This Soil SFA 2.2 Chitin Decomposition Soil Biogeochemistry readme.txt file was generated on 2025-09-23 by Shannon Sheridan GENERAL INFORMATION 1. Title of Dataset: Chitin Decomposition 2.2 Soil Biogeochemistry 2. Principal Researcher: Name: Kirsten Hofmockel Institution: Pacific Northwest National Laboratory Email: kirsten.hofmockel@pnnl.gov 3. Additional Author Contact Information Name: Nicholas Reichart Institution: Pacific Northwest National Laboratory Email: nicholas.reichart@pnnl.gov 4. Information about funding sources supporting the data: DOE BER GSP Soil Microbiome SFA, FWP 5. Geographic location of data collection: 46°15'04"N, 119°43'43"W, Prosser, WA, USA 6. Date of data collection: 2022-10-08 SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: This work is marked with CC0 1.0: https://creativecommons.org/publicdomain/zero/1.0/. The authors do request that you appropriately cite the dataset when referencing or re-using the dataset. 2. Links to publications that cite or use the data: 3. Recommended citation for this dataset: Reichart N.J., S.L. Bell, V.A. Garayburu-Caruso, N.C. Sadler, S. Zhao, and K.S. Hofmockel. 2025. Moisture Effect on Chitin Decomposition Biogeochemistry. [Data Set] PNNL DataHub. https://doi.org/10.11578/2572145 DATA & FILE OVERVIEW 1. File List: chitin.csv: Chitin degradation incubation results. HPLC measured chitin from each sample. enzyme_kinetics.csv: Results on nycodenz extracted cells. Measures degradation of substrate over time for all samples. extracellular_enzyme_assays.csv: ecords the level of activity for several enzyme assays. respiration.csv: Respiration under varying moisture/chitin. Measures CO2 production daily for the course of the incubation. soil_biogeochemistry.csv: Carbon and nitrogen quantitation results. Contains the microbial biomass and salt extractable measurements for carbon and nitrogen 2. Relationship between files, if important: These five sheets describe data collected from different instrument measurements. The variable "SampleID" is the primary key across the files. DATA-SPECIFIC INFORMATION FOR: chitin.csv 1. Number of variables: 8 2. Number of cases/rows: 38, including headers 3. Variable List: SampleID: sample identifier Assay_Concentration: value of chitin extraction recorded on plate assay Day: length of incubation prior to harvest (days) Normalized_Concentration: value of chitin normalized to soil input Chitin: categorical description of chitin treatment [No_Chitin; Chitin] Moisture: Moisture: categorical description of moisture treatment [Low; High] 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: enzyme_kinetics.csv 1. Number of variables: 5 2. Number of cases/rows: 4921, including header 3. Variable List: SampleID: sample identifier Treatment: application of two fluorogenic compounds 4-Methylumbelliferyl β-D-N,N’,N’’-triacetylchitotriose (Chitin) or 4-Methylumbelliferyl N-acetyl-β-D-glucosaminide (NAG). Time: sampling time points when readings were taken: hour Replicate: replicate index Value: fluorescence value converted to concentration via standard curve: µM 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: extracellular_enzyme_assays.csv 1. Number of variables: 11 2. Number of cases/rows: 21, including headers 3. Variable List: SampleID: Sample Identifier Moisture: categorical description of moisture treatment [Low, High]. Samples were collected from the two irrigation plots for low moisture (plot 23, 25% field capacity) and high moisture (plot 42, 100% field capacity) treatments. Chitin: categorical description of chitin treatment [No_Chitin, Chitin] BG_Activity: Release of 4-Methylumbelliferone (MUB) from 4-MUB--D-glucopyranoside. Units- nmol per g dry soil per hour BX_Activity: Release of 4-Methylumbelliferone (MUB) from 4-MUB--D-xyloside. Units- nmol per g dry soil per hour CB_Activity: Release of 4-Methylumbelliferone (MUB) from 4-MUB--D-cellobioside Units- nmol per g dry soil per hour AP_Activity: Release of 4-Methylumbelliferone (MUB) from 4-MUB-phosphate. Units- nmol per g dry soil per hour NAG_Activity: Release of 4-Methylumbelliferone (MUB) from 4-MUB--D-glucosaminide. Units- nmol per g dry soil per hour Chitin_Activity: Release of 4-Methylumbelliferone (MUB) from 4-MUB--D-N,N’,N’’-triacetylchitotriose. Units- nmol per g dry soil per hour Leu_Activity: Release of 4-methylcoumarin (MUC) from L-Leucine-7-amino-4-MUC. Units- nmol per g dry soil per hour Ala_Activity: Release of 4-methylcoumarin (MUC) from L-Alanine-7-amino-4-MUC. Units- nmol per g dry soil per hour 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: respiration.csv 1. Number of variables: 6 2. Number of cases/rows: 141, including header 3. Variable List: SampleID: sample identifier Moisture: categorical description of moisture treatment [Low, High] Chitin: categorical description of chitin treatment [No_Chitin, Chitin] Day: length of incubation prior to headspace sampling (days) Respired_CO2: CO2 respired for each 24 hour period. Units ug CO2-C per g dry soil Cumulative_Respired_CO2: Cumulative CO2 respired for the period up to that period of the incubation. Units ug CO2-C per g dry soil 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: soil_biogeochemistry.csv 1. Number of variables: 9 2. Number of cases/rows: 21, including header 3. Variable List: SampleID: sample identifier Moisture: categorical description of moisture treatment [Low; High] Chitin: categorical description of chitin treatment [No_Chitin; Chitin] MBC: microbial biomass carbon measurement (ug/g dry soil) MBN: microbial biomass nitrogen measurement (ug/g dry soil) MBC_MBN: microbial biomass C:N ratio (unitless) Salt_SOC: salt-extractable carbon measurement (ug/g dry soil) Salt_TN: salt-extractable nitrogen measurement (ug/g dry soil) Salt_C_N: salt-extractable C:N ratio (unitless) 4. Missing data codes: None 5. Specialized formats or other abbreviations used: None METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: File: chitin.csv Chitin