Identifying the Microbial Culprits Initiating Oceanic Nitrogen Loss

Novel lineages of SAR11 clade reveal adaptations to oxygen-poor ocean zones.

The Science

In the Nature paper, the team found functional nitrate reductase pathways, shown on the left-hand side of the nitrogen cycle, in SAR11 microbes. (Nitrogen cycle graphic by Zosia Rostomian, Berkeley Lab)

Oxygen minimum zones (OMZs) extend over about 8 percent of the oceanic surface area, but account for up to 50 percent of the total loss of bioavailable nitrogen and thus play an important role in regulating the ocean’s productivity by substantially impacting the nitrogen cycle. By sequencing single cells and metagenomes from OMZs, researchers identified bacteria of the SAR11 clade as being abundant in these areas, although no previously known anaerobic metabolism had been described for this group. Detailed sequence analysis of SAR11 single cells, followed by functional characterization experiments, revealed the presence of functional nitrate reductase pathways as a key adaptation to oxygen-poor, or anoxic, environments. These results link SAR11, the world’s most abundant organismal group, to oceanic nitrogen loss.

The Impact

Microbes play key roles in maintaining the planet’s biogeochemical cycles, and while the role of SAR11 bacteria in the marine carbon cycle has been well documented, its important role in regulating nitrogen bioavailability was hitherto unknown. In partnering with a national user facility, scientists had access to state-of-the-art single-cell sorting and synthetic biology capabilities at the DOE JGI, enabling them to identify and functionally characterize the role of SAR11 in oxygen minimum zones in the ocean.

Summary

Oxygen minimum zones (OMZs) are regions in the ocean where very low levels of oxygen are available and nitrate to nitrite reduction becomes the dominant oxidative process, impacting the composition of microbial communities and their effect on global biogeochemical cycles. Though SAR11 bacteria are estimated to make up as much as half of the total microbial community in the ocean’s oxygen-rich surface layers, they have also been found to be abundant in OMZs. To understand how SAR11 bacteria can thrive in what was thought to be an inhospitable environment for them, a team led by Georgia Tech scientists and supported by a DOE JGI Community Science Program proposal analyzed single amplified genomes (SAGs) generated from water samples collected in the nitrogen reduction zone of the Eastern Tropical North Pacific OMZ. Located off Mexico, this is the world’s largest OMZ and comprises about 40 percent of the total OMZ surface area. Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, conducted a series of single-cell sorting and synthetic biology experiments, that helped to demonstrate how SAR11 cells adapted to anoxic environments by acquiring the biochemical machinery to respire nitrate, in effect initiating oceanic nitrogen loss. The study appeared online August 3, 2016 in Nature. “Together,” the team concluded, “these findings redefine the ecological niche of one of the planet’s most dominant groups of organisms.”

Contacts

Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

Sam Deutsch
Synthetic Biology Group Lead
DOE Joint Genome Institute
sdeutsch@lbl.gov