Final Report Summary - DICTYTOL (Evolution of Form and Function on a Unique Eukaryotic Organism (Dictyostelia))
Project context and objectives
Dictyostelids are soil-inhabiting amoebae that build multi-cellular fruiting bodies to aid in their dispersal. They have been studied for over 200 years, and include the widely used experimental model, Dictyostelium discoideum. This project aims to characterise the biodiversity and molecular and morphological evolution of the Dictyostelia, and lay the groundwork for broad studies of their ecology and role in the soil. The programme consists of four major lines of work:
1. The Dicty tree of life (DictyTree). The initial dictyostelid phylogeny consisted of 75 species. I aimed to expand the tree to include ~50 new taxa, many of which appeared to be highly distinct and capable of filling critical gaps in dictyostelid evolution;
2. Biodiversity of Dictyostelia (DictyDiv). The diversity of Dictyostelia had previously only been assessed by traditional laboratory culture methods. I aimed to directly assess dictyostelid diversity for the first time by culture-independent sampling (ciPCR), and compare these results with traditional sampling methods;
3. The root of Dictyostelia (DictyRoot). Here I aimed to develop a multi-gene dataset to pinpoint the root of the dictyostelid tree and thereby identify its earliest and most distinct branches;
4. Global trends in dictyostelids (DictyTrends). A large body of data on dictyostelid ecology and morphology was collated and analysed in order to identify major evolutionary trends across the group.
Work performed
During the first year of the Marie Curie fellowship I focused on DictyTree and DictyDiv. Work on DictyTree included sequencing of SSU rDNA from all new isolates, describing all resulting new species based on both morphological and molecular characters, and adding the new species to the molecular phylogeny. DictyDiv work began in the second half of year 1. This involved developing dicty-specific primers and protocols for total soil DNA extraction and analysis (ciPCR). During the summer I collected soil samples from Norway to compare with samples I had previously collected in Sweden. During this time, I also worked part-time on DictyTrends, collating and analysing ecological and morphological observations together with Dr Gonzalez-Voyer (CSIC, ES) and Prof. Schaap (Scotland, UK). During the second year I focused on DictyDiv and DictyTrends, while an MSc bioinformatics student worked on DictyRoot. I had originally planned to develop a three-protein dataset for this objective. However the recent availability of complete genome sequences from all major groups of Dictyostelia allowed for a much more ambitious computer-intensive approach. DictyTrends consisted of statistical and comparative analyses of ecological and morphological datasets from dictyostelid species in order to infer evolutionary trends within the group. Altogether, the project yielded ten publications and five presentations at scientific meetings in five countries.
Main results
During these two years I have developed a fully resolved phylogeny for the Dictyostelids Social Amoeba and expanded the number of species to include 50 recently isolated new isolates from around the world. This changed the number of recognised major Dictyostelia groups from four to eight. The new species also expands the known morphological diversity of the major groups, violating nearly all previously suggested deep morphological patterns. This indicates that dictyostelid morphology is even more plastic and rapidly evolving than previously thought. Nonetheless, through careful analysis, I was also able to identify some deeper patterns of morphological evolution within major groups. I have contributed to the study of dictyostelid diversity and taxonomy by describing many new species from different localities around the world, including Europe, North and South America and Africa.
The second main result from the project has been the development of molecular environmental sampling techniques for the study of the dictyostelids. I designed two sets of primers and amplification protocols, which allowed me to achieve ciPCR sampling of dictyostelids for the first time. These primers have been tested on a broad set of samples and initial analyses of the SSUrDNA sequences from environmental libraries show new deep branches in all major divisions of dictyostelids, and some sequences that appear to represent new major divisions. This confirms that a substantial proportion of dictyostelid diversity remains to be discovered, potentially including major morphotypes and life histories. This also lays the necessary groundwork for future comprehensive and quantitative studies of dictyostelid ecology and the role of these ubiquitous organisms in the soil. In my PhD I conducted an extensive and detailed ecological survey in southwest Europe (the Iberian Peninsula). I applied statistical modelling to this dataset in order to estimate some of the main environmental factors influencing the distribution and diversity of dictyostelids in temperate climates. The results suggested that both water availability and the richness of plant species could facilitate dictyostelid diversity indirectly, via their prey - bacteria. The recently developed ciPCR approaches (DictyDiv) will allow us to examine these questions on a broad scale for the first time.
Through a collaboration with Alejandro Gonzalez Voyer (Doñana, CSIC, ES) and Pauline Schaap (University of Dundee, UK), we applied, for the first time, phylogenetic comparative methods to a detailed morphological dataset for 99 species of the group in order to understand major trends in dictyostelid evolution. Results show that the last common ancestor (LCA) of Dictyostelia formed small fruiting structures. It secreted cAMP to coordinate fruiting body morphogenesis, and another compound to mediate aggregation. Large structures, phototropism and light-orientated migration of sorogens co-evolved as evolutionary novelties within most groups. Overall, dictyostelids showed considerable plasticity in the size and shape of their multi-cellular structures, both within and between species.
