Akhter M S, Hossain S J, Hossain S A, Datta R K. 2012. Isolation and characterization of salinity tolerant Azotobacter sp. Greener Journal of Biological Sciences, 2, 043–051.

Aliyat F Z, Maldani M, El Guilli M, Nassiri L, Ibijbijen J. 2022. Phosphate-solubilizing bacteria isolated from phosphate solid sludge and their ability to solubilize three inorganic phosphate forms: Calcium, iron, and aluminum phosphates. Microorganisms, 10, 980.

Anthony M A, Frey S D, Stinson K A. 2017. Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion. Ecosphere, 8, e01951.

Araujo A S, Pertile M, Costa R M, Costa M K, de Aviz R O, Mendes L W, de Medeiros E V, da Costa D P, Melo V M, de Araujo Pereira A P. 2023. Short-term responses of plant growth-promoting bacterial community to the herbicides imazethapyr and flumioxazin. Chemosphere, 328, 138581.

Bashan Y, Kamnev A A, de-Bashan L E. 2013. Tricalcium phosphate is inappropriate as a universal selection factor for isolating and testing phosphate-solubilizing bacteria that enhance plant growth: A proposal for an alternative procedure. Biology and Fertility of Soils, 49, 465–479.

Beckers B, Op De Beeck M, Weyens N, Boerjan W, Vangronsveld J. Vangronsveld, J. 2017. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome, 5, 25.

Berendsen R L, Vismans G, Yu K, Song Y, de Jonge R, Burgman W P, Burmølle M, Herschend J, Bakker P A, Pieterse C M. 2018. Disease-induced assemblage of a plant-beneficial bacterial consortium. The ISME Journal, 12, 1496–1507.

Bjerketorp J, Levenfors J J, Nord C, Guss B, Öberg B, Broberg A. 2021. Selective isolation of multidrug-resistant Pedobacter spp., producers of novel antibacterial peptides. Frontiers in Microbiology, 12, 642829.

Bokulich N A, Kaehler B D, Rideout J R, Dillon M, Bolyen E, Knight R, Huttley G A, Gregory Caporaso J. 2018. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome, 6, 90.

Braga R M, Padilla G, Araújo W L. 2018. The biotechnological potential of Epicoccum spp.: Diversity of secondary metabolites. Critical Reviews in Microbiology, 44, 759–778.

Callahan B J, McMurdie P J, Rosen M J, Han A W, Johnson A J, Holmes S P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583.

Chen Y, Zhang A F, Wang W X, Zhang Y, Gao T C. 2012. Baseline sensitivity and efficacy of thifluzamide in Rhizoctonia solani. Annals of Applied Biology, 161, 247–254.

Du P Q, Wu X H, Xu J, Dong F S, Liu X G, Zheng Y Q. 2018. Effects of trifluralin on the soil microbial community and functional groups involved in nitrogen cycling. Journal of Hazardous Materials, 353, 204–213.

Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty N K, Bhatnagar S, Eisen J A, Sundaresan V. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences of the United States of America, 112, E911–E920.

El-Nahhal I, El-Nahhal Y. 2021. Pesticide residues in drinking water, their potential risk to human health and removal options. Journal of Environmental Management, 299, 113611.

Elshaghabee F M, Rokana N, Gulhane R D, Sharma C, Panwar H. 2017. Bacillus as potential probiotics: Status, concerns, and future perspectives. Frontiers in Microbiology, 8, 1490.

Fernández-González A J, Cardoni M, Gómez-Lama Cabanás C, Valverde-Corredor A, Villadas P J, Fernández-López M, Mercado-Blanco J. 2020. Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive. Microbiome, 8, 11.

Finkel O M, Salas-González I, Castrillo G, Conway J M, Law T F, Teixeira P J, Wilson E D, Fitzpatrick C R, Jones C D, Dangl J L. 2020. A single bacterial genus maintains root growth in a complex microbiome. Nature, 587, 103–108.

Folman L B, Postma J, van Veen J A. 2003. Characterisation of Lysobacter enzymogenes (Christensen and Cook 1978) strain 3.1T8, a powerful antagonist of fungal diseases of cucumber. Microbiological Research, 158, 107–115.

Galicia-Campos E, García-Villaraco A, Montero-Palmero M B, Gutiérrez-Mañero F J, Ramos-Solano B. 2022. Bacillus H47 triggers Olea europaea metabolism activating DOXP and shikimate pathways simultaneously and modifying leaf extracts’ antihypertensive activity. Frontiers in Microbiology, 13, 1005865.

