPx, and GST contributed the most to the integrated biomarker response (IBR) in earthworm-A when exposed in high-Cd soil for 14 d. Earthworm-B responded with higher GST and GPx activities and decreased protein content in low-Cd soil. For 28 d, the response of earthworm-A was not evident in either low- or high-Cd soil, and the inductive effect of metal stress on earthworm-B tended to be stable, except for the higher MDA content (p < 0.05) when exposed in low-Cd soil. The IBR index of earthworm-B (2.93 and 3.40) in low- and high-Cd soil, respectively, was higher than that of earthworm-A (0.89 and 1.0). Overall, earthworm-A exhibited a detoxification process to resist high-Cd toxicity from low-to high-Cd soil. Earthworm-B exhibited a physiological resilience once its habitat had changed to a normal or low-Cd soil environment, possibly owing to the cost of its resistance adaptation to the historical highly contaminated soil in fields.

Local adaptation fuels cryptic speciation in terrestrial annelids

Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as it is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between 17 populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

Higher than … or lower than ….? Evidence for the validity of the extrapolation of laboratory toxicity test results to predict the effects of chemicals and ionising radiation in the field

Single species laboratory tests and associated species sensitivity distributions (SSDs) that utilise the resulting data can make a key contribution to efforts to prospective hazard assessments for pesticides, biocides, metals and ionising radiation for research and regulatory risk assessment. An assumption that underlies the single species based toxicity testing approach when combined in SSD models is that the assessments of sensitivities to chemical and ionising radiation measured across a range of species in the laboratory can inform on the likely effects on communities present in the field. Potential issues with the validity of this assumption were already recognised by Van Straalen and Denneman (1989) in their landmark paper on the SSD methodology. In this work, they identified eight major factors that could potentially compromise the extrapolation of laboratory toxicity data to the field. Factors covered a range of issues related to differences in chemistry (e.g. bioavailability, mixtures); environmental conditions (optimal, variable), ecological (compensatory, time-scale) and population genetic structure (adaptation, meta-population dynamics). This paper outlines the evidence pertaining to the influence of these different factors on toxicity in the laboratory as compared to the field focussing especially on terrestrial ecosystems. Through radiological and ecotoxicological research, evidence of the influence of each factor on the translation of observed toxicity from the laboratory to field is available in all cases. The importance of some factors, such as differences in chemical bioavailability between laboratory tests and the field and the ubiquity of exposure to mixtures is clearly established and has some relevance to radiological protection. However, other factors such as the differences in test conditions (optimal vs sub-optimal) and the development of tolerance may be relevant on a case by case basis. When SSDs generated from laboratory tests have been used to predict chemical and ionising radiation effects in the field, results have indicated that they may often seem to under-predict impacts, although this may also be due to other factors such as the effects of other non-chemical stressors also affecting communities at polluted sites. A better understanding of the main factors affecting this extrapolation can help to reduce uncertainty during risk assessment.

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.