Orgaaniline aine parasvöötme järvedes – seire ning seosed valgalaga

A Thesis for applying for the degree of Doctor of Philosophy in Applied BiologyOrganic matter (OM) has an important role in lakes as a pH buffer in low alkalinity waters and acting as an energy source for heterotrophic microorganisms. Increasing OM concentrations in lakes have been reported as a dominating trend in various parts of the Northern Hemisphere over the past decades. This phenomenon is called brownification as the brown colour of water increases. Darker water may lead to light limitation of phytoplankton and affect lake productivity at several trophic levels. The organic enrichment with oxygen-consuming substances is also a serious issue in lakes, causing the depletion of dissolved oxygen. The present thesis focused primarily on the monitoring of lake OM and on the connections in temperate lake-catchment systems affecting the amount, properties and cycling of OM. Review of the monitoring programmes showed that European Union (EU) surveillance monitoring does not provide sufficient data for capturing the trends of brownification and organic enrichment in lakes. In 15 EU Member States no OM metric is routinely monitored in lakes. However, our results showed that Sentinel-2 will be a valuable tool for OM monitoring in lakes with remote sensing in addition to traditional methods, as we were able to estimate the OM content in Estonian lakes with different size and optical water properties from Sentinel-2 satellite images. Catchment characteristics have substantial effects on OM and its main component organic carbon (OC) in Estonian lakes and in temperate lakes in general. Our analysis confirmed the role of peatlands as a major source of OM and showed that larger catchments and intensive water exchange result in higher levels of OM. Hydrologically active lakes receive and emit large amounts of OC, whereas seepage lakes mobilise several orders of magnitude less OC and retain nearly all of it. Lakes should be studied as lake-catchment systems for a better insight into their OC cycling and the overall effect on the global carbon cycle.Orgaanilisel ainel on järvedes tähtis roll, näiteks olla pH puhvriks ning mikroobstes protsessides süsinikuallikaks. Paljudes põhjapoolkera järvedes on valgalalt pärineva orgaanilise aine sisaldus viimastel aastakümnetel tõusnud. Seda nimetatakse pruunistumiseks, sest tagajärjeks on tumedam vee värvus. Vähene valgus tumedas vees piirab fotosünteesi, mis mõjutab järve produktiivsust ka järgmistel toiduahela astmetel. Lisaks kahjustab järvi rikastumine kergesti lagunevate orgaaniliste ühenditega ehk orgaaniline reostus, mis põhjustab hapnikupuudust. Käesolevas doktoritöös käsitletakse orgaanilise aine seiret järvedes ning järve-valgala seoseid, mis mõjutavad orgaanilise aine kogust, koostist ja ringet parasvöötme järvedes. Euroopa Liidu (EL) seireprogrammide ülevaade näitas, et seireandmete põhjal ei ole võimalik hinnata üleeuroopalisi pruunistumise ja orgaanilise reostuse trende järvedes. Viieteistkümnes EL liikmesriigis ei mõõdeta järvedes regulaarselt mitte ühtegi orgaanilise aine näitajat. Samas näitasid meie tulemused, et kaugseiresatelliit Sentinel-2 on paljulubav vahend orgaanilise aine seire täiendamiseks traditsiooniliste meetodite kõrval. Suutsime satelliidipiltidelt usaldusväärselt hinnata orgaanilise aine sisaldust erineva suuruse ja vee tumedusega Eesti järvedes. Orgaanilise aine ja selle peamise komponendi, orgaanilise süsiniku kogust, koostist ja ringet Eesti ja parasvöötme järvedes üldiselt mõjutavad oluliselt valgala omadused. Meie tulemused kinnitasid raba rolli orgaanilise aine peamise allikana ning näitasid, et suur valgala ning intensiivne veevahetus tingivad tema kõrgema sisalduse. Intensiivse veevahetusega järvedesse transporditakse suurtes kogustes orgaanilist süsinikku, kuid enamus sellest kantakse järvedest välja. Teisalt on umbjärvedes ringlev kogus väga väike ning eksport olematu. Järvi tuleks uurida kui ühtseid järve-valgala süsteeme, et saada parem ülevaade orgaanilise süsiniku ringest ning võimalikust mõjust globaalsele süsinikuringele.Publication of this thesis is supported by the Estonian University of Life Sciences

