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Detection of nuisance species in ballast waters using eDNA

A group of researchers assessed the diversity of DNA sequences present in ballast waters, during a 3-weeks cruise, using eDNA and Next Generation Sequencing.

In July 2015, Zaiko et al. published a paper entitled “Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring” in the “Marine Environmental Research” journal.

Summary: Detecting the presence of potential invasive species in ballast water is a priority for preventing their spread into new environments. Next generation sequencing technologies are being increasingly used for exploring and assessing biodiversity from environmental samples. Here the authors apply high throughput sequencing from DNA extracted from ballast water (BW) samples employing two different platforms, Ion Torrent and 454, and compare the putative species catalogues from the resulting Operational Taxonomic Units (OTU). Water samples were taken from the RV Polastern ballast tank in five different days between the second and the twentieth navigation day. Pronounced decrease of oxygen concentration and increase of temperature occurred in the BW during this time, coincident with a progressively higher proportion of unassigned OTU and short reads indicating DNA degradation. Discrepancy between platforms for species catalogues was consistent with previously published bias in AT-rich sequences for Ion Torrent platform. Some putative species detected from the two platforms increased in frequency during the Polarstern travel, which suggests they were alive and therefore tolerant to adverse conditions. OTU assigned to the highly invasive red alga Polysiphonia have been detected at low but increasing frequency from the two platforms. Although in this moment NGST could not replace current methods of sampling, sorting and individual taxonomic identification of BW biota, it has potential as an exploratory methodology especially for detecting scarce species.

Reference: Zaiko, A., Martinez, J.L., Ardura, A., Clusa, L., Borrell, Y.J. Samuiloviene, A., Roca, A., Garcia-Vazquez, E. (2015). Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring. Marine Environmental research. In press. doi.10.1016.