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Microbes in ecosystems: weaving intracellular processes into ecological networks
The workshop will be centered about four major, interrelated, topics:
1. Quantitative understanding of community functioning from molecular data. Large scale sequencing (metagenomics) is rapidly providing information on the microbial gene content of many environments. Meta-transcriptomics, meta-proteomics and meta-metabolomics reveal which genes are active. However, these experimental approaches lose the connectivity between genes, mRNAs and proteins (~ the parts) on the one hand and species in which they resided on the other hand. Does deriving the understanding on ecosystem functioning from the part lists require the ability to determine the connectivity between the parts and the involved species? How to determine this connectivity in a quantitative way? May approaches to determine and model part-to-part interactions at the cellular level be extended to microbial ecology?
2. Analysis of fluxes through ecosystems. An important component of ecosystem functioning is the flux of material through an ecosystem and its resistance and resilience to perturbations. Detailed analysis of fluxes through cellular networks of individual species is well possible using fluxomics. Also in ecology, various modeling approaches are available to determine the flux of matter through tropic levels. In ecological models, bacteria are often lumped into a few compartments at most. Nowadays it is possible to track the fate of labeled substrates in microbial communities and through this identify ecological networks to substrate usage. How to integrate these approaches on ecosystems fluxes such that quantitative determination of fluxes through functional groups or even individual microbial species may be obtained?
3. Community assembly and structure. Ecologists put large effort in determining the species abundance and distribution and on the relative importance of species interactions versus selection by the environment. For microorganisms this task is still tremendous and relies on the application of cultivation-independent molecular techniques, targeting informative marker genes. Ideally, we would like to understand what determines the assembly of microbial community structure. We will explore which theoretical and modeling approaches are around in ecology and systems biology to understand the composition of communities.
4. Microbial controls on ecosystem processes. Understanding which species, and which of their intracellular metabolic activities, are relatively important with respect to fluxes through ecosystems and in determining the concentrations of metabolites will allow for rationale engineering of ecosystems such that they provide better services (e.g. enhanced bioremediation, energy production) and for selecting species for environmental conservation. Tools in systemsbiology/molecular biology such as metabolic control analysis and hierarchical regulation analysis have allowed for insight into which enzymes are important and how changes in fluxes are regulated at the metabolic and hierarchical level. First steps to extend these tools to ecological applications have been made. We will explore how these tools can be applied practically. May we specifically modulate and measure the abundance and activity of particular species at the field scale. How to deal with growth of microorganisms? How to explore which processes within relatively important microorganisms contribute to this importance?