Effect of agricultural management approaches on soil microbial diversity and crop production: A meta-analysis

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Anthropogenic activities have a nonnegligible influence on both soil microbial diversity and crop production. Little research has been conducted to quantify the beneficial relationships between microbial diversity and soil productivity. Methods A meta-analysis based on 80 published papers was carried out to clarify the effects of anthropogenic activities including chemical fertilization (CF), organic fertilization (OF), intercropping or rotation (IC) and microbial treatment (MF), on soil microbial diversity and crop yield, and the relationship in between and summarized. Results The results showed that CF had the greatest potential for improving crop yield, whereas it may cause reductions in soil microbial diversity. OF is a sustainable development strategy, which increases both soil microbial diversity and crop yield. Under IC treatment, soil bacterial community diversity was significantly positively correlated with crop productivity, and the average effects of the four management approaches on soil microbial diversity and crop productivity were significantly different under different conditions. Conclusion Overall, our results have great guiding significance for ecological environment protection and crop economic benefits. Agricultural Management Crop Yield Meta-Analysis Microbial Diversity Relationships. Figures Figure 1 Figure 2 Introduction The goal of sustainable agriculture is to allow for the long-term maintenance of productive capacity. Soil functioning is governed by microbial dynamics, and soil productivity largely depends on the microorganisms present in the soil. Microbial properties, including function, enzyme, community composition, and diversity of soil have been numerously studied, and many breakthrough findings were reported (Garland et al. 2021 ; Malik et al. 2018 ). Of them, the microbial diversity is a critical topic that concerns sustainable agriculture and crop production (Kennedy and Smith 1995 ). The maintenance of a viable, diverse and functioning microbial community in the soil is essential to sustainable agriculture. Microorganisms are the main drivers for the biogeochemical behavior of soil nutrients. The plant growth, health, and productivity were significantly affected by the soil microbial communities (Lau and Lennon 2011 ; Sahu et al. 2019 ; Seitz et al. 2021 ). Some reported that a diverse soil microbial community could enhance plant immunity, promote plant growth and improve crop productivity (Delgado-Baquerizo et al. 2017 ; Maherali and Klironomos 2007 ; Wagg et al. 2014 ). Whereas, some researchers found that there was no significant correlation between microbial diversity and plant productivity (Tedersoo et al. 2014 ), and the negative correlation between microbial diversity and soil fertility and plant growth was also reported, pointing out that microbial diversity is not necessarily the decisive factor to increase plant yield (Celestina et al. 2019 ). Therefore, it was argued that the relationship between soil microbial diversity and crop productivity was complex and could not be generalized (Soliveres et al. 2016 ; Wagg et al. 2014 ). The argument concerning the relationship between microbial diversity and productivity was largely depending on the experimental settings and the anthropogenic managements. The impacts of anthropogenic activities on soil microbial communities and the mechanisms by which crop productivity is affected by microbial diversity have important implications for the development of sustainable strategies (Singh et al. 2021 ; Trivedi et al. 2017 ). Common agriculture activities include chemical fertilization, organic fertilization, rotation, microbial inoculation and so on. Wang et al. ( 2021 ) found that the combination of NPK fertilizer and organic fertilizer in rice production significantly improved rice yield, which was closely related to soil bacterial community. Chen et al. ( 2020 ) found that there was a significant positive correlation between soil bacterial community diversity and plant biomass through gradient dilution of soil suspension by inoculation. The relationship between microbial diversity and crop production has also been widely studied under organic fertilization, rotation, and other management (Shu et al. 2022 ; Zhou et al. 2017 ). As experimental settings were different in many aspects, such as soil properties, experimental scales, crop type and else, no constant results have been obtained. Little research has been conducted to quantify the beneficial relationships between microbial diversity and soil productivity. A meta-analysis combines multiple different research information to provide more accurate parameter estimation for the problem (Mengersen et al. 2015 ). Therefore, in this study, we carried out a meta-analysis based on published data, to clarify the conditions underlying the crop production benefit from diverse microbial communities. Specifically, we mainly answer the following questions: (1) What are the effects of different agricultural management approaches on crop yield and microbial diversity? (2) What are the effects of different agricultural management approaches on crop yield and soil microbial diversity at different experimental scales, soil range, plant type and soil pH? (3) What is the relationship between soil microbial diversity and crop yield? Materials And Methods Data selection To carry out the meta-analysis based on published data, we searched for articles published on the Web of Science before December 31, 2021. Searching terms were “Soil or Rhizosphere” and “Microbial community or bacterial community or fungal community or microbiome or microbiota” and “Diversity index or diversity indices or Shannon or Simpson or richness” and “crop or plant or maize or rice or wheat or barley or potato” and “yield or production or productivity”. Only primary studies that satisfied the following criteria were included in this meta-analysis: (1) Soil or rhizosphere microbial community was analyzed. (2) At least one microbial (bacterial or fungal) community diversity indices were or could be calculated. (3) Plant or crop yield or production was recorded. (4) The means and sample sizes of the selected variables were available or could be calculated from the relevant publications. Finally, we get all original data from 80 articles (Note S1). Each article recorded crop yield or productivity, as well as soil microbial (bacterial or fungal) diversity indexes such as Shannon, Simpson, ACE, Chao1, etc. If the longitude and latitude, precipitation, and soil physical and chemical properties during harvesting were described in the article, we recorded them as best as we could. Several experiments extracted from the same article do not affect the independence of the data. In one paper, for example, yields and soil microbial diversity indices for different crops were obtained under the same experimental conditions or experiments with the same crop variety but conducted in different years or under different experimental conditions are considered independent (Lekberg and Koide 2005 ; Zhou et al. 2020 ). The results included in the analysis recorded at least yield or productivity, soil microbial diversity index, experimental scales, whether the soil was rhizosphere or bulk. Finally, 442 experimental results were obtained from 80 articles. Statistical analysis According to the data collected, the main experimental approaches were fertilization, inoculation, intercropping and crop rotation. Therefore, we divided the experimental group into four categories of agricultural measures, namely, organic treatment (OF), inorganic treatment (CF), microbial treatment (MF), and intercropping or rotation (IC). Organic treatments include applying organic fertilizer, or containing organic fertilizer compared with the control. Inorganic treatments include applying chemical fertilizer, or inorganic nitrogen fertilizer, phosphorus fertilizer alone, etc. Microbial treatments for inoculation of microbial flora. Intercropping and rotation treatments for the implementation of intercropping or crop rotation system. In the control group, there was no organic treatment, no inorganic treatment, and no microbial treatment. In the treatment of intercropping or rotation, the control group of intercropping was single cropping, and the control group of rotation was continuous cropping. They were