DATA

Data tables and variables

Table 1: A snippet of sample data categorized into different organic carbon compounds with various management practices and depth intervals.

The concentrations in (Table 1) are displayed as µg/g of soil.

Table 2: Identifying the two predictor variables and their sub classes in this study

The two predictor variables in (Table 2) are manipulated throughout the Breton plot cropping systems over the years and are categorical.

Table 3: Identifying the response variables and it's categories in this study

PyGCMS data obtained from samples consisted of 366 compounds. Through an extensive reference library maintained by the Soil Biogeochemistry Laboratory, these compounds were further categorized into main organic carbon classes identified in (Table 3) before statistical analysis. These class variables will be the response variables in this study.

Data exploration

Data were preliminary analyzed via bar graphs to visually identify the variations of each organic compound in different management practices.

Comparison of WF-NPKS and CG-NPKS Management Practices

Comparison of the wheat fallow (WF) -NPKS and continuous grain (CG) -NPKS treatments to determine the effect of fallow on the soil organic carbon classes. Both of these treatments only contain annual crops, have similar degrees of tillage, and are amended with conventional fertilizer at the same rate during cropped years. This comparison will help evaluate if the use of fallow in the WF-NPKS treatment could be driving differences in soil organic carbon classes.

Figure 4: Comparison of soil organic carbon classes in shallow soil layers in continuous grain (CG) and wheat fallow rotational (WF) management practices to determine the effect of fallow

Figure 5: Comparison of soil organic carbon classes in deep soil layers in continuous grain (CG) and wheat fallow rotational (WF) management practices to determine the effect of fallow

Comparison of 5Y and WF Management Practices

The five year (5Y) and WF systems, encompass three different amendment treatments: control/check, NPKS/fertilizer and manure. These treatments were compared to determine the amendment effects on the soil organic carbon classes. Since the only difference between the amendment sub-treatments within each system is the applied amendment, this would help us understand if the soil organic carbon classes at Breton plots are responding to the amendments with minimal confounding effects of other management practices.

Figure 6: Comparison of soil organic carbon classes in shallow soil layers in five year (5Y) and wheat fallow rotational (WF) management practices to determine the amendment effects: control, fertilizer (striped bars) and manure (dotted bars). 5Y practices are indicated in blue and WF practices are indicated in maroon colors.

Figure 7: Comparison of soil organic carbon classes in shallow soil layers in five year (5Y) and wheat fallow rotational (WF) management practices to determine the amendment effects: control, fertilizer (striped bars) and manure (dotted bars). 5Y practices are indicated in blue and WF practices are indicated in maroon colors.

Comparisons between CG, 5Y-NPKS, 5Y-Manure, 8Y, and CF Treatments

CG, 5Y-NPKS, 5Y-Manure, eight year (8Y), and continuous forage (CF) treatments were further compared to estimate the effects of forage inclusion and green manure on soil organic carbon classes.

Comparing the CG, 5Y-NPKS, and CF where all treatments received conventional fertilizer to determine how increasing the amount of perennial forages in a cropping system can effect can influence soil organic carbon classes. The treatments primarily differ in the degree of perennial forage inclusion (CG - none vs 5Y - every 2/5 years vs CF - continuously for 41 years).

Comparing the 5Y-Manure and 8Y Manure systems to evaluate the effect of manure on soil organic carbon classes, as the 5Y-Manure and 8Y systems are otherwise quite similar.

Figure 8: Comparison of soil organic carbon classes in shallow soil layers in continuous grain (CG) five year (5Y) and eight year (8Y) and continuous forage (CF) management practices to determine the effects of perennial forage and manure. 5Y practices are indicated in blue, 8Y practices are indicated in orange, CF practices are indicated in purple and CG practices are indicated in pink colors. Fertilizer amendments are indicated in stripes and manure amendments in dots.

