More on the department Terrestrial Microbial Ecology

Soil-borne micro-organisms are the greatest reservoirs of biodiversity on the planet and are known to be critical to terrestrial ecosystem functioning. However, our mechanistic understanding of microbial activities in soil and the genetic basis for these activities are still poor, hampering our ability to harness and manage this tremendous diversity.

Soil provides a spatially and temporally heterogeneous environment especially at the scale encountered by microbes. Most soils are variably aerobic and composed of solid, liquid and gaseous phases, with air-filled pores constraining microbial movement.

Energy, i.e. carbon compounds, to the system is provided by plants to the microbial community through exudation and root tissue breakdown. Within this context, niche differentiation and evolution of soil biota, i.e. bacteria and fungi has taken place. Some micro-organisms have become well adapted to grow on exudates of plant roots and/or fungal hyphae, whereas others compete for more recalcitrant compounds. In addition, various mutualistic and pathogenic relationships have developed between bacteria, fungi and plants.

The selective forces of microbial evolution and the mechanisms that drive and maintain this microbial diversity and niche differentiation of soil micro-organisms are only marginally understood.
Plant roots and fungal hyphae can select for bacteria and fungi in the rhizo- (and phylo-) sphere or hyphosphere, which can alter plant and fungal performance e.g. the suppression of plant pathogens or the enhanced supply of nutrients. However, the extent to which this selection occurs in the environment, with resulting feedbacks, is not clear. Barriers to understanding these interactions include the dynamic, heterogeneous nature of soil environments, the vast microbial diversity in soils and the poor culturability of the majority of soil microbes.

Research program
Therefore, the aim of the research program of TME is to obtain basic knowledge on the ecology, diversity and evolution of soil-borne micro-organisms that are associated with plants and fungi. Main focus is on antagonistic (negative) and mutualistic interactions between bacteria and fungi and between plants and micro-organisms. Therefore, special attention is paid to processes and functions in the mycosphere and rhizosphere.

The goals of our department are to provide answers to the following major scientific questions:

Question 1:
What effect do plant roots and fungal hyphae exert on the community composition of plant- and fungal-associated soil microbes and what are the consequences of this selection for the performance of fungi and plants?

Studies focus on factors steering the presence, abundance and distribution of microbial populations, their genes and their possible influence on the fitness of plants and fungi. Research covers e.g. genes involved in the suppression of harmful organisms and production/degradation of plant hormones.

Projects are running on:

Mechanisms, distribution and significance of bacterial mycoparasitism by the bacterial species Collimonas.
Disease-suppression and production functions of soil.
Suppression of plant pathogenic fungi as a result of inter-specific bacterial interactions.
The role of pyrrolizidine alkaloids in shaping the microbial community in the rizosphere of Senecio jacobaea.
BACSIN; assessing the potential of phyllosphere microbiology for the cleanup of environmental wastes.

Question 2:
What are the patterns of microbial diversity associated with plants and fungi, and what factors are responsible for the establishment and maintenance of these patterns?

Here we focus on the nutritional strategies of micro-organism associated with plants and fungi. Furthermore we are interested in the explanation for the tremendous functional redundancy that occurs within soil-borne microbial communities.

Projects are running on:

Global warming induced effects on Antarctic microbial community structure and function.
Functional and phylogenetic micro-array development.
Genomics potential and activity of dominantly active, non-culturable soil bacteria.
Functional biodiversity in agricultural production systems: a synthesis of studies on linking above- and belowground multitrophic interactions and consequences for crop protection.
Development of methodology to assess the risk of transgenic plants on soil processes.

Question 3:
How do interactions influence the functioning of micro-organisms with special focus on mutualistic, pathogenic and antagonistic micro-organisms?

Projects are running on:

Activities of mycorrhizal fungi in soil systems.
The ecology of bacterial individuality.

Research framework
These ecological research questions form the framework for the present research program. The program has developed over years but it ‘s main focus has always been on the microbial ecology of plant-soil systems. Within this research priority, we attempt to gain understanding of functional microbial community dynamics in soil and the rhizosphere, especially in the light of how microbial activities are affected by perturbations to terrestrial ecosystems.

This direction was defined after the separation of the soil faunal research (now at the Department of Multitrophic Interactions, MTI) from the department in 2000, and has since been expanded to include subjects of bacterial-fungal interactions, microbial population biology and environmental genomics. A major stimulus of microbial genomics research in the department has come from the Bsik-funded program on Ecogenomics: 'Assessing the living Soil'.

Recently, the department also received a large impulse within the framework of the ERGO program on the effects of genetically modified plants on soil ecosystems.
Within the framework of two large personal grants to George Kowalchuk (VICI grant) and Johan Leveau (VIDI) a major research effort will be devoted to research on the behaviour of individual bacterial cells in soil ( VCI project Kowalchuk) and phylosphere ( VIDI project Leveau).

The department also aims at translating basic knowledge into applied research projects. Besides basic and applied research, we aim to contribute to technological developments in microbial ecology, in particular, to the developments of molecular biological (including genomics and post-genomics) techniques and methods.

Three members of the department are associated with different universities; Hans van Veen is Professor of Microbial Ecology at the Institute of Biology of Leiden University, George Kowalchuk is extraordinary Professor of Molecular Plant Microbe Interactions at the Institute of Ecological Sciences of the Free University Amsterdam and Johan Leveau is Associate professor of Microbial Ecology at the Department of Plant Pathology of the University of California, Davis (USA)