Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

Abstract

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by <i>Gammaproteobacteria</i>, and culture-based methods revealed communities dominated by <i>Actinobacteria</i>. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to <i>Oceaniovalibus</i>, <i>Psychrobacter</i> and <i>Salegentibacter</i> were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.