Eukaryotic organisms that cannot be classified as animals, land plants, or fungi are termed protists. Despite the fact that protists represent the majority of eukaryotic diversity, these organisms have received relatively little attention from biological researchers beyond morphological characterization. Reasons that likely contributed to their neglect include their mostly microscopic nature, that only a few lineages are the causative agents of human disease, that laboratory cultivation can be challenging, and that species concepts for the majority of protists was vague in many lineages. Initial attempts to resolve relationships among eukaryotes produced the five kingdoms model. This model suggested protists were an evolutionary assemblage separate from the animals, plants, and fungi. Molecular systematics provided a more accurate view of relationships amongst eukaryotic taxa. Results from molecular phylogenetic studies demonstrated that protists were a polyphyletic group made of many assemblages, and that more complex lineages such as plants and animals were nested within these assemblages. This new evolutionary framework brought increased attention to protists. The application of molecular biology, especially genomic and transcriptomic sequencing to protists has allowed researchers to generate meaningful data on poorly understood lineages rapidly. Applying these techniques to understudied amoeboid protists, I demonstrated the presence of a complex life cycle in a well-studied group of opportunistic pathogens and their close relatives that was not previously known, as well as characterized new diversity within the group. I made methodological advances in the field of molecular systematics through development of a novel ortholog collection algorithm that I have included in a phylogenomic package capable of resolving ancient (>100 million years) divergences in the tree of eukaryotes. I used the algorithm to build the packages accompanying manually curated database of 240 homologs from 304 eukaryotic taxa. Using the newly developed software and manually curated gene set has yielded the most complete and highly resolved tree of eukaryotes to date. Finally, I used developmental transcriptomics to demonstrate the amoeba Copromyxa protea evolved a means of simple cooperative multicellularity independently from other more well studied multicellular lineages.

La bioremédiation est une réelle alternative aux techniques invasives de réhabilitation des sols pollués par des hydrocarbures. Cependant, la mise en place et l'optimisation de tels procédés nécessitent une meilleure connaissance des communautés microbiennes impliquées dans la biodégradation de ces polluants. Ainsi, nous avons étudié la structure et la dynamique des communautés bactériennes au cours d'un procédé de biostimulation d'un sol pollué aux hydrocarbures aliphatiques. Outre la caractérisation d' un core set bactérien présent tout au long du procédé, cette étude nous a permis d'identifier des phylotypes potentiellement impliqués dans la biodégradation de ces polluants. Enfin nous nous sommes attachés à mettre au point des outils moléculaires à haut débit, afin d'étudier plus globalement ces communautés environnementales, et ce par le développement d'un logiciel de sélection de sondes sensibles, spécifiques et exploratoires pour biopuces phylogénétiques (PhylArray)

Apusozoa (Protozoa) is a phylum of heterotrophic gliding zooflagellates of unknown taxonomic affiliation, commonly observed in environmental samples. Almost nothing was previously known about the diversity and ecology of apusozoan species though, as bacterivores, they are probably important functional constituents within microbial assemblages. We explored apusozoan morphological and genetic diversity, ecology, and related methodological questions. By culturing environmental material from a range of habitats, we isolated and maintained monocultures of both previously described apusozoan orders, Apusomonadida (apusomonads) and Planomonadida (planomonads). For planomonads, we present a revised taxonomy based on morphology, ultrastructure, and 18S rDNA genetic differences. We describe nine new species and new genera Nutomonas and Fabomonas, and demonstrate ITS2 rDNA secondary structure analysis for species delineation. During our culturing effort, we also isolated two genotypes of a previously unknown flagellate group, shown here to belong to a novel third apusozoan order, Mantamonadida. We designed molecular probes specific to all three orders and applied them to environmental DNA, detecting novel 18S and ITS1 rDNA lineages in a range of habitats. We mined publically available metagenomic and metatranscriptomic sequence databases using 18S rDNA of described species as seeds, identifying hundreds of sequences with affinities to all three orders. Phylogenies featuring newly retrieved lineages with previously described species suggest that direct sequencing of transcriptomic material is more effective than amplification-dependent methods at detecting rare cells in mixed microbial assemblages. Finally, to test potential future applications of our newly isolated strains, we ran microcosm experiments examining the effect of protozoan (Cercozoa) grazing on the structure of bacterial assemblages, demonstrating that closely related and morphologically similar species can have different impacts on their prey base. Taken together, by combining traditional culturing and modern molecular methods, this thesis drastically improves our understanding of apusozoan diversity and sets the scene for future work using next-generation sequencing and ecologically driven functional experiments.

