Amplicon (16S) and shotgun metagenomic sequencing data from nitrite-fed bioreactor communities growing with Nitrobacter winogradskyi.
Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacterwinogradskyi can create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that actively growing N. winogradskyi will select the same heterotrophic functions from contrasting environments even when the selected heterotrophs are different. To test this hypothesis, pure cultures N. winogradskyi were grown in organic carbon-free, mineral medium in continuously fed bioreactors and were inoculated with a suspension from a grassland soil or with dilutedsewage sludge. Samples for chemical and 16S rRNA amplicon sequences analyses were taken after each volume change of the bioreactor. After ten volume changes, samples for shotgun metagenomics were also collected and pure cultures were isolated on solid agar media with different carbon compounds. The enrichment runs were done in three series of three individually inoculated bioreactors each, five with soil suspension and four with dilutedsludge. Based on both 16S rRNA amplicon sequences and shotgun metagenome analyses, the enrichment of heterotrophs from both origins was highly stochastic and yielded different dominant genera in most of the enrichment runs. The enrichments followed a limited number of directions, which were determined in the first couple of volume changes in the bioreactors. The (beta)diversity among the soil-based enrichments was larger than amongthe sewage-based enrichment. Nonetheless, no significant differences in functional homologs were observed between the individual enrichments. Hence, the results did not contradict the hypothesis.