Population Dynamics and Cross-Feeding in an Antibiotic-Degrading Synthetic Ecosystem: Insights from Single-Cell Raman Spectroscopy and Stable Isotope Probing

Abstract We report on commensalism enabling the entire degradation of the sulfadiazine antibiotic by a consortium composed of Microbacterium sp. strain BR1 and Terrabacter. 13C,15N-labeled sulfadiazine was synthesized and used as sole source of carbon in axenic cultures of Microbacterium and Terrabacter as well as cocultures of both genera. HPLC analyses showed that Microbacterium degraded sulfadiazine with accumulation of 2-aminopyrimidine, while the Terrabacter culture did not degrade sulfadiazine. The consortium degraded labeled sulfadiazine without any accumulation of 2-aminopyrimidine. Cross-feeding was efficiently synchronized in the synthetic consortium, and the release of 2-aminopyrimidine from sulfadiazine by Microbacterium is a prerequisite for its degradation by Terrabacter. Raman spectra in the fingerprint region enabled the discrimination of the two genera at the single cell level and the calculation of the cell number ratio, providing quantitative insight into the population dynamics in coculture. The cell counts in axenic culture and coculture were consistent with HPLC analyses, reflecting their metabolic activities and trophic interactions. Stable isotope probing and subsequent analyses of Raman spectra of Terrabacter in the synthetic consortium revealed a significant shift from 1000 cm–1 to 988 cm–1, proving that this bacterium assimilates 2-AP for biomass synthesis and that less than 50% of Terrabacter cells were degrading 2-AP.