Project Area C

Directed Modulation of Complex Biosystems

Whereas the projects in areas A and B explore new community relevant metabolites and regulatory principles, this project area will take these concepts and specifically examine complex communities by using natural products and derivatives as modulators. Multi-organism communities with varying degrees of complexity will be manipulated using natural products or their synthetic analogues and their response will be characterized on different levels. This includes field ecology, work in mesocosms or targeted manipulations of communities in environmental samples.

Focus of project area C will be the effect of mediators on communities.

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Natural products or other chemical compounds with a documented or highly likely potential as mediators of interaction will be used as starting points. Furthermore, the modulating role of metal ions or their depletion due to complexation with natural products will be explored. Non-contact co-culturing allows the effects of direct cell-cell interactions to be separated from the true function of secreted metabolites. This method will be used to study how complex plankton communities respond to chemical signals produced by introducing additional partners.

Field experiments that allow the observation of microbes and plants in their natural environment will directly facilitate the observation of the response of (natural) communities to chemical signals. Synthesis of multimodal peptides will provide a link between metabolic diversity and functional diversity of natural products within stressed and non-stressed bacterial communities. Metallophores will be investigated as mediators for metal cycling to understand how communities can be shaped by metal chelating reagents.

Project C01

Algicidal Bacteria in Plankton Communities: Resistance, Lysis and Heterotrophy


Organisms in the plankton form complex communities that contribute substantially to global primary production and fuel the marine food web. This project focuses on the role of secondary metabolites as mediators of the complex plankton community structure. We focus on the lytic bacterium Kordia algicida that is capable of lysing bloom forming algae and investigate its influence on plankton dynamics. The regulation of algal / bacterial interaction and the cascading effects on the marine food web will be addressed in lab and field experiments.

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Project C02

Are Plant Defenses Chemicals Commonly Sequestered and Metabolized by their Herbivores to Function as Infochemicals in Higher Trophic Level Interactions in Nature?


Plants integrate responses between two spatially separated habitats: air and soil, with different communities of heterotrophs depending on the same host. Little is known about the chemical mediators of interactions between aboveground herbivores and root colonizers. Using metabo-lomics and transcriptomics, we will characterize spatiotemporal changes in roots of herbivore-damaged plants and identify underlying signalling pathways. We will genetically modify identified traits to determine their ecological function in interactions with soil bacteria and mycorrhizal fungi and the consequences for herbivore resistance and plant fitness in field experiments.

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Project C03

Thiopeptide Signals in Actinomycete Communities


Microbial consortia are structured by antibiotics such as thiopeptides (TP) and by environmental factors such as heavy metals (HM). In this project the signaling of sublethal TP doses via the TP-activated TipA receptor and its interaction with HM-stress and resistance mechanisms will be investigated on the molecular, genomic and interspecies level. Ligand function, target genes, and HM-dependence will be clarified in model organisms and microcosms by using targeted mutants, tool compounds, and HM-contaminated soil media.

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Project C04

Metallophores as Mediators for Metal Cycling: Profiling and Ecological Evaluation of Ligands Involved in the Microbial Cycling of Iron in Complex Systems


Iron in complexed form is central to the microbial iron cycle. In this project, we identify and characterize metallophores formed and excreted by bacteria and compare them with the diverse compounds found in nature. The goal is to elucidate the chemical communication of bacteria that use iron in very different forms for energy production. Co-cultivations have shown that biofilm formation plays a key role in the interaction. We want to clarify whether synchronization of lifestyles drives these interactions.

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Project C05

Metallophores as Mediators for Metal Cycling: Development of Libraries for Metal Ion Buffering and as Redox Carriers as well as Profiling of Metallophores

This project aims to identify novel metallophores based on recently developed LC/MS analytical techniques and to unravel their multiple functions particularly in nitrogen-fixing and microbial iron-cycling systems. To mimic natural sources of molybdenum, which is an essential cofactor of nitrogenases, we will develop libraries of synthetic chelating agents for this metal. The resulting complexes serve as “Mo-buffers” to control the availability of molybdenum species in aqueous cultures. To model redox shuttle systems in communities of Fe(II) oxidizers and Fe(III) reducers appropriate ligands as well as metal complexes will be developed.

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Project C07

Complex Ecological Phenomena Arising from Enzymatic Modification of Chemical Effectors


Identification of common patterns across different microbial communities can lead to powerful fundamental insights. Current work in ChemBioSys has identified enzymatic modification of secreted chemical effectors as one such common theme. We propose to investigate the complex temporal and spatial dynamics that can emerge in such systems. Specifically, we will investigate systems where one organism secretes a chemical effector to impact a second organism, while a third organism secretes an enzyme that modifies that effector, changing the ecological outcome. Our project will combine theoretical and experimental methodologies.

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Project C08

Chemical Mediators of Microbiota Composition and Functionality in a Multipartite Defensive Symbiosis


Beneficial microbes are fundamental for plant and animal health, but the molecular factors shaping the composition of symbiotic microbiomes remain poorly understood. Using an experimentally tractable defensive symbiosis in beetles, this project will characterize the secondary metabolites produced by the bacterial community members and elucidate their impact on community structure and on the protective benefit for the host. Through a combination of in vitro assays and manipulative experiments in the host, the results will shed light on the dynamics of competition and facilitation among symbiont strains and thereby provide insights into the processes guiding the assembly of host-associated microbiomes.

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Project C09

Probing the Role of Chemical Signalling in the Interplay of Gut Commensals, Pathogens, and their Phages


When colonizing the human gut, Vibrio cholerae interacts with dozens of commensal microorganisms, their secreted molecules, and numerous phages. In this project, we will investigate the interplay of V. cholerae with microbial competitors in the gut, as well as how phages play into this process. We will focus our investigations on key mediators of collective behavior in V. cholerae and pinpoint their roles in other organisms. We expect that this project will allow us to better understand how microbial commensals and phages influence collective behaviours, such as virulence gene expression and biofilm formation, in the major human pathogen V. cholerae.

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Project C10

Chemical Signaling in Algae-Parasites Communities


Single-cell parasites thrive in aquatic ecosystems and contribute to algal blooms termination, yet the molecular mechanism supporting parasitism is poorly understood. We will explore parasite-induced diseases in diatoms and dinoflagellates and identify the chemical signaling that mediates pathogenesis, host defense and multipartite interactions with the plankton microbiome. The CRC project will provide insights into the fundamental mechanism of alga-parasite interactions that balance the aquatic food web.

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Project T01

Designing Sustainable Strategies to Combat Cabbage Root Fly Infestation in Oil Seed Rape (Brassica napus)


Winter oilseed rape (Brassica napus; OSR) is suffering from severe damage by root-feeding larvae of the cabbage root fly, Delia radicum. We annotated the genome of D. radicum and identified genes participating in isothiocyanate (ITC) detoxification, the typical Brassica defences. The larval gut bacteriome contains SaxA genes involved in ITC detoxification. Here, we join forces with OSR-breeder NPZi to design novel approaches for environmental-friendly D. radicum control. We aim to identify genes for compounds involved in fly attraction and resistance to larvae by screening an OSR mutant population. In parallel, genomic information of D. radicum and its gut microbiome will be used to design RNA interference biopesticides.

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