Skip to Main Content
 

Global Search Box

 
 
 

ETD Abstract Container

Abstract Header

Microbe-Environment Interactions in Arctic and Subarctic Systems

Zayed, Ahmed Abdelfattah
http://orcid.org/0000-0003-2793-2679
http://rave.ohiolink.edu/etdc/view?acc_num=osu1562494472055278

Abstract Details

2019, Doctor of Philosophy, Ohio State University, Microbiology.
The Arctic system has been undergoing a rampant change during the Anthropocene. This anthropogenic change has allowed for additional physical and biological positive feedback processes that in turn accelerate warming in the arctic and subarctic systems. Microbial community/functional dynamics are both (i) dramatically impacted by these rapid changes and (ii) key players in the biological positive feedback process that accelerates the change. Recent technological, analytical, and computational advances have allowed us to ask systems-level questions that encompass microbial and viral community dynamics (along with their potential functional dynamics) and high-resolution environmental measurements. This research took a systems-level approach to look for the first time at (i) the characteristics of Arctic marine viruses in a global context, and (ii) microbial community gene expression in a rapidly changing permafrost thaw gradient. Additionally, novel viral sequences recovered from the marine and terrestrial ecosystems studied here were used to build new resources and tools that accelerate viral discovery in nature. First, studying marine viral macro- and microdiversity from the Arctic Ocean to the Southern Ocean, enabled by the Tara Oceans Expedition, revealed the Arctic Ocean as a hotspot of viral diversity, with ~42% of the recovered viral populations originating from the Arctic Ocean viromes. In total 195,728 viral populations >10 kb were recovered from the global ocean to constitute the Global Ocean Viromes 2.0 (GOV2.0) dataset. Viral communities assorted into five distinct global ecological zones and the arctic viral communities formed their own distinct ecological zone. Additionally, this work revealed unexpected patterns and ecological drivers of viral diversity (at the community, inter-, and intrapopulation levels), within the Arctic Ocean, across latitudes, and across the depth of the global ocean. Second, genome-resolved metaproteomic study of microbial gene expression across a subarctic permafrost thaw gradient in Stordalen Mire, enabled by the IsoGenie project, revealed that (i) all of the carbon degradation pathways relevant to climate feedback were active in at least one habitat, and (ii) microbial lineages of Candidatus Cryosericota, a novel bacterial phylum overwhelmingly abundant under permafrost table but not above, were active in thawing habitats. Additionally, semi-quantitative metaproteomic analysis of community gene expression showed a high degree of concordance between microbial activity and geochemistry measurements, including methane emissions. Third, viral protein families from an extremely conservative subset of viral contigs, recovered in the two projects above, were established and used to build X-fams, the largest viral profile Hidden-Markov-Models (HMMs) database to date. The 43,210 viral HMM profiles in X-fams increased the sensitivity of VirSorter, consistently allowing it to detect up to 41.8% more viral contigs in new viromes and enhancing its recovery of shorter viral contigs. Whenever possible, functional annotations of each viral HMM profile in X-fams were provided along with the search-ready compressed database. In addition to providing valuable resources for viral discovery from the disproportionately understudied arctic metagenomic sequences, insights into microbe-environment interactions in the arctic and subarctic systems are impactful as they will help us fine-tune global climate models and hence better inform our predictions (and decisions) regarding climate change.
Matthew Sullivan (Advisor)
Virginia Rich (Advisor)
Kelly Wrighton (Committee Member)
Alvaro Montenegro (Committee Member)
174 p.
Biogeochemistry; Bioinformatics; Biological Oceanography; Biology; Climate Change; Ecology; Environmental Science; Geobiology; Microbiology; Oceanography; Soil Sciences; Statistics; Virology
viruses; microbial expression; metagenomics; metaproteomics; community ecology; population ecology; community expression; marine biology; peat carbon degradation; permafrost; climate change; diversity gradients; Profile Hidden Markov Models

Recommended Citations

Citations

  • Zayed, A. A. (2019). Microbe-Environment Interactions in Arctic and Subarctic Systems [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1562494472055278

    APA Style (7th edition)

  • Zayed, Ahmed. Microbe-Environment Interactions in Arctic and Subarctic Systems. 2019. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1562494472055278.

    MLA Style (8th edition)

  • Zayed, Ahmed. "Microbe-Environment Interactions in Arctic and Subarctic Systems." Doctoral dissertation, Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1562494472055278

    Chicago Manual of Style (17th edition)

osu1562494472055278
83
© 2019, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.