Master's thesis project
Chasing the most elusive soil amoebae:
environmental sampling of Dictyostelia
General interest
Dictyostelia are a key model system for understanding the genetic basis of social behavior as
well as multicellular development and cell-cell signaling (Williams et al., 2005). It is
fascinating to see that these "social amoebae" can display behaviours such as cooperation and
cheating (Flowers et al., 2010) and even practice "primitive agriculture"(Brock et al., 2011).
Sociability in amoebae breeds sociability in researchers, who are organized in a highly
cooperative network (http://www.dictybase.org/) where you can obtain for free cultures of
any species!
Dictyostelia are easy to isolate and have been found in many types of soil: grasslands (Rollins
et al., 2010), prairies (Sutherland & Raper 1978), forest (Cavender et al., 1995), tundra
(Cavender, 1978; Stephenson et al. 1991), tropical agricultural soils (Cavender et al. 1993),
tropical forests (Stephenson & Landolt 1998) mediterranean forests (Romeralo & Lado 2006),
et cetera; they seem to be widespread and abundant. They are nonetheless absent from
protistan inventories, because their amoebae lack of specific characters - they have to be
allowed to form fruiting bodies to be identified. Therefore, our understanding of their
distribution is still fragmentary.
On the other hand, they are strikingly absent from all soil inventories based on molecular
methods, that is, detecting DNAs or RNAs directly from the environment (ie environmental
sampling). The ~100 species benefit of a comprehensive phylogeny and of a reference
database of 169 18S sequences (Pawlowski et al., 2012), both essential perequisite for being
detected in environmental sampling studies. Hence, how come that Dictyostelia are nearly
never reported? Why are their sequences so elusive?
The master's project
We propose here a project to test possible explanations and in parallel conduct the first
environmental ePCR targeting Dictyostelia. Our assumption is that Dictyostelia, like their
sister-group Myxomycetes, escape molecular detection because of their ample genetic
variation; secondly, they may be more frequent in the litter or in the very upper part of the soil
and are therefore discarded when only the mineral soil is sampled.
You will:

develop and test specific primers for Dictyostelia targeting the V4 region of the 18S
ribosomal gene.

use soils samples from different locations and collected at different depths.

conduct a study on ~10 soil samples of different origins to investigate alpha and beta
diversity of Dictyostelia, in relation with environmental factors.
You will get extensive training in:

Basic molecular techniques: DNA extraction, PCR, cloning, sequencing.

Bioinformatics: primers design, alignments, sequences identification and clustering in
operational taxonomic units, maximum likelihood and Bayesian analyses, evaluating
phylogenetic trees; using GenBank and other databases facilities.

Statistics: multivariate statistics to better understand the distribution of Dictyostelia:
looking for the most significant environmental factors.

Learning the basics of scientific writing with the aim of publishing the results in a
scientific journal.

If desired, culturing and identifying Dictyostelia - just to be familiar with the group.
Expected outcome
This study will be the first one to specifically target by environmental sampling a very
important and most neglected group of soil amoebae. As such, it may be of interest for a
wider public, not only the scientist using Dictyostelia as model organims, but also to
protistologists, soil ecologists and microbiologists. It will contribute to the knowledge of the
distribution and diversity of Dictyostelia, allowing for further functional studies.
Something more about Dictyostelia: Life-cycle
The life cycle of the "social amoebae" includes free-living amoebae that can aggregate in
response to a chemical signal to form "slugs" of few mm that collectively migrate and
ultimately form fruiting bodies bearing spores. During the whole cycle each ameoba keeps its
individuality. In parallel there is a much lesser studied sexual cycle (Fig. 1).
Figure 1. The life cycle of Dictyostelium discoideum. Most of its life, this haploid social amoeba undergoes the
vegetative cycle, preying upon bacteria, and periodically dividing mitotically. When food is scarce, either the
sexual cycle or the social cycle begins. Under the social cycle, amoebae aggregate and form a motile slug, which
ultimately forms a fruiting body. Under the sexual cycle, amoebae aggregate and two cells of opposite mating
types fuse, and then begin consuming the other attracted cells. When cannibalism is complete, the giant diploid
cell or macrocyst eventually undergoes recombination and meiosis. doi:10.1371/journal.pgen.1001013.g001
Phylogeny and taxonomy
Traditionally, Dictyostelia have been divided, according to the fruiting body morphology, into
three genera: A. Dictyostelium, with unbranched or laterally branched fruiting bodies; B.
Polysphondylium, whose fruiting bodies consist of repetitive whorls of regularly spaced side
branches; and C. Acytostelium, which, unlike the other genera, forms acellular fruiting body
stalks. In total, ~100 species are recognized.
Figure 2. Fruiting bodies schematic outlines. A. Dictyostelium. B. Polysphondylium. C. Acytostelium.
Further comprehensive phylogenies have shown the polyphyly of the genera - except
Acytostelium - and the emergence of four groups (Romeralo et al., 2011; Schaap et al., 2006)
(Figure 3). The 34 Mb genome of Dictyostelium discoideum was the first to be sequenced
(Eichinger et al., 2005) now those of few more species are in completion (Romeralo et al.,
2012).
Figure 3. Phylogeny of Dictyostelia according to Schaap et al. 2006.
References
Brock, D.A., Douglas, T.E., Queller, D.C., and Strassmann, J.E. (2011) Primitive agriculture
in a social amoeba. Nature 469: 393-398.
Cavender, J., Cavender-Bares, J., and Hohl, H.R. (1995) Ecological distribution of cellular
slime molds in forest soils of Germany. Bot Helv 105: 199-219.
Eichinger, L., Pachebat, J., Glöckner, G., Rajandream, M.-A., Sucgang, R., Berriman, M. et
al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435: 43-57.
Flowers, J.M., Li, S.I., Stathos, A., Saxer, G., Ostrowski, E.A., Queller, D.C. et al. (2010)
Variation, sex, and social cooperation: molecular population genetics of the social amoeba
Dictyostelium discoideum. PLoS Genet 6: e1001013.
Pawlowski, J., Adl, S.M., Audic, S., Bass, D., Belbahri, L., Berney, C. et al. (2012) CBOL
Protist Working Group: Barcoding eukaryotic richness beyond the animal, plant and fungal
kingdoms. PLoS Biology 10: e1001419.
Rollins, A.W., Landolt, J.C., and Stephenson, S.L. (2010) Dictyostelid cellular slime molds
associated with grasslands of the central and western United States. Mycologia 102: 9961003.
Romeralo, M., Escalante, R., and Baldauf, S.L. (2012) Evolution and diversity of dictyostelid
social amoebae. Protist 163: 327-343.
Romeralo, M., Cavender, J., Landolt, J.C., Stephenson, S.L., and Baldauf, S.L. (2011) An
expanded phylogeny of social amoebas (Dictyostelia) shows increasing diversity and new
morphological patterns. BMC Evol Biol 11: 1-10.
Schaap, P., Winckler, T., Nelson, M., Alvarez-Curto, E., Elgie, B., Hagiwara, H. et al. (2006)
Molecular phylogeny and evolution of morphology in social amoebas. Science 314: 661-663.
Williams, J.G., Noegel, A.A., and Eichinger, L. (2005) Manifestations of multicellularity:
Dictyostelium reports in. Trends Genet 21: 392-398.