Tracking the Evolution of a Methane-Producing Symbiosis in Real Time

Such striking parallel evolution suggests a trade-off between performance in the mutualistic environment and maintaining the flexibility to survive alone.

The Science

Just below the surface of soils and sediments, large portions of Earth’s biosphere exist in the absence of oxygen. The microbial inhabitants of these anoxic environments drive planetary biogeochemical cycles, and their metabolic activities impact the bioavailability of nutrients, metals, and environmental contaminants. To survive in these energy-limited habitats, many microbial species have evolved collaborative symbiotic lifestyles that allow two organisms to perform metabolic processes that neither would be capable of independently (i.e., “mutualistic syntrophy”). In a new study by Lawrence Berkeley National Laboratory scientists, an experimental evolutionary system was constructed that pairs a common sulfate-reducing bacterium, Desulfovibrio vulgaris, with a methane-producing archaea, Methanococcus maripaludis, neither of which is known to grow via mutualistic syntrophy in nature. Experimental conditions were manipulated so that neither organism would have access to an energy source it could use independently. In 21 independent experiments over 1,000 generations, mutualistic syntrophies that closely resembled associations observed in nature evolved between the two organisms 13 times. In these syntrophies, consumption of lactate (a common product of fermentation in anoxic environments) by D. vulgaris provided hydrogen and carbon dioxide to M. maripaludis, which, in turn, produced methane and maintained an energetic environment favorable to continued consumption of lactate by D. vulgaris. The partners quickly improved their performance efficiency for coupled syntrophic growth, but in many cases, D. vulgaris lost its ability to grow in the absence of M. maripaludis even under normal growth conditions. By sequencing the genomes of the evolved strains from the various experimental replicates, it was determined that D. vulgaris quickly accumulated loss of function mutations, particularly in three key sulfate reduction genes needed for independent growth. The team currently is examining the relationship between the loss of capacity for independent growth and improved symbiotic performance. These results provide a fascinating glimpse at the molecular underpinnings of a natural selection process and demonstrate the importance of tradeoffs between growth efficiency and metabolic flexibility during the evolution of a symbiotic partnership. In the broader sense, understanding the molecular factors governing the formation of these associations and their performance under changing environmental conditions could provide valuable new insights into the way that carbon and energy flow through anoxic environments.

The Impact

Because loss-of-function mutations arose rapidly and independently in replicated experiments, and because these mutations were correlated with enhanced growth rate and productivity, gene loss could be attributed to natural selection, even though these mutations should significantly restrict the independence of the evolved D. vulgaris. Together, these data present an empirical demonstration that specialization for a mutualistic interaction can evolve by natural selection shortly after its origin. They also demonstrate that a sulfate-reducing bacterium can readily evolve to become a specialized syntroph, a situation that may have often occurred in nature. This result may explain why sulfate reducers share a common ancestor with many species specialized for cooperation with methanogens.


Hillesland, K. L., S. Lim, J. Flowers, S. Turkarslan, N. Pinel, G. Zane, N. Elliott, Y. Qin, L. Wu, N. Baliga, J. Zhou, J. Wall, and D. Stahl. 2014. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism,” Proceedings of the National Academy of Sciences (USA) 111(41), 14822-827. DOI: 10.1073/pnas.1407986111.