Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
2.8
2.3
Journals
Nitrogen
Special Issues
Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization
share announcement

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

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

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 9834

Special Issue Editor

Dr. Jun Zhou

E-Mail Website
Guest Editor
Laboratoire Chrono-Environnement, UMR 6249 CNRS, Université Bourgogne Franche-Comté, Besançon, France
Interests: plant–microbe interactions; symbiosis; nitrogen uptake
Special Issues, Collections and Topics in MDPI journals

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Nitrogen is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

23 pages, 2149 KB  
Article
Interaction Between Rhizobium leguminosarum bv. viciae and Pseudomonas alkylphenolica Enhances Faba Bean Growth and Resilience to Water Deficit Under Nitrogen-Fixing Conditions
by Mohamed Tamoudjout, Hamid Msaad, Soukaina Lahmaoui, Ahmed El Moukhtari, Cherki Ghoulam and Mohamed Farissi
Nitrogen 2026, 7(1), 7; https://doi.org/10.3390/nitrogen7010007 - 1 Jan 2026
Cited by 1 | Viewed by 1340
Abstract
Water deficit is a major constraint limiting the growth and yield of faba bean (Vicia faba L.). A pot experiment was conducted under controlled conditions to evaluate the effect of inoculation with Rhizobium leguminosarum bv. viciae BIHB 1148 (strain F14) and Pseudomonas [...] Read more.
Water deficit is a major constraint limiting the growth and yield of faba bean (Vicia faba L.). A pot experiment was conducted under controlled conditions to evaluate the effect of inoculation with Rhizobium leguminosarum bv. viciae BIHB 1148 (strain F14) and Pseudomonas alkylphenolica PF9 (strain L13) on faba bean drought resilience. Two irrigation regimes were applied: well-watered (80% of field capacity) versus water-stressed (40% of field capacity). Strain F14 was used to ensure effective biological nitrogen fixation, while strain L13 was applied in co-inoculation to evaluate its biostimulatory effects. The control plants received nitrogen in its chemical form. Results indicated that water deficit significantly (p < 0.001) reduced plant growth, nodulation, and photosynthesis-related parameters, and increased hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels, which are key markers of oxidative stress. However, co-inoculation with strains F14 and L13 significantly enhanced shoot and root biomass, as well as most agro-morphological traits. It also stimulated (p < 0.05) the antioxidant activities of superoxide dismutase (3-fold), guaiacol peroxidase (12%), and catalase (104%), and increased proline content (119%), which led to lower levels of MDA (54% decrease) and H2O2 (55% decrease), improved membrane stability, water status, and enhanced photosynthesis. Overall, co-inoculation of faba bean with Rhizobium leguminosarum bv. viciae BIHB 1148 and Pseudomonas alkylphenolica PF9 offers a promising and sustainable approach to improve plant resilience under water deficit. Full article
(This article belongs to the Special Issue Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization)
►▼ Show Figures

Figure 1

17 pages, 4718 KB  
Article
Managing Nitrogen Sources in Soybean–Rhizobium Symbiosis During Reproductive Phenological Stage: Partitioning Symbiotic and Supplemental N with 15N
by Nicolas Braga Casarin, Cássio Carlette Thiengo, Carlos Alcides Villalba Algarin, Maria Clara Faria Chaves, Gil Miguel de Sousa Câmara, Valter Casarin, Fernando Shintate Galindo and José Lavres
Nitrogen 2026, 7(1), 1; https://doi.org/10.3390/nitrogen7010001 - 22 Dec 2025
Cited by 2 | Viewed by 1274
Abstract
Understanding how supplemental nitrogen (N) interacts with biological N2 fixation (BNF) in modern soybean cultivars is essential for designing fertilization strategies that avoid unnecessary N inputs. We investigated N partitioning among soil, fertilizer and symbiotic sources in soybean grown in a greenhouse [...] Read more.
Understanding how supplemental nitrogen (N) interacts with biological N2 fixation (BNF) in modern soybean cultivars is essential for designing fertilization strategies that avoid unnecessary N inputs. We investigated N partitioning among soil, fertilizer and symbiotic sources in soybean grown in a greenhouse pot experiment on a tropical Oxisol. Plants were inoculated with Bradyrhizobium and subjected to four N managements: no external N, soil-applied 15N-urea (20 kg N ha−1), foliar 15N-urea (2 kg N ha−1, 0.7% w/v), and the combination of soil + foliar N. Using 15N isotope dilution, we quantified N derived from the atmosphere (NDFA), fertilizer (NDFF) and soil (NDFS) at organ and whole-plant scales, and related these fractions to nodulation, nitrogenase activity and yield. In the absence of external N, NDFA exceeded 97% in all organs, indicating a strong reliance on BNF and efficient internal N remobilization during grain filling, accompanied by higher leaf nitrate reductase activity. Soil and soil + foliar N markedly increased NDFF and NDFS while suppressing nodulation (particularly at V4) and reducing nitrogenase activity, yet they did not improve grain yield or vegetative biomass. Foliar N alone had only modest effects on N partitioning and did not enhance yield. Under these tropical soil conditions, symbiotic fixation and internal N remobilization were sufficient to meet grain N demand, highlighting the limited agronomic benefit and potential ecological cost of supplemental N during reproductive growth. Full article
(This article belongs to the Special Issue Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization)
►▼ Show Figures

Figure 1

15 pages, 1885 KB  
Article
Effect of Integrated Nutrient Management Through Targeted Yield Precision Model on Soil Microbes, Root Morphology, Productivity of Hybrid Castor on a Non-Calcareous Alfisol
by Abishek Ravichandran, Santhi Rangasamy, Maragatham Subramaniam, Gopalakrishnan Myleswami, Dhinesh Vadivel, Poovarasan Thangavel, Naveenkumar Arumugam, Vinothini Nedunchezhiyan and Dineshkumar Chandrasekar
Nitrogen 2025, 6(4), 95; https://doi.org/10.3390/nitrogen6040095 - 20 Oct 2025
Viewed by 1033
Abstract
Precision application of fertiliser nutrients based on soil-available nutrients is a vital means of increasing castor (Ricinus communis L.) productivity. Fertiliser application based on the targeted yield model under inorganic fertilisers alone and Integrated Plant Nutrition System (IPNS) differ from the blanket [...] Read more.
Precision application of fertiliser nutrients based on soil-available nutrients is a vital means of increasing castor (Ricinus communis L.) productivity. Fertiliser application based on the targeted yield model under inorganic fertilisers alone and Integrated Plant Nutrition System (IPNS) differ from the blanket recommendation practices. Field experiments were conducted in two locations to validate the Soil Test Crop Response (STCR) targeted yield model developed for hybrid castor on non-calcareous Alfisol. The main objective was to determine the effect of inorganic fertilisers and organic manures on microbial populations, enzyme dynamics in soil, and productivity of castor. Experimental field data revealed that combined application of inorganic fertilisers along with 12.5 t ha−1 farmyard manure increased the soil microbial population and enzyme activity in the rhizosphere soils of castor. Castor responded positively with an increase in highest targeted yield level. The highest yield of 2726 and 2695 kg ha−1 were attained in the treatment T8 (STCR-IPNS −2.75 t ha−1) in both locations, and Treatment T5 (STCR-NPK alone −2.75 t ha−1) was on par with T8. The IPNS treatments showed higher percent achievement than the NPK treatments alone. Root length and dry matter production increased significantly with the application of a higher dose of fertiliser along with farmyard manure. Root dry matter production significantly contributed towards the castor seed yield. More soil-beneficial microorganisms and enzyme dynamics were observed in the IPNS treatment. Full article
(This article belongs to the Special Issue Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization)
►▼ Show Figures

