Submit to Microorganisms Review for Microorganisms Propose a Special Issue

Journal Menu

Journal Browser

Research on Plant—Bacteria Interactions

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

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

Deadline for manuscript submissions: closed (31 July 2024) | Viewed by 14841

Share This Special Issue

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

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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

Published Papers (8 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

22 pages, 10266 KiB

Open AccessArticle

Decoding the Impact of a Bacterial Strain of Micrococcus luteus on Arabidopsis Growth and Stress Tolerance

by Yu-Cheng Chang, Pin-Hsueh Lee, Chao-Liang Hsu, Wen-Der Wang, Yueh-Long Chang and Huey-wen Chuang

Microorganisms 2024, 12(11), 2283; https://doi.org/10.3390/microorganisms12112283 - 10 Nov 2024

Viewed by 1839

Abstract

Microbes produce various bioactive metabolites that can influence plant growth and stress tolerance. In this study, a plant growth-promoting rhizobacterium (PGPR), strain S14, was identified as Micrococcus luteus (designated as MlS14) using de novo whole-genome assembly. The MlS14 genome revealed major gene clusters for the synthesis of indole-3-acetic acid (IAA), terpenoids, and carotenoids. MlS14 produced significant amounts of IAA, and its volatile organic compounds (VOCs), specifically terpenoids, exhibited antifungal activity, suppressing the growth of pathogenic fungi. The presence of yellow pigment in the bacterial colony indicated carotenoid production. Treatment with MlS14 activated the expression of β-glucuronidase (GUS) driven by a promoter containing auxin-responsive elements. The application of MlS14 reshaped the root architecture of Arabidopsis seedlings, causing shorter primary roots, increased lateral root growth, and longer, denser root hairs; these characteristics are typically controlled by elevated exogenous IAA levels. MlS14 positively regulated seedling growth by enhancing photosynthesis, activating antioxidant enzymes, and promoting the production of secondary metabolites with reactive oxygen species (ROS) scavenging activity. Pretreatment with MlS14 reduced H₂O₂ and malondialdehyde (MDA) levels in seedlings under drought and heat stress, resulting in greater fresh weight during the post-stress period. Additionally, exposure to MlS14 stabilized chlorophyll content and growth rate in seedlings under salt stress. MlS14 transcriptionally upregulated genes involved in antioxidant defense and photosynthesis. Furthermore, genes linked to various hormone signaling pathways, such as abscisic acid (ABA), auxin, jasmonic acid (JA), and salicylic acid (SA), displayed increased expression levels, with those involved in ABA synthesis, using carotenoids as precursors, being the most highly induced. Furthermore, MlS14 treatment increased the expression of several transcription factors associated with stress responses, with DREB2A showing the highest level of induction. In conclusion, MlS14 played significant roles in promoting plant growth and stress tolerance. Metabolites such as IAA and carotenoids may function as positive regulators of plant metabolism and hormone signaling pathways essential for growth and adaptation to abiotic stress. Full article

(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)

► Show Figures

Figure 1

13 pages, 2245 KiB

Open AccessArticle

Isolation and Characterization of Plant-Growth-Promoting Bacteria Associated with Salvinia auriculata Aublet

by Jussara Tamires de Souza Silva Goulart, Gabriel Quintanilha-Peixoto, Bruno dos Santos Esteves, Suzane Ariadina de Souza, Pollyanna Santiago Lopes, Nathália Duarte da Silva, Julia Ribeiro Soares, Laura Mathias Barroso, Marina Satika Suzuki and Aline Chaves Intorne

Microorganisms 2024, 12(9), 1842; https://doi.org/10.3390/microorganisms12091842 - 6 Sep 2024

