Background and Research Strategy

The heterogeneous and fluctuating conditions in most current ecosystems, microbial competition and adaptation to biotic and abiotic factors, and consequent evolution, have resulted in the fascinating microbial diversity that is currently found in natural habitats. Microorganisms inhabit almost every thinkable ecological niche on the Planet, and the diversity in the microbial world is daunting by its sheer magnitude. Only a minor fraction of this diversity has been accessed to date. Understanding the ecology of the diverse microbial communities and their interaction with the environment thus represents a major challenge to current microbial ecology research.

 

At present, most of the studies of microbial diversity and function focus on organisms at the community level, using, for instance, the 16S ribosomal RNA (rRNA) gene sequence as a marker of microbial diversity. Thus, an inventory is made of the microbial diversity extant in target ecosystems (soils, aquatic systems), and the putative ecophysiological role of members of that community is inferred from the data. However, finding similar populations of species in similar or different environments does not necessarily mean that these are also functionally identical. In fact, genetic diversification within microbial populations is the key step in microbial adaptation and evolution. Several mutational processes, ranging from horizontal gene transfer through genomic rearrangements to small mutations, may yield variants with traits that enhance fitness. The genetic diversity within a community or population of cells may thus often be missed by 16S rRNA gene-based culture-independent methods, although we do not fully understand the limits to using 16S rRNA genes to infer community function.

 

This lack of sound information provides the rationale for current innovative work that aims to address key questions such as “how well does community structural diversity reflect functional diversity and community functioning” and “how does horizontal gene transfer interfere with the putative relationship between structural and functional diversity”. These issues are being tackled in the research programme in the Microbial Ecology Department, which focuses on:

- The adaptation of prokaryotic microorganisms to a variety of environmental niches, and the ways in which the genomes involved allow plasticity to enhance fitness. Hence, questions in respect of how bacteria adapt genomically to the environmental challenges they encounter, on what occasions they show adaptive responses, how horizontal gene transfer impacts on the adaptational process and at which speed adaptations occur are being addressed.

- The causes and the consequences of microbial diversity. These topics are being tackled by the microbial community ecology group within this department, where we aim to understand questions in respect to how we can infer microbial diversity, how microbial diversity changes through time, what is the impact of microbial diversity for ecosystem processes and services.

 

Research in the Department is strongly driven by the impetus given by the recent development of a range of modern molecular techniques in microbial ecology. Such techniques allow us, for the first time in history, to directly assess the life of microbes in nature on the basis of nucleic acids extracted from environmental samples. In particular, novel methods to fingerprint whole microbial communities are being (further) developed and applied.

 

Collaborations

The Department actively seeks collaboration with internal and external partners. Members of the Department are involved in a range of Dutch national as well as international (EU-sponsored) projects and networks.

 

Projects:

1. Microbial diversity and community functioning. Joana Falcao Salles

2. The baseline of soil functioning across a range of soils. Michele de Cassia Pereira e Silva  and Alexander V. Semenov

3. The functional and structural microbial diversity of soil under potato (baseline). Özgül Inceoğlu

4. The impact of environment on avian immunity – How do birds match their immune system with the pathogen pressure they experience? Stephanie Grizard

5. Microbial diversity and invasiveness. Cyrus Alexander Mallon

6. Adaptation of Escherichia coli to heterogeneous conditions. Pilar Eliana Puentes Téllez

7. Culturing the ‘unculturables’; a challenging approach to recover new species from the rhizosphere - Ecology of Acidobacteria and Verrucomicrobia. Ulisses Nunes da Rocha (in collaboration with Dr. L.S. van Overbeek, Plant Research International)

8. Investigation of habitat specificity for metagenomic exploration of bacterial chitinases and chitin deacetylases. Mariana Silvia Creţoiu and Anna Maria Kielak

9. Monitoring of pathogenic microorganisms in water-development of a multipurpose, generic tool based on pathogenicity traits. Patricia Stevens

10. Fungal-associated bacterial communities and the eco-molecular mechanisms involved. Rashid Nazir
11. Ecology of rice endophytes: How bacteria become endophytes? What are their functions for the plant host? Pablo Rodrigo Hardoim

12. Diversity and beneficial properties of bacterial endophyte communities of arctic plants. Riitta M. Nissinen

13. The significance of plasmids for bacterial fitness in the mycosphere.  Miaozhi Zhang
14. The assembly rules for microbial communities in salt marsh systems.  Francisco Dini Andreote
15. The use of statistics in field testing and the effects of GM crops on soil.  Alexander V. Semenov