classified as the control group of intercropping or rotation. To study the effects of agricultural management approaches on crop yields and soil microbial diversity under different conditions, we chose to transform the response ratio into logarithmic (ln) as the effect size of yield and diversity, which also eliminated the difference between different methods to calculate the microbial diversity index (Chen et al. 2019 ; Hedges et al. 1999 ; Lekberg and Koide 2005 ). Logarithmic transformation can meet the requirements of some statistical analysis, and the transformed data is also used for correlation analysis (Hedges and Pigott 2001 ; 2004 ). For example, the effect size of diversity index is: R diversity = ln (Diversity exp /Diversity con ) (Diversity exp : diversity index of the experimental group, Diversity con : diversity index of the control group). The yield effect size is calculated in the same way as the diversity indices. We also set a priority for the diversity index. For example, if some articles record Shannon and other diversity indexes, Shannon is used; if there is no Shannon but Simpson index is recorded, Simpson index is preferred, and so on. In the meta-analysis, the effect size was weighted to prevent articles with large data from having more weight (Ma and Chen 2016 ). We used the number of replications to weigh the effect size (Allison and Goldberg 2002 ; Ma and Chen 2016 ). If the experimental data only had the mean and the standard deviation was missing, the standard deviation was considered to be one-tenth of the mean. To study the effects of agricultural management approaches, data were analyzed in groups. That is, plants were divided into C 3 and C 4 plants, experimental scales were divided into field, greenhouse and pot experiments, soil samples were divided into rhizosphere and bulk soil, and soil pH was divided into three ranges: =8, Confidence intervals (95%) of mean values of all effect sizes were calculated in MetaWin2.1, The regression analysis and plotting were carried out using Excel 2019 and Origin 2021b. Results A total of 442 available records, with 324 bacterial records and 118 fungal records, were recovered for meta-analysis of the relationship between microbial community and crop production. Also considering that many studies focused on the bacterial rather than the fungal community, we only focused on the bacterial records in the subsequent analyses, and we grouped bacterial records according to soil environment, experimental scales, plant type, and pH range. And when grouped records are less than or equal to 2, they were trimmed. The response ratio plot (Fig. 1 a, b) showed that all agricultural management approaches increased crop yield significantly, with CF having the highest increase response ratio, followed by MF, while OF and IC had similar but the lowest increase response ratio. This can be applied to both fungal and bacterial records. Different from the crop yield, soil microbial diversity had various responses to different approaches (Fig. 1 a, b). The bacterial diversity did not show significant changes in response to CF and MF treatments, but the IC and OF increased the bacterial diversity significantly. Fungal diversity showed significant change only in response to MF treatment. In group analysis, OF increased rhizosphere and bulk bacterial diversity, and the same trend was observed regardless of the experimental scales (field, greenhouse, pot) and plant type (C 3 and C 4 plants). But only the range of pH 6–8, OF significantly affected soil bacterial diversity. IC significantly increased rhizosphere bacterial diversity, and when plants are C 3 types, soil bacterial diversity has a similar response to it. IC had the highest increase response ratio, when experiments were carried out in greenhouse. CF had no significant effect on soil bacterial diversity in most cases, but it increased soil bacterial diversity when the experiment was carried out in pots or with C 4 plants. Only in pot experiments, MF had a positive effect on soil bacterial diversity, while in field experiments or at pH 6 to 8, the effect was reversed (Fig. 1 a). When pH = 8, IC and CF also had no significant effect on the yield. In other cases, agricultural management approaches had a significant effect on crop yields, with CF had the highest increase response ratio (Fig. 1 b). Pearson correlation analysis can visually show the relationship between soil bacterial diversity and plant yield in each management approach. As shown in Fig. 2 , in some cases, soil bacterial diversity and crop yield were significantly positively or negatively correlated (p < 0.05). The remaining cases with no significant correlation are added in the supplementary material (Fig. S1-S5). Discussion Soil productivity largely depends on the microorganisms present in the soil. Soil bacterial diversity is closely related to many biochemical processes occurring in the soil, and thus is important for plant growth (de Vries et al. 2020 ). A lot of attention has been focused on the role of microbial diversity on agriculture production. Although it is generally accepted it was necessary to maintain high biodiversity for sustainable agricultural production, the relationship between biodiversity and agricultural production has rarely been quantified, and there were still arguments that whether plants always benefited from the diverse microbial community. Our results indicated that the relationship between microbial diversity and crop production was significantly affected by anthropogenic activities. Although all treatments could significantly improve crop production (yield), they had different effects on soil bacterial diversity. IC and OF not only increased soil bacterial diversity, but also promoted crop yield. The CF treatment showed the highest efficiency in improving crop productivity, compared to other agricultural strategies (Fig. 1 b), however, it had no positive effects on soil bacterial diversity, suggesting it might not be a sustainable strategy for agriculture production. To pursue high crop production, chemical fertilizers were often used, as they provide direct nutrients to crops, however, the disadvantages of chemical fertilizer application were widely reported. For instance, Long-term chemical fertilizing could lead to environmental risks and soil degradation (Zhou et al. 2015 ), particularly, it enriched microbes with certain functions that had strong competition ability, and therefore, led to community basis. This could explain why CF had negative effects on soil bacterial diversity. To alleviate the negative effects caused by chemical fertilizers, organic matter fertilizers, green manure, plant rotation, or other approaches were often used (Lin et al. 2019 ; Zhang et al. 2020 ). Other than providing the soil with a lot of nutrients, organic fertilizers also improved soil microbial diversity. Although compared to chemical fertilizers, organic fertilizers had relatively weak effects in improving crop yield, they were considered to be a sustainable substance (Li et al. 2017 ; van der Bom et al. 2018 ), as they can improve soil fertility, increase soil bacterial community diversity and beneficial bacteria. It is generally accepted that organic fertilizers affected soil microbial biomass and bacterial community diversity by transporting organic matter to soil (Cookson et al. 2008 ) and the changes in bacterial community diversity would affect soil nutrient supply, thus indirectly affecting the yield (Chen et al. 2017 ; Mikanova et al. 2009 ). IC increased both soil bacterial diversity and crop yield. In addition, soil bacterial diversity showed to have a positive relationship with crop yield under this treatment (p < 0.01, Fig. 2 a, b). The species and types of plants can affect the structure of the soil microbial community through root exudates, intercropping or crop rotation mediated soil microbe pes (Brooker et al. 2015 ; Chadfield et al. 2022 ). Intercropping and rotation affect the composition and diversity of soil bacterial community through the exudates of different plant roots (Bais et al. 2006 ; Ladygina and Hedlund 2010 ), resulting in increased soil microbial diversity and crop yield (Stefan et al. 2021 ). The increase in crop productivity was related to the changing soil microbial community, especially the changes in the bacterial community, which is beneficial to plant growth. Increased diversity in soil bacterial communities can enrich beneficial bacteria, reduce pathogens that cause crop