This DATSETNAMEreadme.txt file was generated on [2020-10-23] by [Jialin Hu] ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Nitrogen-cycle genes and transcripts abundances under agricultural management practices in a long-term continuous cotton field in West TN 2. Author Information Principal Investigator Contact Information Name: Jennifer DeBruyn Institution: Department of Biosystems Engineering and Soil Science, University of Tennessee-Knoxville Address: 2506 EJ Chapman Drive, Knoxville, Tennessee 37996 Email: jdebruyn@utk.edu Associate or Co-investigator Contact Information Name: Jialin Hu Institution: Department of Biosystems Engineering and Soil Science, University of Tennessee-Knoxville Address: 2506 EJ Chapman Drive, Knoxville, Tennessee 37996 Email: jhu30@vols.utk.edu Alternate Contact Information Name: Jennifer DeBruyn Institution: Department of Biosystems Engineering and Soil Science, University of Tennessee-Knoxville Address: 2506 EJ Chapman Drive, Knoxville, Tennessee 37996 Email: jdebruyn@utk.edu 3. Date of data collection (single date, range, approximate date) Soil samples were collected in 2017-04, 2017-05, 2017-10, and 2017-11 Experimental data were collected from 2018-06 to 2019-07 4. Geographic location of data collection (where was data collected?): Soil samples were collected at West Tennessee Research and Education Center. Experimental data were measured at Plant Biotechnology Building 206 DEBRUYN Lab using a Real-Time PCR instrument. 5. Information about funding sources that supported the collection of the data: This research was supported by USDA Award (USDA-NIFA 2015-67019-23604) to Sean Michael Schaeffer and Jennifer Mary DeBruyn 6. Abstract/description of the dataset: Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the abundance (gene copies) and expression (transcript copies) of five bacterial genes involved in soil N cycling (AOB amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). In addition, the abundances of 16S rRNA gene and 16S rRNA were also measured to normalize the abundances of these five N-cycle functional genes and transcripts. 7: Keywords for the dataset (provide 3 - 5): Soil nitrogen, N cycle, Soil microbes, Quantitative PCR (qPCR), Quantitative reverse transcriptase PCR (qRT-PCR) -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: None 2. Links to publications that cite or use the data: DOI: https://doi.org/10.1128/mSphere.01237-20 3. Links to other publicly accessible locations of the data: None 4. Links/relationships to ancillary data sets: None 5. Was data derived from another source? None. If yes, list source(s): 6. Recommended citation for the data: Hu J, Jin VL, Konkel JYM, Schaeffer SM, Schneider LG, DeBruyn JM. 2021. Soil health management enhances microbial nitrogen cycling capacity and activity. mSphere 6:e01237-20. https://doi.org/10.1128/mSphere.01237-20. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: NIFA_Metadata_Table_hjl.csv Short description: Introduction of sample information B. Filename: NIFA_Field_Diagram_hjl.tif Short description: The experiment plot design C. Filename: NIFA_Soil_N-cycle_qPCR_Data_hjl.csv Short description: Including three datasets: 1) primary data; 2) relative abundance data; 3) absolute abundance data; and 4) transcript-to-gene ratio data. 1) The primary qPCR dataset includes five N-cycle genes and gene transcripts, as well as 16S rRNA gene and 16S rRNA. These data were normalized to extracted DNA (for N-cycle genes) or RNA (for N-cycle gene transcripts); 2) The relative abundance dataset includes five N-cycle genes and gene transcripts normalized to 16S rRNA gene and 16S rRNA; 3) The absolute abundance dataset includes five N-cycle genes and gene transcripts, as well as 16S rRNA gene and 16S rRNA. These data were normalized to soil weight (per gram dry weight soil); 4) The transcript-to-gene ratio dataset includes the value of transcript-to-ratio of five N-cycle genes based on absolute abundances of N-cycle genes and transcripts. The transformation methods of datasets in this file were described in section METHODOLOGICAL INFORMATION #2. 2. Relationship between files: File 'NIFA_Metadata_table_hjl.csv' is the information of samples that qPCR data came from; File 'NIFA_Field_Diagram_hjl.tif' shows the schematic diagram of the field that the samples came from; The datasets in File 'NIFA_Soil_N-cycle_qPCR_Data_hjl.csv' are abundances of N-cycle genes and gene transcripts normalized to extracted DNA or RNA, 16S rRNA gene or 16S rRNA, and soil weight, as well as the transcript-to-gene ratio value of N-cycle genes. 