PUBLICATION: Molecular metrics to monitor ecological status of large rivers: Implementation of diatom DNA metabarcoding in the Joint Danube Survey 4
The Joint Danube Survey (JDS) is a regular transnational survey overseen by the International Commission for the Protection of the Danube River (ICPDR) through the Monitoring and Assessment Expert Group, to monitor the quality of the Danube and its main tributaries, in accordance with the Water Framework Directive of the European Union. During the JDS4 in 2019, conventional methods to monitor selected biological quality elements, including benthic diatoms, were complemented with DNA metabarcoding.
Source: https://www.sciencedirect.com/science/article/pii/S1470160X24003406
Phytobenthos samples were collected along the Danube and its major tributaries, and analysed using both light microscopy and DNA metabarcoding amplifying a fragment of the rbcL marker gene. The objectives of the study were to investigate (i) the applicability of DNA metabarcoding to identify diatom communities compared to microscopy; (ii) diversity metrics obtained with DNA metabarcoding and microscopy analysis and finally, (iii) the usability of DNA metabarcoding for routine monitoring and assessment of the Danube under future JDS surveys.
Diatom communities resulting from light microscopy and DNA metabarcoding assessments share 26.5% of all taxa which corresponds to 64.3% when considering relative abundances. Discrepancies originate from biases both from metabarcoding, e.g. missing taxa from the reference library, and from microscopy, e.g. overlooking of hardly visible taxa. Microscopy detected more taxa in total but metabarcoding revealed a higher alpha diversity, detecting also very rare taxa in a given sample. Molecular and microscopy based Specific Pollution Sensitivity Index (IPS) values correlated significantly but differences were detected at several sites due to the differences in community composition and the overestimation of large taxa by metabarcoding. Although both methods showed a decreasing trend of IPS along the Danube, the metabarcoding based IPS covered a higher range of quality classes indicating lower values for downstream sites and the tributaries.
We suggest that metabarcoding provides a standardisable and efficient tool in biomonitoring, being more distinctive among quality classes than microscopy. Due to the high sequencing depth, it is able to detect a higher diversity on genetic level in a time- and cost-efficient manner that should be implemented in future quality assessment tools. We recommend its use in future biomonitoring surveys, for now, as a complementary method to conventional ones.
More details in the OA article:
Kálmán Tapolczai, Teofana Chonova, Dana Fidlerová, Jarmila Makovinská, Demetrio Mora, Alexander Weigand, Jonas Zimmermann (2024). Molecular metrics to monitor ecological status of large rivers: Implementation of diatom DNA metabarcoding in the Joint Danube Survey 4, Ecological Indicators, 160: 111883, https://doi.org/10.1016/j.ecolind.2024.111883.