Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization

A special issue of Nitrogen (ISSN 2504-3129).

Deadline for manuscript submissions: 31 August 2025 | Viewed by 1191

Special Issue Editor

Laboratoire Chrono-Environnement-UMR 6249 CNRS, Université Bourgogne Franche-Comté, Besançon, France
Interests: plant–microbe interactions; symbiosis; nitrogen uptake

Special Issue Information

Dear Colleagues,

Microbial interactions with plants play a crucial role in nitrogen cycling, fundamentally influencing plant growth, soil health, and ecosystem sustainability. While nitrogen-fixing bacteria such as rhizobia have been extensively studied for their symbiotic relationships with legumes, a wider range of microorganisms—including mycorrhizal fungi, free-living nitrogen fixers, and other nitrogen-transforming microbes—have emerged as vital players in enhancing nitrogen availability and uptake for plants. These diverse microbial interactions are key to developing sustainable agricultural practices, reducing dependency on synthetic fertilizers, and supporting more efficient nutrient utilization.

This Special Issue in Nitrogen aims to explore recent advances in our understanding of how microbial partnerships with plants drive nitrogen fixation, enhance nitrogen uptake, and optimize nitrogen utilization. We welcome studies focused on the following topics:

  • Mechanisms of nitrogen fixation, uptake, and assimilation facilitated by various microbial species;
  • The role of symbiotic and associative microbes in boosting plant nitrogen efficiency;
  • Genetic and biotechnological innovations for improving microbial contributions to nitrogen cycling;
  • Applications of microbial inoculants and biofertilizers for sustainable nitrogen management in agriculture.

We welcome original research, comprehensive reviews, and case studies examining the biological, ecological, and applied dimensions of nitrogen-focused plant–microbe interactions, with an emphasis on strategies for enhancing nitrogen sustainability in agricultural systems.

Dr. Jun Zhou
Guest Editor

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Keywords

  • nitrogen fixation
  • nitrogen uptake
  • symbiosis
  • biofertilizers
  • nutrient cycling
  • plant–microbe interactions
  • sustainable nitrogen management
  • nitrogen assimilation
  • rhizobia
  • soil microbiome

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Published Papers (1 paper)

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Research

19 pages, 4249 KiB  
Article
Transcriptome Analysis of Hybrid Progeny of Caucasian Clover and White Clover in the Early Stages of Rhizobia Infection
by Peizhi Zhu, Sijing Wang and Kefan Cao
Nitrogen 2025, 6(1), 11; https://doi.org/10.3390/nitrogen6010011 - 27 Feb 2025
Viewed by 461
Abstract
The hybrid progeny (1-1) resulting from the cross between Caucasian clover and white clover initially demonstrated an inability to fix nitrogen naturally via spontaneous nodulation. However, following inoculation with specific rhizobia strains derived from the Trifolium genus, successful nodulation and nitrogen fixation were [...] Read more.
The hybrid progeny (1-1) resulting from the cross between Caucasian clover and white clover initially demonstrated an inability to fix nitrogen naturally via spontaneous nodulation. However, following inoculation with specific rhizobia strains derived from the Trifolium genus, successful nodulation and nitrogen fixation were observed in the 1-1 progeny, resulting in enhanced biomass production and adaptability. To explore in greater depth the mechanisms driving nitrogen fixation in these hybrid progeny, the inoculation was carried out using the dominant rhizobia strain (No. 5), isolated from Mengnong Clover No. 1. Root samples were collected at 3, 6, and 9 days post inoculation for RNA sequencing. A total of 1755 differentially expressed unigenes were identified between the control and treatment groups. KEGG pathway analysis highlighted key pathways associated with nodule nitrogen fixation. In combination with Weighted Gene Co-expression Network Analysis (WGCNA) and Gene Set Enrichment Analysis (GSEA), several differentially expressed genes were identified, suggesting their potential contribution to nitrogen fixation. Noteworthy among these, the gene TRINITY_DN7551_c0_g1 in the Phenylpropanoid biosynthesis pathway (MAP00940) emerged as a key candidate. This study offers valuable RNA-seq data, contributing significantly to the understanding of the molecular regulatory mechanisms underpinning nodule nitrogen fixation in legumes, thereby laying a solid foundation for future investigations into the hybrid progeny of Caucasian and white clover crosses. Full article
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