DOI: 10.25820/data.006156
title: Polychlorinated biphenyl (PCB) concentration and congener data collected from anaerobic sediment microcosms that harbor organohalide respiring bacteria

description: The data set presented here quantifies individual PCB congeners and total PCB concentrations in sediment microcosms that harbor anaerobic microbial consortium native to PCB-contaminated sediments. The PCB data was collected at day 0 and day 200 from sediment microcosms, and it accompanies a multi-omics dataset that includes 4 metagenomes, 8 metatranscriptomes, 63 metagenome-assembled genomes. As a whole, the combine datasets capture dynamic microbial community interactions, structure, and function relevant to anaerobic PCB biodegradation in the presence of differing PCB concentrations and congener profiles.
description: Sediment Origins and Experimental Setup:

Sediment was collected in 2017 from a PCB contaminated waste water lagoon. For this experiment, we selected sediment from two locations within the lagoon that differed in PCB concentration (indicated by the labels HPCBM and LPCBM). No additional PCBs were spiked into the media. The experiment examines only weathered PCBs present at the field site, and the microbial communities native to those sediments. The native microbial communities served as the only inoculum in the experiments.

PCB Quantification:

GC-MS/MS (Agilent 7890A GC system, Agilent 7000 Triple Quad, Agilent 7693 autosampler) in multiple reaction monitoring mode (MRM) was used for identification and quantification of 209 PCBs as 174 chromatographic peaks. The GC was equipped with a Supelco SPB-Octyl capillary column (50% n-octyl, 50% methyl siloxane, 30 m × 0.25 mm ID, 0.25 µm film thicknesses) with helium as the carrier gas flowing at 0.75 mL/min and nitrogen/ argon as the collision gas. The GC operated in solvent vent injection mode at the following injection conditions: initial temperature 45 °C, initial time 0.06 min, ramp 600 °C/min to inlet temperature 325 °C at 4.4 psi. The GC oven temperature program was 45 °C for 2 min, 45 to 75 °C at 100 °C/min and hold for 5 min, 75 to 150 °C at 15 °C/min and hold for 1 min, 150 to 280 at 2.5 °C/min and final hold 5 min (total run time 70.86 min). The triple quadrupole MS electron ionization source was set to 260 °C. Additional details can be found in the supporting information.

Quality Assurance & Quality Control (QA/QC):

Extraction efficiency, reproducibility, and accuracy was assessed using surrogate standards, replicates of method blanks, and development of QC acceptance criteria. Percentage recoveries of surrogate standards were used to correct congener mass as follows: PCB14 recovery was used to correct PCB1 to PCB39, PCB65-d5 was used to correct PCB40 to PCB127 and PCB166 was used to correct PCB128 to PCB209 (sorted by IUPAC number). PCB congener masses were corrected for surrogate recoveries less than 100%. Samples were processed in two batches with one method blank per batch. All materials used in sample extraction had either been triple rinsed with solvent (methanol, acetone, and hexane) or combusted overnight at 450°C to prevent background PCB contamination. Results from the method blanks were used to determine the limit of quantification (LOQ) as the upper limit of the 95% confidence interval (average mass plus two times the standard deviation).

Description of PCB Extraction Methods:

Slurry samples (2mL) were collected from biological replicate microcosms. PCBs were extracted from the samples with a liquid-liquid extraction (LLE) with an equal volume of hexane (2 mL) added to each. Prior to extraction, the samples were spiked with surrogate standards PCB 14 (50.81 ng; 3,5-dichlorobiphenyl), deuterated PCB 65-d5 (52.5 ng; 2,3,5,6-tetrachlorobiphenyl-d5, deuterated) and PCB166 (52.56 ng; 2,3,4,4′,5,6-hexachlorobiphenyl; Cambridge Isotope Laboratories, Inc.). The slurry and hexane mixture was vortexed and centrifuged. The LLE process was repeated three times. The resulting volume of solvent containing the sample extract was concentrated to approximately 1 mL using a TurboVap II Concentration Workstation (Caliper Life Sciences).

The final hexane extract was passed through a Pasteur pipette filled with 0.1 g of combusted silica gel and 1 g of acidified silica gel (2:1 silica gel:sulfuric acid by weight) and eluted with approximately 10 mL of hexane. Samples were concentrated a final time using a TurboVap II Concentration Workstation (Caliper Life Sciences) to approximately 1 mL and transferred to a gas chromatography vial. The final sample was spiked with internal standards deuterated PCB 30-d5 (19.6 ng; 2,4,6- trichlorobiphenyl-2′,3′,4′,5′,6′-d5, deuterated) and PCB 204 (19.6 ng; 2,2′,3,4,4′,5,6,6′-octachlorobiphenyl; Cambridge Isotope Laboratories, Inc.).