Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment
Abstract
:1. Introduction
2. Materials and Methods
2.1. Site Description and Sample Collection
2.2. Characterization of Sediment Physicochemical Properties
2.3. DNA Extraction, PCR, and Illumina MiSeq Sequencing
2.4. The Diversity and Composition of gcd-Harboring Bacterial Communities Were Assessed Using High-Throughput Sequencing Technique
2.5. Statistical Analysis
3. Results and Discussion
3.1. Physicochemical Properties of the Sediments and Overlying Water
3.2. OTU Classification and Determination and Alpha Diversity of the gcd Gene in Sediments
3.3. Changes in Composition of gcd-Harboring Bacterial Communities
3.3.1. Comparison of gcd-Harboring Bacterial Community Composition Based on Classification Level
3.3.2. Analysis of the Composition of gcd-Harboring Bacterial Communities Based on OTU Level
3.3.3. Comparative Analysis of gcd-Harboring Bacterial Community Composition Based on Beta Diversity
3.4. Correlation between gcd-Harboring Bacterial Communities and Environmental Conditions in the Sediment of Sancha Lake
3.4.1. Linking gcd-Harboring Bacterial Abundance, Diversity, and Community Structure with Environmental Factors
3.4.2. Correlation between Spatial Distribution Characteristics of gcd-Harboring Bacterial Communities and Environmental Conditions
4. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample Site | Geographical Coordinates | Depth (m) | Hydrophyte | Description |
---|---|---|---|---|
L1 | 30°14′52″ N | 13 | Large quantity | Concentrated area of fenced breeding |
104°16′15″ E | ||||
L2 | 30°14′28″ N | 4 | Large quantity | Tail water area of the reservoir |
104°15′32″ E | ||||
L3 | 30°17′25″ N | 26 | Small quantity | Relatively concentrated area of fenced breeding |
104°16′31″ E | ||||
L4 | 30°18′15″ N | 17 | Large quantity | Area with intense human activity |
104°14′31″ E | ||||
L5 | 30°18′18″ N | 30 | Small quantity | Dense area of cage breeding |
104°16′2″ E | ||||
L6 | 30°19′15″ N | 19 | Moderate quantity | Main water entry area of the lake |
104°15′14″ E |
Season | Location | pH | DO (mg·L−1) | T (°C) | DTP (mg·L−1) | TOC (mg·g−1) | TN (mg·g−1) | NH3-N (mg·g−1) | TP (mg·g−1) | OP | IP (mg·g−1) | HCl–P (mg·g−1) | NaOH–P (mg·g−1) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Spring | L1 | 7.38 ± 0.11 | 6.4 ± 1.0 | 13.0 ± 0.3 | 0.088 ± 0.025 | 48.1 ± 5.0 | 6.46 ± 0.46 | 0.387 ± 0.030 | 1.036 ± 0.100 | 0.242 ± 0.042 | 0.790 ± 0.090 | 0.590 ± 0.01 | 0.148 ± 0.008 |
