Multi-omics Analysis of Soil Microbiota and Metabolites in Dryland Wheat Fields Under Different Tillage Methods

Overview

Journal Sci Rep

Specialty Science

Date 2024 Oct 14

PMID 39402065

Authors

Fei Dong

Longxing Wang

Tianjing Xu

Qiuyan Yan

Shuangdui Yan

Feng Li

Lihao Chen

Ruifu Zhang

Affiliations

Soon will be listed here.

Abstract

No-tillage and subsoiling can improve soil aggregate structure and realize a synergistic effect of soil carbon and nitrogen retention compared with deep tillage. This study aimed to investigate the effects of different tillage methods on the microbiome and metabolites in wheat rhizosphere. Results indicated that no significant differences in the diversity of soil bacterial and fungal communities were observed among the tillage methods. Analysis revealed that no-tillage enriched specific genera such as Cryptosporangium, Crossiella, Rhodothermaceae, Leptothrix, Stilbella, Diutina, and Pyrenochaetopsis, while subsoiling was associated with Rubrobacter, Latescibacteraceae, Nitrospira, Rokubacteriales, and Ctenomyces. Deep tillage, on the other hand, showed significant associations with Nocardia, Aeromicrobium, Sphingopyxis, Cordyceps, and Subulicystidium. Metabolomic analysis identified differential metabolites involved in various pathways, including the biosynthesis of plant secondary metabolites, ABC transporters, and starch and sucrose metabolism. Correlation analysis revealed a significant interaction between microorganisms and metabolites in wheat rhizosphere. Bacteria at the genus level exhibited greater associations with differential metabolites. In conclusion, different tillage practices can alter the composition of microbial communities and metabolites in wheat rhizosphere, and their interactions may affect soil fertility and wheat growth.

References

Yamazaki S, Mardani-Korrani H, Kaida R, Ochiai K, Kobayashi M, Nagano A . Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere. Sci Rep. 2021; 11(1):8878. PMC: 8065045. DOI: 10.1038/s41598-021-87384-8. View

Pineda A, Kaplan I, Hannula S, Ghanem W, Bezemer T . Conditioning the soil microbiome through plant-soil feedbacks suppresses an aboveground insect pest. New Phytol. 2019; 226(2):595-608. PMC: 7155073. DOI: 10.1111/nph.16385. View

Huang W, Sun D, Chen L, An Y . Integrative analysis of the microbiome and metabolome in understanding the causes of sugarcane bitterness. Sci Rep. 2021; 11(1):6024. PMC: 7966368. DOI: 10.1038/s41598-021-85433-w. View

Xue J, Ren A, Li H, Gao Z, Du T . Soil physical properties response to tillage practices during summer fallow of dryland winter wheat field on the Loess Plateau. Environ Sci Pollut Res Int. 2017; 25(2):1070-1078. DOI: 10.1007/s11356-017-0684-9. View

DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K . Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069-72. PMC: 1489311. DOI: 10.1128/AEM.03006-05. View

Friberg H, Persson P, Jensen D, Bergkvist G . Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil. FEMS Microbiol Lett. 2019; 366(15). PMC: 6759068. DOI: 10.1093/femsle/fnz189. View

Araujo R . Advances in Soil Engineering: Sustainable Strategies for Rhizosphere and Bulk Soil Microbiome Enrichment. Front Biosci (Landmark Ed). 2022; 27(6):195. DOI: 10.31083/j.fbl2706195. View

Hou X, Qi N, Wang C, Li C, Huang D, Li Y . Hydrogen-rich water promotes the formation of bulblets in Lilium davidii var. unicolor through regulating sucrose and starch metabolism. Planta. 2021; 254(5):106. PMC: 8542194. DOI: 10.1007/s00425-021-03762-6. View

Jaiswal S, Aneja B, Jagannadham J, Pandey B, Chhokar R, Gill S . Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions. Microbiol Spectr. 2022; 10(6):e0263322. PMC: 9769940. DOI: 10.1128/spectrum.02633-22. View

10.

Banerjee S, Walder F, Buchi L, Meyer M, Held A, Gattinger A . Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J. 2019; 13(7):1722-1736. PMC: 6591126. DOI: 10.1038/s41396-019-0383-2. View

11.

Huber K, Vieira S, Sikorski J, Wust P, Fosel B, Grongroft A . Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils. Front Microbiol. 2022; 13:750456. PMC: 8874233. DOI: 10.3389/fmicb.2022.750456. View

12.

Yang L, Wen K, Ruan X, Zhao Y, Wei F, Wang Q . Response of Plant Secondary Metabolites to Environmental Factors. Molecules. 2018; 23(4). PMC: 6017249. DOI: 10.3390/molecules23040762. View

13.

Xu L, Tang G, Tian J, Wang X, Zhang J . Effects of no-tillage sowing on soil properties and forage wheat and Italian ryegrass yields in winter fallow paddy fields. PeerJ. 2021; 9:e10573. PMC: 7847706. DOI: 10.7717/peerj.10573. View

14.

Alsherif E, Khanghahi M, Crecchio C, Korany S, Sobrinho R, AbdElgawad H . Understanding the Active Mechanisms of Plant ( L.) against Heavy Metal Toxicity. Plants (Basel). 2023; 12(3). PMC: 9919468. DOI: 10.3390/plants12030676. View

15.

Chen S, Sun Y, Yang D, Yang S, Yang S, Liang T . Using moss as a bio-indicator to evaluate soil quality in litchi orchard. PLoS One. 2022; 17(12):e0278303. PMC: 9803211. DOI: 10.1371/journal.pone.0278303. View

16.

Zhang D, Yang Z, Song X, Zhang F, Liu Y . TMT-based proteomic analysis of liquorice root in response to drought stress. BMC Genomics. 2022; 23(1):524. PMC: 9297632. DOI: 10.1186/s12864-022-08733-z. View

17.

Cox D, Dyer S, Weir R, Cheseto X, Sturrock M, Coyne D . ABC transporter genes ABC-C6 and ABC-G33 alter plant-microbe-parasite interactions in the rhizosphere. Sci Rep. 2019; 9(1):19899. PMC: 6934816. DOI: 10.1038/s41598-019-56493-w. View

18.

Huang C, Han X, Yang Z, Chen Y, Rengel Z . Sowing Methods Influence Soil Bacterial Diversity and Community Composition in a Winter Wheat-Summer Maize Rotation System on the Loess Plateau. Front Microbiol. 2020; 11:192. PMC: 7040079. DOI: 10.3389/fmicb.2020.00192. View

19.

Zhang R, Wang P, Wang W, Ren A, Noor H, Zhong R . Deep ploughing in the summer fallow season and optimizing nitrogen rate can increase yield, water, and nitrogen efficiencies of rain-fed winter wheat in the Loess Plateau region of China. PeerJ. 2022; 10:e14153. PMC: 9549900. DOI: 10.7717/peerj.14153. View

20.

Yang R, Liu G, Chen T, Li S, An L, Zhang G . Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation. Genomics. 2018; 111(3):356-366. DOI: 10.1016/j.ygeno.2018.02.010. View