Selective effects of transient oxygen and nitrate exposure on sulfate reducing/fermentative consortia

The activity and diversity of prokaryotes is one of the keys to understand element cycling in our environment. Many microbes couple the oxidation of carbon compounds with the reduction of inorganic compounds such as oxygen, nitrogen,manganese, iron and sulfate. The sulfur cycle is one of the most important elements cycles, because of the high abundance of sulfate in the marine environment and the rich speciation of sulfur compounds at different redox states. The most stable and abundant form of sulfur is sulfate which is found in sea water at a high concentration of 28mM. About 50% of the remineralization of organic carbon substrates was suggested to be coupled to sulfate reduction. Sulfate reducers couple the oxidation of organic carbon compounds or hydrogen with the reduction of sulfate to sulfide. Their ability to oxidize organic carbon compounds is known to be mostly limited to those compounds that are produced by fermentative bacteria. However, only few studies directly address the ecological relationship between fermentative and sulfate reducing bacteria. This thesis addresses precisely this point. Consortia of sulfate reducing and fermentative bacteria were enriched in long term continuous culture incubations inoculated with biomass extracted form the top sediment layers of the intertidal flat Janssand in the German Wadden Sea. The cultures were provided with a marine medium that contained, in addition to sulfate, seven different amino acids, glucose and acetate in a ratio that mimicked the composition of decaying biomass (50% protein, 30% polymeric sugars, 20% lipids) in terms of its monomers. Chemical and metagenomic analysis were used to analyze the activity and community composition of the selected consortium. Most cultures were performed under stable, sulfate reducing conditions (Chapter 2). Chapter 3 addresses the effect of transient exposure to oxygen and nitrate on the enrichment of consortia of fermentative/sulfate reducing bacteria. Under all conditions investigated, the enriched sulfate reducers belonged to the Deltaproteobacteria, dominated by Desulfovibrio and Desulfotignum populations. The enriched fermentative bacteria were mainly affiliated with Firmicutes, followed by Spirochaetales. The enrichment and phylogenomic characterization of Candidatus Thammenomicrobium ektimisum , a fermentative representative of the candidate division Hyd24-12 is described in Chapter 4. The results presented in chapters 2 and 3 suggest that hydrogen and acetate were the main fermentation products. Metagenomic, transcriptomic and stoichiometric modeling of microbial metabolism suggested that the sulfate reducers displayed at least partially autotrophic growth by assimilating carbon dioxide, despite the supply of copious carbon sources to the cultures. Transient exposure to oxygen did not result in a strong selective effect, and neither the fermentative nor the sulfate reducing populations showed a strong transcriptional response to exposure to oxygen. Transient availability of nitrate led to the enrichment of a different population of Deltaproteobacteria, affiliated with Desulfuromonadales, in two replicate experiments. This population was apparently incapable of sulfate reduction but performed ammonification of nitrate to ammonia. Overall, the results presented in this thesis provide new insight in the selective pressure exerted by dynamic environmental conditions on sulfate reducing/fermentative consortia.