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40 protocols using model 7890a

1

Fatty Acid Profile Determination in Lipid Extracts

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Fatty acid profile was determined through standard methods (Urzúa & Anger, 2011 (link); Bascur et al., 2018 (link); Bascur et al., 2020 (link)). Specifically, fatty acid methyl esters (FAMEs) were measured after preparation using the sample’s lipid extract. Lipid extracts were esterified at 70 °C for 1 h in a Thermo-Shaker (DBS-001; MRC, Netanya, Israel) using sulfuric acid (1% in methanol) incubations. Then, each sample was vortexed (SBS100-2, Select Vortexer) with 3 mL of n-hexane and centrifuged for 15 s. This process was repeated 3 times and the supernatant was transferred to labeled tubes. Finally, using a nitrogen evaporator (109A YH-1; Glass Col), fatty acids were concentrated. The measurement of FAMEs was performed using a gas chromatograph (Agilent, model 7890A) at set temperature equipped with a DB-225 column (J&W Scientific, 30 m in length, 0.25 internal diameter, and 0.25 µm film). Using chromatography software (Agilent ChemStation, Santa Clara, CA, USA), individual FAMEs were identified by comparison to known standard fatty acids of marine origin (certificate material, Supelco 37 FAME mix 47885-U (Malzahn et al., 2007 (link); Urzúa & Anger, 2011 (link)). Each sample was quantified using a calibration curve for fatty acids, diluting different concentrations of Supelco 37 FAME mix standard.
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2

Fatty Acid Composition Analysis

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The composition of fatty acids was determined in 80 samples (20 individuals per study site) using standard methods [40 (link),41 (link)]. Fatty acid methyl esters (FAMEs) were measured after preparation using the lipid extract of samples (lipid content). Lipid extracts were esterified using sulfuric acid (1% in methanol) incubations at 70°C for 1 h in a Thermo-Shaker (DBS-001, MRC). Then, each sample was mixed with 3 mL of n-hexane and centrifuged for 15 s. This process was repeated three times and the supernatant was transferred to labeled tubes. Finally, fatty acids were concentrated using a nitrogen evaporator (109A YH-1, Glass Col). The measurement of FAMEs was performed using a gas chromatograph (Agilent, model 7890A) at set temperature equipped with a DB-225 column (J&W Scientific, 30 m in length, 0.25 internal diameter, and 0.25 mm film). Using chromatograph software (Agilent ChemStation, USA), individual FAMEs were identified by comparison to known standard fatty acids of marine origin (certificate material, Supelco 37 FAME mix 47885-U [40 (link),42 (link)]. Each sample was quantified using a calibration curve for fatty acids, diluting different concentrations of Supelco 37 FAME mix standard.
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3

Gas Chromatography Lignin Monomer Analysis

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Samples were quantified using gas chromatography (Model 7890 A, Agilent). A 1 μL injection volume was used through a 30 m × 250 μm × 0.25 μm column (DB-1701, Agilent) with a split ratio of 10:1. An inlet temperature of 280 °C and an oven temperature of 50 °C with a 10 °C min−1 ramp to 280 °C was used with an overall run time of 29 min. An FID was used to quantify the products, with dimethoxybenzene as an external standard. Allyl syringol (Alfa Aesar, 98%) and propyl guaiacol (Sigma-Aldrich, 99%) were used as calibration standards Additionally, methyl paraben was not quantified in the monomer yield (although it was detected in every sample) as it is a pendent group to lignin attached by an ester linkage.
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4

GC-MS Analysis of Soursop Seed Extract

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The extract samples obtained by SFE at 30 MPa and 40 °C (based on the high yields and AA; Sections 3.2 and 3.3) and SOX extraction with hexane were selected for GC-MS analysis. The samples were subjected to methylation fractionation reaction (FAME) to assist the analysis of the compounds by GC-MS (O’Fallon, Busboom, Nelson, & Gaskins, 2007 (link)). The identification and relative quantification of the volatile compounds in the soursop seed extract were performed using a gas chromatography system equipped with a mass spectrophotometer (GC-MS, model 7890 A, mass detector 5975C, Agilent Technologies, USA), attached to an HP-5MS column (30 m × 0.32 mm (internal diameter) with a film thickness of 0.25 µm, Agilent Technologies, USA), following the method described by Mazzutti et al. (2018) (link). Helium was used as a carrier gas with a flow rate of 4 mL∙min−1, split ratio of 5:1, injector temperature of 250 °C, and Thermal Aux 2 (MSD Transfer Line). The column temperature was increased from 60 °C to 230 °C at a rate of 3 °C∙min−1, in a total time of 55.56 min, and a quadrupole detector temperature of 150 °C was used. The major components of the selected extracts were identified by comparing the mass spectra and retention times of the compounds to those available in the NIST 11 Mass Spectral Library.
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5