diseases, and facilitate microbial activity and the transport and absorption of nutrients needed by plants, thereby increasing crop yields (Alvey et al. 2003 ; Hauggaard-Nielsen and Jensen 2005 ; Li et al. 2014 ; Warembourg et al. 2003 ). Microbial inoculation can provide soil with high-density microorganisms, causing at least temporary changes in the structure of the soil microbial community (Xi et al. 2015 ). However, our results showed that MF had no significant effect on soil bacterial community diversity in general, but it was also a measure that could improve crop yield (Fig. 1 ). Microbial inoculation may only have a significant impact on the diversity of some specific bacterial communities or some rare communities, so the results have no significant impact on the diversity of the entire soil bacterial community (Mawarda et al. 2020 ). Microbial inoculation can inoculate beneficial bacteria, resist pathogenic bacteria, protect plant health (Arora and Mishra 2017 ), or affect soil microbial diversity, thus affecting nutrient cycling, promoting plant absorption of nutrients, and indirectly increasing yield (Nassal et al. 2018 ). Our results showed that higher soil microbial diversity did not always lead to higher plant productivity. Experimental scales, plant type, soil range, and pH value all affect the effects of agricultural management on soil bacterial diversity and crop yield, and the relationship between them (Fig. 2 , S1-S5). Intercropping and rotation can directly affect the composition and rhizosphere soil bacterial diversity through root exudates, thus improving soil fertility, promoting nutrient cycling and increasing crop yield (Gong et al. 2019 ; Zhalnina et al. 2018 ). The rhizosphere is the area that has been mostly affected by root exudates, whereas the bulk soil was seldom affected (Fan et al. 2018 ; Ling et al. 2022 ). Thus it was not suprising to find bacterial diversity in the rhizosphere and bulk soil responded differently to IC treatment (Fig. 1 a). Changes in the rhizosphere microbial community can affect bulk microbiota (Kent and Triplett 2002 ), the rhizosphere is the main place where soil microorganisms participate in nutrient cycling and metabolite output (Bulgarelli et al. 2013 ). Therefore, intercropping and rotation could also promote crop production by mediating rhizosphere microbial diversity (Fig. 2 a, d and S2). The use of organic fertilizers is helpful to improve the diversity of bacteria community in both bulk and rhizosphere soil (Fig. 2 a). Organic fertilizer can provide the soil with organic matter, reduce soil bulk density, improve microbial activity and diversity throughout the soil, and speed up the process of nutrient cycling (Qaswar et al. 2020 ; Samuel et al. 2018 ). Therefore, it has the same influence trend on the bulk and rhizosphere soil bacterial community and improves yield (Fig. 1 a, b). It should be noted that although CF had no significant effect on the rhizosphere and bulk bacterial diversity, there was a significant negative correlation between the rhizosphere bacterial diversity and crop yield under CF treatment in regression analysis (p < 0.01, Fig. 2 a, c). This may be because the application of chemical fertilizer mainly provides a large amount of nutrients for plant growth, but does not provide too much organic matter to soil. In this case, there is a negative feedback relationship between the two (Ho and Chambers 2019 ; in't Zandt et al. 2019 ; Petermann et al. 2008 ). The effects of agricultural management approaches on soil bacterial diversity and yield will be affected by the experimental scales. In the field experiment, MF reduced soil bacterial diversity, but in the pot experiment, it was the opposite (Fig. 1 a). Compared with field experiments, pot experiments were relatively small and closed systems, with roots able to explore the whole range (Aragao et al. 2020 ). In addition, in the field experiment, the soil microbial environment is relatively complex and easily affected by climate, temperature, precipitation and other external factors, which may be the reason for the inconsistent influence of the two experimental scales in the microbial inoculation experiment (Liu et al. 2017 ). Our results also showed that C 3 and C 4 plant yields and soil bacterial diversity were affected differently by agricultural management approaches (Fig. 1 a, b), this could be due to different metabolisms between C 3 and C 4 plants (Taylor et al. 2010 ). CF could increase the yield of C 3 and C 4 crops, but had different effects on the soil bacterial diversity (Fig. 1 ). The use of inorganic fertilizers, especially nitrogen fertilizers, will affect soil organic matter and carbon cycling (Rubio et al. 2010 ). C 4 plants have higher photosynthetic efficiency than C 3 plants (Zhu et al. 2008 ), and the composition and diversity of soil bacterial community affect C cycle and turnover (Ramirez et al. 2012 ; Zang et al. 2016 ), We speculated that the application of inorganic fertilizer affected the turnover of C, and C 4 plants needed a higher diversity of soil bacterial community to participate in this process, resulting in the different effects of inorganic fertilizer on the diversity of soil bacterial community of C 3 and C 4 plants. pH has a great influence on the diversity and composition of the soil bacterial community (Zhou et al. 2015 ). Only in the pH range of 6–8, OF and MF had an effect on the soil bacterial diversity. Agricultural management approaches had no significant effect on soil bacterial diversity in overly acidic or overly alkaline soils (Fig. 1 a). This may be because the range of pH values suitable for the growth of bacterial community is relatively small, and an overly acidic or alkaline environment is not conducive to the growth of soil bacterial community (Rousk et al. 2010 ). Different agricultural management strategies should be adopted when pursuing different economic benefits and protecting ecological environments. Our study can provide some reference for improving crop yield and soil bacterial diversity, and has certain significance for ecological environment protection and improving crop economy. In the short term, if environmental concerns are not considered and crop yields are pursued, our analysis suggests that chemical fertilizer is a better choice. However, if you want to sustain crop yield while also improving soil fertility, microbial diversity, and the soil environment, you can use organic fertilizer. Although organic fertilizers do not significantly improve crop yields as chemical fertilizers do, they are a sustainable agricultural management strategy that improves soil fertility, microbial activity and diversity, as well as crop yields (Gravuer et al. 2019 ; Li et al. 2021 ; Young et al. 2021 ). Intercropping and crop rotation are also good choices, there are also many studies that combine the advantages of these agricultural management approaches, such as the combined use of organic and inorganic fertilizers or crop rotation and organic fertilizers, to maximize yield and improve soil microbial diversity (Ghaley et al. 2005 ; Li et al. 2022 ; Mei et al. 2021 ; Salehi et al. 2017 ). Conclusions This study elucidated the effects of anthropogenic activities on soil bacterial diversity and crop yield, and explored whether the effects of agricultural management approaches change at different experimental scales, plant types, soil ranges, and pH values. The results showed that CF had the greatest potential for improving crop yield, whereas it had a negative effect on soil microbial diversity. This is because chemical fertilizers can directly provide soil with a lot of readily available nutrient elements required for plant growth, whereas it may also cause enrichment of microbial functional groups and therefore, led to reductions in microbial diversity. Organic fertilizers and rotation can not only improve crop yield, but also increase soil bacterial diversity, which could be used as sustainable agricultural management approaches. Because they may improve soil fertility and increase microbial diversity, and causing continues crop yield increase. This is why they are so called ‘sustainable agricultural approaches’. Crop productivity does not always benefit from higher soil microbial diversity, the relationship is highly dependent on anthropogenic activities. Our results have great guiding significance for ecological environment protection and crop economic benefits. Declarations Funding This work was supported by Natural Science