Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions
Abstract
:1. Introduction
2. Materials and Methods
2.1. Soil Sampling
2.2. DNA Extraction and Metagenomic Sequencing
2.3. Statistical Analysis
3. Results
3.1. Soil Chemical Properties
3.2. Soil Microbiome Community
3.3. Soil Microbiome Functions
3.4. The Soil Microbiome Participating in N Cycling
4. Discussion
4.1. Soil Chemistry Properties
4.2. Soil Microbiome Community and Function
4.3. The Soil Microbiome Participating in the N Cycle
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
Samples | Counting Numbers (×105) | Total Length (bp) (×108) | Largest Length (bp) (×104) | N50 (bp) | Mapped (%) |
---|---|---|---|---|---|
CK | 1.92 ± 0.23 a | 1.34 ± 0.26 b | 4.48 ± 0.17 b | 716.00 ± 29.87 b | 16.56 ± 1.98 b |
NPK | 2.39 ± 0.14 ab | 2.01 ± 0.11 a | 6.03 ± 0.26 a | 779.67 ± 1.53 a | 20.39 ± 1.00 a |
NPK+S0.5 | 2.66 ± 0.10 a | 2.16 ± 0.98 a | 5.82 ± 0.12 a | 758.67 ± 25.42 a | 19.81 ± 0.60 a |
S0.5 | 1.82 ± 0.50 a | 1.13 ± 0.13 c | 4.46 ± 0.11 b | 694.00 ± 14.00 b | 15.26 ± 2.37 b |
DEG Set | DEG Numbers | High Abundance | Low Abundance | COG | GO | KEGG | NR | Pfam | SwissProt |
---|---|---|---|---|---|---|---|---|---|
CK vs. NPK | 1137 | 582 | 555 | 295 | 198 | 173 | 626 | 423 | 263 |
CK vs. NPK+S0.5 | 304 | 153 | 151 | 38 | 27 | 16 | 84 | 64 | 39 |
CK vs. S0.5 | 234 | 161 | 73 | 18 | 19 | 16 | 64 | 46 | 29 |
NPK vs. S0.5 | 1581 | 702 | 879 | 464 | 330 | 310 | 885 | 649 | 444 |
pH | MC | SOM | AP | A-K | NH4+-N | NO3−-N | T-P | T-K | T-N | |
---|---|---|---|---|---|---|---|---|---|---|
Proteobacteria | 0.74 | −0.66 | −0.02 | −0.53 | 0.85 | 0.72 | −0.41 | −0.65 | −0.23 | −0.19 |
Acidobacteria | −0.82 | 0.61 | 0.03 | 0.63 | −0.86 | −0.70 | 0.48 | 0.73 | 0.18 | 0.27 |
Firmicutes | −0.07 | −0.06 | −0.67 | 0.19 | −0.06 | −0.14 | 0.63 | −0.08 | −0.95 * | −0.23 |
Ascomycota | −0.90 | −0.03 | −0.04 | 0.970 * | −0.49 | −0.29 | 0.81 | 0.87 | −0.39 | 0.60 |
Basidiomycota | 0.95 | −0.22 | 0.19 | −0.94 | 0.70 | 0.52 | −0.90 | −0.85 | 0.43 | −0.44 |
Mucoromycota | −0.76 | 0.29 | −0.52 | 0.76 | −0.66 | −0.58 | 0.99 * | 0.58 | −0.74 | 0.14 |
Crenarchaeota | −0.09 | 0.63 | 0.14 | −0.16 | −0.45 | −0.45 | −0.24 | 0.06 | 0.60 | −0.16 |
Euryarchaeota | −0.07 | 0.32 | 0.48 | −0.11 | −0.20 | −0.14 | −0.44 | 0.14 | 0.84 | 0.11 |
Thaumarchaeota | −0.88 | 0.69 | −0.34 | 0.71 | −0.97 * | −0.86 | 0.82 | 0.69 | −0.27 | 0.11 |
Bradyrhizobium | −0.14 | −0.03 | −0.67 | 0.25 | −0.12 | −0.18 | 0.68 | −0.03 | −0.96 * | −0.20 |
Streptomyces | −0.93 | −0.09 | 0.37 | 0.97 * | −0.44 | −0.17 | 0.52 | 0.99 ** | 0.09 | 0.83 |
Mycobacterium | −0.76 | 0.29 | −0.52 | 0.77 | −0.67 | −0.58 | 0.99 | 0.58 | −0.74 | 0.14 |
Sordaria | 0.62 | −0.66 | −0.10 | −0.39 | 0.77 | 0.65 | −0.24 | −0.55 | −0.38 | −0.15 |
Fusarium | −0.33 | −0.79 | 0.43 | 0.59 | 0.35 | 0.55 | 0.18 | 0.51 | −0.11 | 0.79 |
Paracoccidioides | 0.33 | 0.79 | −0.43 | −0.59 | −0.35 | −0.55 | −0.18 | −0.51 | 0.11 | −0.79 |
Halorubrum | −0.19 | −0.32 | −0.39 | 0.37 | 0.07 | 0.08 | 0.59 | 0.12 | −0.82 | 0.10 |
Halococcus | −0.76 | 0.29 | −0.52 | 0.76 | −0.66 | −0.58 | 0.99 * | 0.58 | −0.74 | 0.14 |
Haloferax | 0.43 | −0.98 | 0.70 | −0.18 | 0.93 | 0.99 | −0.63 | −0.14 | 0.38 | 0.48 |
