Chapter 3: EFFECTS OF LAND USE AND MANAGEMENT ON SOIL BACTERIAL
3.3 RESULTS
3.3.3 Analyses of soils at the Mount Edgecombe experimental site
Analysis of evenness (J) at this site showed that land use did not affect bacterial evenness (Appendix A, Table A1), whereas analysis of bacterial diversity by the Shannon Weaver Diversity Index (H’) showed an overall difference in bacterial diversity. Communities under M were separated from those under PF and W but not from those under the other land uses (Table 3.7).
TABLE 3.7 ANOVA of bacterial community diversity and land use means at Baynesfield using the Shannon Weaver Diversity Index (H')
Source of variation d.f. s.s. m.s. f-ratio p-value
Land use 5 7.109 1.421 5.08 0.01
Residual 12 3.357 0.279
Total 17 10.467
Grand mean 2.91
Land use SC a b M a KIKa b NAT a b PF b W b
Mean 2.61 1.72 2.97 3.03 3.54 3.58
Note: Means with common superscript letters are not significantly different (p< 0.05).
Key: SC = sugarcane; M = maize; KIK = kikuyu pasture; NAT = native grassland;
PF = pine plantation; W = wattle plantation.
TABLE 3.8 Means (± sd) for selected physicochemical properties of soils under the four managements at Mount Edgecombe, collected at 0-5cm depth
Trash Management
pH (KCL)
Organic Carbon
Extractable P
Exchangeable cations Exch.
acidity
Total cations (ECEC)
K Ca Mg
% mg kg-1 --- cmolc kg-1 ---
TF 3.7 (0.11) 5.9 (0.61) 33.2 (10.61) 0.61 (0.010) 8.93 (0.942) 3.27 (0.172) 1.82 (0.898) 14.63 (0.642) TFo 4.5 (0.15) 5.1 (0.36) 4.2 (1.24) 0.26 (0.070) 12.27 (1.960) 5.48 (0.385) 0.09 (0.038) 18.11 (1.638) BtoF 3.8 (0.19) 4.2 (0.26) 27.0 (5.35) 0.60 (0.111) 6.34(1.503) 3.06 (0.616) 1.28 (0.854) 11.28 (1.561) BtoFo 4.6 (0.15) 3.9 (0.07) 2.2 (0.06) 0.14 (0.025) 9.30(1.713) 4.93 (0.230) 0.08 (0.020) 14.46 (1.915)
Key: T = green cane harvested with trash retention; Bto = burnt with harvest residues removed; F = fertilized annually with N, P and K; Fo = unfertilized
MRPP of Mount Edgecombe soils, which indicated dissimilarities between all possible soil pairs and also for all land treatments, are shown in Table 3.9. The data obtained for all treatments (T = -4.585, p < 0.001) showed a highly significant overall difference in the experimental soils except between BtoFo and TFo.
TABLE 3.9 Multi-Response Permutation Procedures (MRPP) of soil physicochemical properties, showing pairwise comparisons and a comparison of all soils under different trash managements at Mount Edgecombe
Land treatments Test statistic (T) Probability (p)
BtoF vs. BtoFo -2.791 0.022
BtoF vs. TF -2.245 0.031
BtoF vs. TFo -2.824 0.022
BtoFo vs. TF -2.982 0.021
BtoFo vs. TFo -1.699* 0.061*
TF vs. TFo -2.990 0.021
All treatments -4.585 <0.001
* no significant difference
Key: T = green cane harvested with trash retention; Bto = burnt with harvest residues removed; F = fertilized annually with N, P and K; Fo = unfertilized.
A PCA biplot was used to cluster the three replicate samples of each trash management soil from Mount Edgecombe, on the basis of the compositional relationship among the replicate subsamples. Exchange acidity, P, K, pH and Mg were all highly correlated with PC1 whereas organic C, total cations ECEC and Ca were correlated with PC2. PC1 accounted for 69.6%, PC 2 for 23.2%, and cumulatively, 92.8% of the total variance in the soil data (Figure 3.5). A lower pH was associated with soils from fertilized treatments of both TF and BtoF than with those from the unfertilized treatments TFo and BtoFo. TFo soils were also correlated with high levels of Ca, ECEC and Mg. In contrast, fertilized soils TF and BtoF were associated with higher levels of P, K and acidity than the unfertilized soils. Both trashed treatments, TFo and TF, were associated with higher levels of organic C than the burnt cane harvested managements, BtoFo and BtoF.
