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Quantification of gene expression from metatranscriptomic analysis of a Lake Erie spring diatom bloom

Shupe, Kari L.
http://orcid.org/0000-0002-0945-0097
http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1648659102618346

Abstract Details

2022, Master of Science (MS), Bowling Green State University, Biological Sciences.
Surface water samples, collected on the U.S. EPA Research Vessel Lake Guardian at ice-free sampling stations across Lake Erie on April 7 and 8, 2018, provided a snapshot of the composition of the lower food web, it’s functionality and the physicochemical environment aimed at examining the mechanisms that drive diatom fitness and factors that affect their seasonal contribution to recurring hypoxic conditions in the hypolimnion of the Lake Erie central basin. TN:TP and DIN:TP molar ratios were conversely deficient in the western and central parts of the lake, with the more bioavailable, dissolved inorganic nitrogen deficiency occurring in the central basin. P deficiency occurred for both TN:TP and DIN:TP ratios the eastern basin. Si:TP indicated Si deficiency (<16) in the central basin, flanked by Si-replete conditions in the western and eastern basins. KEGG GhostKOALA taxonomic analysis of station ER42 surface water indicated that diatoms were less abundant at 0.51% than diatom predators such as copepods (Arthropoda) and dinoflagellates (Alveolata) at 7.22% and 2.27% respectively, suggesting spring predation could have been a factor contributing to the fate of the bloom. Parasitic oomycetes, however, were slightly less abundant than diatoms at 0.47%, and chytrids were undetected in the sample. Metatranscriptomic analysis from surface net tow samples at six EPA stations revealed twelve diatom genes exhibiting high expression (TPM ≥ 1001) from KEGG PATHWAY database categories Glycolysis/Gluconeogenesis, Biosynthesis of Cofactors, Photosynthesis, Ribosome and RNA Transport, Phagosome, and Protein Processing. Gene expression involving ribosomal translation was also high and comprised 35% of total gene expression for the Genetic Information Processing pathway, while total expression for replication and transcription was comparatively low. Total gene expression for the five sampling stations in the central and eastern basins was highest at ER15M in the eastern basin, where NO3− and SiO2 concentrations were highest, and lowest at ER30 in the central basin, where NH3 was highest and SiO2 was below detection. Gene expression involving nitrogen assimilation ranged from below detection to low (0–291 TPM), while genes involved with photosynthesis exhibited the highest expression values (0–87,900 TPM), with most expression occurring in the eastern basin.
George Bullerjahn, Ph.D. (Advisor)
Paul Morris, Ph.D. (Committee Member)
Robert Michael McKay, Ph.D. (Committee Member)
81 p.
Biology; Microbiology
diatom; nutrient trends; diatom gene expression; diatom export; Lake Erie taxonomy

Recommended Citations

Citations

  • Shupe, K. L. (2022). Quantification of gene expression from metatranscriptomic analysis of a Lake Erie spring diatom bloom [Master's thesis, Bowling Green State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1648659102618346

    APA Style (7th edition)

  • Shupe, Kari. Quantification of gene expression from metatranscriptomic analysis of a Lake Erie spring diatom bloom. 2022. Bowling Green State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1648659102618346.

    MLA Style (8th edition)

  • Shupe, Kari. "Quantification of gene expression from metatranscriptomic analysis of a Lake Erie spring diatom bloom." Master's thesis, Bowling Green State University, 2022. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1648659102618346

    Chicago Manual of Style (17th edition)

bgsu1648659102618346
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This open access ETD is published by Bowling Green State University and OhioLINK.