Soil fungal community across a 52-year chronosequence of soil recultivation after open-mining in Inden, Germany

The soil fungal community was surveyed across a 52-year chronosequence of soil recultivation after open-mining, during two seasons (March-winter, July-summer). The study sites correspond to agricultural fields located within an area of 25 km 2 (6°15’0’ E to 6°21’0’ E and 50°50’5’ N to 50°53’0’ N) of an open-cast lignite mine at Inden, between Cologne, Aachen, Mönchengladbach, and Düsseldorf. The soil extraction, deposition and recultivation process leads to a chronosequence of fields recultivated from less than one year to fields recultivated for 52 years, at samling time of 2016. During the first three years, fields are permanently covered by alfalfa and never receive artificial fertilisers or biocide treatments (fields recultivated since 2016, 2015, 2014 and 2013, referred to as phase 1). In the following two years, agricultural practises are resumed with barley cropping by RWE Power AG, and a N:P:K (1:0.4:0.6) fertilisation of 437 kg ha−1 a−1 (fields recultivated since 2012 and 2011 referred to as phase 2). Afterwards, fields are returned to farmers and conventionally managed with a crop sequence of winter wheat after sugar beet, one tillage a year to 30 cm depth, and a continuous management practice following area-typical agricultural practice and plant-protection guidelines (fields recultivated since 2006, 1990, 1979, 1971 and 1964, referred to as phase 3). Other agricultural fields that have not yet been subject to extraction were sampled too (referred to as pre-mining phase). They are a total of 115 samples (5 replicates per field x 2 seasons, each field corresponds to a year of recultivation). Four samples were removed due to failed PCR. The soil fungal community was analyzed with 300 bp paired-end Illumina MiSeq sequencing of ITS2 sequences (primers fITS7: 5′‐GTGARTCATCGAATCTTTG‐3′ / ITS4: 5′‐TCCTCCGCTTATTGATATGC‐3′). Amplicon sequence variants (ASVs) were inferred using DADA2 in R. Taxonomic annotations were performed using the IDTaxa algorithm implemented in the DECIPHER R package, against UNITE (version of 10.05.2021). Raw sequencing reads are available at ENA under study project PRJEB51095. The DNA sequences of the fungal amplicon sequence variants are available at ENA under accession numbers OV986018-OV989728. The processed dataset including the ASV count table, ASV taxonomy, and sample metadata compiled as a phyloseq R object stored in a single .RDS R file, as well as ASV guild annotation using Funguild database, are available at figshare at (https://doi.org/10.6084/m9.figshare.20160578). To read the data in the software R, use readRDS() function). Here we upload at the BONARES data centre the relative abundance of each fungal guild (% of DNA sequences) per samples along with basic metadata for easy reuse. The guild name and metadata name is provided in the header of each column. The entire set of measured soil physico-chemical parameters has been deposited at BONARES under reference 72ca6e98-5aab-4884-bf1b-56931482eb94. The publication associated to the dataset can be found at https://doi.org/10.1007/s00248-022-02058-w. Roy J, Reichel R, Brüggemann N, Rillig MC. 2022. Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre mining Initial State After 52 Years of Recultivation. Microbial Ecology. Other publications associated to the datasets are : (1) Reichel R., Hänsch M., Brüggemann N. (2017). Indication of rapid soil food web recovery by nematode-derived indices in restored agricultural soil after open-cast lignite mining. Soil Biology and Biochemistry, 115, 261-264. DOI: 10.1016/j.soilbio.2017.08.020; (2) Roy J., Reichel R., Brüggemann N., Hempel S., Rillig M. (2017). Succession of arbuscular mycorrhizal fungi along a 52-years agricultural recultivation chronosequence. FEMS Microbiology Ecology. DOI: 1093/femsec/fix102

本数据集针对德国因登（Inden）露天褐煤矿区周边的农田开展土壤真菌群落调查，该矿区位于科隆、亚琛、门兴格拉德巴赫与杜塞尔多夫之间，研究区域面积达25 km²，地理坐标为东经6°15′0″至6°21′0″、北纬50°50′5″至50°53′0″。调查覆盖了露天采矿后52年的土壤复垦年限梯度，分两个季节采样：3月冬季期与7月夏季期。

土壤剥离、堆积与复垦过程形成了从复垦不足1年到复垦52年的农田年限梯度，本次采样工作于2016年完成。其中，前三年复垦的农田（2013至2016年复垦的地块，记为阶段1）永久种植紫花苜蓿，且不施用人工肥料或杀生物剂；随后两年复垦的农田（2011、2012年复垦的地块，记为阶段2）由RWE电力股份公司（RWE Power AG）开展大麦种植，施用N:P:K比例为1:0.4:0.6的复合肥，用量为437 kg ha⁻¹ a⁻¹；此后农田交还农户，采用常规农业管理模式：前茬为甜菜，后茬为冬小麦，每年进行一次30 cm深度的耕作，严格遵循区域典型农业操作与植物保护规范（2006、1990、1979、1971、1964年复垦的地块，记为阶段3）。此外，本研究还对尚未进行采矿作业的农田进行了采样（记为采矿前阶段）。

本次实验共计采集115份样品：每个复垦年限农田设置5次生物学重复，分2个季节采样，每个农田对应一个复垦年限。其中4份样品因聚合酶链式反应（Polymerase Chain Reaction, PCR）扩增失败被剔除。

本研究采用Illumina MiSeq平台对ITS2序列进行300 bp双端测序，引物为fITS7（5′‐GTGARTCATCGAATCTTTG‐3′）与ITS4（5′‐TCCTCCGCTTATTGATATGC‐3′），以此解析土壤真菌群落。使用R语言中的DADA2工具推导扩增子序列变体（Amplicon Sequence Variants, ASVs）；依托DECIPHER R包中的IDTaxa算法，结合UNITE数据库（2021年5月10日版本）完成分类学注释。

原始测序数据已提交至欧洲核苷酸档案馆（European Nucleotide Archive, ENA），项目编号为PRJEB51095；真菌扩增子序列变体的DNA序列以登录号OV986018-OV989728提交至ENA。处理后的数据集包含扩增子序列变体计数表、扩增子序列变体分类学信息以及以phyloseq R对象格式存储的样品元数据（保存为单个.RDS文件），同时包含基于Funguild数据库的扩增子序列变体功能群注释，相关数据已上传至figshare（https://doi.org/10.6084/m9.figshare.20160578），可通过R语言的readRDS()函数读取。本次上传至BONARES数据中心的为每份样品中各真菌功能群的相对丰度（以DNA序列占比计）及基础元数据，便于复用，各列的表头已标注功能群名称与元数据名称。全套测定的土壤理化参数已以编号72ca6e98-5aab-4884-bf1b-56931482eb94提交至BONARES。

本数据集关联的已发表论文为Roy J等人2022年发表于《Microbial Ecology》的文章《Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation》（DOI: 10.1007/s00248-022-02058-w）。此外还有两篇关联出版物：(1) Reichel R等人2017年发表于《Soil Biology and Biochemistry》的《Indication of rapid soil food web recovery by nematode-derived indices in restored agricultural soil after open-cast lignite mining》（DOI: 10.1016/j.soilbio.2017.08.020）；(2) Roy J等人2017年发表于《FEMS Microbiology Ecology》的《Succession of arbuscular mycorrhizal fungi along a 52-years agricultural recultivation chronosequence》（DOI: 10.1093/femsec/fix102）