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Microorganisms
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Research on Plant—Bacteria Interactions
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Research on Plant—Bacteria Interactions

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

Deadline for manuscript submissions: 31 July 2024 | Viewed by 5359

Special Issue Editor

Dr. Jérôme Duclercq

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The interaction between plants and beneficial bacteria is a fascinating topic about how bacteria can help plants grow and develop more efficiently. In general, plants can recruit these bacteria by producing organic compounds, such as amino acids and sugars. The beneficial bacteria can then grow in the rhizosphere, the environment surrounding plant roots, and begin to interact with the roots. Some beneficial bacteria can be recognized by specific receptors located on the surface of plant roots. When beneficial bacteria bind to these receptors, the plant can produce signals that stimulate the bacteria to grow in the rhizosphere. Some plants can form symbioses with beneficial bacteria, meaning they work closely together for mutual benefit. For example, bacteria can fix atmospheric nitrogen for the plant, which can improve the growth of the plant and reduce its need for chemical fertilizers. These interactions can improve plant growth, increase plant resistance to disease and environmental stresses, and even help them better withstand climate change. In short, the interaction between plants and beneficial bacteria is an incredible example of natural collaboration that can have a significant impact on plant growth and health.

This Special Issue focuses on original papers dealing with (i) the identification of new beneficial bacterial partners for plants, (ii) the chemical and molecular communication between the partners during the different stages of the interaction, (iii) the factors that influence this communication, and (iv) the effects of these bacteria on the other interactions that the plant may have with its environment.

Dr. Jérôme Duclercq
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

  • plant growth promoting bacteria
  • symbiosis
  • chemical communication
  • molecular dialog
  • environmental stress
  • soil functioning
  • plant protection

Published Papers (5 papers)

