Pre-flooding soil used in monocropping increased strawberry biomass and altered bacterial community composition

References

• Ahn, J. H., J. Song, B. Y. Kim, M. S. Kim, J. H. Joa, and H. Y. Weon. 2012. “Characterization of the Bacterial and Archaeal Communities in Rice Field Soils Subjected to Long-term Fertilization Practices.” Journal of Microbiology 50 (5): 754–765. doi:10.1007/s12275-012-2409-6.
   PubMed Web of Science ®Google Scholar
• Bao, S. D. 2000. Soil and Agricultural Chemistry Analysis. Beijing: China Agricultural Press.
   Google Scholar
• Bokulich, N. A., S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon, R. Knight, D. A. Mills, and J. G. Caporaso. 2013. “Quality-filtering Vastly Improves Diversity Estimates from Illumina Amplicon Sequencing.” Nature Methods 10 (1): 57–59. doi:10.1038/nmeth.2276.
   PubMed Web of Science ®Google Scholar
• Callens, M., H. Watanabe, Y. Kato, J. Miura, and E. Decaestecker. 2018. “Microbiota Inoculum Composition Affects Holobiont Assembly and Host Growth in Daphnia.” Microbiome 6 (1): 56. doi:10.1186/s40168-018-0444-1.
   PubMed Web of Science ®Google Scholar
• Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, et al. 2010. “QIIME Allows Analysis of High-throughput Community Sequencing Data.” Nature Methods 7 (5): 335–336. doi:10.1038/nmeth.f.303.
   PubMed Web of Science ®Google Scholar
• Castrillo, G., P. J. P. L. Teixeira, S. H. Paredes, T. F. Law, L. D. Lorenzo, M. E. Feltcher, O. M. Finkel, et al. 2017. “Root Microbiota Drive Direct Integration of Phosphate Stress and Immunity.” Nature 543 (7646): 513–518. doi:10.1038/nature21417.
   PubMed Web of Science ®Google Scholar
• Chen, P., Y. Z. Wang, Q. Z. Liu, Y. T. Zhang, W. H. Li, H.-Q. Li, and W.-H. Li. 2020. “Phase Changes of Continuous Cropping Obstacles in Strawberry (Fragaria × Ananassa Duch.) Production.” Applied Soil Ecology 155: 103626. doi:10.1016/j.apsoil.2020.103626.
   Web of Science ®Google Scholar
• Christian, Q., P. Elmar, Y. Pelin, G. Jan, S. Timmy, Y. Pablo, P. Jörg, and G. F. Oliver. 2013. “The SILVA Ribosomal RNA Gene Database Project: Improved Data Processing and Web-based Tools.” Nucleic Acids Research 41: 590–596. doi:10.1093/nar/gks1219.
   PubMed Web of Science ®Google Scholar
• De-Campos, A. B., C. H. Huang, and C. T. Johnston. 2011. “Biogeochemistry of Terrestrial Soils as Influenced by Short-term Flooding.” Biogeochemistry 111 (1–3): 239–252. doi:10.1007/s10533-011-9639-2.
   Web of Science ®Google Scholar
• Delgado-Baquerizo, M., P. B. Reich, C. Trivedi, D. J. Eldridge, S. Abades, F. D. Alfaro, F. Bastida, et al. 2020. “Multiple Elements of Soil Biodiversity Drive Ecosystem Functions across Biomes.” Nature Ecology & Evolution 4 (2): 210–220. doi:10.1038/s41559-019-1084-y.
   PubMed Web of Science ®Google Scholar
• Edgar, R. C., B. J. Haas, J. C. Clemente, C. Quince, and R. Knight. 2011. “UCHIME Improves Sensitivity and Speed of Chimera Detection.” Bioinformatics 27 (16): 2194–2200. doi:10.1093/aje/kwu026.
