Effects of bacillus on continuous cropping of sugar beets and their rhizosphere microbial community
AbstractSugar beet is a vital sugar-producing crop, and continuous cropping poses a significant threat to its growth, leading to a decline in yield and quality. This study aimed to investigate the effects of two bacterial agents, Bacillus subtilis and Bacillus mucilaginosus, on the growth, soil physicochemical properties, and rhizosphere microbial community of sugar beet seedlings. We employed pot experiments and amplicon sequencing to analyze the impact of applying two different Bacillus agents on the microbial community structure in the rhizosphere soil of continuously cropped sugar beet and explore the microbial composition, environmental driving factors, and potential functions present within the microbial communities. The results showed that both Bacillus agents and their combination significantly promoted the growth of continuous cropping sugar beet seedlings, reaching or even surpassing the levels observed in crop rotation, improved soil pH, and enhanced soil environment. High-throughput sequencing analysis of the rhizosphere soil revealed that all Bacillus treatments induced changes in the diversity and structural composition of the rhizosphere microbial community, and significantly increased the relative abundance of Proteobacteria, thereby enriching beneficial microorganisms such as Pseudomonas, Novosphingobium, and Sphingomonas compared with that in the control group. Additionally, the application of Bacillus inoculants significantly enhanced the nitrate respiration, nitrogen respiration, and chitinolytic functions. These two bacterial agents optimized soil physicochemical properties and improved the rhizosphere soil microbial community structure, promoting sugar beet seedling growth and effectively mitigating the negative effects of continuous cropping.
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Data availability
The datasets generated during and/or analyzed during the current study are available in the NCBI Sequence Read Archive (SRA) database under accession numbers PRJNA1310802 (ITS) and PRJNA1310801 (16S).
ReferencesSteven, Z., Zhang, R. H. & Stephen, K. In In integrated processing technologies for food and agricultural by-products (ed. Stephen, Z.) 331–351 (Academic Press, Cambridge, 2019).
Google Scholar
Chhikara, N. et al. Bioactive compounds of beetroot and utilization in food processing industry: A critical review. Food Chem. 272, 192–200. https://doi.org/10.1016/j.foodchem.2018.08.022 (2018).
Google Scholar
Mall, A. K. et al. Sugar beet cultivation in India: Prospects for bio-ethanol production and value-added co-products. Sugar Tech. 23(6), 1218–1234. https://doi.org/10.1007/s12355-021-01007-0 (2021).
Google Scholar
Jbawi, E. et al. Genotype: Environment interaction study in sugar beet (Beta vulgaris L.). Int. J. Environ. 5(3), 74–86. https://doi.org/10.3126/ije.v5i3.15706 (2016).
Google Scholar
Holmquist, L. et al. Major latex protein-like encoding genes contribute to Rhizoctonia solani defense responses in sugar beet. Mol. Genet. Genom. 296(1), 155–164. https://doi.org/10.1007/s00438-020-01735-0 (2020).
Google Scholar
Wu, X. et al. The effect of long-term continuous cropping of black pepper on soil bacterial communities as determined by 454 pyrosequencing. PLoS ONE 10(8), e0136946–e0136946. https://doi.org/10.1371/journal.pone.0136946 (2015).
Google Scholar
Zhu, B. et al. Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping. PeerJ 8, e8905. https://doi.org/10.7717/peerj.8905 (2020).
Google Scholar
Tang, J., Xue, Z. Q., Daroch, M. & Ma, J. Impact of continuous Salvia miltiorrhiza cropping onrhizosphere actinomycetes and fungi communities. Ann. Microbiol. 65(3), 1267–1275. https://doi.org/10.1007/s13213-014-0964-2 (2015).
Google Scholar
Cui, R. F. et al. The response of sugar beet rhizosphere micro-ecological environment to continuous cropping. Front. Microbiol. 13, 956785. https://doi.org/10.3389/fmicb.2022.956785 (2022).
Google Scholar
Kui, L. et al. Large-scale characterization of the soil microbiome in ancient tea plantations using high-throughput 16S rRNA and internal transcribed spacer amplicon sequencing. Front. Microbiol. 12, 745225. https://doi.org/10.3389/fmicb.2021.745225 (2021).
Google Scholar
Pimentel, D. et al. Conserving biological diversity in agricultural/forestry systems. Bioscience 42(5), 354–362. https://doi.org/10.2307/1311782 (1992).
Google Scholar
Tkacz, A. et al. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J. 9, 2349–2359 (2015).
