Project

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Genetic microdiversity and ecology of protists

Applicant Lara Enrique
Number 122042
Funding scheme Ambizione
Research institution Institut de Biologie Faculté des Sciences Université de Neuchâtel
Institution of higher education University of Neuchatel - NE
Main discipline Other disciplines of Environmental Sciences
Start/End 01.01.2009 - 31.12.2011
Approved amount 506'571.00
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All Disciplines (3)

Discipline
Other disciplines of Environmental Sciences
Environmental Research
Ecology

Keywords (9)

biogeography; diversity; bioindicator; cryptic species; protists; testate amoebae; biodiversity; biosystematics; molecular phylogeny

Lay Summary (English)

Lead
Lay summary
Protists (eukaryotes excluding plants, animals and fungi) represent a major element on the Earth's biodiversity. They play a key role in all ecosystems through their contribution to processes such as nutrient cycling or photosynthesis. However, our knowledge of their diversity and biology is very limited, which hinders our understanding of the full diversity of live on Earth and the respective roles of different groups of organisms. In this project, we aim to get an accurate picture of the diversity of a model group of protists, the euglyphid testate amoebae, and to understand the evolutionary patterns and phylogenetic relationships among lineages.

Recent research on unicellular eukaryotes has considerably changed our understanding of the diversity, evolution and biology of these microorganisms, but many open questions remain. One of these, which we address in this project, is the long-lasting but still unresolved debate referred to here as the "cosmopolitanism theory": Based on the fact that free-living protists build enormous populations in nature, and also on their high dispersal capacities, it has been argued that most species are cosmopolitan, and can be found wherever suitable conditions for the growth can be met. A corollary of this postulate is that appearance of new species must occur in sympatry (i.e. within the same geographic region), and is therefore a rare event. Accordingly, a relatively small number of species should be found across all ecosystems on Earth. However, environmental surveys of protist genetic diversity are revealing year after year a considerable and mostly unknown diversity. The great amount of genetic data that are accumulating in databases raises the question of the exact roles of these mostly unknown organisms in ecosystems. Thus, there is a conflict between the low diversity of free-living protists that the cosmopolitanism theory predicts and the high taxonomic and supposed related functional diversity observed from environmental DNA surveys.

Studying the huge diversity of eukaryotic microorganisms in a single project is not possible. We therefore decided to focus our investigation on a group of model organisms, the euglyphid testate amoebae. We will first determine the environmental genetic diversity within this group. Furthermore, we will evaluate, for a single species, Assulina seminulum, the correlation between geographical distance and genetic diversity. A third part of the project will be to assess the relative influences of environmental conditions and genetic diversity on the morphological diversity of species.

