References
- Allard, S.M., Walsh, C.S., Wallis, A.E., Ottesen, A.R., Brown, E.W., and Micallef, S.A. 2016. Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers. Science of the Total Environment, 573, 555 ‒ 563. DOI:10.1016/j.scitotenv.2016.08.157.
- Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403 ‒ 10. DOI:10.1016/S0022-2836(05)80360-2.
- Bebber, D.P. and Richards, V.R. (2020). A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity. bioRxiv, DOI:2020.10.04.325373.
- Beecher, G.R. (1998). Nutrient content of tomatoes and tomato products. Experimental Biology and Medicine, 218(2), 98 ‒ 100. DOI:10.3181/00379727-218-44282a.
- Berg, G., Eberl, L., and Hartmann, A. (2005). The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environmental microbiology, 7(11), 1673 ‒ 1685. DOI:10.1111/j.1462-2920.2005.00891.x.
- Bulgarelli, D., Schlaeppi, K., Spaepen, S., Ver Loren van Themaat, E., and Schulze-Lefert, P. (2013). Structure and functions of the bacterial microbiota of plants. Annual Review of Plant Biology, 64, 807 ‒ 38. DOI:10.1146/annurev-arplant-050312-120106.
- Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5), 335 ‒ 336. DOI:10.1038/nmeth.f.303.
- Cheng, D., Tian, Z., Feng, L., Xu, L., and Wang, H. (2019). Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ, 6, e6162. DOI:10.7717/peerj.6162.
- Dombrowski, N., Schlaeppi, K., Agler, M.T., Hacquard, S., Kemen, E., Garrido-Oter, R., Wunder, J., Coupland, G., and Schulze-Lefert, P. (2017). Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time. The Isme Journal, 11(1), 43 ‒ 55. DOI:10.1038/ismej.2016.109.
- Dong, C.-J., Wang, L.-L., Li, Q., and Shang, Q.-M. (2019). Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants. PloS one, 14(11), e0223847-e0223847. DOI:10.1371/journal.pone.0223847.
- Duncan, J. (2005). Composting chicken manure. WSU cooperative extension. King County Master Gardner and Cooperative Extension Livestock Advisor, Washington State University, Pullman. Retrieved 11 Nov 2017.
- Edgar, R.C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460 ‒ 1. DOI:10.1093/bioinformatics/btq461.
- Eo, J. and Park, K.-C. (2016). Long-term effects of imbalanced fertilization on the composition and diversity of soil bacterial community. Agriculture, Ecosystems & Environment, 231, 176 ‒ 182. DOI: org/10.1016/j.agee.2016.06.039.
- Geisseler, D. and Scow, K.M. (2014). Long-term effects of mineral fertilizers on soil microorganisms–A review. Soil Biology and Biochemistry, 75, 54 ‒ 63. DOI:10.1016/j.soilbio.2014.03.023.
- Green, S.J., Prakash, O., Jasrotia, P., Overholt, W.A., Cardenas, E., Hubbard, D., Tiedje, J.M., Watson, D.B., Schadt, C.W., and Brooks, S.C. (2012). Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Applied and Environmental Microbiology, 78(4), 1039 ‒ 1047. DOI:10.1128/AEM.06435-11.
- Guron, G.K., Arango-Argoty, G., Zhang, L., Pruden, A., and Ponder, M.A. (2019). Effects of dairy manure-based amendments and soil texture on lettuce-and radish-associated microbiota and resistomes. Msphere, 4(3), 13 ‒ 19. DOI:10.1128/mSphere.00239-19.
- Haas, D. and Défago, G. (2005). Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology, 3(4), 307 ‒ 319. DOI:10.1038/nrmicro1129.
- Hallmann, J., Quadt-Hallmann, A., Mahaffee, W., and Kloepper, J. (1997). Bacterial endophytes in agricultural crops. Canadian Journal of Microbiology, 43(10), 895 ‒ 914. DOI: 10.1139/M97-131.
- Hartmann, M., Frey, B., Mayer, J., Mäder, P., and Widmer, F. (2015). Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal, 9(5), 1177 ‒ 1194. DOI:10.1038/ismej.2014.210.
- Ji, L., Wu, Z., You, Z., Yi, X., Ni, K., Guo, S., and Ruan, J. (2018). Effects of organic substitution for synthetic N fertilizer on soil bacterial diversity and community composition: A 10-year field trial in a tea plantation. Agriculture, Ecosystems & Environment, 268, 124 ‒ 132. DOI:10.1007/s00374-020-01439-y.
