Sun, Y., Hu, K. L., Zhang, K. F., Jiang, L. H. & Xu, Y. Simulation of nitrogen fate for greenhouse cucumber grown under different water and fertilizer management using the EU-Rotate_N model. Agric. Water Manage. 112, 21–32 (2012).
Google Scholar
Vejan, P., Abdullah, R., Khadiran, T., Ismail, S. & Boyce, A. N. Role of plant growth promoting rhizobacteria in agricultural sustainability—A review. Molecules 21(5), 573. https://doi.org/10.3390/molecules21050573 (2016).
Ferreira, C. M. H., Soares, H. & Soares, E. V. Promising bacterial genera for agricultural practices: An insight on plant growth-promoting properties and microbial safety aspects. Sci. Total Environ. 682, 779–799. https://doi.org/10.1016/j.scitotenv.2019.04.225 (2019).
Google Scholar
Sammauria, R., Kumawat, S., Kumawat, P., Singh, J. & Jatwa, T. K. Microbial inoculants: potential tool for sustainability of agricultural production systems. Arch. Microbiol. 202(4), 677–693 https://doi.org/10.1007/s00203-019-01795-w (2020).
Singh, M. et al. PGPR Amelioration in Sustainable Agriculture 41–66 (Woodhead Publishing, 2019).
Google Scholar
Berg, G. Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl. Microbiol. Biotechnol. 84, 11–18 (2009).
Google Scholar
Olanrewaju, O. S., Glick, B. R. & Babalola, O. O. Mechanisms of action of plant growth promoting bacteria. World J. Microbiol. Biotechnol. 33(11), 197. https://doi.org/10.1007/s11274-017-2364-9 (2017).
Ambrosini, A., de Souza, R. & Passaglia, L. M. P. Ecological role of bacterial inoculants and their potential impact on soil microbial diversity. Plant Soil 400, 193–207. https://doi.org/10.1007/s11104-015-2727-7 (2016).
Google Scholar
O’Callaghan, M. Microbial inoculation of seed for improved crop performance: Issues and opportunities. Appl. Microbiol. Biotechnol. 100, 5729–5746 (2016).
Google Scholar
Kaminsky, L. M., Trexler, R. V., Malik, R. J., Hockett, K. L. & Bell, T. H. The inherent conflicts in developing soil microbial inoculants. Trends Biotechnol. 37, 140–151 (2019).
Google Scholar
Chen, X. H. et al. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat. Biotechnol. 25, 1007–1014 (2007).
Google Scholar
Chowdhury, S. P., Hartmann, A., Gao, X. W. & Borriss, R. Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42—A review. Front. Microbiol. 6, 780. https://doi.org/10.3389/fmicb.2015.00780 (2015).
Han, L. et al. Bacillus amyloliquefaciens B1408 suppresses Fusarium wilt in cucumber by regulating the rhizosphere microbial community. Appl. Soil Ecol. 136, 55–66 (2019).
Google Scholar
Wu, B. et al. Effects of Bacillus amyloliquefaciens ZM9 on bacterial wilt and rhizosphere microbial communities of tobacco. Appl. Soil Ecol. 103, 1–12 (2016).
Google Scholar
Krober, M. et al. Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole rnetagenome sequencing. Front. Microbiol. 5, 252. https://doi.org/10.3389/fmicb.2014.00252 (2014).
Shen, Z. Z. et al. Effect of the combination of bio-organic fertiliser with Bacillus amyloliquefaciens NJN-6 on the control of banana Fusarium wilt disease, crop production and banana rhizosphere culturable microflora. Biocontrol Sci. Technol. 25, 716–731 (2015).
Google Scholar
Shen, Z. Z. et al. Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biol. Fertility Soils 51, 553–562 (2015).
Google Scholar
Li, Q. et al. Rhizosphere microbiome mediated growth-promoting mechanisms of Bacillus amyloliquefaciens FH-1 on rice. Acta Microbiol. Sin. 59, 1–17 (2019).
Google Scholar
Qin, Y. X., Shang, Q. M., Zhang, Y., Li, P. L. & Chai, Y. R. Bacillus amyloliquefaciens L-S60 reforms the rhizosphere bacterial community and improves growth conditions in cucumber plug seedling. Front. Microbiol. 8, 2620. https://doi.org/10.3389/fmicb.2017.02620 (2017).
Idris, E. E., Iglesias, D. J., Talon, M. & Borriss, R. Tryptophan-dependent production of indole-3-acetic acid (IAA) affects level of plant growth promotion by Bacillus amyloliquefaciens FZB42. Mol. Plant-Microbe Interact. 20, 619–626. https://doi.org/10.1094/Mpmi-20-6-0619 (2007).
