Xiaoqin Wu, Sara Gushgari-Doyle, and Mon Oo Yee from Romy Chakraborty’s group in EESA’s Ecology Department and the Department of Biological Engineering at MIT have published a paper in the journal Frontiers in Microbiology describing a study they hope will advance cultivation and isolation strategies for recovering diverse, uncultivable, and novel microorganisms from Earth’s subsurface. This project falls under the DOE-BER ENIGMA SFA, and builds on this previous work by EESA researchers.
Despite advances in modern molecular technology, it remains difficult to recover and cultivate these diverse microorganisms within the laboratory. To be successful in doing so, microbiologists need to develop strategies to closely mimic the bacteria’s ecological habitat.
The research team applied naturally occurring complex carbon (C) sources, including sediment dissolved organic matter (DOM) and bacterial cell lysate, that microbes encounter in their natural habitats to enrich groundwater microbial communities for 30 days. For comparison, the scientists included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins, other popular C choices generally used for this purpose. Their results show that complex but native C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple, often-used C, which yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes). Microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes).
“Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems,” Chakraborty said. “Our findings will benefit future development of effective cultivation/isolation strategies to obtain diverse and ecologically relevant microorganisms from the environment.”