Cited by 1 | Viewed by 1412

Abstract

Salvinia auriculata Aublet is a floating aquatic plant, capable of absorbing the excess of nutrients and water contaminants and can be used in effluent treatment plants. The ability to survive in degraded areas may be related to the association with beneficial bacteria capable of promoting plant growth. However, little is known about the microbiota associated with this aquatic plant and its potential application to the aquatic environment. In this sense, this work aims to identify bacteria associated with S. auriculata that could be able to promote plant growth. Eighteen bacterial strains were identified by sequencing of the 16S rRNA gene, belonging to the genera Agrobacterium, Bacillus, Curtobacterium, Enterobacter, Pseudomonas, Siccibacter, and Stenotrophomonas. All isolates produced indole compounds, 12 fixed N₂, and 16 solubilized phosphate. A new strain of Enterobacter (sp 3.1.3.0.X.18) was selected for inoculation into S. auriculata. For this purpose, 500 mL of nutrient solution and 1 g of the plant were used in the control and inoculated conditions. Enterobacter inoculation promoted a significant increase (p ≤ 0.05) in fresh plant biomass (17%) after 4 days of cultivation. In summary, the present study characterized 18 plant-growth-promoting bacteria isolated from S. auriculata with potential for biotechnological application, such as the production of bioinoculants or biomass resources, to protect or improve plant growth under conditions of stress. Full article

(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)

► Show Figures

Figure 1

22 pages, 9313 KiB

Open AccessArticle

IAA Synthesis Pathway of Fitibacillus barbaricus WL35 and Its Regulatory Gene Expression Levels in Potato (Solanum tuberosum L.)

by Xiaoyu Li, Huan Tao, Shisong Wang, Di Zhang, Xingyao Xiong and Yanfei Cai

Microorganisms 2024, 12(8), 1530; https://doi.org/10.3390/microorganisms12081530 - 26 Jul 2024

Viewed by 1085

Abstract

Indole-3-acetic acid (IAA), as an important regulator of potato growth, seriously affects the growth and yield of potato. Although many studies have reported that IAA-producing Bacillus can promote plant growth, little research has been conducted on its synthesis pathway and molecular mechanisms. In this study, an IAA-producing strain WL35 was identified as Fitibacillus barbaricus, and its yield was 48.79 mg·L⁻¹. The results of the pot experiments showed that WL35 significantly increased plant height, stem thickness, chlorophyll content, and number of leaves of potato plants by 31.68%, 30.03%, 32.93%, and 36.59%, respectively. In addition, in the field experiments, WL35-treated plants increased commercial potato yield by 16.45%, vitamin C content by 16.35%, protein content by 75%, starch content by 6.60%, and the nitrogen, phosphorus, and potassium accumulation by 9.98%, 12.70%, and 26.76%, respectively. Meanwhile, the synthetic pathway of WL35 was found to be dominated by the tryptophan-dependent pathway, the IAM, TAM, and IPA pathways worked together, and the pathways that played a role at different times were different. Furthermore, RNA-seq analysis showed that there were a total of 2875 DEGs regulated in the samples treated with WL35 seed dressing compared with the CK, of which 1458 genes were up-regulated and 1417 genes were down-regulated. Potato roots express differential genes enriched in processes such as carbohydrate metabolism processes and cellular polysaccharide metabolism, which regulate potato plant growth and development. The above results provide a theoretical basis for the further exploration of the synthesis pathway of IAA and its growth-promoting mechanism in potato. Full article

(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)

► Show Figures

Figure 1

16 pages, 4228 KiB

Open AccessArticle

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 - 6 Feb 2024

Cited by 5 | Viewed by 2295

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. During the phylogenetic analysis, it was found that strain IY22 is closely related to P. trifolii strain PETP02^T and P. bourgognense strain STM 201^T. 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)

► Show Figures

Figure 1

11 pages, 4660 KiB

Open AccessCommunication

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

Cited by 1 | Viewed by 1532

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 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)

► Show Figures

Figure 1

23 pages, 3025 KiB

Open AccessArticle

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

Cited by 3 | Viewed by 2005

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 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)

► Show Figures

Figure 1

16 pages, 8371 KiB

Open AccessArticle

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 6 | Viewed by 1805

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.) 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)

► Show Figures

Figure 1

17 pages, 2004 KiB

Open AccessArticle

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 2 | Viewed by 2285

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 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)

► Show Figures

Journal Menu

Journal Browser

Research on Plant—Bacteria Interactions

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (8 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI