Biotic and abiotic predictors of potential N2O emissions from denitrification in Irish grasslands soils: a national-scale field studyItem

<strong>_________________________________________________________________________________________</strong> The datasets are associated with this paper (OA): https://doi.org/10.1016/j.soilbio.2022.108637 If you use this data for your research, please feel free to contact me: [e-mail] <br> <strong>The team that worked on this immense project gives you access to this data. As such, remember to cite the paper and this dataset whenever this data is reused.</strong> <br> <strong>_________________________________________________________________________________________</strong> <br> <strong>The data contains 3 files:</strong> 1) The metadata and soil data: containing the a) description of the samples, b) physicochemical properties of the soil, c) climate conditions extracted from BioClim and d) Soil potential nitrification and denitrification, e) functional gene abundance. 2) An RDS file containing the 16S community matrix and information relating to the community. 3) An RDS file containing the ITS community matrix and information relating to the community. <br> Raw DNA sequencing data are available on the NCBI database under the accession number BioProject PRJNA788893. <br> <br> <strong>The metadata and soil data: “MINEsoilData.csv”</strong> A .csv table containing a) description of the samples, b) physicochemical properties of the soil, c) climate conditions extracted from BioClim and d) Soil potential nitrification and denitrification, e) functional gene abundance. All information relative to the farmer practices and exact location were removed to respect their privacy. The methods to obtain the values of this dataset are in the associated paper. Description of each column: SampleID: sample identification number, which is the sample number used in all the datasets. Site: location where the samples were collected in Ireland. Date: date of sampling soilMoist: soil moisture measured on site with Delta T WET-2 sensor, measures correspond to volumetric soil moisture content (θ, in %). soilCond: soil conductivity measured on site with Delta T WET-2 sensor (mS/m). soilTemp: soil temperature (°C) Altitude: meters above the sea at sampling location. pH: soil pH P_morgans: phosphorus (mg/L soil) K_Morgans: potassium (mg/L soil) Mg_Morgans: magnesium (mg/L soil) Al_Mehlich: aluminium (mg/L soil) Ca_Mehlich: calcium (mg/L soil) Fe_Mehlich: iron (mg/L soil) S: sulfur (mg/L soil) CEC: Cation-exchange capacity (meq/100g) LOI: Loss on ignition (%) NH4_mgL: ammonium (mg/L) NO3_mgL: nitrate (mg/L) sandPerc: soil texture, percentage of sand siltPerc: soil texture, percentage of silt clayPerc: soil texture, percentage of clay TNperc: total nitrogen (percentage) TICperc: total inorganic carbon (percentage) TOCperc: total organic carbon (percentage) TCperc: total carbon (percentage) CuEDTA: copper (mg/L soil) ZnEDTA: zinc (mg/L soil) MnEDTA: manganese (mg/L soil) bulkDens: soil bulk density (g/cm3) Nitrification: soil potential nitrification (mg N / soil kg . day) Denitrification: soil potential denitrification (mg N2O-N / soil kg . day) Ratio_N2O: potential N2O/(N2O + N2) ratio X16s.Bact: Abundance of bacteria based on qPCR (gene copy number / ng DNA) ITS: abundance of fungi (ITS) based on qPCR (gene copy number / ng DNA) X16S.Archae: abundance of archaea (16S) based on qPCR (gene copy number / ng DNA) AOA: abundance of ammonia-oxidizing archaea abundance based on qPCR (gene copy number / ng DNA) AOB: abundance of ammonia-oxidizing bacteria based on qPCR (gene copy number / ng DNA) COMAMMOX: complete ammonia-oxidizing bacterial abundance based on qPCR (gene copy number / ng DNA) NirK: nirK genes’ abundance based on qPCR (gene copy number / ng DNA) NosZI: nosZI genes’ abundance based on qPCR (gene copy number / ng DNA) NosZII: nosZII genes’ abundance based on qPCR (gene copy number / ng DNA) NirS: nirS genes’ abundance based on qPCR (gene copy number / ng DNA) AvgTemp: mean annual temperature (°C) based on BIOClim Prec: mean annual precipitation (mm) based on BIOClim <br> <strong>16S community data: “16Scommunitydata.rds”</strong> This data is compiled in a RDS file containing an ASV table (matrix with sample ID and ASV abundance), the taxonomy table (identity for each ASV) and the object containing the sequences of each ASV. This dataset can be accessed on R. Load the ‘phyloseq’ library and use the function “readRDS()”. <br> <strong>ITS community data: “ITScommunitydata.rds”</strong> This data is compiled in a RDS file containing an ASV table (matrix with sample ID and ASV abundance), the taxonomy table (identity for each ASV) and the object containing the sequences of each ASV. This dataset can be accessed on R. Load the ‘phyloseq’ library and use the function “readRDS()”.

