| Do theories of macro ecology hold for microbial systems? |
Possibility to incorporate microscale habitat structure into microbial model systems. Live imaging of micro-structured chambers and channels where microbial cells can compete or initiate reciprocal resource exploitation. Potential examination of niche differentiation, predator–prey relationships, food web interactions including microfauna, island biogeography (habitat patches within soil aggregates), the connection between microorganism biodiversity and ecosystem function, all with the aid of biosensors such as fluorescent probes. |
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| What are the environmental triggers of microbial behavior and evolution? |
Real-time visual analysis of cell interactions with complex environmental conditions. Monitoring of frequency and triggers of horizontal gene transfer. Controlled microenvironments to study quorum sensing, biofilm formation and community dynamics. Possibility to follow foraging and branching of tip-growing cells to monitor cellular decision making. Model-soil aggregates as evolutionary incubators to study microbial selection pressures. Microscale and in situ sampling (laser microdissection) of cells from chips to characterize gene expression or genetic networks. |
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| How do microbes behave across short and long timescales to chemical cues? |
Controlled chemical gradients or nutrient patches to study chemotaxis of single cells or hyphal tips. Gradients can be time resolved, switched on and off or being reversed. Microorganisms can be exposed to pulses of exudates or signaling molecules of interacting organisms. |
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| What are the stages and preconditions of microbiome formation and succession? |
Empirical platforms for testing stochastic vs deterministic community assembly processes. Time-lapse analysis of micro-structured incubation chambers to simulate soil aggregates and other habitats on a chip. Surface structure simulations from imprints to study microbiome formation, and successional drivers. |
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| What cellular processes are necessary for symbiotic establishment and resource exchange between hosts and their microbes? |
Microscopic channels for growing individual roots with precise control over environmental conditions and timing of symbiont exposure (for example, mycorrhizal fungi or Rhizobia). In situ analysis of signaling molecules. Visualization of direct cell interactions, and nutrient transport via fluorescent labels. |
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| What specific roles do microbes play in the process of soil aggregation and organic matter stabilization? |
Simulation and manipulation of microscale habitat structure to study the importance of organic matter occlusion. Injection of loose microparticles in chambers for the microbes to rearrange and aggregate. Bendable micro-pillars for microbes to physically manipulate. Mineral surface coating to study chemical interactions at microscale. Live visualization of particle aggregation process. |
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| How can we improve and verify computer models of microbial processes, in order to upscale results to global ecosystem models? |
Acquire empirical data of microbial growth, interactions and substrate usage via biosensors and image analysis. Grid-based designs for realistic and highly replicated tests of in silico experiments. Improved empirical base to upscale microbial processes to global models. |
