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There is now a CONTENT FREEZE for Mercury while we switch to a new platform. It began on Friday, March 10 at 6pm and will end on Wednesday, March 15 at noon. No new content can be created during this time, but all material in the system as of the beginning of the freeze will be migrated to the new platform, including users and groups. Functionally the new site is identical to the old one. webteam@gatech.edu
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Summary Sentence: The Spring 2022 OSE Seminar Series -- Roth Conrad, OSE Ph.D. Candidate
Full Summary: The seminar is offered both virtually and in person on the 3rd floor of ES&T in the new Ocean Room.
SP2022 ImageCulture-independent exploration of the ocean has identified cosmopolitan species-like populations of prokaryotes with potential endemic genomic adaptations related to ocean depth or ocean basin. However, these environmental prokaryote populations are not well defined, and how these species-like populations are maintained, the extent of their intra-population structure, and how new species evolve from within these populations remain poorly understood. To provide new insights into these issues, we used metagenomic assembly, binning, and read-recruitment methods with depth stratified short-read shotgun metagenome samples (surface – 5601m) from the Atlantic, Pacific, and Gulf of Mexico to identify and track metagenome-assembled genomes (MAGs) as representatives of (sub)populations. We developed a novel algorithm to define which reads recruited from a metagenome belong to a target population as an alternative to manual determination or the commonly used 95% nucleotide identity threshold. We then related the average nucleotide identity of these recruited reads (ANIr) to nucleotide diversity (p) and used ANIr to quantify the intra-population sequence diversity occurring in the sample where we recovered a MAG relative to other samples where we detected the MAG. Concomitantly, we tracked gene-content changes by identifying genes found at differential frequencies within a population between samples. Our results showed that many populations were abundant or detectable in only one or a few samples of an ocean basin at similar depths while several of these populations were more cosmopolitan between depths and ocean basins. Only two of these cosmopolitan populations spanned more than a few similar depths and were identified as Pseudoalteromonas and Alteromonas, detected at both the surface (0-200m) and the deep (>1000m). Our results also showed decreased ANIr and increased gene-content difference between the population of one sample compared to other samples where a highly or closely related population was detected (e.g., same 95% ANI-based genomospecies or similar 85-95% ANIr) that correlated with distance from the sample of MAG origin. These data suggest that cosmopolitan genomospecies may show endemic adaptation as they disperse indicative of population divergence and speciation. Collectively, these results advance the methods to identify and track sequence-discrete populations and show that discrete units of microbial diversity exist temporally and locally with little to no exceptions.