was hydrolyzed into glucosamine using 100 mg of freeze-dried soil. Derivatized glucosamine peaks were detected on the Shimadzu HPLC 20A with a CTO-20A baseline detector, and SIL-20A HT autoinjector. Glucosamine standards were made using various amounts of D-(+)-glucosamine HCl and derivatized with FMOC-Cl to produce the desired glucosamine product. Samples and standards were run once through the HPLC. An average sum of the external calibration factor was calculated using the standards concentrations 0 – 12.5 µM to solve for the unknown samples’ glucosamine concentrations. File: enzyme_kinetics.csv From the Nycodenz extracted microbial populations (as described above), 100 µL (10 % of the volume) was used for kinetic assays using 4-Methylumbelliferyl β-D-N,N’,N’’-triacetylchitotriose (Chitin) or 4-Methylumbelliferyl N-acetyl-β-D-glucosaminide (NAG). Samples were continuously measured for fluorescence on a BioTek H1 Synergy plate reader (Agilent, Santa Clara, California) measuring once per hour for 40 hours. File: extracellular_enzyme_assays.csv A total of eight potential extracellular enzyme activities were measured from soil samples. These included hydrolytic enzymes for carbon, nitrogen, and phosphorus acquisition. Saturating substrate concentrations were determined during initial testing of Km and linearity of the reactions. Activities were calculated except that net fluorescence, quenching, and emission coefficients were calculated at 1 and 3 hours, and activity was then calculated by the change over time between the two measurements. It is important to note that this assay measures potential rates. Potential enzyme assays are run under saturating substrate concentrations, and in a soil slurry which maximizes physical dispersion of both enzymes and substrates and therefore do not reflect the rate of the reaction occurring in a soil, but rather the size of the enzyme pool. File: respiration.csv Jars were capped with canning jar lids modified with butyl septa. Measurements for CO2 were performed daily by removing 1 mL headspace in a precision gas syringe and injected manually via a valved sample injection loop system into a Licor LI7000 (Licor, Lincoln, Nebraska). After each daily sampling, jars were uncapped for 5 minutes inside a biological safety cabinet to equilibrate to room air and then recapped for the following day’s measurement. Cumulative respiration among treatments were calculated as the sum of the daily CO2 produced (µg CO2-C per g_dry_wt_soil) over the 7-day incubation. File: soil_biogeochemistry.csv We used a sequential chloroform fumigation extraction (CFE) method for salt extractable and microbial biomass C and N pool quantification. Using a 50 mL conical tube, 8 g subsamples were shaken at 200 rpm at room temperature for 2 hours in 24 mL of 0.5 M K2SO4. After, subsamples were centrifuged at 4000 rpm for 20 minutes. Then, the supernatant was filtered through quantitative ashless filter paper (Whatman No. 42), which had been pre-leached three times with 0.5 M K2SO4 and one time with ultrapure water. Two to three drops of phosphoric acid were added to the filtrate for preservation then frozen in -20 °C for storage until total organic carbon (TOC) and total nitrogen (TN) analysis. The same initial 8 g of soil pellet was then reused in sequence to measure microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Two milliliters of ethanol-free chloroform (VWR# BJ049-1L) was added to each subsample and incubated at room temperature in the dark for 24 hrs. Chloroform was allowed to evaporate from the samples for 48 hours. The 0.5 M K2SO4 extraction was then repeated according to the same protocol. Acidified extracts were analyzed with a Vario TOC Cube analyzer (Elementar, Germany) to quantify non-purgeable organic C and TN. 2. Methods for processing the data: Data was collected from various instruments and formatted for ease of reading into these CSV files. Later processing described in manuscript for analysis of files and generation of figures. 3. Instrument- or software-specific information needed to interpret the data: N/A 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: Field Sampling On October 18th, 2022, just after the fall harvest, soil was collected from plots planted with the Alkar cultivar of Tall Wheatgrass. Samples were collected from the two irrigation plots for low moisture (plot 23, 25% field capacity) and high moisture (plot 42, 100% field capacity) treatments. Five replicate cores (5 cm diameter) from 0-15 cm depth were collected from each plot. Irrigation water used for the field site was collected from the adjacent irrigation channel, which is fed from the Yakima River , and used for moisture control in the lab-based incubations. Incubation Setup Replicate cores were combined and gently homogenized while maintaining aggregation. Roots, plant detritus, and rocks were picked out with sterile tools. Gravimetric water content was collected by drying 10 g soil at 60oC for 48 hours. For each moisture level (25% and 100%), 80 g of field moist soil was weighed into ten autoclaved sterile replicate 237mL wide mouth canning jars (20 jars total). All jars were preincubated at 15.3oC for 4 days. The experiment was initiated by adding 1000ppm chitin (Bean Town Chemical, Hudson, New Hampshire) (1 mg/g dry soil) to five replicate jars of each moisture level (25% and 100%) and stirred to homogenize with sterile spatulas. Ten replicate non-chitin control jars (five at each moisture level) were also stirred for consistency in disturbance across treatments. All samples (n = 20) were brought back to field moisture with 0.22µm sterilized irrigation water from the site. Samples were incubated at 15.3oC for 7 days. 6. Describe any quality-assurance procedures performed on the data: N/A 7. People involved with sample collection, processing, analysis and/or submission: Sheryl Bell, Sharon Zhou, Natalie Sadler, Vanessa Garayburu-Caruso, Nicholas Reichart, Kirsten Hofmockel