Biogeography of nitrogen-cycling microbial communities in San Francisco Bay
Abstract/Contents
- Abstract
- Nitrogen is an essential element to all of life on earth, and its bioavailability in the environment is governed by the activities of microorganisms that transform nitrogen species through redox processes such as denitrification, nitrification, and anammox. In this study, we survey the nitrogen-cycling microbial populations in the sediments of San Francisco Bay, using diverse DNA-based methods to address questions about microbial population dynamics across space, time, and the environmental gradients typical of an estuary. Our results include: a comparison of the abundance and community structures of nirK-type and nirS-type denitrifying bacteria; a novel use of next-generation sequencing for surveying functional gene diversity in the environment and a demonstration of machine-learning techniques for identifying ecological trends in that sequence data; and finally, deep sequencing of the 16S rRNA gene to survey and compare several N-cycling functional communities at once. Overall, we observe strong spatial structure in each nitrogen-cycling functional group as well as in the total microbial community, a strong response of all groups to salinity and to sediment nitrogen content, and marked differences in the temporal variability of communities in different sites. This survey of microbial diversity in San Francisco Bay contributes to our understanding of the processes influencing sediment biota in the estuary, and forms a foundation for future studies in the functioning of these nitrogen-cycling communities.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2015 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Lee, Jessica Audrey |
|---|---|
| Associated with | Stanford University, Department of Environmental Earth System Science. |
| Primary advisor | Francis, Christopher |
| Thesis advisor | Francis, Christopher |
| Thesis advisor | Bhaya, Devaki, 1957- |
| Thesis advisor | Casciotti, Karen Lynn, 1974- |
| Thesis advisor | Fendorf, Scott |
| Advisor | Bhaya, Devaki, 1957- |
| Advisor | Casciotti, Karen Lynn, 1974- |
| Advisor | Fendorf, Scott |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Jessica Audrey Lee. |
|---|---|
| Note | Submitted to the Department of Environmental Earth System Science. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Jessica Audrey Lee
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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