Next-generation sequencing in environmental monitoring

In this post, Kathrin Theissinger informs about the project “Effects of mining effluents on species composition and stress gene activation in aquatic macroinvertebrates in Finland”.

In this project, Dr. Jenny Makkonen focuses on the characterization of the aquatic environment under the influence of the mining industry. The two macroinvertebrate species groups selected as target organisms are representing the opposite heads in respect to the tolerance of the mining-derived pollution. The chironomids, being highly tolerant against the toxic effects of mining effluents, can even be found from close locations of the mines, while the crayfish, as highly sensitive species, can reflect the effects of the mining-derived substances on transcriptional level even from far distances of the actual mining industry.

Taking chironomid core samples from a frozen lake with mining-derived pollution (photo by K. Väänänen

Taking chironomid core samples from a frozen lake with mining-derived pollution (photo by K. Väänänen)

The Background:

Contamination of the ecosystem resulting from anthropogenic activities is a major ecological concern. Mining activities cause great environmental modifications of the landscape outline, chemistry and biology. The abandoned or inactive mines are of particular concern and require continuous control and monitoring. The effluent discharges into the aquatic environment of the mines are often heavy metals, salts or organic compounds, and the run-off waters are often acidic. The highest environmental risks are presumably linked to the metallic sulfides, causing acidification of the surrounding environment. An ecotoxicological characterization of the aquatic environment is necessary to better understand the toxic effects and consequences of the chemicals on aquatic biota.

The non-biting midges (Chironomidae, Diptera) are one of the most dominant groups among the aquatic macroinvertebrates and they are commonly used in biomonitoring or -assessments of aquatic ecosystems. The reason for using these species lies in their ubiquity, species richness, high ecological diversity and very high number of individuals in all kind of lotic systems. However, many groups have excluded chironomids from the analyses, since the species determination above the family level is highly demanding, leaving a lot of room for errors. However, metabarcoding has recently become a new powerful tool for environmental monitoring. The DNA based assays to monitor the species abundance and biodiversity in aquatic ecosystems has been shown to be a rapid and efficient tool in biomonitoring.

On the other side of the aquatic macroinvertebrate species spectrum is the freshwater crayfish which is commonly used as a target species in the biomonitoring of aquatic environment. The crayfish-based biomonitoring has been mainly concentrating to study the bioaccumulation of heavy metals, but also the stress related gene activation due to toxic exposure has been recently studied with transcriptomics approach. In Finland, the highly sensitive native noble crayfish (Astacus astacus) stocks, considered as an indicator of superior water quality, mostly disappeared from the sphere of mining influence. The transcriptional effects of environmental stress has been widely studied in Drosophila melanogaster and a high number of genes and regulatory mechanisms involved in maintaining heavy metal homeostasis, metal export and import have been recognized. Furthermore, it has been shown that the transcriptomic effects-based monitoring reflects chemical pollution gradients, thus holding promise for assessment of relative contributions of point sources to pollution and the efficacy of pollution remediation. Therefore, the crayfish, being one of the most sensitive aquatic macroinvertebrates, could act as an excellent target species in transcriptomics-based biomonitoring of the aquatic environment.

For more info regarding this project click HERE.