Foundation of Changsha (Grant numbers [No. kq2202089]). Competing Interests The authors have no relevant financial or non-financial interests to disclose. Author Contributions Delong Meng, Junliang Zou, Xueduan Liu, and Huaqun Yin designed the research, data collection were performed by Lei Xing, Tianbo Liu, Yongjun Liu and data analysis were performed by JingYi Huang, Delong Meng, Junliang Zou. The manuscript was written by Jingyi Huang. All authors discussed the results and approved the final manuscript. Data Availability The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request. Acknowledgements This work was supported by Natural Science Foundation of Changsha (grant, No. kq2202089). We would like to thank Dr. Wieland Fricke from University College Dublin, Ireland for giving very constructive suggestions. References Allison VJ, Goldberg DE (2002) Species-level versus community-level patterns of mycorrhizal dependence on phosphorus: an example of Simpson's paradox. Funct Ecol 16:346–352. https://doi.org/10.1046/j.1365-2435.2002.00627.x Alvey S, Yang CH, Buerkert A, Crowley DE (2003) Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils. Biol Fert Soils 37:73–82. https://doi.org/10.1007/s00374-002-0573-2 Aragao OOD, Leite RD, Araujo AP, Jesus ED (2020) Effect of Pot Size on the Growth of Common Bean in Experiments with Rhizobium. 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Curr Opin Biotech 19:153–159. https://doi.org/10.1016/j.copbio.2008.02.004 Supplementary Files Supplementarydata.docx 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-2303140","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":154978141,"identity":"6626ab19-4f70-4c4e-b5ac-adcc17e6058a","order_by":0,"name":"Jingyi Huang","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jingyi","middleName":"","lastName":"Huang","suffix":""},{"id":154978142,"identity":"8d6e3f1f-38c4-459f-bfa1-7b318435e0ec","order_by":1,"name":"Junliang Zou","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Junliang","middleName":"","lastName":"Zou","suffix":""},{"id":154978143,"identity":"18570904-d0d8-4c1d-bb74-a2f223459af1","order_by":2,"name":"Lei Xing","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Lei","middleName":"","lastName":"Xing","suffix":""},{"id":154978144,"identity":"f912c726-0e93-4e12-8bbc-8399c743e00c","order_by":3,"name":"Yongjun Liu","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Yongjun","middleName":"","lastName":"Liu","suffix":""},{"id":154978145,"identity":"cc615b45-71f1-4bbe-b173-aa4932af1302","order_by":4,"name":"Tianbo Liu","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Tianbo","middleName":"","lastName":"Liu","suffix":""},{"id":154978146,"identity":"b0b77b72-e98d-4be9-93d4-918c28c52118","order_by":5,"name":"Huaqun Yin","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Huaqun","middleName":"","lastName":"Yin","suffix":""},{"id":154978147,"identity":"4a3d03e3-5d14-4894-ad2a-3a362450e698","order_by":6,"name":"Xueduan Liu","email":"","orcid":"","institution":"","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Xueduan","middleName":"","lastName":"Liu","suffix":""},{"id":154978148,"identity":"6e2fc437-6127-4f05-bf19-f8d9b4a109d4","order_by":7,"name":"Delong Meng","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA9UlEQVRIiWNgGAWjYDCCA8wNMCbjAwidQEgLI1wLswHJWtgkiNLCd7yx8XHBL4Zofun2axU//hxm4GfPMWD4uQO3FskzB5uNZ/Yx5M6cc6bsZm/bYQbJnjcGjL1ncGsxuJHYJs3bw5C74UZO2m3GhsNAkRwDZsY2PFruP4Ro2Q/UUswAdJg9QS03GNukeX4AbZFIP8bMwAa0RYKAFskzic3GvA0SuTNu5DBL9ral80iceVZwsBePFr7jhw8+5vljk9s/I/3hhx9/rOX425M3PviJRwsYMLaBYoQHHJM8IOIAAQ1A8AdEsD8grHAUjIJRMApGJAAAm95WF4TmqfoAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0003-0448-6856","institution":"Central South University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Delong","middleName":"","lastName":"Meng","suffix":""}],"badges":[],"createdAt":"2022-11-23 02:13:13","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-2303140/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-2303140/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":29678521,"identity":"4e7676ac-0b59-4b31-a2c4-45b3fdb12353","added_by":"auto","created_at":"2022-11-29 18:35:53","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":69786,"visible":true,"origin":"","legend":"\u003cp\u003eThe average effects of agricultural management approaches on soil microbial diversity and crop yield. (a) soil microbial diversity. (b) crop yield. Dots are the posterior mean of the effect size, the entire range represents a 95% confidence interval. when there is an intersection between confidence interval and zero effect line, it indicates that the influence is not significant; otherwise, it has significant influence. The numbers in brackets represent the total number.\u003c/p\u003e","description":"","filename":"Onlinefloatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-2303140/v1/9532bd7934c8205b61b0ff9c.png"},{"id":29678522,"identity":"f454c728-d773-4df6-ac69-df5ac00c8a4c","added_by":"auto","created_at":"2022-11-29 18:35:54","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":145086,"visible":true,"origin":"","legend":"\u003cp\u003eRelationship between soil bacterial diversity and crop yield under different conditions. (a) Pearson correlation analysis. Note: *p\u0026lt;0.05; **p\u0026lt;0.01. (b)~(k) Soil bacterial diversity was significantly correlated with crop productivity under certain conditions. (b) Only under IC treatment (c) Rhizosphere environment and CF treatment (d) Rhizosphere environment and IC treatment (e) Field experiment and MF treatment (f) Greenhouse experiment and OF treatment (g) Greenhouse experiment and IC treatment (h) Pot experiment and MF treatment (i) C3 plants and IC treatment (j) C4 plants and OF treatment (k) pH range 6 to 8 and MF treatment.\u003c/p\u003e","description":"","filename":"Onlinefloatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-2303140/v1/848396795737504cd89037f0.png"},{"id":31518246,"identity":"78174c7b-775e-42e1-a055-a2cc5badd5a3","added_by":"auto","created_at":"2023-01-13 06:50:46","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":833142,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-2303140/v1/af3aa7e8-66ea-4713-bb52-6b28839dc0bf.pdf"},{"id":29678523,"identity":"b23036de-2acf-4701-9fbf-d9eeb5cc8b1e","added_by":"auto","created_at":"2022-11-29 18:35:54","extension":"docx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":2523428,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementarydata.docx","url":"https://assets-eu.researchsquare.com/files/rs-2303140/v1/a5c7cc89fdbf5746ab7c1361.docx"}],"financialInterests":"","formattedTitle":"Effect of agricultural management approaches on soil microbial diversity and crop production: A meta-analysis","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe goal of sustainable agriculture is to allow for the long-term maintenance of productive capacity. Soil functioning is governed by microbial dynamics, and soil productivity largely depends on the microorganisms present in the soil. Microbial properties, including function, enzyme, community composition, and diversity of soil have been numerously studied, and many breakthrough findings were reported (Garland et al. \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Malik et al. \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Of them, the microbial diversity is a critical topic that concerns sustainable agriculture and crop production (Kennedy and Smith \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e1995\u003c/span\u003e). The maintenance of a viable, diverse and functioning microbial community in the soil is essential to sustainable agriculture.