L2 | 7.52 ± 0.13 | 6.4 ± 0.9 | 12.9 ± 0.1 | 0.092 ± 0.040 | 36.9 ± 4.0 | 4.30 ± 0.30 | 0.057 ± 0.007 | 0.715 ± 0.015 | 0.229 ± 0.090 | 0.617 ± 0.017 | 0.550 ± 0.010 | 0.047 ± 0.010 | |
L3 | 7.52 ± 0.10 | 5.8 ± 0.2 | 12.6 ± 0.3 | 0.035 ± 0.005 | 76.6 ± 8.0 | 10.15 ± 1.00 | 0.017 ± 0.007 | 3.069 ± 0.092 | 0.562 ± 0.062 | 2.687 ± 0.087 | 2.248 ± 0.100 | 0.367 ± 0.060 | |
L4 | 7.46 ± 0.10 | 6.7 ± 1.1 | 13.2 ± 0.2 | 0.069 ± 0.002 | 55.0 ± 6.0 | 4.87 ± 0.87 | 0.021 ± 0.000 | 1.120 ± 0.120 | 0.189 ± 0.046 | 0.824 ± 0.004 | 0.786 ± 0.050 | 0.099 ± 0.009 | |
L5 | 7.45 ± 0.09 | 5.1 ± 0.5 | 12.6 ± 0.2 | 0.033 ± 0.003 | 55.6 ± 5.0 | 6.57 ± 0.50 | 0.067 ± 0.007 | 1.376 ± 0.109 | 0.311 ± 0.011 | 1.162 ± 0.10 | 0.556 ± 0.010 | 0.340 ± 0.020 | |
L6 | 7.67 ± 0.21 | 9.0 ± 1.0 | 12.7 ± 0.3 | 0.065 ± 0.005 | 25.4 ± 3.0 | 1.66 ± 0.06 | 0.096 ± 0.006 | 0.696 ± 0.100 | 0.099 ± 0.009 | 0.481 ± 0.090 | 0.406 ± 0.006 | 0.077 ± 0.007 | |
Autumn | L1 | 7.54 ± 0.10 | 5.6 ± 0.1 | 15.4 ± 0.4 | 0.057 ± 0.007 | 47.5 ± 2.0 | 4.49 ± 0.49 | 0.244 ± 0.034 | 2.874 ± 0.074 | 0.317 ± 0.017 | 2.603 ± 0.060 | 1.088 ± 0.088 | 0.172 ± 0.002 |
L2 | 6.89 ± 0.19 | 5.5 ± 0.1 | 17.2 ± 1.0 | 0.051 ± 0.002 | 34.8 ± 1.8 | 3.18 ± 0.28 | 0.035 ± 0.005 | 1.153 ± 0.053 | 0.444 ± 0.021 | 0.782 ± 0.030 | 0.450 ± 0.050 | 0.395 ± 0.005 | |
L3 | 7.11 ± 0.10 | 4.1 ± 0.1 | 14.6 ± 0.6 | 0.012 ± 0.001 | 83.2 ± 3.2 | 10.77 ± 1.74 | 0.539 ± 0.039 | 5.005 ± 0.202 | 0.609 ± 0.041 | 3.882 ± 0.080 | 3.517 ± 0.017 | 1.007 ± 0.007 | |
L4 | 7.16 ± 0.06 | 5.5 ± 0.2 | 16.3 ± 0.9 | 0.055 ± 0.005 | 54.2 ± 2.4 | 3.99 ± 0.41 | 0.141 ± 0.004 | 2.661 ± 0.060 | 0.295 ± 0.010 | 1.897 ± 0.070 | 1.949 ± 0.049 | 0.222 ± 0.022 | |
L5 | 7.02 ± 0.02 | 4.5 ± 0.1 | 14.1 ± 0.1 | 0.015 ± 0.005 | 47.8 ± 2.0 | 5.25 ± 0.79 | 0.071 ± 0.001 | 1.454 ± 0.054 | 0.369 ± 0.009 | 1.051 ± 0.051 | 0.554 ± 0.054 | 0.611 ± 0.011 | |
L6 | 7.18 ± 0.18 | 5.9 ± 0.3 | 16.5 ± 0.5 | 0.025 ± 0.005 | 32.9 ± 1.7 | 2.28 ± 0.18 | 0.265 ± 0.006 | 0.629 ± 0.029 | 0.167 ± 0.007 | 0.444 ± 0.024 | 0.343 ± 0.033 | 0.104 ± 0.004 |
Season | Sampling Site | Reads | Chao1 | Shannon | Coverage | OTUs | No. of Phyla | No. of Classes | No. of Orders | No. of Families | No. of Genera |
---|---|---|---|---|---|---|---|---|---|---|---|
spring | L1 | 32,585 ± 150 | 234.55 ± 33.05 | 3.365 ± 0.040 | 0.9993 ± 0.0004 | 226 ± 6 | 6 | 9 | 13 | 19 | 22 |
L2 | 23,251 ± 120 | 156.18 ± 21.04 | 2.777 ± 0.067 | 0.9985 ± 0.0012 | 150 ± 4 | 5 | 9 | 12 | 15 | 23 | |
