Global analysis of biomineralization genes in magnetotactic bacteria

Magnetotactic bacteria (MTB) are a phylogenetically diverse group of bacteria remarkable for their ability to biomineralize magnetite (Fe3O4) or greigite (Fe3S4) in organelles called magnetosomes. MTB can account for up to 30% of the microbial biomass in a an aquatic habitat [1]. MTB also take up large amounts of iron from the environment in order to form magnetosomes—they are estimated to take up anywhere from ~1-50% of dissolved iron inputs into the ocean [2]. However, relatively little is known about the ecology of MTB, other than species diversity in sampled habitats [3]. On the contrary, much is known about the genetics and cell biology of MTB. The majority of genes required for magnetosome formation are encoded by a magnetosome gene island (MAI) and many of their functions are known. However, no previous studies have involved unbiased genetic analysis of biomineralization genes. This work expands the genetic toolset for studying MTB in the lab and identifies novel genes—or functions of genes—that have an impact on biomineralization. Importantly, this dissertation also lays the groundwork to bridge the gap between genetic and environmental studies of MTB./nThe first chapter of this dissertation, a published review article, covers the work that has been done on the genetics of MTB and where the field is headed. We focus on the genetics behind the formation of magnetosomes and biomineralization. Then, we cover the history of genetic discoveries in MTB and key insights that have been found in recent years and provide a perspective on the future of genetic studies in MTB./nThe second chapter of this dissertation, a published primary research article, takes an unbiased approach to study genes, both inside and outside the MAI, needed for magnetosome formation under different growth conditions. First, we developed the use of random barcoded transposon mutagenesis (RB-TnSeq) in Magnetospirillum magneticum AMB-1 and generated a library of tens of thousands of unique mutant strains. The RB-TnSeq library allowed us to determine the essential gene set of AMB-1 under standard growth conditions. We also performed magnetic selection screen in varied growth conditions to uncover novel genes required for biomineralization in high iron and anaerobic growth conditions. We discovered more nuanced functions for the MAI gene mamT and several ex-MAI genes that may be important for biomineralization./nThe third chapter of this dissertation, a published review article written in collaboration with Dr. Andy Tay, covers the potential uses for microfluidics devices for studying MTB from separating cells based on magnetic properties to directed evolution to single cell analysis. Being able to study magnetotactic bacteria in highly controlled, quantifiable environments will be a boon to the field. Additionally, using microfluidics devices to mimic natural environments will be valuable for linking the cell biology and genetics of MTB to their ecology. I end the dissertation with a concluding chapter on the future prospects for employing genetics to understand the molecular mechanisms of biomineralization in a variety of environmental contexts.

Advisor: Komeili, Arash