Google Scholar
Tong, J., Cao, M. & Wang, R. Effects of restoration time on microbial diversity in rhizosphere and non-rhizosphere soil of Bothriochloa ischaemum. Int. J. Environ. Res. Public Health. 15, 2155. https://doi.org/10.3390/ijerph15102155 (2018).
Google Scholar
Zheng, X. et al. Effects of a microbial restoration substrate on plant growth and rhizo-sphere bacterial community in a continuous tomato crop-ping greenhouse. Sci. Rep. 10, 13729. https://doi.org/10.1038/s41598-020-70737-0 (2020).
Google Scholar
Cao, B. et al. Insight into the variation of bacterial structure in atrazine-contaminated soil regulating by potential phytoremediator: Pennisetum americanum (L.) K. Schum.. Front Microbiol. 9, 864. https://doi.org/10.3389/fmicb.2018.00864 (2018).
Google Scholar
Das, S. et al. Taxonomic and functional responses of soil microbial communities to slag-based fertilizer amendment in rice cropping systems. Environ. Int. 127, 531–539. https://doi.org/10.1016/j.envint.2019.04.012 (2019).
Google Scholar
Kang, P. et al. A comparison of microbial composition under three tree ecosystems using the stochastic process and network complexity approaches. Front. Microbiol. 13, 1018077. https://doi.org/10.3389/fmicb.2022.1018077 (2022).
Google Scholar
Zhang, X. et al. Plant growth and development of tropical seagrass deter-mined rhizodeposition and its related microbial community. Mar Pollut Bull. 199, 115940. https://doi.org/10.1016/j.marpolbul (2024).
Google Scholar
Liu, J. et al. Development of a soil quality index for Camellia oleifera forestland yield under three different parent materials in Southern China. Soil Till Res. 176, 45–50. https://doi.org/10.1016/j.still.2017.09.013 (2018).
Google Scholar
Qi, R. M. et al. Temperature effects on soil organic carbon, soil labile organic carbon fractions, and soil enzyme activities under long-term fertilization regimes. Appl. Soil Ecol. 102, 36–45. https://doi.org/10.1016/j.apsoil.2016.02.004 (2016).
Google Scholar
Ahsan, T. et al. Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system. J. Adv. Res. 64, 1–13. https://doi.org/10.1016/j.jare.2023.11.028 (2024).
Google Scholar
Li, M. et al. Effects of continuous cropping of sugar beet (Beta vulgaris L.) on its endophytic and soil bacterial community by high-throughput sequencing. Ann. Microbiol. 70, 39. https://doi.org/10.1186/s13213-020-01583-8 (2020).
Google Scholar
Sun, R. C. et al. 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 Biol. Biochem. 88, 9–18. https://doi.org/10.1016/j.soilbio.2015.05.007 (2015).
Google Scholar
Zhang, S. N. et al. Cow manure application effectively regulates the soil bacterial community in tea plantation. BMC Microbiol. 20(1), 190. https://doi.org/10.1186/s12866-020-01871-y (2020).
Google Scholar
Cai, X. Y. et al. Effects and mechanisms of symbiotic microbial combination agents to control tomato fusarium crown and root rot disease. Front. Microbiol. 12, 629793. https://doi.org/10.3389/fmicb.2021.629793 (2021).
Google Scholar
Duan, Y. N. et al. The phlorizin-degrading Bacillus licheniformis XNRB-3 mediates soil microorganisms to alleviate apple replant disease. Front. Microbiol. 13, 839484. https://doi.org/10.3389/fmicb.2022.839484 (2022).
Google Scholar
Olanrewaju, O. S., Ayilara, M. S., Ayangbenro, A. S. & Babalola, O. O. Genome mining of three plant growth-promoting bacillus species from maize rhizosphere. Appl. Biochem. Biotechnol. 193(12), 3949–3969. https://doi.org/10.1007/s12010-021-03660-3 (2021).
Google Scholar
Solanki, M. K. et al. Diversity and antagonistic potential of Bacillusspp. associated to the rhizosphere of tomato for the management of Rhizoctonia solani. Biocontrol. Sci. Technol. 22(2), 203–217. https://doi.org/10.1080/09583157.2011.649713 (2012).
Google Scholar
Chen, X. R. et al. Bacillus velezensis strain GUMT319 reshapes soil microbiome biodiversity and increases grape yields. Biology. 11(10), 1486–1486. https://doi.org/10.3390/biology11101486 (2022).
