Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2025 Jan 8

PMID 39766799

Authors

Xiangqin Xu

Xi Gao

Chen Gui

Hang Wang

Xiaowen Liu

Guoxing Wu

Affiliations

Soon will be listed here.

Abstract

Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, and were strongly associated with soil organic nitrogen content. The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes.

References

Zhou Y, Selvam A, Wong J . Evaluation of humic substances during co-composting of food waste, sawdust and Chinese medicinal herbal residues. Bioresour Technol. 2014; 168:229-34. DOI: 10.1016/j.biortech.2014.05.070. View

Wu C, Yan B, Wei F, Wang H, Gao L, Ma H . Long-term application of nitrogen and phosphorus fertilizers changes the process of community construction by affecting keystone species of crop rhizosphere microorganisms. Sci Total Environ. 2023; 897:165239. DOI: 10.1016/j.scitotenv.2023.165239. View

Fang W, Wang X, Huang B, Zhang D, Liu J, Zhu J . Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition. Ecotoxicol Environ Saf. 2019; 187:109850. DOI: 10.1016/j.ecoenv.2019.109850. View

Liu L, Zheng N, Yu Y, Zheng Z, Yao H . Soil carbon and nitrogen cycles driven by iron redox: A review. Sci Total Environ. 2024; 918:170660. DOI: 10.1016/j.scitotenv.2024.170660. View

Kartal B, Maalcke W, de Almeida N, Cirpus I, Gloerich J, Geerts W . Molecular mechanism of anaerobic ammonium oxidation. Nature. 2011; 479(7371):127-30. DOI: 10.1038/nature10453. View

Butala N, Falkinham J . Nitrate and nitrite reductase activities of . Int J Mycobacteriol. 2018; 7(4):328-331. DOI: 10.4103/ijmy.ijmy_118_18. View

Berendsen R, Pieterse C, Bakker P . The rhizosphere microbiome and plant health. Trends Plant Sci. 2012; 17(8):478-86. DOI: 10.1016/j.tplants.2012.04.001. View

Zhu F, Xiao J, Zhang Y, Wei L, Liang Z . Dazomet application suppressed watermelon wilt by the altered soil microbial community. Sci Rep. 2020; 10(1):21668. PMC: 7730150. DOI: 10.1038/s41598-020-78839-5. View

Cheng L, Booker F, Tu C, Burkey K, Zhou L, Shew H . Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2. Science. 2012; 337(6098):1084-7. DOI: 10.1126/science.1224304. View

10.

Wang Q, Ma Y, Yang H, Chang Z . Effect of biofumigation and chemical fumigation on soil microbial community structure and control of pepper Phytophthora blight. World J Microbiol Biotechnol. 2013; 30(2):507-18. DOI: 10.1007/s11274-013-1462-6. View

11.

Li Q, Zhang D, Song Z, Ren L, Jin X, Fang W . Organic fertilizer activates soil beneficial microorganisms to promote strawberry growth and soil health after fumigation. Environ Pollut. 2021; 295:118653. DOI: 10.1016/j.envpol.2021.118653. View

12.

Naylor D, Fansler S, Brislawn C, Nelson W, Hofmockel K, Jansson J . Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. mBio. 2020; 11(4). PMC: 7343995. DOI: 10.1128/mBio.01349-20. View

13.

Fang W, Huang B, Sun Y, Yan D, Li Y, Bruno T . Soil amendments promoting nitrifying bacteria recovery faster than the denitrifying bacteria at post soil fumigation. Sci Total Environ. 2023; 908:168041. DOI: 10.1016/j.scitotenv.2023.168041. View

14.

Song L, Yang T, Xia S, Yin Z, Liu X, Li S . Soil depth exerts stronger impact on bacterial community than elevation in subtropical forests of Huangshan Mountain. Sci Total Environ. 2022; 852:158438. DOI: 10.1016/j.scitotenv.2022.158438. View

15.

Castellano-Hinojosa A, Karlsen-Ayala E, Boyd N, Strauss S . Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system. Sci Total Environ. 2024; 919():170659. DOI: 10.1016/j.scitotenv.2024.170659. View

16.

Jiao S, Chu H, Zhang B, Wei X, Chen W, Wei G . Linking soil fungi to bacterial community assembly in arid ecosystems. Imeta. 2024; 1(1):e2. PMC: 10989902. DOI: 10.1002/imt2.2. View

17.

Luo G, Xue C, Jiang Q, Xiao Y, Zhang F, Guo S . Soil Carbon, Nitrogen, and Phosphorus Cycling Microbial Populations and Their Resistance to Global Change Depend on Soil C:N:P Stoichiometry. mSystems. 2020; 5(3). PMC: 7329320. DOI: 10.1128/mSystems.00162-20. View

18.

Ouchene R, Intertaglia L, Zaatout N, Kecha M, Suzuki M . Selective isolation, antimicrobial screening and phylogenetic diversity of marine actinomycetes derived from the Coast of Bejaia City (Algeria), a polluted and microbiologically unexplored environment. J Appl Microbiol. 2021; 132(4):2870-2882. DOI: 10.1111/jam.15415. View

19.

Zhang D, Yan D, Cheng H, Fang W, Huang B, Wang X . Effects of multi-year biofumigation on soil bacterial and fungal communities and strawberry yield. Environ Pollut. 2019; 256:113415. DOI: 10.1016/j.envpol.2019.113415. View

20.

Wang Z, Su J, Ali A, Gao Z, Zhang R, Li Y . Microbially induced calcium precipitation driven by denitrification: Performance, metabolites, and molecular mechanisms. J Environ Manage. 2023; 338:117826. DOI: 10.1016/j.jenvman.2023.117826. View