This thesis investigates the diversity of two silica-scaled protist groups, Paraphysomonadida and Thaumatomonadida by light and electron microscopical observations and sequencing (rDNA) on novel clonal cultures. Despite these groups of protist dominating pelagic, littoral as well as inland freshwater and soil habitats, they are taxonomically poorly understood to the extent that any progress in ecological theory is hampered. Now that environmental DNA sequencing is being carried out faster than we can characterise protists from culture it is important that we understand how molecular and physical diversity match up, especially because so many protists are morphospecies. Nearly one hundred isolates were cultured on which both morphological and molecular data was carried out in parallel to reveal around 50 new species of protist from eight different genera: two heterokont genera, Paraphysomonas and Incisomonas n. gen., and six cercozoan genera, Thaumatomonas, Allas, Reckertia, Thaumatospina n. gen., Cowlomonas n. gen., and Scutellomonas n. gen. These data make major contributions to taxonomy and understanding aspects of protist diversity where previously morphological diversity was heavily biased towards over- generalized morphotypes. This thesis quickly showed that gross lumping of morphospecies was true of Paraphysomonas, for which many of the isolates cultured herein might have been regarded as one species (not more than 20). The many cultured isolates exhibited varied cell and scale morphology, and by sequencing (rDNA), it was possible to see the evolution of scale morphology map on to trees. This marriage of molecular and morphological data made it possible to view distinct groups of species that shared scale detail that might have otherwise been overlooked had either method been used alone. This research has shed significant light on how scale morphology can be used as reliable taxonomic marker for protists, the insights of which can be applied to make taxonomic improvements to other silica-scaled protist groups.

<p>Докторска дисертација представља таксономску студију тестатних амеба Источне&nbsp; Херцеговине&nbsp; базирану&nbsp; искључиво&nbsp; на&nbsp; резултатима&nbsp; сопствених истраживања с обзиром да на овом подручју тестатне амебе до сада нису проучаване,&nbsp; те&nbsp; не&nbsp; постоје&nbsp; историјске&nbsp; музејске&nbsp; колекције.&nbsp; На&nbsp; подручју Источне Херцеговине регистровано је 40 врста тестатних амеба које су сврстане у 10 фамилија и један род без јасног места у класификационом систему.&nbsp; Сви&nbsp; регистровани&nbsp; таксони&nbsp; тестатних&nbsp; амеба&nbsp; су&nbsp; нови&nbsp; за&nbsp; фауну Босне и Херцеговине. Укупно је анализирано 24.549 јединки, од чега су 23.242&nbsp; јединке&nbsp; припадале&nbsp; групи&nbsp; тестатних&nbsp; амеба&nbsp; са&nbsp; лобоподијама (супергрупа&nbsp; Amoebozoa),&nbsp; а&nbsp; 1307&nbsp; јединки&nbsp; је&nbsp; припадало&nbsp; групи&nbsp; тестатних амеба са филоподијама (супергрупа Cercozoa). Најзначајнији резултат ове дисертације&nbsp; је&nbsp; опис&nbsp; пет&nbsp; нових&nbsp; врста&nbsp; за&nbsp; науку&nbsp; које&nbsp; припадају&nbsp; родовима<br />Centropyxis, Heleopera и Nebela. Морфотип означен као C.&nbsp; cf.