De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies

BACKGROUND: Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression. RESULTS: This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. To identify differentially expressed transcripts; each of the original sequence files were aligned to the de novo assembled transcriptome using Bowtie and then RSEM was used to estimate expression values based on the alignment. EdgeR was used to calculate differential expression between the two conditions, with an FDR corrected P value cut off of 0.001, this returned six significantly differentially expressed genes. Initial BLASTX hits of these putative genes included hits with annelid ferritin and lysozyme proteins, as well as fungal NADH cytochrome b5 reductase and senescence associated proteins. At a cut off of P = 0.01 there were a further 26 differentially expressed genes. CONCLUSION: These data have been made publicly available, and to our knowledge represent the most comprehensive available transcriptome for E. fetida assembled from RNA sequencing data. This provides important groundwork for subsequent ecotoxicogenomic studies exploring the impact of the environment on global gene expression in E. fetida and other earthworm species.

Ecotoxicological evaluation of sediments applied to environmental forensic investigation / Avaliação ecotoxicológica de sedimentos aplicada à perícia criminal ambiental

Abstract The present study aimed to evaluate the potential for using toxicity assays with sediment samples for the detection of water pollution caused by the discharge of tannery effluents into water bodies and its application to environmental forensic investigation. The study included ecotoxicological evaluation of sediments, survey of benthic organisms in the field, as well as chromium, cadmium and lead dosage which provided data for a sediment quality triad evaluation. The sediment samples showed acute and chronic toxicity to the bioindicators, low biodiversity of benthic macrofauna and high chromium concentration, reaching up to 4365 mg.Kg–1. A close relationship was observed between the separate results of ecotoxicological sediment evaluation and the sediment quality triad. The sediment ecotoxicological assessment proved to be applicable to tracking sources of contamination related to tanneries and similar activities in environmental forensics.

Resumo O objetivo do presente estudo foi avaliar o potencial de aplicação de ensaios de toxicidade com amostras de sedimento para constatação de poluição aquática causada por lançamentos de efluentes de curtumes em cursos d’água e seu emprego na perícia criminal ambiental. O estudo incluiu avaliação ecotoxicológica de sedimentos, avaliação da fauna bentônica local e dosagem de cromo, cádmio e chumbo que forneceram dados para avaliação da tríade de qualidade dos sedimentos. As amostras de sedimentos mostraram efeito de toxicidade aguda e crônica aos bioindicadores, baixa biodiversidade da macrofauna bentônica e altas concentrações de cromo que chegaram a 4365 mg.Kg–1. Houve uma estreita relação entre os resultados isolados da avaliação ecotoxicológica e a tríade de qualidade de sedimentos. A avaliação ecotoxicológica demonstrou ser aplicável na identificação de fontes de contaminação relacionadas a curtumes e atividades similares em perícias ambientais.

Influence of antifouling paint on freshwater invertebrates (Mytilidae, Chironomidae and Naididae): density, richness and composition / Influência de revestimentos antiincrustantes em invertebrados aquáticos (Mytilidae, Chironomidae and Naididae): densidade, riqueza e composição

Abstract We conducted a study about invertebrates on artificial substrates with different antifouling paints in order to answer the following questions 1) is there lower accumulation of organic matter on substrates with antifouling paints, 2) is invertebrate colonization influenced by the release of biocides from antifouling paints, 3) is the colonization of aquatic invertebrates positively influenced by the material accumulated upon the substrate surface and 4) is the assemblage composition of invertebrates similar among the different antifouling paints? To answer these questions, four structures were installed in the Baía River in February 1st, 2007. Each structure was composed of 7 wood boards: 5 boards painted with each type of antifouling paints (T1, T2, T3, T4 and T5), one painted only with the primer (Pr) and the other without any paint (Cn). After 365 days, we observed a greater accumulation of organic matter in the substrates with T2 and T3 paint coatings. Limnoperna fortunei was recorded in all tested paints, with higher densities in the control, primer, T2 and T3. The colonization of Chironomidae and Naididae on the substrate was positively influenced by L. fortunei density. The non-metric multidimensional scaling (NMDS) of the invertebrate community provided evidence of the clear distinction of invertebrate assemblages among the paints. Paints T2 and T3 were the most similar to the control and primer. Our results suggest that antifouling paints applied on substrates hinder invertebrate colonization by decreasing the density and richness of invertebrates.

