Niche differentiation between ammonia-oxidizing bacteria in aquatic environments

Abstract

The aim of the studies presented in this thesis was the search for niche differentiation between the ammonia-oxidizing bacteria in aquatic environments. Ammonia-oxidizing bacteria are chemolitho-autotrophic microorganisms responsible for the first, mostly rate-limiting step of the nitrification process, i.e. the conversion of ammonia into nitrite. The recent development of molecular techniques had overcome the difficulties inherent to the classic cultivation-based methods applied to these slow-growing bacteria. Finally, a large diversity of ammonia-oxidizing bacteria has been uncovered in several aquatic environments. However, only a few studies focused on niche differentiation between these bacteria within the same estuarine or freshwater environment. The studies reported in this thesis demonstrated the existence of an intriguing niche differentiation between ammonia-oxidizing bacteria driven by different factors, such as ammonia and oxygen availability, salinity, tidal regime, physical-chemical characteristics of the substrate for the biofilm formation and anthropogenic influences. In particular, in shallow freshwater lakes dominated by submerged macrophytes ammonia-oxidizing bacteria appeared to utilize the epiphyton as a niche in addition to the benthic and pelagic compartments (Chapters II and III). The molecular detection of ammonia-oxidizing bacteria on the leaves of submerged macrophytes, like Potamogeton pectinatus, is the first time ever to be reported (Chapter II and III). Diversity, numbers and activity of benthic, pelagic and epiphytic ammonia-oxidizing bacteria was influenced by the characteristics of both the compartments and the lakes in which the samples were collected (Chapter III). Ammonia-oxidizing bacteria showed higher diversity, numbers and activity in the benthic compartment in comparison to the pelagic compartment (Chapter III). Members of the Nitrosomonas oligotropha lineage dominated the pelagic compartment and were present in the benthic section together with members of the clusters 0 and 3 of the Nitrosospira lineage. The epiphyton was colonized by both pelagic and benthic ammonia-oxidizing bacteria. The dynamics of colonization of the epiphyton by benthic and pelagic ammonia-oxidizing bacteria were investigated in a microcosm experiment (Chapter IV). Results showed that benthic ammonia oxidizers colonized the surface of the macrophytes both during the sprouting of the tubers and the resuspension of sediment particles. Moreover, being attached to the macrophytes surface appeared to be favorable for pelagic species that were otherwise not detectable in their original compartment. Restoration procedures applied to the lakes in the past at different intensities, appeared to influence the overall fitness of ammonia-oxidizing bacteria negatively (Chapter III). Briefly, the best restored lake, i.e. Lake Nuldernauw, nowadays colonized by a Charophytes meadow showed the lowest diversity, numbers and potential activity of ammonia-oxidizing cells. The influence of anthropogenic inputs on the niche differentiation of ammonia-oxidizing bacteria was also shown in a study along a freshwater-estuarine gradient in addition to the effects of salinity as well as ammonia and oxygen availability (Chapter V). Salinity showed to be a steering factor for the succession from salt-sensitive to salt-tolerant ammonia-oxidizing species in freshwater sediment during a microcosm experiment with controlled environmental perturbations (Chapter VI). Finally, the studies presented in this thesis contributed to the knowledge on the niche differentiation between ammonia-oxidizing bacteria in freshwater and estuarine ecosystems by describing the epiphyton of submerged macrophytes as a novel niche for ammonia oxidizers and by describing the response of these bacteria to natural and anthropogenic environmental perturbations