Soil Biological Fertility and Bacterial Community Response to Land Use Intensity: A Case Study in the Mediterranean Area
Abstract
:1. Introduction
2. Materials and Methods
2.1. Measurements
2.2. Soil Microbial Biomass
2.3. Microbial Respiration
2.4. Biological Fertility Index
2.5. Soil DNA Extraction
2.6. Real-Time Quantitative PCR Analysis (qPCR)
2.7. Analyses of 16S rRNA Gene Sequence, Species Richness and Diversity
2.8. Statistical Analysis
3. Results
3.1. Chemical and Microbial Parameters
3.2. Soil Biological Fertility Index
3.3. Nucleic Acid Concentration
3.4. Bacterial Quantification
3.5. Correlation Coefficients among Parameters
3.6. Bacterial α Diversity and Community Composition
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Land Use | Area (Ha) | Cultivation History (Year) | Management | Irrigation and Fertilization |
---|---|---|---|---|
Cereal field | 2.4 | 7 | Soil tillage (40 cm), residues removal from the field, integrated pest management, | No irrigation (dryland farming), chemical fertilization before seeding |
Grass-covered vineyard | 4.9 | 10 | No tillage, residues left on the field, integrated pest management, | Drip irrigation with continuous mixed fertilization (chemical–organic) |
Cherry farm | 1.2 | 10 | Soil tillage (40 cm), residues removal from the farm, integrated pest management | Drip irrigation with continuous chemical fertilization |
Parameters | Scores | ||||
---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | |
Soil organic matter, SOM (%) | <1.0 | ≥1.0 | >1.5 | >2.0 | >3.0 |
≤1.5 | ≤2.0 | ≤3.0 | |||
Basal soil respiration, BSR (mg CO2–C kg−1 soil d−1) | <5 | ≥5 | >10 | >15 | >20 |
≤10 | ≤15 | ≤20 | |||
Cumulative soil respiration, CSR (mg CO2–C kg−1 soil) | <100 | ≥100 | >250 | >400 | >600 |
≤250 | ≤400 | ≤600 | |||
Microbial biomass carbon, MBC (mg C kg−1 soil) | <100 | ≥100 | >200 | >300 | >400 |
≤200 | ≤300 | ≤400 | |||
Metabolic quotient, qCO2 (mg CO2–C 10−2 h−1 mg MBC −1) | ≥0.4 | ≥0.4 | <0.3 | <0.2 | <0.1 |
≤0.3 | ≥0.2 | ≥0.1 | |||
Mineralization quotient, qM (%) | <1.0 | ≥1 | >2 | >3 | >4 |
≤2 | ≤3 | ≤4 | |||
Classes of the Biological Fertility Index (BFI) | |||||
Fertility class | I | II | III | IV | V |
Stress | Pre-stress (alarm) | Medium | Good | High | |
BFI scores sum | 6 | 7–12 | 13–18 | 19–24 | 25–30 |
Parameter | Unit | Land Use | ||
---|---|---|---|---|
Cereal Field | Grass-Covered Vineyard | Cherry Farm | ||
Soil pH | 7.95 ± 0.04 | 7.95 ± 0.01 | 7.98 ± 0.04 | |
Soil texture | Sandy Clay Loam | |||
SOC | % | 1.69 ± 0.17 a | 1.82 ± 0.13 a | 1.36 ± 0.11 b |
SOM | % | 2.91 ± 0.29 a | 3.13 ± 0.22 a | 2.35 ± 0.19 b |
MBC | μg C g−1 soil | 197.08 ± 18.76 a | 201.92 ± 20.81 a | 186.45 ± 14.19 b |
CUE | μg C g−1 soil | 117.06 ± 1.14 b | 110.53 b ± 4.96 | 138.08 a ± 12.98 |
BSR | mg CO2–C kg−1 soil d−1 | 9.73 ± 0.87 b | 11.84 ± 0.66 a | 10.51 ± 1.11 ab |