Figure 9: Comparison of soil organic carbon classes in shallow soil layers in continuous grain (CG) five year (5Y) and eight year (8Y) and continuous forage (CF) management practices to determine the effects of perennial forage and manure. 5Y practices are indicated in blue, 8Y practices are indicated in orange, CF practices are indicated in purple and CG practices are indicated in pink colors. Fertilizer amendments are indicated in stripes and manure amendments in dots.

Pairwise comparison of all treatments

Confidence level used: 0.95

> pairs(out2, adjust="sidak")

contrast estimate SE df t.ratio p.value

5Y Check - 5Y Manure -2043 687 92 -2.975 0.1261

5Y Check - 5Y NPKS -1136 567 92 -2.003 0.8305

5Y Check - 8Y Manure -3617 620 92 -5.836 <.0001

5Y Check - CF NPKS -3053 812 92 -3.762 0.0106

5Y Check - CG NPKS -1034 812 92 -1.274 0.9998

5Y Check - WF Check 1111 930 92 1.195 0.9999

5Y Check - WF Manure -496 930 92 -0.533 1.0000

5Y Check - WF NPKS 890 722 92 1.233 0.9999

5Y Manure - 5Y NPKS 907 547 92 1.657 0.9783

5Y Manure - 8Y Manure -1574 601 92 -2.617 0.3126

5Y Manure - CF NPKS -1010 798 92 -1.266 0.9998

5Y Manure - CG NPKS 1009 798 92 1.265 0.9998

5Y Manure - WF Check 3154 918 92 3.438 0.0313

5Y Manure - WF Manure 1548 918 92 1.686 0.9726

5Y Manure - WF NPKS 2933 706 92 4.153 0.0026

5Y NPKS - 8Y Manure -2481 461 92 -5.388 <.0001

5Y NPKS - CF NPKS -1917 698 92 -2.748 0.2294

Confidence level used: 0.95

> pairs(out2, adjust="sidak")

contrast estimate SE df t.ratio p.value

5Y NPKS - WF Check 2248 832 92 2.701 0.2572

5Y NPKS - WF Manure 641 832 92 0.770 1.0000

5Y NPKS - WF NPKS 2027 591 92 3.429 0.0322

8Y Manure - CF NPKS 564 741 92 0.762 1.0000

8Y Manure - CG NPKS 2584 741 92 3.487 0.0267

8Y Manure - WF Check 4729 869 92 5.443 <.0001

8Y Manure - WF Manure 3122 869 92 3.594 0.0188

8Y Manure - WF NPKS 4508 642 92 7.026 <.0001

CF NPKS - CG NPKS 2019 907 92 2.225 0.6469

CF NPKS - WF Check 4164 1010 92 4.105 0.0031

CF NPKS - WF Manure 2558 1010 92 2.521 0.3852

CF NPKS - WF NPKS 3944 828 92 4.761 0.0003

CG NPKS - WF Check 2145 1010 92 2.115 0.7442

CG NPKS - WF Manure 538 1010 92 0.531 1.0000

CG NPKS - WF NPKS 1924 828 92 2.323 0.5572

WF Check - WF Manure -1607 1110 92 -1.446 0.9973

WF Check - WF NPKS -221 944 92 -0.234 1.0000

WF Manure - WF NPKS 1386 944 92 1.468 0.9965

PCA Analysis

Understanding the variation of SOC classes across the different management practices in Breton Plot samples.

Figure 10: (Top) Scree plot indicating the point of inertia at PC2.

Figure 11: (Right) PCA biplot of samples categorized by depth (0-7.5 cm / shallow and 7.5-15 cm / deep) and various agricultural management practices.

PC1 and PC2 in the PCA biplot explain the majority of the variation in the data, with PC1 capturing the largest variability (84%) and a cumulative variability of 95%. SOC-Nitrogen Compounds stand out strongly negatively along PC2. Other SOC classes (ex: carbohydrates) have a negative loading on PC1 and a small positive loading on PC2.

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