Google Scholar
Shao, F. F., Tao, W. H., Yan, H. K. & Wang, Q. J. Effects of microbial organic fertilizer (MOF) application on desert soil enzyme activity and jujube yield and quality. Agronomy 13(9), 2427–2427. https://doi.org/10.3390/agronomy13092427 (2023).
Google Scholar
Gajbhiye, A., Rai, A. R. & Meshram, S. U. Isolation, evaluation and characterization of Bacillus subtilis from cotton rhizospheric soil with biocontrol activity against Fusarium oxysporum. World. J. Microb. Biot. 26(7), 1187–1194. https://doi.org/10.1007/s11274-009-0287-9 (2009).
Google Scholar
Govindasamy, V. et al. Bacillus and Paenibacillus spp.: Potential PGPR for sustainable agriculture. 18. https://doi.org/10.1007/978-3-642-13612-2_15 (2010).Qiao, J. Q. et al. Addition of plant-growth-promoting Bacillus subtilis PTS-394 on tomato rhizosphere has no durable impact on composition of root microbiome. BMC Microbiol. 17(1), 131. https://doi.org/10.1186/s12866-017-1039-x (2017).
Google Scholar
Sui, J. K. et al. Effects of Bacillus subtilis T6–1 on the rhizosphere microbial community structure of continuous cropping poplar. Biology. 11(5), 791–791. https://doi.org/10.3390/biology11050791 (2022).
Google Scholar
Wang, D. et al. Genomic insights and functional analysis reveal plant growth promotion traits of Paenibacillus mucilaginosus G78. Genes 14(2), 392–392. https://doi.org/10.3390/genes14020392 (2023).
Google Scholar
Lu, R. K. Soil and agricultural chemistry analysis (ed. Lu, R. K.) pp. 248–254 (1999).Huang, W. J. et al. Effects of continuous sugar beet cropping on rhizospheric microbial communities. Genes 11(1), 13–13. https://doi.org/10.3390/genes11010013 (2019).
Google Scholar
Kõljalg, U. et al. The taxon hypothesis paradigm: On the unambiguous detection and communication of taxa. Microorganisms. 8(12), 1910–1910. https://doi.org/10.3390/microorganisms8121910 (2020).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41(D1), D590–D596. https://doi.org/10.1093/nar/gks1219 (2012).
Google Scholar
Li, Q., Huang, Y., Xin, S. & Li, Z. Y. Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status. Sci. Rep. 10(1), 22296. https://doi.org/10.1038/s41598-020-78459-z (2020).
Google Scholar
Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75(23), 7537–7541. https://doi.org/10.1128/AEM.01541-09 (2009).
Google Scholar
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genomebiology.com (London. Print) 12 (6): R60-R60. http://genomebiology.com/2011/11/6/R60 (2011).Yuan, M. M. et al. Climate warming enhances microbial network complexity and stability. Nat. Clim. Change. 11(4), 343–348. https://doi.org/10.1038/s41558-021-00989-9 (2021).
Google Scholar
Xu, W. F. et al. Structure and ecological function of the soil microbiome associated with ‘Sanghuang’ mushrooms suffering from fungal diseases. BMC Microbiol. 23(1), 218. https://doi.org/10.1186/s12866-023-02965-z (2023).
Google Scholar
Richard, M. C., David, W. H. & Joseph, W. K. Rhizobacterial colonization of bermudagrass by Bacillus spp. in a Marvyn loamy sand soil. Appl. Soil Ecol. 141, 10–17. https://doi.org/10.1016/j.apsoil.2019.04.018 (2019).
Google Scholar
Zhang, Q. X. et al. Wheat rhizosphere colonization by Bacillus amyloliquefaciens W10 and Pseudomonas protegens FD6 suppress soil and in planta abundance of the sharp eyespot pathogen Rhizoctonia cerealis. J. Appl. Microbiol. 134, 1–11. https://doi.org/10.1093/jambio/lxad101 (2023).
Google Scholar
Chen, W. M. et al. Biochar combined with Bacillus subtilis SL-44 as an eco-friendly strategy to improve soil fertility, reduce Fusarium wilt, and promote radish growth. Ecotoxicol. Environ. Saf. 251, 114509. https://doi.org/10.1016/j.ecoenv.2023.114509 (2023).
Google Scholar
Han, S. C., Kim, K., Maung, C. E. H. & Kim, K. Y. Growth enhancement of tomato by a plant growth promoting bacterium, bacillus subtilis PE7. Korean J. Soil Sci. Fertil. 56(4), 398–406. https://doi.org/10.7745/kjssf.2023.56.4.398 (2023).
