Microbial Oceanography Research Lab

Methane production in the ocean

My research seeks to understand the ecological processes that control the microbial production of methane in marine environments. Methane is often supersaturated in marine waters, a phenomenon indicative of in situ biological production, and yet the contribution to methane production by different microbial methanogenic processes identified therein remains largely unconstrained. My lab employs a combined approach of metagenomics, microbial culturing techniques, analytical chemistry, and biogeochemistry to elucidate these processes.

Methanogenesis by the C-P lyase pathway

Of special interest in my lab is a pathway known as the carbon-phosphorus (C-P) lyase, a multi-enzyme complex that breaks down an organophosphorus compound known as methylphosphonate into phosphate and methane. Phosphonates are synthesized by a wide range of organisms, including marine Archaea and Cyanobacteria, and constitute a large fraction of the dissolved organic phosphorus pool in the ocean. The gene encoding C-P lyase, phnJ, is enriched in bacterioplankton populations inhabiting phosphate-depleted surface waters in the Mediterranean Sea and the North Atlantic Subtropical Gyre, where methylphosphonate and other phosphonates are likely an important source of phosphorus for microorganisms. You can read the article here. These marine regions are expected to produce significant amounts of methane annually in response to phosphate stress and methylphosphonate turnover. My goal is to determine the principal processes that control methane production from methylphosphonate and to measure methane concentrations and outputs in surface waters in these marine regions. This research is expected to help constrain and model natural methane emissions from oceanic ecosystems.

Microbial utilization and competition for phosphonates

The C-P lyase enzyme is not the only pathway to break down methylphosphonate. The high-light adapted unicellular photosynthetic cyanobacterium Prochlorococcus strain MIT9301 carries a pair of genes, phnY and phnZ, that code for a phosphonate oxidative pathway that converts methylphosphonate into phosphate and formic acid. You can read the article here. This suggests that methane may not be the only fate of methylphosphonate in the marine environment. Similar to the C-P lyase gene, the phnY and phnZ genes in Prochlorococcus genomes occur at a higher rate in phosphate-depleted marine surface waters that in other ocean regions, indicating that this cyanobacterium may also utilize, and perhaps compete for, methylphosphonates in response to phosphate stress. My lab is currently investigating if and how Prochlorococcus populations can metabolize phosphonates in marine dissolved organic matter.


Sosa, O. A., J. R. Casey, and D. M. Karl. 2019. Methylphosphonate oxidation in Prochlorococcus strain MIT9301 supports phosphate acquisition, formate excretion, and carbon assimilation into purines. Applied and Environmental Microbiology 85(13): e00289-19. doi:10.1128/aem.00289-19. See article here.

Sosa, O. A., D. J. Repeta, E. F. DeLong, M. D. Ashkezari, and D. M. Karl. 2019. Phosphate‐limited ocean regions select for bacterial populations enriched in the carbon‐phosphorus lyase pathway for phosphonate degradation. Environmental Microbiology 21(7): 2402-2414. doi:10.1111/1462-2920.14628. See article here.

Sosa, O. A. 2017. Phosphorus redox reactions as pinch hitters in microbial metabolism. Proceedings of the National Academy of Sciences of the United States of America 115(1): 7-8. doi:10.1073/pnas.1719600115. See commentary here.

Sosa, O. A., D. J. Repeta, S. Ferrón, J. A. Bryant, D. R. Mende, D. M. Karl, and E. F. DeLong. 2017. Isolation and characterization of bacteria that degrade phosphonates in marine dissolved organic matter. Frontiers in Microbiology 8: 1786. doi:10.3389/fmicb.2017.01786. See article here.

Repeta, D. J., S. Ferrón, O. A. Sosa, C. G. Johnson, L. D. Repeta, M. Acker, E. F. DeLong, and D. M. Karl. 2016. Marine methane paradox explained by bacterial degradation of dissolved organic matter. Nature Geoscience 9: 884–887. doi:10.1038/ngeo2837. See article here.

Gifford, S. M., J. W. Becker, O. A. Sosa, D. J. Repeta, and F. Delong. 2016. Quantitative transcriptomics reveals the growth- and nutrient-dependent response of a streamlined marine methylotroph to methanol and naturally occurring dissolved organic matter. mBio 7: e01279-16. doi:10.1128/mBio.01279-16. See article here.

Sosa, O. A., S. M. Gifford, D. J. Repeta, and E. F. DeLong. 2015. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. The ISME Journal 9: 2725–2739. doi:10.1038/ismej.2015.68. See article here.