A Caltech Library Service

Diazotrophy in the Deep: An Analysis of the Distribution, Magnitude, Geochemical Controls, and Biological Mediators of Deep-Sea Benthic Nitrogen Fixation


Dekas, Anne Elizabeth (2013) Diazotrophy in the Deep: An Analysis of the Distribution, Magnitude, Geochemical Controls, and Biological Mediators of Deep-Sea Benthic Nitrogen Fixation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/H9F5-T161.


Biological nitrogen fixation (the conversion of N2 to NH3) is a critical process in the oceans, counteracting the production of N2 gas by dissimilatory bacterial metabolisms and providing a source of bioavailable nitrogen to many nitrogen-limited ecosystems. One currently poorly studied and potentially underappreciated habitat for diazotrophic organisms is the sediments of the deep-sea. Although nitrogen fixation was once thought to be negligible in non-photosynthetically driven benthic ecosystems, the present study demonstrates the occurrence and expression of a diversity of nifH genes (those necessary for nitrogen fixation), as well as a widespread ability to fix nitrogen at high rates in these locations. The following research explores the distribution, magnitude, geochemical controls, and biological mediators of nitrogen fixation at several deep-sea sediment habitats, including active methane seeps (Mound 12, Costa Rica; Eel River Basin, CA, USA; Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA), whale-fall sites (Monterey Canyon, CA), and background deep-sea sediment (off-site Mound 12 Costa Rica, off-site Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA). The first of the five chapters describes the FISH-NanoSIMS method, which we optimized for the analysis of closely associated microbial symbionts in marine sediments. The second describes an investigation of methane seep sediment from the Eel River Basin, where we recovered nifH sequences from extracted DNA, and used FISH-NanoSIMS to identify methanotrophic archaea (ANME-2) as diazotrophs, when associated with functional sulfate-reducing bacterial symbionts. The third and fourth chapters focus on the distribution and diversity of active diazotrophs (respectively) in methane seep sediment from Mound 12, Costa Rica, using a combination of 15N-labeling experiments, FISH-NanoSIMS, and RNA and DNA analysis. The fifth chapter expands the scope of the investigation by targeting diverse samples from methane seep, whale-fall, and background sediment collected along the Eastern Pacific Margin, and comparing the rates of nitrogen fixation observed to geochemical measurements collected in parallel. Together, these analyses represent the most extensive investigation of deep-sea nitrogen fixation to date, and work towards understanding the contribution of benthic nitrogen fixation to global marine nitrogen cycling.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Nitrogen fixation, diazotrophy, deep-sea, methane seep, ANME archaea, anaerobic oxidation of methane, NanoSIMS
Degree Grantor:California Institute of Technology
Division:Geological and Planetary Sciences
Major Option:Geobiology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Orphan , Victoria J.
Thesis Committee:
  • Kirschvink, Joseph L. (chair)
  • Sessions, Alex L.
  • Orphan, Victoria J.
  • Newman, Dianne K.
  • Howard, James B.
Defense Date:17 October 2012
Record Number:CaltechTHESIS:12192012-141624638
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Chapter 1. adapted for Chapter 2.
Dekas, Anne Elizabeth 0000-0001-9548-8413
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7347
Deposited By: Anne Dekas
Deposited On:02 Jan 2013 20:25
Last Modified:03 Oct 2019 23:57

Thesis Files

PDF - Final Version
See Usage Policy.


Repository Staff Only: item control page