UC Irvine

Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, our understanding of their biogeographic patterns and the processes that drive those patterns is underdeveloped. My dissertation provides a comprehensive analysis of bacterial biogeographic patterns and investigates how dispersal into soil impacts microbiome assembly. To establish global biogeographic patterns, I analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project (Chapter 1). This study compared bacterial diversity trends across habitats and provided a big-picture analysis that linked multiple smaller-scale studies. From this study, I found that soils contained the highest bacterial richness within a single sample, prompting a follow-up field experiment to study how dispersal may drive the high diversity found in soils.

Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly and diversity. Dispersal may be particularly important to leaf litter, the top layer of soil, which is exposed to microbial immigration from multiple sources and plays a key role in nutrient cycling in soils. However, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. To fill this gap, I characterized the rate and composition of bacteria dispersing into leaf litter via three dispersal routes (through the air, from nearby vegetation, and up from the bulk soil) and simultaneously quantified the impact of those routes on soil microbiomes (Chapter 2). I found that dispersal from vegetation changed the microbiome composition and functioning, driving the decomposition of leaf litter. That result led to another field experiment to characterize immigration rates and composition of microorganisms dispersing from the plant communities of two ecosystems: a grassland and a shrubland (Chapter 3). Immigrating microorganisms were strongly correlated with the local vegetation, although only within 1 m – a much shorter dispersal distance than previously assumed. Overall, my dissertation highlights the high microbial diversity found in soils and suggests that dispersal into leaf litter from local vegetation plays a central role in the assembly of soil microbiomes.