Geiger F, Bengtsson J, Berendse F, Weisser W W, Emmerson M, Morales M B, Ceryngier P, Liira J, Tscharntke T, Winqvist C, Eggers S. 2010. Persistent negative effects of pesticides on biodiversity and biological control potential on European farmland. Basic and Applied Ecology, 11, 97–105.

Gu S H, Wei Z, Shao Z Y, Friman V P, Cao K H, Yang T J, Kramer J, Wang X F, Li M, Mei X L, Xu Y C, Shen Q R, Kümmerli R, Jousset A. 2020. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nature Microbiology, 5, 1002–1010.

Gu Y A, Banerjee S, Dini-Andreote F, Xu Y C, Shen Q R, Jousset A, Wei Z. 2022. Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations. The ISME Journal, 16, 2448–2456.

Guo A Y, Pan C G, Ma J Y, Bao Y Y. 2020. Linkage of antibiotic resistance genes, associated bacteria communities and metabolites in the wheat rhizosphere from chlorpyrifos-contaminated soil. Science of the Total Environment, 741, 140457.

Guo Y P, Li W, Sun H Y, Wang N, Yu H S, Chen H G. 2012. Detection and quantification of Rhizoctonia cerealis in soil using real-time PCR. Journal of General Plant Pathology, 78, 247–254.

Haney C H, Samuel B S, Bush J, Ausubel F M. 2015. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nature Plants, 1, 1–9.

He E K, Qiu R L, Cao X D, Song L, Peijnenburg W J, Qiu H. 2020. Elucidating toxicodynamic differences at the molecular scale between ZnO nanoparticles and ZnCl2 in Enchytraeus crypticus via nontargeted metabolomics. Environmental Science & Technology, 54, 3487–3498.

Huang A C, Jiang T, Liu Y X, Bai Y C, Reed J, Qu B, Goossens A, Nützmann H W, Bai Y, Osbourn A. 2019. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science, 364, eaau6389.

Imfeld G, Vuilleumier S. 2012. Measuring the effects of pesticides on bacterial communities in soil: A critical review. European Journal of Soil Biology, 49, 22–30.

Jacobson A R, Dousset S, Guichard N, Baveye P, Andreux F. 2005. Diuron mobility through vineyard soils contaminated with copper. Environmental Pollution, 138, 250–259.

Jinal N H, Amaresan N. 2020. Evaluation of biocontrol Bacillus species on plant growth promotion and systemic-induced resistant potential against bacterial and fungal wilt-causing pathogens. Archives of Microbiology, 202, 1785–1794.

Kõljalg U, Larsson K H, Abarenkov K, Nilsson R H, Alexander I J, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T. 2005. UNITE: A database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytologist, 166, 1063–1068.

Kremer R, Means N, Kim S. 2005. Glyphosate affects soybean root exudation and rhizosphere micro-organisms. International Journal of Environmental Analytical Chemistry, 85, 1165–1174.

Kushwaha P, Kashyap P L, Srivastava A K, Tiwari R K. 2020. Plant growth promoting and antifungal activity in endophytic Bacillus strains from pearl millet (Pennisetum glaucum). Brazilian Journal of Microbiology, 51, 229–241.

Li H, Wang Y X, Zhu X L, Yang G F. 2021. Discovery of a fungicide candidate targeting succinate dehydrogenase via computational substitution optimization. Journal of Agricultural and Food Chemistry, 69, 13227–13234.

Li S Z, Deng Y, Lian S Y, Dai C X, Ma Q, Qu Y Y. 2022. Succession of diversity, functions, and interactions of the fungal community in activated sludge under aromatic hydrocarbon stress. Environmental Research, 204, 112143.

Liu C Y, Guo W, Wang Y, Fu B S, Doležel J, Liu Y, Zhai W L, Said M, Molnár I, Holušová K, Zhang R Q, Wu J Z. 2023. Introgression of sharp eyespot resistance from Dasypyrum villosum chromosome 2VL into bread wheat. The Crop Journal, 11, 1512–1520.

Liu Y P, Zhang H H, Wang J, Gao W T, Sun X T, Xiong Q, Shu X, Miao Y Z, Shen Q R, Xun W B, Zhang R F. 2024. Nonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant “cry for help” response to assemble disease suppressing and growth promoting rhizomicrobiome. Nature Communications, 15, 1907.

Louden B C, Haarmann D, Lynne A M. 2011. Use of blue agar CAS assay for siderophore detection. Journal of Microbiology & Biology Education, 12, 51–53.

Lupwayi N Z, Blackshaw R E, Geddes C M, Dunn R, Petri R M. 2022. Multi-year and multi-site effects of recurrent glyphosate applications on the wheat rhizosphere microbiome. Environmental Research, 215, 114363.

Matsumoto H, Fan X Y, Wang Y, Kusstatscher P, Duan J, Wu S L, Chen S L, Qiao K, Wang Y, Ma B, Zhu G N, Hashidoko Y, Berg G, Cernava T, Wang M C. 2021. Bacterial seed endophyte shapes disease resistance in rice. Nature Plants, 7, 60–72.

Miller S A, Ferreira J P, LeJeune J T. 2022. Antimicrobial use and resistance in plant agriculture: A one health perspective. Agriculture-Basel, 12, 289.

Nagaoka T, Goto K, Watanabe A, Sakata Y, Yoshihara T. 2001. Sesquiterpenoids in root exudates of Solanum aethiopicum. Zeitschrift für Naturforschung (Section C: A Journal of Biosciences), 56, 707–713.

Nguyen N H, Song Z, Bates S T, Branco S, Tedersoo L, Menke J, Schilling J S, Kennedy P G. 2016. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, 20, 241–248.

Raaijmakers J M, Mazzola M. 2012. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annual Review of Phytopathology, 50, 403–424.

Satola B, Wübbeler J H, Steinbüchel A. 2013. Metabolic characteristics of the species Variovorax paradoxus. Applied Microbiology and Biotechnology, 97, 541–560.

Shi W C, Li M C, Wei G S, Tian R M, Li C P, Wang B, Lin R S, Shi C Y, Chi X L, Zhou B, Gao Z. 2019. The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome. Microbiome, 7, 14.

Singh R P, Singh P K, Rutkoski J, Hodson D P, He X, Jørgensen L N, Hovmøller M S, Huerta-Espino J. 2016. Disease impact on wheat yield potential and prospects of genetic control. Annual Review of Phytopathology, 54, 303–322.

Sivakumar G, Briccoli Bati C, Uccella N. 2007. Demethyloleuropein and β-glucosidase activity in olive fruits. Biotechnology Journal, 2, 381–385.

Soltani A A, Khavazi K, Asadi-Rahmani H, Omidvari M, Dahaji P A, Mirhoseyni H. 2010. Plant growth promoting characteristics in some Flavobacterium spp. isolated from soils of Iran. Journal of Agricultural Science, 2, 106.

Toole D R, Zhao J, Martens-Habbena W, Strauss S L. 2021. Bacterial functional prediction tools detect but underestimate metabolic diversity compared to shotgun metagenomics in southwest Florida soils. Applied Soil Ecology, 168, 104129.

Wang Y H, Men J N, Zheng T, Ma Y L, Li W S, Cernava T, Bai L Y, Jin D. 2023. Impact of pyroxasulfone on sugarcane rhizosphere microbiome and functioning during field degradation. Journal of Hazardous Materials, 455, 131608.

Wang Z H, Song Y. 2022. Toward understanding the genetic bases underlying plant-mediated “cry for help” to the microbiota. iMeta, 1, e8.

Xie J B, Wicaksono W A, Lv Z Y, Berg G, Cernava T, Ge B B. 2023. Rhizosphere bacteria show a stronger response to antibiotic-based biopesticide than to conventional pesticides. Journal of Hazardous Materials, 458, 132035.

Xiong W, Li R, Ren Y, Liu C, Zhao Q Y, Wu H S, Jousset A, Shen Q R. 2017. Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease. Soil Biology and Biochemistry, 107, 198–207.

Yang X X, Dai Z A, Yuan R W, Guo Z H, Xi H X, He Z L, Wei M. 2023. Effects of salinity on assembly characteristics and function of microbial communities in the phyllosphere and rhizosphere of salt-tolerant Avicennia marina mangrove species. Microbiology Spectrum, 11, e03000–e03022.

Yao X F, Liu Y, Liu X, Qiao Z H, Sun S, Li X D, Wang J, Zhang F W, Jiang X Y. 2022. Effects of thifluzamide on soil fungal microbial ecology. Journal of Hazardous Materials, 431, 128626.

Yin C T, Casa Vargas J M, Schlatter D C, Hagerty C H, Hulbert S H, Paulitz T C. 2021. Rhizosphere community selection reveals bacteria associated with reduced root disease. Microbiome, 9, 86.

Zhang Y, Lu J L, Wang J X, Zhou M G, Chen C J. 2015. Baseline sensitivity and resistance risk assessmemt of Rhizoctonia cerealis to thifluzamide, a succinate dehydrogenase inhibitor. Pesticide Biochemistry and Physiology, 124, 97–102.