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Microorganisms
Special Issues
Exploring the Impact of Beneficial Plant-Associated Microbes on Host Plants
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Exploring the Impact of Beneficial Plant-Associated Microbes on Host Plants

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

Deadline for manuscript submissions: closed (30 March 2025) | Viewed by 5999

Special Issue Editor

Dr. Gary Harman

E-Mail Website
Guest Editor
School of Integrative Plant Science Horticulture Section, Cornell University—Horticultural Sciences, 630 W. North St. Geneva, Geneva, NY 14456, USA
Interests: plant–microbe interactions; biocontrol; biochemistry

Special Issue Information

Dear Colleagues,

The upcoming Special Issue aims to delve into the diverse influence of beneficial plant-associated microbes on host plants, elucidating their pivotal roles in enhancing plant health, growth, and stress resilience. This issue seeks to highlight the multifaceted effects these symbiotic organisms exert on their hosts, including enhanced nutrient uptake, improved pathogen resistance, and mitigation of abiotic stressors such as drought and salinity.

Furthermore, research has revealed that these interactions extend to the modulation of plant hormone levels, positively influencing developmental processes and overall fitness. Additionally, these associations impact the host's immune system, contributing to improved defense mechanisms, while some microbes produce bioactive compounds with potential pharmaceutical and agricultural applications.

We invite contributions that delve into the intricate mechanisms by which beneficial plant-associated microbes affect host plants, whether related to the ecological dynamics underlying these interactions, the molecular basis of symbiosis, or the practical implications for sustainable agriculture. By fostering collaborative insights and advancements in this area, we aim to pave the way for innovative strategies harnessing the beneficial effects of plant-associated microbes, ultimately leading to enhanced plant health and agricultural sustainability.

Dr. Gary Harman
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • mechanisms of nutrient exchange and metabolic interactions
  • modulation of plant defense responses
  • abiotic stress tolerance enhancement
  • bioactive compounds production and applications
  • ecological dynamics of beneficial plant-associated microbial communities
  • microbes enhancing photosynthesis in association with plants
  • nitrogen fixation by beneficial plant-associated microbes (emphasis on monocots)

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

Published Papers (4 papers)

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Research

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17 pages, 2852 KiB  
Article
Development of an Engineered Bacterial Endophyte: Promoting Plant Growth Through Pyrroloquinoline Quinone (PQQ) Synthesis
by Ti Fang, Shou-Chen Lo, Yu-Ning Yu, Nga-Lai Sou, Shih-Hsun Walter Hung, Jian-Hau Peng, En-Pei Isabel Chiang and Chieh-Chen Huang
Microorganisms 2025, 13(2), 293; https://doi.org/10.3390/microorganisms13020293 - 28 Jan 2025
Viewed by 902
Abstract
Endophytic bacteria are a group of microorganisms that can intercellularly colonize plant hosts without causing apparent damage or disease. Our previous works found that a pyrroloquinoline quinone (PQQ)-producing endophyte could promote plant growth and systemic tolerance. To demonstrate this PQQ-producing endophyte’s beneficial role [...] Read more.
Endophytic bacteria are a group of microorganisms that can intercellularly colonize plant hosts without causing apparent damage or disease. Our previous works found that a pyrroloquinoline quinone (PQQ)-producing endophyte could promote plant growth and systemic tolerance. To demonstrate this PQQ-producing endophyte’s beneficial role in plants, a set of five PQQ synthesis genes from Gluconobacter oxydans was introduced into both Escherichia coli JM109 and Bacillus subtilis RM125, a BsuM-deficient mutant of laboratory strain B. subtilis 168. Interestingly, both strains harboring the PQQ synthesis genes exhibited significantly higher optimal optical density than control strains. In a carbon flux analysis, both strains showed a noticeable increase in their citric acid, alpha-ketoglutaric acid, and succinic acid levels. Conversely, in E. coli, pyruvic acid, malic acid, and fumaric acid levels decreased. These results suggest that PQQ impacts various host species differently. Furthermore, the presence of PQQ in fermentation broth was also confirmed in the RM125 PQQ synthesis recombinant strain. Subsequent experiments by inoculating those Bacillus strains revealed that the laboratory host strain could function as an endophyte, and the PQQ transgenic strain could further promote the growth of Arabidopsis thaliana and increase the number of siliques. These findings confirm PQQ’s vital role in endophyte-mediated plant growth promotion and also suggest the potential of B. subtilis transformed with PQQ genes as an engineered endophyte for studying PQQ’s biological functions in plants. This research is a step forward in understanding how specific substances can beneficially influence plant growth and systemic tolerance through endophytic mechanisms. Full article
(This article belongs to the Special Issue Exploring the Impact of Beneficial Plant-Associated Microbes on Host Plants)
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20 pages, 3029 KiB  
Article
Orchid Mycorrhizal Association of Cultivated Dendrobium Hybrid and Their Role in Seed Germination and Seedling Growth
by R. M. S. Ruwan Chamara, Kazumitsu Miyoshi, Tomohisa Yukawa, Nobuyuki Asai and Yuki Ogura-Tsujita
Microorganisms 2024, 12(6), 1176; https://doi.org/10.3390/microorganisms12061176 - 10 Jun 2024
Viewed by 1518
Abstract
Orchids are crucial for the horticulture industry. Mycorrhizal fungi benefit crops by improving nutrition, plant growth, and disease resistance. However, the mycorrhizal association of horticultural hybrid orchids is poorly understood. To address this, we investigated mycorrhizal colonization in the entire root system and [...] Read more.
Orchids are crucial for the horticulture industry. Mycorrhizal fungi benefit crops by improving nutrition, plant growth, and disease resistance. However, the mycorrhizal association of horticultural hybrid orchids is poorly understood. To address this, we investigated mycorrhizal colonization in the entire root system and assessed the mycorrhizal community using a Dendrobium cultivar, D. Stardust ‘Firebird’, obtained from three nurseries. Additionally, we isolated and tested mycorrhizal fungi in symbiotic culture to assess their role in the seed germination and growth of Dendrobium species. All plants were colonized by mycorrhizal fungi, with a higher colonization rate in mature than in juvenile plants. Molecular identification of mycorrhizal fungi by Sanger and high-throughput sequencing revealed that the cultivar was associated with a phylogenetically diverse group of fungi, including mycorrhizal fungi from Tulasnellaceae, and several wood-decaying fungi. The Tulasnellaceae isolates significantly enhanced the seed germination of three Dendrobium species and increased the survival rate and growth of asymbiotic seedlings of D. moniliforme. This study is the first comprehensive examination of mycorrhizal associations in horticultural orchid hybrids, providing valuable insights for commercial production. Full article
(This article belongs to the Special Issue Exploring the Impact of Beneficial Plant-Associated Microbes on Host Plants)
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Review

