Trace metal uptake and use in soil diazotrophs and marine Vibrios: Alternative nitrogenases, siderophores, and quorum sensing OR Efforts of the very small to acquire the very scarce

Abstract

The need for living things to obtain trace elements creates a fundamental interaction between Life and Earth. Iron (Fe), and a handful of other metals, are used ubiquitously in biochemistry, yet must be extracted from insoluble minerals. The major biogeochemical cycles occurring at the Earth’s surface are also catalyzed by metalloenzymes. Trace elements therefore form one of the strongest links in the coupling of geologic and biologic processes and their use is key to understanding the co-evolution of Life and Earth. This thesis explores two microbial solutions to the problem of trace metal scarcity: the substitution of different trace elements in enzymes and the production of siderophores or small molecules that aid in trace metal uptake. I use high-throughput sequencing and newly developed isotopic techniques to determine that ‘alternative’ nitrogenases – containing vanadium (V) or Fe-only instead of molybdenum (Mo) – can make substantial (>20%) contributions to nitrogen fixation and nitrogenase diversity in coastal sediments, raising questions about their overall role in nitrogen cycling. My experiments with nitrogen-fixing Azotobacter vinelandii cultures show that the siderophore protochelin is co-regulated by limitation for both Fe and the nitrogenase cofactor Mo. Protochelin complexes Mo, and up-regulation under Mo-limitation is consistent with its long hypothesized role as a molybdophore. Additionally, I report that A. vinelandii can invest > 30% of fixed nitrogen in siderophores and that this nitrogen is isotopically distinct from biomass. Under conditions of iron-limitation siderophore production changes the isotopic composition (δ15N) of A. vinelandii biomass, a result that may help to explain variations in δ15N from laboratory and field studies of diazotrophs. Finally, I investigate the regulation of siderophore production by Fe and quorum sensing (QS, a microbial counting technique that allows bacteria to tailor their gene expression to their cell density). I find that the marine bacterium Vibrio harveyi uses a single gene cluster to produce both strong, cell-bound siderophores as well as weak soluble siderophores and that QS allows V. harveyi to calibrate its siderophore production to its cellular iron uptake capacity. This final chapter highlights ‘biotic’ and ‘abiotic’ controls on siderophore production and the potential importance of microbial interactions in geobiological processes.