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.

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 to Tylodelphys clavata. CONCLUSIONS: High intraspecific diversity of T. clavata indicates 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.

Do organic matter metrics included in lake surveillance monitoring in Europe provide a broad picture of brownification and enrichment with oxygen consuming substances?

Organic matter (OM) has numerous geochemical and ecological functions in inland waters and can affect water quality. Different parameters of aquatic OM are measured with various methods as no single analytical tool can provide definitive structural or functional information about it. In the present paper we review different OM metrics used in the European Union (EU) lake surveillance monitoring programmes and assess their suitability to provide sufficient data about the brownification and enrichment with oxygen consuming substances in European lakes. In the EU Water Framework Directive (WFD), metrics of OM are not mandatory physico-chemical parameters, but only recommended parameters to characterize water transparency, oxygenation conditions or acidification status. Our analysis shows that, as lake OM is monitored under the WFD in only 14 countries, no Europe-wide conclusions on the situation regarding brownification and organic enrichment can be drawn based on these data. Applied parameters in lake surveillance monitoring programmes are biochemical oxygen demand (BOD), chemical oxygen demand (COD), total organic carbon (TOC), dissolved organic carbon (DOC), water colour (WCol), and yellow substance. Different national OM metrics used avoid getting a broad picture of lake OM concentration changes in Europe over the last decades. Furthermore, our results demonstrate that the possibilities to convert different OM parameters to each other are limited because empirical relationships between them are region-specific. OM sensors for continuous measurements and remote sensing surveys could improve the effectiveness of lake OM monitoring, especially its temporal and spatial representativeness. It would be highly suggested to include in lake monitoring programmes also methods (e.g. absorbance or fluorescence spectroscopy) allowing to characterize the composition of OM as it influences strongly the biogeochemical role of OM in lakes.