Google Scholar
Torres, M. et al. Growth promotion on horticultural crops and antifungal activity of Bacillus velezensis XT1. Appl. Soil Ecol. 150, 103453. https://doi.org/10.1016/j.apsoil.2019.103453 (2020).
Google Scholar
Shen, Z. Z. et al. Effect of biofertilizer for suppressing Fusarium wilt disease of banana as well as enhancing microbial and chemical properties of soil under greenhouse trial. Appl. Soil Ecol. 93, 111–119. https://doi.org/10.1016/j.apsoil.2015.04.013 (2015).
Google Scholar
Wu, L. X., Wang, Y., Lyu, H. & Chen, X. D. Effects of a compound Trichoderma agent on Coptis chinensis growth, nutrients, enzyme activity, and microbial community of rhizosphere soil. PeerJ 11, e15652. https://doi.org/10.7717/peerj.15652 (2023).
Google Scholar
Asaf, S., Numan, M., Khan, A. L. & Al-Harrasi, A. Sphingomonas: From diversity and genomics to functional role in environmental remediation and plant growth. Crit. Rev. Biotechnol. 40(2), 138–152. https://doi.org/10.1080/07388551.2019.1709793 (2020).
Google Scholar
Li, Q. et al. Plant growth-promoting rhizobacterium Pseudomonas sp. CM11 specifically induces lateral roots. New Phytol. 235(4), 1575–1588. https://doi.org/10.1111/nph.18199 (2022).
Google Scholar
Wang, Q. et al. The endophytic bacterium Sphingomonas SaMR12 alleviates Cd stress in oilseed rape through regulation of the GSH-AsA cycle and antioxidative enzymes. BMC Plant Biol. 20, 63. https://doi.org/10.1186/s12870.-020-2273-1 (2020).
Google Scholar
Song, J. et al. Rhizosphere microbiomes of potato cultivated under bacillus subtilis treatment influence the quality of potato tubers. Int. J. Mol. Sci. 22(21), 12065–12065. https://doi.org/10.3390/ijms222112065 (2021).
Google Scholar
Zhao, J. et al. The rhizosphere microbial community response to a bio-organic fertilizer: Finding the mechanisms behind the suppression of watermelon Fusarium wilt disease. Acta Physiol. Plant. 40(1), 17. https://doi.org/10.1007/s11738-017-2581-8 (2017).
Google Scholar
Li, X. Y. et al. Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity. Front. Bioeng. Biotechnol. 10, 1062351. https://doi.org/10.3389/fbioe.2022.1062351 (2022).
Google Scholar
Download referencesAcknowledgementsThis research was made possible through the collaboration and support of the National Sugar Crop Improvement Centre of Heilongjiang University and Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region.FundingThis research was funded by the Heilongjiang Provincial Postdoctoral Research Funding Program (LBH-Z23255).Author informationAuthors and AffiliationsCollege of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150000, ChinaYanchun Sun, Qun Song, Zenghao Wang, Youkai Gao, Liuli Wei, Yuguang Wang, Rui Chen & Gui GengAuthorsYanchun SunView author publicationsSearch author on:PubMed Google ScholarQun SongView author publicationsSearch author on:PubMed Google ScholarZenghao WangView author publicationsSearch author on:PubMed Google ScholarYoukai GaoView author publicationsSearch author on:PubMed Google ScholarLiuli WeiView author publicationsSearch author on:PubMed Google ScholarYuguang WangView author publicationsSearch author on:PubMed Google ScholarRui ChenView author publicationsSearch author on:PubMed Google ScholarGui GengView author publicationsSearch author on:PubMed Google ScholarContributionsQun Song and Zenghao Wang: Conceptualization, Methodology, Writing-Original draft preparation; Youkai Gao, Liuli Wei, Rui Chen: Data curation, Sample analysis; Yanchun Sun: Conceptualization, Resources, Supervision, Writing-Reviewing; Gui Geng, Yuguang Wang: Methodology, Writing-Reviewing. All authors contributed to the article and approved the submitted version.Corresponding authorsCorrespondence to
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Reprints and permissionsAbout this articleCite this articleSun, Y., Song, Q., Wang, Z. et al. Effects of bacillus on continuous cropping of sugar beets and their rhizosphere microbial community.
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KeywordsBacterial agentsSuccessive cropping obstacleRhizosphere microorganismsMicrobial diversity More
