Competition in nitrate-reducing microbial communities

Abstract

The biogeochemical nitrogen cycle, including nitrate reduction processes, is highly affected by human activity such as fertilization and ammonia deposition caused by fossil fuel burning. Consequently, gaining a better understanding about the ecophysiology of nitrate-reducing microbial communities is crucial for inferring the impact of anthropogenic nitrogen input. Different nitrate-reducing pathways compete with each other for the electron acceptor nitrate: Denitrifiers reduce nitrate to dinitrogen and nitrous oxide while dissimilatory nitrate reducers reduce nitrate to ammonium. The outcome of this competition has important environmental consequences: denitrification removes fixed nitrogen from the ecosystem, while dissimilatory nitrite reduction to ammonium (DNRA) keeps fixed nitrogen bioavailable. Although a lot of studies have been performed on this topic, no conclusive factors responsible for the dominance of one or the other process could be identified so far. In this thesis, the competition between nitrate reduction pathways was addressed by combining continuous culture incubations of natural microbial communities with stable isotope labeling and metagenomics, complemented with metatranscriptomics and metaproteomics in order to gain insight into the identity, function and interaction of the enriched microbial populations. To be able to make the best use of the obtained metagenomic data a new metagenomic binning procedure was developed. Before the competition between two different nitrate reduction pathways was studied, the relationship between functional and compositional stability over time within one nitrate reduction pathway was investigated: In a heterotrophic denitrifying microbial community, enriched from a marine intertidal flat, strong community dynamics were occurring under constant conditions and during stable conversion of substrates. A stable metabolic interaction between the denitrifying populations and co-enriched fermenting microbes persisted throughout the experiment unaffected by the ongoing population dynamics. This indicated that functional stability was independent of the community composition. Apparently, only the persistence of the overall metabolic potential was important to maintain functional stability. This suggested that stochastic as well as deterministic processes are responsible for the observed community composition. Once the functional stability of denitrification was confirmed and interactions with other microbial guilds were known the competition between DNRA and denitrification was addressed. Several parallel continuous culture incubations that differed in one condition but were otherwise constant led to the identification of the generation time as most important control on the competition between DNRA and denitrification. The organic carbon to nitrate ratio and the kind of electron acceptor supplied (nitrate or nitrite) were identified as further controlling factors that together with the generation time discriminated between the two pathways. The metabolic interaction between nitrate- reducing and fermenting populations was stable under both pathways. One quarter of the nitrate reduction was coupled to the oxidation of sulfide, which was produced in the enrichment culture by microbial sulfate reduction, constituting a strong link between the nitrogen and sulfur cycle. All in all, this thesis provides new insights into the ecophysiology of microbial nitrate reducers by unraveling the driving forces of the competition between different nitrate reduction pathways and by revealing important metabolic interactions with other microbial guilds.