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Microbial Activity and Chemoautotrophy in the Deep Sea

The deep sea covers nearly two thirds of the Earth’s surface, contains ~75% of marine water by volume, and is home to ~55% of all marine microorganisms. Deep-sea microorganisms have the potential to play important roles in shaping global chemistry and climate, including by producing and consuming greenhouse gases (e.g., CO2 and N2O). However, the microbiology of deep-sea waters is sorely understudied relative to that of the surface ocean. Recent estimates suggest that ~60% of microbial species in the deep sea are novel. This project investigates the metabolic activity of deep-sea microorganisms with a focus on chemoautotrophy and the carbon cycle. Chemoautotrophy is a microbial metabolism in which inorganic carbon (e.g., CO2) is converted to sugar and biomass using chemical energy. Using a combination of metabolic rate measurements (using nanoSIMS) and metagenomics, this project investigates which species conduct chemoautotrophy (who?), what types of chemical energy support it (how?), and at what rate it occurs (how much?) throughout the deep sea. Answering these questions provides insight into deep-sea microbial ecology as well as quantitative data on the sources and sinks of carbon in deep waters. This is essential to understanding the ability of our oceans to sequester CO2 on long timescales, and how it will be affected by changing climate.

Nitrogen Fixation in Deep-Sea Sediments

The deep ocean floor is an enormous habitat for microbial life, covering ~2/3 of the entire planet and hosting up to 1000X the microbial cell density of overlying water. The activity of these microbes is essential for local ecosystem functioning, global elemental cycling, and—since they consume and produce greenhouse gases—climate stability. However, the benthic deep sea is among the most under-studied habitats on earth. In particular, the cycling of nitrogen, an essential nutrient for growth and substrate for catabolic metabolism, is poorly understood in deep marine sediments. Our goal in this project is to characterize a critical pathway in the nitrogen cycle, the biological conversion of N2 to NH3 (N2 fixation), in deep-sea sediments. We aim to quantify the rates of N2 fixation, identify the microorganisms mediating it, and determine the biological and physicochemical parameters influencing when, where, and how much it occurs.

Activity and Metabolic Capabilities of Uncultured Archaea

Archaea are unicellular organisms comprising the most recently recognized and the most poorly described domain of life. Although initially thought to be exclusively extremophilic, they are widespread in temperate environments, from mamalian guts to the open ocean. In fact, one phylum of archaea, the Thaumarcheota (“thaumas” from the Greek “wonder”), comprise about 20% of all of the microbial cells in the oceans. Despite the abundance of archaea in the environment, much about their activity and contribution to global biogeochemical cycles remains unknown. In this project, we are studying the distribution, activity, and metabolic flexibility of pelagic and benthic marine archaea using culture-independent techniques. Our goal is to understand their role in local ecosystems and global biogeochemical cycles, and ultimately to understand how their activity may change in a changing climate.

Microbial Ecology at Marine Methane Seeps

Methane is a potent greenhouse gas, and it is naturally produced and stored in marine sediments. At some sites on the seafloor, high methane production and/or release results in natural methane seepage. At these sites, 80% of the methane is consumed within the sediments by microorganisms: anaerobic methanotrophic archaea living symbiotically with sulfate reducing bacteria. Understanding the ecology of seep microorganisms is therefore important to understand methane emissions, and temperature trends and anomalies, today and throughout time. The oxidation of methane is the first step in the food chain at methane seeps—like photosynthesis on the surface of the earth—and is responsible for fueling the diverse and visually bizzarre animal communities at seeps.  In this study, we are using samples collected at methane seeps in Monterey Bay and off the coast of the eastern U.S. to understand the distribution of these microorganisms and their patterns of activity. 

Single-Cell Analysis with NanoSIMS

In the Dekas Lab, we specialize in measuring the activity of bacteria and archaea on the single-cell level using nanoscale secondary ion mass spectrometry (NanoSIMS). This powerful technique measures elemental and isotopic composition at 50 nm resolution, allowing the anabolic activity of individual cells to be quantified even when closely associated with other microbial cells, particles, or host tissue. We are currently working on methods to improve our ability to quantify microbial activity on this scale, and increase sample throughput. In addition to using the NanoSIMS to characterize microbial activity in our own marine samples, we collaborate with researchers interested in single-cell activity in diverse habitats, from terrestrial hot springs to pine forests. We are eager to continue expanding the breadth of microbial interactions characterized at this scale, and to link these observations with ecosystem functioning at the local and global scales. Visit the Stanford Nano Shared Facility to learn more about the CAMECA NanoSIMS 50L on campus.


We are supported by:

  • The National Science Foundation (Division of Ocean Sciences)
  • National Aeronautics and Space Administration (Exobiology)
  • Simons Foundation (Life Sciences)
  • Center for Dark Energy Biosphere Investigations
  • Joint Genome Institute
  • The TomKat Center for Sustainable Energy