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Impacts of Bacillus velezensis inoculation on exogenous organic carbon mineralization and bacterial community composition in fumigated continuous-cropping obstacle soils
Yixian Liu1, 2, Runa Zhang1, 2, Shuai Ding1, 2#, Shuang Wang1, 2, Liang Wei1, 2, Cuiyan Wu3, Wensheng Fang4, Qiuxia Wang4, Dongdong Yan4, Aocheng Cao4, Jianping Chen1, 2, Tida Ge1, 2, Zhenke Zhu1, 2#
1 State Key Laboratory for Quality and Safety of Agro-products/Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Rural Affairs/Key Laboratory of Green Plant Protection of Zhejiang Province/Institute of Plant Virology, Ningbo University, Ningbo 315211, China
2 International Science and Technology Cooperation Base for the Regulation of Soil Biological Functions and One Health of Zhejiang Province, Ningbo University, Ningbo 315211, China
3 School of Materials and Chemical Engineering, Ningbo University of Technology, Ningbo 315211, China
4 Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China

 Highlights 

● Dazomet and dimethyl disulfide fumigation suppress exogenous organic carbon (C) mineralization.

● Bacillus velezensis inoculation restores C mineralization and increases microbial respiration.

● Bacillus velezensis reshapes bacterial communities and strengthens bacterial interactions.

● Microbial remediation can restore soil function in intensive agricultural systems.

● Dazomet and dimethyl disulfide fumigation suppress exogenous organic carbon (C) mineralization.

● Bacillus velezensis inoculation restores C mineralization and increases microbial respiration.

● Bacillus velezensis reshapes bacterial communities and strengthens bacterial interactions.

● Microbial remediation can restore soil function in intensive agricultural systems. -->

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摘要  

化学熏蒸剂如棉隆(DZ)和二甲基二硫(DMDS)能够有效抑制土传病害,但熏蒸后的连作障碍土壤生态功能恢复存在不确定性,例如由微生物介导的有机碳循环。然而,微生物修复措施如何增强熏蒸后连作土壤微生物碳矿化活性的作用机制仍不明确。本研究通过土壤培养实验,探究了接种贝莱斯芽孢杆菌(Bacillus velezensis)连作障碍土壤熏蒸后外源有机碳(EOC)矿化以及细菌群落组成和互作的影响。与化学熏蒸处理相比,额外接种B.velezensis使DZ熏蒸处理土壤的EOC累积矿化量提高了27%,DMDS熏蒸处理土壤提高了22%。贝莱斯芽孢杆菌接种促进外源碳矿化主要是因为核心类群和关键种的富集, 增强了土壤微生物碳代谢活性。结构方程模型分析进一步表明,核心微生物类群(OTU56,属于Bacillus)能够与土著细菌产生积极互作,从而促进EOC 矿化。研究表明B.velezensis通过选择性地重塑细菌群落并增强细菌协作网络,促进了熏蒸后连作障碍土壤微生物代谢功能的快速恢复。本研究为化学熏蒸连作障碍土壤生态功能恢复提供了理论支撑,并为化学胁迫农田生态系统发展可持续管理措施提供了科学依据。



Abstract  
Chemical fumigants such as dazomet (DZ) and dimethyl disulfide (DMDS) effectively suppress soil-borne pathogens but  there  is  uncertainty  regarding  the  restoration  of  soil  ecological  functions  in  continuous  cropping  obstacles  after fumigation, such as microbe-mediated organic carbon cycling.   However, the mechanism by which microbial remediation measures enhance carbon mineralization activity after soil fumigation remains unclear.   In  this study, we conducted microcosm experiments to investigate the impacts of Bacillus velezensis inoculation on exogenous organic carbon (EOC) mineralization and bacterial community composition and interactions following chemical fumigation.  Relative to fumigation alone, Bvelezensis addition increased cumulative EOC mineralization by 27% in DZ-treated soils and by 22% in DMDS- treated soils.  This enhancement was associated with the enrichment of core taxa and keystone species, which collectively increased microbial activity.   Structural equation modeling further confirmed that core taxa (OTU56, belonging to Bacillus) induced positive interactions with indigenous species, which drove the observed enhancement in EOC mineralization. We conclude that Bvelezensis facilitates the rapid recovery of soil carbon mineralization after fumigation by selectively reshaping the bacterial community and strengthening bacterial cooperative networks.   This work provides a mechanistic framework for microbially driven ecological restoration of fumigant-impacted continuous-cropping obstacle soils and informs the development of sustainable soil-management practices in chemically challenged agroecosystems.


Keywords:  continuous cropping obstacles       chemical fumigation       B. velezensis       microbial community structure       organic carbon mineralization  
Online: 02 January 2026  
Fund: 

This work was supported by the National Key Research and Development Program of China (2023YFD1701200), the Beijing Natural Science Foundation, China (6232034).

