Molecular ecology and biogeochemical activity of nitrifying archaea and bacteria across spatial and temporal scales in the nitrogen-rich San Francisco Bay
Abstract/Contents
- Abstract
- San Francisco Bay (SFB) is a large and heavily nitrogen-polluted estuary on the west coast of the United States. The community dynamics of nitrogen-cycling microorganisms, especially the bacteria and archaea responsible for nitrification (the oxidation of ammonia to nitrite and then nitrate), are particularly relevant in the ammonia-rich waters of SFB. Despite the critical role of pelagic nitrifiers in transforming ammonia within SFB waters, they have received little attention. In this dissertation, I explore the ecology of pelagic microorganisms in the water column using several time series of microbial data and further focus on the distribution and activity of nitrifying guilds. I investigate the general structure of the bacterial and archaeal community in San Francisco Bay using a two-year monthly time series in conjunction with water quality data, documenting a bloom of ammonia-oxidizing archaea (AOA) associated with nitrite accumulation in South SFB. I then use metagenomic data to uncover dynamics of two dominant ammonia-oxidizing archaea lineages in SFB, including the bloom AOA in South SFB. I generate nitrification rate and microbial data, including metagenomes and metatranscriptomes, over a 1-year time series with targeted sampling over the course of an AOA bloom in autumn of 2018. I analyze both microbial time series datasets together to assess the AOA bloom organism over time (2012 to 2019). I also explore the 50-year timeseries of water quality data available for SFB, primarily focusing on the most recent 9 complete years of data (2012-2020) because of more consistent nitrite measurements. Overall, this dissertation characterizes a previously unknown and recurring massive AOA-bloom in SFB, delving into which AOA lineage blooms, the activity of AOA and other microbes during the bloom, and the conditions conducive to recurring and massive blooms.
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 | Rasmussen, Anna Nichole |
|---|---|
| Degree committee member | Casciotti, Karen Lynn, 1974- |
| Degree committee member | Dekas, Anne |
| Degree committee member | Francis, Christopher |
| Degree committee member | Fukami, Tadashi, 1972- |
| Thesis advisor | Casciotti, Karen Lynn, 1974- |
| Thesis advisor | Dekas, Anne |
| Thesis advisor | Francis, Christopher |
| Thesis advisor | Fukami, Tadashi, 1972- |
| Associated with | Stanford University, Department of Earth System Science |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Anna Rasmussen. |
|---|---|
| Note | Submitted to the Department of Earth System Science. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/hf338nk1401 |
Access conditions
- Copyright
- © 2022 by Anna Nichole Rasmussen
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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