Euglyphid testate amoebae are sensitive to environmental gradients and are therefore useful bioindicators for environmental change. Fossil remains of testate amoebae preserved in peat and lake sediments are increasingly used to reconstruct past climates and to monitor the effects of global change on ecosystems. The use of testate amoebae in ecology and palaeoecology requires a sound taxonomy, but this is clearly missing and this project will contribute towards this goal. To a further extent, euglyphid testate amoebae are used as model organisms to understand the mechanisms of lineage differentiation in protists. Findings in this area can be extended to other groups; possible outcomes are not only academic, as some protists have a tremendous impact on human health as parasites (ex: Plasmodium, the agent of malaria) or agricultural pests (Phytophtora infestans, the agent of potato blight, responsible of 19th century famine in Ireland).
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Amphitremida (Poche, 1913) Is a New Major, Ubiquitous Labyrinthulomycete Clade
Gomaa F., Mitchell E.A.D., Lara E. (2013), Amphitremida (Poche, 1913) Is a New Major, Ubiquitous Labyrinthulomycete Clade, in plos one, 8(1), e53046-..
Time to regulate microbial eukaryote nomenclature.
Lahr DJG, Lara E, Mitchell EAD (2012), Time to regulate microbial eukaryote nomenclature., in Biological Journal of the Linnean Society, 107, 469-476.
Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae).
Kosakyan A., Gomaa F., Mitchell E. A. D., Heger T. J., Lara E. (2012), Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae)., in European Journal of Protistology, 49, 222-237.
COI gene and ecological data suggest size-dependent high dispersal and low intra-specific diversity in free-living terrestrial protists (Euglyphida: Assulina)
Lara E., Heger T. J., Scheihing R., Mitchell E. A. D. (2011), COI gene and ecological data suggest size-dependent high dispersal and low intra-specific diversity in free-living terrestrial protists (Euglyphida: Assulina), in Journal of Biogeography, 38, 640-650.
Comparing Potential COI and SSU rDNA Barcodes for Assessing the Diversity and Phylogenetic Relationships of Cyphoderiid Testate Amoebae (Rhizaria: Euglyphida)
Heger T. J., Pawlowski J., Lara E., Leander B. S., Todorov M., Golemansky V., Mitchell E. A. D. (2011), Comparing Potential COI and SSU rDNA Barcodes for Assessing the Diversity and Phylogenetic Relationships of Cyphoderiid Testate Amoebae (Rhizaria: Euglyphida), in Protist, 162, 131-141.
Highly Diverse and Seasonally Dynamic Protist Community in a Pristine Peat Bog
Lara E., Mitchell E. A. D., Moreira D., Garcia P. L. (2011), Highly Diverse and Seasonally Dynamic Protist Community in a Pristine Peat Bog, in Protist, 162, 14-32.
SSU rRNA reveals major trends in oomycete evolution
Lara E., Belbahri L. (2011), SSU rRNA reveals major trends in oomycete evolution, in Fungal Diversity, 49, 93-100.
The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms
Lahr D. J. G., Parfrey L. W., Mitchell E. A. D., Katz L. A., Lara E. (2011), The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms, in Proceedings of the Royal Society B-Biological Sciences, 278, 2081-2090.
Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil
Jousset A., Lara E., Nikolausz M., Harms H., Chatzinotas A. (2010), Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil, in Science of the Total Environment, 408, 1221-1225.
Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent
Heger T. J., Mitchell E. A. D., Todorov M., Golemansky V., Lara E., Leander B. S., Pawlowski J. (2010), Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent, in Molecular Phylogenetics and Evolution, 55, 113-122.
A molecular perspective on ciliates as soil bioindicators
Lara Enrique, Acosta-Mercado Dimaris, A molecular perspective on ciliates as soil bioindicators, in European Journal of Soil Biology.
COI Barcoding of Nebelid Testate Amoebae (Arcellinida): Extensive Pseudocryptic Diversity and Redefinition of Family Nebelidae
Kosakyan A., Heger T. J., Leander B. S., Todorov M., Mitchell E. A. D., Lara E., COI Barcoding of Nebelid Testate Amoebae (Arcellinida): Extensive Pseudocryptic Diversity and Redefinition of Family Nebelidae, in Protist.
SSU rRNA Phylogeny of Arcellinida (Amoebozoa) Reveals that the Largest Arcellinid Genus, Difflugia Leclerc 1815, is not Monophyletic
Gomaa Fatma, Todorov Milcho, Heger Thierry J., Mitchell Edward A. D., Lara Enrique, SSU rRNA Phylogeny of Arcellinida (Amoebozoa) Reveals that the Largest Arcellinid Genus, Difflugia Leclerc 1815, is not Monophyletic, in Protist.

Collaboration

Group / person Country
Types of collaboration
RWTH Aachen Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Université de Genève Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
University of British Columbia Canada (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Bulgarian Academy of Sciences Bulgaria (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Universidad de Puerto Rico Puerto Rico (South America)
- Publication
University of Sao Paulo Brazil (South America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
CECS, Valdivia Chile (South America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
International Symposition on Testate Amoebae (ISTA-6) Talk given at a conference A molecular perspective on testate amoebae 15.10.2012 Xiamen, China Lara Enrique;
Barcoding Swiss Biodiversity meeting Talk given at a conference Soil eukaryotic diversity: A new world under our shoes 09.09.2011 Genève, Switzerland Roussel-Delif Ludovic; Lara Enrique;
PSA-ISOP Annual Meeting Talk given at a conference Euglyphid diversity : business as usual or terra incognita? 13.07.2011 Seattle, United States of America Lara Enrique; Roussel-Delif Ludovic;
Soil organisms as bioindicators: methods, applications, and current research priorities Talk given at a conference Cryptic species diversity and potential implications for bioindication: 1. Protists 17.06.2010 Université de Neuchâtel, Switzerland Lara Enrique; Roussel-Delif Ludovic;
Fifth International Symposium on Testate Amoebae Talk given at a conference Pseudocryptic speciation and long-range migration in the euglyphid testate amoeba genus Assulina 14.09.2009 Montbéliard, France Lara Enrique;
Workshop on Molecular Systematics of Amoebozoa and Rhizaria Talk given at a conference Environmental diversity of eukaryotes: what clone libraries can tell us 12.01.2009 Genève, Switzerland Lara Enrique;


Self-organised

Title Date Place
Workshop on protist taxonomy and morphological identification 25.10.2011 Neuchâtel, Switzerland
Workshop on Microbial Diversity 05.09.2011 Neuchâtel, Switzerland

Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Festival de la Salamandre Performances, exhibitions (e.g. for education institutions) 23.10.2010 Morges/VD, Switzerland Roussel-Delif Ludovic; Lara Enrique;
Salon du Livre, Genève Performances, exhibitions (e.g. for education institutions) 01.05.2010 Genève, Switzerland Lara Enrique; Roussel-Delif Ludovic;


Communication with the public

Communication Title Media Place Year
Media relations: radio, television les amibes ne sont pas chastes! RSR la 1ère-impatience Western Switzerland 2011
Media relations: print media, online media Les amibes s'envoient en l'air L'Express Western Switzerland 2011
New media (web, blogs, podcasts, news feeds etc.) Petite révolution dans l'histoire du sexe étudiants.ch Western Switzerland 2011

Associated projects

Number Title Start Funding scheme
139482 Genetic microdiversity and ecology of protists-follow up 01.01.2012 Ambizione
143960 Is everything everywhere? A metabarcoding approach to protist biogeography 01.02.2013 Project funding (Div. I-III)

Abstract

The study of the diversity and functional roles of free-living unicellular eukaryotes is an extremely dynamic field of research. Many important recent new finding have considerably changed our understanding of these still little known organisms. This project addresses a long-lasting but still unresolved debate referred to here as the “cosmopolitanism theory”: Based on the fact that free-living protists build enormous populations in nature, and also on their high dispersal capacities, it has been argued that most species are cosmopolitan, and can be found wherever suitable conditions for the growth can be met. A corollary of this postulate is that cladogenesis must occur in sympatry, and is therefore a rare event. Accordingly, a relatively small number of morphospecies should be found across all ecosystems on earth. Furthermore, most of the molecular diversity encountered should be the result of neutral mutations, which would not be reflected in functional diversity. However, environmental surveys of protist genetic diversity are revealing year after year a wealth of new clades at all levels of the eukaryotic tree of life. These new clades have regularly brought scientists to rethink the evolutionary relationships among groups or eukaryotes as attested by the changing number and names of eukaryotic supergroups. In addition, the increasing number of new sequences that are accumulating in databases raises the question of the exact roles of these mostly unknown organisms in the ecosystems. Thus, there is a conflict between the low diversity of free-living protests that would be predicted by the cosmopolitanism theory and the high taxonomic and supposed related functional diversity observed from environmental DNA surveys. In this project, I will use testate amoebae as model organisms. Testate amoebae are ideal models because they are very abundant and diverse (ca. 2-3000 described taxa), the shell they produce has taxonomic value and remains after the death of the organism, and they span the range of sizes that are considered to be critical for long-distance dispersal.I will test two hypotheses related to the cosmopolitanism theory and carry out a third exploratory study related to the same topic: H1) There is no correlation between genetic diversity and geographic distance. To test this hypothesis, I have chosen a well-defined testate amoeba morphospecies :Assulina seminulum. This species is frequent in acidic peat bogs, but very rare or absent in other habitats. The shell it produces is well-preserved in peat and this species is one of the many testate amoebae used in paleoecology to reconstruct past climates. As peat bogs are discontinuous in Central Europe as well as at a broader scale, the repartition of the populations is patchy. Several genetic markers will be amplified on single cells, and the spatial repartition of genotypes will permit to test whether geographic distance has an impact on genetic diversity. H2) There is no ecological and genetic cryptic diversity within a given morphospecies. Individual cells from a ubiquitous testate amoeba morphospecies (Trinema enchelys) will be isolated from different environments and will be grown into clonal cultures. The growth kinetics of each isolate will be determined as well as the genetic distances among strains. These experiments will show if there is a cryptic diversity of ecologically and genetically distinct forms within this morphospecies. 3) I will finally explore the possible presence of an unsuspected diversity within a given group of protists. Here, environmental sequences of euglyphids will be obtained in order to detect possible novel forms (e.g. naked taxa as observed in foraminifera (Pawlowski et al., 1999) or morphologically divergent groups) within this morphologically well-characterised group of protists. Because the study will target a specific group for which some sequences are available, I expect to obtain a good estimate of the total diversity within this group and within the studied samples. This diversity can then be compared to the diversity of morphotypes to assess how well the molecular diversity matches the morphological diversity. This project will contribute towards a better understanding of the evolution, diversity and roles of protists in ecosystems. Furthermore, this project improves our understanding of the phenomena of cladogenesis in protists. Finally, as testate amoebae are increasingly used as proxies for monitoring climate change, this project will contribute to improving the taxonomy which is a basic requirement for such studies.
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