- Kamau, D., Spiertz, J., and Oenema, O. (2008). Carbon and nutrient stocks of tea plantations differing in age, genotype and plant population density. Plant and Soil, 307(1), 29 ‒ 39. DOI:10.1007/s11104-008-9576-6.
- Lee, S.A., Kim, Y., Kim, J.M., Chu, B., Joa, J.-H., Sang, M.K., Song, J. and Weon, H.-Y. (2019). A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments. Scientific Reports, 9(1), 1 ‒ 15. DOI: org/10.1038/s41598-019-45660-8.
- Li, C., Yan, K., Tang, L., Jia, Z., and Li, Y. (2014). Change in deep soil microbial communities due to long-term fertilization. Soil Biology and Biochemistry, 75, 264 ‒ 272. DOI:10.1016/j.soilbio.2014.04.023.
- Lin, L., Ge, H.M., Yan, T., Qin, Y.H., and Tan, R.X. (2012). Thaxtomin A-deficient endophytic Streptomyces sp. enhances plant disease resistance to pathogenic Streptomyces scabies. Planta, 236(6), 1849 ‒ 1861. DOI:10.1007/s00425-012-1741-8.
- Loper, J.E., Hassan, K.A., Mavrodi, D.V., Davis II, E.W., Lim, C.K., Shaffer, B.T., Elbourne, L.D., Stockwell, V.O., Hartney, S.L., and Breakwell, K. (2012). Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet, 8(7), e1002784. DOI:10.1371/journal.pgen.1002784.
- Lundberg, D.S., Lebeis, S.L., Paredes, S.H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., and Del Rio, T.G. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86 ‒ 90. DOI:10.1038/nature11237.
- Luo, L., Wang, P., Zhai, Z., Su, P., Tan, X., Zhang, D., Zhang, Z., and Liu, Y. (2019). The effects of Rhodopseudomonas palustris PSB06 and CGA009 with different agricultural applications on rice growth and rhizosphere bacterial communities. AMB Express, 9(1), 1 ‒ 10. DOI:10.1186/s13568-019-0897-z.
- Magoč, T. and Salzberg, S.L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21), 2957 ‒ 63. DOI:10.1093/bioinformatics/btr507.
- Manching, H.C., Balint-Kurti, P.J., and Stapleton, A.E. (2014). Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization. Frontiers in Plant Science, 5, 403. DOI:10.3389/fpls.2014.00403.
- Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal, 17(1), 10. DOI:10.14806/ej.17.1.200.
- Peiffer, J.A., Spor, A., Koren, O., Jin, Z., Tringe, S.G., Dangl, J.L., Buckler, E.S., and Ley, R.E. (2013). Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences, 110(16), 65486553. DOI:10.1073/pnas.1302837110.
- Schreiter, S., Babin, D., Smalla, K., and Grosch, R. (2018). Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale. Frontiers in Microbiology, 9, 97. DOI:10.3389/fmicb.2018.00097.
- Smit, E., Leeflang, P., Gommans, S., van den Broek, J., van Mil, S., and Wernars, K. (2001). Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Applied and Environmental Microbiology, 67(5), 2284 ‒ 2291. DOI:10.1128/AEM.67.5.2284-2291.2001.
- Sturz, A.V., Christie, B.R., and Nowak, J. (2000). Bacterial endophytes: potential role in developing sustainable systems of crop production. Critical Reviews in Plant Sciences, 19(1), 1 ‒ 30. DOI:10.1080/07352680091139169.
- Tian, B., Zhang, C., Ye, Y., Wen, J., Wu, Y., Wang, H., Li, H., Cai, S., Cai, W., and Cheng, Z. (2017). Beneficial traits of bacterial endophytes belonging to the core communities of the tomato root microbiome. Agriculture, Ecosystems & Environment, 247, 149 ‒ 156. DOI:10.1016/j.agee.2017.06.041.
- Torsvik, V. and Øvreås, L. (2002). Microbial diversity and function in soil: from genes to ecosystems. Current Opinion in Microbiology, 5(3), 240 ‒ 245. DOI:10.1016/s1369-5274(02)00324-7.
- Turner, T.R., James, E.K., and Poole, P.S. (2013). The plant microbiome. Genome Biol, 14(6), 209. DOI:10.1186/gb-2013-14-6-209.
