Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area and Sample Collection
2.2. Physicochemical Analysis
2.3. DNA Extraction and Illumina Sequencing
2.4. Bioinformatic Analysis
2.5. Statistical Analysis
3. Results
3.1. Bacteria–Archaea Co-Occurrence Network Structure
3.2. Keystone Species and Their Taxonomic Distributions
3.3. The Topological Properties of the Co-Occurrence Networks
3.4. Potential Driving Factors of Bacteria–Archaea Co-Existence Patterns
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Networks | Number of Nodes | Number of Edges (Spearman’s r > 0.6, FDR-p < 0.01) | MD b | MDr b | CC b | CCr b | APL b | APLr b | σ b |
---|---|---|---|---|---|---|---|---|---|
Two seasons | 838 | 16,309 | 0.658 | 0.010 | 0.642 | 0.047 | 3.763 | 2.111 | 7.663 |
Spring (dry season) | 971 | 22,394 | 0.300 | 0.084 | 0.536 | 0.047 | 3.456 | 2.058 | 6.791 |
Autumn (wet season) | 1071 | 10,192 | 0.688 | 0.160 | 0.457 | 0.018 | 3.892 | 2.689 | 17.541 |
Jiulong River microbial network | 2194 | 44,680 | 0.672 | 0.087 | 0.511 | 0.0190 | 3.918 | 2.442 | 16.7628758 |
Jiulong River normal season subnetwork | 1036 | 16,912 | 0.620 | 0.110 | 0.572 | 0.0320 | 4.540 | 2.314 | 9.110737885 |
Jiulong River dry season subnetwork | 869 | 9078 | 0.423 | 0.151 | 0.526 | 0.0240 | 4.921 | 2.567 | 11.43265258 |
Jiulong River wet season subnetwork | 1145 | 6879 | 0.549 | 0.205 | 0.415 | 0.0100 | 6.107 | 3.093 | 21.01842148 |
Marine microbial network | NA | NA | NA | NA | 0.270 | 0.0440 | 2.990 | 2.620 | 5.37701429 |
Food webs | NA | NA | NA | NA | 0.02–0.43 | 0.03–0.33 | 1.33–3.74 | 1.41–3.73 | <1 |
Pollinator-plant networks | NA | NA | NA | NA | 0.72–1.00 | 0.08–1.00 | 1.00–2.31 | NA | NA |
Microbial database network | NA | NA | NA | NA | 0.501 | NA | 6.300 | NA | NA |
Functional microbial networks | NA | NA | NA | NA | 0.10–0.22 | 0.028–0.099 | 3.09–4.21 | 3.00–3.84 | <1 |
Caenorhabditis elegans, neural network | NA | NA | NA | NA | 0.28 | 0.05 | 2.65 | 2.25 | 4.754716981 |
Escherichia coli, metabolic network | NA | NA | NA | NA | 0.32–0.59 | 0.026–0.09 | 2.62–2.90 | 1.98–3.04 | <1 |
Power grid | NA | NA | NA | NA | 0.08 | 0.005 | 18.7 | 12.4 | 10.60962567 |
Actors | NA | NA | NA | NA | 0.79 | 0.00027 | 3.65 | 2.99 | 2396.854389 |
Internet, domain level | NA | NA | NA | NA | 0.18–0.3 | 0.001 | 3.70–3.76 | 6.18–6.36 | >295 |
Groups | Phylum-1 | Phylum-2 | Phylum-1-Node Number | Phylum-2-Node Number | Edge Number | O(%) | R(%) | O/R-Ratio |
---|---|---|---|---|---|---|---|---|
Both seasons | Actinobacteria | Actinobacteria | 94 | 94 | 732 | 4.49 | 1.25 | 3.60 |
Bacteroidetes | Bacteroidetes | 112 | 112 | 512 | 3.14 | 1.77 | 1.77 | |
Bathyarchaeota | Bathyarchaeota | 68 | 68 | 1642 | 10.07 | 0.65 | 15.50 | |
Cyanobacteria | Cyanobacteria | 43 | 43 | 112 | 0.69 | 0.26 | 2.67 | |
Euryarchaeota | Euryarchaeota | 104 | 104 | 804 | 4.93 | 1.53 | 3.23 | |
