Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.3
3.6
Journals
Agriculture
Special Issues
Crop Microbiome and Stress: Interactions, Mechanisms, and Applications
share announcement

Crop Microbiome and Stress: Interactions, Mechanisms, and Applications

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Production".

Deadline for manuscript submissions: 15 September 2026 | Viewed by 1487

Special Issue Editors

Dr. Soon-Jae Lee

E-Mail Website
Guest Editor
1. Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
2. The Swiss National Centre of Competence in Microbiomes Research, 1015 Lausanne, Switzerland
3. African Genome Centre, UM6P, Ben Guerir 43150, Morocco
Interests: mycorrhizal symbiosis; arbuscular mycorrhizal fungi; genetics; rhizosphere; plant physiology; holobiont; holobiont chronobiology; co-evolution; ecology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Li Wang

E-Mail Website
Guest Editor
College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
Interests: agroecology; crop physiological and biotechnological breeding; crop cultivation; mycorrhizal symbiosis; genetics; rhizosphere
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Understanding and harnessing plant microbiomes—which encompass the rhizosphere, endosphere, and phyllosphere communities—are essential for improving nutrient cycling, suppressing pathogens, and enhancing stress resilience in agriculture. Nonetheless, the efficacy of microbial inoculants in field trials is frequently constrained by edaphic heterogeneity, climatic fluctuations, and context-dependent plant–microbe interactions, including cultivar-specific responses. Mechanistic insights into signalling networks, metabolite exchange, and community assembly remain scarce, and multi-omics datasets are often analysed in silos.

This Special Issue tackles these bottlenecks by spotlighting high-throughput metaomics for capturing microbial diversity, spatial metabolomics to map in situ chemical dialogues, and emerging genome- and microbiome-editing tools. Systems-level modelling and machine learning approaches enable the rational design of synthetic consortia, while root-exudate engineering and holobiont-based breeding integrate microbes into plant improvement programmes. We will also address the regulatory, ethical, and socio-economic frameworks that shape field deployment.

Together, these contributions will bridge lab and field settings, offering a novel framework to harness beneficial microbiomes for use in sustainable, climate-resilient agriculture worldwide.

Dr. Soon-Jae Lee
Prof. Dr. Li Wang
Guest Editors

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. Agriculture is an international peer-reviewed open access semimonthly 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 2600 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

  • crop holobiont
  • host–microbiome interaction
  • co-evolution
  • carbon sequestration
  • climate change
  • organism–environment crosstalk

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.

Published Papers (3 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

Jump to: Other

13 pages, 1987 KB  
Article
Effects of Parametarhizium changbaiense on the Growth and Physiological Characteristics of Sugar Beet Seedlings Under Salt–Alkali Stress
by Lin Wang, Hao Wang, Lijian Xu and Wenbo Tan
Agriculture 2026, 16(11), 1224; https://doi.org/10.3390/agriculture16111224 - 1 Jun 2026
Abstract
Global crop production faces serious threats from soil salinization. Microbial resources are often exploited to be used as fertilizers or seed coatings to address this issue. Parametarhizium changbaiense, as a novel beneficial microorganism, has been discovered to be capable of assisting limited [...] Read more.
Global crop production faces serious threats from soil salinization. Microbial resources are often exploited to be used as fertilizers or seed coatings to address this issue. Parametarhizium changbaiense, as a novel beneficial microorganism, has been discovered to be capable of assisting limited crops such as mung bean in resisting salt–alkali stress. To investigate the effects of P. changbaiense on sugar beet under salt–alkali stress, the salt (NaCl:Na2SO4, molar ratio 9:1) and alkali (NaHCO3:Na2CO3, molar ratio 9:1) stress were set on sugar beet germplasm 780016B. Results demonstrated that P. changbaiense improved the phenotypic characteristics of sugar beet seedlings under salt–alkali stress. The biomass parameters such as plant height and fresh weight significantly increased by growth-promoting effect. The elevated antioxidant enzyme activity could help protect plants from ROS damage induced by stress. Relative electrical conductivity and MDA content decreased with inoculation, thereby mitigating membrane lipid peroxidation and improving membrane system stability. The higher content of soluble sugar could maintain cell turgor pressure and alleviate osmotic stress. Inoculation with P. changbaiense enhanced chlorophyll content, fluorescence, and photosynthetic capacity. The more superior root vitality and architecture were suitable for the functions of metabolism and absorption. P. changbaiense could promote the growth and physiological characteristics under salt–alkali stress, so it has practical application value in agricultural production. Full article
(This article belongs to the Special Issue Crop Microbiome and Stress: Interactions, Mechanisms, and Applications)
►▼ Show Figures