-1.0 -0.5 0.0 0.5 1.0 -1.0
-0.5 0.0 0.5 1.0
P K
Ca
Mg Acidity
Cations pH
OrgC
TF1
TF2 TF3 TFo1
TFo3 TFo2
BtoF1 BtoF2
BtoF3 BtoFo1
BtoFo2
BtoFo3
SPECIES
SAMPLES
TF TFo BtoF BtoFo
FIGURE 3.5 Plot of samples and soil variables along the first two axes of a standardised and centred PCA of different land treatments at Mount Edgecombe.
The PC1 (horizontal) and PC2 (vertical) components accounted for 69.6% and 23.2%
respectively, and cumulatively, for 92.8% of the total variance in the soil data.
Key: T = green cane harvested with trash retention; Bto = burnt with harvest residues removed; F = fertilized annually with N, P and K; Fo = unfertilized.
A two-way ANOVA of the main effects of (i) trash mulch/no mulch, (ii) fertilizer/no fertilizer and (iii) the interaction of trash × fertilizer on soil variables, showed that there were no significant interactive effects of trash × fertilizer on any of the selected soil variables. However, fertilizer addition had a significant effect on pH, P, K, and Mg (p < 0.001), Ca (p = 0.008), ECEC (p = 0.005), exchange acidity (p = 0.003) and organic C (p = 0.034). The effects of trashing were seen only on organic C (p <
0.001), ECEC (p = 0.004) and Ca (p = 0.016).
CCA analysis showed the effects of selected soil physicochemical variables on bacterial community composition at site 2, (Figure 3.6). Eigen values for axes 1 and 2 were 0.228 and 0.160 respectively. CCA1 accounted for 30.1% and CCA2 for 21.1%
of the total variability, and for 58.7% and 41.3% respectively, (cumulatively 100%) of the variability in bacterial community composition related to the selected soil variables. To reduce collinearity, variables were by forward selection. The soils were significantly correlated with variation on axis 1 (p = 0.004) and along all canonical axes (p = 0.002). Organic C was closely correlated with CCA1 and Mg with CCA2.
FIGURE 3.6 Plot of samples (classified by land treatment) and soil variables along the first two axes of a CCA of the effect of selected soil variables on bacterial composition (band presence) at Mount Edgecombe.
Soils were significantly related to variation on the first axis (p = 0.004) and along all the canonical axes (p = 0.002) (Monte Carlo Permutation test: n = 499).
Key: T = green cane harvested with trash retention; Bto = burnt with harvest residues removed; F = fertilized annually with N, P and K; Fo = unfertilized.
-1.0 -0.5 0.0 0.5 1.0 1.5
-1.0 -0.5 0.0 0.5 1.0 1.5
Mg
Organic C
BtoF
BtoF2 BtoF3
BtoFo1
BtoFo2
BtoFo3
TF1
TF2 TF3
TFo1
TFo2 TFo3
ENV. VARIABLES
SAMPLES
BtoF BtoFo TF TFo
CCA1 (30.1%)
CCA2 (21.1%)
The statistical significance of the relationship between environmental variables and variation in the DGGE profiles was tested by the Monte Carlo permutation test (n = 499). Organic C was shown to be the most significant variable affecting the bacterial communities at Mount Edgecombe, followed by Mg. These variables together accounted for 100% of the total variance explained by all the soil properties tested (Table 3.10). Correlations between the soil variables used in the CCA and the ordination axes are shown in Table 3.11.
TABLE 3.10 Conditional effects of variables in a stepwise selection test in the CCA of soils on bacterial community composition at Mount Edgecombe
Variable Eigenvalue P F
Organic C 0.23 0.002 4.29
Mg 0.16 0.006 3.91
K 0.08 0.112 2.21
P 0.06 0.156 1.76
Ca 0.02 0.612 0.76
Exchange acidity 0.03 0.618 0.67
pH 0.01 0.756 0.46
ECEC 0.01 0.996 0.04
Note: All variables (in bold) were used in the CCA (significant effects on composition).
TABLE 3.11 Correlation between soil variables used in the CCA and compositional gradients (ordination axes)
Variable CCA1 CCA2
Mg -0.2321 -0.9079
Organic C 0.9252 0.0654