Application of sedaDNA...

Application of sedaDNA to increase the interpretational potential of rotifer resting eggs (Rotifera) in paleolimnological research



Among three main groups of freshwater zooplankton – Cladocera, Copepoda and Rotifera, it is the latter one that exhibits the highest potential for infering the trophic status of lakes. This is mainly due to lower dependence of taxonomic composition of Rotifer communities from predatory pressure than e.g. Cladocera [1]. Nevertheless, Cladocera remains are widely use in the inference of past trophic status of lakes. This results from the traditional paleoecological approach, based entirely on the morphological identification of fossil remains. In this approach, the lack of fossil remains which can be isolated from sediment and visually identyfied, clearly eliminates many groups of organisms - including soft-bodied rotifers - as the potential paleoecological indicators.

Unlike the fragile  body, the durable resting eggs of Rotifers (RRS) are well preserved in sediment.  Produced sesonally and induced by various environmantal stressors RRS are commonly noticed as the additional findings in many paleolimnological analysis. However, apart from few individual cases [2,3], they are not identified to morphotype or taxon level, nor used in further paleoenvironmental inference. This is mainly due to concerns  regarding the incomplete reflection of the Rotifer population in the resting egg banks, as not all taxa (Bdelloidea) have the capacity to produce resting eggs.

Given the above, the aim of the study is to determine the gap caused by underrepresentation of  some rotifer taxa in sediment archives and its importance for paleoenvironmental inference. This will be achieved by applying set of mehods based on DNA sequencing. Although this approach (DNA metabarcoding and high troughtput sequencing of ancient sediment samples) is still innovative and at early stage of application, there is the consensus that in the forthcoming years these methods derived from molecular biology will not only significantly supplement, but even revolutionize paleoenvironmental research [4].

The project framework covers: (i) acquireing the data on the variability of the RRE composition (identification of morphotypes and determination of its abundance) followed by DNA analysis of individual RRE for the most detailed taxonomic identification (DNA barcoding) (ii) metabarcoding of environmental samples (detection in the sediment of all organisms present in a given niche based on short fragments of their DNA - in this case, the target group are rotifers, and method enables also detection of taxa not producing resting eggs).

References:
[1] Ejsmont-Karabin 2012. The usefulness of zooplankton as lake ecosystem indicators: rotifer trophic state index. Polish Journal of Ecology, 60(2), 339-350. [2] Nykänen et al. 2008. Rotifer resting eggs in the sediment indicate trophic changes in Lake Vesijärvi. Int. Ver. fur Limnologie: Verhandlungen, 30(3), 441-445. [3] Piscia et al. 2016. Unexpected increases in rotifer resting egg abundances during the period of contamination of Lake Orta. Journal of Limnology, 75. [4] Domaizon et al. 2017. DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity. Journal of Paleolimnology, 58(1), 1-21.

 


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