Resumo O estudo dos invertebrados em substrato artificial com diferentes revestimentos antiincrustantes foi realizado com o intuito de responder as seguintes questões 1) Há menor acumulação de material orgânico nos substratos com revestimentos antiincrustantes? 2) A colonização de invertebrados é afetada pela liberação de biocidas dos revestimentos antiincrustantes? 3) A colonização dos invertebrados aquáticos é facilitada por material acumulado sobre a superfície do substrato? 4) A composição da assembléia é similar entre os diferentes revestimentos? Para realização deste estudo, quatro estruturas foram instaladas em 01 de fevereiro de 2007 no rio Baía. Em cada estrutura foram colocadas sete placas de madeira: cinco placas com aplicação de um tipo de revestimentos antiincrustantes (T1, T2, T3, T4 e T5), uma placa apenas com a aplicação do primer (Pr) e a outra placa permaneceu sem aplicação de nenhum revestimento (Cn). Ao final dos 365 dias em que os substratos ficaram submersos observou-se maior acumulação de material orgânico nos substratos dos revestimentos T2 e T3. Limnoperna fortunei foi registrada em todos os revestimentos testados, com maiores densidades encontradas no controle, primer, T2 e T3. A colonização de Chironomidae e Naididae sobre os substratos foi influenciada pela densidade de L. fortunei. A ordenação (NMDS) evidenciou a separação da assembléia de invertebrados entre os revestimentos. Os revestimentos T2 e T3 foram os mais similares ao controle e ao primer. Os resultados obtidos sugerem que revestimentos antiicrustantes aplicados sobre substratos dificultam a colonização de invertebrados, reduzindo a densidade e riqueza de invertebrados.

Biomanagement of sago-sludge using an earthworm, Eudrilus eugeniae.

Sago, the tapioca starch is manufactured by over 800 small-scale units located in the Salem district, Tamil Nadu, India. During the processing of sago it generates huge quantities of biodegradable solid waste, as crushed tubers. In present study an attempt was made to convert these biodegradable solid sago tubers into value added compost using an exotic earthworm, Eudrilus eugeniae. The experiments were carried out in a plastic tray at various concentrations of sago-sludge (50% 75% and 100%) for a period of 90 days. During the vermicomposting, data were collected on life form (cocoon, non clitellates, clitellates) of earthworm and it was found to be high in 50% followed by 75% and 100% concentrations. Chemical analysis of worked substrates showed a step wise increase of nitrogen and phosphorus. The fold increase of phosphorus and nitrogen were found to be high for sago-sludge undergoing vermicomposting than the control. During the composting period the organic carbon decreased from its initial value of 58, 76 and 107 mg/kg to 21, 24 and 65 mg/kg for 50, 70 and 100%, respectively The microbial analysis showed that after 75 days of composting, their population stabilized and further increase in composting period did not increase their population size. The results indicate that 50% and 75% concentration of sludge mixed with bedding material was ideal for the vermicomposting.

Impact of soil types and petroleum effluents on the earthworm, Eudrilus eugeniae.

Earthworm, Eudrilus eugeniae, exposed to different concentrations of dump-site soil and petroleum effluents exhibited different morbidity and mortality responses. Lake sediments caused varied fluctuations in weight over a 20 day exposure period. Colour changes and mortality up to 15% were observed in earthworms cultured in 100% lake sediment, while weight loss, coiling and sluggish movement were observed in 50% lake water. The effects of 100% dump-site soils were more pronounced as 40% death, swelling, body lesions, stiffening, coiling and low reproduction were recorded. Earthworms were useful as an organism in testing the toxicity of dump-site soils and effluent from a petroleum industry. Dump-site soils and soils polluted with petroleum effluent reduced populations of earthworms and this could subsequently affect other components of the ecosystems associated with earthworm activities.

