Immediate Effects of Chemical Fertilization on Crop Yield and Soil Bacterial Diversity: Insights for Sustainable Agriculture

Immediate Effects of Chemical Fertilization on Crop Yield and Soil Bacterial Diversity: Insights for Sustainable Agriculture | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Immediate Effects of Chemical Fertilization on Crop Yield and Soil Bacterial Diversity: Insights for Sustainable Agriculture Hamad Sawaed, Elhanan Gigi, Hanan Goldschmidt, Bar Dahan, Yarden Hadad, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6534195/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The use of chemical fertilizers is widespread in modern agriculture due to their proven benefits for crop productivity. In this study, we examined the immediate effects of the slow-release chemical fertilizer Osmocote® on plant growth and soil microbial communities in a mono and poly culture regime in controlled pot experiment over a single growth season compared to organic soil amendment treatments- Black soldier fly frass and Humus. Osmocote® addition significantly enhanced the growth rate and yield of cherry tomato (Solanum lycopersicum), basil (Ocimum basilicum), and onion (Allium cepa), confirming its effectiveness in plant growth promotion. However, parallel analysis of soil bacterial communities revealed a substantial decline in overall microbial diversity following Osmocote treatment. This reduction was particularly pronounced among bacterial groups involved in key nutrient cycling processes, such as nitrogen and organic matter turnover. Conversely, Osmocote-treated soils showed an increase in the relative abundance of bacterial taxa known for producing broad-spectrum antibacterial compounds. This shift suggests the possible emergence of a suppressive environment that may hinder microbial recolonization and compromise long-term soil health, even after fertilizer application ceases. In contrast, soils amended with organic fertilizers maintained or enriched microbial diversity. Similarly, the presence of plants positively influenced soil bacterial diversity, with some species exerting stronger effects than others. Notably, co-planting multiple species within a pot elevated microbial diversity to levels comparable to those observed with the most beneficial single species. These observations highlight the potential of integrative strategies combining organic and chemical fertilization, alongside diverse plantings, to support both high crop productivity and sustainable soil microbial ecology. Our findings underscore the immediate negative effects of chemical fertilization, which may have long-term consequences for soil function and plant growth potential and suggest more sustainable alternatives. Figures Figure 1 Figure 2 Figure 3 Figure 4 Background Sustainable agriculture seeks to balance high crop productivity with the preservation of integrity[ 1 ]. A central component of this balance is soil fertility management, where chemical fertilizers have long played a dominant role in enhancing agronomic performance[ 2 ]. These fertilizers are valued for their rapid nutrient release and ability to support vigorous plant growth. However, their intensive and widespread use has raised significant concerns about long-term environmental impacts, particularly on soil health and microbial diversity[ 3 – 5 ]. Numerous studies have shown that chemical fertilizers can reduce soil organic matter and alter microbial communities, which are essential for nutrient cycling and ecosystem stability[ 6 , 7 ]. Prolonged use has been linked to declines in microbial diversity and shifts in community composition, potentially impairing soil resilience and key ecological function[ 6 , 8 – 11 ]. More studies have explored the impacts of chemical fertilization practices on soil microbial communities and crop yields[ 12 – 15 ]. Hartmann et al. (2015)[ 3 ] conducted a comprehensive study comparing long-term organic and conventional farming systems, revealing significant differences in soil microbial diversity and function. Similarly, Geisseler and Scow (2014)[ 6 ] reviewed the long-term effects of mineral fertilizers on soil microorganisms, demonstrating that intensive chemical fertilization can diminish soil microbial diversity and health. These studies emphasize the potential ecological consequences of chemical fertilizer use, including reduced soil resilience and altered nutrient cycles[ 16 , 17 ]. While much of this evidence focuses on long-term applications, the short-term effects of chemical fertilizers on soil microbial ecology remain less explored. The present study addresses this gap by investigating the immediate impact of a slow-release chemical fertilizer (Osmocote®) on plant productivity and soil bacterial communities over a single growing season. Focusing on three economically important crop species—tomato ( Solanum lycopersicum ), basil ( Ocimum basilicum ), and onion ( Allium cepa )—we assessed both plant performance and microbial diversity. Our research utilized high-throughput 16S rRNA sequencing to analyze the taxonomic composition and diversity of soil bacterial populations[ 18 , 19 ], offering insights into the broader ecological impacts of chemical fertilization practices. As expected our findings indicate that chemical fertilization significantly enhances plant growth and crop yields for all three examined plant species. Nevertheless, our findings reveal that even short-term chemical fertilization significantly reduces soil bacterial diversity, particularly among taxa involved in nutrient cycling (e.g., Nitrosomonadaceae , Hyphomicrobium ), while promoting antibiotic-producing bacteria (e.g., Streptomyces , Kitasatospora ). In contrast, organic fertilizers such as commercially used humus[ 20 ] and homemade black soldier fly frass[ 21 ] enriched soil microbial diversity. Additionally, the presence and identity of plants—particularly tomato—positively influenced bacterial diversity, with co-planting strategies showing additive effects. In accordance with previous studies the plant effect seemed to depend on the plant[ 22 ]. Overall it appears that while no doubtfully chemical fertilizers help enhance plant productivity - using chemical fertilizers on their own is harmful for the soil even after a short period of usage. Soil treatment strategies, perhaps combining organic additives, or multispecies cultures should be considered for a long term, sustainable solution. Materials and Methods Multi-Species Pot Cultivation Seedlings of tomato ( Solanum lycopersicum ), basil ( Ocimum basilicum ), and onion ( Allium cepa ) were individually transplanted into 10-liter pots. Each pot contained either a monoculture, a two-species combination, or all three species, arranged according to a factorial design to assess interspecies interactions. The pots were filled with a standardized substrate composed of 9 liters of red Tuf 4–8 soil (commercially sourced) and 1 liter of indigenous forest soil, serving as a source of native microbiota. Slow-release chemical fertilizer (Osmocote®) was applied to designated treatments at manufacturer-recommended rates. In treatments using organic fertilizers (humus and black soldier fly FRASS), nitrogen levels were matched to those in the Osmocote treatments. Ten replicates were prepared for each treatment, and all plants were cultivated in a spacious greenhouse located at the Matityahoo farm in the eastern upper Galilee region. The temperature in the greenhouse ranged from 14–49 ̊C with an average of 32 ̊C. The soil pH was mostly between 7–8 for all treatments but occasional drops to 5.5–6.5 were observed, mostly in pots treated with osmocote but not only. Organic soil amendments Two organic soil amendments were used in this experiment: a . commercially purchased organic Humus produced Eisenia fetida red warms from household organic waste. b . homemade Back Soldier Fly Frass: Neonate-stage larvae of Hermetia illucens were purchased from FreezeM and fed a diet of 55% apple waste, 30% brewery yeast liquid, and 15% dried brewery malt. Larvae were reared in a temperature-controlled room (28 ± 2°C) in three stages: (1) initial acclimation with small amounts of diet added to neonate bottles; (2) transfer of 5 g larvae to 2-liter containers with 1 kg substrate for one week; (3) subsequent transfer