TY - JOUR T1 - Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria JF - bioRxiv DO - 10.1101/517854 SP - 517854 AU - Xiaoqin Wu AU - Sarah Spencer AU - Eric J. Alm AU - Jana Voriskova AU - Romy Chakraborty Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/01/13/517854.abstract N2 - Improved and innovative enrichment/isolation techniques that yield to relevant isolates representing the true diversity of environmental microbial communities would significantly advance exploring the physiology of ecologically important taxa in ecosystems. Traditionally, either simple organic carbon (C) or yeast extract is used as C source in culture medium for microbial enrichment/isolation in laboratory. In natural environment, however, microbial population and evolution are greatly influenced by the property and composition of natural organic C. In this study, 8 types of organic C sources were fed to intrinsic groundwater microbes collected at Oak Ridge Reservation Field Research Center (ORR-FRC) background site for a 30-day incubation period to investigate the response of indigenous bacterial communities to different C sources. The tested C sources included simple organic C (glucose, acetate, benzoate, oleic acid, and cellulose) that are either traditionally used as C source in bacterial culture medium or present in natural environments; naturally occurring undefined complex C (bacterial cell lysate and sediment-derived natural organic matter (NOM)); as well as vitamin mixture which is a commonly used ingredient in culture medium. Our results clearly indicate that natural complex C substrates served better in enriching diverse bacteria compared to other C sources. Microcosms amended with small organic C (glucose, acetate, benzoate, or oleic acid) showed significantly lower biodiversity than control groups, dominated by only a few phyla of bacteria such as Proteobacteria and Bacteroidetes which are commonly isolated and already have diverse representative isolates, while those amended with natural complex C (cell lysate or NOM) displayed significantly higher biodiversity than control groups, in which three phyla (Verrucomicrobia, Planctomycetes, and Armatimonadetes) that are poorly represented in published culture collections were abundantly enriched. Further isolation of pure bacterial strains from complex C-amended enrichments led to 51 species representing 4 phyla, 13 orders. Furthermore, 5 isolates with low similarities to published strains were considered to be novel. Results from this study will aid in the design of better cultivation and isolation strategy for maximize the diversity of organisms recovered from subsurface environment. ER -