Efecto de sedimentos naturales enriquecidos con zinc, en modelos aislados y en microcosmos, sobre tres especies de invertebrados bentónicos / Effect of zinc-enriched sediments, in open and isolated systems, on three species of benthonic invertebrates

Availability of toxics in aquatic bodies is limited by the physicochemical characteristics of sediments and water, as well as by the interactions between the different xenobiotics and inhabits species. The aim of this work was to relate the effect produced by zinc (Zn) spiked in sediments of the Ignacio Ramirez dam (PIR), in isolated and microcosms models, on ATP concentration of three benthic organisms with the metal biodisponibility. The selected species were a crustacean, an annelid and a mollusk: Hyalella azteca (Amphipoda: Hyalellidae), Limnodrilus hoffmeisteri (Oligochaeta: Tubificidae) and Stagnicola attenuata (Basommatophora: Lymnaeidae), species that are found at high proportions in the reservoir and use different spaces in the benthos. Samples of sediments and organisms were collected from the PIR during the dry season (February of 1999). Metal concentration (Zn, Fe, Cu and Ni), pH, texture, particle size, total nitrogen and organic matter were determined in sediments. Sublethal studies were carried out using two types of static systems (organisms isolated and in microcosms). Both models contained PIR sediments enriched with Zn (nominal concentration of 0.8129 mg/kg) and synthetic water in a proportion of 1:4. The test organisms were added to the systems once the equilibrium was reached (2 hr) considering the biomass quantity with respect to volume (1.0 g of organism by each 100 ml of water:sediment). After 0, 12, 24, 36, 48 and 72 hr of exposure, samples of sediment and hydrobionts were taken, and Zn content was quantified by atomic absorption. ATP concentration was also determined in organisms. The effect produced by natural sediments spiked with Zn is increased by the presence of more than one specie in the system (microcosm). With respect to Zn levels, two of the organisms tend to lose this metal in isolated and microcosm models, probably as a regulation strategy in its accumulation, as well as Fe presence in the reservoir sediments. Therefore...

En los cuerpos acuáticos la disponibilidad de los tóxicos es limitada por las características fisicoquímicas de los sedimentos y agua, así como por las interacciones entre los diversos xenobióticos y entre las especies que los habitan. Por lo anterior, el objetivo del presente trabajo fue relacionar el efecto producido por el zinc (Zn) sembrado en sedimentos del embalse Ignacio Ramírez (PIR), en modelos aislados y en microcosmos, sobre el ATP de res organismos bentónicos con la biodisponibilidad del metal. Las especies seleccionadas fueron: Hyalella azteca, Limnodrilus hoffmeisteri y Stagnicola attenuata, dado que se encuentran en altas proporciones en el embalse y ocupan espacios diferentes en el bentos. Las muestras de sedimentos y organismos se colectaron en la estación de sequía (febrero de 1999). A los primeros se les determinó el pH, textura, tamaño de partícula, nitrógeno total, materia orgánica y concentración de metales (Zn, Fe, Cu y Ni). Posteriormente se realizó un estudio de toxicidad subletal utilizando dos tipos de sistemas estáticos (organismos aislados y en microcosmos). Ambos modelos contenían sedimentos de la PIR enriquecidos con Zn (concentración nominal de 0.8129 mg/kg) y agua sintética en una proporción de 1:4. Los organismos de prueba fueron adicionados una vez alcanzado el equilibrio (2 hr) considerando la cantidad de biomasa con respecto al volumen (1.0 g de organismo por cada 100 ml de agua:sedimento). Después de 0, 12, 24, 36, 48 y 72 hr de exposición se tomaron muestras del sedimento y de los hidrobiontes, a los cuales se les cuantificó el contenido de Zn por absorción atómica. A los organismos también se les determinó la concentración de ATP. Los resultados obtenidos muestran que el efecto producido por los sedimentos naturales enriquecidos se ve potenciado por la presencia de más de una especie en el sistema (microcosmos). Con respecto a los niveles de Zn, dosde los organismos (L. hoffmeisteri y S. attenuata) tienden a...

Impact of copper application on soil metabolism, energy budget and formation of stable aggregates by anecic earthworm in tea plantations.

The preparation of daily energy budget of earth worm Lampito mauritii showed (i) decrease in consumption by about 66%, (ii) decrease of egestion 97%, (iii) decrease in growth by 80%, and (iv) enhancement in maintenance cost by about 31.5% on exposure to 8 ppm copper in comparison to zero level exposure. The stable aggregate formations also decreased by 67.6% at 8 ppm copper as compared to zero level exposure. Two way ANOVA showed significant decrease in stable aggregate formation and biomass at 5% level of significance on exposure to 8 ppm copper. The soil metabolism also increased under the negative impact of copper.