   PubMed Web of Science ®Google Scholar
• Edgar, R. C. 2013. “UPARSE: Highly Accurate OTU Sequences from Microbial Amplicon Reads.” Nature Methods 10 (10): 996–998. doi:10.1038/NMETH.2604.
   PubMed Web of Science ®Google Scholar
• Fan, K., M. Delgado-Baquerizo, X. Guo, D. Wang, Y. G. Zhu, and H. Chu. 2021. “Biodiversity of Key-stone Phylotypes Determines Crop Production in a 4-decade Fertilization Experiment.” The ISME Journal 15 (2): 550–561. doi:10.1038/s41396-020-00796-8.
   PubMed Web of Science ®Google Scholar
• Fierer, N. 2017. “Embracing the Unknown: Disentangling the Complexities of the Soil Microbiome.” Nature Reviews. Microbiology 15 (10): 579–590. doi:10.1038/nrmicro.2017.87.
   PubMed Web of Science ®Google Scholar
• Fitzpatrick, C. R., J. Copeland, P. W. Wang,D, S. Guttman, P. M. Kotanen, and M. T. J. Johnson. 2018. “Assembly and Ecological Function of the Root Microbiome across Angiosperm Plant Species.” Proceedings of the National Academy of Sciences of the United States of America 115 (6): E1157–E1165. doi:10.1073/pnas.1717617115.
   PubMed Web of Science ®Google Scholar
• García-Fraile, P., E. Menéndez, and R. Rivas. 2015. “Role of Bacterial Biofertilizers in Agriculture and Forestry.” AIMS Bioengineering 2 (3): 183–205. doi:10.3934/bioeng.2015.3.183.
   Web of Science ®Google Scholar
• Griffiths, B. S., S. Caul, J. Thompson, A. N. E. Birch, J. Cortet, M. N. Andersen, and P. H. Krogh. 2007. “Microbial and Microfaunal Community Structure in Cropping Systems with Genetically Modified Plants.” Pedobiologia 51 (3): 195–206. doi:10.1016/j.pedobi.2007.04.002.
   Web of Science ®Google Scholar
• Huang, X. Q., T. Wen, J. B. Zhang, L. Meng, T. B. Zhu, L. L. Liu, and Z. C. Cai. 2015. “Control of Soil-borne Pathogen Fusarium Oxysporum by Biological Soil Disinfestation with Incorporation of Various Organic Matters.” European Journal of Plant Pathology 143 (2): 223–235. doi:10.1007/s10658-015-0676-x.
   Web of Science ®Google Scholar
• Jorquera, M. A., F. Maruyama, A. V. Ogram, O. U. Navarrete, L. M. Lagos, N. G. Inostroza, J. J. Acuña, J. I. Rilling, and M. D. L. L. Mora. 2016. “Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments.” Microbial Ecology 72 (3): 633–646. doi:10.1007/s00248-016-0813-x.
   PubMed Web of Science ®Google Scholar
• Kang, S. M., A. L. Khan, M. Waqas, Y. H. You, M. Hamayun, G. J. Joo, R. Shanzad, K. S. Choi, and I. J. Lee. 2015. “Gibberellin-producing Serratia Nematodiphila PEJ1011 Ameliorates Low Temperature Stress in Capsicum Annuum L.” European Journal of Soil Biology 68: 85–93. doi:10.1016/j.ejsobi.2015.02.005.
   Web of Science ®Google Scholar
• Lauber, C. L., M. S. Strickland, M. A. Bradford, and N. Fierer. 2008. “The Influence of Soil Properties on the Structure of Bacterial and Fungal Communities across Land-use Types.” Soil Biology & Biochemistry 40 (9): 2407–2415. doi:10.1016/j.soilbio.2008.05.021.
   Web of Science ®Google Scholar
• Li, X., A. Jousset, W. D. Boer, V. C. J. Carrión, T. Zhang, X. Wang, and E. E. Kuramae. 2019. “Legacy of Land Use History Determines Reprogramming of Plant Physiology by Soil Microbiome.” The ISME Journal 13 (3): 738–751. doi:10.1038/s41396-018-0300-0.
