Fig. 1

A workflow for culturing, archiving, and characterizing sediment microbiotas. Schematic diagram of the workflow, encompassing bacterial culturing and genomics to isolate and characterize bacterial species from a marine sediment microbiota. The process incorporates the following steps: resuscitation cultures (0–30 days), restreaking, archiving, and phenotyping. First, fresh sediment samples are cultured in the enrichment culture medium for the isolation of bacteria. The anaerobic enrichment cultures are diluted serially diluted, and aliquots of the homogenate are subsequently inoculated on MA to isolate bacteria. Second, isolates are identified by selecting single colonies that are streaked to purity, and full-length 16S rRNA genes are amplified and sequenced. Third, each unique, novel, desired isolate is archived frozen in a culture collection, and a whole-genome sequence is generated. Finally, a metatranscriptomic analysis of the microbiota during each period of resuscitation culturing is conducted and combined with information from environmental factors, comparative genomic analysis, and a local BLAST of cultured strains