Google Scholar
Mendes, R. et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100 (2011).
Google Scholar
Panke-Buisse, K., Poole, A. C., Goodrich, J. K., Ley, R. E. & Kao-Kniffin, J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J 9, 980–989. https://doi.org/10.1038/ismej.2014.196 (2015).
Google Scholar
de Vries, F. T., Griffiths, R. I., Knight, C. G., Nicolitch, O. & Williams, A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science 368, 270 (2020).
Google Scholar
Rodriguez, P. A. et al. Systems biology of plant–microbiome interactions. Mol. Plant 12, 804–821. https://doi.org/10.1016/j.molp.2019.05.006 (2019).
Google Scholar
Trabelsi, D. & Mhamdi, R. Microbial inoculants and their impact on soil microbial communities: A review. Biomed. Res. Int. 2013, 863240. https://doi.org/10.1155/2013/863240 (2013).
Google Scholar
Gu, Y. et al. The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion. Plant Soil 452, 105–117. https://doi.org/10.1007/s11104-020-04545-w (2020).
Google Scholar
Ke, X. B. et al. Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere. Syst. Appl. Microbiol. 42, 248–260 (2019).
Google Scholar
Barberan, A., Bates, S. T., Casamayor, E. O. & Fierer, N. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 6, 343–351. https://doi.org/10.1038/ismej.2011.119 (2012).
Google Scholar
Kong, Z. Y. et al. Co-occurrence patterns of microbial communities affected by inoculants of plant growth-promoting bacteria during phytoremediation of heavy metal contaminated soils. Ecotoxicol. Environ. Saf. 183, 109504. https://doi.org/10.1016/j.ecoenv.2019.109504 (2019).
Newman, M. E. Modularity and community structure in networks. Proc. Natl. Acad. Sci. USA 103, 8577–8582. https://doi.org/10.1073/pnas.0601602103 (2006).
Google Scholar
Mendes, R. & Raaijmakers, J. M. Cross-kingdom similarities in microbiome functions. ISME J. 9, 1905–1907. https://doi.org/10.1038/ismej.2015.7 (2015).
Google Scholar
Mueller, U. G. & Sachs, J. L. Engineering microbiomes to improve plant and animal health. Trends Microbiol. 23, 606–617. https://doi.org/10.1016/j.tim.2015.07.009 (2015).
Google Scholar
Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).
Google Scholar
Chowdhury, S. P. et al. Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community. Plos One 8(7), e68818. https://doi.org/10.1371/journal.pone.0068818 (2013).
Correa, O. S. et al. Bacillus amyloliquefaciens BNM122, a potential microbial biocontrol agent applied on soybean seeds, causes a minor impact on rhizosphere and soil microbial communities. Appl. Soil Ecol. 41, 185–194 (2009).
Google Scholar
Wan, T. T., Zhao, H. H. & Wang, W. Effect of biocontrol agent Bacillus amyloliquefaciens SN16-1 and plant pathogen Fusarium oxysporum on tomato rhizosphere bacterial community composition. Biol. Control 112, 1–9 (2017).
Google Scholar
Wan, T. T., Zhao, H. H. & Wang, W. Effects of the biocontrol agent Bacillus amyloliquefaciens SN16-1 on the rhizosphere bacterial community and growth of tomato. J. Phytopathol. 166, 324–332 (2018).
Google Scholar
Nautiyal, C. S. et al. Plant growth-promoting bacteria Bacillus amyloliquefaciens NBRISN13 modulates gene expression profile of leaf and rhizosphere community in rice during salt stress. Plant Physiol. Biochem. 66, 1–9 (2013).
Google Scholar
Kumar, S., Suyal, D. C., Yadav, A., Shouche, Y. & Goel, R. Microbial diversity and soil physiochemical characteristic of higher altitude. Plos One 14(3), e0213844. https://doi.org/10.1371/journal.pone.0213844 (2019).
Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A. & Kuramae, E. E. The ecology of acidobacteria: Moving beyond genes and genomes. Front. Microbiol. 7, 744. https://doi.org/10.3389/fmicb.2016.00744 (2016).
Ul-Hassan, A. & Wellington, E. M. Actinobacteria in Encyclopedia of Microbiology (Third Edition) (ed Schaechter, M.) 25–44 (Academic Press, 2009).
Zhang, M., Powell, C. A., Guo, Y., Benyon, L. & Duan, Y. Characterization of the microbial community structure in Candidatus Liberibacter asiaticus-infected citrus plants treated with antibiotics in the field. BMC Microbiol. 13, 112. https://doi.org/10.1186/1471-2180-13-112 (2013).
