Spatiotemporal patterns of prokaryotic communities in New Zealand agricultural soils

Abstract

New Zealand pasture soils are an important resource, contributing significantly to the economy and global food security. However, the sustainability of current land management practices is of great concern, leading researchers to investigate indicators of soil health. Soils house a wealth of microbial diversity that contributes significantly to ecosystem function. However, questions remain about the ecology of soil microbes, and how intensification of land management practices such as oversowing, increased stocking rate and fertilization impact soil microbial populations. In order to address these concerns, it is important to establish a baseline characterization of microbial community ecology in managed soils. To this end, the current work aims to identify factors that influence microbial community diversity, structure and composition over space and time, and in response to disturbance. This work employs high throughput sequencing of the 16S rRNA gene in order to capture a preponderance of prokaryotic diversity in order to link community shifts to physicochemical properties of interest.

This thesis employs a landscape-scale field study, exploring a group of 24 sites representing the three main land uses in New Zealand (dairy, sheep and beef and high country) in order to explore community differences in land uses of differing intensities. Samples were also taken over a seasonal cycle, after treatment with two fertilizers (phosphate and lime) to observe temporal and disturbance dynamics. The study integrates a number of physicochemical properties, revealing insights into the relative impacts of pH, land use, soil order, season and fertilization on prokaryotic communities. Results reveal strong relationships between community diversity, structure and composition and physicochemical factors (pH, land use intensity and soil order) showing landscape-scale relationships with pH and land use intensity that are sustained across time and with treatment, supporting previous results that show a strong relationship between pH and global prokaryotic communities. Links between prokaryotic communities and soil order when controlling for land use intensity provide insight into the impact of intensification on belowground communities, showing that the connection between prokaryotic communities and inherent soil properties (i.e. bedrock) weakens with increased intensification. This study also provides insight into the underexplored rare biosphere, showing that conditionally rare taxa in soils may not be responsible for overall community patterns, a result that does not match with findings for other environments. Overall, this thesis provides new insights into patterns of prokaryotic communities in pasture soils, highlighting the ways in which microbes may reflect the condition of the soils they inhabit, and consequently, general soil health.