Beneficial Microorganisms for Plants

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 6861

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Guest Editor
Unité Écologie et Dynamique des Systèmes Anthropisés (EDYSAN UMR CNRS 7058 CNRS), Université de Picardie Jules Verne, UFR des Sciences, 80029 Amiens, France
Interests: Plant-Growth-Promoting Rhizobacteria (PGPR); soil microbial communities; sphingomonas; plant–bacteria interaction
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Special Issue Information

Dear Colleagues,

Microorganisms have been successfully used in agriculture as a strategy to sustainably improve plant growth and health. However, these approaches are still limited to a small number of organisms and their effectiveness is often limited when transferred from the laboratory to the field. Conversely, the impact of these microbial inputs on microbial communities is generally neglected, while the introduction of high densities of microorganisms can affect the complex and dynamic balance of soil microbial communities.

This Special Issue is devoted to original papers dealing with (i) the use of microorganisms (alone, in combination, or at the community level) to improve plant growth and health; (ii) the factors that influence or improve the efficiency of these beneficial microorganisms; and (iii) the effects of these microorganisms on native microbial communities, especially in a laboratory-to-field transfer approach.

Dr. Jérôme Duclercq
Guest Editor

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Keywords

  • plant-growth-promoting rhizobacteria (PGPR)
  • mycorrhizal fungi
  • beneficial microorganisms
  • soil microbial communities

Published Papers (5 papers)

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Research

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17 pages, 3970 KiB  
Article
Microbacterium azadirachtae CNUC13 Enhances Salt Tolerance in Maize by Modulating Osmotic and Oxidative Stress
by Huan Luo, Chaw Su Win, Dong Hoon Lee, Lin He and Jun Myoung Yu
Biology 2024, 13(4), 244; https://doi.org/10.3390/biology13040244 - 07 Apr 2024
Viewed by 349
Abstract
Soil salinization is one of the leading threats to global ecosystems, food security, and crop production. Plant growth-promoting rhizobacteria (PGPRs) are potential bioinoculants that offer an alternative eco-friendly agricultural approach to enhance crop productivity from salt-deteriorating lands. The current work presents bacterial strain [...] Read more.
Soil salinization is one of the leading threats to global ecosystems, food security, and crop production. Plant growth-promoting rhizobacteria (PGPRs) are potential bioinoculants that offer an alternative eco-friendly agricultural approach to enhance crop productivity from salt-deteriorating lands. The current work presents bacterial strain CNUC13 from maize rhizosphere soil that exerted several PGPR traits and abiotic stress tolerance. The strain tolerated up to 1000 mM NaCl and 30% polyethylene glycol (PEG) 6000 and showed plant growth-promoting (PGP) traits, including the production of indole-3-acetic acid (IAA) and siderophore as well as phosphate solubilization. Phylogenetic analysis revealed that strain CNUC13 was Microbacterium azadirachtae. Maize plants exposed to high salinity exhibited osmotic and oxidative stresses, inhibition of seed germination, plant growth, and reduction in photosynthetic pigments. However, maize seedlings inoculated with strain CNUC13 resulted in significantly improved germination rates and seedling growth under the salt-stressed condition. Specifically, compared with the untreated control group, CNUC13-treated seedlings exhibited increased biomass, including fresh weight and root system proliferation. CNUC13 treatment also enhanced photosynthetic pigments (chlorophyll and carotenoids), reduced the accumulation of osmotic (proline) and oxidative (hydrogen peroxide and malondialdehyde) stress indicators, and positively influenced the activities of antioxidant enzymes (catalase, superoxide dismutase, and peroxidase). As a result, CNUC13 treatment alleviated oxidative stress and promoted salt tolerance in maize. Overall, this study demonstrates that M. azadirachtae CNUC13 significantly enhances the growth of salt-stressed maize seedlings by improving photosynthetic efficiency, osmotic regulators, oxidative stress resilience, and antioxidant enzyme activity. These findings emphasize the potential of utilizing M. azadirachtae CNUC13 as a bioinoculant to enhance salt stress tolerance in maize, providing an environmentally friendly approach to mitigate the negative effects of salinity and promote sustainable agriculture. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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18 pages, 2330 KiB  
Article
PGPR-Soil Microbial Communities’ Interactions and Their Influence on Wheat Growth Promotion and Resistance Induction against Mycosphaerella graminicola
by Erika Samain, Jérôme Duclercq, Essaïd Ait Barka, Michael Eickermann, Cédric Ernenwein, Candice Mazoyon, Vivien Sarazin, Frédéric Dubois, Thierry Aussenac and Sameh Selim
Biology 2023, 12(11), 1416; https://doi.org/10.3390/biology12111416 - 10 Nov 2023
Cited by 1 | Viewed by 1053
Abstract
The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR Paenibacillus sp. strain [...] Read more.
The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR Paenibacillus sp. strain B2 (PB2), PB2 in co-inoculation with Arthrobacter agilis 4042 (Mix 2), or with Arthrobacter sp. SSM-004 and Microbacterium sp. SSM-001 (Mix 3). Inoculation of PB2, Mix 2, and Mix 3 into non-sterile field soil had a positive effect on root and aboveground dry biomass, depending on the wheat cultivar. The efficiency of the PGPR was further confirmed by the protection they provided against Mycosphaerella graminicola, the causal agent of Septoria leaf blotch disease. PB2 exhibited protection of ≥37.8%, while Mix 2 showed ≥47.9% protection in the four cultivars tested. These results suggest that the interactions between PGPR and native soil microbial communities are crucial for promoting wheat growth and protection. Additionally, high-throughput sequencing of microbial communities conducted 7 days after PGPR inoculations revealed no negative effects of PB2, Mix 2, and Mix 3 on the soil microbial community structure. Interestingly, the presence of Arthrobacter spp. appeared to mitigate the potential negative effect of PB2 on bacterial community and foster root colonization by other beneficial bacterial strains. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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15 pages, 2075 KiB  
Article
What If Root Nodules Are a Guesthouse for a Microbiome? The Case Study of Acacia longifolia
by Joana G. Jesus, Cristina Máguas, Ricardo Dias, Mónica Nunes, Pedro Pascoal, Marcelo Pereira and Helena Trindade
Biology 2023, 12(9), 1168; https://doi.org/10.3390/biology12091168 - 24 Aug 2023
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Abstract
Acacia longifolia is one of the most aggressive invaders worldwide whose invasion is potentiated after a fire, a common perturbation in Mediterranean climates. As a legume, this species establishes symbioses with nitrogen-fixing bacteria inside root nodules; however, the overall microbial diversity is still [...] Read more.
Acacia longifolia is one of the most aggressive invaders worldwide whose invasion is potentiated after a fire, a common perturbation in Mediterranean climates. As a legume, this species establishes symbioses with nitrogen-fixing bacteria inside root nodules; however, the overall microbial diversity is still unclear. In this study, we addressed root nodules’ structure and biodiversity through histology and Next-Generation Sequencing, targeting 16S and 25S-28S rDNA genes for bacteria and fungi, respectively. We wanted to evaluate the effect of fire in root nodules from 1-year-old saplings, by comparing unburnt and burnt sites. We found that although having the same general structure, after a fire event, nodules had a higher number of infected cells and greater starch accumulation. Starch accumulated in uninfected cells can be a possible carbon source for the microbiota. Regarding diversity, Bradyrhizobium was dominant in both sites (ca. 77%), suggesting it is the preferential partner, followed by Tardiphaga (ca. 9%), a non-rhizobial Alphaproteobacteria, and Synechococcus, a cyanobacteria (ca. 5%). However, at the burnt site, additional N-fixing bacteria were included in the top 10 genera, highlighting the importance of this process. Major differences were found in the mycobiome, which was diverse in both sites and included genera mostly described as plant endophytes. Coniochaeta was dominant in nodules from the burnt site (69%), suggesting its role as a facilitator of symbiotic associations. We highlight the presence of a large bacterial and fungal community in nodules, suggesting nodulation is not restricted to nitrogen fixation. Thus, this microbiome can be involved in facilitating A. longifolia invasive success. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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26 pages, 7375 KiB  
Article
Transcriptome Analysis Reveals That C17 Mycosubtilin Antagonizes Verticillium dahliae by Interfering with Multiple Functional Pathways of Fungi
by Qi Zhang, Rongrong Lin, Jun Yang, Jingjing Zhao, Haoran Li, Kai Liu, Xiuhua Xue, Huixin Zhao, Shengcheng Han and Heping Zhao
Biology 2023, 12(4), 513; https://doi.org/10.3390/biology12040513 - 29 Mar 2023
Cited by 2 | Viewed by 1552
Abstract
Verticillium wilt is a kind of soil-borne plant fungal disease caused by Verticillium dahliae (Vd). Vd 991 is a strong pathogen causing cotton Verticillium wilt. Previously, we isolated a compound from the secondary metabolites of Bacillus subtilis J15 (BS J15), which showed a [...] Read more.
Verticillium wilt is a kind of soil-borne plant fungal disease caused by Verticillium dahliae (Vd). Vd 991 is a strong pathogen causing cotton Verticillium wilt. Previously, we isolated a compound from the secondary metabolites of Bacillus subtilis J15 (BS J15), which showed a significant control effect on cotton Verticillium wilt and was identified as C17 mycosubtilin. However, the specific fungistatic mechanism by which C17 mycosubtilin antagonizes Vd 991 is not clear. Here, we first showed that C17 mycosubtilin inhibits the growth of Vd 991 and affects germination of spores at the minimum inhibitory concentration (MIC). Morphological observation showed that C17 mycosubtilin treatment caused shrinking, sinking, and even damage to spores; the hyphae became twisted and rough, the surface was sunken, and the contents were unevenly distributed, resulting in thinning and damage to the cell membrane and cell wall and swelling of mitochondria of fungi. Flow cytometry analysis with ANNEXINV-FITC/PI staining showed that C17 mycosubtilin induces necrosis of Vd 991 cells in a time-dependent manner. Differential transcription analysis showed that C17 mycosubtilin at a semi-inhibitory concentration (IC50) treated Vd 991 for 2 and 6 h and inhibited fungal growth mainly by destroying synthesis of the fungal cell membrane and cell wall, inhibiting its DNA replication and transcriptional translation process, blocking its cell cycle, destroying fungal energy and substance metabolism, and disrupting the redox process of fungi. These results directly showed the mechanism by which C17 mycosubtilin antagonizes Vd 991, providing clues for the mechanism of action of lipopeptides and useful information for development of more effective antimicrobials. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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Review

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25 pages, 2417 KiB  
Review
Coffee-Associated Endophytes: Plant Growth Promotion and Crop Protection
by Suhail Asad, Alviti Kankanamalage Hasith Priyashantha, Saowaluck Tibpromma, Yinling Luo, Jianqiang Zhang, Zhuqing Fan, Likun Zhao, Ke Shen, Chen Niu, Li Lu, Itthayakorn Promputtha and Samantha C. Karunarathna
Biology 2023, 12(7), 911; https://doi.org/10.3390/biology12070911 - 25 Jun 2023
Cited by 2 | Viewed by 1900
Abstract
Endophytic microbes are a ubiquitous group of plant-associated communities that colonize the intercellular or intracellular host tissues while providing numerous beneficial effects to the plants. All the plant species are thought to be associated with endophytes, majorly constituted with bacteria and fungi. During [...] Read more.
Endophytic microbes are a ubiquitous group of plant-associated communities that colonize the intercellular or intracellular host tissues while providing numerous beneficial effects to the plants. All the plant species are thought to be associated with endophytes, majorly constituted with bacteria and fungi. During the last two decades, there has been a considerable movement toward the study of endophytes associated with coffee plants. In this review, the main consideration is given to address the coffee-associated endophytic bacteria and fungi, particularly their action on plant growth promotion and the biocontrol of pests. In addition, we sought to identify and analyze the gaps in the available research. Additionally, the potential of endophytes to improve the quality of coffee seeds is briefly discussed. Even though there are limited studies on the subject, the potentiality of coffee endophytes in plant growth promotion through enhancing nitrogen fixation, availability of minerals, nutrient absorption, secretion of phytohormones, and other bioactive metabolites has been well recognized. Further, the antagonistic effect against various coffee pathogenic bacteria, fungi, nematodes, and also insect pests leads to the protection of the crop. Furthermore, it is recognized that endophytes enhance the sensory characteristics of coffee as a new field of study. Full article
(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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