Testing the role of fine-scale diversity for local adaptation and population stability in Synechococcus
A major challenge in marine microbial ecology is understanding the origins and functional role of taxonomic and genomic diversity among microorganisms in the ocean. Within a species, strains can demonstrate markedly different genomic properties, physiologies, and ecologies — termed microdiversity. Since its discovery in 1950, numerous studies have identified phylogenetically and ecologically distinct lineages or ecotypes. Even within ecotypes, subpopulations of Synechococcus have been identified, separated by genomic areas of flexibility hypothesized to confer ecological distinction and protection from viral lysis and grazing. Given their global abundance, ecological importance, and genetic tractability, Synechococcus provides an excellent model system to explore the factors controlling fine-scale population genome variation.
Whole-genome sequencing of freshwater bacteria using long-read sequencing (Nanopore)
The Laurentian Great Lakes (LGL) represent environmentally diverse, hydrologically connected ecosystems where primary production ranges from extremely low (Superior) to locally very high due to recurring harmful algal blooms. The LGL have been exposed to numerous environmental perturbations that have altered water quality, primary producers, nutrient composition, and water clarity. These changes likely have cascading effects on community assemblages and subpopulation dynamics. As part of ongoing research with the EPA and NOAA, the Coleman Lab has collected 9 years of water samples across the LGL for community-based sequencing (e.g., amplicon, meta-‘omic- based). A recent study found that despite the large environmental heterogeneity, numerous taxa such as Limnohabitans and Methylophilaceae had wide distributions across the LGL; however, whether these cosmopolitan taxa are truly identical at a genetic and functional level, is still unknown. This knowledge gap precludes our ability to estimate the ecosystem function of a taxon.
High-throughput cultivation of bacterioplankton from the coastal Northern Gulf of Mexico
Cultivar representatives from diverse lineages and locations are essential for the elucidation of fundamental microbiological questions and hypotheses. Over 3 years, we conducted over 17 DTE experiments totaling 7,820 individual incubations , yielding 328 repeatably transferable isolates. These isolates represented many previously uncultivated and underrepresented lineages such as SAR11 LD12, Gammaproteobacteria OM252, and Actinobacteria acIV. Moreover, cultivars allowed for important inferences into their ecophysiology and evolutionary history, as well as vastly expanded the geographic representation of their clade.
Mississippi River Microbiome
The Mississippi River and its tributaries are an essential resource to millions of people for clean drinking water, transportation, recreation, agriculture, and industry. However, water quality has rapidly declined over the past century due to human activity and is directly linked to the seasonal hypoxia zone, “the Dead Zone”, found in the northern Gulf of Mexico. Acting as first responders, microorganisms can mitigate, exacerbate, and/or serve as predictors for water quality, yet we know little about their community structure or ecology at the whole river scale for large rivers. In collaboration with the nonprofit Ocean Adventure Rowing & Education (OAR) Northwest, water chemistry and filtered samples were collected over a 2900 km (39 sites) transect of the Mississippi River using human-powered row boats to help elucidate what impacts rive order and water quality have on the native microbial communities that inhabit the Mississippi River
The Microbes of the Mississippi River – A Rowing Adventure for Science in The Pursuit Blog
LSU scientist teams with rowboat team to research Mississippi River water in The Advocate Newspaper
The first cultivar from SAR11 LD12
Characterized by small streamlined genomes and high core genome conservation, SAR11 microorganisms are found throughout aquatic environments including open oceans, brackish estuaries, and freshwater lakes and rivers. The SAR11 clade, family Pelagibacterales, contains a diverse group of subclades with unique spatial and temporal distributions, however, all freshwater members belong to a single subclade, LD12. Like its marine counterparts, LD12 can comprise up to 21% of the freshwater bacterioplankton. Our existing knowledge regarding the underlying genomic basis for the SAR11 shift to freshwater ecosystems comes from culture independent methods: metagenomics and single-cell genomics, hampering a more thorough understanding of its biology. Here, we present the first cultivated representative from SAR11 LD12 and its associated genome.