3. Additional related data collected that was not included in the current data package: Soil properties, including N2O flux (N2O-N), soil water content (SWC), soil pH, NO3-N, NH4-N, total extractable N (TEN), total extractable C (TEC), total soil C (TC), total soil N (TN), soil ratio of C to N (C:N ratio), microbial biomass N (MBN), microbial biomass C (MBC), field net nitrification rate (field nitrification), field net N mineralization rate (field N mineralization), incubated net nitrification rate (incubated nitrification), and incubated net N mineralization rate (incubated N mineralization). 4. Are there multiple versions of the dataset? yes/no No. If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Soil samples were collected at a long-term continuous cotton conservation agriculture field implementing a randomized complete block design with split-split plot treatment arrangements in four replicates, established 1981, at the University of Tennessee West Tennessee Research and Education Center (WTREC) in Jackson, Tennessee. For tilled plots, tillage was done twice before planting by a standard disc harrow followed by smoothing and breaking up of clods by a triple-K harrow. Field operations for these plots, including cover crop termination, cotton planting, and phosphorus and potassium fertilizer application are described in more detail in previous studies of this site: 1) Mbuthia LW, Acosta-Martínez V, DeBruyn J, Schaeffer S, Tyler D, Odoi E, Mpheshea M, Walker F, Eash N. 2015. Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: implications for soil quality. Soil Biol Biochem 89:24-34. 2) Nouri A, Lee J, Yin X, Tyler DD, Saxton AM. 2019. Thirty-four years of no-tillage and cover crops improve soil quality and increase cotton yield in Alfisols, Southeastern USA. Geoderma 337:998-1008. Subsamples (2.5 cm diameter by 7.5 cm long cores) of soil were collected from ten random locations in each experimental sub-sub-plot, composited, sieved through a 2 mm mesh, then refrigerated until analysis. Collections were obtained four times corresponding to different stages of crop growth in 2017, including cover crop harvest (April, immediately following cover crop harvest), spring crop transition (May, after cotton planting and before fertilizer application), cotton crop peak (October, before cotton harvest), and fall crop transition (November, after cotton harvest and before winter cover crop planting). DNA and RNA were extracted from the collected soil samples. cDNA was produced from RNA using SuperScript IV Reverse Transcriptase. For both DNA and cDNA samples, qPCR of nifH, amoA, nirK, nirS, and nosZ were performed on a CFX96 Optical Real-Time Detection System (Bio-Rad, Laboratories Inc., Hercules, CA, USA). Quantitative PCR of 16S rRNA genes and 16S rRNA was done using Femto™ Bacterial DNA Quantification Kit (Zymo Research Corp., CA, USA) following the manufacturer’s protocols. 2. Methods for processing the data: 1) Soil water content was calculated as SWC (%) = [(fresh weight soil – dry weight soil)/dry weight soil] × 100%, which was used for the calculation of functional gene and transcript absolute abundances (copies/dry weight soil). 2) In order to mitigate the impact of DNA and RNA extraction efficiency on data accuracy, the abundances of functional genes and transcripts were normalized by the abundances of 16S rRNA genes and 16S rRNA, respectively. Therefore, the relative abundance of N-cycle genes and transcripts used in this study were calculated by the formula: 1) N-cycle gene relative abundance = (N-cycle gene copies/ug DNA extract)/(16S rRNA gene copies/ug DNA extract); 2) N-cycle transcript relative abundance = (N-cycle transcript copies/ug RNA extract)/(16S rRNA copies/ug RNA extract). 3) The absolute abundances (copies/g dry weight soil) of each functional gene and transcript as well as 16S rRNA genes and 16S rRNA were also reported to compare with their relative abundance (16S-normalized data) in 1). 