Marine Biogeochemistry and the Carbon Cycle

We are interested in understanding the biogeochemical processes that transform organic matter in marine sediments.


We focus on marine sediments, because they are important repositories of carbon. They also function as a major fork in the global carbon cycle, where organic matter is either preserved over geological time, or broken down and eventually returned to the atmosphere in the form of carbon dioxide.


The vast majority of organic matter in the environment is highly degraded, and is structurally and compositionally complex. To study how this material cycles in the environment, we harness naturally occurring isotopes of carbon to identify pools of organic matter with contrasting provenance and history. We build conceptual and numerical models of organic matter degradation and oxidation to interpret experimental and field-based data. We also assess analytical methods that enable us to better address the questions of our interest.

Production and cycling of dissolved organic matter in marine sediments

Organic matter in sediments is broken down primarily through microbial processes. In order for the microbial community to utilize sedimentary organic matter as an energy source, it must first convert particulate organic matter into soluble components, or dissolved organic matter (DOM). We study the composition and reactivity of DOM in the interstitial waters of sediments (pore waters) for important clues about the mechanisms behind sedimentary organic matter degradation and preservation.


By studying pore-water DOM, we also aim to shed light on the role sediments play in the marine DOM cycle. DOM generated in the sediments is not completely utilized by the benthic microbial community, and the excess is exported out to the overlying water column. Understanding the molecular composition and production pathways of pore-water DOM should help determine whether DOM from sediments persist in the long term and contribute to the deep-sea DOM pool.

Collaborators:    Hussain Abdulla, Texas A&M University, Corpus Christi

David Burdige, Old Dominion University

James Lewicki, Lawrence Livermore National Laboratory

Jeffrey Chanton, Florida State University 

Organic carbon preservation in salt marshes

Recent reports identify salt marshes as globally important sites of organic carbon burial. While peaty marshes accumulate organic carbon that is ~100% of local production, minerogenic salt marshes, such as those in San Francisco Bay, accumulate organic carbon from both local and external sources, such as upland soils. Quantifying these two types of organic carbon is imperative to understanding the role of minerogenic salt marshes in the sequestration of atmospheric carbon dioxide, but the complexity of sedimentary organic matter makes this a challenging task.

We are examining the fate of locally-produced (autochthonous) and imported (allochthonous) organic carbon in C4-dominated minerogenic salt marshes in San Francisco Bay, California, by harnessing a well-tested concept from the soil science literature: association with minerals increases organic matter stability against degradation. We take advantage of the fact that autochthonous organic matter enters the sediments free of minerals, while most allochthonous organic matter is deposited in close association with minerals. C4-macrophyte and allochthonous organic matter have distinct stable carbon isotope signatures, opening the possibility to evaluate their fates using this geochemical tracer.

Estuary & Ocean Science Center, San Francisco State University | 3150 Paradise Drive, Tiburon, California 94920 USA

© 2023 by HARMONY. Proudly created with

This site was designed with the
website builder. Create your website today.
Start Now