Searching for the Bacteria that Drive the Ocean’s Carbon Cycle

EMBARGOED UNTIL: Sunday 5/19, 3 PM MDT

(Symposium Session 69, Paper )

SCOTT GIFFORD
Massachusetts Institute of Technology
Cambridge, MA, United States
Phone: (614) 406-0117
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With billions of cells in every liter of seawater and highly diverse metabolic capabilities, bacteria serve as the engines of the ocean’s geochemical cycles. Therefore, understanding bacterial activities has implications for our ability to predict how energy and materials move around the planet. In this study we found that a specific group of bacteria called methylotrophs may have an important role in controlling the flux of the ocean’s dissolved organic matter (DOM), one of earth’s largest carbon pools that has a close connection with atmospheric CO2 concentrations. A role for methylotrophs in DOM cycling was surprising given that they have evolved metabolic capabilities focused on degrading the simplest of organic molecules, while in contrast the current model of ocean DOM suggests that it is a highly complex substance. By identify the organisms and genes that influence these global carbon cycles, this work will help us understand how bacterial processes will respond to an ocean increasingly altered by human activities.

 This research is being conducted by Scott Gifford, Oscar Sosa, and Ed DeLong of the Massachusetts Institute of Technology and Dan Repeta of the Woods Hole Oceanographic Institute. The results of this work will be presented at the America Society of Microbiology (ASM) general meeting in Denver, Colorado on Sunday, May 19th. The research is supported by a grant from the Gordon and Betty Moore Foundation to Edward DeLong and Dan Repeta

Background: The ocean plays an important role in the cycling and sequestration of carbon, both natural and anthropogenic.  Atmospheric CO2 absorbed in the ocean’s surface layer is converted to organic carbon when photosynthetic plankton incorporate it into their biomass. Once fixed, this organic carbon has many possible fates, all of which are dictated by a community of microbes and viruses that is astounding in its size and complexity.  One possible fate for the phytoplankton-fixed carbon is release into the surrounding waters due to viral infection, bacterial attacks, or grazing by larger organisms. Once released, it becomes dissolved organic matter (DOM).

The open ocean is greatly depleted in nutrients and labile carbon, so the release of phytoplankton DOM is a sudden injection of a wealth of nutrients and energy to the surrounding bacterial community that is starving for such resources. Most released DOM is therefore rapidly taken up and consumed by bacteria in the water column within hours of its release. Interestingly though, there is a very large standing stock of DOM in the ocean (equivalent to all of the carbon in the atmosphere), so it’s unlikely that all of the DOM released by phytoplankton is quickly turned into bacterial biomass or used for energy. And importantly, when the age of that DOM standing stock is measured, it’s estimated to be 1000 to 2000 years old. This is bit of a mystery, as DOM seems to stick around for a very long time but we know that bacteria are growing on it because 1) the DOM pool seems to be in steady state, neither increasing or decreasing in concentration with time and 2) bacteria in the deep ocean seem to be actively growing, so there must be some component of the DOM pool that is ‘edible’ by them. But what is it about the DOM that limits bacteria from rapidly taking it up? Why does it take so long to turnover? Is there only a subset of the bacterial community that is able to degrade it? If so which bacterial taxa are they and what genes give them the capability to do so? Answering these questions will allow us to better understand how microbes control the flow of carbon in the world’s oceans, and how those roles may change as the ocean becomes warmer and more acidic due to human influence.

One way to investigate these questions is to isolate a DOM degrading bacterium and experiment on it in a laboratory setting. But isolating such an organism requires that you are able to 1) separate it from the hundreds (if not thousands) of different taxa in the community and 2) have a method to select for only those community members that are actively degrading the DOM. Furthermore, since we don’t know what oceanic DOM is composed of, a method is required of collecting and concentrating natural ocean DOM for the cells to grow on; a difficult task considering the extremely dilute DOM concentrations in seawater (one thousandth of a gram per liter).

In this study, a cultivation technique called dilution-to-extinction was used to capture the most common, indigenous microbes in culture, and bring them into the laboratory for study.   Bacterial cells are diluted so that each cell gets distributed into its own “personal” culture tube.  This dilution culturing has been one of the most important methods for trapping the most abundant microbes in the wild and domesticating them for laboratory studies.  This study adds a new twist on traditional dilution-to-extinction culturing by adding natural DOM from the ocean to subsets of the wells in the hopes of enriching for DOM degrading isolates.

After extended incubations, the cultures were screened for growth using flow cytometry, enabling the counting of thousands of cells per second. Surprisingly, only 1 culture out of 800 from the no DOM control showed positive growth.  In contrast, 42 and 50 wells had significant growth in the 5X and 10X DOM treatments, respectively.   This shows that the naturally occurring DOM had a positive effect on growth of indigenous microbes.  The DOM effect was verified by taking the 93 isolates and exposing them to increasing DOM concentrations. As before, the results showed that higher cell yields were proportional to the DOM added.

Interestingly, over 85% of the isolates belonged to one important group of bacteria, the Methylophilales. These organisms are methylotrophs that specialize in the breakdown of compounds with just one carbon atom.  That was a surprise since the DOM is likely comprised of high molecular weight carbon composed of many carbon atoms linked together. Our findings suggest that methylotrophs may have the capability to chip off single carbon compounds from high molecular weight DOM.  So even though they are thought to specialize in eating single carbon compounds, it appears they can also degrade polymeric carbon composed of chains of carbon atoms.   Our conclusion is that methylotrophs may be important in the turnover of high molecular weight DOM in the sea, an unexpected result.  We are currently analyzing the genomes of our isolates to identify potential genetic mechanisms used for DOM degradation, and future studies will couple this genetic information with genome wide expression studies to identify the molecular mechanisms these organisms actively turn on when exposed to DOM.

This study represents a significant step in understanding not only the bacterial activities that control the flux of ocean carbon, but it will likely provide insights into the molecular composition of the DOM; a crucial element to understanding how this large, seemingly old pool of carbon originates and is transformed. In doing so, we will begin to understand how these small organisms have a big impact on the flow of carbon on our planet, and how those activities may be altered in a changing ocean.