CSR | mg CO2–C kg−1 soil | 153.91 ± 10.77 b | 214.49 ± 13.69 a | 226.90 ± 18.88 a |
qCO2 | mg CO2–C 10−2 h−1 mg MBC−1 | 0.050 ± 0.004 b | 0.058 ± 0.005 a | 0.056 a ± 0.004 |
qM | % | 0.91 ± 0.08 c | 1.17 ± 0.10 b | 1.66 ± 0.15 a |
Nucleic acid concentration | ngµL−1 0.5 g−1 | 154.8 ± 6.01 b | 160.6 ± 5.49 a | 143.7 ±5.94 c |
16S rRNA- CN | g−1 DS | 8.06 ± 1.28 × 107 a | 1.82 ± 0.51 × 107 c | 5.18± 0.32 × 107 b |
Land Use | Equation | R Square | Constant | b1 | b2 | b3 |
---|---|---|---|---|---|---|
Cereal field | Cubic | 0.98 ** | 18.28 | 1.57 | −0.18 | 0.004 |
Grass-covered vineyard | Cubic | 0.95 ** | 38.79 | −0.75 | −0.12 | 0.004 |
Cherry farm | Cubic | 0.99 ** | 61.92 | −8.11 | 0.44 | −0.008 |
Land Use | SOM | BSR | CSR | MBC | qCO2 | qM | BFI Score | BFI Class |
---|---|---|---|---|---|---|---|---|
Cereal field | 4 | 2 | 2 | 2 | 5 | 1 | 16 | III (medium) |
Grass-covered vineyard | 5 | 3 | 2 | 3 | 5 | 2 | 20 | IV (good) |
Cherry farm | 4 | 3 | 2 | 2 | 5 | 2 | 18 | III (medium) |
Model | Independent Variables | Standardized Coefficients (Beta) | t | Significance Level | |
---|---|---|---|---|---|
1 | (Constant) | 1.059 | 0.401 | ||
SOM | 1.119 | 0.932 | 0.450 | ||
BSR | 0.501 | 0.603 | 0.608 | ||
CSR | 1.230 | 1.352 | 0.309 | ||
MBC | −1.411 | −0.550 | 0.638 | ||
qCO2 | −1.448 | −0.625 | 0.596 | ||
qM | −0.466 | −0.980 | 0.430 | ||
2 | (Constant) | 3.756 | 0.033 | ||
SOM | 0.519 | 1.181 | 0.323 | ||
BSR | 0.208 | 0.372 | 0.735 | ||
CSR | 0.792 | 2.061 | 0.131 | ||
qCO2 | −0.206 | −0.454 | 0.680 | ||
qM | −0.426 | −1.035 | 0.377 | ||
3 | (Constant) | 4.827 | 0.008 | ||
SOM | 0.650 | 2.782 | 0.050 | ||
CSR | 0.896 | 3.835 | 0.019 | ||
qCO2 | −0.046 | −0.363 | 0.735 | ||
qM | −0.445 | −1.229 | 0.286 | ||
4 | (Constant) | 5.318 | 0.003 | ||
SOM | 0.641 | 3.035 | 0.029 | ||
CSR | 0.903 | 4.269 | 0.008 | ||
qM | −0.484 | −1.544 | 0.183 | ||
5 | (Constant) | 5.703 | 0.001 | ||
SOM | 0.931 | 8.765 | 0.000 | ||
CSR | 0.612 | 5.761 | 0.001 | ||
Model Summary | |||||
Model | R | R2 | Adjusted R2 | Std. Error of the Estimate | |
1 | 0.983 | 0.966 | 0.863 | 0.46969 | |
2 | 0.980 | 0.961 | 0.895 | 0.41147 | |
3 | 0.979 | 0.959 | 0.918 | 0.36447 | |
4 | 0.978 | 0.957 | 0.932 | 0.33132 | |
5 | 0.968 | 0.937 | 0.916 | 0.36752 |
Parameters | SOM | BSR | CSR | MBC | qCO2 | qM | Nucleic Acid Concentration | 16S rRNA- CN |
---|---|---|---|---|---|---|---|---|
SOM | 1 | |||||||
BSR | 0.25 ns | 1 | ||||||
CSR | −0.27 ns | 0.60 ns | 1 | |||||
MBC | 0.78 * | −0.10 ns | −0.09 ns | 1 | ||||
qCO2 | −0.41 ns | 0.68 * | 0.44 ns | −0.79 * | 1 | |||
qM | −0.76 * | 0.27 ns | 0.76 * | −0.58 ns | 0.59 ns | 1 | ||
Nucleic acid concentration | 0.91 ** | 0.31 ns | −0.21 ns | 0.68 * | −0.33 ns | −0.69 * | 1 | |
16S rRNA- CN | −0.15 ns | −0.71 * | −0.68 * | −0.00 ns | −0.45 ns | −0.25 ns | −0.27 ns | 1 |