   PubMed Web of Science ®Google Scholar
• Li, X., Y. Deng, Q. Li, C. Lu, J. Wang, H. Zhang, J. Zhu, et al. 2013. “Shifts of Functional Gene Representation in Wheat Rhizosphere Microbial Communities under Elevated Ozone.” The ISME Journal 7 (3): 660. doi:10.1038/ismej.2012.120.
   PubMed Web of Science ®Google Scholar
• Lou, Y., M. Xu, W. Wang, X. Sun, and K. Zhao. 2011. “Return Rate of Straw Residue Affects Soil Organic C Sequestration by Chemical Fertilization.” Soil and Tillage Research 113 (1): 70–73. doi:10.1016/j.still.2011.01.007.
   Web of Science ®Google Scholar
• Lu, P., L. D. Bainard, B. Ma, and J. H. Liu. 2020. “Bio-fertilizer and Rotten Straw Amendments Alter the Rhizosphere Bacterial Community and Increase Oat Productivity in a Saline–alkaline Environment.” Scientific Reports 10 (1): 19896. doi:10.1038/s41598-020-76978-3.
   PubMed Web of Science ®Google Scholar
• Mago, T., and S. L. Salzberg. 2011. “FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies.” Bioinformatics 27 (21): 2957–2963. doi:10.1093/bioinformatics/btr507.
   PubMed Web of Science ®Google Scholar
• Marina, R. S., J. Chen, F. Multinu, A. Hokenstad, T. J. Distad, E. H. Cheek, G. L. Keeney, et al. 2016. “Potential Contribution of the Uterine Microbiome in the Development of Endometrial Cancer.” Genome Medicine 8 (1): 122. doi:10.1186/s13073-016-0368-y.
   PubMed Web of Science ®Google Scholar
• Ning, Q., L. Chen, Z. Jia, C. Zhang, D. Ma, F. Li, J. Zhang, et al. 2019. “Multiple Long-term Observations Reveal a Strategy for Soil pH-dependent Fertilization and Fungal Communities in Support of Agricultural Production.” Agriculture, Ecosystems & Environment 293 :106837–106846. doi:10.1016/j.agee.2020.106837.
   Web of Science ®Google Scholar
• Olsen, S. R. 1954. Estimation of Available Phosphorus in Soils by Extraction with Sodium Bicarbonate. Washington: United States Department Of Agriculture.
   Google Scholar
• Peiffer, J. A., A. Spor, O. Koren, Z. Jin, S. G. Tringe, J. L. Dangl, E. S. Buckler, et al. 2013. “Diversity and Heritability of the Maize Rhizosphere Microbiome under Field Conditions.” Proceedings of the National Academy of Sciences of the United States of America 110 (16): 6548–6553. doi:10.1073/pnas.1302837110.
   PubMed Web of Science ®Google Scholar
• Rath, K. M., N. Fierer, D. V. Murphy, and J. Rousk. 2019. “Linking Bacterial Community Composition to Soil Salinity along Environmental Gradients.” The ISME Journal 13 (3): 836–846. doi:10.1038/s41396-018-0313-8.
   PubMed Web of Science ®Google Scholar
• Sanford, R. A., K. G. Lloyd, K. T. Konstantinidis, and F. E. Löffler. 2020. “Microbial Taxonomy Run Amok.” Trends in Microbiology 29 (5): 394–404. doi:10.1016/j.tim.2020.12.010.
   Web of Science ®Google Scholar
• Stover, R. H. 1962. Fusarial Wilt (Panama Disease) of Bananas and Other Musa Species. Kew: Commonwealth Mycological Institute.
