Data for: Forest organic matter removal leads to long-term reductions in bacterial and fungal abundance

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.本Excel文件记录的数据为美国南部松林的土壤细菌与真菌丰度。本研究的样地为位于美国德克萨斯州东部的火炬松（Pinus taeda, loblolly pine）林，地理坐标为31°06’32.48’’N，95°09’59.15’’W。实验设置了两种不同的OMR强度：低强度采伐（仅伐干采伐，bole-only harvest, BO）与高强度采伐（全树采伐+枯落物层移除，whole-tree harvest + forest floor removal, WT+FF），并设置未采伐的对照样地，每种处理设置3次生物学重复。所有采伐处理于1996年实施，之后以2.5 m×2.5 m的株行距重新栽植容器化火炬松幼苗。研究于1年内按季节采集土壤样本，采样时间分别为2014年6月、2014年9月、2014年12月及2015年3月。每次采样时，在每个重复样地内采集4个土芯，采样深度达1 m，并按土层深度划分为0-10 cm、10-30 cm、30-60 cm及60-100 cm四个层级。随后将每个样地的4个土芯按同一土层层级混合均质化，为每个重复样地制备一份均质混合样本，从中提取代表性子样本并置于-80℃低温保存，用于后续分子生物学分析。土壤微生物DNA的提取方法参照Mushinski等人（2017）的实验方案。采用定量聚合酶链式反应（quantitative-PCR, qPCR）测定总细菌与真菌的丰度：细菌扩增使用引物对1100F/1492R，真菌扩增使用引物对ITS1F/ITS5.8S。25 μL的反应体系包含13 μL SYBR Green实时荧光定量PCR预混液（5Prime，美国马里兰州盖瑟斯堡）、0.5 μL的每种引物（浓度为10 mM）、1 μL DNA模板以及10 μL分子级纯水。每个分析批次均在96孔板上设置标准品、阴性对照以及重复样本（n=3）。针对细菌的16S rRNA基因，qPCR反应程序为：95℃预变性10 min；95℃变性30 s、53℃退火30 s，共40个循环；72℃延伸1 min。针对真菌的ITS区域，qPCR反应程序为：94℃预变性5 min；94℃变性30 s、57℃退火45 s，共30个循环；72℃延伸1.5 min。本实验采用Mastercycler® ep realplex实时荧光定量PCR仪（Eppendorf, 德国汉堡）完成qPCR反应。细菌与真菌的扩增效率分别为77%-80%与84%-86%，二者的决定系数r²均大于0.96。实验中使用携带16S rRNA基因与ITS片段插入序列的质粒绘制标准曲线。参考文献：Mushinski, R.M., Gentry, T.J., Dorosky, R.J., Boutton, T.W., 2017. 森林采伐强度与土壤深度对无机氮库大小及氨氧化微生物群落组成的影响. 土壤生物学与生物化学, 112, 216-227.