DOI: 10.5061/dryad.jh9w0vtqt
title: Soil structure changes under reduced tillage and cover cropping enhance carbon mineralization in Mediterranean croplands

description: This dataset contains soil physical, chemical, and biological measurements
 from a long-term conservation agriculture experiment at the Conservation
 Agriculture Systems Innovation (CASI) site in Five Points, California.
 Data were collected from undisturbed soil cores sampled in October 2019,
 after 19 years of differential management comparing conservation tillage
 with cover crops (CTCC) versus standard tillage without cover crops
 (STNC). The dataset includes: (1) soil water retention curves measured
 using the HYPROP evaporation method; (2) time-series CO2 efflux
 measurements across a controlled moisture gradient from saturation to
 approximately -80 kPa; (3) total carbon and nitrogen content determined by
 elemental combustion; (4) bulk density and porosity measurements; and (5)
 fitted van Genuchten-PDI model parameters for each soil core. These data
 support the finding that conservation management significantly increases
 soil carbon stocks while simultaneously enhancing carbon-specific
 respiration rates under wet conditions, with implications for carbon
 sequestration in irrigated agricultural systems.
description: # Soil physical properties, carbon and nitrogen stocks, and heterotrophic
 respiration data from a 19-year conservation agriculture experiment in
 California's San Joaquin Valley **Authors:** Jennifer
 Alvarez-Sagrero, Stephany S. Chacon, Jeffrey P. Mitchell, Teamrat Afewerki
 Ghezzehei **Corresponding Authors:** * Jennifer Alvarez-Sagrero
 ([jalvarez88@ucmerced.edu](mailto:jalvarez88@ucmerced.edu)) * Teamrat
 Afewerki Ghezzehei
 ([taghezzehei@ucmerced.edu](mailto:taghezzehei@ucmerced.edu)) **Associated
 Publication:** Alvarez-Sagrero J, Chacon SS, Mitchell JP, Ghezzehei TA.
 (2025) Soil Structure Changes Under Reduced Tillage and Cover Cropping
 Enhance Carbon Mineralization in Mediterranean Croplands. *Vadose Zone
 Journal*.
 [https://doi.org/10.1002/vzj2.70065](https://doi.org/10.1002/vzj2.70065)
 --- ## Table of Contents * [Abstract](#abstract) * [Study
 Site](#study-site) * [Experimental Design](#experimental-design) *
 [Software](#software) * [Data Description](#data-description) *
 [Repository Structure](#repository-structure) * [Methods
 Summary](#methods-summary) * [Code and Analysis
 Scripts](#code-and-analysis-scripts) * [Usage Notes](#usage-notes) *
 [Funding](#funding) * [License](#license) * [Keywords](#keywords) --- ##
 Abstract This dataset contains soil physical, chemical, and biological
 measurements from a long-term conservation agriculture experiment at the
 Conservation Agriculture Systems Innovation (CASI) site in Five Points,
 California. Data were collected from undisturbed soil cores sampled in
 October 2019, after 19 years of differential management comparing
 conservation tillage with cover crops (CTCC) versus standard tillage
 without cover crops (STNC). The dataset includes: (1) soil water retention
 curves measured using the HYPROP evaporation method; (2) time-series CO2
 efflux measurements across a controlled moisture gradient from saturation
 to approximately -80 kPa; (3) total carbon and nitrogen content determined
 by elemental combustion; (4) bulk density and porosity measurements; and
 (5) fitted van Genuchten-PDI model parameters for each soil core. These
 data support the finding that conservation management significantly
 increases soil carbon stocks while simultaneously enhancing
 carbon-specific respiration rates under wet conditions, with implications
 for carbon sequestration in irrigated agricultural systems. **Data
 Distribution:** This dataset is distributed in two zip files:
 **repository.zip** (main data on Dryad under CC0 license) and
 **outputs.zip** (supplemental figures/tables on Zenodo under CC BY 4.0
 license). See [Repository Structure](#repository-structure) section for
 details. --- ## Study Site * **Location:** Conservation Agriculture
 Systems Innovation (CASI) site * **Coordinates:** 36.34°N, 120.12°W *
 **Region:** Five Points, San Joaquin Valley, California, USA * **Soil
 type:** Panoche clay loam (fine-loamy, mixed, superactive, thermic Typic
 Haplocambids) * **Climate:** Mediterranean (178 mm mean annual
 precipitation, primarily November–April) * **Experiment established:**
 1999 * **Sampling date:** October 2019 --- ## Experimental Design
 **Treatments:** * **CTCC:** Conservation tillage with winter cover crops
 (reduced tillage/no-till with legume-grass cover crop mixture) * **STNC:**
 Standard tillage without cover crops (conventional disk and subsoil
 tillage, 8+ passes annually) **Sampling depths:** * 0–5 cm * 5–10 cm
 **Replication:** * 7 undisturbed soil cores per treatment per depth * 28
 total cores (2 treatments × 2 depths × 7 replicates) **Core dimensions:**
 * 250 cm³ volume (8 cm diameter × 5 cm height) * Collected using METER
 HYPROP stainless steel cylinders --- ## Software * The HYPROP data were
 visualized and analyzed using HYPROP VIEW software, whcih has been renamed
 as LABROS. LABROS is backward compatible and can be downloaded for free
 from [METERGROUP Inc](https://metergroup.com). * CO2 concentration data
 were loged using Gaslab software, which is availbale from
 [co2meter.com](https://www.co2meter.com) * Lab environment data was logged
 using Logger Pro, available from [Vernier
 Inc](https://www.vernier.com/downloads/). --- ## Data Description ### 1.
