Final blog post

20160729_113234Well everyone, this is it, my final blog post for the summer.  I’ve learned a lot and spent some great moments here at UTMSI and I’d like to thank everyone that made it possible.  Our mentors provided us with useful advice and lessons that will definitely help us in our future years.  And finally my fellow REUs made the entire experience that much greater, we had many laughs and moments we’ll never forget.  It was definitely an unforgetable experience from which we all learned a lot, and I’m sure going to miss everyone. But as is the custom, here is the abstract for my seminar presentation.


In recent years there has been a large expansion of the tree of life from the massive number of novel genomes that have been obtained using metagenomics in recent years. Examination of commonly used amplification primers for 16S rRNA gene diversity surveys revealed that they overlook many newly discovered archaeal groups. Thus, we redesigned universal PCR primers 530F and 907R that target novel archaeal groups. The community structure of the Mission Aransas NERR Research Reserve (near Port Aransas, TX) shallow estuary sediments has not been previously explored.  To investigate the diversity of these communities we sectioned (3 cm intervals, down to 15 cm) sediment cores from 3 different sites (east and west Copano Bay and Mesquite Bay) in the reserve.  Dissolved oxygen, nitrate, and nitrite porewater concentrations were measured in the sediments and the cores were subdivided to extract total DNA and RNA.  Phylogenetic analyses revealed the presence of several novel lineages including 4 archaeal phyla and 9 different bacterial phyla in Copano Bay. The archaea belong to phyla that have been previously associated with marine and estuary sediments around the world including 2 clades (Altiarchaeales and a novel lineage) within the DPANN superphylum, Euryarchaeota (Marine Benthic Group D), and Bathyarcheota. The bacteria include Planctomycetes, Betaproteobacteria, Deltaproteobacteria, and candidate phyla WS3 and OP8, and what appears to be a novel phylum.  This novel phylum is related to sequences previously recovered from South Pacific deep abyssal sediments. While these new primers revealed there is substantial novel diversity present in the NERR reserve, much work remains to be done involving the geochemical properties of the sediments and the ecological roles of these organisms.

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