Diversity of the autotrophic, nitrate-reducing, Fe(II)-oxidizing enrichment culture KS

The enrichment culture KS is one of the few existing autotrophic, nitrate-reducing Fe(II)-oxidizing cultures that can be continuously transferred without an organic carbon source. We used a combination of Catalyzed Amplification Reporter Deposition Fluorescence In-Situ Hybridization (CARD-FISH) and Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) to analyze community dynamics, single-cell activities and interactions among the two most abundant microbial community members (i.e., Gallionellaceae sp. and Bradyrhizobium spp.) under autotrophic and heterotrophic growth conditions. CARD-FISH cell counts showed the dominance of the Fe(II)-oxidizer Gallionellaceae sp. under autotrophic conditions as well as of Bradyrhizobium spp. under heterotrophic conditions. We used NanoSIMS to follow the fate of 13C-labeled bicarbonate and acetate as well as 15N-labeled ammonium at the single-cell level for both taxa. Under autotrophic conditions only the Gallionellaceae sp. was actively incorporating 13C-labeled bicarbonate and 15N-labeled ammonium. Interestingly, both Bradyrhizobium spp. and Gallionellaceae sp. became enriched in 13C-acetate and 15N-ammonium under heterotrophic conditions. Our experiments demonstrated that Gallionellaceae sp. was capable of assimilating 13C-acetate while Bradyrhizobium spp. were not able to fix CO2, although a metagenomics survey of culture KS recently revealed that Gallionellaceae sp. lacks genes for acetate uptake and that the Bradyrhizobium sp. carries the genetic potential to fix CO2. The results presented in this study emphasize the importance of performing physiological growth and stable-isotope labeling experiments to verify hypotheses of potential species functions and interactions in microbial communities derived from (meta)genomics. The study furthermore extends our understanding of the microbial reactions that interlink the nitrogen and Fe cycles in the environment.