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

Deadline for manuscript submissions: 30 August 2026 | Viewed by 12931

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Dr. Tim J. Dumonceaux

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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
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Dr. Christina Eynck

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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

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Keywords

abiotic stress
biotic stress
biocontrol
biofertilizer
plant–microbe interaction

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Published Papers (10 papers)

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Research

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19 pages, 2831 KB

Open AccessArticle

Enhancement of Sweet Corn Seed Quality and Early Seedling Vigor by Priestia sp. RMT2NF4: Functional and Genomic Characterization of a Plant Growth-Promoting Strain

by Tawanchai Khuendee, Yupa Chromkaew, Nuttapon Khongdee, Rattanaphon Chaima, Phanumat Ainta, Narin Iamthongin, Nichakarn Pota, Benyapa Kitwetch and Toungporn Uttarotai

Microorganisms 2026, 14(7), 1388; https://doi.org/10.3390/microorganisms14071388 (registering DOI) - 23 Jun 2026

Abstract

The development of sustainable microbial inoculants for crop production requires strains with demonstrated plant growth-promoting performance and well-characterized functional potential. This study evaluated the effect of Priestia sp. RMT2NF4, isolated from the rice rhizosphere, on sweet corn (Zea mays L.) seed physiological quality and early seedling vigor, supported by whole-genome sequencing analysis. Seed treatment effects were evaluated using a between-paper germination assay under controlled conditions at 25 °C for 7 days. Seed treatment with RMT2NF4 significantly increased germination percentage, germination index, and seedling growth rate by 13.26%, 21.30%, and 23.71%, respectively (p < 0.05). Inoculated seedlings also exhibited significantly greater shoot length, while root length and abnormal seedling proportion showed numerical but non-significant improvements. Genomic analysis identified genes putatively associated with tryptophan biosynthesis, nutrient acquisition, and stress adaptation. The integration of phenotypic validation and genome-informed functional profiling highlights the potential of RMT2NF4 and provides a basis for further evaluation of RMT2NF4 as a candidate plant growth-promoting bacterium to support sustainable sweet corn production and reduce reliance on chemical inputs. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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19 pages, 2024 KB

Open AccessArticle

Halotolerant Rhizobacteria from Phragmites Communis: A Controlled Proof-of-Concept for Crop Improvement in Degraded Sandy Soils

by Kadir Sinan Arslan, Meriam Bouri, Aissa Bakelli and Fikrettin Şahin

Microorganisms 2026, 14(5), 1120; https://doi.org/10.3390/microorganisms14051120 - 14 May 2026

Cited by 1 | Viewed by 298

Abstract

Halotolerant plant growth-promoting rhizobacteria (PGPR) represent a promising strategy for enhancing crop productivity in degraded soils. This study evaluated 51 bacterial strains isolated from the rhizosphere of the Saharan halophyte Phragmites communis L. for their capacity to improve the performance of wheat (Triticum aestivum L.) and pepper (Capsicum annuum L.) under nutrient-deficient sandy soil conditions. The selection of halotolerant isolates was based on their potential for cross-tolerance, assuming that their adaptive mechanisms against salinity could also mitigate the osmotic and nutritional constraints inherent to nutrient-poor sandy substrates. Two strains, XE-15 and XR-18, were selected based on in vitro screening and tentatively assigned to the genera Pseudomonas and Bacillus, respectively, using 16S rRNA sequencing and multilocus sequence analysis (MLSA). Greenhouse experiments demonstrated that bacterial inoculation significantly increased plant biomass (up to ~2-fold compared to control) and enhanced pepper fruit yield (0.68 g vs. 0.20 g in control). XR-18 notably increased Fe (up to 198.65 mg kg⁻¹) and P (7.98 mg kg⁻¹) accumulation in wheat, while XE-15 exhibited substantial concentrations of nitrogen (1.08%) and magnesium (4.11 mg kg⁻¹) and zinc (102.3 mg kg⁻¹). Soil properties were also improved, including increased water-holding capacity (~30%) and enhanced micronutrient availability. Zinc showed the most pronounced strain-specific response, increasing by 84% under XE-15 and by more than 160% under XR-18. However, taxonomic resolution remains tentative in the absence of genome-level analyses, and mechanistic insights are primarily inferred from in vitro traits. The simplified greenhouse system further limits ecological interpretation. These findings highlight the potential of halotolerant PGPR in degraded soils while emphasizing the need for genomic validation, mechanistic studies, and field-scale evaluation. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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26 pages, 5194 KB

Open AccessArticle

Comparative Effects of Exogenous Organic Amendments on Rhizosphere Microbial Communities and Soil Properties in Continuous Cropping Watermelon

by Wen Pan, Li Gao, Yanjun Xu, Hongmei Guo, Ainiwar Abdulla, Alim Abdurim, Xiangyu Liu, Xingwang Gao and Haibo Wu

Microorganisms 2026, 14(4), 837; https://doi.org/10.3390/microorganisms14040837 - 8 Apr 2026

