UC Berkeley

Despite recent advances in microbial ecology, including the widespread use of high- throughput sequencing and micro-array technologies, microbial taxonomic, phylogenetic, and functional diversity remain understudied and poorly understood compared to our knowledge of macrofaunal diversity. In this dissertation, I work to close this gap by: (1) addressing the challenges of quantifying and comparing modern microbial data, (2) elucidating the changes to soil microbial diversity caused by widespread land-use change in tropical ecosystems, and (3) modeling the unique evolution of marine diatoms.

The dissertation begins in Chapter 1 with a general overview of the three original research projects that were carried out. In Chapter 2, I explore the use of diversity profiles, which are a novel way to analyze microbial datasets. Diversity profiles may be better suited than traditional ecological indices for quantifying data spanning multiple domains of life and dimensions of diversity. I evaluate the use of diversity profiles for analyzing microbial assemblages in order to determine whether the inclusion of rarity and similarity information changes the interpretation of comparative studies of microbial community diversity.

In Chapter 3, I assess the effects of anthropogenic land-use change, soil abiotic factors, and geographic distance on the taxonomic, phylogenetic, and functional gene diversity of soil microbes. I discover and quantify multiple dimensions of bacterial, archaeal, and fungal diversity in five different land-use types (Primary Forest, Secondary Forest, Oil Palm, Rubber, and Rice) throughout a dipterocarp forest landscape in Peninsular Malaysia. In Chapter 4, I identify major shifts in lineage diversification rates during diatom evolution by building a new diatom phylogenetic tree with significantly more environmental diatom sequences than previously published phylogenies.

The dissertation concludes in Chapter 5 with a summary of key findings: Microbial diversity comparisons may vary when taxa rarity and similarity information are considered by diversity profiles. Incorporating this information can greatly alter our comparisons and conclusions of microbial diversity in multi-community studies (Chapter 2); conversion of Primary Forest to other land-use types led to the loss of rare microbial OTUs (Chapter 3); fungal diversity was more strongly affected by land-use type than bacterial and archaeal diversity (Chapter 3); functional gene diversity was most strongly linked to abiotic soil environment (Chapter 3); and analyses of the global diatom phylogenetic tree yield estimates of diversification rate shifts across the tree with all but one of the estimated shifts corresponding to net increases in diversification rates (Chapter 4).