 Water Retention Data * Matric potential (kPa) measured at 10-minute
 intervals during evaporative drying * Volumetric water content (cm³/cm³)
 calculated from mass loss * Air-filled porosity derived from total
 porosity minus water content * Range: saturation (0 kPa) to approximately
 -80 kPa ### 2. CO2 Efflux Data * Headspace CO2 concentration (ppm)
 measured at 10-second intervals during 6-minute chamber closures * 2–6
 flux measurements per day throughout drying cycle (~12 days per core) *
 CO2 flux calculated using nonlinear diffusion model * Paired with
 concurrent matric potential measurements ### 3. Carbon and Nitrogen Data *
 Total carbon (%) and nitrogen (%) by dry combustion (Costech 4010
 Elemental Analyzer) * Carbon and nitrogen stocks (kg/m²) calculated using
 bulk density * C:N ratios * Isotopic composition (δ13C and δ15N) ### 4.
 Physical Properties * Bulk density (g/cm³) * Total porosity (%) * Fitted
 bimodal van Genuchten-PDI parameters: * Φ (total porosity) * θr (residual
 water content) * α1, α2 (inverse air entry pressure for textural and
 structural pores) * n1, n2 (pore size distribution indices) * w2
 (weighting factor for structural pores) --- ## Repository Structure This
 dataset is distributed in two zip files: * **repository.zip** - Main data
 package containing all raw data, processed data, and analysis scripts
 (uploaded to Dryad) * **outputs.zip** - Supplemental information
 containing publication-quality figures and tables (uploaded to Zenodo via
 Dryad, released under CC BY 4.0 license) ### Root Directory Files (in
 repository.zip) * **0_gaslab_file_formatter.R** - Script to format and
 clean raw CO2 concentration data from the Gaslab system *
 **1_pre-process_gaslab.R** - Pre-processing script for Gaslab respiration
 measurements * **2_main_analysis.R** - Main analysis script for data
 processing, statistical analysis, and figure generation * **fluxCalc.R** -
 Function definitions for calculating CO2 flux from concentration time
 series using nonlinear diffusion model * **flux_derivation.nb** -
 Mathematica notebook with derivation of flux calculation equations ###
 data/ (in repository.zip) #### Raw Data Folders: **Gaslab/** - CO2
 respiration measurement data * `raw/` - 176 CSV files of raw headspace CO2
 concentration data (YYYY-MM-DD-HHMM.csv format) * `cleaned/` - 229 CSV
 files of cleaned and formatted CO2 data with timestamps converted to
 elapsed time (seconds) and columns labeled by core ID * `GaslabLogs/` -
 System log files from CO2 analyzer (18 files) * `2022-01-10-1350.csv` -
 Additional CO2 measurement file * `Before round 1 Hyprop.gmbl` -
 Environmental monitoring log (Logger Pro file) containing room temperature
 and pressure data from preliminary measurements (see File Format Guide
 below) * Note: Each measurement file contains up to six concurrent
 readings from the six HYPROP cores being measured simultaneously
 **Hyprop/** - Soil water retention and hydraulic properties * `Hyprop Raw
 Data/` - 64 raw data files from HYPROP-View software for all soil cores
 (the software has been renamed to LABROS and backward compatible with
 older files). * `Five Points/` - HYPROP-View binary data files (.bhdx
 format) for all 28 soil cores plus some merged/alternate versions (31
 files total; see File Format Guide below) * `Hyprop+ WP4C.xlsx` - Combined
 water retention data including WP4C dewpoint potentiometer measurements
 for dry range extension (Excel format with formulas for database
 integration) * `Jennifer Hyprop+ Five Points.xlsx` - Consolidated HYPROP
 measurements with metadata (Excel format with formulas for database
 integration) * `CSV_converted/` - Water retention data in open CSV format
 without formulas (14 files total): * 5 files from Jennifer Hyprop+ Five
 Points dataset (one per replicate round) * 9 files from Hyprop+ WP4C
 dataset (including extended dry range measurements) * `PDI_bimodal/` -
 Fitted bimodal van Genuchten-PDI model outputs for each soil core: * 28
 Excel files (.xlsx) with formulas for all 15 data sheets per core * 140
 PNG diagnostic plots showing retention curves, conductivity curves, and
