Molecular characterization of bacterial diversity in New Zealand groundwater

Groundwater is a globally important natural resource and an integral part of the water supply in New Zealand. Due to high demand, the quality and availability of groundwater are both extensively monitored in New Zealand and globally, under State-of-the-Environment (SOE) monitoring programmes. SOE groundwater monitoring in New Zealand mainly evaluates hydrochemistry and until this thesis has largely overlooked the biotic component. Microbes including bacteria play a crucial role in ecosystem functioning by mediating biogeochemical processes in subsurface environments. Therefore, analysis of microbiological content will enable better evaluation of the health of groundwater ecosystems that is not fully reflected by chemical data alone. This project characterizes the bacterial diversity in New Zealand groundwater at national and regional scales using molecular methods and explores the underlying factors that shape the bacterial community structure. A simple molecular profiling tool, Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine community structure at local and national scales. The results revealed considerable diversity that was driven by groundwater chemistry. Roche 454-pyrosequencing was then used to obtain a deeper insight into New Zealand groundwater ecosystems, and showed that bacterial communities have many low abundance taxa and relatively few highly abundant species. In addition, microbial diversity is mainly related to the redox potential of the groundwater. But, despite this relationship, Pseudomonas spp. were the dominant genus at many sites even those with diverse chemistries and environmental factors. The final phase of the project set the platform to test whether these Pseudomonas spp. have acquired genetic material from other species via horizontal gene transfer (HGT) enabling them to adapt into a diverse range of habitats. A whole-genome sequencing approach (Illumina MiSeq platform) was used to develop six metagenomic databases as a resource to test this hypothesis. Initial results show some evidence for HGT and further investigations are underway. Overall, the knowledge generated across all phases of this project provides novel insights into New Zealand groundwater ecosystems and creates a scientific basis for the future inclusion of microbial status assessment criteria into regional and national groundwater monitoring programmes and related policies in New Zealand.