Viewed by 632

Abstract

Continuous cropping obstacles in watermelon are closely linked to rhizosphere microbial imbalance, posing a major threat to the sustainability of the industry in Xinjiang. Exogenous additives are widely used to regulate soil health, yet comprehensive comparisons of their mechanisms and effects remain limited. In this study, a field experiment was conducted under continuous watermelon cropping conditions in Xinjiang to evaluate the impact of eight treatments, including chemical fertilizer (NPK) alone and its combination with organic fertilizer (NPKM), glucose (NPKG), oxalic acid (NPKOA), amino acids (NPKGA), citric acid (NPKCA), and acetic acid (NPKAA), with unfertilized soil as the control (CK). Treatment effects were assessed through soil physicochemical analysis, fruit quality evaluation, and high-throughput sequencing (16S rRNA and ITS). Among all treatments, NPKM showed the greatest improvement in soil fertility, increasing soil organic matter by 13.91%, total nitrogen by 23.08%, and single fruit weight by 35.75% compared to CK. NPKGA also enhanced fruit weight (+33.06% vs. CK) and increased catalase activity, while oxalic acid exhibited the strongest activation of alkaline phosphatase. Microbiome analysis revealed that NPKM and NPKAA significantly reshaped both bacterial and fungal community structures. NPKM enriched beneficial taxa such as unclassified Chitinophagaceae and Lophotrichus, whereas NPKCA enriched the biocontrol bacterium Pseudomonas chlororaphis. Soil organic matter and total nitrogen were identified as key environmental drivers, showing significant positive correlations with core bacterial genera (Dokdonella) and negative correlations with the pathogenic fungus Alternaria. Collectively, this study elucidates the distinct mechanisms of various additives by linking treatment-specific microbial shifts to key soil factors and crop performance, providing a theoretical and technical framework for mitigating watermelon continuous cropping obstacles through rhizosphere environmental regulation. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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16 pages, 2396 KB

Open AccessArticle

Contrasting Effects of Grass-Derived Endophytic Fungal VOCs on Early Growth of Spring Barley and Red Clover: From Stimulation to Suppression

by Izolda Pašakinskienė, Saulė Matijošiūtė, Violeta Stakelienė, Marius Rimkevičius and Jurga Būdienė

Microorganisms 2026, 14(3), 533; https://doi.org/10.3390/microorganisms14030533 - 25 Feb 2026

Viewed by 1083

Abstract

Endophytic fungi can influence plant development through diverse molecular mechanisms; however, their volatile organic compound VOC-mediated effects on agriculturally relevant crops remain insufficiently characterized. In this study, we examined the effects of VOCs produced by six grass-root-associated endophytic fungi—Cadophora fastigiata, Cordyceps fumosorosea, Chaetomium funicola, Epicoccum nigrum, Microdochium bolleyi, and Plectosphaerella cucumerina—on early growth of spring barley (Hordeum vulgare) and red clover (Trifolium pratense). In plate-in-plate VOC exposure assays, we assessed root system traits, root hair formation, and biomass accumulation. Responses to fungal VOCs were fungal species-specific but similar across barley and red clover. VOCs emitted by C. fastigiata and P. cucumerina were consistently associated with increased root growth, root hair proliferation, and seedling biomass, whereas VOCs from M. bolleyi and C. funicola resulted in neutral or growth-suppressing effects. A complementary seed inoculation experiment was conducted with barley, which showed fungal species–dependent contrasting effects consistent with the observations of VOCs treatment. Gas chromatography–mass spectrometry (GC–MS) analysis revealed that C. fastigiata, the isolate associated with the strongest growth-promoting responses, emitted a diverse VOC profile dominated by sesquiterpenes, with 22 compounds identified. Together, these results demonstrate that VOCs emitted by grass-root-associated endophytic fungi exert reproducible, species-specific effects on early plant development occurring in phylogenetically distant species. The findings highlight the value of VOC-based assays for comparative functional screening of fungal isolates, providing a foundation for future studies that aim to link individual VOCs to plant growth responses. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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20 pages, 5556 KB

Open AccessArticle

Isolation of Siderophore-Producing Bacteria from Extreme Environments and Their Role in Improving Maize Salinity–Alkalinity Tolerance

by Yuanyuan Huang, Yuansheng Xu, Zhe Chen, Xiaomei Dong, Yuxia Mei, Zhufeng Zhang and Min Ren

Microorganisms 2026, 14(2), 452; https://doi.org/10.3390/microorganisms14020452 - 12 Feb 2026

