How epigenetics contribute to an environmental response

Conditions at the geothermal field include high soil temperature, exceptionally high carbon dioxide (CO2) and low oxygen levels, and raised metal bioavailability. Such a stressful environment would be lethal for most organisms, therefore an EU-funded initiative studied L. rubellus to determine how it can tolerate its surroundings.

The EPIWORM (Finding the ghost in the genome: Assessing the contribution of epigenetics to environmental plasticity in the soil sentinel Lumbricus rubellus) project investigated alterations in the epigenetic landscape caused by exposure to environmental contaminants. The consortium wished to determine whether epigenetic control is an additional mechanism for regulating genome responses by earthworm populations.

Project partners posited that environmental stressors in the form of contaminants directly influence the expression of specific genes. The result is increased phenotypic plasticity and a mechanistic basis that underpins the organism's response to the stress-inducing causative stimuli.

Two sites were selected in São Miquel. The first was Furnas, which displays the greatest volcanic activity in the entire Azores archipelago, and the second was Macela, which displays no volcanic activity. Although metal concentrations were similar at the two sites, the soil at Furnas was characterised by high temperature, relative hypoxia, extremely high levels of CO2 and accompanying acidity.

Researchers mapped the epigenetic changes by performing methylated DNA immunoprecipitation on samples of powdered earthworms. This constituted the first description of the methylation patterns in earthworms.

The data also led to the development of software capable of rapidly performing investigative analysis of large-scale epigenetic data sets. In addition, researchers prepared libraries for small RNA sequencing and identified microRNA (miRNA) for the earthworm Amynthas gracilis for the first time. The miRNA appeared important for the organism's adaptation to the volcanic conditions as well as having population-specific regulatory functions.

Scientists also investigated the spatial association of epigenetic modifications with loci displaying altered expression by generating RNA-sequencing data. This revealed a number of pathways associated with survival in a multi-stressor environment, including genes involved in the organism's response to hypoxia, hypercapnia, heat stress and metals.

EPIWORM also studied the epidermis of earthworms in volcanic and non-volcanic soils to determine the functional relationship between epigenetic changes and phenotypic responses. Results showed that earthworms respond to changes from the epigenetic point of view by regulating changes in gene expression, as well as the basal sequence information, which is modified as a result of adaptation.