Award: OCE-1931113

The SAR11 clade of bacterioplankton comprises the most numerous microorganisms in the oceans. SAR11 have specialized into distinct groups with unique spatio-temporal distributions, including subclade IIIa, that is adapted to brackish waters, and LD12, a freshwater clade. Both of these groups are highly abundant in coastal and estuarine systems where fresh water outflow to the ocean is prevalent. Given their high abundance in these environments, SAR11 IIIa and LD12 organisms are important for coastal elemental cycles like those of carbon and nitrogen. The goal of this research was to investigate how salinity dynamics affect the population structure and physiology of these organisms so that we can gain predictive capacity for how future changes in salinity, e.g., those brought about by sea level rise, will affect these taxa and their contributions to biogeochemical cycles. The outcomes of this work were multifold: i) we generated new data on the growth physiology of these two SAR11 groups using pure culture representatives, ii) we cataloged the population dynamics of subclades IIIa and LD12 across a coastal time series dataset using whole community genome sequencing (a.k.a. metagenomics), iii) we involved undergraduate students in real research by building curricula for first year university biology laboratory classes that incorporate experiments to measure microbial physiology and perform comparative genomics. The pure culture work investigated the hypothesis that these different subclades of SAR11 are adapted to specialized salinities through alterations in their genentic capabilities to manage osmotic stress. Osmotic stress management is frequently done through the production or import of compatible solutes- small molecules that can balance the internal ionic strength of the cell with that of the external environment. Using strains that represented the two subclades, LSUCC0261 (IIIa) and LSUCC0530 (LD12), we measured the transcription and internal metabolite profiles of these cells. These data are the first for organisms in these SAR11 subclades, and provide new insight into how these organisms regulate their genes and manage their metabolite pools, including compatible solutes. The coastal time series metagenomes spanned four sites in the northern Gulf of Mexico across over 460 km (286 mi) of coastline. We collected data at all sites over the course of 11 months and sequenced seven samples from each site to provide coverage across that time period for the four locations (a total of 28 metagenomes). The metagenomic sequencing provided DNA sequences for the free-living microbial community members (those not attached to large particles) in these samples. These DNA sequences were used to assess the relative abundance of organisms for which we already have genome sequences (e.g., our SAR11 IIIa and LD12 representatives) through a process of matching the sequence reads to the genomes and quantifying the differences in sequence matches (a.k.a. read recruitment). The DNA sequences were also used to assemble new genomes, a process called metagenomic assembly and binning. These new genomes will give us the ability to more deeply explore how microbial populations change over space and time with differences in salinity and other environmental parameters that we measured at each site (e.g., nitrogen concentrations, temperature, etc.). These data are the most comprehensive microbial survey done for this coastal region, and one of the most extensive coastal metagenomic time series data sets collected anywhere. Simultaneously, we developed curricula for undergraduate biology laboratory sections that involved college students in real research. These Course-based Undergraduate Research Experiences (CUREs) contrast with traditional biology laboratories that repeat experiments with known outcomes for training purposes. CUREs allow students to perform experiments where the outcome is not yet known, using samples/specimens relevant to active research, and do so in a course setting to facilitate greater participation than can be accomodated by placing undergraduates into research laboratories. Our CUREs engaged nearly 250 students at two universities during the course of the grant. Students were involved in measureing the growth and physiology of multiple different marine bacteria, as well as in predicting metabolism through examination of microbial genome sequences. Last Modified: 04/26/2023 Submitted by: Cameron Thrash