Viewed by 1201

Abstract

Soil salinization represents a significant abiotic constraint to global agricultural sustainability. The potential of extremophile plant growth-promoting bacteria (PGPB) to alleviate such stress in maize was investigated in this study. Siderophore-producing PGPB enhance plant growth and improve the rhizosphere microenvironment by increasing nutrient availability and inducing systemic resistance. Two salt-tolerant, high-siderophore-producing PGPB strains, Bacillus toyonensis TRM58010 and Peribacillus frigoritolerans TRM58009, were isolated and identified from soil samples collected on the Pamir Plateau. In this study, we found that B. toyonensis TRM58010 synthesized catechol-type siderophores, which enhanced iron availability for maize in saline–alkaline conditions, thereby improving iron nutrition and directly promoting root and stem growth under salt stress. P. frigoritolerans TRM58009 produced hydroxamate-type siderophores, which increased maize iron uptake and stimulated antioxidant enzyme activity, mitigating oxidative stress caused by salinity and alkalinity and supporting overall plant health. Both strains demonstrated robust tolerance to extreme alkaline and saline conditions. Hydroponic and pot experiments showed that these strains significantly improved maize germination rate, root and stem development, plant height, leaf growth, antioxidant enzyme activities, and chlorophyll content under saline–alkaline stress. Notably, the application of P. frigoritolerans TRM58009 bacterial suspension increased maize leaf catalase, peroxidase, and superoxide dismutase activities by 15.712%, 11.584%, and 2.820%, respectively (all p < 0.05), while decreasing malondialdehyde (MDA) content by 15.685% (p < 0.05). P. frigoritolerans TRM58009 elevated chlorophyll a content by 23.4% (p < 0.05). These findings demonstrate the potential of extremophile PGPB strains to mitigate the impact of saline–alkaline stress on maize growth. The distinct growth-promoting effects of these strains, isolated from Pamir Plateau meadow soils, present a promising strategy for bioremediation of saline–alkaline lands and the development of efficient microbial fertilizers. By advancing the use of salt-tolerant siderophore-producing bacteria, this study lays the foundation for innovative approaches to enhance crop resilience and productivity in challenging environments. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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23 pages, 4580 KB

Open AccessArticle

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

Cited by 4 | Viewed by 1475

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 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

Open AccessArticle

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 4 | Viewed by 2281

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 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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33 pages, 5615 KB

Open AccessReview

Microorganism-Based Biological Products for Agriculture: From Strain Selection to Production Organization

by Amankeldi K. Sadanov, Gul Baimakhanova, Baiken B. Baimakhanova, Saltanat Orazymbet, Irina A. Ratnikova, Irina Smirnova, Gulzat S. Aitkaliyeva, Ayaz M. Belkozhayev and Bekzhan D. Kossalbayev

Microorganisms 2026, 14(4), 775; https://doi.org/10.3390/microorganisms14040775 - 29 Mar 2026

Cited by 1 | Viewed by 989

Abstract

Plant growth-promoting microorganisms (PGPMs) and microbial biocontrol agents have emerged as key tools for improving crop productivity while maintaining environmental sustainability. However, central questions remain regarding which factors determine their consistent field performance and how these factors interact under real agronomic conditions. Previous research has demonstrated that PGPMs enhance nutrient acquisition, regulate phytohormone balance, improve stress tolerance, and suppress plant pathogens through diverse biochemical and ecological mechanisms. Advances in omics technologies, genome mining, and synthetic microbial communities have further expanded understanding of their functional potential. Nevertheless, many studies rely on laboratory-scale experiments or short-term trials, with limited multi-season and cross-regional validation. This gap contributes to inconsistent field outcomes and restricts large-scale agricultural adoption. Long-term multi-season validation and reproducibility assessment remain essential priorities for improving reliability of microbial agricultural products. This review synthesizes recent advances in PGPM-based biofertilizers and microbial biocontrol technologies, critically examining their mechanisms of action, scalability constraints, formulation challenges, and regulatory limitations. It identifies major translational barriers, including context dependency, mechanistic uncertainties, reproducibility gaps, and insufficient systems-level integration. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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19 pages, 760 KB

Open AccessReview

Beyond the Single Isolate: Leveraging Plant-Associated Microbial Communities for Crop Resilience

by Ashish Kumar Sarker, Karishma D. Kuar, Esha Kuriakose, C. Oliver Morton, Colin M. Stack and Michelle C. Moffitt

Microorganisms 2026, 14(2), 456; https://doi.org/10.3390/microorganisms14020456 - 13 Feb 2026

Cited by 2 | Viewed by 1119

Abstract

The future of sustainable agriculture will require practical microbial solutions that reduce chemical inputs while maintaining productivity. While existing literature reviews focus on laboratory science, they rarely address the practicalities of farm implementation. Low rates of adoption suggest a translational gap. This review translates current scientific insights for the relevant end user (farmers). Pesticides and fertilisers disrupt naturally occurring microbial communities that maintain plant health and resilience. Applications of beneficial microbes to restore plant health or improve productivity currently employ single-strain inoculants. The targeted application of a consortium of multiple microorganisms, a “synthetic community” (SynCom), including biocontrol agents, biostimulants and biofertilisers, is superior. The “SynCom” approach could be considered the Swiss army knife of sustainable agriculture, with each member of the community performing overlapping functions. While SymComs have shown success in laboratory and greenhouse trials, field reliability has been inconsistent, either due to variability in production or stability issues in the field. The future of sustainable agriculture will require greater collaboration between scientists and farmers at a local level, specifically, the application of microbes from local soils that are adapted to local environmental conditions, investment in monitoring successes and failures, and application via seed coating using currently available infrastructure. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

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29 pages, 2787 KB

Open AccessReview

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

Cited by 7 | Viewed by 1917

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 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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