Land Use | CHAO1 | Simpson | Shannon | Goods-Coverage |
---|---|---|---|---|
Cherry farm | 4882.3 ± 108.95 a | 0.85 ± 0.00 a | 9.93 ± 0.8 a | 0.99 ± 0.00 a |
Cereal field | 4558.8 ± 97.04 a | 0.87 ± 0.00 a | 9.84 ± 0.05 a | 0.99 ± 0.00 a |
Grass-covered vineyard | 4973.2 ± 61.94 a | 0.85 ± 0.00 a | 10.14 ± 0.4 a | 0.99 ± 0.00 a |
(A) | Land Use | |||
Phylum | Cherry Farm (%) | Cereal Field (%) | Grass-Covered Vineyard (%) | |
Proteobacteria | 26.38 ± 0.58 b | 29.29 ± 0.79 a | 26.43 ± 0.23 b | |
Actinobacteria | 22.88 ± 0.25 b | 23.71 ± 1.05 b | 25.51 ± 1.41 a | |
Bacteroidetes | 7.58 ± 0.99 a | 8.82 ± 0.46 a | 6.88 ± 0.35 a | |
Planctomycetes | 5.03 ± 0.19 a | 4.13 ± 0.21 ab | 3.98 ± 0.28 b | |
Verrucomicrobia | 4.67 ± 0.11 ab | 5.28 ± 0.51 a | 3.09 ± 0.11 b | |
Chloroflexi | 4.33 ± 0.66 a | 3.85 ± 0.27 a | 3.89 ± 0.23 a | |
Firmicutes | 3.25 ± 0.39 ab | 2.32 ± 0.20 b | 3.45 ± 0.14 a | |
Gemmatimonadetes | 2.00 ± 0.04 a | 1.31 ± 0.05 c | 1.64 ± 0.10 b | |
Acidobacteria | 1.23 ± 0.07 b | 0.95 ± 0.03 c | 1.38 ± 0.02 a | |
(B) | ||||
Phylum | Family | Cherry Farm (%) | Cereal Field (%) | Grass-Covered Vineyard (%) |
Actinobacteria | Rubrobacteraceae | 7.20 ± 0.35 b | 6.09 ± 0.27 b | 8.68 ± 0.28 a |
Proteobacteria | Bradyrhizobiaceae | 2.33 ± 0.29 a | 2.56 ± 0.08 a | 2.78 ± 0.13 a |
Firmicutes | Bacillaceae | 2.10 ± 0.31 a | 1.23 ± 0.14 b | 2.02 ± 0.16 a |
Actinobacteria | Solirubrobacteraceae | 2.56 ± 0.58 a | 1.87 ± 0.02 b | 2.42 ± 0.19 a |
Bacteroidetes | Chitinophagaceae | 2.75 ± 0.24 b | 2.81 ± 0.02 b | 3.87 ± 0.32 a |
Planctomycetes | Gemmataceae | 2.55 ± 0.04 a | 1.26 ± 0.10 b | 1.61 ± 0.13 b |
Gemmatimonadetes | Gemmatimonadaceae | 2.00 ± 0.04 a | 1.31 ± 0.05 c | 1.64 ± 0.10 b |
Proteobacteria | Rhodospirillaceae | 1.66 ± 0.08 b | 1.97 ± 0.04 ab | 2.59 ± 0.17 a |
Proteobacteria | Sinobacteraceae | 2.04 ± 0.08 a | 2.11 ± 0.22 a | 1.37 ± 0.12 b |
Verrucomicrobia | Pedosphaeraceae | 2.31 ± 0.33 a | 1.65 ± 0.05 b | 8.68 ± 0.28 a |
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Yaghoubi Khanghahi, M.; Murgese, P.; Strafella, S.; Crecchio, C. Soil Biological Fertility and Bacterial Community Response to Land Use Intensity: A Case Study in the Mediterranean Area. Diversity 2019, 11, 211. https://doi.org/10.3390/d11110211
Yaghoubi Khanghahi M, Murgese P, Strafella S, Crecchio C. Soil Biological Fertility and Bacterial Community Response to Land Use Intensity: A Case Study in the Mediterranean Area. Diversity. 2019; 11(11):211. https://doi.org/10.3390/d11110211
Chicago/Turabian StyleYaghoubi Khanghahi, Mohammad, Pasqua Murgese, Sabrina Strafella, and Carmine Crecchio. 2019. "Soil Biological Fertility and Bacterial Community Response to Land Use Intensity: A Case Study in the Mediterranean Area" Diversity 11, no. 11: 211. https://doi.org/10.3390/d11110211