at the third instar to stainless steel trays (51×30×11 cm), each containing 4 kg substrate. Trays were stacked vertically with 13 cm spacing for air circulation. Larvae were harvested at the fifth instar, separated using a dual-mesh sieve (1 cm² and 0.4 cm²) from "Koraleck Almog Ltd." After removal of the top dried layer, frass was collected, dried to constant weight, ground to 0.4 cm² particles, and refrigerated to prevent fermentation until use in the experiment. Plant Growth Monitoring Plants were monitored weekly to assess growth and development. Detailed measurements of plant height and growth stage were recorded for each plant in every pot, considering the specific plantation arrangement and fertilization treatment. Soil parameters, including pH and moisture levels, were measured to monitor soil conditions. Environmental conditions within the greenhouse, such as temperature and radiation levels, were documented regularly. Any signs of plant stress, such as drought, disease symptoms, or pest presence, were carefully recorded. Tomato growth was classified into four stages: (1) vegetative (leaf and stem development), (2) flowering (onset of floral structures), (3) early fruit (immature fruits visible), and (4) mature fruit (full-sized, ripe fruits ready for harvest). Productivity Measurements Weekly yield was measured as the fresh (wet) weight of harvested crops. For tomatoes, only ripe fruits were harvested; for basil and onion, edible aerial parts were collected. The weekly average crop yield was calculated for each treatment and used as a measure of plant productivity. Soil Sampling Soil was sampled monthly from the rhizosphere (at 5–10 cm depth below soil surface) of each plant using a sterile spatula, targeting soil directly adjacent to the root system, avoiding root damage. Five samples per treatment were collected every month into sterile 1.5 ml Eppendorf tubes and kept at − 80 ̊C until analysis. Soil DNA Extraction Total soil DNA was extracted using the Qiagen DNeasy PowerSoil Pro Kit (Cat. No. 47014). Samples of 50 µl, at 1 µg/ml DNA concentration, were submitted for 16S rRNA gene sequencing (V3–V4 region) by CosmosID. The samples were sequenced in two batches: The first batch consisted of 50 samples of soil collected 1–3 months into the experiment, 25 samples treated with osmocote® and 25 samples with no fertilization treatment. Each fertilization treatment contained 5–8 sample repeats of each plant species. Soil controls with no growing plant were analyzed as well. The second batch contained additional 37 samples and included 13 samples treated with organic fertilizers. 16S Amplicon Classification Taxonomic classification of 16S rRNA amplicons was performed by CosmosID using their proprietary analysis pipeline. Raw reads were quality-filtered, trimmed, and joined (if paired-end), then converted to FASTA format. OTU picking was performed via QIIME using a closed-reference approach (97% similarity threshold) against the SILVA v138 database. Resulting tables included OTU ID, taxonomic assignment, frequency, and relative abundance. Statistical Analysis Alpha diversity (Chao1 index) and relative abundance analyses were conducted using the CosmosID-HUB platform. Differential abundance analysis was performed using the platform’s Advanced Statistics Module, which incorporates multivariable linear modeling tools such as MaAsLin2 and MaAsLin3 ( Multivariable Association with Linear Models ). These tools identify associations between microbial features and metadata while controlling for potential confounding factors and applying multiple testing corrections (e.g., False Discovery Rate). Statistical significance was determined at p < 0.05. Results Plant Growth and Productivity All three crop species examined: tomato, basil, and onion — grew significantly faster when the soil was enriched with the chemical fertilizer Osmocote (Fig. 1 A-C). Additionally, crop yield production was markedly higher in Osmocote-treated soil (Fig. 1 D). The substantial improvements in plant growth and development, as well as increased crop yield explain the widespread use of chemical fertilizers in agriculture despite their cost and harmful environmental impact. Fertilization Impact on Bacterial Diversity The addition of chemical fertilizer to the soil significantly reduced overall bacterial diversity (Fig. 2 ). Notably, bacterial species associated with nutrient recycling experienced a marked decline (Fig. 3 A-D) (Table 1 ). In contrast, groups producing antimicrobial molecules thrived under these conditions (Fig. 3 E-H) (Table 1 ). These findings highlight a shift in the soil bacterial community structure, indicating that even short exposure to chemical fertilization may cause substantial changes in soil bacterial populations. The application of the organic fertilizers Humus and black soldier fly FRASS did not reduce soil bacterial abundance, and have even contributed to it, suggesting that the observed microbial shifts were not solely due to NPK concentration, as equivalent nutrient levels from organic fertilizers did not produce similar effects (Fig. 2 C). Table 1 Known function within soil of bacterial groups presented in Fig. 3 . Bacterial Group Typical function in soil Hyphomicrobium Involved in nitrogen cycle, specifically in the oxidation of methanol and other C1 compounds. Contributes to soil fertility by recycling essential nutrients and degrading organic pollutants. Myxococcales Known for predatory behavior against other microorganisms, helping control soil pathogen populations. Produces antibiotics and enzymes that contribute to soil health and plant growth. Nitrosomonadaceae Important nitrifiers in the nitrogen cycle, oxidizing ammonia to nitrite. This process is crucial for nitrogen transformation, making nitrogen available to plants in a usable form and maintaining soil fertility. Rhodospirillaceae Involved in nitrogen fixation, converting atmospheric nitrogen into forms that plants can absorb and use. Particularly important in soils with low nitrogen availability. Streptomyces (species 1 & 2) Produces a wide range of antibiotics that help suppress soil-borne plant pathogens. Produces plant growth-promoting substances such as indole acetic acid (IAA) and siderophores, enhancing nutrient availability and uptake by plants. Amycolatopsis Produces antibiotics and other bioactive compounds. Involved in the degradation of complex organic materials, contributing to soil organic matter turnover and nutrient cycling. Kitasatospora Produces various secondary metabolites, including antibiotics, which help control harmful soil microorganisms. Contributes to organic matter decomposition and nutrient cycling, supporting plant growth. Plant Impact on Bacterial Diversity The plant presence influenced the soil microbial community, with overall plant presence contributing positively to soil microbial diversity (Fig. 4 A). Co-plantation of more than one plant species in a pot did not significantly alter this positive effect observed for single species presence, but the bacterial diversity in those pots did seem to be higher than the diversity observed for some of the single plant species alone (Fig. 4 B). This suggests that co-plantation may be a strategy to increase bacterial diversity within the soil, but the plant species should be examined individually – as some species tend to promote bacterial richness more than others. Discussion This study aimed to examine the immediate effects of chemical fertilization on both crop yield and the composition of soil bacterial communities. Our findings show that while soil treatment with the chemical fertilizer (Osmocote®) significantly improved plant growth and productivity (Fig. 1 ), it also caused a rapid decline in overall bacterial diversity within the soil (Fig. 2 ). Similar effects have been reported in long-term studies of chemically fertilized soils, including in the root zones of cultivated walnut trees[ 10 ], and in agricultural soil dedicated to wheat and soybean cultivation[ 23 ]. Furthermore, the addition of the chemical fertilizer in our case appeared to specifically decrease the presence of bacterial groups associated with soil nutrient cycles, while having a significant positive impact on the abundance of bacterial species known for their high antimicrobial substance production (Fig. 3 , Table 1 ). The significant rise in abundance of antibacterial compounds within the soil may prevent nutrient recycling bacteria from re-establishing within the previously fertilized soil, even when fertilization is no longer applied. Thus, long term soil productivity reduction in chemically fertilized agricultural soil[ 15 , 24 ], in fact appears to initiate early on with fertilization application potentially making chemical fertilization even less forgiving than previously considered. In addition to fertilizer type, we found that plant presence and species composition also influenced soil bacterial diversity. These factors seemed to have immediate positive effects on soil bacterial diversity. Thus, the application of organic fertilizers such as humus and black soldier fly frass (Fig. 2 C), and the very presence of plants in the soil (Fig. 4 ) elevated bacterial richness within the soil. Co-planting species appeared to elevate overall bacterial diversity to the level associated with the species that contributed most strongly to microbial enrichment. These findings were in accordance with previous work showing that organic fertilizers tend to contribute to soil bacterial diversity in rice fields[ 25 , 26 ], grape rhizosphere[ 27 ], garlic[ 28 ], and tea ( Camelia sinensis )[ 29 ]; and showing that multi crop planting has effectively increased soil bacterial diversity[ 30 ]. Unlike previous studies focusing on long-term effects, our findings demonstrate that significant changes in microbial community composition can occur within just 3 months of cultivation. Recent efforts have focused on promoting the combined use of organic and chemical fertilizers in the aim of achieving a healthy balance between high crop yields on one hand, while maintaining soil health which is emphasized by diverse bacterial community, specifically capable of nutrient recycling on the other hand[ 31 – 33 ]. Our findings strongly support this approach, highlighting the immediate and pronounced shifts in bacterial communities following chemical fertilizer application on agricultural soils even when the benefits to crop yield are clear. Declarations Author Contribution H.G, E.G, L.S and R.C.K planned the greenhouse growth experiments H.G and E.G were responsible for the physical work and data collection, R.C.K has analyzed the data.H.S, B.D, and Y.H extracted the soil DNA and prepared it for sequencing with help from S.O.O and R.C.K R.C.K has analyzed the DNA sequencing data using the CosmosID hubR.C.K wrote the manuscript, L.S added methodology regarding organic fertilization, all authors reviewed the manuscript Acknowledgement This research was funded by the Israel Chief Scientist Foundation of the Ministry of Agriculture (ICSFA). Project number 21-02-0011- Using frass derived from black soldier larvae treatment of agricultural plant waste as a product enhancing plant protection and growth. References Pretty J, Benton TG, Bharucha ZP, Dicks LV, Flora CB, Godfray HCJ, et al. Global assessment of agricultural system redesign for sustainable intensification. Nature Sustainability. 2018;1(8):441–6; doi: 10.1038/s41893-018-0114-0 . Kumar R, Kumar R, Prakash O. Chapter-5 the impact of chemical fertilizers on our environment and ecosystem. Chief Ed. 2019;35(69):1173–89. Hartmann M, Frey B, Mayer J, Mäder P, Widmer F. Distinct soil microbial diversity under long-term organic and conventional farming. The ISME journal. 2015;9(5):1177–94. Penuelas J, Coello F, Sardans J. A better use of fertilizers is needed for global food security and environmental sustainability. Agriculture & Food Security. 2023;12(1):1–9. Powlson DS, Gregory PJ, Whalley WR, Quinton JN, Hopkins DW, Whitmore AP, et al. Soil management in relation to sustainable agriculture and ecosystem services. Food policy. 2011;36:S72-S87. Geisseler D, Scow KM. Long-term effects of mineral fertilizers on soil microorganisms–A review. Soil Biology and Biochemistry. 2014;75:54–63. Bender SF, Wagg C, van der Heijden MG. An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends in ecology & evolution. 2016;31(6):440–52. Yan D, Wang D, Yang L. Long-term effect of chemical fertilizer, straw, and manure on labile organic matter fractions in a paddy soil. Biology and Fertility of Soils. 2007;44:93–101. Beltran-Garcia MJ, Martínez-Rodríguez A, Olmos-Arriaga I, Valdes-Salas B, Di Mascio P, White JF. Nitrogen fertilization and stress factors drive shifts in microbial diversity in soils and plants. Symbiosis. 2021;84(3):379–90. Bai Y-C, Chang Y-Y, Hussain M, Lu B, Zhang J-P, Song X-B, et al. Soil chemical and microbiological properties are changed by long-term chemical fertilizers that limit ecosystem functioning. Microorganisms. 2020;8(5):694. Meena RS, Kumar S, Datta R, Lal R, Vijayakumar V, Brtnicky M, et al. Impact of agrochemicals on soil microbiota and management: A review. Land. 2020;9(2):34. Dincă LC, Grenni P, Onet C, Onet A. Fertilization and soil microbial community: a review. Applied Sciences. 2022;12(3):1198. Guo Z, Wan S, Hua K, Yin Y, Chu H, Wang D, et al. Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystem. Applied Soil Ecology. 2020;149:103510. Li J, Cooper JM, Lin Za, Li Y, Yang X, Zhao B. Soil microbial community structure and function are significantly affected by long-term organic and mineral fertilization regimes in the North China Plain. Applied Soil Ecology. 2015;96:75–87. Pahalvi HN, Rafiya L, Rashid S, Nisar B, Kamili AN. Chemical fertilizers and their impact on soil health. Microbiota and Biofertilizers, Vol 2: Ecofriendly tools for reclamation of degraded soil environs. 2021:1–20. Deshoux M, Sadet-Bourgeteau S, Gentil S, Prévost-Bouré NC. Effects of biochar on soil microbial communities: a meta-analysis. Science of the Total Environment. 2023;902:166079. Zhang Z, Zhan Y, Zhang Z, Liu Y, Xu T, Wei Y, et al. Tomato endophyte bacteria diversity under long-term organic agricultural manipulation systems. 2021. Peng M, Zi X, Wang Q. Bacterial community diversity of oil-contaminated soils assessed by high throughput sequencing of 16S rRNA genes. International Journal of Environmental Research and Public Health. 2015;12(10):12002–15. Armougom F, Raoult D. Exploring microbial diversity using 16S rRNA high-throughput methods. J Comput Sci Syst Biol. 2009;2(1):74–92. Senesi N. Composted materials as organic fertilizers. Science of the Total Environment. 1989;81:521–42. Abd Manan F, Yeoh Y-K, Chai T-T, Wong F-C. Unlocking the potential of black soldier fly frass as a sustainable organic fertilizer: A review of recent studies. Journal of Environmental Management. 2024;367:121997. Zhang J, Liu Y-X, Zhang N, Hu B, Jin T, Xu H, et al. NRT1. 1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature biotechnology. 2019;37(6):676–84. Sun R, Zhang X-X, Guo X, Wang D, Chu H. Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw. Soil Biology and Biochemistry. 2015;88:9–18. Edmeades DC. The long-term effects of manures and fertilisers on soil productivity and quality: a review. Nutrient Cycling in Agroecosystems. 2003;66(2):165–80; doi: 10.1023/A:1023999816690 . Liu J, Shu A, Song W, Shi W, Li M, Zhang W, et al. Long-term organic fertilizer substitution increases rice yield by improving soil properties and regulating soil bacteria. Geoderma. 2021;404:115287. Zhang Z, Liu H, Liu X, Chen Y, Lu Y, Shen M, et al. Organic fertilizer enhances rice growth in severe saline–alkali soil by increasing soil bacterial diversity. Soil Use and Management. 2022;38(1):964–77. Wu L, Jiang Y, Zhao F, He X, Liu H, Yu K. Increased organic fertilizer application and reduced chemical fertilizer application affect the soil properties and bacterial communities of grape rhizosphere soil. Scientific Reports. 2020;10(1):9568. Ma Y, Shen S, Wan C, Wang S, Yang F, Zhang K, et al. Organic fertilizer substitution over six years improves the productivity of garlic, bacterial diversity, and microbial communities network complexity. Applied Soil Ecology. 2023;182:104718. Gu S, Hu Q, Cheng Y, Bai L, Liu Z, Xiao W, et al. Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils. Soil and Tillage Research. 2019;195:104356. Tang H, Liu Y, Yang X, Huang G, Liang X, Shah AN, et al. Multiple cropping effectively increases soil bacterial diversity, community abundance and soil fertility of paddy fields. BMC Plant Biology. 