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Rubisco is the main CO2-fixing enzyme in the biosphere and sustains the vast majority of food chains on Earth. Although Rubisco catalysis is currently an area of active study, there is still a strong debate about the main drivers shaping Rubisco evolution. Thus, an integrative and complete meta-analysis of study-to-study normalized Rubisco kinetic data becomes an essential requisite to succeed in providing new relevant information on Rubisco phylogenetic evolution and environmental adaptation. The aim of this study was to undertake an exhaustive compilation of all the data published so far on the in vitro Rubisco catalytic parameters of autotrophic organisms containing Rubisco, from bacteria to vascular plants. Rubisco evolution was re-evaluated in the context of its environmental drivers and the effectiveness of CO2 concentrating mechanisms (CCMs). The phylogenetic signal in Rubisco catalysis was also analyzed by evaluating the dependence of variation in kinetic traits on the phylogenetic tree constructed from the Rubisco large subunit sequence. Our results showed that phylogenetic constraints in Rubisco adaptation mostly determine the specificity factor values of current species. However, the adaptation of the Rubisco affinity for CO2 and carboxylation efficiency has been more influenced by the environmental conditions than by phylogenetic constraints, either provoking an evolution of a more CO2-affine and efficient Rubisco enzyme under limiting intracellular CO2 conditions, or a relaxation of CO2 affinity and efficiency when co-evolved with CCMs. Importantly, this analysis questions the canonical trade-off between Rubisco kinetic traits previously described for Spermatophyta and recognizes a larger plasticity of Rubisco kinetics than previously thought. This information will be especially useful for understanding the effects in the productivity and ecological success of the different aquatic organisms in future scenarios of Global Change.

Väitekirja elektrooniline versioon ei sisalda publikatsioone., Eluslooduse süsteemi põhiühik on liik, kuid seni pole õnnestunud rakendada ühesuguseid liigikriteeriume kogu eluslooduse mitmekesisusele. Ebapüsiv või ekslik taksonoomia võib põhjustada isegi mittevajalikke rahalisi kulutusi, näiteks kaitsealuste, invasiivsete või patogeensete liikide piiritlemisel või valestimääramisel. Samblikud on sümbiootilised organismid, koosnedes vähemalt kahest komponendist – seenest ning selle sees elavast ja fotosünteesivast rohevetikast ja/või tsüanobakterist. Süstemaatiliselt käsitletakse samblike seentena, mis toituvad oma partneri fotosünteesiproduktist. Mitmeid samblike saab kasutada keskkonna kvaliteedi hindamiseks, kuid paljude liikide määramine on jätkuvalt keeruline ning nende piirid ebaselged. Pärilikkusaine ehk DNA uuringud võimaldavad liigikontseptsioonide ning liigipiiride ühtlustamist, rakendades liigile ühise eellase (monofüleetilisuse) kriteeriumit. Uurisin oma doktoritöös sugulussuhted ning liikide piiritlemist kolmes sambliku moodustava seene rühmas, kasutades morfoloogilisi, keemilisi, anatoomilisi ja geneetilisi tunnuseid. Lisaks küsisin, kas samblike on võimalik määrata kasutades DNA järjestusi. Oma töös leidsin, et paljud morfoloogiliste tunnuste alusel kirjeldatud samblikud ei esinda jätkuvalt loomulikke, geneetiliselt eristunud liike ning seetõttu vajavad taksonoomilist korrastamist. Rebasesamblikud ja habesamblikud sektsioonist Usnea esindavad hiljuti lahknenud noorte liikide komplekse, mida iseloomustavad konfliktne geneetiline info ja ebaselged liigipiirid. Tõestasin, et sellistes rühmades on põhjendatud uudsete liigipuu ja liikide piiritlemise meetodite kasutamine. Helksamblike liigid on seevastu hästi eristunud ning kasutatavad tunnused valdavalt asjakohased. Uurimus näitas, et isendite üldine haabitus ja paljunemisviis ei pruugi olla piisavad nende samblike õigeks määramiseks ning lisaks tuleks uurida samblike keemiat ja kasutada DNA infot., Species is a fundamental unit in biology but debate continues over boundaries, numbers of species, and identification methods. Unstable or erroneous taxonomy can even have financial ramifications when, for example, protected, invasive, or pathogenic species are falsely identified or delimited. Lichens are systematically considered as mostly sac fungi that are able to form intimate and long-term symbiotic associations with photosynthetic algae or cyanobacteria. Lichens are known for their tolerance for extreme conditions in arctic areas, and at the same time, for their vulnerability – many lichens can be used as bio-indicators in monitoring environmental quality. However, accurate identification of lichenized fungal species remains challenging due to complex diagnostic characters and unsettled species boundaries in many groups. In my doctorate thesis I studied species boundaries and evolutionary relationships in lichenized fungal genera Cetrelia, Usnea section Usnea, and Vulpicida. Also I attempted to identify lichenized fungal species using DNA sequences, and estimate its usage and accuracy. I found that many taxa of lichen fungi are still in need of taxonomic revision. The genera Vulpicida and Usnea section Usnea represent recently diverged species complexes with conflicting genetic signal and unclear species relationships. Here, I established that using novel species tree and species delimitation methods should be preferred over traditional gene tree approach. Cetrelia, on the other hand, represented a lengthier evolutionary history, with relatively well-circumscribed species and justified diagnostic characters. I found that the general appearance of specimens and their reproductive mode might not always be sufficient in delimiting genetically isolated fungal lineages. DNA-based identification could be used as an alternative species identification method but is efficient in a system of well-circumscribed taxa and a high-quality reference database.