   Google Scholar
• Strickland, T. C., and P. Sollins. 1987. “Improved Method for Separating Light- and Heavyfraction Organic Material from Soil.” Soil Science Society of America Journal 51 (5): 1390–1393. doi:10.2136/sssaj1987.03615995005100050056x.
   Web of Science ®Google Scholar
• Tian, Y., B. Wu, and Y. Zheng. 2013. “Modeling the Surface Water-groundwater Interaction in Arid and Semi-arid Regions Impacted by Agricultural Activities.” Agu Fall Meeting, December 9-13 , San Francisco.
   Google Scholar
• Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. “Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy.” Applied and Environmental Microbiology 73 (16): 5261–5267. doi:10.1128/AEM.00062-07.
   PubMed Web of Science ®Google Scholar
• Wang, Q., M. Ma, X. Jiang, B. Zhou, D. Guan, F. Cao, S. Chen, et al. 2019. “Long-term N Fertilization Altered 13 C-labeled Fungal Community Composition but Not Diversity in Wheat Rhizosphere of Chinese Black Soil.” Soil Biology & Biochemistry 135 :117–126. doi:10.1016/j.soilbio.2019.04.009.
   Web of Science ®Google Scholar
• Wang, Q., X. Jiang, D. Guan, D. Wei, B. Zhao, M. Ma, S. Chen, et al. 2018. “Long-term Fertilization Changes Bacterial Diversity and Bacterial Communities in the Maize Rhizosphere of Chinese Mollisols.” Applied Soil Ecology 125 :88–96. doi:10.1016/j.apsoil.2017.12.007.
   Web of Science ®Google Scholar
• Warncke, D., and J. R. Brown. 1998. “Potassium and Other Basic Cations.” Recommended Chemical Soil Test Procedures for the North Central Region 100: 31.
   Google Scholar
• Wei, G., M. Li, W. Shi, R. Tian, C. Chang, Z. Wang, N. Wang, et al. 2020. “Similar Drivers but Different Effects Lead to Distinct Ecological Patterns of Soil Bacterial and Archaeal Communities.” Soil Biology & Biochemistry 144 :107759. doi:10.1016/j.soilbio.2020.107759.
   Web of Science ®Google Scholar
• Wright, M. L., H. Jonathan, A. J. Gordon, and L. Adam. 2015. “Upper Midwest Climate Variations: Farmer Responses to Excess Water Risks.” Journal of Environmental Quality 44 (3): 810–822. doi:10.2134/jeq2014.08.0352.
   PubMed Web of Science ®Google Scholar
• Wu, A. L., X. Y. Jiao, F. F. Fan, J. S. Wang, J. Guo, E. W. Dong, L. G. Wang, et al. 2019. “Effect of Continuous Sorghum Cropping on the Rhizosphere Microbial Community and the Role of Bacillus Amyloliquefaciens in Altering the Microbial Composition.” Plant Growth Regulation 89 (3): 299–308. doi:10.1007/s10725-019-00533-y.
   Web of Science ®Google Scholar
• Xiong, W., S. Guo, A. Jousset, Q. Zhao, H. Wu, R. Li, G. A. Kowalchuk, et al. 2017. “Bio-fertilizer Application Induces Soil Suppressiveness against Fusarium Wilt Disease by Reshaping the Soil Microbiome.” Soil Biology & Biochemistry 114 :238–247. doi:10.1016/j.soilbio.2017.07.016.
   Web of Science ®Google Scholar
• Yang, L., X. Zhou, Y. Liao, Y. Lu, J. Nie, and W. Cao. 2019. “Co-incorporation of Rice Straw and Green Manure Benefits Rice Yield and Nutrient Uptake.” Crop Science 59 (2): 749–759. doi:10.2135/cropsci2018.07.0427.
   Web of Science ®Google Scholar
• Ye, C., O. M. Butler, C. Chen, W. Liu, Q. Zhang, and Q. Zhang. 2019. “Shifts in Characteristics of the Plant-soil System Associated with Flooding and Revegetation in the Riparian Zone of Three Gorges Reservoir, China.” Geoderma 361: 114015. doi:10.1016/j.geoderma.2019.114015.
