Building Sphagnum Genomic Resources - DOE Joint Genome Institute

Sphagnome data would enable researchers’ insights on their potential carbon cycling impact.

The Science

Enabled by the JGI’s Community Science Program (CSP), researchers are developing a number of resources to build up Sphagnum as a plant model system focused on carbon cycling studies, rather than for food or fuel applications.

The Impact

Sphagnum fallax is one of two high quality reference genomes for peat-forming species being sequenced through the JGI’s Community Science Program. Its genome is available on Phytozome. (Karl-Ludwig Poggemann on Flickr, CC BY 2.0)

Sphagnum’s impact on global carbon cycling and climate is estimated to be larger than any other single plant genus. Peatlands accumulate partially decomposed matter, and researchers estimate that they hold about 25 percent of the world’s soil carbon. In high latitudes, sphagnum can also act as a protective layer insulating permafrost from the warming regional temperatures. For this reason, the U.S. Department of Energy is overseeing the SPRUCE (Spruce and Peatland Responses Under Changing Environments) project, assessing how northern peatland ecosystems respond to increases in temperature and elevated concentrations of atmospheric carbon dioxide.

Summary

Sphagnum (peat moss) is an unassuming plant, but it thrives in nutrient-poor, acidic and waterlogged environments, occupying every continent except Antarctica. Researchers estimate a quarter of the world’s terrestrial carbon is stored in peatlands, which make up nearly 3 percent of the earth’s land surface. In the New Phytologist, researchers led by David Weston of Oak Ridge National Laboratory make the case for sphagnum as “an unparalleled model system for ecological and evolutionary genomics.” Understanding the nature and genetic basis of functional traits in sphagnum growth and decomposition is critical to predicting the ecosystem response to climate change. Through the CSP, researchers are aiming to have two high quality reference genomes for peat-forming species that occupy different microhabitats – Sphagnum fallax and S. magellanicum. The draft genome for S. fallax is already available on the JGI plant portal Phytozome, and the S. magellanicum genome is currently being assembled. These resources would provide the research community with the ability to address questions such as sphagnum’s associations with methane oxidizing bacteria, nutrient uptake, and its productivity and decomposition rates.

Peatlands, like other wetlands, can act as a carbon sink or carbon source. Sulfur cycling is a carbon flux regulator since sulfate-reducing microbes prevent methane production by routing the carbon away from methanogens. In The ISME Journal, a team led by researchers from the University of Konstanz and the University of Vienna reported recovering draft metagenome-assembled genomes for seven novel species of Acidobacteria through an approved CSP proposal. The researchers found that these species encode a sulfate reduction pathway, but also have genes for sulfide oxidation. The findings lead them to speculate that these microbes could use the same pathway for either sulfur reduction or sulfur oxidation. The pathway’s reversibility could be a factor in determining if the peatlands act as a carbon sink or a carbon source.

These research results, building on the availability of genomic information from two distinct environments, strengthen the case for Sphagnum as a versatile model system for studies of carbon cycling in diverse environments. In addition, this work reflects a collaboration between two programs within different Divisions of the Office of Biological and Environmental Research, the Joint Genome Institute supported by the Biological Systems Science Division and the Spruce and Peatland Responses Under Changing Environments (SPRUCE) program of the Terrestrial Ecosystem Science program, supported by the Climate and Environmental Sciences Division.

BER 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

Daniel Stover, Ph.D.
Program Manger
Climate and Environmental Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Daniel.stover@science.doe.gov

PI Contacts

David Weston
Oak Ridge National Laboratory
westondj@ornl.gov

Michael Pester
Leibnitz Institute DSMZ, Germany
Michael.pester@dsmz.de

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. For the sphagnome project, germplasm establishment and maintenance is supported by the US DOE, Office of Science, Office of Biological and Environmental Research, Early Career Research Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. Funding for the peatlands work was also supported by the Austrian Science Fund (FWF, P23117-B17, P25111-B22, P26392-B20, and I1628-B22), the JGI (CSP 605), the German Research Foundation (DFG, PE 2147/1-1), the European Union (FP7-People-2013-CIG, Grant No PCIG14-GA-2013-630188 and Marie Skłodowska-Curie Grant No 660280), and the VILLUM FONDEN (research grant 15510).

Publications

Weston DJ et al. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. New Phytol. 2018 Jan;217(1):16-25. doi: 10.1111/nph.14860.
Hausmann B et al. Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J. 2018 Feb 23. doi: 10.1038/s41396-018-0077-1. [Epub ahead of print]