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Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.

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Title: Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.
Authors: Shittu OE; Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa., Enagbonma BJ; Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa., Babalola OO; Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa.; Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK.
Source: MicrobiologyOpen [Microbiologyopen] 2026 Jun; Vol. 15 (3), pp. e70307.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Wiley-Blackwell Country of Publication: England NLM ID: 101588314 Publication Model: Print Cited Medium: Internet ISSN: 2045-8827 (Electronic) Linking ISSN: 20458827 NLM ISO Abbreviation: Microbiologyopen Subsets: MEDLINE
Imprint Name(s): Original Publication: Oxford : Wiley-Blackwell
MeSH Terms: Allium*/microbiology , Bacteria*/classification , Bacteria*/genetics , Bacteria*/isolation & purification , Fertilizers*/analysis , Rhizosphere* , Metagenomics* , Microbiota*, Soil/chemistry ; Soil Microbiology
Abstract: Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.
(© 2026 The Author(s). MicrobiologyOpen published by John Wiley & Sons Ltd.)
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Grant Information: International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB
Contributed Indexing: Keywords: agricultural sustainability; biofertilizer; food security; leek; shotgun sequencing
Substance Nomenclature: 0 (Fertilizers)
0 (Soil)
Entry Date(s): Date Created: 20260610 Date Completed: 20260612 Latest Revision: 20260726
Update Code: 20260726
PubMed Central ID: PMC13251443
DOI: 10.1002/mbo3.70307
PMID: 42267859
Database: MEDLINE
Description
ISSN:2045-8827
DOI:10.1002/mbo3.70307