From genes to ecosystems: Understanding the role of agricultural management on soil biodiversity and functioning

Abstract

Soil, one of the most complex ecosystems on Earth, harbors a diverse array of organisms that profoundly influence nutrient cycling, plant health, and pollutant degradation. Despite decades of scientific inquiry, there are still significant gaps in knowledge about how different factors drive community composition in soils, including agricultural management and spatial and temporal factors. This thesis aimed to comprehensively investigate the effect of agricultural management on holistic biodiversity in New Zealand vineyards in space and time via short amplicon sequencing, and RNAseq to evaluate the impact of fungicide application on soil microbial function. The first data chapter found the strength of factors contributing to community assemblage at sub-regional (<15 km) spatial scales is hierarchically ordered habitat > site > agricultural management regime, with the effect of management being either very weak or absent. It appears that within habitats, vineyard sites represent discrete homogenized biodiversity islands, and while biodiversity differs between sites, the distance by which they are separated does not define how different they are. The second data chapter analyzed data collected over five years and again revealed that the effect of agricultural management on community composition was weak, and also showed it was inconsistent in both space and time for all taxa. In line with the findings from the first data chapter, biodiversity in each vineyard had a different response to management, and further analyses revealed each site had a distinct spray schedule, soil chemistry, and biology. Lastly, the third data chapter directly evaluated the response of microbes to fungicide applications in soil mesocosms and revealed that synthetic (but not non-synthetic) fungicides had a small effect on predominantly soil fungal community composition only in soils without previous exposure to fungicides. Differential transcription analysis revealed an effect of both types of fungicides on microbial function with the metabolism of aromatic compounds and sulfur upregulated. Although the response of soils with previous exposure to the same fungicides was minimal, it was recognizable. This thesis adds a significant body of knowledge to better understand how agricultural management affects soil biodiversity and offers compelling evidence on how other factors impact community assemblages in agricultural settings. The results from this thesis can be used to inform future best practice in agriculture and represent an important step towards sustainable agriculture.