   Web of Science ®Google Scholar
• Zeng, J., X. Liu, L. Song, X. Lin, H. Zhang, C. Shen, and H. Chu. 2016. “Nitrogen Fertilization Directly Affects Soil Bacterial Diversity and Indirectly Affects Bacterial Community Composition.” Soil Biology & Biochemistry 92: 41–49. doi:10.1016/j.soilbio.2015.09.018.
   Web of Science ®Google Scholar
• Zhang, K., Y. Shi, X. Cui, P. Yue, K. Li, X. Liu, B. M. Tripathi, et al. 2019. “Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem.” mSystems 4 (1): e00225–18. doi:10.1128/mSystems.00225-18.
   PubMed Web of Science ®Google Scholar
• Zhou, D., S. Wu, C. Chu, Z. Zhao, and Q. Wang. 2020a. “The Isolation of a Bacillus Velezensis and Its Application.” CN patant. CN202010175169.6, March 13.
   Google Scholar
• Zhou, G., S. Gao, Y. Lu, Y. Liao, J. Nie, and W. Cao. 2020b. “Co-incorporation of Green Manure and Rice Straw Improves Rice Production, Soil Chemical, Biochemical and Microbiological Properties in a Typical Paddy Field in Southern China.” Soil and Tillage Research 197: 104499. doi:10.1016/j.still.2019.104499.
   Web of Science ®Google Scholar
• Zhou, J., D. Guan, B. Zhou, B. Zhao, M. Ma, J. Qin, and X. Jiang, et al 2015. “Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China.” Soil Biology and Biochemistry 90: 42–51. https://doi.org/10.1016/j.soilbio.2015.07.005
   Web of Science ®Google Scholar
• Zhou, J., X. Jiang, B. Zhou, B. Zhao, M. Ma, D. Guan, J. Li, et al. 2016. “Thirty Four Years of Nitrogen Fertilization Decreases Fungal Diversity and Alters Fungal Community Composition in Black Soil in Northeast China.” Soil Biology & Biochemistry 95 :135–143. doi:10.1016/j.soilbio.2015.12.012.
   Web of Science ®Google Scholar
• Zhou, X., D. Gao, J. Liu, P. Qiao, X. Zhou, H. Lu, X. Wu, et al. 2014. “Changes in Rhizosphere Soil Microbial Communities in a Continuously Monocropped Cucumber (Cucumis Sativus L.) System.” European Journal of Soil Biology 60 :1–8. doi:10.1016/j.ejsobi.2013.10.005.
   Web of Science ®Google Scholar
• Zhou, X., and F. Wu. 2012. “Dynamics of the Diversity of Fungal and F Usarium Communities during Continuous Cropping of Cucumber in the Greenhouse.” FEMS Microbiology Ecology 80 (2): 469–478. doi:10.1111/j.1574-6941.2012.01312.x.
   PubMed Web of Science ®Google Scholar
• Zuppinger-Dingley, D., B. Schmid, J. S. Petermann, V. Yadav, G. B. D. Deyn, and D. F. B. Flynn. 2014. “Selection for Niche Differentiation in Plant Communities Increases Biodiversity Effects.” Nature 515 (7525): 108–111. doi:10.1038/nature13869.
   PubMed Web of Science ®Google Scholar
• Zwetsloot, M. J., J. M. Ucros, K. Wickings, R. C. Wilhelm, J. Sparks, D. H. Buckley, and T. L. Bauerle. 2020. “Prevalent Root-derived Phenolics Drive Shifts in Microbial Community Composition and Prime Decomposition in Forest Soil.” Soil Biology & Biochemistry 145: 107797. doi:10.1016/j.soilbio.2020.107797.
   Web of Science ®Google Scholar