Methane is formed by methanogens. One way to do it would be to aerate your sample more to remove anaerobic organisms. Other methods that are used to sterilize wastewater can be applied too (UV, chlorine, etc.). You could also try to increase the number of oxygenating microorganisms as well like microalgae through inoculation.
Where did you learn microbiology or anaerobic digestion which say that methane is formed by bacteria? Can you provide reference methane forming bacteria?
Methanogenesis is the production of methane from Archaea, though some newer studies have pointed to pathways in bacteria for methane production ( https://www.nature.com/articles/s41564-017-0091-5). Archaea and bacteria are both prokaryotes, so confusing them isn't to be unexpected once in a while. Clearly the question was focused on ways to kill the methanogens, but your response neither constructive nor conducive to finding a solution.
1. Your comments clearly says that your understanding about methanogenesis needs more efforts. Changing "bacteria" to "methanotrophs", in you provious post does not help, as it becomes more incorrect. With methanotrophs you are saying methane is formed by methane eaters. Incorrect grammatically and conceptually. As you are an engineer, I understand that biology is not our field of expertise.
2. I also recommend you to review the reference your providing to support the idea of bacteria forming methane. The paper says, in certain condition (co-culture or expressing enzyme etc.), the test bacteria produces methane, and that too in very small amount. Thus, that methane is not produced by methanogenesis pathway. Therefore, it can not be generalized.
3. Furthermore, the minor amount of methane (as a metabolic bi-product) is formed by phototrophic/aerobic bacteria, and I don't see the reference fitting in anaerobic digestion system or waste water treatment.
4. Sure one can give hundred answer to a question as per the interpretation, but if the questioner does not know what is he/she asking, it is equally senseless to answer. With the question itself it is clear that questioner is neither have enough experience in the process operation nor the experience. So, it would be better for him to understand the basics and realize there is a lot to learn.