&nbsp; aerophila&nbsp; се од врсте&nbsp; C. aerophila&nbsp; разликује по томе што се на крају љуштурице не налази пар крупних честица кварца,а и љуштурица је нешто дужа (46‒81 &mu;m код врсте C. aerophila према 67‒ 88 &mu;m код врсте C. cf. aerophila). Морфотип означен као C. cf. platystoma значајно се пре свега морфолошки разликује од врсте&nbsp; C. platystoma, те је закључено да се ради о неописаној врсти.У оквиру рода Heleopera описан је нови морфотип сличан врсти H. rosea који&nbsp; представља&nbsp; нову&nbsp; врсту&nbsp; за&nbsp; науку.&nbsp; Морфометријске&nbsp; разлике&nbsp; су релативне, тј. нису строго дискриминаторне, те се морају комбиновати са морфолошким&nbsp; разликама&nbsp; које&nbsp; су&nbsp; такође&nbsp; тешко&nbsp; yочљиве.&nbsp; Наиме,&nbsp; поред разлике&nbsp; у&nbsp; боји&nbsp; љуштурице,&nbsp; најбољи&nbsp; дискриминаторни&nbsp; морфолошки карактер&nbsp; је&nbsp; општи&nbsp; облик&nbsp; љуштурице.&nbsp; Љуштурице&nbsp; врсте&nbsp; H.&nbsp; rosea&nbsp; су робусног&nbsp; облика,&nbsp; док&nbsp; су&nbsp; љуштурице&nbsp; врсте&nbsp; Heleopera&nbsp; cf.&nbsp; rosea&nbsp; знатно елегантније&nbsp; ‒&nbsp; уже&nbsp; су&nbsp; и&nbsp; имају&nbsp; облије&nbsp; ивице.&nbsp; Највеће&nbsp; морфометријске разлике&nbsp; у&nbsp; индексним&nbsp; карактерима&nbsp; су&nbsp; забележене&nbsp; за&nbsp; однос&nbsp; ширине&nbsp; и дужине љуштурице и однос ширине апертуре и ширине љуштурице.Морфотип&nbsp; Nebela&nbsp; cf.&nbsp; collaris&nbsp; се од&nbsp; врсте&nbsp; N. collaris&nbsp; јасно разликује&nbsp; пре свега&nbsp; морфолошки&nbsp; и&nbsp; еколошки,&nbsp; а&nbsp; морфометријски&nbsp; веома&nbsp; мало.&nbsp; Наиме, најважнија морфолошка одлика која морфотип&nbsp; N.&nbsp; cf.&nbsp; collaris&nbsp; раздваја од врсте&nbsp; N.&nbsp; collaris&nbsp; су&nbsp; таласасте&nbsp; ивице&nbsp; љуштурице,&nbsp; а&nbsp; еколошка&nbsp; разлика&nbsp; се јавља&nbsp; у&nbsp; смислу&nbsp; да&nbsp; врста&nbsp; N.&nbsp; collaris&nbsp; насељава&nbsp; зелене&nbsp; маховине&nbsp; док морфотип N. cf. collaris&nbsp; насељава сфагнумске маховине. Морфотип N. cf. tincta&nbsp; var. major&nbsp; се од морфотипа N.&nbsp; cf. collaris&nbsp; разликује пре свега по јасно израженом сужењу у делу близу апертуре, тј. израженом врату. Такође, морфотип N. cf. tincta var. major никада нема таласасте ивице љуштурице,док&nbsp; се&nbsp; код&nbsp; јединки&nbsp; морфотипа&nbsp; N.&nbsp; cf.&nbsp; collaris&nbsp; ова&nbsp; карактеристика&nbsp; често јасно уочава.</p> / <p>Doktorska disertacija predstavlja taksonomsku studiju testatnih ameba Istočne&nbsp; Hercegovine&nbsp; baziranu&nbsp; isključivo&nbsp; na&nbsp; rezultatima&nbsp; sopstvenih istraživanja s obzirom da na ovom području testatne amebe do sada nisu proučavane,&nbsp; te&nbsp; ne&nbsp; postoje&nbsp; istorijske&nbsp; muzejske&nbsp; kolekcije.&nbsp; Na&nbsp; području Istočne Hercegovine registrovano je 40 vrsta testatnih ameba koje su svrstane u 10 familija i jedan rod bez jasnog mesta u klasifikacionom sistemu.&nbsp; Svi&nbsp; registrovani&nbsp; taksoni&nbsp; testatnih&nbsp; ameba&nbsp; su&nbsp; novi&nbsp; za&nbsp; faunu Bosne i Hercegovine. Ukupno je analizirano 24.549 jedinki, od čega su 23.242&nbsp; jedinke&nbsp; pripadale&nbsp; grupi&nbsp; testatnih&nbsp; ameba&nbsp; sa&nbsp; lobopodijama (supergrupa&nbsp; Amoebozoa),&nbsp; a&nbsp; 1307&nbsp; jedinki&nbsp; je&nbsp; pripadalo&nbsp; grupi&nbsp; testatnih ameba sa filopodijama (supergrupa Cercozoa). Najznačajniji rezultat ove disertacije&nbsp; je&nbsp; opis&nbsp; pet&nbsp; novih&nbsp; vrsta&nbsp; za&nbsp; nauku&nbsp; koje&nbsp; pripadaju&nbsp; rodovima<br />Centropyxis, Heleopera i Nebela. Morfotip označen kao C.