About author:  Yixian Li, E-mail: 2311130026@nbu.edu.cn; #Correspondence Shuai Ding, E-mail: dingshuai@nbu.edu.cn; Zhenke Zhu, E-mail: zhuzhenke@nbu.edu.cn

Cite this article: 

Yixian Liu, Runa Zhang, Shuai Ding, Shuang Wang, Liang Wei, Cuiyan Wu, Wensheng Fang, Qiuxia Wang, Dongdong Yan, Aocheng Cao, Jianping Chen, Tida Ge, Zhenke Zhu. 2026. Impacts of Bacillus velezensis inoculation on exogenous organic carbon mineralization and bacterial community composition in fumigated continuous-cropping obstacle soils. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.12.076

Abs E, Chase A B, Manzoni S, Ciais P, Allison S D. 2024. Microbial evolution-An under-appreciated driver of soil carbon cycling. Global Change Biology, 30, e17268.

Barnett S E, Shade A. 2024. Arrive and wait: Inactive  bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance. Ecology Letters, 27, e14393.

Bissett A, Brown M V, Siciliano S D, Thrall P H. 2013. Microbial community responses to anthropogenically induced environmental change: Towards a systems approach. Ecology Letters16, 128–139.

Brookes P C, Landman A, Pruden G, Jenkinson D S. 1985. Chloroform fumigation and the release of soil nitrogen: A rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biology and Biochemistry, 17, 837–842.

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

Cao T, Luo Y, Shi M, Tian X, Kuzyakov Y. 2024. Microbial interactions for nutrient acquisition in soil: Miners, scavengers, and carriers. Soil Biology and Biochemistry, 188, 109215.

Carini P, Marsden P J, Leff J W, Morgan E E, Strickland M S,   Fierer

N. 2016. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nature Microbiology, 2, 1–6.

Castellano-Hinojosa A, Boyd N S, Strauss S L. 2022. Impact of fumigants on non-target soil microorganisms: A review. Journal of Hazardous Materials, 427, 128149.

Chen H, Ma K, Lu M, Fu Q, Qiu Y, Zhao J, Huang Y, Yang Y, Schadt C W, Chen H. 2022. Functional redundancy in soil microbial community based on metagenomics across the globe. Frontiers in Microbiology, 13, 878978.

Chen Y, Feng X, Zhao X, Hao X, Tong L, Wang S, Ding R, Kang S. 2025. Biochar application enhances soil quality by improving soil physical structure under particular water and salt conditions in arid region of Northwest China. Journal of Integrative Agriculture24, 3242–3263. Chowdhury S, Farrell M, Bolan N. 2014. Priming of soil organic carbon by malic acid addition is differentially affected by nutrient availability.

Soil Biology and Biochemistry, 77, 158–169.

Cui J, Zhu Z, Xu X, Liu S, Jones D L, Kuzyakov Y, Shibistova O, Wu J, Ge T. 2020. Carbon and nitrogen recycling from microbial necromass to cope with C:N stoichiometric imbalance by priming. Soil Biology and Biochemistry, 142, 107720.

Deng X, Zhang N, Shen Z, Zhu C, Liu H, Xu Z, Li R, Shen Q, Salles J

F. 2021. Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum. NPJ Biofilms and Microbiomes, 7, 33.

Dungan R S, Gan J, Yates S R. 2003. Accelerated degradation of methyl isothiocyanate in soil. WaterAirand Soil Pollution142, 299–310. Fang W, Wang X, Huang B, Zhang D, Liu J, Zhu J, Yan D, Wang Q, Cao A, Han Q. 2020. Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition. Ecotoxicology and Environmental

Safety, 187, 109850.

Ge T, Wei X, Razavi B S, Zhu Z, Hu Y, Kuzyakov Y, Jones D L, Wu J. 2017. Stability and dynamics of enzyme activity patterns in the rice rhizosphere: Effects of plant growth and temperature. Soil Biology and Biochemistry, 113, 108–115.

Del Giorgio P A, Cole J J. 1998. Bacterial growth efficiency in natural aquatic systems. Annual Review of Ecology and Systematics29, 503–541.

de Graaff M A, Adkins J, Kardol P, Throop H L. 2015. A meta-analysis of soil biodiversity impacts on the carbon cycle. Soil, 1, 257–271.

Guo Z, Lu Z, Liu Z, Zhou W, Yang S, Lv J, Wei M. 2024. Difference in the effect of applying Bacillus to control tomato Verticillium wilt in black and red soil. Microorganisms, 12, 797.