Planctomycetes | Planctomycetes | 29 | 29 | 94 | 0.58 | 0.12 | 4.98 | |
Proteobacteria | Proteobacteria | 200 | 200 | 1190 | 7.30 | 5.67 | 1.29 | |
Thaumarchaeota | Thaumarchaeota | 67 | 67 | 317 | 1.94 | 0.63 | 3.08 | |
Actinobacteria | Bacteroidetes | 94 | 112 | 826 | 5.06 | 3.00 | 1.69 | |
Actinobacteria | Chloroflexi | 94 | 13 | 155 | 0.95 | 0.35 | 2.73 | |
Actinobacteria | Cyanobacteria | 94 | 43 | 213 | 1.31 | 1.15 | 1.13 | |
Actinobacteria | Gemmatimonadetes | 94 | 5 | 95 | 0.58 | 0.13 | 4.35 | |
Actinobacteria | Planctomycetes | 94 | 29 | 410 | 2.51 | 0.78 | 3.23 | |
Actinobacteria | Proteobacteria | 94 | 200 | 1300 | 7.97 | 5.36 | 1.49 | |
Actinobacteria | Verrucomicrobia | 94 | 12 | 123 | 0.75 | 0.32 | 2.34 | |
Bacteroidetes | Chloroflexi | 112 | 13 | 104 | 0.64 | 0.42 | 1.54 | |
Bacteroidetes | Gemmatimonadetes | 112 | 5 | 88 | 0.54 | 0.16 | 3.38 | |
Bacteroidetes | Planctomycetes | 112 | 29 | 367 | 2.25 | 0.93 | 2.43 | |
Bacteroidetes | Proteobacteria | 112 | 200 | 1131 | 6.93 | 6.39 | 1.09 | |
Bacteroidetes | Verrucomicrobia | 112 | 12 | 132 | 0.81 | 0.38 | 2.11 | |
Bathyarchaeota | YNPFFA (archaea) | 68 | 4 | 151 | 0.93 | 0.08 | 11.94 | |
Bathyarchaeota | Euryarchaeota | 68 | 104 | 1544 | 9.47 | 2.02 | 4.69 | |
Bathyarchaeota | Thaumarchaeota | 68 | 67 | 465 | 2.85 | 1.30 | 2.19 | |
Chloroflexi | Proteobacteria | 13 | 200 | 166 | 1.02 | 0.74 | 1.37 | |
Cyanobacteria | Planctomycetes | 43 | 29 | 105 | 0.64 | 0.36 | 1.81 | |
Gemmatimonadetes | Proteobacteria | 5 | 200 | 152 | 0.93 | 0.29 | 3.27 | |
Planctomycetes | Proteobacteria | 29 | 200 | 521 | 3.19 | 1.65 | 1.93 | |
Proteobacteria | Verrucomicrobia | 200 | 12 | 165 | 1.01 | 0.68 | 1.48 | |
Spring | Actinobacteria | Actinobacteria | 74 | 74 | 218 | 0.97 | 0.57 | 1.70 |
Bacteroidetes | Bacteroidetes | 119 | 119 | 358 | 1.60 | 1.49 | 1.07 | |
Bathyarchaeota | Bathyarchaeota | 115 | 115 | 4240 | 18.93 | 1.39 | 13.60 | |
Euryarchaeota | Euryarchaeota | 137 | 137 | 1488 | 6.64 | 1.98 | 3.36 | |
Thaumarchaeota | Thaumarchaeota | 87 | 87 | 391 | 1.75 | 0.79 | 2.20 | |
Aenigmarchaeota | Bathyarchaeota | 8 | 115 | 453 | 2.02 | 0.20 | 10.35 | |
Aenigmarchaeota | Euryarchaeota | 8 | 137 | 260 | 1.16 | 0.23 | 4.99 | |
Altiarchaeota | Bathyarchaeota | 8 | 115 | 178 | 0.79 | 0.20 | 4.07 | |
Altiarchaeota | Euryarchaeota | 8 | 137 | 126 | 0.56 | 0.23 | 2.42 | |
Bathyarchaeota | YNPFFA (archaea) | 115 | 5 | 193 | 0.86 | 0.12 | 7.06 | |
Bathyarchaeota | Euryarchaeota | 115 | 137 | 3772 | 16.84 | 3.35 | 5.03 | |
Bathyarchaeota | Hadesarchaea | 115 | 2 | 144 | 0.64 | 0.05 | 13.17 | |
Bathyarchaeota | Lokiarchaeota | 115 | 10 | 204 | 0.91 | 0.24 | 3.73 | |
Bathyarchaeota | Miscellaneous-Euryarchaeotal -Group (MEG) | 115 | 5 | 127 | 0.57 | 0.12 | 4.64 | |
Bathyarchaeota | Thaumarchaeota | 115 | 87 | 1814 | 8.10 | 2.12 | 3.81 | |
Bathyarchaeota | Woesearchaeota | 115 | 23 | 146 | 0.65 | 0.56 | 1.16 | |