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Eutrophication and geochemistry drive pelagic calcite precipitation in lakes

Pelagic calcification shapes the carbon budget of lakes and the sensitivity of dissolved inorganic carbon (DIC) responses to lake metabolism. This process, being tightly linked to primary production, needs to be understood within the context of summer eutrophication which is increasing due to human stressors and global change. Most lake carbon budget models do not account for calcification because the conditions necessary for its occurrence are not well constrained. This study aims at identifying ratios between calcification and primary production and the drivers that control these ratios in freshwater. Using in situ incubations in several European freshwater lakes, we identify a strong relationship between calcite saturation and the ratio between calcification and net ecosystem production (NEP) (p-value < 0.001, R2 = 0.95). NEP-induced calcification is a short-term process that is potentiated by the increase in calcite saturation occurring at longer time scales, usually reaching the highest levels in summer. The resulting summer calcification event has effects on the DIC equilibria, causing deviations from the metabolic 1:1 stoichiometry between DIC and dissolved oxygen (DO). The strong dependency of the ratio between NEP and calcification on calcite saturation can be used to develop a suitable parameterization to account for calcification in lake carbon budgets

Catchment land cover and soil as predictors of organic carbon, nitrogen, and phosphorus levels in temperate lakes : [presentation]

The presentation took place at the 10th International Conference on Shallow Lakes in 2021.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 951963. This study was funded by the Estonian Research Council grants PUTJD954, PRG705, and PRG709, and by the European Regional Development Fund through Estonian University of Life Sciences ASTRA project “Value-chain based bio-economy”. The Estonian Ministry of Environment and the Estonian Environment Agency supported data collection in the national monitoring program.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 951963. This study was funded by the Estonian Research Council grants PUTJD954, PRG705, and PRG709, and by the European Regional Development Fund through Estonian University of Life Sciences ASTRA project “Value-chain based bio-economy”. The Estonian Ministry of Environment and the Estonian Environment Agency supported data collection in the national monitoring program

A Future Tale of Two Winters? Sediment-water interface nitrogen dynamics in Lake Võrtsjärv (Estonia) during the ice-free winter 2019/2020 : [presentation]

The presentation took place at the Lahti Lakes 2021 Symposium.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 95196. Estonian University of Life Sciences ASTRA project “Value-chain based bio-economy”.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 95196. Estonian University of Life Sciences ASTRA project “Value-chain based bio-economy”

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

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

Roiu paisjärve tervendamise eeltööd – limnoloogiline hinnang

Uuring lähtub veekogude tervendamisel üldisest EL Veepoliitika Raamdirektiivi eesmärgist, mille järgi peavad siseveekogud saavutama hea ökoloogilise seisundi. Siseveekogude seisund on hea või väga hea, kui vee-ökosüsteemi esmasproduktsioon ja lagundamine on tasakaalus. Sellest lähtudes on oluline hinnata ideaalvariandis kogu elustikku, setete koostist, levikut, toitesoolade sisebilanssi, välisbilanssi ja veebilanssi. Roiu paisjärv on tehisveekogu, pindalalt (5,5 ha) ja mahult väike. Seepärast koguti setteproove kolmest punktist, planktoni ja vee omaduste proovid ühest punktist. Seevastu taimi uuriti üle kogu järve. EMÜ PKI Limnoloogiakeskus pole Roiu paisjärve varem uurinud. Seepärast on suurt rõhku pööratud inventuurile. Töös kirjeldatakse veekogu, esitatakse eripärad, funktsioneerimise peamised mõjurid, liikide seisund, veekogu ökoloogiline seisund. Hinnatakse koormustaluvust. Uuringu raames uuritakse kõiki paisjärve sissevoole, mis võivad olla oluliseks surveteguriks paisjärve seisundile. Lisaks tuleb tuvastada sissevooludest paisjärve suunatav reostuskoormus ning anda soovitused nende mõju vähendamiseks. Antakse järve seisundi tervendamiseks soovitused. Töödest võtsid osa järgmised EMÜ PKI Limnoloogiakeskuse töötajad: prof. I. Ott; PhD. H. Timm; PhD. H. Tammert; MSc. K. Saar; BSc. R. Laarmaa; MSc. M. Lehtpuu; MSc. T. Krause; MSc. A. Palm; MSc. M. Sepp, K. Ott; PhD. E.-J. Haberman

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.</div