Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch

Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance

Phosphorus Retention as the Function of External Loading, Hydraulic Turnover Time, Area and Relative Depth in 54 Lakes and Reservoirs

We analysed phosphorus retention as the function of external loading, hydraulic turnover time, area and relative depth on the basis of published data on 54 lakes and reservoirs in different climate regions around the world. The results of our study generally supported the earlier suggestion by many authors that the waterbodies with longer hydraulic retention time retain the higher percentage of the externally received phosphorus. We could also partly confirm our hypothesis that the waterbodies with the bigger relative depth might retain higher proportion of the external phosphorus than larger and shallower waterbodies with lower relative depth. The latter assumption was, however, valid only in some specific type of waterbodies ¿ small and medium-sized with the intensive hydraulic turnover. The lakes that received higher areal loading of P also retained more P per m2 but the proportion of the retained external P loading remained generally independent from the amount of areal P input that waterbody received. However the waterbodies with rather small relative depth retained higher proportion of external P input towards the decreasing gradient of the areal P loading.JRC.H.1-Water Resource

Effect of Chlorophyll Sampling Design on Water Quality Assessment in Thermally Stratified Lakes

In order to adequately assess the ecological status of thermally stratified lakes based on chlorophyll, the sampling must cover all productive layers of the water column. Missing the deep chlorophyll maxima (DCM) that often occur in the meta- or hypolimnion of transparent lakes supported by sufficient illumination and good nutrient availability, may cause serious underestimation of the productivity and lead to misclassification of the lake ecological status. There is no commonly accepted sampling design for stratified lakes and various monitoring guides suggest controversial designs. Our aim was to find some robust criteria to assess the probability of occurrence of a DCM and estimate the differences in measured mean chlorophyll concentrations caused by various sampling designs. Our theoretical model showed that the probability of occurrence of a DCM increases with increasing water transparency and decreasing lake size. Empirical data from Italian and Estonian stratified lakes confirmed the results. Testing of different sampling designs on lakes with full measured chlorophyll profiles available showed that taking only surface layer samples will lead with a high probability to an underestimation of the chlorophyll concentration in the trophogenic layer. In order not to miss the Chl peak in stratified lakes, in most cases it would be more precautious not to limit the sampling with the well-mixed epilimnion but to extend it to the euphotic layer. Sampling epilimnion instead of euphotic zone could cause up to 70% underestimation of Chl concentration, an error that would cause a misclassification of the lake by one or even two status classes in a 5-class assessment system. In most cases, the 2.5*Secchi depths proved a suitable criterion of the sampling depth and only in case of surface scums, sampling of a 3*Secchi depth layer would be recommended in order to not miss the deep chlorophyll maximum.JRC.H.1-Water Resource

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

Background: Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses.Methods: We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in 14 lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach.Results: Whole eye transcriptome results revealed overexpression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned toTylodelphys clavata.Conclusions: High intraspecific diversity ofT. clavataindicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites