Rhizosphere bacteriome of Allium cepa after the application of chemical and endophyte-based fertilizer

AbdElgawad, 2020, Actinomycetes enrich soil rhizosphere and improve seed quality as well as productivity of legumes by boosting nitrogen availability and metabolism, Biomolecules, 10, 1675, 10.3390/biom10121675 Assefa, 2019, The principal role of organic fertilizer on soil properties and agricultural productivity-a review, Agri. Res. Tech Open Access J., 22, 556192 Banerjee, 2016, Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil, Soil Biol. Biochem., 97, 188, 10.1016/j.soilbio.2016.03.017 Berg, 2009, Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere, FEMS Microbiol. Ecol., 68, 1, 10.1111/j.1574-6941.2009.00654.x Brady, 2008, vol. 13, 662 Bray, 1945, Determination of total, organic, and available forms of phosphorus in soils, Soil Sci., 59, 39, 10.1097/00010694-194501000-00006 Bremner, 1982, Total nitrogen in page Calle, 2019, Statistical analysis of metagenomics data, Genomics Informatics, 17, 10.5808/GI.2019.17.1.e6 Cao, 2020, Phylogenetic structure of soil bacterial communities along age sequence of subtropical cunninghamia lanceolata plantations, Sustainability, 12, 1864, 10.3390/su12051864 Culligan, 2014, Metagenomics and novel gene discovery: promise and potential for novel therapeutics, Virulence, 5, 399, 10.4161/viru.27208 Dai, 2018, Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe, Glob. Chang. Biol., 24, 3452, 10.1111/gcb.14163 Daims, 2015, Complete nitrification by Nitrospira bacteria, Nature, 528, 504, 10.1038/nature16461 Figueiredo, 2020, Clostridium, 477 Gamalero, 2022, Current techniques to study beneficial plant-microbe interactions, Microorganisms, 10, 1380, 10.3390/microorganisms10071380 Ganeshamoorthi, 2008, Plant growth promoting rhizobacterial (PGPR) bioconsortia mediates induction of defense-related proteins against infection of root rot pathogen in mulberry plants, J. Plant Interact., 3, 233, 10.1080/17429140802088097 Gardner, 2011, Soil rhizosphere microbial communities and enzyme activities under organic farming in Alabama, Diversity, 3, 308, 10.3390/d3030308 Guo, 2021, Effect of agricultural subsidies on the use of chemical fertilizer, J. Environ. Manag., 299, 10.1016/j.jenvman.2021.113621 Heuer, 2012, Plasmids foster diversification and adaptation of bacterial populations in soil, FEMS Microbiol. Rev., 36, 1083, 10.1111/j.1574-6976.2012.00337.x Hussain, 2021, Phosphorus availability and leaching losses in annual and perennial cropping systems in an upper US Midwest landscape, Sci. Rep., 11, 20367, 10.1038/s41598-021-99877-7 Isobe, 2019, Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents, Nat. Commun., 10, 2499, 10.1038/s41467-019-10390-y Isobe, 2020, Phylogenetic conservation of soil bacterial responses to simulated global changes, Philos. Trans. R. Soc. B, 375, 20190242, 10.1098/rstb.2019.0242 Javed, 2022, Soil fertility: factors affecting soil fertility, and biodiversity responsible for soil fertility, Int. J. Plant Animal Environ. Sci., 12, 21, 10.26502/ijpaes.202129 Kalam, 2020, Recent understanding of soil acidobacteria and their ecological significance: a critical review, Front. Microbiol., 11, 10.3389/fmicb.2020.580024 Khairina, 2021, Indigenous bacteria, an excellent reservoir of functional plant growth promoters for enhancing duckweed biomass yield on site, Chemosphere, 268, 10.1016/j.chemosphere.2020.129247 Khandagale, 2020, Omics approaches in Allium research: Progress and way ahead, PeerJ, 8, 10.7717/peerj.9824 Khanghahi, 2022, Shifts in the rhizosphere and endosphere colonizing bacterial communities under drought and salinity stress as affected by a biofertilizer consortium, Microb. Ecol., 84, 483, 10.1007/s00248-021-01856-y Lin, 2021, Antifungal weapons of Lysobacter, a mighty biocontrol agent, Environ. Microbiol., 23, 5704, 10.1111/1462-2920.15674 Liu, 2021, A practical guide to amplicon and metagenomic analysis of microbiome data, Protein Cell, 12, 315, 10.1007/s13238-020-00724-8 Mahmud, 2021, Rhizosphere microbiome manipulation for sustainable crop production, Curr. Plant Biol., 27, 10.1016/j.cpb.2021.100210 Miljaković, 2020, The significance of Bacillus spp. in disease suppression and growth promotion of field and vegetable crops, Microorganisms, 8, 1037, 10.3390/microorganisms8071037 Mizrahi-Man, 2013, Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs, PLoS One, 8, 10.1371/journal.pone.0053608 Mujakić, 2022, Phylum Gemmatimonadota and its role in the environment, Microorganisms, 10, 151, 10.3390/microorganisms10010151 Mwende Muindi, 2019, Understanding soil phosphorus, Int. J. Plant Soil Sci., 31, 1, 10.9734/ijpss/2019/v31i230208 Olibone, 2010, Phosphate fertilization and phosphorus forms in an Oxisol under no-till, Sci. Agric., 67, 465, 10.1590/S0103-90162010000400014 Pahalvi, 2021, Chemical fertilizers and their impact on soil health. Microbiota and biofertilizers, vol 2, 1 Parihar, 2022, Spatial metagenomic analysis in understanding the microbial diversity of Thar Desert, Biology, 11, 461, 10.3390/biology11030461 Pronk, 2022, The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts, Environ. Microbiol., 24, 3273, 10.1111/1462-2920.15968 Saptana Gunawan, 2021, The competitiveness analysis of shallot in Indonesia: a policy analysis matrix, PLoS One, 16, e0256832, 10.1371/journal.pone.0256832 Savci, 2012, Investigation of effect of chemical fertilizers on environment, Apcbee Procedia, 1, 287, 10.1016/j.apcbee.2012.03.047 Schefe, 2007, Soil amendments modify phosphate sorption in an acid soil: the importance of P source (KH2PO4, TSP, DAP), Soil Res., 45, 246, 10.1071/SR07001 Schirawski, 2018, Plant–microbe interaction 2017—the good, the bad and the diverse, Int. J. Mol. Sci., 19, 1374, 10.3390/ijms19051374 Shukla, 2017, Comprehensive study of excess phosphate response reveals ethylene mediated signaling that negatively regulates plant growth and development, Sci. Rep., 7, 3074, 10.1038/s41598-017-03061-9 Silber, 2002, Interrelationship between phosphorus toxicity and sugar metabolism in Verticordia plumosa L, Plant Soil, 245, 249, 10.1023/A:1020432512980 Simon, 2009, Achievements and new knowledge unraveled by metagenomic approaches, Appl. Microbiol. Biotechnol., 85, 265, 10.1007/s00253-009-2233-z Simon, 2011, Metagenomic analyses: past and future trends, Appl. Environ. Microbiol., 77, 1153, 10.1128/AEM.02345-10 Sipriyadi, 2023, Bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum, Can. J. Microbiol., 10.1139/cjm-2022-0256 Spain, 2009, Abundance, composition, diversity and novelty of soil Proteobacteria, ISME J., 3, 992, 10.1038/ismej.2009.43 Sreevidya, 2016, Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea, Braz. J. Microbiol., 47, 85, 10.1016/j.bjm.2015.11.030 Sun, 2019, The insight and survey on medicinal properties and nutritive components of shallot, J. Med. Plants Res., 13, 452, 10.5897/JMPR2019.6836 Tayoh, 2016, Chemical fertilizer application and farmers perception on food safety in Buea, Cameroon, Agric. Sci. Res. J, 6, 287 Timofeeva, 2022, Prospects for using phosphate-solubilizing microorganisms as natural fertilizers in agriculture, Plants, 11, 2119, 10.3390/plants11162119 Too, 2018, Microbial community structure in a Malaysian tropical peat swamp forest: the influence of tree species and depth, Front. Microbiol., 9, 2859, 10.3389/fmicb.2018.02859 Van Reeuwijk, 2002, Procedures for soil analysis Vuolo, 2022, Impact of plant-beneficial bacterial Inocula on the resident Bacteriome: current knowledge and future perspectives, Microorganisms, 10, 2462, 10.3390/microorganisms10122462 Walkley, 1934, Estimation of soil organic carbon by the chromic acid digestion method, Soil Sci., 63, 251, 10.1097/00010694-194704000-00001 Woo, 2018, Microbial consortia: promising probiotics as plant biostimulants for sustainable agriculture, Front. Plant Sci., 9, 1801, 10.3389/fpls.2018.01801 Xu, 2023, Plant and microbial communities responded to copper and/or tetracyclines in mycorrhizal enhanced vertical flow constructed wetlands microcosms with Canna indica L, J. Hazard. Mater., 451, 10.1016/j.jhazmat.2023.131114 Zainuddin, 2022, Effect of integrated biofertilizers with chemical fertilizers on the oil palm growth and soil microbial diversity, Biocatal. Agricult. Biotechnol., 39