Mighty Microbes Roil Oceans

New model reveals the significant role of microbes in oceanic nutrient and energy.

Image courtesy of the U.S. Department of Energy’s Environmental Molecular Sciences Laboratory

The Science

A single drop of seawater can contain a million microorganisms, but these microorganisms have a much bigger influence than their size would imply. For example, microbes influence an ocean’s nutrient and energy cycles, and in turn, these cycles affect atmospheric levels of carbon dioxide, methane, and other gases. Traditional models of the Earth system do not include the influence of microbes in these cycles. Now, researchers have developed a model that explains key microbial metabolic processes and their influence on greenhouse gas production and consumption in a model marine ecosystem. The new model uses information about the ocean’s geochemistry in combination with genomic and metabolic information about the microbes.

The Impact

Within the ocean, oxygen-starved zones affect the productivity of fisheries, emissions of greenhouse gases, biodiversity in coastal zones, and more. The results of this work significantly improve the crude models of microbial activity in these important oceanic zones. And, these results not only provide holistic insights into how microbes drive nutrient and energy flow within the oceanic environment but also how they influence the atmospheric ecosystem.

Summary

Oxygen minimum zones are widespread areas in the ocean. In these zones, oxygen is depleted due to the metabolic activity of microbes. Rising temperatures drive expansion of oxygen minimum zones, making these areas especially relevant as model ecosystems for climate science. In turn, microbial metabolic networks in these areas are predicted to have a growing influence on nutrient and energy cycling in the ocean. These cycles will affect atmospheric levels of greenhouse gases such as carbon dioxide, methane, and nitrous oxide. Despite important interactions between microbial activity and global biogeochemical processes, climate models have largely neglected modern molecular sequencing data containing critical information about metabolic networks. Moreover, climate models often do not incorporate sufficient information about biogeochemical processes in the ocean. Researchers from the University of British Columbia, University of Minnesota, Canadian Institute for Advanced Research, and Max Planck Institute for Marine Microbiology worked together to develop a biogeochemical model. The model integrates observational geochemical data with metagenomic, metatranscriptomic, and metaproteomic sequence data on the distribution of DNA, messenger RNA (mRNA), and proteins from waters in the Saanich Inlet, British Columbia, Canada. This site is serving as a model ecosystem for studying key metabolic processes of the oceanic microbial community and their responses to oxygen minimum zone expansion. The team used resources from two U.S. Department of Energy Office of Science user facilities: the DOE Joint Genome Institute and EMSL, the Environmental Molecular Sciences Laboratory. The new model reproduced measured biogeochemical reaction rates as well as DNA, mRNA, and protein concentration profiles at the ecosystem scale. Moreover, simulations predicted the role of ubiquitous microorganisms in mediating carbon, nitrogen, and sulfur cycling. These results quantitatively improve previous conceptual models describing microbial metabolic networks in oxygen minimum zones. The integration of real geochemical and multiomic sequence data in a biogeochemical model provides holistic insight into microbial metabolic networks driving nutrient and energy flow at ecosystem scales.

Contact

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contacts
Steve Hallam
University of British Columbia
shallam@mail.ubc.ca

Ljiljana Paša-Tolić
Environmental Molecular Sciences Laboratory
ljiljana.pasatolic@pnnl.gov

Funding

This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, including support of the Joint Genome Institute and Environmental Molecular Sciences Laboratory, both DOE Office of Science user facilities; G. Unger Vetlesen and Ambrose Monell foundations; Tula Foundation; Natural Sciences and Engineering Research Council of Canada; Genome British Columbia; Canada Foundation for Innovation; and Canadian Institute for Advanced Research.

Publications

S. Louca, A.K. Hawley, S. Katsev, M. Torres-Beltran, M.P. Bhatia, S. Kheirandish, C.C. Michiels, D. Capelle, G. Lavik, M. Doebeli, S.A. Crowe, and S.J. Hallam, “Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.” Proceedings of the National Academy of Sciences (USA) 113(40), E5925-E5933 (2016). [DOI: 10.1073/pnas.1602897113]