From deep sea to deep time : investigations into benthic marine biological nitrogen fixation and the origins of diazotrophy
Abstract/Contents
- Abstract
- Nitrogen-fixing microorganisms (i.e., diazotrophs) play a critical role in the marine environment. Through the reduction of nitrogen gas to ammonia, diazotrophs supply bioavailable nitrogen to ecosystems where productivity is nitrogen limited. Although the ecological and biogeochemical importance of diazotrophs in both the surface ocean and shallow marine sediments is well documented, we know comparatively little about diazotrophic communities in deep-sea sediments (greater than 200 m water depth). Recent work, however, suggests diazotrophs are active at some deep-sea sites. These findings call for additional investigations into the phylogenetic diversity and ecology of diazotrophs in the deep-sea benthos to assess the potential environmental controls on their activity. Additionally, since diazotrophy is the only known mechanism by which organisms offset ecosystem fixed nitrogen losses, understanding its evolutionary origins would offer insight into the evolution of a key component of Earth's nitrogen cycle. Interestingly, previous work has found that genes essential for nitrogen fixation are evolutionarily related to those in other geobiologically important metabolisms (e.g., photosynthesis, methanogenesis, the reductive acetyl-CoA pathway), but these evolutionary relationships remain unresolved. In this dissertation, I address these knowledge gaps by: (1) studying the phylogenetic diversity and ecology of diazotrophs (both active and inactive) in deep-sea sediments collected offshore Northern California and (2) investigating the evolutionary history of nitrogenase reductase (NifH), an essential protein in nitrogen fixation. In Chapter 1, I combine stable isotope and molecular techniques to identify active diazotrophs in a deep-sea sediment core collected from Monterey Canyon, California. In Chapter 2, I develop an open-source R package (Phylogenetic Placement for Inferring Taxonomy; PPIT) that assigns taxonomy to nifH sequences using phylogenetic placement and sequence identity approaches. In Chapter 3, I examine the distribution, taxonomic identity, and ecology of potential diazotrophs in sediments along a 267 km transect offshore San Francisco, California. I apply PPIT to nifH amplicon sequences recovered from continental shelf to abyssal plain and leverage paired geochemical measurements to identify environmental parameters influencing the composition of the nifH-containing community. In Chapter 4, I explore the evolutionary history of the protein family containing NifH using publicly available amino acid sequence data in phylogenetic and comparative sequence conservation analyses. Together, these studies significantly advance our understanding of diazotrophy in deep-sea sediments and link its evolution to the origins of ancient metalloclusters, pigments, and a self-organizing molecular system.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2022; ©2022 |
| Publication date | 2022; 2022 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Kapili, Bennett James |
|---|---|
| Degree supervisor | Dekas, Anne |
| Thesis advisor | Dekas, Anne |
| Thesis advisor | Francis, Christopher |
| Thesis advisor | Spormann, Alfred M |
| Thesis advisor | Welander, Paula |
| Degree committee member | Francis, Christopher |
| Degree committee member | Spormann, Alfred M |
| Degree committee member | Welander, Paula |
| Associated with | Stanford University, Department of Earth System Science |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Bennett James Kapili. |
|---|---|
| Note | Submitted to the Department of Earth System Science. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/kh223nb9875 |
Access conditions
- Copyright
- © 2022 by Bennett James Kapili
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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