Microbial diversity (bacteria, fungi, protists)

5 September 2011

A joint workshop with CUSO Doctoral Program in Microbial Sciences


  • Jan Pawlowski , University of Geneva, Switzerland - Topic: Amoboid protists, molecular diversity and phylogeny
  • Télesphore Sime-Ngando , LMGE, Université Blaise Pascal Clermont-Ferrand, France - Topic: Virus and microbial metabolisms in aquatic environment
  • Frederick W. Spiegel , University of Arkansas, USA - Topic: Systematics, ecology and biogeography of Protostelids and other mycetozoans
  • Micah Dunthorn , University of Kaiserslautern, Germany - Topic: Diversity, Ecology and Evolution of microeukaryotes in extreme marine environments
  • Pilar Junier , University of Neuchâtel
  • Enrique Lara , University of Neuchâtel


  • To understand the theoretical background and methods of microbial diversity research.
  • To get a multidisciplinary view on the advantages and limitations of morphological, culture-based and molecular approaches to the study of microbial diversity.
  • To get insights on new emerging research themes in microbial diversity.



Participants are encouraged to present their research. If you would like to present a poster, please contact Enrique Lara and send him the title of your poster.

Program (updated 30.08.2011)

  • Micah Dunthorn

    Diversity and Biogeography of Ciliates

    Ciliates are central in the study of the diversity and biogeography of microbial eukaryotes. Four aspects of ciliate biology that affect their usefulness as a model taxon will be reviewed. First, ciliates have a relatively high number of morphological characters that have been used by taxonomists to describe numerous species and establish an extensive classification. Ecologists have used these morphological taxa to both derive and test hypotheses of microbial biogeography. Second, due to the effects from the peculiar genetics of ciliate dimorphic nuclei, molecular systematists are limited in the number of genes available for testing morphological and ecological hypotheses, and estimates of abundances can be spuriously skewed. Third, the presence of sex in most ciliate lineages has led to extensive cryptic species that are often missed in morphological and ecological studies. The putative absence of sex in one lineage makes it difficult to know if their diversity and biography should be best compared to other ciliates and eukaryotes or to bacteria. Fourth, while ciliates are found in most environments, our understanding of which species are present depends on who is looking and which methods are being used.

  • Enrique Lara

    Personal web site.

    Barcoding of soil protists: the example of testate amoebae

    Estimating soil organisms’ diversity is the first step towards understanding and perhaps modeling the functioning of the “biological black box” as it is still considered by many researchers and environmental managers. Eukaryotic microbes play an important role in soil ecosystems as decomposers and predators. Because of the many difficulties encountered in their identification, and also because many of them cannot be isolated and cultured, a molecular bar-coding approach is an essential approach for the estimation of their diversity. Here, our focus will be centered on a group of conspicuous protists, the testate amoebae as an example of the challenges that are encountered when barcoding soil microbial eukaryotes.

  • Jan Pawlowski

    Personal web site

    Barcoding Protists: new - old challenges

    Recent explosion of high-throughput DNA sequencing technologies has prompted a lot of interest in metabarcoding of protists. Several environmental DNA surveys revealed huge hidden richness of protistan species. The use of new molecular tools promised more accurate assessment of protist diversity and better understanding of their geographic distribution. However, the analysis of metagenetic data also raises important questions concerning the definition of protistan species, the genetic variability and its relation to morphological features. Answering these questions has been haunting the community of protistologists since the dawn of molecular systematics. In my talk, I will present the current advances in DNA barcoding of different groups of protists and I will discuss some problems related to molecular identification of protistan species.

  • Télesphore Sime-Ngando

    Personal web site

    Disregarded microbial diversity in aquatic ecosystems: Viruses from unexplored environments and other unexplored microbial parasites

