Dataset: SRA accession and experiment metadata for Chesapeake Bay sediment incubation in 2019

A time series incubation experiment was performed to investigate potential interactions between marine cable bacteria and their associated microbial community. Sediment was collected from the main channel of Chesapeake Bay from a mesohaline region that experiences severe and prolonged seasonal oxygen depletion. The upper 10 cm of sediments were homogenized under a gentle N2 gas stream to minimize oxidation, and re-packed into polycarbonate core liners (Ø = 2.5 cm, height = 8 cm), sealed with a silicone stopper at the bottom, and left open to aquarium water at the top. The sediment cores were constructed so that the sediment surface was flush with the core liner. Sediment cores were incubated in continuously aerated aquaria maintained at bottom water temperature (16oC), in artificial seawater (Red Sea Salts TM), in the dark, at bottom water salinity (S=15.5), and this enabled a rapid proliferation of cable bacteria. Water level and salinity in the aquaria was monitored daily and topped with deionized water as necessary to maintain water level and salinity (approximately twice weekly). At six time points (Days 3, 6, 10, 14, 20, 46), triplicate cores were selected at random for microsensor profiling, followed by destructive sampling. One sediment core was sampled for microscopy and nucleic acid preservation, and a separate sediment core was sampled under anaerobic conditions for porewater geochemistry. Sediment cores were each sectioned at 0.5 cm increments to 3 cm. In a subset of sediment cores, downward growth of cable bacteria was blocked by embedding a 25 mm filter (0.2 μm polycarbonate; Millipore) at 0.5 cm depth. The filter was held in place with a specially constructed filter-holder equipped with a rubber Oring to ensure a water-tight seal. Sediment cores with barrier filters were similarly sampled on Days 3, 20, 46 for microsensor profiling, microscopy, nucleic acid analyses, and porewater geochemistry.

For nucleic acid sequencing analysis, sediments were collected in cryogenic tubes, flash frozen in liquid nitrogen, and stored at -80oC. DNA and RNA were extracted separately. Extracted RNA was purified with Norgen CleanAll DNA/RNA Clean-Up and Concentration Kit (Norgen Biotek). Residual DNA in the RNA extracts was digested with two rounds of TURBO DNAse treatment (Invitrogen) and cDNA synthesis was accomplished by reverse transcription-polymerase chain reaction using SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen), according to manufacturer’s protocol. DNA and cDNA concentrations were quantitated with Qubit dsDNA Broad Range assay kits using Qubit 2.0 fluorometer (Invitrogen). The V4-V5 region of the microbial 16S rRNA gene (DNA and cDNA) was amplified using the modified primer pair of the Earth Microbiome Project (515F-Y/926R; Parada et al., 2016). For DNA samples, amplicons were amplified, barcoded, and sequenced at Bioanalytical Services Laboratory (Baslab) at the Institute of Marine and Environmental Technology (IMET; Baltimore, MD, USA) using an Illumina Miseq platform (2 x 300 bp). For RNA samples, cDNA amplicons were sequenced using an Illumina Miseq platform (2 x 250 bp) by Genewiz (NJ, USA).