The Influence of microbial communities and nitrogen contamination on each other in groundwater.
Creators: name: Morrissy, Justin
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 310703
subject: Microbial ecology
classificationCode: 370703
subject: Groundwater hydrology
classificationCode: 4104
subject: Environmental management
classificationCode: 410404
subject: Environmental management

description: This study was originally intended to be a laboratory study on the effects of different physicochemical conditions on groundwater. This was to be represented by controlled, lab scale microcosms inoculated with a microbial community from an aquifer contaminated with multiple nitrogen sources. Instead, due to COVID-19 restrictions this study utilised a next generation sequencing and physicochemical data set that was collected early in the project and studied the effects of nitrogen contamination on the microbial communities in an aquifer contaminated with multiple sources. Nitrogen is both an essential nutrient for life and a limiting nutrient in groundwater ecosystems. This presents a difficult case as fluctuating natural concentrations of nitrogen in the environment can make it difficult to determine the extent and impact of the nitrogen contamination. The overarching aims of this study were to: (1) review and discuss the causes, impacts and remediation of nitrogen contamination and its interactions with its surroundings; (2) characterise the microbial communities in a nitrogen contaminated aquifer and determine the effects of different nitrogen molecules on the microbial communities within the aquifer; (3) determine if nitrogen contamination is having an effect on the structure and ecosystem functions of the microbial communities; (4) analyse the use of clear and functional definitions in the scientific literature and the importance of the relationship between science and the legislative process.

Through a review of the scientific literature, nitrogen was shown to be accumulating in the environment due to the artificial synthesis of nitrogen increasing the fixation of nitrogen beyond the capacity of natural nitrogen degradation back into N2 gas. Nitrogen contamination was shown to originate from both diffuse sources such as agriculture and point sources such as wastewater treatment plants. Additionally, nitrogen contamination was shown to cause multiple human health effects and severe environmental damage through processes such as eutrophication. The costs of nitrogen contamination to the global economy were shown to be in the range of multiple billions of dollars. The efficiency and effectiveness of current and past remediation techniques were discussed, and the pros and cons of potential future remediation techniques such as biostimulation and bioaugmentation were discussed.

Using next generation sequencing and various chemical testing the physicochemical properties and microbial communities in a nitrogen contaminated aquifer were characterised. Proteobacteria was shown to be one of the most abundant phyla across all the sampling locations and nitrate (NO3-) and ammonium (NH4+) were shown to be the main contaminants in the region. Nitrate was found to increase overall richness in the microbial communities whereas NH4+ was found to decrease overall richness. The microbial communities were further analysed in terms of the ecosystem functions performed by the most abundant species. The sites contaminated with NO3- typically had an increase in the abundance and variety of species capable of nitrate reduction while still maintaining many other ecosystem functions. Contrastingly the NH4+ contaminated sites showed a significant spike in the abundance of species in the Planctomycetes phylum and much fewer ecosystem functions. The analysis of the microbial communities showed that the Planctomycetes phylum had a significant relationship (P-value &lt;0.01) with the presence of NH4+. Further analysis of this relationship revealed that the Planctomycetes phylum is the only phylum capable of anaerobic ammonium oxidation (ANAMMOX) which is the likely cause for this relationship.

The scientific literature was found to have multiple, sometimes conflicting definitions of words important to environmental science such as ‘background’, ‘contamination’ and ‘pollution’. The dictionary definition and multiple definitions for these words were studied and clear, functional and encompassing definitions for these words were proposed. Several legislative documents were then analysed for their use of these words and potentially incorrect, misleading or confusing uses of these words were discussed. Additionally, it was determined that though the appropriate legislation should be acknowledged in the scientific literature, the use of legislation to define scientific concepts such as contamination or pollution progresses neither science nor legislation. 

The major findings of this study include (1) the increased ease and accuracy of accessing information surrounding nitrogen contamination in the environment (2) the effects of NO3- and NH4+ on the structure of microbial communities in groundwater (3) the effects of NO3- and NH4+ on the ecosystem functions of the microbial communities in groundwater and the identification of Planctomycetes as potential indicator organisms for NH4+ contamination (4) the clarification of several ambiguous definitions within the literature. This study highlights how a relatively short-term study can significantly increase our understanding of the extent and impacts of nitrogen contamination in groundwater. Additionally, the identification of Planctomycetes as potential indicator organisms has large implications not only in the identification of NH4+ contamination at this and other sites but it also highlights the usefulness of indicator organisms in the tracking of contamination in groundwater.