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Metabolic Symbiomics

Lead: Michael Wagner (Uni Vienna)

Rationale

For many invertebrates obligate endosymbiotic bacteria have been described and phylogenetically analyzed, but in most cases an in-depth understanding of the physiology of the symbionts and of the metabolic interaction with their hosts is lacking. Furthermore, several animals like mussels and sponges play host to multiple bacterial symbionts and we still know very little about functional complementation between these microbes. (Meta)genomic sequencing alone, which is now frequently applied in symbiosis research, provides important hypotheses regarding the metabolic potential of symbionts, but cannot close these knowledge gaps due to the inherent limitations of in silico annotation and missing information on expressed and functional proteins. Recent methodological advances now enable microbiologists to directly investigate the proteome and metabolome of microbes and to study their physiology at the single cell level in the natural habitat by advanced isotope techniques. For this work package, the combined application of these innovative approaches will help us decipher key functional traits of selected invertebrate-microbe symbioses.

Objectives

We propose to use advanced proteomic, metabolomic and isotope-detection techniques to reveal the function of amoebal, sponge and mussel symbionts (Projects_7, 9 and 10). More specifically, the physiological properties of different growth stages of a chlamydial symbiont of amoebae, its extracellular metabolic activities, and its metabolome will be characterized (Project_7). Furthermore, more complex symbiont communities consisting of two (Project_9) or multiple members (Project_10) will be investigated to reveal key functional properties of a recently discovered and numerically dominant gammaproteobacterial sponge symbiont (Project_10) and to understand physiological complementation and specific adaptations of sulfur- and methane-oxidizing mussel symbionts (Project_9). Due to the great methodological challenges associated with metabolomic analyses of intracellular symbionts (and symbiont communities), Project_8 focuses on adaptation of various metabolome tools for endosymbiosis research (using marine invertebrate symbionts as examples) and makes them accessible for other Projects.

Key methods

This work package integrates a wide range of state of the art methods for functional characterization of microbes. Most of the suggested method combinations in the four Projects of this work package have not been previously applied for the investigation of invertebrate symbionts. Applied methods include for example metagenome sequencing and annotation (Projects 9 and 10), cytoplasmic and membrane proteomics (Projects 9 and 10), metabolome analyses via HPLC-MS and quantitative GC/MS- and NMR, NMR and LC/MS-, and GC/MS profiling (Projects 7, 8 and 9), as well as isotope labeling and subsequent detection in single symbiont cells via confocal Raman microspectroscopy and Nano-Secondary Ion Mass Spectrometry (NanoSIMS) (Projects 7, 9 and 10).