&nbsp; cf.&nbsp; aerophila&nbsp; se od vrste&nbsp; C. aerophila&nbsp; razlikuje po tome što se na kraju ljušturice ne nalazi par krupnih čestica kvarca,a i ljušturica je nešto duža (46‒81 &mu;m kod vrste C. aerophila prema 67‒ 88 &mu;m kod vrste C. cf. aerophila). Morfotip označen kao C. cf. platystoma značajno se pre svega morfološki razlikuje od vrste&nbsp; C. platystoma, te je zaključeno da se radi o neopisanoj vrsti.U okviru roda Heleopera opisan je novi morfotip sličan vrsti H. rosea koji&nbsp; predstavlja&nbsp; novu&nbsp; vrstu&nbsp; za&nbsp; nauku.&nbsp; Morfometrijske&nbsp; razlike&nbsp; su relativne, tj. nisu strogo diskriminatorne, te se moraju kombinovati sa morfološkim&nbsp; razlikama&nbsp; koje&nbsp; su&nbsp; takođe&nbsp; teško&nbsp; yočljive.&nbsp; Naime,&nbsp; pored razlike&nbsp; u&nbsp; boji&nbsp; ljušturice,&nbsp; najbolji&nbsp; diskriminatorni&nbsp; morfološki karakter&nbsp; je&nbsp; opšti&nbsp; oblik&nbsp; ljušturice.&nbsp; LJušturice&nbsp; vrste&nbsp; H.&nbsp; rosea&nbsp; su robusnog&nbsp; oblika,&nbsp; dok&nbsp; su&nbsp; ljušturice&nbsp; vrste&nbsp; Heleopera&nbsp; cf.&nbsp; rosea&nbsp; znatno elegantnije&nbsp; ‒&nbsp; uže&nbsp; su&nbsp; i&nbsp; imaju&nbsp; oblije&nbsp; ivice.&nbsp; Najveće&nbsp; morfometrijske razlike&nbsp; u&nbsp; indeksnim&nbsp; karakterima&nbsp; su&nbsp; zabeležene&nbsp; za&nbsp; odnos&nbsp; širine&nbsp; i dužine ljušturice i odnos širine aperture i širine ljušturice.Morfotip&nbsp; Nebela&nbsp; cf.&nbsp; collaris&nbsp; se od&nbsp; vrste&nbsp; N. collaris&nbsp; jasno razlikuje&nbsp; pre svega&nbsp; morfološki&nbsp; i&nbsp; ekološki,&nbsp; a&nbsp; morfometrijski&nbsp; veoma&nbsp; malo.&nbsp; Naime, najvažnija morfološka odlika koja morfotip&nbsp; N.&nbsp; cf.&nbsp; collaris&nbsp; razdvaja od vrste&nbsp; N.&nbsp; collaris&nbsp; su&nbsp; talasaste&nbsp; ivice&nbsp; ljušturice,&nbsp; a&nbsp; ekološka&nbsp; razlika&nbsp; se javlja&nbsp; u&nbsp; smislu&nbsp; da&nbsp; vrsta&nbsp; N.&nbsp; collaris&nbsp; naseljava&nbsp; zelene&nbsp; mahovine&nbsp; dok morfotip N. cf. collaris&nbsp; naseljava sfagnumske mahovine. Morfotip N. cf. tincta&nbsp; var. major&nbsp; se od morfotipa N.&nbsp; cf. collaris&nbsp; razlikuje pre svega po jasno izraženom suženju u delu blizu aperture, tj. izraženom vratu. Takođe, morfotip N. cf. tincta var. major nikada nema talasaste ivice ljušturice,dok&nbsp; se&nbsp; kod&nbsp; jedinki&nbsp; morfotipa&nbsp; N.&nbsp; cf.&nbsp; collaris&nbsp; ova&nbsp; karakteristika&nbsp; često jasno uočava.</p> / <p>The&nbsp; PhD&nbsp; thesis&nbsp; is&nbsp; a&nbsp; taxonomic&nbsp; study&nbsp; of&nbsp; testate&nbsp; amoebae&nbsp; from&nbsp; East Herzegovina based exclusively on the results of our own research, given that testate amoebae have not been studied in this region so far, and there are no historical museum collections. In the region&nbsp; of East Herzegovina,40 testate amoeba species have been registered, which are classified into 10&nbsp; families&nbsp; and&nbsp; one&nbsp; genus&nbsp; without&nbsp; a&nbsp; clear&nbsp; place&nbsp; in&nbsp; the&nbsp; classification system. All registered testate amoeba taxa are new to the fauna of Bosnia and Herzegovina.