Luis Cunha

Bioavailable metals and cellular effects in the digestive gland of marine limpets living close to shallow water hydrothermal vents

The pressure exerted by shallow water hydrothermal vents on edible gastropods and their cellular responses triggered by these stresses are almost unknown. The aims of this study were to evaluate the bioavailability of metals in the Macaronesian endemic limpet Patella candei gomesii living close to shallow water hydrothermal vents, and the structural differences in their digestive gland as well as the levels of apoptosis in that organ. Limpets were sampled in four sites, two with the presence of hydrothermalism and the other two without it. Whole body concentrations of several metals (Ca, Cd, Cs, Co, Cu, Fe, Hg, Mg, Mn, Pb, Rb, Se, Sr, and Zn) were obtained, morphometry analysis of the digestive gland and TUNEL test for apoptosis were also performed. Results revealed that the presence of shallow water hydrothermal vents is a source of chronic metal stress to limpets, imposing modifications in the morphometry and cell composition of the digestive gland of those limpets that may constitute cell and tissue adaptations to the environment they live in. This study sets up new baseline data for further research on the influence of shallow water hydrothermal vents over communities living in these habitats.

Bioavailability of heavy metals and their effects on the midgut cells of a phytopaghous insect inhabiting volcanic environments

Organisms living in volcanic environments are chronically exposed to metals, either as particles or associated with gases, from volcanic emissions, being therefore potential sentinels of the effects derived from such exposure. Concentrations of Ca, Cd, Cu, Mg, Mn, Pb, Rb, and Zn were measured in soil, grass (Lolium perenne), and larvae of Pseudaletia uninpuncta captured in sites exposed and non-exposed to volcanic activity. The midgut epithelial cell morphometry and apoptosis of P. unipuncta larvae were also analyzed. Larvae from the site with volcanic activity showed higher levels of Cu, Mn, Rb and Zn. Metals such as Pb, Cd and Mg levels of P. unipuncta larvae were similar between sites. Apoptosis was higher in cells from digestive epithelium of larvae exposed to volcanic activity. Soils and grass not exposed to volcanic activity showed higher levels for most of the analyzed elements with the exception of Rb. Such result when compared with metal levels of larvae may reveal that bioavailability of elements differs between sites. The higher levels of Cd, Zn and Mg in soils and grass from the site with no volcanic activity are probably related to the severe artificial fertilization in the studied pastures. Such result, when compared with metal levels of larvae, suggest that the bioavailability of metals differs between sites.

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.

Soil animals and pedogenesis: The role of earthworms in anthropogenic soils

Abstract The role of earthworms as one of the most important groups of ecosystem engineers in human-modified and natural environments has been increasingly recognized only during the last 30 years, yet earthworms and humans have been acting together in building landscapes for millennia. This relationship is well represented in the pre-Columbian raised fields, in flood-prone savannas around the rim of Amazonia, but also by the potentially significant role of earthworms in the formation and resilience of Amazonian Dark Earths. Through the bioturbating action of earthworms, soil is biologically, chemically, and physically altered; nutrients are translocated; organic matter is decomposed and transformed; and the surrounding biota interacts as a large orchestra where the soil musicians play together on the various instruments but where earthworms take a leading role, enhancing microbial activity and generally stimulating plant growth. In this article, we assess the remarkable role of earthworms at the center of soil pedogenetic processes within anthropogenic landscapes, dissecting their functions with a special focus on Amazonian Dark Earths.

Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae)

Earthworm taxonomy and evolutionary biology remain a challenge because of their scarce distinct morphological characters of taxonomic value, the morphological convergence by adaptation to the uniformity of the soil where they inhabit, and their high plasticity when challenged with stressful or new environmental conditions. Here we present a phylogenomic study of the family Hormogastridae, representing also the first piece of work of this type within earthworms. We included seven transcriptomes of the group representing the main lineages as previously-described, analysed in a final matrix that includes twelve earthworms and eleven outgroups. While there is a high degree of gene conflict in the generated trees that obscure some of the internal relationships, the origin of the family is well resolved: the hormogastrid Hemigastrodrilus appears as the most ancestral group, followed by the ailoscolecid Ailoscolex, therefore rejecting the validity of the family Ailoscolecidae. Our results place the origin of hormogastrids in Southern France, as previously hypothesised.

Morphometry of the epidermis of an invasive megascoelecid earthworm (Amynthas gracilis, Kinberg 1867) inhabiting actively volcanic soils in the Azores archipelago

For the first time, the structure, dimensions, and composition of the epidermis of an invasive earthworm species that has successfully colonized hostile conditions in actively volcanic soil on São Miguel (Azores) have been measured. Metal concentrations in actively volcanic (Furnas) and volcanically inactive (Fajã) soils were similar; however, Furnas soil was characterised by elevated temperature (10°C differential), relative hypoxia, extremely high CO(2) tension, and accompanying acidity. The epidermis of earthworms resident at Fajã was approximately twice the thickness of the epidermis of conspecifics resident in Furnas soil. Reference worms transferred to Furnas soil for 14 days experienced an epidermal thinning of approximately 51%. In comparison, when Furnas earthworms were transferred to mesocosms at the relatively benign Fajã site, their epidermal thickness increased by approximately 21% over 14 days. Earthworms resident in Furnas soil had higher goblet cell counts than the residents of volcanically inactive soil on a neighbouring island (S. Maria). Transferring worms from S. Maria to mesocosms at Furnas induced a significant increase in goblet cell counts. Clearly, the active volcanic environment at Furnas poses a multifactorial stress challenge to the epigeic A. gracilis colonizer.

A case of simultaneous hermaphroditism in the Azorean endemic limpet Patella candei gomesii (Mollusca: Patellogastropoda), a gonochoristic species

Summary A case of simultaneous hermaphroditism was observed in Patella candei gomesii, an Azorean endemic species, which has been considered a gonochoristic species. Here we show that simultaneous hermaphroditism can occur within the family Patellidae.

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

BackgroundPopulations 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.ResultsUsing 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.ConclusionsThough 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.

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae : evolutionary signatures of a pathogenic lifestyle

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.

The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning

Abstract Pontoscolex corethrurus (Müller, 1857) plays an important role in tropical soil ecosystems and has been widely used as an animal model for a large variety of ecological studies in particular due to its common presence and generally high abundance in human-disturbed tropical soils. In this study we describe the complete mitochondrial genome of the peregrine earthworm P. corethrurus. This is the first record of a mitochondrial genome within the Rhinodrilidae family. Its mitochondrial genome is 14 835 bp in length containing 37 genes (13 protein-coding genes (PCG) 2 rRNA genes and 22 tRNA genes). It has the same gene content and structure as in other sequenced earthworms but unusual among invertebrates it hasseveral overlapping open reading frames. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND3 which uses GTG as the start codon. The A+T content of the mitochondrial genome is 59.9% (31.8% A 28.1% T 14.6% G and 25.6% for C). The annotated genome sequence has been deposited in GenBank under the accession number KT988053.