Archaeal and bacterial community dynamics in enrichments from anaerobic estuarine sediments

Biddle, Jennifer F.Archaea from anaerobic marine sediments are understudied and challenging to culture in the lab. Without enriching microbes in culture, genomic data is the only means for garnering information about microbial community structure and potential metabolic activities. Archaea are common members in microbial communities, and understanding their roles in the environment is one of the keys to better understanding global microbial ecology. The microbial community at Oyster Rocks, an estuarine site near Delaware Bay, has a diverse set of archaeal clades and a high relative abundance of “deeply-branching” archaea. Here in this study, we are aiming to achieve stable archaeal enrichments in the lab via applying different chemical and physical treatments to differentially stimulate the archaeal growth while minimizing bacterial growth. Seven sets of cultures with differing media components and supplementary nutrients were diluted using sediments from Oyster Rocks. Additives included both complex and simple carbon compounds to find to provide energy and carbon sources to the media. An extracellular electron carrier was also tested to see the effects of increased electron exchange between organisms. Our second set of cultures were supplemented with autoclaved sediment from Oyster Rocks to provide a more diverse suite of nutrients specific to the environment they were sampled from. Finally, we incubated our cultures with a reducing agent and a media including volatile fatty acids to test a range of redox potentials with a rich media. The effect of each condition was assessed using qPCR and 16S rRNA gene analysis to quantitatively and qualitatively address the changes that took place on microbial communities. Interestingly, a culture with the rich media including volatile fatty acids, an electron carrier, a low redox potential, and a methane headspace, substantially stimulated the growth of Archaea approximately 600-fold, and nearly excluded bacteria from the enrichment. In future attempts to enrich anaerobic sedimentary archaea in the lab, this media recipe would be advantageous for archaeal growth. These results can inform future archaeal culturing in order to better understand them in the context of their microbial ecology.University of Delaware, School of Marine Science and PolicyM.S