Spatial Distribution of Specific N-cycle Microorganisms in Oxic River Sediments

Anthropogenic nitrogen (N) inputs cause considerable damage to aquatic ecosystems. Anaerobic ammonia oxidising bacteria (anammox bacteria or AnAOB) have an important role in the removal of fixed N in oxic sediments, despite being obligate anaerobes. AnAOB are also important in wastewater bioreactors. Specifically, in complete autotrophic nitrogen removal over nitrite (CANON) bioreactors, AnAOB interact with other N-cycle groups such as ammonia oxidising bacteria (AOB), archaea (AOA), complete ammonia oxidation (comammox) bacteria and denitrifiers. This thesis aims to investigate the spatial localisation of N-cycle groups in relation to AnAOB in oxic river sediments. Here, imaging techniques such as confocal microscopy and catalysed reporter deposition fluorescent in situ hybridisation (CARD-FISH) were utilised. In addition, a novel negative staining technique was developed to analyse sediment grain microtopology. This technique allows accurate 3D measurements of nominally non-fluorescent objects using confocal microscopy - in this case the surface of sediment grains. This thesis found that AnAOB exhibit a chasmoendolithic lifestyle – inhabiting anoxic pores on sediment grain surfaces – a strategy not previously observed in bioreactors. Furthermore, analysis of the spatial interactions of AnAOB with complete ammonia oxidising (comammox) bacteria show 35.2% of AnAOB colonies are found within 1 μm of comammox bacteria colonies, suggesting some form of beneficial relationship. In conclusion, we have a previously unknown oxygen avoidance strategy in AnAOB and have further analysed the relationship of AnAOB with other N-cycle groups in oxic sediments.