L3 | 12,834 ± 60 | 98.60 ± 19.04 | 1.539 ± 0.030 | 0.9986 ± 0.0007 | 85 ± 2 | 2 | 4 | 7 | 11 | 16 | |
L4 | 41,828 ± 200 | 185.27 ± 29.04 | 2.622 ± 0.064 | 0.9993 ± 0.0005 | 158 ± 4 | 1 | 3 | 5 | 10 | 17 | |
L5 | 12,151 ± 60 | 140.69 ± 18.09 | 3.167 ± 0.071 | 0.9983 ± 0.0002 | 130 ± 3 | 3 | 5 | 7 | 10 | 13 | |
L6 | 13,357 ± 65 | 322.14 ± 36.64 | 3.397 ± 0.075 | 0.9958 ± 0.0017 | 291 ± 7 | 3 | 6 | 9 | 17 | 32 | |
autumn | L1 | 95,695 ± 50 | 163.05 ± 23.04 | 2.943 ± 0.040 | 0.9978 ± 0.0014 | 154 ± 4 | 5 | 8 | 12 | 16 | 22 |
L2 | 10,880 ± 54 | 143.96 ± 20.05 | 1.259 ± 0.014 | 0.9983 ± 0.0004 | 121 ± 3 | 2 | 4 | 5 | 5 | 15 | |
L3 | 3199 ± 10 | 43.00 ± 1.00 | 1.307 ± 0.016 | 0.9974 ± 0.0000 | 29 ± 0 | 1 | 3 | 5 | 6 | 10 | |
L4 | 10,852 ± 54 | 80.20 ± 3.04 | 1.939 ± 0.029 | 0.9984 ± 0.0006 | 62 ± 2 | 1 | 3 | 5 | 7 | 10 | |
L5 | 30,857 ± 150 | 139.38 ± 17.04 | 2.432 ± 0.039 | 0.9994 ± 0.0001 | 118 ± 3 | 2 | 3 | 5 | 8 | 12 | |
L6 | 18,415 ± 92 | 157.53 ± 22.04 | 2.273 ± 0.027 | 0.9992 ± 0.0005 | 152 ± 3 | 5 | 8 | 13 | 21 | 23 |
Environmental Factor | PH | DO | T | TN | TOC | TP | HCl-P | NaOH-P | DTP |
---|---|---|---|---|---|---|---|---|---|
OTUs | 0.422 a/0.172 b | 0.346/0.271 | 0.239/0.454 | –0.577/0.05 * | –0.631/0.028 * | –0.698/0.012 * | –0.687/0.014 * | –0.624/0.03 * | 0.915/0.000 ** |
Chao1 | 0.043/0.894 | 0.391/0.211 | –0.063/0.846 | –0.604/0.037 * | –0.6/0.039 * | –0.619/0.032 * | –0.653/0.021 * | –0.32/0.311 | 0.643/0.024 * |
Shannon | 479/0.115 | 0.251/0.432 | 0.278/0.382 | –0.574/0.051 | –0.619/0.032 * | –702/0.011 * | –0.672/0.017 * | –0.635/0.26 | 0.921/0.000 ** |
No. of filtered reads | 0.371/0.236 | 0.907/0.002 ** | 0.12/0.711 | –0.093/0.773 | –0.191/0.553 | –0.464/0.129 | –0.457/0.135 | –514/0.088 | 0.602/0.039 * |
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Li, Y.; Zhang, J.; Gong, Z.; Xu, W.; Mou, Z. Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment. Int. J. Environ. Res. Public Health 2019, 16, 1. https://doi.org/10.3390/ijerph16010001
Li Y, Zhang J, Gong Z, Xu W, Mou Z. Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment. International Journal of Environmental Research and Public Health. 2019; 16(1):1. https://doi.org/10.3390/ijerph16010001
Chicago/Turabian StyleLi, Yong, Jianqiang Zhang, Zhiliang Gong, Wenlai Xu, and Zishen Mou. 2019. "Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment" International Journal of Environmental Research and Public Health 16, no. 1: 1. https://doi.org/10.3390/ijerph16010001