Euryarchaeota | Lokiarchaeota | 137 | 10 | 177 | 0.79 | 0.29 | 2.72 | |
Euryarchaeota | Miscellaneous-Euryarchaeotal -Group (MEG) | 137 | 5 | 113 | 0.50 | 0.15 | 3.47 | |
Euryarchaeota | Thaumarchaeota | 137 | 87 | 956 | 4.27 | 2.53 | 1.69 | |
Euryarchaeota | Woesearchaeota | 137 | 23 | 153 | 0.68 | 0.67 | 1.02 | |
Autumn | Acidobacteria | Acidobacteria | 33 | 33 | 70 | 0.69 | 0.09 | 7.45 |
Actinobacteria | Actinobacteria | 98 | 98 | 449 | 4.41 | 0.83 | 5.31 | |
Bacteroidetes | Bacteroidetes | 141 | 141 | 281 | 2.76 | 1.72 | 1.60 | |
Bathyarchaeota | Bathyarchaeota | 63 | 63 | 868 | 8.52 | 0.34 | 24.99 | |
Cyanobacteria | Cyanobacteria | 67 | 67 | 334 | 3.28 | 0.39 | 8.49 | |
Euryarchaeota | Euryarchaeota | 92 | 92 | 592 | 5.81 | 0.73 | 7.95 | |
Proteobacteria | Proteobacteria | 295 | 295 | 925 | 9.08 | 7.57 | 1.20 | |
Thaumarchaeota | Thaumarchaeota | 68 | 68 | 288 | 2.83 | 0.40 | 7.11 | |
Acidobacteria | Actinobacteria | 33 | 98 | 68 | 0.67 | 0.56 | 1.18 | |
Acidobacteria | Planctomycetes | 33 | 41 | 53 | 0.52 | 0.24 | 2.20 | |
Acidobacteria | Proteobacteria | 33 | 295 | 324 | 3.18 | 1.70 | 1.87 | |
Actinobacteria | Bacteroidetes | 98 | 141 | 381 | 3.74 | 2.41 | 1.55 | |
Actinobacteria | Chloroflexi | 98 | 23 | 64 | 0.63 | 0.39 | 1.60 | |
Actinobacteria | Planctomycetes | 98 | 41 | 77 | 0.76 | 0.70 | 1.08 | |
Bacteroidetes | Cyanobacteria | 141 | 67 | 179 | 1.76 | 1.65 | 1.07 | |
Bacteroidetes | Planctomycetes | 141 | 41 | 107 | 1.05 | 1.01 | 1.04 | |
Bathyarchaeota | YNPFFA (archaea) | 63 | 4 | 57 | 0.56 | 0.04 | 12.72 | |
Bathyarchaeota | Cyanobacteria | 63 | 67 | 209 | 2.05 | 0.74 | 2.78 | |
Bathyarchaeota | Euryarchaeota | 63 | 92 | 606 | 5.95 | 1.01 | 5.88 | |
Bathyarchaeota | Thaumarchaeota | 63 | 68 | 167 | 1.64 | 0.75 | 2.19 | |
Cyanobacteria | Planctomycetes | 67 | 41 | 65 | 0.64 | 0.48 | 1.33 | |
Euryarchaeota | Thaumarchaeota | 92 | 68 | 267 | 2.62 | 1.09 | 2.40 | |
Gemmatimonadetes | Proteobacteria | 7 | 295 | 56 | 0.55 | 0.36 | 1.52 | |
Nitrospirae | Proteobacteria | 5 | 295 | 66 | 0.65 | 0.26 | 2.52 |
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Du, W.; Li, J.; Zhang, G.; Yu, K.; Liu, S. Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River. Microorganisms 2024, 12, 1282. https://doi.org/10.3390/microorganisms12071282
Du W, Li J, Zhang G, Yu K, Liu S. Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River. Microorganisms. 2024; 12(7):1282. https://doi.org/10.3390/microorganisms12071282
Chicago/Turabian StyleDu, Wenran, Jiacheng Li, Guohua Zhang, Ke Yu, and Shufeng Liu. 2024. "Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River" Microorganisms 12, no. 7: 1282. https://doi.org/10.3390/microorganisms12071282
APA StyleDu, W., Li, J., Zhang, G., Yu, K., & Liu, S. (2024). Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River. Microorganisms, 12(7), 1282. https://doi.org/10.3390/microorganisms12071282