Dictyostelids are soil-inhabiting amoebae that build multi-cellular fruiting bodies to aid in their dispersal. They have been studied for over 200 years, and include the widely used experimental model, Dictyostelium discoideum. This project aims to characterise the biodiversity and molecular and morphological evolution of the Dictyostelia, and lay the groundwork for broad studies of their ecology and role in the soil. The programme consists of four major lines of work:
1. The Dicty tree of life (DictyTree). The initial dictyostelid phylogeny consisted of 75 species. I aimed to expand the tree to include ~50 new taxa, many of which appeared to be highly distinct and capable of filling critical gaps in dictyostelid evolution;
2. Biodiversity of Dictyostelia (DictyDiv). The diversity of Dictyostelia had previously only been assessed by traditional laboratory culture methods. I aimed to directly assess dictyostelid diversity for the first time by culture-independent sampling (ciPCR), and compare these results with traditional sampling methods;
3. The root of Dictyostelia (DictyRoot). Here I aimed to develop a multi-gene dataset to pinpoint the root of the dictyostelid tree and thereby identify its earliest and most distinct branches;
4. Global trends in dictyostelids (DictyTrends). A large body of data on dictyostelid ecology and morphology was collated and analysed in order to identify major evolutionary trends across the group.
Work performed
During the first year of the Marie Curie fellowship I focused on DictyTree and DictyDiv. Work on DictyTree included sequencing of SSU rDNA from all new isolates, describing all resulting new species based on both morphological and molecular characters, and adding the new species to the molecular phylogeny. DictyDiv work began in the second half of year 1. This involved developing dicty-specific primers and protocols for total soil DNA extraction and analysis (ciPCR). During the summer I collected soil samples from Norway to compare with samples I had previously collected in Sweden. During this time, I also worked part-time on DictyTrends, collating and analysing ecological and morphological observations together with Dr Gonzalez-Voyer (CSIC, ES) and Prof. Schaap (Scotland, UK). During the second year I focused on DictyDiv and DictyTrends, while an MSc bioinformatics student worked on DictyRoot. I had originally planned to develop a three-protein dataset for this objective. However the recent availability of complete genome sequences from all major groups of Dictyostelia allowed for a much more ambitious computer-intensive approach. DictyTrends consisted of statistical and comparative analyses of ecological and morphological datasets from dictyostelid species in order to infer evolutionary trends within the group. Altogether, the project yielded ten publications and five presentations at scientific meetings in five countries.
Main results
During these two years I have developed a fully resolved phylogeny for the Dictyostelids Social Amoeba and expanded the number of species to include 50 recently isolated new isolates from around the world. This changed the number of recognised major Dictyostelia groups from four to eight. The new species also expands the known morphological diversity of the major groups, violating nearly all previously suggested deep morphological patterns. This indicates that dictyostelid morphology is even more plastic and rapidly evolving than previously thought. Nonetheless, through careful analysis, I was also able to identify some deeper patterns of morphological evolution within major groups. I have contributed to the study of dictyostelid diversity and taxonomy by describing many new species from different localities around the world, including Europe, North and South America and Africa.
The second main result from the project has been the development of molecular environmental sampling techniques for the study of the dictyostelids. I designed two sets of primers and amplification protocols, which allowed me to achieve ciPCR sampling of dictyostelids for the first time. These primers have been tested on a broad set of samples and initial analyses of the SSUrDNA sequences from environmental libraries show new deep branches in all major divisions of dictyostelids, and some sequences that appear to represent new major divisions. This confirms that a substantial proportion of dictyostelid diversity remains to be discovered, potentially including major morphotypes and life histories. This also lays the necessary groundwork for future comprehensive and quantitative studies of dictyostelid ecology and the role of these ubiquitous organisms in the soil. In my PhD I conducted an extensive and detailed ecological survey in southwest Europe (the Iberian Peninsula). I applied statistical modelling to this dataset in order to estimate some of the main environmental factors influencing the distribution and diversity of dictyostelids in temperate climates. The results suggested that both water availability and the richness of plant species could facilitate dictyostelid diversity indirectly, via their prey - bacteria. The recently developed ciPCR approaches (DictyDiv) will allow us to examine these questions on a broad scale for the first time.
Through a collaboration with Alejandro Gonzalez Voyer (Doñana, CSIC, ES) and Pauline Schaap (University of Dundee, UK), we applied, for the first time, phylogenetic comparative methods to a detailed morphological dataset for 99 species of the group in order to understand major trends in dictyostelid evolution. Results show that the last common ancestor (LCA) of Dictyostelia formed small fruiting structures. It secreted cAMP to coordinate fruiting body morphogenesis, and another compound to mediate aggregation. Large structures, phototropism and light-orientated migration of sorogens co-evolved as evolutionary novelties within most groups. Overall, dictyostelids showed considerable plasticity in the size and shape of their multi-cellular structures, both within and between species.