2024;24(1):715. Wan L-J, Tian Y, He M, Zheng Y-Q, Lyu Q, Xie R-J, et al. Effects of chemical fertilizer combined with organic fertilizer application on soil properties, citrus growth physiology, and yield. Agriculture. 2021;11(12):1207. Han J, Dong Y, Zhang M. Chemical fertilizer reduction with organic fertilizer effectively improve soil fertility and microbial community from newly cultivated land in the Loess Plateau of China. Applied Soil Ecology. 2021;165:103966. Jin N, Jin L, Wang S, Li J, Liu F, Liu Z, et al. Reduced chemical fertilizer combined with bio-organic fertilizer affects the soil microbial community and yield and quality of lettuce. Frontiers in Microbiology. 2022;13:863325. Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6534195","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":449542133,"identity":"960c3846-7f7c-4e56-925a-a42fd0584860","order_by":0,"name":"Hamad Sawaed","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Hamad","middleName":"","lastName":"Sawaed","suffix":""},{"id":449542134,"identity":"e2d283e8-d0cd-4170-a279-39ce96b9a60e","order_by":1,"name":"Elhanan Gigi","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Elhanan","middleName":"","lastName":"Gigi","suffix":""},{"id":449542135,"identity":"1b89dc35-3808-4fc2-9391-015dbd80c613","order_by":2,"name":"Hanan Goldschmidt","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Hanan","middleName":"","lastName":"Goldschmidt","suffix":""},{"id":449542136,"identity":"501e836c-1e9f-48b3-89d5-a8734849b752","order_by":3,"name":"Bar Dahan","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Bar","middleName":"","lastName":"Dahan","suffix":""},{"id":449542137,"identity":"8a1d7487-aaa4-43fb-91aa-5df55e0215a8","order_by":4,"name":"Yarden Hadad","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Yarden","middleName":"","lastName":"Hadad","suffix":""},{"id":449542138,"identity":"280abb4c-7d65-4679-87fc-67bf2f3b5c98","order_by":5,"name":"Liora Shaltiel","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Liora","middleName":"","lastName":"Shaltiel","suffix":""},{"id":449542139,"identity":"764da0ef-dc47-40cf-be63-992da437bbd8","order_by":6,"name":"Shira Ohr Omer","email":"","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":false,"prefix":"","firstName":"Shira","middleName":"Ohr","lastName":"Omer","suffix":""},{"id":449542140,"identity":"fd89c128-d7aa-43b5-92cb-3f4e0ed344c4","order_by":7,"name":"Ruth Cohen-Khait","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAyklEQVRIiWNgGAWjYHACNgaGCgYeBgbmBgiXnaAOZqCWMyAtjFAtzMRoYWwDMaBaGAhpMZ+Rf+zBz3nbZOTdDzYwfNxTy8BHSIvMjWR2w95tt3kMzyQ2MM54dpywwyQkktmkGUFaGhIbmHkOHCNWyxyglv6HJGlpuM0jLwG2pYYILTyPzSR7jt3mMZB42HBwxoEDPIS1sCc+k/hRc9tevj/54IMPB+rk5NsbCOiBAYMDDAxAdJiHSPVAIA8xu454HaNgFIyCUTBiAACHBzqiVrfDGwAAAABJRU5ErkJggg==","orcid":"","institution":"Migal - Galilee Technology Center","correspondingAuthor":true,"prefix":"","firstName":"Ruth","middleName":"","lastName":"Cohen-Khait","suffix":""}],"badges":[],"createdAt":"2025-04-26 09:53:17","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6534195/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6534195/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":81704200,"identity":"0271ea53-3345-48ad-98f8-16e894ff903e","added_by":"auto","created_at":"2025-04-30 13:17:44","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":158819,"visible":true,"origin":"","legend":"\u003cp\u003ePlant Growth Parameters. \u003cstrong\u003eA-C\u003c/strong\u003e Average plant height (cm) measured weekly throughout the experiment. Error bars represent standard error, when N=20-40 individual measurements for each data point. \u003cstrong\u003eA\u003c/strong\u003e Tomato \u003cstrong\u003eB\u003c/strong\u003e Basil \u003cstrong\u003eC\u003c/strong\u003eOnion. \u003cstrong\u003eD\u003c/strong\u003e Average wet plant crop yield (in grams) measured weekly post-harvest. Error bars represent standard error. N=6 for each treatment, each measurement represents the weekly average of the specific crop harvest at each treatment. Each panel includes a comparison between plants grown in Osmocote-treated soil and control soil.\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-6534195/v1/0005f1bc863b8467a1aa6d7f.png"},{"id":81704196,"identity":"0d523a29-f01b-43b0-a327-822b35ca93a4","added_by":"auto","created_at":"2025-04-30 13:17:44","extension":"jpeg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":635558,"visible":true,"origin":"","legend":"\u003cp\u003eEffect of Chemical Fertilization on Plant-Soil Associated Bacterial Population. \u003cstrong\u003eA\u003c/strong\u003eAlpha diversity Chao 1 index of the bacterial population detected by 16S rRNA analysis of the V3-V4 gene region across different treatments. N=25 samples for each fertilization treatment. Analyzed samples were collected 1-3 months after plantation, and include 5-8 representatives of each plant species and soil controls emphasizing on the fertilization effect beyond crop identity. \u003cstrong\u003eB\u003c/strong\u003eHeat map showing the relative abundance of bacterial taxa across different soil samples. \"U_S\" denotes undefined species. Each row represents a different bacterial taxon, and each column represents a single sample within the treatment (the same data set as shown in panel A). \u003cstrong\u003eC\u003c/strong\u003e Alpha diversity Chao 1 index of the bacterial population detected by 16S rRNA analysis of the V3-V4 gene. Number of analyzed samples for each treatment: N=37 for no fertilizer, N=37 for osmocote, N=6 for frass, N=7 for humus. The samples were taken at different time points ranging from 1-3 months after inoculation, and have representatives of all plant species including no plant soil controls. Statistical significance across all panels is indicated as follows: ns p\u0026gt;0.05, * p \u0026lt; 0.05, ** p\u0026lt;0.01, *** p\u0026lt;0.001, **** p\u0026lt;0.0001.\u003c/p\u003e","description":"","filename":"floatimage2.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6534195/v1/787001910fa474f94e93913b.jpeg"},{"id":81704197,"identity":"565d4217-03a0-4ede-bf91-756ae0cc215c","added_by":"auto","created_at":"2025-04-30 13:17:44","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":221373,"visible":true,"origin":"","legend":"\u003cp\u003eRelative abundance of bacterial species which are strongly influenced by chemical fertilization. These analyses were made on the same data set described in Fig. 2A. Each panel shows the relative abundance of a bacterial group which is indicated at its title. The specific properties of each bacterial group are deliberated in Table 1. Statistical significance across all panels is indicated as follows: ns p\u0026gt;0.05, * p \u0026lt; 0.05, ** p\u0026lt;0.01, *** p\u0026lt;0.001, **** p\u0026lt;0.0001.\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-6534195/v1/f99f514cd9eba9eab27c36b7.png"},{"id":81705320,"identity":"8c1f8614-c346-4321-affa-9d77106134e2","added_by":"auto","created_at":"2025-04-30 13:25:44","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":87804,"visible":true,"origin":"","legend":"\u003cp\u003eThe influence of plant species on soil bacterial diversity. The plants were subject to different fertilization treatments, the influence of the fertilization factor is presented in Fig 2C, the present analysis examines whether \u003cstrong\u003eA\u003c/strong\u003ethe plant species or \u003cstrong\u003eB\u003c/strong\u003e the plant’s neighbors have any influence on the overall bacterial diversity at the plant’s rhizosphere, beyond the fertilization effect. Abbreviations in \u003cstrong\u003eB\u003c/strong\u003e NP=No Plant, T=Tomato, B=Basil, O=Onion. Statistical significance across all panels is indicated as follows: ns p\u0026gt;0.05, * p \u0026lt; 0.05, ** p\u0026lt;0.01, *** p\u0026lt;0.001, **** p\u0026lt;0.0001.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-6534195/v1/61e3da62327654c0e38a1e87.png"},{"id":85209770,"identity":"9b9d8e37-2cfa-4b99-9943-7b319ba94872","added_by":"auto","created_at":"2025-06-23 12:17:11","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1701942,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6534195/v1/cdf8eb84-bdb1-4891-82f4-eb81e951f01b.