Soil Microbiological data (OTU) from Casey Station, including from the remediation project biopiles.

Soil Microbiological data from Casey Station, including from the remediation project biopiles. Operational Taxonomic Unit (OTU) data obtained from soil samples taken from locations in and around Casey station (including Shirley Island). It also includes samples from biopiles 3 and 4 and the control “test plot” established at Casey station, Antarctica, for the purpose of the remediation of petroleum hydrocarbon contaminants present in the soil.16S data was used as the basis for building a proteomic database for analytical comparison.MethodsDNA was extracted from soils using the MPbiomedicals FastDNA spin kit for soil (manual attached). This Protocol is known to produce low 260/230 ratios (low DNA to high salt/ethanol contaminants).Extracted DNA was sent for sequencing at Ramacciotti Centre for Genomics (UNSW) for short read DNA sequencing target V1-V3 hyper variable regions for the 16s rRNA. Primers used 27F(AGA GTT TGA TYM TGG CTC AG) and 534R(ATT ACC GCG GCT GCT GG).The file zOTU pipeline.txt contains information on the processing performed on the raw data. QC analysis was conducted in Mothur (for removal of low quality reads).Dereplication of reads and sorting of unique reads by abundance was done using USEARCH Amplicon Analysis (https://drive5.com/usearch/). Denoising and building of the abundance profile also conducted in unoise (https://www.drive5.com/usearch/manual/unoise_algo.html) Taxonomic classification performed by mothur (https://github.com/mothur/mothur.github.io) using silva.nr_v138_1.tax databaseData processing included removal of mitochondrial DNA, unclassified Eucaryotic DNA and Chloroplast entries in R. The proteomic database was built from the 100 most abundant genera from Shirley Island, the Casey Biopile and Casey Test plot soils. Some of the most abundant genera were common between the three soil groups, resulting in a database with less than 300 genera.Proteins associated with the genera in were searched in uniprot and the relevant fasta files downloaded. The downloaded fasta files were then matched against the raw spectral reads from the tandem mass spec output in proteome discoverer 3.1.

南极凯西站（Casey Station）土壤微生物组数据，涵盖该站点修复项目生物堆（biopiles）相关样本。数据包含从凯西站及周边区域（包括雪莉岛Shirley Island）采集的土壤样本的操作分类单元（Operational Taxonomic Unit, OTU）信息，同时纳入了来自生物堆3号、4号以及南极凯西站为修复土壤中石油烃污染物所设立的对照“试验样地”的样本。本数据集以16S数据为基础构建蛋白质组数据库，用于分析比对。

实验方法：采用MPbiomedicals公司的FastDNA土壤离心提取试剂盒（操作手册随附）完成土壤DNA提取，该方法的已知特性为260/230比值偏低（即DNA占比相对较低，盐/乙醇污染物残留较高）。提取得到的DNA被送至拉马乔蒂基因组中心（Ramacciotti Centre for Genomics，新南威尔士大学UNSW），针对16S rRNA的V1-V3高变区进行短读长DNA测序，所用扩增引物为27F(AGA GTT TGA TYM TGG CTC AG)与534R(ATT ACC GCG GCT GCT GG)。

文件zOTU pipeline.txt记录了原始测序数据的处理流程。质控分析通过Mothur工具完成，用于剔除低质量读段；读段去重及按丰度对唯一读段进行排序的步骤通过USEARCH扩增子分析工具完成（https://drive5.com/usearch/）；降噪及丰度谱构建步骤同样通过unoise算法完成（https://www.drive5.com/usearch/manual/unoise_algo.html）；分类学注释由Mothur工具基于silva.nr_v138_1.tax数据库完成（https://github.com/mothur/mothur.github.io）。

数据处理阶段在R语言环境中完成，移除了线粒体DNA、未分类的真核生物DNA以及叶绿体序列。蛋白质组数据库由雪莉岛、凯西生物堆及凯西试验样地土壤中丰度排名前100的菌属构建而成，由于三类土壤样本共享部分高丰度菌属，最终数据库涵盖不足300个菌属。针对上述菌属的蛋白质序列在UniProt数据库中检索，并下载对应的FASTA文件；随后将下载的FASTA文件与蛋白质组发现者3.1（Proteome Discoverer 3.1）输出的串联质谱原始光谱读段进行比对分析。