Bakalaureusetöö Vee ja maismaa ökosüsteemide rakendusbioloogia õppekaval Bioindikatsioonilised uuringud oma ajaloolises järjepidevuses võimaldavad uurida pikemajaliste keskkonnamuutuste mõju organismidele. Viimane lihhenoindikatsiooniline töö Tartu linna õhukvaliteedi hindamiseks tehti 18 aastat tagasi, sellepärast on antud teema Tartu linna jaoks taaskord aktuaalne. Käesoleva bakalaureusetöö eesmärgiks oli: kirjanduse põhjal väljavalitud samblike indikaatorliikide leviku kaardistamine Tartu linnas, samblike indikaatorliikide levikumustrite võrdlemine varasemate lihhenoindikatsiooni uuringutega Tartu linnas ning õhu seisundi hindamine Tartu linnas indikaatorliikide levikukaartide põhjal. Töö metoodika põhines 2001. aastal Tiiu Tõrra poolt Tartus tehtud ja 2004. aastal koostatud lihhenoindikatsioonilisel uuringul. Käesoleva bakalaureusetöö välitööd teostati ajavahemikul 7.10. – 23.10. 2019. Uurimistöö käigus koguti andmeid 59-lt proovialalt, uuriti kokku 479 puud: 151 vahtrat, 183 pärna ja 145 tamme. Hinnati uuritud indikaatorliikide eelistusi substraadiks valitud pärna ja vahtra suhtes. Andmete põhjal koostati kaardid, mis näitavad indikaatorsamblike levikut Tartu linnas ja liikide esinemisesageduste tabelid, mida võrreldi uurimustega varasematest töödest. Uuringus leiti, et happeline saastus pole Tartu linnast kadunud ning piirab jätkuvalt sellele tundlikumate liikide linna naasmist. Samblike esinemissagedused on selle aja jooksul suurenenud ja erinevate indikaatorliikide levik on enam-vähem ühtlustunud. Samblikukõrbeid ei leitud ning see viitab, et õhuseisund Tartus on paranenud. Vitality and distribution of indicator species of known tolerance or quantitative characteristics of lichen communities has been used to estimate the effects of long-term environmental changes on organisms. The latest lichen indicator work on the air quality assessment of Tartu was done 18 years ago, so this topic is again relevant for the city of Tartu. The aim of this work was to determine the distribution of lichen indicator species in Tartu by the method of mapping, to compare the distribution of lichen indicator species with previous researches, and to assess the state of the air in Tartu based on distribution maps of species-indicators. The results were compared with earlier papers on the same subject. The methodology of the work was based on the study of lichens in 2001 by Tiiu Tõrra in Tartu and compiled in 2004. The fieldwork of current study took place during 7.10. - 23.10. 2019. The data were collected from 59 monitoring sites and from 479 trees: 151 maples, 183 limes and 145 oaks. The preferences of the indicator species studied in relation to tree species were assessed. On the bases of these data, maps showing the distribution of indicator lichens in Tartu and tables of occurrence frequencies of species were compiled and compared with previous studies. Results show, that acid pollution has not disappeared from the city of Tartu and continues to restrict the return of more sensitive species to the city. Nevertheless, the frequency of occurrence of studied lichens has increased, and the distribution of various indicator species has increased in the city almost evenly. Lichen deserts were also not found, and this indicates that the air condition in Tartu has improved.