Expanding the Knowledgebase of Earth’s Microbiome Using Culture Dependent and Independent Methods

Author

Trevor Murphy, Southern Illinois University CarbondaleFollow

Date of Award

6-1-2021

Degree Name

Master of Science

Department

Molecular Biology Microbiology and Biochemistry

First Advisor

Hamilton-Brehm, Scott

Abstract

Microorganisms exist ubiquitously on Earth, yet their functions and ecological roles remain elusive. Investigating these microbes is accomplished by using culture-dependent and culture-independent methodologies. This study employs both methodologies to characterize: 1) the genomic potential of the novel deep-subsurface bacterial isolate Thermanaerosceptrum fracticalcis strain DRI-13T by combining next-generation and nanopore sequencing technologies and 2) the microbiome of the artificial marine environment for the Hawaiian Bobtail Squid in aquaculture using next-generation sequencing of 16S rRNA gene. Microbial ecology of the deep-subsurface remains understudied in terms of microbial diversity and function. The genomic information of DRI-13T revealed a potential for syntrophic relationships, diverse metabolic potential including prophages/antiviral defenses, and novel methylation motifs. Artificial marine environments housing marine the Hawaiian Bobtail Squid (Euprymna scolopes) contain microorganisms that can directly influence animal and aquaculture health. No studies presently show if bacterial communities of the tank environment correlate with the health and productivity of E. scolopes. This study sought to address this by sampling from a year of unproductive aquaculture yield and comparing the bacterial communities from productive cohorts. Bacterial communities from unproductive samples show less bacterial diversity and abundance coupled with shifts in bacterial composition. Nitrate and pH levels between the tanks were found to be strong influences on determining the bacterial populations of productive and unproductive cohorts.