Alphabaculovirus | −0.67 | −0.30 | −0.05 | 0.83 | −0.19 | −0.02 | 0.72 | 0.67 | −0.52 | 0.57 |
Jd18virus | 0.50 | −0.86 | 0.82 | −0.31 | 0.90 | 0.96 * | −0.83 | −0.19 | 0.64 | 0.44 |
Betabaculovirus | 0.738 | −0.685 | 0.011 | −0.524 | 0.863 | 0.738 | −0.424 | −0.639 | −0.213 | −0.17 |
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Samples | Clean Reads (107) | Base Sum (1010) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|
CK | 3.65 ± 0.02 a | 1.09 ± 0.05 a | 97.38 ± 0.04 a | 93.15 ± 0.08 a | 63.67 ± 0.08 a |
NPK | 3.35 ± 0.02 a | 0.98 ± 0.04 a | 97.42 ± 0.01 a | 93.25 ± 0.02 a | 63.69 ± 0.18 a |
NPK+S0.5 | 3.81 ± 0.02 a | 1.14 ± 0.06 a | 97.39 ± 0.05 a | 93.16 ± 0.12 a | 64.14 ± 0.49 a |
S0.5 | 3.40 ± 0.02 a | 1.02 ± 0.05 a | 97.43 ± 0.06 a | 93.17 ± 0.05 a | 65.13 ± 1.52 a |
CK | NPK | NPK+S0.5 | S0.5 | ||
---|---|---|---|---|---|
(%) | (%) | (%) | (%) | ||
Bacteria | Proteobacteria | 51.89 ± 0.47 b | 57.32 ± 1.26 a | 51.85 ± 3.65 b | 51.71 ± 1.99 c |
Acidobacteria | 42.53 ± 0.27 b | 37.12 ± 1.36 c | 43.43 ± 3.66 a | 43.26 ± 1.78 a | |
Firmicutes | 1.16 ± 0.03 b | 1.24 ± 0.08 a | 1.22 ± 0.30 a | 1.13 ± 0.11 b | |
Fungi | Ascomycota | 87.40 ± 0.22 d | 87.81 ± 1.04 c | 89.77 ± 0.98 a | 88.62 ± 0.55 b |
Basidiomycota | 10.39 ± 0.43 b | 10.57 ± 0.83 a | 8.43 ± 0.93 d | 9.71 ± 0.41 c | |
Mucoromycota | 0.94 ± 0.26 a | 1.41 ± 0.22 a | 1.20 ± 0.33 a | 0.99 ± 0.21 a | |
Archaea | Crenarchaeota | 95.87 ± 0.03 c | 97.78 ± 0.05 a | 97.39 ± 0.09 b | 96.16 ± 0.22 bc |
Euryarchaeota | 2.56 ± 0.20 a | 1.08 ± 0.12 c | 1.45 ± 0.28 c | 2.17 ± 0.37 b | |
Thaumarchaeota | 1.46 ± 0.16 b | 1.01 ± 0.12 c | 1.05 ± 0.19 c | 1.51 ± 0.16 a | |
Bacteria | Bradyrhizobium | 7.66 ± 0.08 b | 10.33 ± 0.10 a | 10.75 ± 0.11 a | 6.75 ± 0.07 b |
Streptomyces | 7.34 ± 0.07 a | 6.8 ± 0.07 a | 7.86 ± 0.08 a | 7.64 ± 0.08 a | |
Mycobacterium | 3.78 ± 0.04 b | 4.13 ± 0.04 b | 4.96 ± 0.05 a | 3.84 ± 0.04 b | |
Fungi | Sordaria | 5.83 ± 0.06 b | 11.02 ± 0.11 a | 7.03 ± 0.07 b | 5.63 ± 0.06 b |
Fusarium | 2.41 ± 0.02 a | 2.64 ± 0.03 a | 2.58 ± 0.03 a | 3.15 ± 0.03 a | |
Paracoccidioides | 2.8 ± 0.03 a | 1.95 ± 0.02 b | 1.85 ± 0.02 b | 2.2 ± 0.02 b | |
Archaea | Halorubrum | 13.84 ± 0.14 a | 14.36 ± 0.14 a | 14.47 ± 0.12 a | 13.92 ± 0.09 a |
Halococcus | 9.48 ± 0.09 ab | 9.01 ± 0.09 b | 9.62 ± 0.10 a | 9.27 ± 0.09 ab | |
Haloferax | 6.85 ± 0.07 a | 7.1 ± 0.07 a | 6.88 ± 0.05 a | 7.04 ± 0.07 a | |
Viruses | Alphabaculovirus | 10.67 ± 0.11 a | 13.33 ± 0.13 a | 14.67 ± 0.15 a | 13 ± 0.13 a |
Jd18virus | 11.00 ± 0.11 a | 14.33 ± 0.14 a | 10.33 ± 0.10 a | 14.33 ± 0.14 a | |
Betabaculovirus | 1.00 ± 0.01 a | 2.00 ± 0.02 a | 1.33 ± 0.01 a | 1.33 ± 0.01 a |
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Li, Y.; Wang, C.; Wang, T.; Liu, Y.; Jia, S.; Gao, Y.; Liu, S. Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions. Land 2020, 9, 329. https://doi.org/10.3390/land9090329
Li Y, Wang C, Wang T, Liu Y, Jia S, Gao Y, Liu S. Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions. Land. 2020; 9(9):329. https://doi.org/10.3390/land9090329
Chicago/Turabian StyleLi, Yanan, Chengyu Wang, Tianye Wang, Yutao Liu, Shuxia Jia, Yunhang Gao, and Shuxia Liu. 2020. "Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions" Land 9, no. 9: 329. https://doi.org/10.3390/land9090329