\u003c/p\u003e \u003cp\u003eMicroorganisms are the main drivers for the biogeochemical behavior of soil nutrients. The plant growth, health, and productivity were significantly affected by the soil microbial communities (Lau and Lennon \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e2011\u003c/span\u003e; Sahu et al. \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Seitz et al. \u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). Some reported that a diverse soil microbial community could enhance plant immunity, promote plant growth and improve crop productivity (Delgado-Baquerizo et al. \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Maherali and Klironomos \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e2007\u003c/span\u003e; Wagg et al. \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2014\u003c/span\u003e). Whereas, some researchers found that there was no significant correlation between microbial diversity and plant productivity (Tedersoo et al. \u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e2014\u003c/span\u003e), and the negative correlation between microbial diversity and soil fertility and plant growth was also reported, pointing out that microbial diversity is not necessarily the decisive factor to increase plant yield (Celestina et al. \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Therefore, it was argued that the relationship between soil microbial diversity and crop productivity was complex and could not be generalized (Soliveres et al. \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e2016\u003c/span\u003e; Wagg et al. \u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e2014\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe argument concerning the relationship between microbial diversity and productivity was largely depending on the experimental settings and the anthropogenic managements. The impacts of anthropogenic activities on soil microbial communities and the mechanisms by which crop productivity is affected by microbial diversity have important implications for the development of sustainable strategies (Singh et al. \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Trivedi et al. \u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). Common agriculture activities include chemical fertilization, organic fertilization, rotation, microbial inoculation and so on. Wang et al. (\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e2021\u003c/span\u003e) found that the combination of NPK fertilizer and organic fertilizer in rice production significantly improved rice yield, which was closely related to soil bacterial community. Chen et al. (\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2020\u003c/span\u003e) found that there was a significant positive correlation between soil bacterial community diversity and plant biomass through gradient dilution of soil suspension by inoculation. The relationship between microbial diversity and crop production has also been widely studied under organic fertilization, rotation, and other management (Shu et al. \u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Zhou et al. \u003cspan citationid=\"CR74\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). As experimental settings were different in many aspects, such as soil properties, experimental scales, crop type and else, no constant results have been obtained. Little research has been conducted to quantify the beneficial relationships between microbial diversity and soil productivity.\u003c/p\u003e \u003cp\u003eA meta-analysis combines multiple different research information to provide more accurate parameter estimation for the problem (Mengersen et al. \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Therefore, in this study, we carried out a meta-analysis based on published data, to clarify the conditions underlying the crop production benefit from diverse microbial communities. Specifically, we mainly answer the following questions:\u003c/p\u003e \u003cp\u003e(1) What are the effects of different agricultural management approaches on crop yield and microbial diversity?\u003c/p\u003e \u003cp\u003e(2) What are the effects of different agricultural management approaches on crop yield and soil microbial diversity at different experimental scales, soil range, plant type and soil pH?\u003c/p\u003e \u003cp\u003e(3) What is the relationship between soil microbial diversity and crop yield?\u003c/p\u003e"},{"header":"Materials And Methods","content":"\u003cp\u003eData selection\u003c/p\u003e \u003cp\u003eTo carry out the meta-analysis based on published data, we searched for articles published on the Web of Science before December 31, 2021. Searching terms were \u0026ldquo;Soil or Rhizosphere\u0026rdquo; and \u0026ldquo;Microbial community or bacterial community or fungal community or microbiome or microbiota\u0026rdquo; and \u0026ldquo;Diversity index or diversity indices or Shannon or Simpson or richness\u0026rdquo; and \u0026ldquo;crop or plant or maize or rice or wheat or barley or potato\u0026rdquo; and \u0026ldquo;yield or production or productivity\u0026rdquo;. Only primary studies that satisfied the following criteria were included in this meta-analysis: (1) Soil or rhizosphere microbial community was analyzed. (2) At least one microbial (bacterial or fungal) community diversity indices were or could be calculated. (3) Plant or crop yield or production was recorded. (4) The means and sample sizes of the selected variables were available or could be calculated from the relevant publications. Finally, we get all original data from 80 articles (Note S1).\u003c/p\u003e \u003cp\u003eEach article recorded crop yield or productivity, as well as soil microbial (bacterial or fungal) diversity indexes such as Shannon, Simpson, ACE, Chao1, etc. If the longitude and latitude, precipitation, and soil physical and chemical properties during harvesting were described in the article, we recorded them as best as we could. Several experiments extracted from the same article do not affect the independence of the data. In one paper, for example, yields and soil microbial diversity indices for different crops were obtained under the same experimental conditions or experiments with the same crop variety but conducted in different years or under different experimental conditions are considered independent (Lekberg and Koide \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e2005\u003c/span\u003e; Zhou et al. \u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). The results included in the analysis recorded at least yield or productivity, soil microbial diversity index, experimental scales, whether the soil was rhizosphere or bulk. Finally, 442 experimental results were obtained from 80 articles.\u003c/p\u003e \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eStatistical analysis\u003c/h2\u003e \u003cp\u003eAccording to the data collected, the main experimental approaches were fertilization, inoculation, intercropping and crop rotation. Therefore, we divided the experimental group into four categories of agricultural measures, namely, organic treatment (OF), inorganic treatment (CF), microbial treatment (MF), and intercropping or rotation (IC). Organic treatments include applying organic fertilizer, or containing organic fertilizer compared with the control. Inorganic treatments include applying chemical fertilizer, or inorganic nitrogen fertilizer, phosphorus fertilizer alone, etc. Microbial treatments for inoculation of microbial flora. Intercropping and rotation treatments for the implementation of intercropping or crop rotation system. In the control group, there was no organic treatment, no inorganic treatment, and no microbial treatment. In the treatment of intercropping or rotation, the control group of intercropping was single cropping, and the control group of rotation was continuous cropping. They were classified as the control group of intercropping or rotation.\u003c/p\u003e \u003cp\u003eTo study the effects of agricultural management approaches on crop yields and soil microbial diversity under different conditions, we chose to transform the response ratio into logarithmic (ln) as the effect size of yield and diversity, which also eliminated the difference between different methods to calculate the microbial diversity index (Chen et al. \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Hedges et al. \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e1999\u003c/span\u003e; Lekberg and Koide \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e2005\u003c/span\u003e). Logarithmic transformation can meet the requirements of some statistical analysis, and the transformed data is also used for correlation analysis (Hedges and Pigott \u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e2001\u003c/span\u003e; \u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e2004\u003c/span\u003e). For example, the effect size of diversity index is:\u003c/p\u003e \u003cp\u003eR\u003csub\u003ediversity\u003c/sub\u003e = ln (Diversity\u003csub\u003eexp\u003c/sub\u003e/Diversity\u003csub\u003econ\u003c/sub\u003e)\u003c/p\u003e \u003cp\u003e(Diversity\u003csub\u003eexp\u003c/sub\u003e: diversity index of the experimental group, Diversity\u003csub\u003econ\u003c/sub\u003e: diversity index of the control group). The yield effect size is calculated in the same way as the diversity indices. We also set a priority for the diversity index. For example, if some articles record Shannon and other diversity indexes, Shannon is used; if there is no Shannon but Simpson index is recorded, Simpson index is preferred, and so on. In the meta-analysis, the effect size was weighted to prevent articles with large data from having more weight (Ma and Chen \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). We used the number of replications to weigh the effect size (Allison and Goldberg \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2002\u003c/span\u003e; Ma and Chen \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e2016\u003c/span\u003e). If the experimental data only had the mean and the standard deviation was missing, the standard deviation was considered to be one-tenth of the mean.