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15 pages, 1751 KiB  
Review
Maximizing Photosynthesis and Plant Growth in African Legumes Through Rhizobial Partnerships: The Road Behind and Ahead
by Sanjay K. Jaiswal and Felix D. Dakora
Microorganisms 2025, 13(3), 581; https://doi.org/10.3390/microorganisms13030581 - 4 Mar 2025
Cited by 1 | Viewed by 684
Abstract
The interplay between soil rhizobial bacteria and leguminous plants, particularly in Africa, has a profound impact on photosynthetic efficiency and overall crop productivity. This review explores the critical role of rhizobia in enhancing photosynthesis through nitrogen fixation, a process crucial for sustainable agriculture. [...] Read more.
The interplay between soil rhizobial bacteria and leguminous plants, particularly in Africa, has a profound impact on photosynthetic efficiency and overall crop productivity. This review explores the critical role of rhizobia in enhancing photosynthesis through nitrogen fixation, a process crucial for sustainable agriculture. Rhizobial bacteria residing in root nodules provide legumes with symbiotic nitrogen that significantly boosts plant growth and photosynthetic capacity. Recent advances in molecular genomics have elucidated the genetic frameworks underlying this symbiosis, identifying key genes involved in root nodule formation and nitrogen fixation. Comparative genomics of Bradyrhizobium species have revealed seven distinct lineages, with diverse traits linked to nodulation, nitrogen fixation, and photosynthesis. Field studies across Africa demonstrate that rhizobial inoculation can markedly increase nodulation, nitrogen fixation, and grain yields, though outcomes vary depending on local soil conditions and legume species. Notable findings include enhanced nutrient uptake and photosynthetic rates in inoculated legumes compared with nitrate-fed plants. This review highlights the potential of utilizing indigenous rhizobia to improve photosynthesis and crop resilience. Future prospects involve leveraging genomic insights to optimize rhizobial inoculants and enhance legume productivity in water-limited environments. As climate change intensifies, integrating these advancements into agricultural practices could play a crucial role in improving food security and sustainable soil health in Africa. Full article
(This article belongs to the Special Issue Exploring the Impact of Beneficial Plant-Associated Microbes on Host Plants)
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13 pages, 281 KiB  
Review
Integrated Benefits to Agriculture with Trichoderma and Other Endophytic or Root-Associated Microbes
by Gary E. Harman
Microorganisms 2024, 12(7), 1409; https://doi.org/10.3390/microorganisms12071409 - 12 Jul 2024
Cited by 1 | Viewed by 2163
Abstract
The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte–plant relationship and the fungi and bacteria [...] Read more.
The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte–plant relationship and the fungi and bacteria involved. Their abilities to alleviate biotic (diseases and pests) and abiotic stresses (drought, salt, and flooding) to remediate pollution and increase photosynthetic capabilities will be described. Their mechanisms of action will be elucidated. These frequently result in increased plant yields. Finally, methods and practices for formulation and commercial use will be described. Full article
(This article belongs to the Special Issue Exploring the Impact of Beneficial Plant-Associated Microbes on Host Plants)
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