Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system

dc.contributor.authorJalloh, Abdul A.
dc.contributor.authorKhamis, Fathiya Mbarak
dc.contributor.authorYusuf, Abdullahi Ahmed
dc.contributor.authorSubramanian, Sevgan
dc.contributor.authorMutyambai, Daniel Munyao
dc.date.accessioned2024-08-06T05:24:59Z
dc.date.available2024-08-06T05:24:59Z
dc.date.issued2024-03
dc.descriptionDATA AVAILABILITY STATEMENT: The unprocessed sequencing datasets generated during the current study have been deposited in GenBank, NCBI under BioProject PRJNA1015669. The 16S (V1-V2, V3-V4) metagenome data were registered as Biosamples SAMN37384180 – SAMN37384217 and the sequences assigned SRA accessions SRR26087688 – SRR26087719. The ITS (ITS1-ITS2) metagenome data were registered as Biosamples SAMN37384218 – SAMN37384250 and the sequences assigned SRA accessions SRR26087651 – SRR26087687. We also provide the R scripts for data analysis along with all the necessary input files as Additional file 2A and B. The data for soil physicochemical properties and GPS coordinates were provided as Additional files 3 and 4.en_US
dc.descriptionSUPPORTING INFORMATION: FILE S1: Availability of data and materials: The unprocessed sequencing datasets generated during the current study have been deposited in GenBank, NCBI under BioProject PRJNA1015669. The 16S (V1-V2, V3-V4) metagenome data were registered as Biosamples SAMN37384180 – SAMN37384217 and the sequences assigned SRA accessions SRR26087688 – SRR26087719. The ITS (ITS1-ITS2) metagenome data were registered as Biosamples SAMN37384218 – SAMN37384250 and the sequences assigned SRA accessions SRR26087651 – SRR26087687. We also provide the R scripts for data analysis along with all the necessary input files as Additional file 2A and B. The data for soil physicochemical properties and GPS coordinates were provided as Additional files 3 and 4.en_US
dc.description.abstractBACKGROUND: The soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push–pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with those obtained from maize-monoculture (Mono) cropping system. RESULTS: The PPT cropping system changed the composition and diversity of soil and maize-root microbial communities, and led to notable improvements in soil physicochemical characteristics compared to that of the Mono cropping system. Distinct bacterial and fungal genera played a crucial role in influencing the variation in microbial diversity within these cropping systems. The relative abundance of fungal genera Trichoderma, Mortierella, and Bionectria and bacterial genera Streptomyces, RB41, and Nitrospira were more enriched in PPT. These microbial communities are associated with essential ecosystem services such as plant protection, decomposition, carbon utilization, bioinsecticides production, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Conversely, pathogenic associated bacterial genus including Bryobacter were more enriched in Mono-root. Additionally, the Mono system exhibited a high relative abundance of fungal genera such as Gibberella, Neocosmospora, and Aspergillus, which are linked to plant diseases and food contamination. Significant differences were observed in the relative abundance of the inferred metabiome functional protein pathways including syringate degradation, L-methionine biosynthesis I, and inosine 5’-phosphate degradation. CONCLUSION: Push–pull cropping system positively influences soil and maize-root microbiomes and enhances soil physicochemical properties. This highlights its potential for agricultural and environmental sustainability. These findings contribute to our understanding of the diverse ecosystem services offered by this cropping system where it is practiced regarding the system’s resilience and functional redundancy. Future research should focus on whether PPT affects the soil and maize-root microbial communities through the release of plant metabolites from the intercrop root exudates or through the alteration of the soil’s nutritional status, which affects microbial enzymatic activities.en_US
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_US
dc.description.sdgSDG-02:Zero Hungeren_US
dc.description.sdgSDG-12:Responsible consumption and productionen_US
dc.description.sdgSDG-15:Life on landen_US
dc.description.sponsorshipIntegrated pest management strategy to counter the threat of invasive FAW to food security in eastern Africa, the Swiss Agency for Development and Cooperation (SDC); Swedish International Development Cooperation Agency (Sida); Australian Centre for International Agricultural Research (ACIAR); the Norwegian Agency for Development Cooperation (Norad); the German Federal Ministry for Economic Cooperation and Development (BMZ); and the Government of the Republic of Kenya for core support to icipe, the German Academic Exchange Service (DAAD)-In-Region Postgraduate Scholarship through the African Regional Postgraduate Programme in Insect Science (ARPPIS), as well as the University of Pretoria (UP) postgraduate doctoral bursary for the 2023 academic year.en_US
dc.description.urihttps://bmcmicrobiol.biomedcentral.com/en_US
dc.identifier.citationJalloh, A.A., Khamis, F.M., Yusuf, A.A. et al. Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system. BMC Microbiology 24, 92 (2024). https://doi.org/10.1186/s12866-024-03238-z.en_US
dc.identifier.issn1471-2180 (online)
dc.identifier.other10.1186/s12866-024-03238-z
dc.identifier.urihttp://hdl.handle.net/2263/97438
dc.language.isoenen_US
dc.publisherBMCen_US
dc.rights© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.subjectAgroecosystem sustainabilityen_US
dc.subjectAmplicon sequencingen_US
dc.subjectCropping systemen_US
dc.subjectEcosystem servicesen_US
dc.subjectSoil and maize-root microbiomesen_US
dc.subjectSoil healthen_US
dc.subjectSDG-02: Zero hungeren_US
dc.subjectSDG-12: Responsible consumption and productionen_US
dc.subjectSDG-15: Life on landen_US
dc.subjectPush–pull technology (PPT)en_US
dc.titleLong-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming systemen_US
dc.typeArticleen_US

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