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Microorganisms
Special Issues
Beneficial Microorganisms for Sustainable Agriculture
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Beneficial Microorganisms for Sustainable Agriculture

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 3900

Special Issue Editors

Dr. Tim J. Dumonceaux

E-Mail Website
Guest Editor
Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
Interests: molecular diagnostics; agricultural microbiology; microbial communities; biofuels; plant pathology
Special Issues, Collections and Topics in MDPI journals
Dr. Christina Eynck

E-Mail Website
Guest Editor
Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
Interests: agronomy; genomics; plant pathology; phenomics; crop breeding and genetics; alternative cropping systems; oilseeds; biofuels; camelina; carinata
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The plant holobiont includes an array of microorganisms from all domains of life that interact in a wide variety of ways with the host plant and with one another. These interactions can have an important effect on plant health and productivity. Studies of these interactions have typically focused on the negative impacts of plant pathogens and how they lead to decreased productivity and plant vitality. More recently, the less clear beneficial impacts of environmental microorganisms on plant health have become the focus of significant research. It is clear that individual microorganisms or microbial communities, often actively recruited by the plant through a variety of chemical messages (volatiles, root exudates, and others), can strongly support plant resilience to biotic and abiotic threats such as pathogens, insects, drought, and salinity. Analytical tools suitable for studying these interactions are becoming increasingly sophisticated, leading to important insights into beneficial plant–microbe interactions, along with microbial products intended to support plant growth and resilience (biofertilizers) or resistance to biotic threats (biocontrol agents). In this collection, we aim to highlight the vast array of scientific activity in this area, with a special emphasis on the discovery and application of microorganisms to support plant growth and resilience to biotic and abiotic stresses. We encourage the submission of high-quality manuscripts spanning the continuum from basic discovery, such as microbial community analyses that can identify microbial taxa and illuminate mechanisms of microbial community assembly, to application, including the use of individual microbes or defined synthetic communities to support plant growth. Comprehensive literature review articles, or manuscripts describing novel methods to address these questions, are also welcomed.

Dr. Tim J. Dumonceaux
Dr. Christina Eynck
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. Microorganisms is an international peer-reviewed open access monthly 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 2700 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

  • abiotic stress
  • biotic stress
  • biocontrol
  • biofertilizer
  • plant–microbe interaction

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Published Papers (3 papers)