 tension/weight measurements * Note: Excel data also available in CSV
 format in `PDI_bimodal_CSV/` folder (see below) * `PDI_bimodal_CSV/` -
 Fitted bimodal model parameters and curves in CSV format without formulas
 (150 files total, with ~15 files per soil core containing measurements,
 evaluations, fitting parameters, and statistical analyses) *
 `PDI_unimodal/` - Unimodal van Genuchten model fits for comparison: * 5
 Excel files (.xlsx) with formulas for selected cores * 30 PNG diagnostic
 plots for selected cores * `Environmental Data/` - Laboratory
 environmental monitoring logs (4 .gmbl files containing room temperature
 and pressure data recorded during measurements; see File Format Guide
 below) **TCN/** - Total Carbon and Nitrogen elemental analysis * `TCN.csv`
 - Primary dataset containing total C and N content, C:N ratios, isotopic
 composition (δ13C, δ15N), and clay content for all samples *
 `EA20221209_corrected.csv` - Raw output from elemental analyzer with
 corrections **KSAT/** - Saturated hydraulic conductivity measurements from
 falling head permeameter * 36 CSV files containing time-series
 measurements of water level decline during permeability tests for
 individual soil cores **historical_C_N_BD/** - Historical carbon,
 nitrogen, and bulk density data from earlier sampling campaigns *
 `C_N_BD.csv` - Historical measurements for context and temporal comparison
 #### Processed Data: **processed/** - Analysis-ready datasets *
 `respiration_flux.csv` - Complete time series of calculated CO2 flux rates
 (μmol m⁻² s⁻¹) paired with matric potential, temperature, soil organic
 carbon content, and quality metrics for all measurements (9,755
 observations) * `respiration_flux_withstats.csv` - Summary respiration
 data with statistical parameters * `respiration_wrc_interpolated.csv` -
 Water retention and respiration data interpolated to standard matric
 potential values for statistical comparison #### Metadata: *
 `sample_plot_IDs.csv` - Sample identification codes linking cores to field
 plots * `Fivepoints GPS Fall 2023.csv` - GPS coordinates for sampling
 locations ### outputs/ (in outputs.zip - Supplemental Information on
 Zenodo) **Note:** The outputs folder contains creative works (figures and
 tables) and is released separately on Zenodo under CC BY 4.0 license
 (requires attribution). Access via the "Related works" link on
 the Dryad dataset page. **figures/** - Publication-quality figures (9 PDF
 files) * `chemical_properties.pdf` - Carbon and nitrogen content by
 treatment and depth * `core_physical_properties.pdf` - Bulk density and
 porosity measurements * `Cstock_CN.pdf` - Carbon stocks and C:N ratios *
 `methods_schema.pdf` - Schematic diagram of experimental methods *
 `physical_properties.pdf` - Summary of physical soil properties *
 `resp_relative.pdf` - Normalized respiration rates (κ) across moisture
 gradient * `sup_CN.pdf` - Supplementary carbon and nitrogen figures *
 `sup_isotope.pdf` - Supplementary isotopic composition figures *
 `sup_swc.pdf` - Supplementary soil water content figures **tables/** -
 Statistical analysis results and summary tables (8 CSV/TEX files) *
 `air_porosity_diffusion_differences.csv` - Air-filled porosity and gas
 diffusivity comparisons * `bulk_results_2018.csv` - Bulk soil property
 measurements * `interpolated_vwc_air_diff_resp.csv` - Interpolated
 volumetric water content, air diffusivity, and respiration data for
 statistical testing * `pore_diameter.csv` - Calculated pore size
 distributions * `ratio_table_2018.csv` - Various ratio calculations *
 `stats_of_bulk_soil_properties.csv` - Descriptive statistics for bulk
 properties * `swc_parameters.tex` - Water retention curve parameters in
 LaTeX format * `t_test_of_bulk_soil_properties.csv` - Welch's t-test
 results comparing treatments **fitFigs/** - Individual diagnostic plots
 (30 files) showing model fits for water retention curves and other fitted
 parameters --- ## File Format Guide ### Proprietary File Formats This
 dataset includes two proprietary file formats from specialized measurement
 software: **`.bhdx`** **files** - Binary HYPROP Data eXchange format *
 Contains raw measurement data from HYPROP evaporation experiments * Stores
 tensiometer readings, mass measurements, timestamps, and sample metadata *
 Can only be opened with HYPROP-View software, renamed LABROS (METER Group,
 Inc., version 4.0 or later) * Free download available at:
 https://metergroup.com/meter-products/software/?srsltid=AfmBOopWtrlQYeK3SFgoOiSVMuA_zBXiflHRxKgG5Z3hiX_MBfpSjzwJ  * Files are located in: `data/Hyprop/Five Points/` * Note: Some files have different extensions (.bhdix) or represent merged datasets; these are variations of the same binary format **`.gmbl`** **files** - Logger Pro environmental data logs * Environmental monitoring data logs containing room temperature and pressure measurements * Generated by Logger Pro software (Vernier Software & Technology) * Used to monitor and document environmental consistency during laboratory measurements * Can be opened with Logger Pro software (available from Vernier) * Files are located in: `data/Gaslab/` and `data/Hyprop/Environmental Data/` * Provided for completeness to document experimental conditions **Alternative data access:** For users without access to the proprietary software listed above, the essential data have been extracted and provided in multiple formats: **Excel format (with formulas):** * `data/Hyprop/Hyprop+ WP4C.xlsx` - Consolidated water retention with extended dry range (includes formulas for database integration) * `data/Hyprop/Jennifer Hyprop+ Five Points.xlsx` - Consolidated HYPROP measurements with metadata (includes formulas for data manipulation) * `data/Hyprop/PDI_bimodal/` - 28 Excel files with fitted bimodal van Genuchten-PDI parameters (15 sheets per file with formulas) * `data/Hyprop/PDI_unimodal/` - 5 Excel files with fitted unimodal van Genuchten parameters (formulas included) **CSV format (open access, no formulas):** * `data/Hyprop/CSV_converted/` - Consolidated water retention measurements from all measurement rounds, including extended dry range data from WP4C dewpoint potentiometer (14 CSV files) * `data/Hyprop/PDI_bimodal_CSV/` - Fitted bimodal van Genuchten-PDI parameters, retention curves, conductivity curves, and statistical analyses for all soil cores (150 CSV files) **Image format (diagnostic plots):** * `data/Hyprop/PDI_bimodal/` and `data/Hyprop/PDI_unimodal/` - Diagnostic plots in PNG format **Analysis-ready format:** * `data/processed/respiration_wrc_interpolated.csv` - Processed and interpolated water retention data ready for statistical analysis Note: Both Excel and CSV formats are provided to accommodate different user needs. Excel files contain formulas useful for database integration, while CSV files offer maximum accessibility and compatibility for downstream analysis. --- ## Methods Summary ### Water Retention Measured using HYPROP system (METER Group, Inc.) with extended evaporation method. Dual tensiometers recorded matric potential at 1.25 and 3.25 cm from core bottom during controlled evaporative drying. Low water content range extended using WP4C dewpoint potentiometer. Van Genuchten-PDI bimodal model fitted to capture both textural and structural porosity. ### Respiration Custom chamber system with NDIR CO2 sensor (K-33FR, CO2meter.com; ±30 ppm accuracy). Chambers sealed for 6-minute measurement periods, conducted 2–6 times daily during the drying cycle. Flux calculated using nonlinear diffusion model accounting for concentration-dependent feedback on diffusion and respiration rate (see `fluxCalc.R` and `flux_derivation.nb`). ### Elemental Analysis Dry combustion using Costech 4010 Elemental Analyzer coupled with Delta V Plus Isotope Ratio Mass Spectrometer. Samples ground to &lt;150 μm. Provides total carbon, total nitrogen, C:N ratios, and stable isotope ratios (δ13C, δ15N). ### Statistical Analysis Welch's t-tests conducted at interpolated matric potential values to account for heteroscedasticity between treatments. Uncertainty propagation using standard error methods. All analyses performed in R (see analysis scripts). --- ## Code and Analysis Scripts ### Processing Workflow 1. **0_gaslab_file_formatter.R** - Formats raw Gaslab CO2 data * Converts timestamps to elapsed time (seconds) * Assigns column names by core ID * Creates cleaned CSV files 2. **1_pre-process_gaslab.R** - Pre-processes respiration data * Calculates CO2 flux from concentration time series * Links flux measurements to concurrent matric potential data * Quality control and outlier detection 3. **2_main_analysis.R** - Main analysis pipeline * Imports and merges all datasets * Interpolates water retention and respiration data to standard matric potentials * Performs statistical analyses (Welch's t-tests) * Generates all manuscript figures and tables * Calculates carbon stocks and normalized respiration rates ### Dependencies **R packages required:** * tidyverse (data manipulation and visualization) * lubridate (date/time handling) * nlme or lme4 (if mixed models used) * Standard R stats packages **Other software:** * HYPROP-View (METER Group) for water retention analysis * Mathematica (optional, for flux derivation verification) --- ## Usage Notes ### File Formats * **Dual format provision**: Key water retention datasets are provided in both Excel (.xlsx) and CSV formats * Excel files retain formulas useful for database integration and custom calculations * CSV files provide open-access format with all formulas pre-calculated, suitable for any data analysis platform * This addresses accessibility while maintaining utility for users needing formula-based workflows ### Data Values and Units * All matric potential values are reported as negative numbers (kPa) or positive numbers (hPa) where 1 kPa = 10 hPa * Water content is volumetric (cm³ water / cm³ soil) * CO2 flux units: μmol CO2 m⁻² s⁻¹ (or mg-C g-SOC⁻¹ d⁻¹ for carbon-specific rates) * Normalized respiration (κ) units: yr⁻¹ * Missing values indicated as `NA` * Quality flags included in flux data: "good" indicates reliable fit, "not good" indicates poor model fit (low R²) and data should be used with caution * Temperature reported in °C * Core IDs follow format: `[TREATMENT][DEPTH CODE][REPLICATE]` (e.g., CTCC11 = CTCC treatment, 0-5 cm depth, replicate 1) --- ## Funding This research was supported by: * California Department of Water Resources (Grant Number 4600012156) * University of California F3 Innovation Initiative * Economic Development Administration BBBR iCREATE project * USDA Hispanic Serving Institutions Education Grants Program (Grant #2021-77040-34903) --- ## License This dataset is distributed with two different licenses: * **repository.zip (Main Data on Dryad):** Released under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. To the extent possible under law, the authors have waived all copyright and related rights to this dataset. * **outputs.zip (Supplemental Information on Zenodo):** Creative works (figures and tables) are released under CC BY 4.0, requiring attribution when used. This dataset is intended for research and educational purposes. Please cite the associated publication when using these data. --- ## Keywords conservation agriculture, no-tillage, cover crops, soil carbon sequestration, heterotrophic respiration, soil water retention, soil structure, Mediterranean climate, irrigated agriculture, carbon mineralization, San Joaquin Valley, van Genuchten model, pore size distribution, carbon-specific respiration, HYPROP --- ## Citation When using this dataset, please cite: Alvarez-Sagrero J, Chacon SS, Mitchell JP, Ghezzehei TA. (2025) Soil Structure Changes Under Reduced Tillage and Cover Cropping Enhance Carbon Mineralization in Mediterranean Croplands. *Vadose Zone Journal*. [https://doi.org/10.1002/vzj2.70065](https://doi.org/10.1002/vzj2.70065) --- ## Contact For questions about this dataset or to report issues, please contact: * Jennifer Alvarez-Sagrero: [jalvarez88@ucmerced.edu](mailto:jalvarez88@ucmerced.edu) * Teamrat Afewerki Ghezzehei: [taghezzehei@ucmerced.edu](mailto:taghezzehei@ucmerced.edu) Environmental Systems Graduate Program University of California, Merced Merced, CA 95343, USA