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Immediate Effects of Chemical Fertilization on Crop Yield and Soil Bacterial Diversity: Insights for Sustainable Agriculture","fulltext":[{"header":"Background","content":"\u003cp\u003eSustainable agriculture seeks to balance high crop productivity with the preservation of integrity[\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. A central component of this balance is soil fertility management, where chemical fertilizers have long played a dominant role in enhancing agronomic performance[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. These fertilizers are valued for their rapid nutrient release and ability to support vigorous plant growth. However, their intensive and widespread use has raised significant concerns about long-term environmental impacts, particularly on soil health and microbial diversity[\u003cspan additionalcitationids=\"CR4\" citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eNumerous studies have shown that chemical fertilizers can reduce soil organic matter and alter microbial communities, which are essential for nutrient cycling and ecosystem stability[\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Prolonged use has been linked to declines in microbial diversity and shifts in community composition, potentially impairing soil resilience and key ecological function[\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan additionalcitationids=\"CR9 CR10\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. More studies have explored the impacts of chemical fertilization practices on soil microbial communities and crop yields[\u003cspan additionalcitationids=\"CR13 CR14\" citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. Hartmann et al. (2015)[\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e] conducted a comprehensive study comparing long-term organic and conventional farming systems, revealing significant differences in soil microbial diversity and function. Similarly, Geisseler and Scow (2014)[\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e] reviewed the long-term effects of mineral fertilizers on soil microorganisms, demonstrating that intensive chemical fertilization can diminish soil microbial diversity and health. These studies emphasize the potential ecological consequences of chemical fertilizer use, including reduced soil resilience and altered nutrient cycles[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e, \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. While much of this evidence focuses on long-term applications, the short-term effects of chemical fertilizers on soil microbial ecology remain less explored.\u003c/p\u003e \u003cp\u003eThe present study addresses this gap by investigating the immediate impact of a slow-release chemical fertilizer (Osmocote\u0026reg;) on plant productivity and soil bacterial communities over a single growing season. Focusing on three economically important crop species\u0026mdash;tomato (\u003cem\u003eSolanum lycopersicum\u003c/em\u003e), basil (\u003cem\u003eOcimum basilicum\u003c/em\u003e), and onion (\u003cem\u003eAllium cepa\u003c/em\u003e)\u0026mdash;we assessed both plant performance and microbial diversity. Our research utilized high-throughput 16S rRNA sequencing to analyze the taxonomic composition and diversity of soil bacterial populations[\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e, \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e], offering insights into the broader ecological impacts of chemical fertilization practices.\u003c/p\u003e \u003cp\u003eAs expected our findings indicate that chemical fertilization significantly enhances plant growth and crop yields for all three examined plant species. Nevertheless, our findings reveal that even short-term chemical fertilization significantly reduces soil bacterial diversity, particularly among taxa involved in nutrient cycling (e.g., \u003cem\u003eNitrosomonadaceae\u003c/em\u003e, \u003cem\u003eHyphomicrobium\u003c/em\u003e), while promoting antibiotic-producing bacteria (e.g., \u003cem\u003eStreptomyces\u003c/em\u003e, \u003cem\u003eKitasatospora\u003c/em\u003e). In contrast, organic fertilizers such as commercially used humus[\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e] and homemade black soldier fly frass[\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e] enriched soil microbial diversity. Additionally, the presence and identity of plants\u0026mdash;particularly tomato\u0026mdash;positively influenced bacterial diversity, with co-planting strategies showing additive effects. In accordance with previous studies the plant effect seemed to depend on the plant[\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. Overall it appears that while no doubtfully chemical fertilizers help enhance plant productivity - using chemical fertilizers on their own is harmful for the soil even after a short period of usage. Soil treatment strategies, perhaps combining organic additives, or multispecies cultures should be considered for a long term, sustainable solution.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eMulti-Species Pot Cultivation\u003c/h2\u003e \u003cp\u003eSeedlings of tomato (\u003cem\u003eSolanum lycopersicum\u003c/em\u003e), basil (\u003cem\u003eOcimum basilicum\u003c/em\u003e), and onion (\u003cem\u003eAllium cepa\u003c/em\u003e) were individually transplanted into 10-liter pots. Each pot contained either a monoculture, a two-species combination, or all three species, arranged according to a factorial design to assess interspecies interactions. The pots were filled with a standardized substrate composed of 9 liters of red Tuf 4\u0026ndash;8 soil (commercially sourced) and 1 liter of indigenous forest soil, serving as a source of native microbiota. Slow-release chemical fertilizer (Osmocote\u0026reg;) was applied to designated treatments at manufacturer-recommended rates. In treatments using organic fertilizers (humus and black soldier fly FRASS), nitrogen levels were matched to those in the Osmocote treatments. Ten replicates were prepared for each treatment, and all plants were cultivated in a spacious greenhouse located at the Matityahoo farm in the eastern upper Galilee region. The temperature in the greenhouse ranged from 14\u0026ndash;49 ̊C with an average of 32 ̊C. The soil pH was mostly between 7\u0026ndash;8 for all treatments but occasional drops to 5.5\u0026ndash;6.5 were observed, mostly in pots treated with osmocote but not only.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eOrganic soil amendments\u003c/h3\u003e\n\u003cp\u003eTwo organic soil amendments were used in this experiment: \u003cb\u003ea\u003c/b\u003e. commercially purchased organic Humus produced \u003cem\u003eEisenia fetida\u003c/em\u003e red warms from household organic waste. \u003cb\u003eb\u003c/b\u003e. homemade Back Soldier Fly Frass: Neonate-stage larvae of \u003cem\u003eHermetia illucens\u003c/em\u003e were purchased from FreezeM and fed a diet of 55% apple waste, 30% brewery yeast liquid, and 15% dried brewery malt. Larvae were reared in a temperature-controlled room (28\u0026thinsp;\u0026plusmn;\u0026thinsp;2\u0026deg;C) in three stages: (1) initial acclimation with small amounts of diet added to neonate bottles; (2) transfer of 5 g larvae to 2-liter containers with 1 kg substrate for one week; (3) subsequent transfer at the third instar to stainless steel trays (51\u0026times;30\u0026times;11 cm), each containing 4 kg substrate. Trays were stacked vertically with 13 cm spacing for air circulation. Larvae were harvested at the fifth instar, separated using a dual-mesh sieve (1 cm\u0026sup2; and 0.4 cm\u0026sup2;) from \"Koraleck Almog Ltd.\" After removal of the top dried layer, frass was collected, dried to constant weight, ground to 0.4 cm\u0026sup2; particles, and refrigerated to prevent fermentation until use in the experiment.\u003c/p\u003e\n\u003ch3\u003ePlant Growth Monitoring\u003c/h3\u003e\n\u003cp\u003ePlants were monitored weekly to assess growth and development. Detailed measurements of plant height and growth stage were recorded for each plant in every pot, considering the specific plantation arrangement and fertilization treatment. Soil parameters, including pH and moisture levels, were measured to monitor soil conditions. Environmental conditions within the greenhouse, such as temperature and radiation levels, were documented regularly. Any signs of plant stress, such as drought, disease symptoms, or pest presence, were carefully recorded. Tomato growth was classified into four stages: (1) vegetative (leaf and stem development), (2) flowering (onset of floral structures), (3) early fruit (immature fruits visible), and (4) mature fruit (full-sized, ripe fruits ready for harvest).