Effect of intermittent opening of breathable culture plugs and aeration of headspace on the structure of microbial communities in shake-flask culture

In this study, we found that opening breathable culture plugs for 30 s during periodic and aseptic sampling affects the community structure of cultured soil microbes. Similar effects were observed using an automatic aeration flask system that mimics aseptic opening of the breathable culture plug during sampling, but without interruption in shaking. Thus, the observed changes in the microbial consortia appear to be due exclusively to the intermittent ventilation of the flask headspace. To elucidate the mechanism driving this phenomenon, we monitored CO2 and O2 concentrations in both headspace and culture broth using the new system termed as circulation direct monitoring and sampling system. The data show that the CO2 concentration in the culture broth temporarily decreased with the CO2 concentration in the headspace, strongly suggesting that the effect of intermittent ventilation of the headspace on the microbial consortia depends on CO2. Importantly, the data also imply that environmental variables during shake flask culture, especially CO2 concentration, is important for screening aerobic microorganisms.