A Source of Deep DOM

by Carly Buchwald, Woods Hole Oceanographic Institution

Morning rainbow off the port side of Knorr.
(Sarah Hurley, Harvard Univ.)

There is a unique and abundant, but often less-well-known group of microbes in the ocean known as chemoautotrophs. Like phytoplankton, as described in Gwenn’s previous blog, they are autotrophs, meaning they get their carbon from inorganic sources such as carbon dioxide (CO2) and bicarbonate (HCO3-). Unlike phytoplankton, however, which get their energy from sunlight, chemoautotrophs get their energy by oxidizing inorganic materials, such as ammonia, nitrite, and sulfide, which means they can survive in the deep ocean.

The main purpose of this cruise is to focus on the sources and sinks of dissolved organic matter (DOM). Other researchers on the cruise are targeting the surface sources of DOM, while others are looking at the meso (mid-water) and bathy-pelagic (deep) heterotrophic sinks of this DOM. I’m here on the R/V Knorr working for Dr. Alyson Santoro, a research scientist at Horn Point Laboratory in Cambridge, Maryland, studying a specific type of chemoautotroph known as microbial nitrifying organisms. Nitrifying organisms include bacteria and archaea that get their energy by oxidizing ammonia and urea, a dissolved organic nitrogen compound, to produce nitrite. We want to determine the importance of this deep autotrophic source of DOM, in particular how it affects the composition of deep DOM.

Who are they and where are they?

Carly Buchwald filtering seawater with peristaltic pumps.
(Winn Johnson, WHOI)

As micro-bio-geo-chemists [it sometimes helps to add all the hyphens, ed.], our research lies at the boundary of biological and chemical oceanography. We are using a variety of microbiological and geochemical techniques to assess the importance of nitrification in the deep ocean. One way of determining which and how many nitrifying organisms are in the ocean is to use gene quantitative PCR (qPCR).

This technique targets a specific gene, in our case the gene used by organisms to oxidize ammonia (ammonia monooxygenase), amplifying and measuring the quantity of this gene at different depths in the water column. This will give us an idea of where nitrifying organisms are most abundant. On the cruise this means filtering many liters of water using a peristaltic pump, collecting the filters (now full of microbes), and freezing them for analysis back on land.  

What are they doing and how fast are they doing it? 

--> 0.2 um filter after filtering 4 liters of water
from the deep chlorophyll maximum at
105 meters. (Carly Buchwal, WHOI) Although knowing the organisms are present is important, this does not tell us what they are actually doing. So, our second goal is to measure the rates of nitrification and carbon fixation using incubations with special isotopically labeled substrates. To one set of incubations we add isotopically labeled ammonia or urea that we can track as it is incorporated into nitrite and nitrate over time. To measure carbon fixation, we add labeled bicarbonate and track the label as it is incorporated into particulate organic carbon.

In addition to these incubations we will also be conducting novel experiments using a new and powerful mass spectrometry tool called nanoSIMS. This tool allows us to track the incorporation of isotopic labels into individual cells, which means that, along with our bulk oxidation and fixation rates, we will be able to track rates in individual cells, as well as learn where the nitrogen and carbon is going inside the cell. Nitrification, particularly by archaea, still presents many unknowns. For example, the use of urea in nitrification was only recently discovered. Our experiments on this cruise will not only teach us about the mechanisms used by these organisms, but also how important they are globally as a primary producer, as a carbon dioxide sink, and as a source of dissolved organic matter in the deep ocean.