Google Scholar
Albuquerque, L., Johnson, M. M., Schumann, P., Rainey, F. A. & da Costa, M. S. Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. Nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis. Syst. Appl. Microbiol. 37, 235–243. https://doi.org/10.1016/j.syapm.2014.03.001 (2014).
Google Scholar
Egas, C. et al. Complete genome sequence of the radiation-resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand. Genomic. Sci. 9(3), 1062–1075. https://doi.org/10.4056/sigs.5661021 (2014).
Ge, S. M., Zhou, M. H., Dong, X. J., Lu, Y. & Ge, S. C. Distinct and effective biotransformation of hexavalent chromium by a novel isolate under aerobic growth followed by facultative anaerobic incubation. Appl. Microbiol. Biotechnol. 97, 2131–2137 (2013).
Google Scholar
Sturm, G., Jacobs, J., Sproer, C., Schumann, P. & Gescher, J. Leucobacter chromiiresistens sp. nov., a chromate-resistant strain. Int. J. Syst. Evol. Microbiol. 61, 956–960 (2011).
Google Scholar
Muir, R. E. & Tan, M. W. Virulence of Leucobacter chromiireducens subsp. solipictus to Caenorhabditis elegans: Characterization of a novel host-pathogen interaction. Appl. Environ. Microbiol. 74, 4185–4198 (2008).
Google Scholar
Zhang, Y. et al. Abundance and diversity of candidate division JS1-and Chloroflexi-related bacteria in cold seep sediments of the northern South China Sea. Front. Earth Sci. Prc. 6, 373–382. https://doi.org/10.1007/s11707-012-0324-0 (2012).
Google Scholar
Bennett, A. C., Murugapiran, S. K. & Hamilton, T. L. Temperature impacts community structure and function of phototrophic Chloroflexi and Cyanobacteria in two alkaline hot springs in Yellowstone National Park. Environ. Microbiol. Rep. https://doi.org/10.1111/1758-2229.12863 (2020).
Google Scholar
Devos, D. P. Gemmata obscuriglobus. Curr. Biol. 23, R705-707. https://doi.org/10.1016/j.cub.2013.07.013 (2013).
Google Scholar
Dong, L. L. et al. Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng. Chin. Med. UK 13, 41. https://doi.org/10.1186/s13020-018-0198-5 (2018).
Ma, Q. et al. Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing. Bioresour. Technol. 179, 436–443 (2015).
Google Scholar
Kepel, B. J. F., Gani, M. A. & Tallei, T. E. Comparison of bacterial community structure and diversity in traditional gold mining waste disposal site and rice field by using a metabarcoding approach. Int. J. Microbiol. 2020, 1858732. https://doi.org/10.1155/2020/1858732 (2020).
Google Scholar
Chouari, R. et al. Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. Appl. Environ. Microbiol. 69, 7354–7363. https://doi.org/10.1128/aem.69.12.7354-7363.2003 (2003).
Google Scholar
Zhao, Y. et al. Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae. Plos One 12(10), e0185907. https://doi.org/10.1371/journal.pone.0185907 (2017).
Banerjee, S. et al. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. https://doi.org/10.1038/s41396-019-0383-2 (2019).
Google Scholar
Faust, K. & Raes, J. Microbial interactions: From networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).
Google Scholar
Olesen, J. M., Bascompte, J., Dupont, Y. L. & Jordano, P. The modularity of pollination networks. Proc. Natl. Acad. Sci. USA 104, 19891–19896 (2007).
Google Scholar
Kang, Y., Shen, M., Wang, H. & Zhao, Q. A possible mechanism of action of plant growth-promoting rhizobacteria (PGPR) strain Bacillus pumilus WP8 via regulation of soil bacterial community structure. J. Gen. Appl. Microbiol. 59, 267–277 (2013).
Google Scholar
Wang, J. et al. Traits-based integration of multi-species inoculants facilitates shifts of indigenous soil bacterial community. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.01692 (2018).
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing (2020).
Xiong, J. et al. Evidence of bacterioplankton community adaptation in response to long-term mariculture disturbance. Scientific Report 5, 15274. https://doi.org/10.1038/srep15274 (2015).
Google Scholar
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12(6), R60. https://doi.org/10.1186/gb-2011-12-6-r60 (2011).
Jiang, Y. J. et al. Plant cultivars imprint the rhizosphere bacterial community composition and association networks. Soil Biol. Biochem. 109, 145–155 (2017).
Google Scholar
Ju, F., Xia, Y., Guo, F., Wang, Z. P. & Zhang, T. Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants. Environ. Microbiol. 16, 2421–2432 (2014).
Google Scholar
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