4) The transcript-to-gene copy number ratio for each gene was also calculated to provide a means to determine whether transcript variation was due to changes in population sizes (i.e. genes) or changes in expression (i.e. transcripts) and was calculated by the method in File C: NIFA_Soil_qPCR_Data_Transformation_hjl.pdf. 3. Instrument- or software-specific information needed to interpret the data: qPCR data were generated from Bio-Rad CFX96 Optical Real-Time Detection System Bio-Rad CFX Manager Software was used for preliminary data analysis 4. Standards and calibration information, if appropriate: Ten-fold serial dilutions of the plasmid DNA (10^2 to 10^8 copies/μl) were used during qPCR assays to generate standard curves for quantifying N-cycle genes and transcripts in soil samples. 5. Environmental/experimental conditions: qPCR assays were conducted in a PCR workstation in a biosafety level 2 laboratory. 6. Describe any quality-assurance procedures performed on the data: Melt curve procedure was added after the major qPCR procedure to make sure no nonspecific amplification. 7. People involved with sample collection, processing, analysis and/or submission: Brian Kozlowski and the staff of the West Tennessee Research and Education Center - manage and maintain the field trials; Julie Konkel, Megan Davis, Lydia Turpin, Lidong Li and Kelly Cobaugh for field sampling and data collection; Jialin - DNA and RNA extraction, molecular cloning, qPCR assay, data analysis, and submission; Jennifer DeBruyn - data analysis and submission. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [NIFA_Soil_N-cycle_qPCR_Data_hjl.csv] ----------------------------------------- 1. Number of variables: 44 2. Number of cases/rows: 192 3. Variable List A. Name: [Season] Description: [Collections were obtained four times corresponding to different stages of crop growth in 2017, including cover crop harvest (April, immediately following cover crop harvest), spring crop transition (May, after cotton planting and before fertilizer application), cotton crop peak (October, before cotton harvest), and fall crop transition (November, after cotton harvest and before winter cover crop planting)] April: cover crop harvest May: spring transition October: cotton crop peak November: fall crop transition B. Name: [Tillage] Description: [two types of tillage, including conventional tillage and no tillage. For conventional tillage, tillage was done twice before planting by a standard disc harrow followed by smoothing and breaking up of clods by a triple-K harrow] CT: conventional tillage NT: no tillage C. Name: [Cover_crop] Description: [Three types of winter cover crops [hairy vetch (Vicia villosa Roth; V), winter wheat (Triticum aestivum L.; W), no cover crop (NC)]] NC: no cover crop V: hairy vetch W: winter wheat D. Name: [Nitrogen_fertilization_rate] Description: [2 levels of NH4NO3 fertilization rates [0, 67 kg N/ha (0N, 67N, respectively)]] 0N: no nitrogen fertilizer addition 67N 67 kg N/ha fertilizer addition E. Name: [Block] Description: [The field study implemented a randomized complete block design with split-split plot treatment arrangements in four blocks, which can be seen as four replicates] F. Name: [nifH_gene_ugDNA] Description: [the copy numbers of nitrogen fixation gene nifH normalized to extracted DNA, the unit is copies/ug DNA] G. Name: [amoA_gene_ugDNA] Description: [the copy numbers of ammonia oxidation gene amoA normalized to extracted DNA, the unit is copies/ug DNA] H. Name: [nirK_gene_ugDNA] Description: [the copy numbers of nitrite reduction gene nirK normalized to extracted DNA, the unit is copies/ug DNA] I. Name: [nirS_gene_ugDNA] Description: [the copy numbers of nitrite reduction gene nirS normalized to extracted DNA, the unit is copies/ug DNA] J. Name: [nosZ_gene_ugDNA] Description: [the copy numbers of nitrous oxide reduction gene nosZ normalized to extracted DNA, the unit is copies/ug DNA] K. Name: [16S rRNA_gene_ugDNA] Description: [the copy numbers of 16S rRNA gene normalized to extracted DNA, the unit is copies/ug DNA] L. Name: [nifH_transcript_ugRNA] Description: [the copy numbers of nitrogen fixation gene transcript normalized to extracted RNA, the unit is copies/ug RNA] M. Name: [amoA_transcript_ugRNA] Description: [the copy numbers of ammonia oxidation gene transcript normalized to extracted RNA, the unit is copies/ug RNA] N. Name: [nirK_transcript_ugRNA] Description: [the copy numbers of nitrite reduction gene transcript normalized to extracted RNA, the unit is copies/ug RNA] O. Name: [nirS_transcript_ugRNA] Description: [the copy numbers of nitrite reduction gene transcript normalized to extracted RNA, the unit is copies/ug RNA] P. Name: [nosZ_transcript_ugRNA] Description: [the copy numbers of nitrous oxide reduction gene transcript