Cornell University researchers reveal that, after years of producing methane, microbial communities can quickly switch to producing hydrogen sulfide.
Aug 25, 2020

The Bioreactor Battle: Understanding the Switch from Methane to Hydrogen Sulfide

The Science

Microbial communities are often flexible in how they get their energy. Even inside a methane-producing bioreactor that has been stable for years, community dynamics can be quickly disrupted. For example, introduction of sulfate could result in the production of hydrogen sulfide gas (H2S) instead of methane in a matter of hours. H2S is a corrosive gas and an unwanted side product during methane production. This study discovered the mechanism behind the rapid switch. Some core members of the community are always ready to use sulfate as an energy source. And over time, those that are not may disappear from the community entirely.

The Impact

The controlled production of methane is an important biofuel source. Introduction of sulfate could result in a switch to hydrogen sulfide gas (H2S), which is corrosive and smells like rotten eggs. Even after years as a stable methanogenic bioreactor, H2S production can start in a matter of hours. Understanding fine-scale community shifts are important for maintaining stable bioreactor conditions for biofuel production.


A stable methane-producing bioreactor was used to explore how a microbial community responds to the addition of sulfate as an alternative energy source. Samples were taken from a control bioreactor (no sulfate) and an experimental bioreactor after the addition of sulfate at 6, 24, and 48 hours. The samples were processed by the Joint Genome Institute. 

Representative genomes for 5 of the core bioreactor community members were analyzed using KBase. Gene activity for each community member was compared between the control (no sulfate) and the experiment (with sulfate). Within 6 hours, these microbes had already started to adjust to the new conditions (compared to the stable control system). Several members turned on genes responsible for sulfate uptake from the environment and sulfate metabolism. By 24 hours, genes capable of producing molecular hydrogen are active. At 48 hours, one of the methane producing microbes is still functioning, while another member is unable to persist. Explore an example of the analyses for yourself via their public KBase Narratives.


A.R. St. James, R.E. Richardson. “Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions.” FEMS Microbiology Ecology 96, fiaa050 (2020). [10.1093/femsec/fiaa050]

Related Links

Metagenome-discovered food webs in a long-term methanogenic bioreactor and rapid switch to sulfate reducing conditions, KBase Published Narrative


The research highlighted was supported by a microbial/metagenome project (CSP 503205) through the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02–05CH11231. Additional funding was provided by the Cornell University Program in Cross-Scale Biogeochemistry and Climate, which is supported by the National Science Foundation Integrative Graduate Education and Research Traineeship Program (NSF-IGERT) and the Atkinson Center for a Sustainable Future.

DOE Systems Biology Knowledgebase (KBase) is funded by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886. 

Elisha Wood-Charlson
Elisha Wood-Charlson | Engagement Lead
Lawrence Berkeley National Laboratory

Elisha M Wood-Charlson is KBase’s User Engagement Lead. She has a PhD and 10+ years of experience as a microbial ecologist focused on host-microbe-virus interactions in the marine environment. Since leaving the research bench, she has moved into the realm of scientific community engagement, with the goal of making microbiome data science more efficient through effective collaboration, building trust in online communities, and developing shared ownership throughout the scientific process.