\u003c/p\u003e \u003cp\u003eTo study the effects of agricultural management approaches, data were analyzed in groups. That is, plants were divided into C\u003csub\u003e3\u003c/sub\u003e and C\u003csub\u003e4\u003c/sub\u003e plants, experimental scales were divided into field, greenhouse and pot experiments, soil samples were divided into rhizosphere and bulk soil, and soil pH was divided into three ranges: \u0026lt;=6, 6\u0026ndash;8, \u0026gt;=8, Confidence intervals (95%) of mean values of all effect sizes were calculated in MetaWin2.1, The regression analysis and plotting were carried out using Excel 2019 and Origin 2021b.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cp\u003eA total of 442 available records, with 324 bacterial records and 118 fungal records, were recovered for meta-analysis of the relationship between microbial community and crop production. Also considering that many studies focused on the bacterial rather than the fungal community, we only focused on the bacterial records in the subsequent analyses, and we grouped bacterial records according to soil environment, experimental scales, plant type, and pH range. And when grouped records are less than or equal to 2, they were trimmed.\u003c/p\u003e \u003cp\u003eThe response ratio plot (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea, b) showed that all agricultural management approaches increased crop yield significantly, with CF having the highest increase response ratio, followed by MF, while OF and IC had similar but the lowest increase response ratio. This can be applied to both fungal and bacterial records. Different from the crop yield, soil microbial diversity had various responses to different approaches (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea, b). The bacterial diversity did not show significant changes in response to CF and MF treatments, but the IC and OF increased the bacterial diversity significantly. Fungal diversity showed significant change only in response to MF treatment.\u003c/p\u003e \u003cp\u003eIn group analysis, OF increased rhizosphere and bulk bacterial diversity, and the same trend was observed regardless of the experimental scales (field, greenhouse, pot) and plant type (C\u003csub\u003e3\u003c/sub\u003e and C\u003csub\u003e4\u003c/sub\u003e plants). But only the range of pH 6\u0026ndash;8, OF significantly affected soil bacterial diversity. IC significantly increased rhizosphere bacterial diversity, and when plants are C\u003csub\u003e3\u003c/sub\u003e types, soil bacterial diversity has a similar response to it. IC had the highest increase response ratio, when experiments were carried out in greenhouse. CF had no significant effect on soil bacterial diversity in most cases, but it increased soil bacterial diversity when the experiment was carried out in pots or with C\u003csub\u003e4\u003c/sub\u003e plants. Only in pot experiments, MF had a positive effect on soil bacterial diversity, while in field experiments or at pH 6 to 8, the effect was reversed (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eWhen pH\u0026thinsp;\u0026lt;\u0026thinsp;=\u0026thinsp;6, MF had no significant effect on crop yield, and when pH\u0026thinsp;\u0026gt;\u0026thinsp;=\u0026thinsp;8, IC and CF also had no significant effect on the yield. In other cases, agricultural management approaches had a significant effect on crop yields, with CF had the highest increase response ratio (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eb).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003ePearson correlation analysis can visually show the relationship between soil bacterial diversity and plant yield in each management approach. As shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e, in some cases, soil bacterial diversity and crop yield were significantly positively or negatively correlated (p\u0026thinsp;\u0026lt;\u0026thinsp;0.05). The remaining cases with no significant correlation are added in the supplementary material (Fig. S1-S5).\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eSoil productivity largely depends on the microorganisms present in the soil. Soil bacterial diversity is closely related to many biochemical processes occurring in the soil, and thus is important for plant growth (de Vries et al. \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). A lot of attention has been focused on the role of microbial diversity on agriculture production. Although it is generally accepted it was necessary to maintain high biodiversity for sustainable agricultural production, the relationship between biodiversity and agricultural production has rarely been quantified, and there were still arguments that whether plants always benefited from the diverse microbial community. Our results indicated that the relationship between microbial diversity and crop production was significantly affected by anthropogenic activities. Although all treatments could significantly improve crop production (yield), they had different effects on soil bacterial diversity. IC and OF not only increased soil bacterial diversity, but also promoted crop yield. The CF treatment showed the highest efficiency in improving crop productivity, compared to other agricultural strategies (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eb), however, it had no positive effects on soil bacterial diversity, suggesting it might not be a sustainable strategy for agriculture production. To pursue high crop production, chemical fertilizers were often used, as they provide direct nutrients to crops, however, the disadvantages of chemical fertilizer application were widely reported. For instance, Long-term chemical fertilizing could lead to environmental risks and soil degradation (Zhou et al. \u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e2015\u003c/span\u003e), particularly, it enriched microbes with certain functions that had strong competition ability, and therefore, led to community basis. This could explain why CF had negative effects on soil bacterial diversity.\u003c/p\u003e \u003cp\u003eTo alleviate the negative effects caused by chemical fertilizers, organic matter fertilizers, green manure, plant rotation, or other approaches were often used (Lin et al. \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Zhang et al. \u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Other than providing the soil with a lot of nutrients, organic fertilizers also improved soil microbial diversity. Although compared to chemical fertilizers, organic fertilizers had relatively weak effects in improving crop yield, they were considered to be a sustainable substance (Li et al. \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; van der Bom et al. \u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e2018\u003c/span\u003e), as they can improve soil fertility, increase soil bacterial community diversity and beneficial bacteria. It is generally accepted that organic fertilizers affected soil microbial biomass and bacterial community diversity by transporting organic matter to soil (Cookson et al. \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e2008\u003c/span\u003e) and the changes in bacterial community diversity would affect soil nutrient supply, thus indirectly affecting the yield (Chen et al. \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Mikanova et al. \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2009\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eIC increased both soil bacterial diversity and crop yield. In addition, soil bacterial diversity showed to have a positive relationship with crop yield under this treatment (p\u0026thinsp;\u0026lt;\u0026thinsp;0.01, Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea, b). The species and types of plants can affect the structure of the soil microbial community through root exudates, intercropping or crop rotation mediated soil microbe pes (Brooker et al. \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Chadfield et al. \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Intercropping and rotation affect the composition and diversity of soil bacterial community through the exudates of different plant roots (Bais et al. \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e2006\u003c/span\u003e; Ladygina and Hedlund \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2010\u003c/span\u003e), resulting in increased soil microbial diversity and crop yield (Stefan et al. \u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). The increase in crop productivity was related to the changing soil microbial community, especially the changes in the bacterial community, which is beneficial to plant growth. Increased diversity in soil bacterial communities can enrich beneficial bacteria, reduce pathogens that cause crop diseases, and facilitate microbial activity and the transport and absorption of nutrients needed by plants, thereby increasing crop yields (Alvey et al. \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2003\u003c/span\u003e; Hauggaard-Nielsen and Jensen \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2005\u003c/span\u003e; Li et al. \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2014\u003c/span\u003e; Warembourg et al. \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e2003\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eMicrobial inoculation can provide soil with high-density microorganisms, causing at least temporary changes in the structure of the soil microbial community (Xi et al. \u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). However, our results showed that MF had no significant effect on soil bacterial community diversity in general, but it was also a measure that could improve crop yield (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Microbial inoculation may only have a significant impact on the diversity of some specific bacterial communities or some rare communities, so the results have no significant impact on the diversity of the entire soil bacterial community (Mawarda et al. \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Microbial inoculation can inoculate beneficial bacteria, resist pathogenic bacteria, protect plant health (Arora and Mishra \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e2017\u003c/span\u003e), or affect soil microbial diversity, thus affecting nutrient cycling, promoting plant absorption of nutrients, and indirectly increasing yield (Nassal et al. \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e2018\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eOur results showed that higher soil microbial diversity did not always lead to higher plant productivity. Experimental scales, plant type, soil range, and pH value all affect the effects of agricultural management on soil bacterial diversity and crop yield, and the relationship between them (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e, S1-S5).\u003c/p\u003e \u003cp\u003eIntercropping and rotation can directly affect the composition and rhizosphere soil bacterial diversity through root exudates, thus improving soil fertility, promoting nutrient cycling and increasing crop yield (Gong et al. \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Zhalnina et al. \u003cspan citationid=\"CR70\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). The rhizosphere is the area that has been mostly affected by root exudates, whereas the bulk soil was seldom affected (Fan et al. \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2018\u003c/span\u003e; Ling et al. \u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Thus it was not suprising to find bacterial diversity in the rhizosphere and bulk soil responded differently to IC treatment (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea). Changes in the rhizosphere microbial community can affect bulk microbiota (Kent and Triplett \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2002\u003c/span\u003e), the rhizosphere is the main place where soil microorganisms participate in nutrient cycling and metabolite output (Bulgarelli et al. \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2013\u003c/span\u003e). Therefore, intercropping and rotation could also promote crop production by mediating rhizosphere microbial diversity (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea, d and S2). The use of organic fertilizers is helpful to improve the diversity of bacteria community in both bulk and rhizosphere soil (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea). Organic fertilizer can provide the soil with organic matter, reduce soil bulk density, improve microbial activity and diversity throughout the soil, and speed up the process of nutrient cycling (Qaswar et al. \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Samuel et al. \u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e2018\u003c/span\u003e). Therefore, it has the same influence trend on the bulk and rhizosphere soil bacterial community and improves yield (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea, b). It should be noted that although CF had no significant effect on the rhizosphere and bulk bacterial diversity, there was a significant negative correlation between the rhizosphere bacterial diversity and crop yield under CF treatment in regression analysis (p\u0026thinsp;\u0026lt;\u0026thinsp;0.01, Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea, c). This may be because the application of chemical fertilizer mainly provides a large amount of nutrients for plant growth, but does not provide too much organic matter to soil. In this case, there is a negative feedback relationship between the two (Ho and Chambers \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; in't Zandt et al. \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Petermann et al. \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e2008\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe effects of agricultural management approaches on soil bacterial diversity and yield will be affected by the experimental scales. In the field experiment, MF reduced soil bacterial diversity, but in the pot experiment, it was the opposite (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea). Compared with field experiments, pot experiments were relatively small and closed systems, with roots able to explore the whole range (Aragao et al. \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). In addition, in the field experiment, the soil microbial environment is relatively complex and easily affected by climate, temperature, precipitation and other external factors, which may be the reason for the inconsistent influence of the two experimental scales in the microbial inoculation experiment (Liu et al. \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2017\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eOur results also showed that C\u003csub\u003e3\u003c/sub\u003e and C\u003csub\u003e4\u003c/sub\u003e plant yields and soil bacterial diversity were affected differently by agricultural management approaches (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea, b), this could be due to different metabolisms between C\u003csub\u003e3\u003c/sub\u003e and C\u003csub\u003e4\u003c/sub\u003e plants (Taylor et al. \u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e2010\u003c/span\u003e). CF could increase the yield of C\u003csub\u003e3\u003c/sub\u003e and C\u003csub\u003e4\u003c/sub\u003e crops, but had different effects on the soil bacterial diversity (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The use of inorganic fertilizers, especially nitrogen fertilizers, will affect soil organic matter and carbon cycling (Rubio et al. \u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e2010\u003c/span\u003e). C\u003csub\u003e4\u003c/sub\u003e plants have higher photosynthetic efficiency than C\u003csub\u003e3\u003c/sub\u003e plants (Zhu et al. \u003cspan citationid=\"CR75\" class=\"CitationRef\"\u003e2008\u003c/span\u003e), and the composition and diversity of soil bacterial community affect C cycle and turnover (Ramirez et al. \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e2012\u003c/span\u003e; Zang