\u003c/p\u003e\n\u003ch3\u003eProductivity Measurements\u003c/h3\u003e\n\u003cp\u003eWeekly yield was measured as the fresh (wet) weight of harvested crops. For tomatoes, only ripe fruits were harvested; for basil and onion, edible aerial parts were collected. The weekly average crop yield was calculated for each treatment and used as a measure of plant productivity.\u003c/p\u003e\n\u003ch3\u003eSoil Sampling\u003c/h3\u003e\n\u003cp\u003eSoil was sampled monthly from the rhizosphere (at 5\u0026ndash;10 cm depth below soil surface) of each plant using a sterile spatula, targeting soil directly adjacent to the root system, avoiding root damage. Five samples per treatment were collected every month into sterile 1.5 ml Eppendorf tubes and kept at \u0026minus;\u0026thinsp;80 ̊C until analysis.\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eSoil DNA Extraction\u003c/h2\u003e \u003cp\u003eTotal soil DNA was extracted using the Qiagen DNeasy PowerSoil Pro Kit (Cat. No. 47014). Samples of 50 \u0026micro;l, at 1 \u0026micro;g/ml DNA concentration, were submitted for 16S rRNA gene sequencing (V3\u0026ndash;V4 region) by CosmosID. The samples were sequenced in two batches: The first batch consisted of 50 samples of soil collected 1\u0026ndash;3 months into the experiment, 25 samples treated with osmocote\u0026reg; and 25 samples with no fertilization treatment. Each fertilization treatment contained 5\u0026ndash;8 sample repeats of each plant species. Soil controls with no growing plant were analyzed as well. The second batch contained additional 37 samples and included 13 samples treated with organic fertilizers.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003e16S Amplicon Classification\u003c/h3\u003e\n\u003cp\u003eTaxonomic classification of 16S rRNA amplicons was performed by CosmosID using their proprietary analysis pipeline. Raw reads were quality-filtered, trimmed, and joined (if paired-end), then converted to FASTA format. OTU picking was performed via QIIME using a closed-reference approach (97% similarity threshold) against the SILVA v138 database. Resulting tables included OTU ID, taxonomic assignment, frequency, and relative abundance.\u003c/p\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eStatistical Analysis\u003c/h2\u003e \u003cp\u003eAlpha diversity (Chao1 index) and relative abundance analyses were conducted using the CosmosID-HUB platform. Differential abundance analysis was performed using the platform\u0026rsquo;s Advanced Statistics Module, which incorporates multivariable linear modeling tools such as MaAsLin2 and MaAsLin3 (\u003cem\u003eMultivariable Association with Linear Models\u003c/em\u003e). These tools identify associations between microbial features and metadata while controlling for potential confounding factors and applying multiple testing corrections (e.g., False Discovery Rate). Statistical significance was determined at p\u0026thinsp;\u0026lt;\u0026thinsp;0.05.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\n \u003ch2\u003ePlant Growth and Productivity\u003c/h2\u003e\n \u003cp\u003eAll three crop species examined: tomato, basil, and onion \u0026mdash; grew significantly faster when the soil was enriched with the chemical fertilizer Osmocote (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eA-C). Additionally, crop yield production was markedly higher in Osmocote-treated soil (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eD). The substantial improvements in plant growth and development, as well as increased crop yield explain the widespread use of chemical fertilizers in agriculture despite their cost and harmful environmental impact.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\n \u003ch2\u003eFertilization Impact on Bacterial Diversity\u003c/h2\u003e\n \u003cp\u003eThe addition of chemical fertilizer to the soil significantly reduced overall bacterial diversity (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e). Notably, bacterial species associated with nutrient recycling experienced a marked decline (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003eA-D) (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). In contrast, groups producing antimicrobial molecules thrived under these conditions (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003eE-H) (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). These findings highlight a shift in the soil bacterial community structure, indicating that even short exposure to chemical fertilization may cause substantial changes in soil bacterial populations. The application of the organic fertilizers Humus and black soldier fly FRASS did not reduce soil bacterial abundance, and have even contributed to it, suggesting that the observed microbial shifts were not solely due to NPK concentration, as equivalent nutrient levels from organic fertilizers did not produce similar effects (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003eC).\u003c/p\u003e\n \u003cdiv class=\"gridtable\"\u003e\n \u003ctable id=\"Tab1\" border=\"1\"\u003e\n \u003ccaption\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eKnown function within soil of bacterial groups presented in Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBacterial Group\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eTypical function in soil\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eHyphomicrobium\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eInvolved in nitrogen cycle, specifically in the oxidation of methanol and other C1 compounds. Contributes to soil fertility by recycling essential nutrients and degrading organic pollutants.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eMyxococcales\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eKnown for predatory behavior against other microorganisms, helping control soil pathogen populations. Produces antibiotics and enzymes that contribute to soil health and plant growth.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eNitrosomonadaceae\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eImportant nitrifiers in the nitrogen cycle, oxidizing ammonia to nitrite. This process is crucial for nitrogen transformation, making nitrogen available to plants in a usable form and maintaining soil fertility.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eRhodospirillaceae\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eInvolved in nitrogen fixation, converting atmospheric nitrogen into forms that plants can absorb and use. Particularly important in soils with low nitrogen availability.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eStreptomyces\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003e(species 1 \u0026amp; 2)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eProduces a wide range of antibiotics that help suppress soil-borne plant pathogens. Produces plant growth-promoting substances such as indole acetic acid (IAA) and siderophores, enhancing nutrient availability and uptake by plants.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eAmycolatopsis\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eProduces antibiotics and other bioactive compounds. Involved in the degradation of complex organic materials, contributing to soil organic matter turnover and nutrient cycling.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003eKitasatospora\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eProduces various secondary metabolites, including antibiotics, which help control harmful soil microorganisms. Contributes to organic matter decomposition and nutrient cycling, supporting plant growth.