Dataset: Microbial gene abundance of coastal wetland soil cores collected in June 2018 from Barataria Bay, Louisiana

Nine coastal wetland soil cores were collected in June 2018 from Barataria Bay, Louisiana, a shallow open water basin located west of the Mississippi River Delta.  Soil cores were collected along three transects, roughly 1 meter apart, that consisted of three points:  the coastal fringe (0 m inland), 1 meter inland, and 2 meters inland. Soil cores were collected in polycarbonate tubes via the push core method to a depth of 150 cm, and field-extruded into 15 separate 10-cm intervals. Soils were stored  in polyethylene bags on ice and immediately transported back to the laboratory, where they were kept at 4 °C until sample analysis was complete.  

This dataset includes analyses of microbial gene abundance.  Quantitative PCR analysis on a CFX96 Touch Real-Time PCR Detection system was used to measure the number of gene copies of bacteria (16S), sulfate reduction (dsRa), and archaea (Arch) genes.  

Soil samples were sieved through a 2mm seive, then centrifuged at 4000 rpm at 25°C for 1 minute, and excess water decanted.  DNA was extracted from soil subsamples (0.25 grams each) following DNAeasy PowerSoil Extraction Kit (QIAGEN, Hilden, Germany).  Primers were selected to amplify specific taxonomic and functional genes of interest within the samples -- sulfate reduction (dsrA), all bacteria (16S), and all archaea (Arch).  Genomic DNA from Desulfobacterium autotrophicum (Strain DSM 3382) was used to establish standard curves for both amplification of the 16S gene and the dsrA gene, while Methanococcus voltae (Strain A3) was used to establish standard curves for amplification of the Arch gene. Each 25 microliter reaction contained 5 microliters DNA, 1.25 microliters of each 0.1uM primer (forward and reverse), 12.5 microliters of SYBR green MasterMix, and 12.5 microliters of PCR-grade water. Each reaction initially proceeded through steps at 50°C and 95°C, then through 50 cycles of denaturing at 95°C, annealing, and extending at 72°C.  

[For details on primers and primer annealing temperatures, see Steinmuller and Chambers (2019)].