Ecological and evolutionary perspectives on bacterial resource use

Abstract

Bacterial metabolism mediates many biochemical transformations important to the stability and health of a diverse range of ecosystem types. In my dissertation, I examine the evolutionary and ecological context of a subset of bacterial metabolic pathways related to energy and metabolic precursor production that are crucial for bacterial growth. Specifically, I examine whether these pathways are conserved across a large, phylogenetically diverse set of organisms, whether related organisms respond similarly to differences in resource inputs, and whether knowledge of these pathways or phylogenetic relatedness can aid in the prediction of bacterial growth rates across a wide range of C substrates. While I found only a weak phylogenetic signal in the presence or absence of these pathways, there was strong evidence that constraints have limited the number of observed combinations of these pathways. Only 265 (6.5%) of the 4096 potential pathway combinations were found in this dataset of 8178 genomes. I propose this may suggest strong environmental selection acting to rapidly change pathway presence or absence, regardless of past evolutionary history. In order for this suggestion to be feasible, organisms must respond to their environment in a phylogeny-independent manner. To address this, I compared taxa response using 16S amplicon libraries from plots with substantial variation in C and N availability resulting from plant species identity in a long-term field experiment. I found an inconsistent response of soil bacteria at higher taxonomic levels to resource variation, in agreement with organisms responding to environment in a phylogeny-independent manner. I then cultured 56 bacterial isolates from these plots to examine the relative strength of phylogeny versus metabolic pathways in explaining growth responses of isolates across a range of substrates. Phylogenetic relatedness and similarities in energy metabolism each explained about 30% of the observed variation in patterns of bacterial growth, with about 50% overlap between the two approaches. Both phylogeny and energy metabolism are important in determining bacterial growth; however, environmental selection may lead to convergence towards a small number of ecotypes within a system despite high levels of phylogenetic diversity. The strength and consequences of such environmental optimization of metabolism warrant further study.