Dataset: Microscopy counts (Beggiatoa-like filaments, Cable bacteria), together with in situ temperature and salinity and surface sediment chlorophyll concentrations, of ex situ sediment cores collected in the Chesapeake Bay during 2017-2018

Methodology:
Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter).

In the lab, surficial sediments were sectioned at 0.5 cm depth increments from which aliquots were collected for microscope enumeration of Beggiatoa-like filaments and cable bacteria filaments. Beggiatoa-like filament enumeration proceeded by methods adapted from Jorgensen et al. 2010 (doi: 10.1111/j.1574-6941.2010.00918), using inverted light microscopy (Zeiss AxioVert A1) with Utermöhl well slides. Filaments were identified as living Beggiatoa-like filaments if they were motile, unpigmented, and contained refractive sulfur granules. The length and diameter of each Beggiatoa-like filament encountered was recorded. Data are reported as volumetric density of Beggiatoa-like filaments (computed assuming a cylindrical shape), integrated to 5.0 cm depth.

To enumerate cable bacteria, cells were first detached from sediment particles using methods adapted from Kallmeyer et al. 2008, using density centrifugation with Nycodenz (50% wt/vol), and finally captured on filters (0.2 µm cellulose acetate). The identity of cable bacteria was first confirmed using fluorescent in situ hybridization (FISH) with the DSB706 oligoprobe (Schauer et al. 2014) on a subset of samples, and then enumerated following staining by Sybr Green I. A minimum of 200 randomly selected fields were viewed at 630X (Zeiss Axio Imager 2). Data are reported as cumulative length of cable bacteria filaments per volume of sediment, and as cumulative volume of cable bacteria computed assuming a cylindrical shape and cell diameter of 1 micron, each integrated to 4.0 cm depth.

For analysis of chlorophyll a (Chla) concentration in surface sediments (0-0.5 cm), pigments were extracted into 90% acetone, applying agitation by gentle sonication, and pooling 2-3 successive extractions. Pigment concentration was determined colorimetrically (ThermoScientific Evolution 60S), applying the empirical formula of (Jeffrey et al. 1975).

Sampling and Analytical Procedures:
Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm). Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter). Cores were then capped, 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. Core sectioning was conducted within 1 day of core retrieval.