et al. \u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e2016\u003c/span\u003e), We speculated that the application of inorganic fertilizer affected the turnover of C, and C\u003csub\u003e4\u003c/sub\u003e plants needed a higher diversity of soil bacterial community to participate in this process, resulting in the different effects of inorganic fertilizer on the diversity of soil bacterial community of C\u003csub\u003e3\u003c/sub\u003e and C\u003csub\u003e4\u003c/sub\u003e plants. pH has a great influence on the diversity and composition of the soil bacterial community (Zhou et al. \u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Only in the pH range of 6\u0026ndash;8, OF and MF had an effect on the soil bacterial diversity. Agricultural management approaches had no significant effect on soil bacterial diversity in overly acidic or overly alkaline soils (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea). This may be because the range of pH values suitable for the growth of bacterial community is relatively small, and an overly acidic or alkaline environment is not conducive to the growth of soil bacterial community (Rousk et al. \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2010\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eDifferent agricultural management strategies should be adopted when pursuing different economic benefits and protecting ecological environments. Our study can provide some reference for improving crop yield and soil bacterial diversity, and has certain significance for ecological environment protection and improving crop economy. In the short term, if environmental concerns are not considered and crop yields are pursued, our analysis suggests that chemical fertilizer is a better choice. However, if you want to sustain crop yield while also improving soil fertility, microbial diversity, and the soil environment, you can use organic fertilizer. Although organic fertilizers do not significantly improve crop yields as chemical fertilizers do, they are a sustainable agricultural management strategy that improves soil fertility, microbial activity and diversity, as well as crop yields (Gravuer et al. \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2019\u003c/span\u003e; Li et al. \u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Young et al. \u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). Intercropping and crop rotation are also good choices, there are also many studies that combine the advantages of these agricultural management approaches, such as the combined use of organic and inorganic fertilizers or crop rotation and organic fertilizers, to maximize yield and improve soil microbial diversity (Ghaley et al. \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2005\u003c/span\u003e; Li et al. \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Mei et al. \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Salehi et al. \u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e2017\u003c/span\u003e).\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eThis study elucidated the effects of anthropogenic activities on soil bacterial diversity and crop yield, and explored whether the effects of agricultural management approaches change at different experimental scales, plant types, soil ranges, and pH values. The results showed that CF had the greatest potential for improving crop yield, whereas it had a negative effect on soil microbial diversity. This is because chemical fertilizers can directly provide soil with a lot of readily available nutrient elements required for plant growth, whereas it may also cause enrichment of microbial functional groups and therefore, led to reductions in microbial diversity. Organic fertilizers and rotation can not only improve crop yield, but also increase soil bacterial diversity, which could be used as sustainable agricultural management approaches. Because they may improve soil fertility and increase microbial diversity, and causing continues crop yield increase. This is why they are so called \u0026lsquo;sustainable agricultural approaches\u0026rsquo;. Crop productivity does not always benefit from higher soil microbial diversity, the relationship is highly dependent on anthropogenic activities. Our results have great guiding significance for ecological environment protection and crop economic benefits.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was supported by Natural Science Foundation of Changsha (Grant numbers [No. kq2202089]).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting Interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors have no relevant financial or non-financial interests to disclose.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDelong Meng, Junliang Zou, Xueduan Liu, and Huaqun Yin designed the research, data collection were performed by Lei Xing, Tianbo Liu, Yongjun Liu and data analysis were performed by JingYi Huang, Delong Meng, Junliang Zou. The manuscript was written by Jingyi Huang. All authors discussed the results and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.\u003c/p\u003e\n\u003cp\u003eAcknowledgements\u003c/p\u003e\n\u003cp\u003eThis work was supported by Natural Science Foundation of Changsha (grant, No. kq2202089). We would like to thank Dr. Wieland Fricke from University College Dublin, Ireland for giving very constructive suggestions.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eAllison VJ, Goldberg DE (2002) Species-level versus community-level patterns of mycorrhizal dependence on phosphorus: an example of Simpson's paradox. 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Curr Opin Biotech 19:153\u0026ndash;159. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.copbio.2008.02.004\u003c/span\u003e\u003cspan address=\"10.1016/j.copbio.2008.02.004\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\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":"Agricultural Management, Crop Yield, Meta-Analysis, Microbial Diversity, Relationships. ","lastPublishedDoi":"10.21203/rs.3.rs-2303140/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-2303140/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003eBackground and Aims\u003c/em\u003e Microbial diversity is a critical topic that concerns sustainable agriculture and crop production. Anthropogenic activities have a nonnegligible influence on both soil microbial diversity and crop production. Little research has been conducted to quantify the beneficial relationships between microbial diversity and soil productivity.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eMethods\u003c/em\u003e A meta-analysis based on 80 published papers was carried out to clarify the effects of anthropogenic activities including chemical fertilization (CF), organic fertilization (OF), intercropping or rotation (IC) and microbial treatment (MF), on soil microbial diversity and crop yield, and the relationship in between and summarized.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eResults\u003c/em\u003e The results showed that CF had the greatest potential for improving crop yield, whereas it may cause reductions in soil microbial diversity. OF is a sustainable development strategy, which increases both soil microbial diversity and crop yield. Under IC treatment, soil bacterial community diversity was significantly positively correlated with crop productivity, and the average effects of the four management approaches on soil microbial diversity and crop productivity were significantly different under different conditions.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eConclusion\u003c/em\u003e Overall, our results have great guiding significance for ecological environment protection and crop economic benefits.\u003c/p\u003e","manuscriptTitle":"Effect of agricultural management approaches on soil microbial diversity and crop production: A meta-analysis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2022-11-29 18:35:49","doi":"10.21203/rs.3.rs-2303140/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":"b30e4ee4-ec4e-439b-955d-1c70433924ba","owner":[],"postedDate":"November 29th, 2022","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2023-05-09T09:00:18+00:00","versionOfRecord":[],"versionCreatedAt":"2022-11-29 18:35:49","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-2303140","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-2303140","identity":"rs-2303140","version":["v1"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}