Hui C, Sun P, Guo X, Jiang H, Zhao Y, Xu L. 2018. Shifts in microbial community structure and soil nitrogen mineralization following short- term soil amendment with the ammonifier Bacillus amyloliquefaciens DT. International Biodeterioration & Biodegradation, 132, 40–48.

Ibekwe A M, Papiernik S K, Gan J, Yates S R, Yang C H, Crowley D E.


 

2001. Impact of fumigants on soil microbial communities. Applied and Environmental Microbiology, 67, 3245–3257.

Jiang Z, Vancov T, Fang Y, Tang C, Zhang W, Xiao M, Song X, Zhou J, Ge T, Cai Y. 2025. Sustained superiority of biochar over straw for enhancing soil biological-phosphorus via the mediation of phoD- harboring bacteria in subtropical Moso bamboo forests. Forest Ecology and Management, 584, 122606.

Kalam S, Basu A, Ahmad I, Sayyed R, El-Enshasy H A, Dailin D J, Suriani N L. 2020. Recent understanding of soil Acidobacteria and their ecological significance: A critical review. Frontiers in Microbiology, 11, 580024.

Li J, Song Z, Wang Y, Chen C, Jiang H, Ding T, Xie S. 2025. Root exudates mediate Bacillus velezensis FZB42’s colonization- independent biocontrol in maize. Journal of Agricultural and Food Chemistry, 73, 22.

Liang C, Schimel J P, Jastrow J D. 2017. The importance of anabolism in microbial control over soil carbon storage. Nature Microbiology, 2, 17105.

Liang Y, Cao D, Ma Z, Wu R, Zhang H, Fang Y, Shahbaz M, Liu X J A, Kuzyakov Y, Chen J. 2024. Stoichiometry regulates rice straw- induced priming effect: The microbial life strategies. Soil Biology and Biochemistry, 196, 109514.

Liu Q, Zhu Z, Wei L, Zhang W, Wang S, Yuan H, Chen J, Ge T, Xu M, Kuzyakov Y. 2025. Bacterial necromass decomposition and priming effects in paddy soils depend on long-term fertilization. Soil Biology and Biochemistry, 211, 109992.

Malik A A, Puissant J, Buckeridge K M, Goodall T, Jehmlich N, Chowdhury S, Gweon H S, Peyton J M, Mason K E, van Agtmaal

M. 2018. Land use driven change in soil pH affects microbial carbon cycling processes. Nature Communications, 9, 3591.

Mawarda P C, Lakke S L, van Elsas J D, Salles J F. 2022. Temporal dynamics of the soil bacterial community following Bacillus invasion. iScience, 25, 104029.

de Mills S, Ijaz U Z, Lens P N L. 2025. Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems. NPJ Biofilms and Microbiomes, 11, 54.

Mosela M, Andrade G, Massucato L, de Araújo Almeida S, Nogueira A, de Lima Filho R, Zeffa D, Mian S, Higashi A, Shimizu G. 2022. Bacillus velezensis strain Ag75 as a new multifunctional agent for biocontrol, phosphate solubilization and growth promotion in maize and soybean crops. Scientific Reports, 12, 15284.

Nielsen U N, Ayres E, Wall D H, Bardgett R D. 2011. Soil biodiversity and carbon cycling: A review and synthesis of studies examining diversity–function relationships. European Journal of Soil Science, 62, 105–116.

Pan T, Chen Y, Li S, Wang L, Muramoto J, Shennan C, Tian J, Cai K. 2025. Anaerobic soil disinfestation rather than Bacillus velezensis Y6 inoculant suppresses tomato bacterial wilt by improving soil quality and manipulating bacterial communities. Journal of Integrative Agriculture, 24, 754–768.

Philippot L, Chenu C, Kappler A, Rillig M C, Fierer N. 2024. The interplay between microbial communities and soil properties. Nature Reviews Microbiology, 22, 226–239.

Prider J, Williams A. 2014. Using dazomet to reduce broomrape seed banks in soils with low moisture content. Crop Protection59, 43–50. Qiao Y, Wang T, Huang Q, Guo H, Zhang H, Xu Q, Shen Q, Ling

N. 2024. Core species impact plant health by enhancing soil microbial cooperation and network complexity during community coalescence. Soil Biology and Biochemistry, 188, 109231.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner F O. 2012. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41, D590–D596.

Schulte-Uebbing L F, Beusen A H, Bouwman A F, De Vries W. 2022. From planetary to regional boundaries for agricultural nitrogen pollution. Nature, 610, 507–512.

Sennett L B, Burton D L, Goyer C, Zebarth B J. 2022. Chemical fumigation alters soil carbon and nitrogen dynamics in soils amended with substrates of contrasting carbon availability. Geoderma, 419, 115878.