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Research

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23 pages, 4580 KB  
Article
Bacillus velezensis 7-A as a Biocontrol Agent Against Fusarium verticillioides, the Causal Agent of Rice Sheath Rot Disease
by Boyu Liu, Qunying Qin, Jianchao Hu, Jiayi Wang, Juan Gan, Ye Zhuang, Zhengxiang Sun and Yi Zhou
Microorganisms 2025, 13(11), 2511; https://doi.org/10.3390/microorganisms13112511 - 31 Oct 2025
Viewed by 745
Abstract
Rice sheath rot has progressively developed into a growing threat to global rice production, particularly in intensively managed systems conducive to disease development. Therefore, accurate identification of the causal pathogen and the development of sustainable management strategies represent urgent scientific requirements. In this [...] Read more.
Rice sheath rot has progressively developed into a growing threat to global rice production, particularly in intensively managed systems conducive to disease development. Therefore, accurate identification of the causal pathogen and the development of sustainable management strategies represent urgent scientific requirements. In this study, we isolated the causal organism of rice sheath rot from infected rice tissues and identified it as Fusarium verticillioides based on multi-locus sequence analysis. Eight endophytic bacterial strains were recovered from healthy rice root systems. Among the isolates, Bacillus velezensis isolate 7-A exhibited the strongest antifungal activity against F. verticillioides. This isolate demonstrated broad-spectrum antifungal activity, with inhibition rates ranging from 54.8% to 71.8%. Phylogenetic analysis based on 16S rRNA and gyrB gene sequences identified it as B. velezensis. Further characterization revealed that B. velezensis 7-A is capable of secreting proteases and synthesizing siderophores. The filtered liquid from sterile fermentation markedly inhibited the growth of mycelium in F. verticillioides and induced marked morphological abnormalities. Liquid LC-MS analysis identified multiple antifungal active substances, including camphor, ginkgolides B, salicin, cinnamic acid, hydroxygenkwanin, stearamide, β-carotene, and others. A pot experiment demonstrated that the fermentation broth of B. velezensis 7-A effectively suppressed the occurrence of rice sheath rot, achieving a relative control efficacy of 61.3%, which is comparable to that of a 10% carbendazim water-dispersible granule (WDG). Additionally, isolate 7-A enhances plant disease resistance by activating the activities of key defense enzymes. These findings provide preliminary insights into its potential application in integrated and sustainable disease management programs. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)
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14 pages, 1131 KB  
Article
Enzymatic Activity and Organic Acid Profile of Phosphate-Solubilizing Bacterial Inoculants and Their Agronomic Effectiveness in Soybean
by Luana Rainieri Massucato, Mayara Barbosa Silva, Mirela Mosela, Lycio Shinji Watanabe, Leandro Afonso, Antoni Wallace Marcos, Alison Fernando Nogueira, Nicholas Vieira de Sousa, Ricardo Cancio Fendrich, Marcos Ventura Faria and Leandro Simões Azeredo Gonçalves
Microorganisms 2025, 13(9), 2016; https://doi.org/10.3390/microorganisms13092016 - 29 Aug 2025
Cited by 2 | Viewed by 1281
Abstract
Low phosphorus (P) availability in tropical soils is one of the main constraints to agricultural productivity and the sustainability of cropping systems. In this study, we evaluated the functional potential of four bacterial strains, including those present in two commercial inoculants: Nodubiophos (Ag87-CCT [...] Read more.
Low phosphorus (P) availability in tropical soils is one of the main constraints to agricultural productivity and the sustainability of cropping systems. In this study, we evaluated the functional potential of four bacterial strains, including those present in two commercial inoculants: Nodubiophos (Ag87-CCT 8090 and Ag94-CCT 8108), and Biomaphos (B119 and B2084), focusing on their production of phosphatase and phytase enzymes, organic acids, and their agronomic efficacy in soybean cultivation. In vitro assays showed that all strains exhibited phytase and both acid and alkaline phosphatase activities, with B2084 and Ag94 standing out in phytase-mediated mineralization. In contrast, B119 and B2084 showed the highest phosphatase activity. Organic acid production varied among strains and was influenced by the phosphate source, indicating a highly responsive metabolic regulation. Strains Ag87 and Ag94 were particularly effective in producing lactic, malic, and gluconic acids, displaying distinct profiles modulated by the available P source. In field trials, combined inoculation with Ag87 and Ag94 led to increased soybean yield, achieving performance comparable to conventional fertilization at 50% and 100% of the recommended P rate, despite applying only 30% of the total P. The results highlight complementary metabolic strategies among the evaluated strains, with the ability to solubilize and mineralize phosphorus through different mechanisms. They support their potential use as bioinoculants to enhance nutrient use efficiency and reduce fertilizer dependency in soybean cultivation. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)
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Review

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29 pages, 2787 KB  
Review
Role of the Plant–Microbiome Partnership in Environmentally Harmonious 21st Century Agriculture
by Shashi B. Sharma, Kiran P. Raverkar, Suhas P. Wani, Davis Joseph Bagyaraj, Annapurna Kannepalli, Diwakar R. W. Kandula, Aram Mikaelyan, Minshad A. Ansari, S. Patricia Stock, Keith G. Davies and Rajan Sharma
Microorganisms 2025, 13(12), 2839; https://doi.org/10.3390/microorganisms13122839 - 13 Dec 2025
Viewed by 446
Abstract
The 21st century calls for a paradigm shift in agricultural practices to address the pressing issues of regeneration of soil health, climate change, environmental degradation, sustainability under growing population pressures, and food security challenges. This article reviews the potential of the plant–microbiome approach [...] Read more.
The 21st century calls for a paradigm shift in agricultural practices to address the pressing issues of regeneration of soil health, climate change, environmental degradation, sustainability under growing population pressures, and food security challenges. This article reviews the potential of the plant–microbiome approach as a key driver for eco-conscious green farming. The focus is on the diverse roles of microbial communities in close association with plants in improving plant health, crop productivity, and soil ecosystem functions, and in enhancing environmental sustainability, with focus on four key areas: (1) Soil health and fertility through microbial partnerships; (2) Ecosystem sustainability through microbial functions; (3) Plant health, productivity and food security through microbial innovations emphasising the potential of microbial applications (biofertilisers, bioprotectants, and biostimulants) in sustainable agriculture; (4) Standardisation and stewardship in microbial agriculture highlighting the need for standardisation and quality control in microbial product development and use, and the concept of microbial stewardship and its importance in long-term agricultural sustainability. By synthesising current knowledge and identifying future challenges, this review underscores the transformative potential of the plant-associated microbiome approach in creating resilient, productive, and environmentally harmonious agricultural systems. We highlight current research gaps and future directions, arguing that embracing microbial solutions is not just an option but a necessity for ensuring food security and environmentally benign sustainability in the face of global challenges. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)
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