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Research

16 pages, 4228 KiB  
Article
Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of “Candidatus Phyllobacterium onerii” sp. nov. Isolated from Endemic Astragalus flavescens
by Asiye Esra Eren Eroğlu, Volkan Eroğlu and İhsan Yaşa
Microorganisms 2024, 12(2), 336; https://doi.org/10.3390/microorganisms12020336 - 06 Feb 2024
Viewed by 881
Abstract
A novel strain of Gram-negative, rod-shaped aerobic bacteria, identified as IY22, was isolated from the root nodules of Astragalus flavescens. The analysis of the 16S rDNA and recA (recombinase A) gene sequences indicated that the strain belongs to the genus Phyllobacterium. [...] Read more.
A novel strain of Gram-negative, rod-shaped aerobic bacteria, identified as IY22, was isolated from the root nodules of Astragalus flavescens. The analysis of the 16S rDNA and recA (recombinase A) gene sequences indicated that the strain belongs to the genus Phyllobacterium. During the phylogenetic analysis, it was found that strain IY22 is closely related to P. trifolii strain PETP02T and P. bourgognense strain STM 201T. The genome of IY22 was determined to be 6,010,116 base pairs long with a DNA G+C ratio of 56.37 mol%. The average nucleotide identity (ANI) values showed a range from 91.7% to 93.6% when compared to its close relatives. Moreover, IY22 and related strains had digital DNA-DNA hybridization (dDDH) values ranging from 16.9% to 54.70%. Multiple genes (including nodACDSNZ, nifH/frxC, nifUS, fixABCJ, and sufABCDES) associated with symbiotic nitrogen fixation have been detected in strain IY22. Furthermore, this strain features genes that contribute to improving plant growth in various demanding environments. This study reports the first evidence of an association between A. flavescens and a rhizobial species. Native high-altitude legumes are a potential source of new rhizobia, and we believe that they act as a form of insurance for biodiversity against the threats of desertification and drought. Full article
(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)
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11 pages, 4660 KiB  
Communication
Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths
by Adesuwa Sylvia Erhunmwunse, Victor Alonso Guerra, Jung-Chen Liu, Cheryl L. Mackowiak, Ann Rachel Soffes Blount, José Carlos Batista Dubeux, Jr. and Hui-Ling Liao
Microorganisms 2023, 11(12), 3002; https://doi.org/10.3390/microorganisms11123002 - 18 Dec 2023
Viewed by 698
Abstract
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant–soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing [...] Read more.
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant–soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3–V4 regions. We observed that a well-established RP–bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures. Full article
(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)
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23 pages, 3025 KiB  
Article
Metagenomic Approach Deciphers the Role of Community Composition of Mycobiome Structured by Bacillus velezensis VB7 and Trichoderma koningiopsis TK in Tomato Rhizosphere to Suppress Root-Knot Nematode Infecting Tomato
by Vinothini Kamalanathan, Nakkeeran Sevugapperumal, Saranya Nallusamy, Suhail Ashraf, Kumanan Kailasam and Mohd Afzal
Microorganisms 2023, 11(10), 2467; https://doi.org/10.3390/microorganisms11102467 - 30 Sep 2023
Viewed by 1065
Abstract
The soil microbiome is crucial for maintaining the sustainability of the agricultural environment. Concerning the role of diverse mycobiomes and their abundance toward the suppression of root-knot nematode (RKN) infection in vegetable crops, our understanding is unclear. To unveil this issue, we examined [...] Read more.
The soil microbiome is crucial for maintaining the sustainability of the agricultural environment. Concerning the role of diverse mycobiomes and their abundance toward the suppression of root-knot nematode (RKN) infection in vegetable crops, our understanding is unclear. To unveil this issue, we examined the fungal microbiome in tomato rhizosphere augmented with bioagents challenged against RKN at taxonomic and functional levels. Composition of the mycobiome in tomato rhizosphere treated with Bacillus velezensis VB7 and Trichoderma koningiopsis TK differed significantly from the infected tomato rhizosphere. The abundance and diversity of fungal species, however, were significantly higher in the combined treatments of bioagents than for individual treatments. Fungal microbiome diversity was negatively correlated in the RKN-associated soil. Network analysis of the fungal biome indicated a larger and complex network of fungal biome diversity in bioagent-treated soil than in nematode-associated tomato rhizosphere. The diversity index represented by that challenging the RKN by drenching with consortia of B. velezensis VB7 and T. koningiopsis TK, or applying them individually, constituted the maximum abundance and richness of the mycobiome compared to the untreated control. Thus, the increased diverse nature and relative abundance of the mycobiome in tomato rhizosphere was mediated through the application of either T. koningiopsis TK or B. velezensis VB7, individually or as a consortium comprising both fungal and bacterial antagonists, which facilitated engineering the community composition of fungal bioagents. This in turn inhibited the infestation of RKN in tomato. It would be interesting to explore further the possibility of combined applications of B. velezensis VB7 and T. koningiopsis TK to manage root-knot nematodes as an integrated approach for managing plant parasitic nematodes at the field level. Full article
(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)
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16 pages, 8371 KiB  
Article
Optimizing Crop Production with Bacterial Inputs: Insights into Chemical Dialogue between Sphingomonas sediminicola and Pisum sativum
by Candice Mazoyon, Stéphane Firmin, Lamine Bensaddek, Audrey Pecourt, Amélie Chabot, Michel-Pierre Faucon, Vivien Sarazin, Fréderic Dubois and Jérôme Duclercq
Microorganisms 2023, 11(7), 1847; https://doi.org/10.3390/microorganisms11071847 - 21 Jul 2023
Cited by 4 | Viewed by 984
Abstract
The use of biological inputs is an interesting approach to optimize crop production and reduce the use of chemical inputs. Understanding the chemical communication between bacteria and plants is critical to optimizing this approach. Recently, we have shown that Sphingomonas (S.) [...] Read more.
The use of biological inputs is an interesting approach to optimize crop production and reduce the use of chemical inputs. Understanding the chemical communication between bacteria and plants is critical to optimizing this approach. Recently, we have shown that Sphingomonas (S.) sediminicola can improve both nitrogen supply and yield in pea. Here, we used biochemical methods and untargeted metabolomics to investigate the chemical dialog between S. sediminicola and pea. We also evaluated the metabolic capacities of S. sediminicola by metabolic profiling. Our results showed that peas release a wide range of hexoses, organic acids, and amino acids during their development, which can generally recruit and select fast-growing organisms. In the presence of S. sediminicola, a more specific pattern of these molecules took place, gradually adapting to the metabolic capabilities of the bacterium, especially for pentoses and flavonoids. In turn, S. sediminicola is able to produce several compounds involved in cell differentiation, biofilm formation, and quorum sensing to shape its environment, as well as several molecules that stimulate pea growth and plant defense mechanisms. Full article
(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)
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17 pages, 2004 KiB  
Article
Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR
by Jordan Valente, Florence Gerin, Agathe Mini, Rohan Richard, Jacques Le Gouis, Claire Prigent-Combaret and Yvan Moënne-Loccoz
Microorganisms 2023, 11(6), 1615; https://doi.org/10.3390/microorganisms11061615 - 19 Jun 2023
Cited by 1 | Viewed by 1370
Abstract
Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the [...] Read more.
Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains. Full article
(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)
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