- van Elsas, J.D., Chiurazzi, M., Mallon, C.A., Elhottova, D., Kristufek, V., and Salles, J.F. (2012). Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences of the USA, 109(4), 1159 ‒ 64. DOI:10.1073/pnas.1109326109.
- Wang, X., Van Nostrand, J.D., Deng, Y., Lü, X., Wang, C., Zhou, J., and Han, X. (2015). Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiology Ecology, 91(12). DOI:10.1093/femsec/fiv133.
- Weller, D.M., Raaijmakers, J.M., Gardener, B.B.M., and Thomashow, L.S. (2002). Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annual Review of Phytopathology, 40(1), 309 ‒ 348. DOI:10.1146/annurev.phyto.40.030402.110010.
- Xiao, Y., Liu, X., Meng, D., Tao, J., Gu, Y., Yin, H., and Li, J. (2018). The role of soil bacterial community during winter fallow period in the incidence of tobacco bacterial wilt disease. Applied Microbiology and Biotechnology, 102(5), 2399 ‒ 2412. DOI:10.1007/s00253-018-8757-3.
- Xu, W., Wang, F., Zhang, M., Ou, T., Wang, R., Strobel, G., Xiang, Z., Zhou, Z., and Xie, J. (2019). Diversity of cultivable endophytic bacteria in mulberry and their potential for antimicrobial and plant growth-promoting activities. Microbiological Research, 229, 126328. DOI:10.1016/j.micres.2019.126328.
- Yang, H., Li, J., Xiao, Y., Gu, Y., Liu, H., Liang, Y., Liu, X., Hu, J., Meng, D., and Yin, H. (2017). An integrated insight into the relationship between soil microbial community and tobacco bacterial wilt disease. Frontiers in Microbiology, 8, 2179. DOI:10.3389/fmicb.2017.02179.
- Ye, G., Banerjee, S., He, J.-Z., Fan, J., Wang, Z., Wei, X., Hu, H., Zheng, Y., Duan, C., Wan, S., Chen, J., and Yongxin, L. (2021). Manure application increases microbiome complexity in soil aggregate fractions: Results of an 18-year field experiment. Agriculture Ecosystems & Environment, 307, 107249. DOI:10.1016/j.agee.2020.107249.
- Yilmaz, P., Parfrey, L.W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., Schweer, T., Peplies, J., Ludwig, W., and Glöckner, F.O. (2014). The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research, 42(D1), D643 ‒ 648. DOI:10.1093/nar/gkt1209.
- Zhang, S., Sun, L., Wang, Y., Fan, K., Xu, Q., Li, Y., Ma, Q., Wang, J., Ren, W., and Ding, Z. (2020a). Cow manure application effectively regulates the soil bacterial community in tea plantation. BMC Microbiology, 20(1), 190. DOI:10.1186/s12866-020-01871-y.
- Zhang, X., Zhang, Q., Liang, B., and Li, J. (2017). Changes in the abundance and structure of bacterial communities in the greenhouse tomato cultivation system under long-term fertilization treatments. Applied Soil Ecology, 121, 82 ‒ 89. DOI:10.1016/j.apsoil.2017.08.016.
- Zhang, Y.J., Hu, H.W., Chen, Q.L., Singh, B.K., Yan, H., Chen, D., and He, J.Z. (2019). Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes. Environment International, 130, 104912. DOI:10.1016/j.envint.2019.104912.
- Zhang, Y.J., Hu, H.W., Chen, Q.L., Yan, H., Wang, J.T., Chen, D., and He, J.Z. (2020b). Manure application did not enrich antibiotic resistance genes in root endophytic bacterial microbiota of cherry radish plants. Applied and Environmental Microbiology, 86(2). DOI:10.1128/AEM.02106-19.
- Zhen, Z., Liu, H., Wang, N., Guo, L., Meng, J., Ding, N., Wu, G., and Jiang, G. (2014). Effects of manure compost application on soil microbial community diversity and soil microenvironments in a temperate cropland in China. PLOS ONE, 9(10), e108555. DOI:10.1371/journal.pone.0108555.
- Zhong, X.-Z., Ma, S.-C., Wang, S.-P., Wang, T.-T., Sun, Z.-Y., Tang, Y.-Q., Deng, Y., and Kida, K. (2018). A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics. Bioresource Technology, 247, 443 ‒ 452. DOI:10.1016/j.biortech.2017.09.