    Microbial parasites typically are characterized by their small size, short generation time, and high potential rates of reproduction, with simple life cycle occurring generally within a single host. They are diverse and ubiquitous in aquatic ecosystems, comprising viruses, prokaryotes and eukaryotes. This presentation focus on viruses from unexplored environments and on eukaryotic parasites of microbes, in a scientific context where technical and analytical advances are expected to continuously increase our knowledge of the reservoir of novel 'species', genes, and metabolic pathways, together with the related ecological potentials in aquatic ecosystems. The unexplored environments include the hypersaline tropical waters of Lake Retba (Senegal), and the 6,000 years old anoxic sediments of the unique meromictic Lake Pavin (French Massif Central) that preserves records of the geologic past exceptionally well. In these environments, we have recently unveiled viruses with particular morphotypes, typical of archaeal viruses. Concerning the unexplored eukaryotic parasites, they are known from recent surveys of the 18S ribosomal DNA and developments in sequencing technology and the use of SSU rRNA hypervariable tag sequencing, both of which have unveiled a large reservoir of unexpected diversity of small eukaryotes in both marine and freshwater ecosystems, suggesting significant ecological roles in ecosystem functions, and opening new perspectives in the context of aquatic food web dynamics. These microparasites are highly complex in terms of phylogenetic affiliation, belonging to diverse subgroups of the kingdoms Alveolata, Heterokonta, Fungi, and Rhizaria. Exciting future lines of environmental research on the unexplored viral and microbial parasites and their effects on the food web dynamics are thus expected in the decade to come.

  • Frederick W. Spiegel

    Personal web site

    Systematics and phylogeny of the slime molds, the sporocarpic and sorocarpic amoebae

    The fruiting amoeboid organisms known as slime molds have been treated as the intellectual “property” of mycologists for a very long time, and mycologists tend to focus on fruiting structures associated with sporulation, i.e., the “mold-like” aspects of slime molds. The amoebal aspects have been underemphasized. For various reasons, slime molds have been treated as if they were all closely related. However, recent phylogenetic work has shown that slime molds, s.l., are spread among several supergroups in the Eukaryote Tree of Life. There are two modes of slime mold development. Sporocarpic forms develop when a single amoeboid cell fruits. Examples of these are the myxogastrids and protosteloid amoebae, and this type of development is found only among Amoebozoa. Sorcarpic forms develop when many individual cells aggregate and produce a multicellular structure the matures into a fruiting structure. These have also been called the cellular slime molds. Sorocarpic amoebae are found among Amoebozoa, Opisthokonta, Excavata, and SAR. The general distinguishing characteristics of each major clade of slime molds will be covered, and the hypothesis will be presented that suggests that the last common ancestor of the supergroup Amoebozoa was a terrestrial sexual flagellate which was sporocarpic.

  • Pilar Junier

    Personal web site.

    Bacterial diversity: from cultures to DNA and back to cultures

General information

Dates:  Monday 5 September 2011

Schedule : 8.55 - 17.00

Location : University of Neuchâtel, Faculté des sciences, UniMail, building C  (C001 Animalerie)

Credit points : 0.5 credit point (attendance only)  & 1.0 credit point  (with poster or oral presentation)  (Scientific activity, DP) 

Evaluation : Full attendance and active participation

Information : Please contact the scientific organizers Edward Mitchell or Enrique Lara, or the doctoral program coordinator Christiane Bobillier (administration)

Registration fee :

  • free for PhD students registered in the CUSO Doctoral Program in Microbial Sciences or PhD students (who are not members of a CUSO University) registered in the Interuniversity Doctoral Program in Organismal Biology (includes 2 coffee breaks and lunch).
  • free for Master students (includes 2 coffee breaks, but lunch not included)
  • for ALL other participants, the registration cost is CHF 20.00 (includes 2 coffee breaks and lunch).

Travel expenses : participants in the Interuniversity Doctoral Program in Organismal Biology and CUSO doctoral program are eligible for reimbursement of incurred travel expenses by train (half-fare card, and 2nd class).

  • for CUSO Doctoral Program participants: see information on the web site.
  • for Interuniversity Doctoral Program in Organismal Biology participants who are not members of a CUSO University. Send the original tickets (no copies, except for the general abonnement) with the reimbursement form  to Dr. Christiane Bobillier. No reimbursement for bus, taxi or car travel expenses will be paid.

TAKE your ATTESTATION of ATTENDANCE (distributed at the end of the workshop)
(no attestation will be sent by mail)


  • This workshop is opened to all Ph.D. students. Registration priority until 30 June 2011.
  • Post-docs and master students are welcome as long as places are available.
  • Maximum number of participants: 40. 

Registration : CLOSED 

Please note the cancellation policy (CHF 20) .

Deadline: 30 August 2011