Figure 1

19 pages, 2643 KB  
Article
Characterisation of Bacillus BacMix-Linked Metabolic Response in Strawberry and Descriptive Leaf Microbiome Signatures
by Ingrida Mažeikienė, Edvinas Misiukevičius, Darius Černauskas, Lina Trakšelė and Neringa Rasiukevičiūtė
Agriculture 2026, 16(6), 662; https://doi.org/10.3390/agriculture16060662 - 14 Mar 2026
Viewed by 553
Abstract
Sustainable indoor growing management requires biological alternatives that protect against pathogens, preserve fruit quality and minimise chemical inputs in strawberries. We compared the impacts of a four-strain Bacillus consortium (BacMix) and chemical fungicides on two cultivars (cv. Elsanta and cv. Sonsation) by evaluating [...] Read more.
Sustainable indoor growing management requires biological alternatives that protect against pathogens, preserve fruit quality and minimise chemical inputs in strawberries. We compared the impacts of a four-strain Bacillus consortium (BacMix) and chemical fungicides on two cultivars (cv. Elsanta and cv. Sonsation) by evaluating the metabolite outcomes—the free amino acids (FAAs) in the leaves and the sugars in the fruits. Furthermore, the descriptive shotgun metagenomics provides a functional context for these biochemical traits. The BacMix increased the total FAAs in the leaves and stabilised the fruit sugar profiles, maintaining moderate–high sucrose with controlled glucose and fructose. The chemically treated plants showed significant reductions in both FAAs and sugars. The metagenomic data showed BacMix-related shifts in the microbial functional potential in the leaves, but the biological agent did not affect diversity. An increased representation of genes involved in amino acid biosynthesis (aminoacyl tRNA pathway) and secondary metabolite biosynthesis was observed, along with changes in the relative CAZy signals. The direction of these metagenomic trends aligned with the metabolite outcomes, suggesting that BacMix influences the endophytic microbiome in a way that supports nitrogen-related metabolism and carbohydrate stability during the vegetation period. The cultivar-independent metabolic improvements emphasise the benefits of BacMix and highlight microbiome-based interventions as promising tools for sustainable, chemical-reduced strawberry production. Full article
(This article belongs to the Special Issue Crop Microbiome and Stress: Interactions, Mechanisms, and Applications)
►▼ Show Figures

Graphical abstract

Other

Jump to: Research

23 pages, 8298 KB  
Systematic Review
Arbuscular Mycorrhizal Fungal Symbiosis Enhances Crop Photosynthetic Traits Under Drought Stress—A Meta-Analysis
by Xiaoqian Shang, Yun Nie, Pandeng Wang, Hanwen Cao, Mohamed Hijri, Soon-Jae Lee, Shoujiang Feng, Gary Y. Gan and Li Wang
Agriculture 2026, 16(11), 1180; https://doi.org/10.3390/agriculture16111180 - 27 May 2026
Viewed by 295
Abstract
The benefits of arbuscular mycorrhizal fungi (AMF) in alleviating plant abiotic and biotic stresses have been well documented; however, how AMF modulate photosynthesis-related processes under different drought intensities is poorly understood. This study quantified the impact of different AMF formulations on the photosynthetic [...] Read more.
The benefits of arbuscular mycorrhizal fungi (AMF) in alleviating plant abiotic and biotic stresses have been well documented; however, how AMF modulate photosynthesis-related processes under different drought intensities is poorly understood. This study quantified the impact of different AMF formulations on the photosynthetic traits in different host plant types under different intensities of drought stress. A total of 52 published studies were included in a meta-analysis with a random-effects model. Synthesizing the research findings revealed that, under drought stress, AMF significantly improved plant photosynthetic rates and nutrient absorption, with the strongest effect on phosphorus absorption (the effect size Hedges’ g = 3.85, 95% CI: 2.76–4.95, p < 0.001). Overall, the between-study heterogeneity was moderate to high (I2 = 64.7%, τ2 = 0.38), indicating variability among the included studies. As drought intensity increased, the effect of AMF on the net photosynthetic rate decreased, with the transpiration rate (Tr) and stomatal conductance (Gs) first increasing and then diminishing. Drought intensity exceeding the ‘moderate’ threshold inhibited both Tr and Gs. The AMF effect on chlorophyll content differed among the plant types, with Hedges’ g being 1.656, 2.715, and 3.231 for herbaceous, grass, and woody plants, respectively. Inoculation with multiple AMF species provided greater benefits than single AMF strains in promoting chlorophyll content (Hedges’ g = 1.949 for single vs. 3.217 for mixture) and net photosynthetic rate (Hedges’ g = 2.242 for single vs. 3.986 for mixture). We conclude that the AMF–plant symbiotic association alleviates drought stress by adjusting the net photosynthetic rate, transpiration rate, and stomatal conductance. The magnitude of these responses varies depending on plant functional type, drought intensity, and AM fungal formulation. Full article
(This article belongs to the Special Issue Crop Microbiome and Stress: Interactions, Mechanisms, and Applications)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop