Over the past decade, metagenomics and advanced sequencing tools have uncovered a broad diversity of microbes in different environments, yet only a small component of this diversity (< 1%) has been successfully cultivated to date. Improved and innovative enrichment/isolation techniques yielding isolates representing this diversity would benefit exploring the physiology of more than 95% of ecologically important taxa in different ecosystems. The properties and composition of carbon (C) influences the structure of microbial communities in natural ecosystems. Traditionally, simple small organic compounds such as glucose, acetate, lactate, are the C of choice in enrichment/isolations. In our study, we fed a variety of different C to groundwater microbes for a 30-day incubation period to investigate the response of indigenous microbes to C sources. Eight different C were tested, including simple small organic C (glucose, acetate, benzoate, and oleic acid); naturally occurring complex C (cell lysate and sediment-extracted natural organic matter (NOM)); polysaccharide (cellulose), and vitamin mixture. Our hypothesis was providing naturally occurring complex C to enrichments would result in substantially diverse microbial communities compared to small organic C.
Results/Conclusions
The community composition of enrichments was greatly affected by C substrates. Enrichments amended with naturally occurring complex C displayed high diversity, while those amended with small organic C showed much lower diversity, dominated by only a few orders such as Cytophagales, Burkholderiales, Rhodocyclales, and Caulobacterales. In microcosms amended with NOM, Verrucomicrobia, which is poorly respresented in culture collections were present. Halomonas sp., Pelomonas sp., Sediminibacterium sp., and Shewanella sp. were enriched in all groups in this study, indicating that they are ‘generalists’, and likely harbor metabolic potential of utilizing diverse C sources, from simple small organic C to complex C. NOM enriched ‘specialists’ than observed with other C sources. Our results suggest that isolation of diverse microbes from environment would benefit from the use of naturally occurring complex C substrates, and will contribute significantly in uncovering the diversity of microbes recovered from the environment.