normalized to extracted RNA, the unit is copies/ug RNA] Q. Name: [16S rRNA_ugRNA] Description: [the copy numbers of 16S rRNA normalized to extracted RNA, the unit is copies/ug RNA] R. Name: [nifH_gene_16S] Description: [the 16S rRNA gene normalized copy numbers of nitrogen fixation gene nifH, the unit is copies/16S rRNA gene copies] S. Name: [amoA_gene_16S] Description: [the 16S rRNA gene normalized copy numbers of ammonia oxidation gene amoA, the unit is copies/16S rRNA gene copies] T. Name: [nirK_gene_16S] Description: [the 16S rRNA gene normalized copy numbers of nitrite reduction gene nirK, the unit is copies/16S rRNA gene copies] U. Name: [nirS_gene_16S] Description: [the 16S rRNA gene normalized copy numbers of nitrite reduction gene nirS, the unit is copies/16S rRNA gene copies] V. Name: [nosZ_gene_16S] Description: [the 16S rRNA gene normalized copy numbers of nitrous oxide reduction gene nosZ, the unit is copies/16S rRNA gene copies] W. Name: [nifH_transcript_16S] Description: [the 16S rRNA normalized copy numbers of nitrogen fixation gene transcript, the unit is copies/16S rRNA copies] X. Name: [amoA_transcript_16S] Description: [the 16S rRNA normalized copy numbers of ammonia oxidation gene transcript, the unit is copies/16S rRNA copies] Y. Name: [nirK_transcript_16S] Description: [the 16S rRNA normalized copy numbers of nitrite reduction gene transcript, the unit is copies/16S rRNA copies] Z. Name: [nirS_transcript_16S] Description: [the 16S rRNA normalized copy numbers of nitrite reduction gene transcript, the unit is copies/16S rRNA copies] AA. Name: [nosZ_transcript_16S] Description: [the 16S rRNA normalized copy numbers of nitrous oxide reduction gene transcript, the unit is copies/16S rRNA copies] AB. Name: [nifH_gene_gdw] Description: [nitrogen fixation gene nifH copy numbers normalized to soil weight (gram dry weight soil (gdw)), the unit is copies/g dry weight soil] AC. Name: [amoA_gene_gdw] Description: [ammonia oxidation gene amoA copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AD. Name: [nirK_gene_gdw] Description: [nitrite reduction gene nirK copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AE. Name: [nirS_gene_gdw] Description: [nitrite reduction gene nirS copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AF. Name: [nosZ_gene_gdw] Description: [nitrous oxide reduction gene nosZ copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AG. Name: [16S rRNA_gene] Description: [16S rRNA gene copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AH. Name: [nifH_transcript_gdw] Description: [nitrogen fixation gene transcript copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AI. Name: [amoA_transcript_gdw] Description: [ammonia oxidation gene transcript copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AJ. Name: [nirK_transcript_gdw] Description: [nitrite reduction gene transcript copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AK. Name: [nirS_transcript_gdw] Description: [nitrite reduction gene transcript copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AL. Name: [nosZ_transcript_gdw] Description: [nitrous oxide reduction gene transcript copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AM. Name: [16S rRNA_gdw] Description: [16S rRNA copy numbers normalized to soil weight, the unit is copies/g dry weight soil] AN. Name: [nifH_transcript-to-gene ratio] Description: [the ratio of nifH gene transcript copies to nifH gene copies, the unit is (transcript copies/g dry weight soil)/(gene copies/g dry weight soil)] AO. Name: [amoA_transcript-to-gene ratio] Description: [the ratio of amoA gene transcript copies to amoA gene copies, the unit is (transcript copies/g dry weight soil)/(gene copies/g dry weight soil)] AP. Name: [nirK_transcript-to-gene ratio] Description: [the ratio of nirK gene transcript copies to nirK gene copies, the unit is (transcript copies/g dry weight soil)/(gene copies/g dry weight soil)] AQ. Name: [nirS_transcript-to-gene ratio] Description: [the ratio of nirS gene transcript copies to nirS gene copies, the unit is (transcript copies/g dry weight soil)/(gene copies/g dry weight soil)] AR. Name: [nosZ_transcript-to-gene ratio] Description: [the ratio of nosZ gene transcript copies to nosZ gene copies, the unit is (transcript copies/g dry weight soil)/(gene copies/g dry weight soil)] 4. Missing data codes: Code/symbol Definition Code/symbol Definition 5. Specialized formats of other abbreviations used None.