&nbsp; A total of 24,549 individuals belonged to the group of testate&nbsp; amoebae&nbsp; with&nbsp; lobopodia&nbsp; (supergroup&nbsp; Amoebozoa),&nbsp; and&nbsp; 1307 individuals&nbsp; belonged&nbsp; to&nbsp; the&nbsp; group&nbsp; of&nbsp; testate&nbsp; amoebae&nbsp; with&nbsp; filopodia (supergroup Cercozoa). The most significant results of this PhD thesis are the descriptions of five new species for science belonging to the genera Centropyxis, Heleopera, and Nebela. The morphotype&nbsp; Centropyxis&nbsp; cf.&nbsp; aerophila&nbsp; differs from&nbsp; C. aerophila&nbsp; in that&nbsp; there&nbsp; is&nbsp; no&nbsp; large&nbsp; quartz&nbsp; particles&nbsp; at&nbsp; the&nbsp; shell&nbsp; end,&nbsp; and&nbsp; the&nbsp; shell&nbsp;&nbsp; is slightly&nbsp; longer&nbsp; (46‒81&nbsp; &mu;m&nbsp; in&nbsp; C.&nbsp; aerophila&nbsp; versus&nbsp; 67‒88&nbsp; &mu;m&nbsp; in&nbsp; C.&nbsp; cf. aerophila).&nbsp; The&nbsp; morphotype&nbsp; C.&nbsp; cf.&nbsp; platystoma&nbsp; differs&nbsp; significantly morphologically&nbsp; from&nbsp; C.&nbsp; platystoma,&nbsp; so&nbsp; it&nbsp; was&nbsp; concluded&nbsp; that&nbsp; it&nbsp; is&nbsp; an undescribed species. Within the genus&nbsp; Heleopera&nbsp; a new &nbsp; morphotype similar to&nbsp; H. rosea&nbsp; has been&nbsp; described,&nbsp; representing&nbsp; a&nbsp; new&nbsp; species&nbsp; for&nbsp; science.&nbsp; Morphometric differences are relative, i.e. they are not strictly discriminatory, and must be combined with morphological differences that are difficult to detect. Namely, in addition to the difference in the color of the shell, the best discriminatory morphological character is the general shell shape. Shells of&nbsp; H. rosea&nbsp; are red and robust in shape, while shells of&nbsp; H.&nbsp; cf. rosea&nbsp; are volet and much more&nbsp; elegant ‒&nbsp; they are narrower and have rounded edges. The&nbsp; largest&nbsp; morphometric&nbsp; differences&nbsp; in&nbsp; the&nbsp; index&nbsp; characters&nbsp; were observed for shell width/shell length ratio and aperture width/shell width ratio. The&nbsp; morphotype&nbsp; Nebela&nbsp; cf.&nbsp; collaris&nbsp; clearly&nbsp; differs&nbsp; from&nbsp; N.&nbsp; collaris primarily&nbsp; morphologically&nbsp; and&nbsp; ecologically,&nbsp; but&nbsp; morphometrically&nbsp; very little.&nbsp; Namely,&nbsp; the&nbsp; most&nbsp; important&nbsp; morphological&nbsp; character&nbsp; that&nbsp; N.&nbsp; cf. collaris separates from N. collaris are the wavy edges of the shell, and the&nbsp; ecological difference occurs in the sense that&nbsp; N. collaris&nbsp; inhabits green mosses while &nbsp; N. cf. collaris inhabits Sphagnum mosses. The morphotype N.&nbsp; cf.&nbsp; tincta&nbsp; var.&nbsp; major&nbsp; from&nbsp; the&nbsp; morphotype&nbsp; N.&nbsp; cf.&nbsp; collaris&nbsp; differs primarily by a clearly pronounced narrowing in the part near the aperture, i.e. pronounced neck. Also, the morphotype N. &nbsp; cf. tincta var. major never has a wavy edge of the shell, while in&nbsp; N.&nbsp; cf.&nbsp; collaris&nbsp; this feature is often clearly observed.</p>