Emil Ruff
Contact Information
Ph.D., Microbial Ecology, University of Bremen/ Max Planck Institute for Marine Microbiology, 2013
Diplom (MSc equiv.), Technical Biology, University of Stuttgart, 2010
MBL Affiliation
Research Area
Lab Website

Emil Ruff is a microbial ecologist at the Ecosystems Center and Bay Paul Center. His research focuses on microbial interactions and population dynamics as drivers of community function. To disentangle microbial food webs, Emil mainly studies ecosystems with reduced complexity, such as natural or laboratory enrichment cultures, microbial blooms or extreme habitats. His work has improved our understanding of the sources and sinks of the greenhouse gas methane in seafloor ecosystems and groundwater aquifers. Currently, he is investigating the effect of bioirrigation on the removal of methane from wetland sediments. He has just received a 2021 Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution Award to study mutualistic interactions between anoxygenic phototrophs and sulfur-reducing bacteria. His lab is also involved in projects studying i) the effect of pollutants on the microbiome of sea anemones, ii) the interactions between sulfur-cycling bacteria and cord grass roots in salt marshes, iii) plastics degradation in the deep sea, and iv) microbial degradation of macromolecules in hydrothermal sediments.

Bloom of anoxygenic phototrophs
Bloom of anoxygenic phototrophs - Trunk River lagoon is the only ecosystem known to date in which anoxygenic phototrophic Chlorobiales thrive at the water surface in the presence of substantial dissolved oxygen concentrations. The photo shows Molly Moynihan inmidst the bloom during a sampling campaign. The yellow-green color of the microbes is due to the presence of sulfur and bacteriochlorophylls, pigments that the cells use to harvest light (Photo: Katie Crowley).
Selected Publications

Pérez Castro S, Borton MA, Regan K, Hrabe de Angelis I, Wrighton KC, Teske AP, Strous M, Ruff SE.* (2021) “Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments.” The ISME Journal (advanced online). https://doi.org/10.1038/s41396-021-01026-5

SouzaFFC, Mathai PP, Pauliquevis T,, Balsanelli E, Pedrosa FO, Souza EM, Baura VA, Monteiro RA, Cruz LM, Souza RAF, Andreae MO, Barbosa CGG; Hrabe de Angelis I, Sánchez-Parra B, Pӧhlker C, Weber B, Ruff SE, Reis RA, Godoi RHM, Sadowsky MJ, Huergo LF. (2021) “Influence of Seasonality on the Aerosol Microbiome of the Amazon Rainforest.” Science of the Total Environment, 760, 144092. https://www.sciencedirect.com/science/article/pii/S0048969720376233?via%3Dihub

Chakraborty, A.; Ruff, S. E.; Dong, X.; Ellefson, E. D.; Li, C.; Brooks, J. M.; Bernard, B. B.; Hubert, C. J. R. (2020) “Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres.“ Proceedings of the National Academy of Sciences USA, 117, 11029-11037. https://www.pnas.org/content/117/20/11029

Bhatnagar, S.; Cowley, E. S.; Kopf, S. H.; Pérez Castro, S.; KearneyS.; Dawson, S. C.; Hanselmann, K.; Ruff*, S. E. (2020) „Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom.“ Environmental Microbiome, 15:3. https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-019-0348-0

Ruff*, S. E.; Felden, J.; Gruber-Vodicka, H. R.; Marcon, Y.; Knittel, K.; Ramette, A.; Boetius, A. (2019). In situ development of a methanotrophic microbiome in deep-sea sediments.” The ISME Journal13, 197-213. https://www.nature.com/articles/s41396-018-0263-1