UC Irvine

Nutrient supply regulates the activity of phytoplankton, but the global biogeography of nutrient limitation and co-limitation are poorly understood. Bottle incubation experiments have revealed patterns of nutrient limitation but have limited spatial coverage, and surface nutrient concentrations are below detection limits in much of the oligotrophic ocean. In my first chapter I used genomic changes as an indicator of adaptation to nutrient stress. We collected 909 surface metagenomes from the Atlantic, Pacific, and Indian Ocean, quantified the global genome content of Prochlorococcus and inferred local nutrient stress based on shifts in nitrogen, phosphorus, and iron assimilation genes. Our ‘omics-based description of phytoplankton resource use provided a nuanced and highly resolved quantification of nutrient stress in the global ocean.We see a clear association between genome content and nutrient limitation, but the underlying population genetics of these genomic differences and the mechanisms by which they arise are unknown. In my second chapter, I described the functional diversity found within Prochlorococcus and captured the link between low nutrient adaptation and phylogeography. I analyzed 630 surface ocean metagenomes and quantified global variation in gene abundance, phylogeny, and genomic structure through consensus marker genes and metagenomically assembled genomes (MAGs). The analysis of functional diversity and phylogeography revealed widespread flexibility in genomic content, with a phylogenetically conserved haplotype driven by P limitation. While omics-based analysis can give a detailed representation of a microbial community, these methods are spatially and temporally limited to the time and location of sampling. Remote sensing-based descriptions of microbial nutrient limitation have been proposed but have never been validated in situ. For my third chapter, I combined remote sensing and metagenomically derived estimates of nutrient limitation to expand both the temporal and spatial extent of our characterization of nutrient limitation. Based on this in situ validation of the remote sensing products I analyzed the past 10 years of data and captured novel seasonal variation and a recent reduction in global nutrient limitation.