Data for: Forest organic matter removal leads to long-term reductions in bacterial and fungal abundance
Description
Data noted in the excel file is of soil bacterial and fungal abundance in a southern pine forest. The study area was a Pinus taeda (loblolly pine) forest located in eastern Texas USA (31° 06’ 32.48’’ N, 95° 09’ 59.15’’W). In brief, the experimental design consisted of two different OMR intensities (low-intensity: bole-only harvest, BO; high intensity: whole-tree harvest + forest floor removal, WT+FF) and unharvested control forest plots, with three replicates per treatment. Treatments were harvested in 1996, and replanted with containerized P. taeda seedlings at 2.5 m x 2.5 m spacing. Soil was sampled seasonally for 1 year (June 2014, September 2014, December 2014, and March 2015). At each sample date, 4 cores were taken within each replicate plot to a depth of 1 m, and separated into depth increments (0-10, 10-30, 30-60, and 60-100 cm). The four cores/plot were then pooled by depth increment and homogenized to create a single homogenous sample for each replicate plot, from which a representative subsample was removed and stored at -80 °C for molecular analyses. Microbial DNA was extracted from soil as noted in Mushinski et al. (2017). Quantitative-PCR (qPCR) targeting total bacteria and fungi was performed using primer pairs 1100F/1492R for bacteria and ITS1F/ITS5.8S for fungi . The 25 μl reaction mixture contained 13 μl SYBR green real master mix (5Prime, Gaithersburg, MD), 0.5 μl of each primer (concentration 10 mM), 1 μl DNA template, and 10 μl molecular-grade water. Each analytical run included a set of standards, negative controls, and replicated samples (n = 3) on a 96-well plate. For the 16S rRNA gene, the qPCR conditions were as follows: 95 °C for 10 min; 95 °C for 30 sec, 53 °C for 30 sec (40 cycles); 72 °C for 1 min. For the ITS region, the qPCR was run with the following conditions: 94 °C for 5 min; 94 °C for 30 sec, 57 °C for 45 sec (30 cycles); 72 °C for 1.5 min. The qPCR was performed using a Mastercycler® ep realplex thermal cycler (Eppendorf, Hamburg, Germany). Amplification efficiencies of 77-80% and 84-86% were obtained for bacteria and fungi, with r2 values > 0.96. Plasmids containing 16S and ITS inserts were used for the standard curves. References Mushinski, R.M., Gentry, T.J., Dorosky, R.J., Boutton, T.W., 2017. Forest harvest intensity and soil depth alter inorganic nitrogen pool sizes and ammonia oxidizer community composition. Soil Biol. Biochem. 112, 216-227.