From March of 2017 to August of 2018, sediments samples were collected at two Chesapeake Bay stations: CB4.3C (38.55505 N -76.42794 W; 26 m depth) and CB4.3W (38.55728 N -76.49402 W; 9m depth).

Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate controlled room. From each station, one sediment core was subsampled for nucleic acids, microscopy, and chlorophyll a (Chl a) analyses, two cores were used for microsensor profiling. Sampling was undertaken from small vessels (Parker or Wetsig boats). Surface sediments (0–0.5 cm) were transferred to 5-mL cryovials, rapidly frozen in a liquid nitrogen-charged dry shipper, and stored at -80 degC.

This data set refers to the DNA samples. DNA was extracted from a thawed sediment aliquot. Prior to cell lysis, carbonates were dissolved in an acetate buffer–PBS solution with gentle mixing, and soluble (extracellular) DNA was removed by washing in Tris- EDTA buffer with gentle mixing. Cell lysis was achieved using a combination of bead-beating, repeated heat-thaw cycling, and chemical lysis. Extracted DNA was purified by two washes with a chloroform–isoamyl alcohol solution and then precipitated with a PEG 8000-NaCl solution in the presence of linear polyacrylamide at room temperature. A final wash was made in 70% ethanol, and the resultant DNA pellet was allowed to air dry and then dissolved in water. Extracted DNA quality was checked by agarose gel electrophoresis, and its concentration was measured by fluorometry (Qubit 2.0 fluorometer; Invitrogen) using Qubit dsDNA assay kits. Further purification was found to be unnecessary. The hypervariable region V4-V5 of the 16S rRNA gene was targeted for amplification, using the modified primer pair515F-Y/926R (GTG YCA GCM GCC GCG GTA A)/(CCG YCA ATT YMT TTR AGT TT) (Parada et al. 2015). Amplification, barcoding, and sequencing were performed at the Bioanalytical Services Laboratory (BASLAB, IMET). Amplification proceeded via two steps, first for gene amplification and the second for adding indexes, and clean-up was accomplished using AMPure XP beads (Beckman Coulter). Amplicons were sequenced using an Illumina MiSeq platform (2 x 300 nt paired-end reads).