Figure 1

17 pages, 7385 KB  
Article
Microbial Alliance of Paenibacillus sp. SPR11 and Bradyrhizobium yuanmingense PR3 Enhances Nitrogen Fixation, Yield, and Salinity Tolerance in Black Gram Under Saline, Nutrient-Depleted Soils
by Praveen Kumar Tiwari, Anchal Kumar Srivastava, Rachana Singh and Alok Kumar Srivastava
Nitrogen 2025, 6(3), 66; https://doi.org/10.3390/nitrogen6030066 - 7 Aug 2025
Cited by 1 | Viewed by 1682
Abstract
Salinity is a major abiotic stress limiting black gram (Vigna mungo) productivity, particularly in arid and semi-arid regions. Saline soils negatively impact plant growth, nodulation, nitrogen fixation, and yield. This study evaluated the efficacy of co-inoculating salt-tolerant plant growth-promoting bacteria Paenibacillus [...] Read more.
Salinity is a major abiotic stress limiting black gram (Vigna mungo) productivity, particularly in arid and semi-arid regions. Saline soils negatively impact plant growth, nodulation, nitrogen fixation, and yield. This study evaluated the efficacy of co-inoculating salt-tolerant plant growth-promoting bacteria Paenibacillus sp. SPR11 and Bradyrhizobium yuanmingense PR3 on black gram performance under saline field conditions (EC: 8.87 dS m−1; pH: 8.37) with low organic carbon (0.6%) and nutrient deficiencies. In vitro assays demonstrated the biocontrol potential of SPR11, inhibiting Fusarium oxysporum and Macrophomina phaseolina by 76% and 62%, respectively. Germination assays and net house experiments under 300 mM NaCl stress showed that co-inoculation significantly improved physiological traits, including germination rate, root length (61.39%), shoot biomass (59.95%), and nitrogen fixation (52.4%) in nitrogen-free media. Field trials further revealed enhanced stress tolerance markers: chlorophyll content increased by 54.74%, proline by 50.89%, and antioxidant enzyme activities (SOD, CAT, PAL) were significantly upregulated. Electrolyte leakage was reduced by 55.77%, indicating improved membrane stability. Agronomic performance also improved, with co-inoculated plants showing increased root length (7.19%), grain yield (15.55 q ha−1; 77.04% over control), total biomass (26.73 q ha−1; 57.06%), and straw yield (8.18 q ha−1). Pod number, seed count, and seed weight were also enhanced. Nutrient analysis showed elevated uptake of nitrogen, phosphorus, potassium, and key micronutrients (Zn, Fe) in both grain and straw. To the best of our knowledge, this is the very first field-based report demonstrating the synergistic benefits of co-inoculating Paenibacillus sp. SPR11 and Bradyrhizobium yuanmingense PR3 in black gram under saline, nutrient-poor conditions without external nitrogen inputs. The results highlight a sustainable strategy to enhance legume productivity and resilience in salt-affected soils. Full article
(This article belongs to the Special Issue Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization)
►▼ Show Figures

Graphical abstract

10 pages, 1280 KB  
Article
Analysis of GmERF5 Response to the Rhizobial Type III Effector NopAA Underlying the Nodule in Soybeans
by Lianheng Xia, Yunshan Song, Tong Yu, Ying Pei, Hongwei Jiang, Qingshan Chen and Dawei Xin
Nitrogen 2025, 6(2), 38; https://doi.org/10.3390/nitrogen6020038 - 21 May 2025
Viewed by 1214
Abstract
Soybean, an important leguminous crop valued for its high protein and oil content, obtains most of its nitrogen through symbiotic fixation processes. The symbiosis between soybeans and rhizobium can provide sufficient nitrogen for soybean growth. However, the signaling pathways underlying the establishment of [...] Read more.
Soybean, an important leguminous crop valued for its high protein and oil content, obtains most of its nitrogen through symbiotic fixation processes. The symbiosis between soybeans and rhizobium can provide sufficient nitrogen for soybean growth. However, the signaling pathways underlying the establishment of the symbiosis are not so clear, especially the rhizobial type III effector-induced host response. In this study, we found that the single mutant HH103 nopAA::kan significantly affected the nodule number in soybeans. To further demonstrate the NopAA-triggered response in soybeans. Initial quantitative real-time PCR (qRT-PCR) tests showed that NopAA affects the expression of the soybean gene GmERF5, which was significantly upregulated upon inoculation with HH103 nopAA::kan, acting as a positive regulator of nodulation. The direct interaction between NopAA and GmERF5 was confirmed through yeast-two hybrid analysis. Furthermore, overexpression of GmERF5 in hairy roots indicated that GmERF5 may underlie the nodule phenotype of soybeans in response to NopAA. These findings provide new insights into the mechanisms by which soybean genes respond to rhizobial type III effectors to regulate symbiosis. Full article
(This article belongs to the Special Issue Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization)
►▼ Show Figures

Figure 1

19 pages, 4249 KB  
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 1410
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
(This article belongs to the Special Issue Microbial Interactions with Plants: Advancing Nitrogen Fixation, Uptake, and Utilization)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6
Back to TopTop