Quantitative Analysis of Short-Chain Fatty Acids

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Frozen cecal contents (100–300mg) or frozen supernatants from in vitro growth curves were resuspended in 0.1% formic acid in water (Honeywell) and blended with a pellet pestle (Kimble chase). Acetate, butyrate, lactate, propionate and succinate standards were included in each run to generate standard curves for quantification. The samples were acidified (37% HCl), and SCFAs were extracted (500μl diethyl ether/extraction; 2 cycles). Each sample was derivatized with N-tert-butyldimethylsilyl-N-methyltrifluoracetamide (MTBSTFA; Sigma Aldrich) and quantified using a gas chromatograph (Model 7890A; Agilent Technologies, Santa Clara, CA) coupled to mass spectrometer detector (Model 5975C; Agilent Technologies). Analyses were carried out in a split mode (1:100) on a DB-5MSUI capillary column (30 m×0.25 mm, 0.25 μm film thickness, Agilent Technologies) using electronic impact (70 eV) as ionization mode and scan in m/z 50–550 mass range. The column head-pressure was 12 p.s.i. Injector, source and quadrupole temperatures were 250, 280 and 150 °C, respectively. The GC oven was programmed as follow: 75 °C held for 2 min, increased to 120 °C at 40 °C min−1, 120 °C held for 5 min, increased to 320 °C at 20 °C min−1 and held at 320 °C for 7 min.
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6

Fatty Acid Profiling by GC-FID

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Fatty acid methyl esters were separated and quantified by gas-liquid chromatography (Model 7890A, Agilent Technologies, USA) using a 30 m×0.32 mm i.d. capillary column (SP-2330, Supelco, Inc., Bellefonte, PA, USA). The hydrogen was used as the carrier gas at 40 mL/min. The injector temperature was programmed at 240°C and the detector temperature was 250°C. The column temperature program started to run at 140°C, for 2 min, warmed to 158°C at 1°C/min, held for 28 min, warmed to 220°C at 1°C/min and then held for 20 min to achieve satisfactory separation. The identification of the peaks was made by comparison of equivalent chain lengths with those of authentic fatty acid methyl esters (37 Component FAME mix, Supelco, Bellefonte, PA). Peak areas were determined automatically using the Agilent gas chromatography chemstation software (Agilent Technologies, USA). The fatty acid concentrations are expressed as percentage of the sum of total identified peaks measured in each sample.
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7

SCFA Analysis of Piglet Fecal Samples

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SCFA analysis of piglet fecal samples was performed using a GC-FID system (model 7890A; Agilent Technologies, Santa Clara, CA, USA) equipped with an AOC-20s autosampler, a capillary column (HP-INNOWAX (19091N-133), 30 m × 0.53 mm × 1.0 µm) and a flame ionization detector. Specifically, 2 g of piglet feces was macerated in 2 mL of ultrapure water in a freezer at 4 °C for 48 h. The feces were then centrifuged at 10,000 rpm/min for 10 min at 4 °C, and this step was repeated twice. Filtration of the supernatant was carried out using a 0.22 μm filter membrane. Finally, the filtrate was combined with an internal standard solution (25% metaphosphate solution containing crotonic acid) at a volume ratio of 5:1. The injector temperature, detector temperature and oven temperature were set to 230 °C, 240 °C and 180 °C, respectively, and the pressure was set to 90kPa. The flow rates of nitrogen, air and hydrogen were 20, 400 and 30 mL/min, respectively.
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8

Gas Chromatography-Mass Spectrometry Analysis

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Gas chromatography (Model 7890 A, Agilent technologies, USA) with a single quadruple mass Spectrometry detector (Model 5975 C, Agilent technologies, USA) equipped with split/splitless injector and an Agilent auto-sampler with a HP-5 19091S-436 Agilent capillary column (60 m × 0.25 mm I.D., 0.25 μm film thicknesses) was used.
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9

Fatty Acid Composition Analysis by GC

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The fatty acid composition was determined by gas chromatography (GC) as described previously (Hao et al., 2020 ). First, the LDM samples were extracted with a mixture of chloroform and methanol (2:1; vol/vol). Approximately 20 g of each LDM sample was weighed and dried in an oven at 105 °C for 1 h, and then 1 g of each dried sample was weighed and leached with petroleum ether for 3 h. A total of 60 mg of the extracted fat was placed in a test tube, 4 mL of isooctane was added to fully dissolve the sample, and then 200 μL potassium hydroxide-methanol and 1 g of sodium bisulfate were added. After salt precipitation, the solution containing the methyl esters was drawn into the upper layer and stored in a refrigerator at 4 °C. Each sample was filtered through a 0.22-nm filter membrane before GC detection (Model 7890 A, Agilent Technologies, Palo Alto, CA, USA). Finally, the fatty acid concentration was analyzed by GC ChemStation software (Agilent Technologies, Palo Alto, CA, USA).
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10

Soil N2O Emissions Measurement Protocol

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Soil N2O emissions were measured in the four replicates per treatment two or three times per week during the first month after treatments application. Afterwards, measurements were continued at a frequency of once per week until the end of the experiment. For each measurement, the jars were hermetically sealed with a lid supporting a butyl rubber septum and 20 mL of the inner headspace air were collected using a gas-tight syringe at 0, 45 and 90 min after sealing the jars. Gas samples were stored at overpressure in pre-evacuated 12 mL glass vials and analyzed using a gas chromatograph (GC, Model 7890A, Agilent Tech., USA), equipped with an electron capture detector (ECD) to quantify N2O. A capillary column (IA KRCIAES 6017: 240 °C, 30 m × 320 μm) was used and the samples were injected by means of a headspace autosampler (Teledyne Tekmar HT3) connected to the GC. Standards of N2O were analyzed at the same time as the samples. Fluxes were calculated on a daily basis from the linear increase in concentration in the jars headspace over the 90 minute incubation time33 (link). Cumulative N2O emissions were estimated by multiplying the average of two consecutive measurements by the time period between those measurements and adding that amount to the previous cumulative value.
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