\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e\n \u003ch2\u003ePlant Impact on Bacterial Diversity\u003c/h2\u003e\n \u003cp\u003eThe plant presence influenced the soil microbial community, with overall plant presence contributing positively to soil microbial diversity (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eA). Co-plantation of more than one plant species in a pot did not significantly alter this positive effect observed for single species presence, but the bacterial diversity in those pots did seem to be higher than the diversity observed for some of the single plant species alone (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003eB). This suggests that co-plantation may be a strategy to increase bacterial diversity within the soil, but the plant species should be examined individually \u0026ndash; as some species tend to promote bacterial richness more than others.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eThis study aimed to examine the immediate effects of chemical fertilization on both crop yield and the composition of soil bacterial communities. Our findings show that while soil treatment with the chemical fertilizer (Osmocote\u0026reg;) significantly improved plant growth and productivity (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e), it also caused a rapid decline in overall bacterial diversity within the soil (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Similar effects have been reported in long-term studies of chemically fertilized soils, including in the root zones of cultivated walnut trees[\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e], and in agricultural soil dedicated to wheat and soybean cultivation[\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Furthermore, the addition of the chemical fertilizer in our case appeared to specifically decrease the presence of bacterial groups associated with soil nutrient cycles, while having a significant positive impact on the abundance of bacterial species known for their high antimicrobial substance production (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The significant rise in abundance of antibacterial compounds within the soil may prevent nutrient recycling bacteria from re-establishing within the previously fertilized soil, even when fertilization is no longer applied. Thus, long term soil productivity reduction in chemically fertilized agricultural soil[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e], in fact appears to initiate early on with fertilization application potentially making chemical fertilization even less forgiving than previously considered.\u003c/p\u003e \u003cp\u003eIn addition to fertilizer type, we found that plant presence and species composition also influenced soil bacterial diversity. These factors seemed to have immediate positive effects on soil bacterial diversity. Thus, the application of organic fertilizers such as humus and black soldier fly frass (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC), and the very presence of plants in the soil (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e) elevated bacterial richness within the soil. Co-planting species appeared to elevate overall bacterial diversity to the level associated with the species that contributed most strongly to microbial enrichment. These findings were in accordance with previous work showing that organic fertilizers tend to contribute to soil bacterial diversity in rice fields[\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e], grape rhizosphere[\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e], garlic[\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e], and tea (\u003cem\u003eCamelia sinensis\u003c/em\u003e)[\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]; and showing that multi crop planting has effectively increased soil bacterial diversity[\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. Unlike previous studies focusing on long-term effects, our findings demonstrate that significant changes in microbial community composition can occur within just 3 months of cultivation.\u003c/p\u003e \u003cp\u003eRecent efforts have focused on promoting the combined use of organic and chemical fertilizers in the aim of achieving a healthy balance between high crop yields on one hand, while maintaining soil health which is emphasized by diverse bacterial community, specifically capable of nutrient recycling on the other hand[\u003cspan additionalcitationids=\"CR32\" citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. Our findings strongly support this approach, highlighting the immediate and pronounced shifts in bacterial communities following chemical fertilizer application on agricultural soils even when the benefits to crop yield are clear.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eH.G, E.G, L.S and R.C.K planned the greenhouse growth experiments H.G and E.G were responsible for the physical work and data collection, R.C.K has analyzed the data.H.S, B.D, and Y.H extracted the soil DNA and prepared it for sequencing with help from S.O.O and R.C.K R.C.K has analyzed the DNA sequencing data using the CosmosID hubR.C.K wrote the manuscript, L.S added methodology regarding organic fertilization, all authors reviewed the manuscript\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eThis research was funded by the Israel Chief Scientist Foundation of the Ministry of Agriculture (ICSFA). Project number 21-02-0011- Using frass derived from black soldier larvae treatment of agricultural plant waste as a product enhancing plant protection and growth.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003ePretty J, Benton TG, Bharucha ZP, Dicks LV, Flora CB, Godfray HCJ, et al. Global assessment of agricultural system redesign for sustainable intensification. Nature Sustainability. 2018;1(8):441\u0026ndash;6; doi: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41893-018-0114-0\u003c/span\u003e\u003cspan address=\"10.1038/s41893-018-0114-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKumar R, Kumar R, Prakash O. Chapter-5 the impact of chemical fertilizers on our environment and ecosystem. Chief Ed. 2019;35(69):1173\u0026ndash;89.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHartmann M, Frey B, Mayer J, M\u0026auml;der P, Widmer F. Distinct soil microbial diversity under long-term organic and conventional farming. The ISME journal. 2015;9(5):1177\u0026ndash;94.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePenuelas J, Coello F, Sardans J. A better use of fertilizers is needed for global food security and environmental sustainability. Agriculture \u0026amp; Food Security. 2023;12(1):1\u0026ndash;9.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePowlson DS, Gregory PJ, Whalley WR, Quinton JN, Hopkins DW, Whitmore AP, et al. Soil management in relation to sustainable agriculture and ecosystem services. Food policy. 2011;36:S72-S87.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGeisseler D, Scow KM. Long-term effects of mineral fertilizers on soil microorganisms\u0026ndash;A review. Soil Biology and Biochemistry. 2014;75:54\u0026ndash;63.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBender SF, Wagg C, van der Heijden MG. An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability. Trends in ecology \u0026amp; evolution. 2016;31(6):440\u0026ndash;52.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYan D, Wang D, Yang L. Long-term effect of chemical fertilizer, straw, and manure on labile organic matter fractions in a paddy soil. Biology and Fertility of Soils. 2007;44:93\u0026ndash;101.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBeltran-Garcia MJ, Mart\u0026iacute;nez-Rodr\u0026iacute;guez A, Olmos-Arriaga I, Valdes-Salas B, Di Mascio P, White JF. Nitrogen fertilization and stress factors drive shifts in microbial diversity in soils and plants. Symbiosis. 2021;84(3):379\u0026ndash;90.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBai Y-C, Chang Y-Y, Hussain M, Lu B, Zhang J-P, Song X-B, et al. Soil chemical and microbiological properties are changed by long-term chemical fertilizers that limit ecosystem functioning. Microorganisms. 2020;8(5):694.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMeena RS, Kumar S, Datta R, Lal R, Vijayakumar V, Brtnicky M, et al. Impact of agrochemicals on soil microbiota and management: A review. Land. 2020;9(2):34.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDincă LC, Grenni P, Onet C, Onet A. Fertilization and soil microbial community: a review. Applied Sciences. 2022;12(3):1198.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGuo Z, Wan S, Hua K, Yin Y, Chu H, Wang D, et al. Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystem. Applied Soil Ecology. 2020;149:103510.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi J, Cooper JM, Lin Za, Li Y, Yang X, Zhao B. Soil microbial community structure and function are significantly affected by long-term organic and mineral fertilization regimes in the North China Plain. Applied Soil Ecology. 2015;96:75\u0026ndash;87.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePahalvi HN, Rafiya L, Rashid S, Nisar B, Kamili AN. Chemical fertilizers and their impact on soil health. Microbiota and Biofertilizers, Vol 2: Ecofriendly tools for reclamation of degraded soil environs. 2021:1\u0026ndash;20.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDeshoux M, Sadet-Bourgeteau S, Gentil S, Pr\u0026eacute;vost-Bour\u0026eacute; NC. Effects of biochar on soil microbial communities: a meta-analysis. Science of the Total Environment. 2023;902:166079.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang Z, Zhan Y, Zhang Z, Liu Y, Xu T, Wei Y, et al. Tomato endophyte bacteria diversity under long-term organic agricultural manipulation systems. 2021.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePeng M, Zi X, Wang Q. Bacterial community diversity of oil-contaminated soils assessed by high throughput sequencing of 16S rRNA genes. International Journal of Environmental Research and Public Health. 2015;12(10):12002\u0026ndash;15.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eArmougom F, Raoult D. Exploring microbial diversity using 16S rRNA high-throughput methods. J Comput Sci Syst Biol. 2009;2(1):74\u0026ndash;92.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSenesi N. Composted materials as organic fertilizers. Science of the Total Environment. 1989;81:521\u0026ndash;42.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAbd Manan F, Yeoh Y-K, Chai T-T, Wong F-C. Unlocking the potential of black soldier fly frass as a sustainable organic fertilizer: A review of recent studies. Journal of Environmental Management. 2024;367:121997.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang J, Liu Y-X, Zhang N, Hu B, Jin T, Xu H, et al. NRT1. 1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature biotechnology. 2019;37(6):676\u0026ndash;84.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSun R, Zhang X-X, Guo X, Wang D, Chu H. Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw. Soil Biology and Biochemistry. 2015;88:9\u0026ndash;18.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEdmeades DC. The long-term effects of manures and fertilisers on soil productivity and quality: a review. Nutrient Cycling in Agroecosystems. 2003;66(2):165\u0026ndash;80; doi: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1023/A:1023999816690\u003c/span\u003e\u003cspan address=\"10.1023/A:1023999816690\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu J, Shu A, Song W, Shi W, Li M, Zhang W, et al. Long-term organic fertilizer substitution increases rice yield by improving soil properties and regulating soil bacteria. Geoderma. 2021;404:115287.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang Z, Liu H, Liu X, Chen Y, Lu Y, Shen M, et al. Organic fertilizer enhances rice growth in severe saline\u0026ndash;alkali soil by increasing soil bacterial diversity. Soil Use and Management. 2022;38(1):964\u0026ndash;77.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWu L, Jiang Y, Zhao F, He X, Liu H, Yu K. Increased organic fertilizer application and reduced chemical fertilizer application affect the soil properties and bacterial communities of grape rhizosphere soil. Scientific Reports. 2020;10(1):9568.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMa Y, Shen S, Wan C, Wang S, Yang F, Zhang K, et al. Organic fertilizer substitution over six years improves the productivity of garlic, bacterial diversity, and microbial communities network complexity. Applied Soil Ecology. 2023;182:104718.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGu S, Hu Q, Cheng Y, Bai L, Liu Z, Xiao W, et al. Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils. Soil and Tillage Research. 2019;195:104356.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTang H, Liu Y, Yang X, Huang G, Liang X, Shah AN, et al. Multiple cropping effectively increases soil bacterial diversity, community abundance and soil fertility of paddy fields. BMC Plant Biology. 2024;24(1):715.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWan L-J, Tian Y, He M, Zheng Y-Q, Lyu Q, Xie R-J, et al. Effects of chemical fertilizer combined with organic fertilizer application on soil properties, citrus growth physiology, and yield. Agriculture. 2021;11(12):1207.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHan J, Dong Y, Zhang M. Chemical fertilizer reduction with organic fertilizer effectively improve soil fertility and microbial community from newly cultivated land in the Loess Plateau of China. Applied Soil Ecology. 2021;165:103966.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJin N, Jin L, Wang S, Li J, Liu F, Liu Z, et al. Reduced chemical fertilizer combined with bio-organic fertilizer affects the soil microbial community and yield and quality of lettuce. Frontiers in Microbiology. 2022;13:863325.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-6534195/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6534195/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe use of chemical fertilizers is widespread in modern agriculture due to their proven benefits for crop productivity. In this study, we examined the immediate effects of the slow-release chemical fertilizer Osmocote\u0026reg; on plant growth and soil microbial communities in a mono and poly culture regime in controlled pot experiment over a single growth season compared to organic soil amendment treatments- Black soldier fly frass and Humus. Osmocote\u0026reg; addition significantly enhanced the growth rate and yield of cherry tomato (Solanum lycopersicum), basil (Ocimum basilicum), and onion (Allium cepa), confirming its effectiveness in plant growth promotion. However, parallel analysis of soil bacterial communities revealed a substantial decline in overall microbial diversity following Osmocote treatment. This reduction was particularly pronounced among bacterial groups involved in key nutrient cycling processes, such as nitrogen and organic matter turnover. Conversely, Osmocote-treated soils showed an increase in the relative abundance of bacterial taxa known for producing broad-spectrum antibacterial compounds. This shift suggests the possible emergence of a suppressive environment that may hinder microbial recolonization and compromise long-term soil health, even after fertilizer application ceases. In contrast, soils amended with organic fertilizers maintained or enriched microbial diversity. Similarly, the presence of plants positively influenced soil bacterial diversity, with some species exerting stronger effects than others. Notably, co-planting multiple species within a pot elevated microbial diversity to levels comparable to those observed with the most beneficial single species. These observations highlight the potential of integrative strategies combining organic and chemical fertilization, alongside diverse plantings, to support both high crop productivity and sustainable soil microbial ecology. Our findings underscore the immediate negative effects of chemical fertilization, which may have long-term consequences for soil function and plant growth potential and suggest more sustainable alternatives.\u003c/p\u003e","manuscriptTitle":"Immediate Effects of Chemical Fertilization on Crop Yield and Soil Bacterial Diversity: Insights for Sustainable Agriculture","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-04-30 13:17:39","doi":"10.21203/rs.3.rs-6534195/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"3c3240ec-af3c-4616-be91-051e46f9a68f","owner":[],"postedDate":"April 30th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-06-23T12:09:03+00:00","versionOfRecord":[],"versionCreatedAt":"2025-04-30 13:17:39","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6534195","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6534195","identity":"rs-6534195","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}