From biogeography to bioindicators: Exploring New Zealand’s soil bacteria

Abstract

Soil bacteria are indispensable members of the soil environment, vital for supporting both natural ecosystems and agricultural land. It is therefore crucial that we understand how natural and anthropogenic driven variation in the soil impacts bacterial communities and their functional contributions. This thesis applied next-generation sequencing technology to investigate patterns in soil bacteria biogeography at small and large spatial scales to ultimately determine how bacterial communities can be used to inform on soil quality. A methods study was conducted to identify a DNA extraction protocol which can be universally applied to investigate bacterial communities, and eukaryotic taxa, across a wide range of environment types. This method was then employed to extract DNA from soil, stream sediment and stream water samples collected across small spatial scales (e.g., tens to hundreds of metres) within a native forest catchment. Amplicon sequencing of these samples revealed transient connectivity between bacterial communities in terrestrial and aquatic environments. Large scale investigations of soil bacterial communities in ~5,000 samples collected across New Zealand confirmed that pH and soil nutrient content strongly correlated with changes in bacterial community composition, more so than spatial or climatic variables. These soil variable changes were closely linked to land use, and land use history impacted bacterial community composition and functional potential. Even eight years after conversion from pine plantation to grazed pasture, bacterial communities within the soil were distinct to those found within long term reference sites for both the historic and current land uses. Finally, the relationships between soil bacterial communities, land use and soil physicochemical variables were shown to be predictable to the extent where bacterial community composition can be used to determine the quality of the soil. This thesis greatly advances our understanding of the factors which govern the distribution and functional potential of soil bacterial communities across New Zealand and helps to close the gaps in global bacterial diversity data. Importantly, the implications of human land use on soil microbial communities are highlighted and crucial evidence is provided for how soil monitoring can be improved by incorporating bacterial data. The results from this thesis can be used to advise best-practice guidelines for soil monitoring that ultimately ensures the long-term sustainability of our agricultural and pastoral industries, while caring for our natural environments.