Microbes in Ecosystems: Weaving intracellular processes into ecological networks


Ecosystems often contain thousands of microbial species, each with their own geno- and phenotypes. Ecosystem functioning relies on interactions among these microorganisms and between microorganisms and their environment. For a long time it was very hard to study microbial community structure and functioning at high spatial and temporal resolution. Recent technologies allow now for the generation of large data sets on complex microbial communities and the cellular composition of these communities, by addressing genomic information on the species present and their genes (metagenomics), their gene expression (metatranscriptomics), proteins (metaproteomics) and metabolites (metametabolomics).  However, the field of microbial ecology still is largely descriptive. Through integration of the emerging fields of microbial ecology and systems biology and cross-fertilisation by assembly theory, we wanted in this workshop to address the question how to move microbial ecology towards a scientific discipline that yields a more quantitative and mechanistic understanding of microbial community structure and functioning.


Within general ecology, a number of theories have been developed on community assembly and ecosystems stability and functioning. Few of those concepts have so far been applied to microbial ecology. Systems biology is another rapidly developing field and aims at understanding how dynamic interactions between components of living systems, but also between living systems in interaction with their environment, give rise to their functioning. This is achieved by an iterative approach of modeling and experimentation integrating large data sets into mathematical models to quantitatively describe and predict system functioning. Systems biology approaches focused so far almost exclusively on molecular interactions within individual species. This has led to fundamental new insights into the functioning of individual species. Systems biology has the ambition to go beyond intracellular processes and aims at connecting different levels of biological organization, from the functioning of genomes to communities and ecosystems. Cross fertilization between microbial ecology and systems biology should aid in designing approaches to modulate community structure development and functioning, which will contribute to combating environmental (e.g. climate change), societal (e.g. energy shortage, pollution) and health (e.g. human diseases) threats.


To achieve our goal, we brought together 41 academics from seven countries and with various backgrounds ((theoretical) ecologists, microbial physiologists, microbial ecologists, bioinformaticians, biogeochemists and systems biologists) to present and discuss integrative approaches and concepts to study multi-species interactions in simple artificial experimental systems and in real environments. The majority of the participants were senior scientists, but during the first two days also about 10 junior scientists (PhD students, post docs) attended the workshop.


The workshop consisted of two well-connected parts: during the first two days four major, interrelated topics were introduced, while in the last two days we discussed how those topics should be integrated scientifically. The four topics were:

1. Quantitative understanding of community functioning from molecular data.

2. Analysis of fluxes through ecosystems.

3. Community assembly and structure.

4. Microbial controls on ecosystem processes

For each topic, three plenary lectures were presented, introducing the status of the field and visions for the future. The presentations were in general of high level and led to lively discussion afterwards. The presentations also nicely reflected the multidisciplinary character of the workshop. The third and fourth day were spent on discussing the four topics, in order to proceed towards a concept that allows for better understanding of community functioning, in particular the distribution and control of fluxes in microbial networks and the associated resistance and resilience towards disturbances. Twenty-six invited senior participants were divided over four small working groups. Each group discussed a particular topic on basis of three statements and prepared a presentation. These presentations were discussed, and subsequently the working groups were changed: all participants moved to another working group in order to allow all participants to contribute to two different topics. During the fourth day the discussion was centered around one plenary discussion. The workshop ended with an excellent presentation by Ian Head.


We observed that the participants could roughly be divided into two groups: those who work top-down and try to understand ecosystems by the application of large scale meta-omics techniques, and those who work more bottom-up and try to understand ecosystems starting from simple, controlled, systems. These differences in approaches and visions could not completely be reconciled, but a proposal was presented in the final discussion on how these two approaches can be brought closer together in order to achieve better understanding on microbial ecosystem functioning. We aim to write a perspective paper on the outcome of the workshop, together with other participants of the workshop. We feel that the workshop brought many scientists closer to each other, and will lead to new research cooperations.


We thank the Lorentz center, in particular Auke Planjer and Pauline Vincenten, for the excellent organization, facilities and suggestions they provided us with. We also thank the Lorentz center, the Netherlands Institute of Systems Biology and KNAW for financially supporting the workshop.


Wilfred Röling (VU University Amsterdam)

Peter van Bodegom (VU University Amsterdam)

Nico van Straalen (VU University Amsterdam)