<strong>_________________________________________________________________________________________</strong> 本数据集关联本文（开放获取（Open Access，OA））：https://doi.org/10.1016/j.soilbio.2022.108637。若您在研究中使用本数据，可随时联系作者：[e-mail]<br><strong>参与本大型项目的团队向您开放本数据集。因此，在重复使用本数据时，请务必引用本文及本数据集。</strong><br><strong>_________________________________________________________________________________________</strong><br><strong>本数据集包含3个文件：</strong>1) 元数据与土壤数据：包含a) 样本描述、b) 土壤理化性质、c) 从BioClim提取的气候数据、d) 土壤潜在硝化与反硝化活性、e) 功能基因丰度。2) 一个RDS文件，包含16S群落矩阵及群落相关信息。3) 一个RDS文件，包含ITS群落矩阵及群落相关信息。原始DNA测序数据已上传至美国国家生物技术信息中心（National Center for Biotechnology Information，NCBI）数据库，获取编号为BioProject PRJNA788893。<br><br><strong>元数据与土壤数据: "MINEsoilData.csv"</strong>该CSV表格包含a) 样本描述、b) 土壤理化性质、c) 从BioClim提取的气候数据、d) 土壤潜在硝化与反硝化活性、e) 功能基因丰度。为保护农户隐私，所有与农户耕作方式及精确地理位置相关的信息已被移除。本数据集各参数的获取方法详见关联论文。各字段说明如下：SampleID：样本识别编号，为本数据集所有文件通用的样本编号。Site：样本采集地点（位于爱尔兰）。Date：采样日期。soilMoist：使用Delta T WET-2传感器在现场测定的土壤含水率，结果为体积含水量（θ，单位：%）。soilCond：使用Delta T WET-2传感器在现场测定的土壤电导率（单位：mS/m）。soilTemp：土壤温度（单位：°C）。Altitude：采样点海拔高度（单位：米，相对于海平面）。pH：土壤pH值。P_morgans：土壤磷含量（单位：mg/L 土壤）。K_Morgans：土壤钾含量（单位：mg/L 土壤）。Mg_Morgans：土壤镁含量（单位：mg/L 土壤）。Al_Mehlich：土壤铝含量（单位：mg/L 土壤）。Ca_Mehlich：土壤钙含量（单位：mg/L 土壤）。Fe_Mehlich：土壤铁含量（单位：mg/L 土壤）。S：土壤硫含量（单位：mg/L 土壤）。CEC：阳离子交换量（Cation-exchange capacity，单位：meq/100g）。LOI：烧失量（单位：%）。NH4_mgL：土壤铵态氮含量（单位：mg/L）。NO3_mgL：土壤硝态氮含量（单位：mg/L）。sandPerc：土壤机械组成，砂粒百分比含量。siltPerc：土壤机械组成，粉粒百分比含量。clayPerc：土壤机械组成，黏粒百分比含量。TNperc：总氮含量（单位：%）。TICperc：总无机碳含量（单位：%）。TOCperc：总有机碳含量（单位：%）。TCperc：总碳含量（单位：%）。CuEDTA：土壤铜含量（单位：mg/L 土壤）。ZnEDTA：土壤锌含量（单位：mg/L 土壤）。MnEDTA：土壤锰含量（单位：mg/L 土壤）。bulkDens：土壤容重（单位：g/cm³）。Nitrification：土壤潜在硝化活性（单位：mg N / 土壤kg · 天）。Denitrification：土壤潜在反硝化活性（单位：mg N2O-N / 土壤kg · 天）。Ratio_N2O：N2O/(N2O + N2) 潜在比值。X16s.Bact：基于定量PCR（quantitative Polymerase Chain Reaction，qPCR）测定的细菌丰度（基因拷贝数 / ng DNA）。ITS：基于定量PCR（qPCR）测定的真菌丰度（ITS区域，基因拷贝数 / ng DNA）。X16S.Archae：基于定量PCR（qPCR）测定的古菌丰度（16S区域，基因拷贝数 / ng DNA）。AOA：基于定量PCR（qPCR）测定的氨氧化古菌丰度（基因拷贝数 / ng DNA）。AOB：基于定量PCR（qPCR）测定的氨氧化细菌丰度（基因拷贝数 / ng DNA）。COMAMMOX：基于定量PCR（qPCR）测定的完全氨氧化细菌丰度（基因拷贝数 / ng DNA）。NirK：基于定量PCR（qPCR）测定的nirK基因丰度（基因拷贝数 / ng DNA）。NosZI：基于定量PCR（qPCR）测定的nosZI基因丰度（基因拷贝数 / ng DNA）。NosZII：基于定量PCR（qPCR）测定的nosZII基因丰度（基因拷贝数 / ng DNA）。NirS：基于定量PCR（qPCR）测定的nirS基因丰度（基因拷贝数 / ng DNA）。AvgTemp：基于BioClim数据集得到的年平均气温（单位：°C）。Prec：基于BioClim数据集得到的年平均降水量（单位：mm）。<br><strong>16S群落数据: "16Scommunitydata.rds"</strong>本数据存储于RDS文件中，包含扩增子序列变体（Amplicon Sequence Variant，ASV）表（以样本ID和ASV丰度构成的矩阵）、分类学注释表（各ASV的物种分类信息）以及包含各ASV序列的对象。可在R语言环境中加载使用：先调用`phyloseq`包，再使用`readRDS()`函数读取该文件。<br><strong>ITS群落数据: "ITScommunitydata.rds"</strong>本数据存储于RDS文件中，包含扩增子序列变体（ASV）表（以样本ID和ASV丰度构成的矩阵）、分类学注释表（各ASV的物种分类信息）以及包含各ASV序列的对象。可在R语言环境中加载使用：先调用`phyloseq`包，再使用`readRDS()`函数读取该文件。