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All box cores were subsampled for sediment water content and porosity estimates using cutoff 60-ml syringes extruded over 1-cm vertical depth intervals. Sediment was weighed wet and dry (70°C). Porosity was estimated from water content assuming a particle density of 2.6 g cm−3.

Reactive Fe, Mn, and Al were estimated by leaching tube linings or sediment with 1 N HCl for 16 hours at 22°C. Fe and Mn were measured spectrophotometrically using ferrozine and formaldoxime (32, 33) and Al using graphite furnace atomic absorption. Solid-phase S was measured as CRS at 22°C using passive distillation (34).

Sediment samples for direct epifluorescence counts of free-living bacteria cell and cable bacteria distributions were obtained using cutoff 3-ml plastic syringes inserted at the same locations as Rhizon ports and immediately preserved with 2% formaldehyde in sterile seawater (3% salt) and refrigerated. Sample syringes sometimes intersected tubes but did not pierce the tough lining material. These samples were used to enumerate total free-living bacteria cells and cable bacteria, the latter identifiable by the unmistakable filament morphology, after staining with acridine orange (AO) (35, 36). Confirmation of cable bacteria identity was made on subsamples at all array locations, and radial intervals by fluorescence in situ hybridization (FISH) with a Desulfobulbaceae-specific oligonucleotide probe (DSB706; 5′-ACCCGTATTCCTCCCGAT-3′) (37), EUB338 probe mixture (38), and probe NON338 (39) were used as positive and negative controls, respectively, with FISH protocols according to (40) and probe hybridization conditions after (25). The length of filaments and number of cells were made from the AO-stained samples, which not only were larger than the FISH confirmation samples but also were minimally disturbed as opposed to the smaller subsamples used for FISH. AO-stained black 0.2-μm neutron track-etched polycarbonate membrane filters with 100-fold diluted samples of sediment for direct counts of bacteria by epifluorescence microscopy after (35) (precision better than 5.0%). Free-living cells within 10 randomly selected fields defined by a Whipple reticle (0.1 mm by 0.1 mm) of 100 0.01 mm by 0.01 mm squares were counted, while cable cells were counted or filament lengths (including any that extended beyond the grid field) recorded within at least 20 fields systematically covering the filter. The number of individual cable cells per filament of a given length was calculated on the basis of repeated measurements of five cells across a reticle grid square. After removal of subsamples for bacterial counts and wet-dry weight conversion, the remaining sediment was stained with rose bengal, allowed to sit for several hours to overnight, collected on a 0.44-μm nylon-mesh screen, and rinsed with distilled water, and nematodes were enumerated under a dissecting microscope.

For radiochemical analyses (7Be), sediment cores (9.5 cm ID) were obtained at multiple times in 2009–2010 and 2018 at the sampling site using 10-cm outside diameter cellulose acetate butyrate (CAB) corer tubes as subcorers of larger box cores obtained by divers. These cylindrical cores were sectioned at 1- to 3-cm intervals, dried, ground, and γ-counted for 7Be (477 keV; Canberra 3 K LeGe). Counting error was used as a measure of analytical precision. Example profiles from July to October 2009 and September 2018 are reported here. These sampling periods are from the same seasons as box cores obtained for analyses of cable bacteria.

In the case of radial sampling, tubes from both sampling sites were also removed from sediment and cleaned of agglutinated mud by scrapping and sonification in seawater followed by a single rinse with distilled water to remove salt, and the microstructure was examined by scanning electron microscopy (SEM)/EDS. A cylindrical core containing a Chaetopterus tube collected from Smithtown Bay, LIS, USA (17) was sectioned horizontally during extrusion, and pH distributions were measured in horizontal planes radially around the tube at multiple depths.

2D pH distributions were measured using reversible planar optodes either placed horizontally directly onto sectioned core surfaces or inserted vertically along the sides of box corers (41).

Dissolved Fe2+ and H2S (as dissolved H2S only) distributions were measured using irreversible planar sensors inserted vertically into sediment cores next to Chaetopterus tubes and/or allowed to equilibrate for 3 to 5 min (23, 42). X-radiography of sedimentary structure was performed on 2.5-cm-thick vertical subcores of box cores or separate diver-taken box cores 2.5 cm in thickness using a Kramex portable x-ray source (80 kilovolt peak, 10 mA; 0.04 s) and a Samsung LTX 1717 digital x-ray detector.

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