Shu X, Hu Y, Liu W, Xia L, Zhang Y, Zhou W, Liu W, Zhang Y. 2023. Linking between soil properties, bacterial communities, enzyme activities, and soil organic carbon mineralization under ecological restoration in an alpine degraded grassland. Frontiers in Microbiology, 14, 1131836.

Sinsabaugh R L, Follstad Shah J J. 2012. Ecoenzymatic stoichiometry and ecological theory. Annual Review of Ecology, Evolutionand Systematics, 43, 313–343.

Sun X, Xu Z, Xie J, Hesselberg-Thomsen V, Tan T, Zheng D, Strube M L, Dragoš A, Shen Q. 2022. Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. ISME Journal, 16, 774–787.

Trabelsi D, Mhamdi R. 2013. Microbial inoculants and their impact on soil microbial communities: A review. BioMed Research International, 2013, 863240.

Walters W, Hyde E R, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert J A, Jansson J K, Caporaso J G, Fuhrman J

A. 2016. Improved bacterial 16S rRNA gene (V4 and V4–5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems, 1, e00009–16.

Wang C, Liu D, Bai E. 2018. Decreasing soil microbial diversity is associated with decreasing microbial biomass under nitrogen addition. Soil Biology and Biochemistry, 120, 126–133.

Wei X, Ge T, Wu C, Wang S, Mason-Jones K, Li Y, Zhu Z, Hu Y, Liang C. 2021. T4-like phages reveal the potential role of viruses in soil organic matter mineralization. Environmental Science & Technology, 55, 6440–6448.

Wu J, Pommerening B, Chaussod R, Brookes P. 1990. Measurement of soil microbial biomass C by fumigation-extraction-an automated procedure. Soil Biology and Biochemistry, 22, 1167–1169.

Wu R, Zhang Z, Li G, Wang X, Fang Y, Kuzyakov Y, Xu X, Chen J, Ge T, Zhu Z. 2026. Frequency and C:N:P stoichiometry of organic inputs determines intensity of net C balance in paddy soils. Soil Biology and Biochemistry, 214, 110051.

Xiong J, Du L, Li N, Wu X, Xiang Y, Li S, Zou L, Liu D, Huang D, Xie Z F. 2024. Pigmentiphaga kullae CHJ604 improved the growth of tobacco by degrading allelochemicals and xenobiotics in continuous cropping obstacles. Journal of Hazardous Materials465, 133466. Yan D, Cao A, Wang Q, Li Y, Canbin O, Guo M, Guo X. 2019. Dimethyl disulfide (DMDS) as an effective soil fumigant against nematodes

in China. PLoS ONE, 14, e0224456.

Yan D, Liu J, Wang X, Fang W, Li Y, Cao A, Wang Q. 2025. A review on the mechanisms of fumigant action. New Plant Protection, 2, e27. Zargar A N, Lymperatou A, Skiadas I, Kumar M, Srivastava P. 2022. Structural and functional characterization of a novel biosurfactant from Bacillus sp. IITD106. Journal of Hazardous Materials,   423,

127201.

Zegeye E K, Brislawn C J, Farris Y, Fansler S J, Hofmockel K S, Jansson J K, Wright A T, Graham E B, Naylor D, McClure R S. 2019. Selection, succession, and stabilization of soil microbial consortia. mSystems, 4, 00055–00019.

Zhao Y, Guan D, Liu X, Gao G F, Meng F, Liu B, Xing P, Jiang X, Ma M, Cao F. 2022. Profound change in soil microbial assembly process and co-occurrence pattern in co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35–5 on soybean. Frontiers in Microbiology, 13, 846359.

Zhou J S, Tang C X, Vancov T, Fu S L, Fang Y Y, Ge T D, Dong Y F, Luo Y, Yu B, Cai Y J, White J C, Li Y F. 2026. Biochar mitigates the suppressive effects of nitrogen deposition on soil methane uptake in a subtropical forest. Agriculture, Ecosystems & Environment, 395, 109951.

Zhu X, Li Y, Wang H, Zhang L. 2024. Biochar regulates the functions of keystone taxa to reduce p-coumaric acid accumulation in soil. Frontiers in Microbiology, 15, 1458185.

Zhu Z, Fang Y, Liang Y, Li Y, Liu S, Li Y, Li B, Gao W, Yuan H, Kuzyakov

Y. 2022. Stoichiometric regulation of priming effects and soil carbon balance by microbial life strategies. Soil Biology and Biochemistry, 169, 108669.

Zhu Z, Ge T, Luo Y, Liu S, Xu X, Tong C, Shibistova O, Guggenberger G, Wu J. 2018. Microbial stoichiometric flexibility regulates rice straw mineralization and its priming effect in paddy soil. Soil Biology and Biochemistry, 121, 67–76.

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