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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: 15 January 2025 | Viewed by 9050

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Dr. Taegun Seo

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Department of Life Science, Dongguk University, Goyang 10326, Republic of Korea
Interests: symbiosis; plant growth promoting rhizobacteria (PGPR); rhizosphere; endophytes; plant-microbe interactions
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issues, “Rhizosphere Microbial Community”, “Rhizosphere Microbial Community 2.0”.

The bacterial community found in the rhizosphere, known for its colonization around the roots due to the availability of nutrients, plays an important role in plant growth and adaptability both directly and indirectly. Various bacteria promote plant root growth to establish their ecological niche in the rhizosphere. Rhizobacteria are involved in plant-growth promotion and are often utilized to improve crop health and productivity. The rhizosphere microbe community has been the focus of extensive research during recent decades, due to its impact on plant sustainability.

More than 99% of soil bacterial species are assumed to be uncultured bacteria. The development of a next-generation sequencing (NGS) technique has allowed us to explore bacterial diversity, providing additional information about culturable and non-culturable plant-associated bacteria. In recent years, many studies have shown that bacterial populations associated with plants have allowed the identification of a large number of novel genera and species. Moreover, whole genome sequencing has enhanced our knowledge of the metabolism and relationship between bacteria and their host.

This Special Issue seeks contributions that explore the native bacterial community and diversity in the rhizosphere of plants, with the aim of sharing new findings on microorganisms’ interactions with plants in the rhizosphere environment. Moreover, it will consist of articles that cover the isolation and characterization of microbes, genomic analyses and agronomic applications. Submissions of research articles, review articles, or short communications related to the rhizosphere microbial community are all welcome, and will help us to make unexpected new discoveries in this area.

Dr. Taegun Seo
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.

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Keywords

rhizosphere
endophytes
plant-microbe interactions

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Related Special Issues

Rhizosphere Microbial Community in Microorganisms (8 articles)
Rhizosphere Microbial Community 2.0 in Microorganisms (10 articles)

Published Papers (10 papers)

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Research

17 pages, 3270 KiB

Open AccessArticle

Bacillus subtilis PE7-Mediated Alleviation of Phosphate Starvation and Growth Promotion of Netted Melon (Cucumis melo L. var. reticulatus Naud.)

by Seong Eun Han, Kil Yong Kim and Chaw Ei Htwe Maung

Microorganisms 2024, 12(12), 2384; https://doi.org/10.3390/microorganisms12122384 - 21 Nov 2024

Viewed by 405

Abstract

Members of Bacillus species are able to enhance the level of available phosphorus (P) for plant absorption through mechanisms of P solubilization and mineralization. In our study, B. subtilis PE7 showed P-solubilizing activity in simple phosphate broth (SPB) medium, and acetic acid, iso-butyric acid, and iso-valeric acid were major organic acids responsible for the increase in soluble P and decrease in pH of SPB medium. In addition, strain PE7 released phytase on phytase-screening agar (PSA) medium, and analysis of semi-quantitative reverse transcription and polymerase chain reaction (sqRT-PCR) revealed that the phyC gene expression was the highest at 1 day after incubation. A low concentration of KH₂PO₄ in SPB medium induced more biofilm formation than a high concentration of KH₂PO₄. Strain PE7 showed swimming and swarming motilities in TY and TrA agar media. Under P starvation, inoculation with higher cell numbers of strain PE7 enhanced biomass and nutrient acquisition by melon plants, resulting in higher values of growth parameters and nutrient contents. Moreover, the persistence of bacterial cells on the root surface and in the rhizosphere of melon plants indicated colonization of the plants by strain PE7. Due to its capacity for P solubilization and mineralization, B. subtilis PE7 could be utilized as an alternative to synthetic fertilizer for P deficient-stress management in crop plantation. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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17 pages, 2854 KiB

Open AccessArticle

Two Novel Bacterial Species, Rhodanobacter lycopersici sp. nov. and Rhodanobacter geophilus sp. nov., Isolated from the Rhizosphere of Solanum lycopersicum with Plant Growth-Promoting Traits

by Haejin Woo, Inhyup Kim, Geeta Chhetri, Sunho Park, Hyunji Lee, Subin Yook and Taegun Seo

Microorganisms 2024, 12(11), 2227; https://doi.org/10.3390/microorganisms12112227 - 3 Nov 2024

Viewed by 719

Abstract

Two novel bacterial species were isolated from the rhizosphere of Solanum lycopersicum (tomato plant), both exhibiting plant growth-promoting properties. Two isolated strains, Rhodanobacter lycopersici sp. nov. Si-c^T and Rhodanobacter geophilus sp. nov. S2-g^T, were classified through a polyphasic approach, confirming their novel status within the Rhodanobacter genus. The strains demonstrated a remarkable tolerance to extreme pH conditions, with R. lycopersici Si-c^T surviving in pH 3.0–13.0 and R. geophilus S2-g^T tolerating pH 2.0–13.0. Additionally, both strains exhibited multiple plant growth-promoting traits, including indole-3-acetic acid and ammonia production, phosphate solubilization, and siderophore formation. These characteristics suggest that the two strains may play an important role in promoting plant growth, especially in soils with variable pH levels. However, since the direct impact on plant growth was not experimentally tested, the potential of these bacteria for agricultural applications remains to be confirmed through further research. This study expands our understanding of the diversity within the Rhodanobacter genus and provides insights into the potential use of these novel species in sustainable agriculture. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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21 pages, 2946 KiB

Open AccessArticle

Combination of Silicate-Based Soil Conditioners with Plant Growth-Promoting Microorganisms to Improve Drought Stress Resilience in Potato

by Abdullah Al Mamun, Günter Neumann, Narges Moradtalab, Aneesh Ahmed, Fahim Nawaz, Timotheus Tenbohlen, Jingyu Feng, Yongbin Zhang, Xiaochan Xie, Li Zhifang, Uwe Ludewig, Klára Bradáčová and Markus Weinmann

Microorganisms 2024, 12(11), 2128; https://doi.org/10.3390/microorganisms12112128 - 24 Oct 2024

Viewed by 765

Abstract

Due to shallow root systems, potato is a particularly drought-sensitive crop. To counteract these limitations, the application of plant growth-promoting microorganisms (PGPMs) is discussed as a strategy to improve nutrient acquisition and biotic and abiotic stress resilience. However, initial root colonization by PGPMs, in particular, can be affected by stress factors that negatively impact root growth and activity or the survival of PGPMs in the rhizosphere. In this study, perspectives for the use of commercial silicate-based soil conditioners (SCs) supposed to improve soil water retention were investigated. The SC products were based on combinations with lignocellulose polysaccharides (Sanoplant^® = SP) or polyacrylate (Geohumus^® = GH). It was hypothesized that SC applications would support beneficial plant–inoculant interactions (arbuscular mycorrhiza, AM: Rhizophagus irregularis MUCL41833, and Pseudomonas brassicacearum 3Re2-7) on a silty loam soil–sand mixture under water-deficit conditions (6–12 weeks at 15–20% substrate water-holding capacity, WHC). Although no significant SC effects on WHC and total plant biomass were detectable, the SC-inoculant combinations increased the proportion of leaf biomass not affected by drought stress symptoms (chlorosis, necrosis) by 66% (SP) and 91% (GH). Accordingly, osmotic adjustment (proline, glycine betaine accumulation) and ROS detoxification (ascorbate peroxidase, total antioxidants) were increased. This was associated with elevated levels of phytohormones involved in stress adaptations (abscisic, jasmonic, salicylic acids, IAA) and reduced ROS (H₂O₂) accumulation in the leaf tissue. In contrast to GH, the SP treatments additionally stimulated AM root colonization. Finally, the SP-inoculant combination significantly increased tuber biomass (82%) under well-watered conditions, and a similar trend was observed under drought stress, reaching 81% of the well-watered control. The P status was sufficient for all treatments, and no treatment differences were observed for stress-protective nutrients, such as Zn, Mn, or Si. By contrast, GH treatments had negative effects on tuber biomass, associated with excess accumulation of Mn and Fe in the leaf tissue close to toxicity levels. The findings suggest that inoculation with the PGPMs in combination with SC products (SP) can promote physiological stress adaptations and AM colonization to improve potato tuber yield, independent of effects on soil water retention. However, this does not apply to SC products in general. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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16 pages, 4288 KiB

Open AccessArticle

Bacillus subtilis Strain YJ-15, Isolated from the Rhizosphere of Wheat Grown under Saline Conditions, Increases Soil Fertility and Modifies Microbial Community Structure

by Junkang Sui, Chenyu Wang, Pengfei Chu, Changqing Ren, Feifan Hou, Yuxuan Zhang, Xueting Shang, Qiqi Zhao, Xuewen Hua and Hengjia Zhang

Microorganisms 2024, 12(10), 2023; https://doi.org/10.3390/microorganisms12102023 - 6 Oct 2024

Viewed by 783

Abstract

Soil salinization during wheat cultivation considerably diminishes soil fertility and impedes wheat growth, primarily due to rhizosphere microbial community changes. Our study investigates the application of Bacillus subtilis YJ-15, a strain isolated from the rhizosphere of wheat cultivated in salinized soil, as a soil remediation agent. This strain has demonstrated significant salt tolerance, disease suppression capabilities, and growth-promoting attributes in previous studies. The wheat rhizosphere was examined to assess the impact of Bacillus subtilis YJ-15 on microbial community composition and soil fertility. Fertility of soil in saline soil was significantly increased by inoculating wheat with YJ-15. The microbial community structure within the wheat rhizosphere inoculated with Bacillus subtilis YJ-15 was analyzed through sequencing on the Illumina MiSeq platform. Phyla Proteobacteria and Acidobacteria were identified as the dominant bacteria. Basidiomycota, Mortierellomycota, and Ascomycota dominated the fungal phyla. Among the bacterial genera, Pseudomonas, Arthrobacter, and Bacillus were predominant. The predominant fungal genera included Alternaria, Cephalotrichum, Mortierella, and Chaetomium. A significant increase in Gaiella and Haliangium levels was observed in the YJ group compared to the control group. Additionally, the fungal genera Epicoccum, Sporidiobolus, and Lecythophora have significantly increased in YJ abundance. One of the potential benefits of Bacillus subtilis YJ-15 in the cultivation of wheat on salinized land is its ability to enhance the rhizosphere microbial community structure and improve soil fertility. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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14 pages, 3147 KiB

Open AccessArticle

Sex-Dependent Rhizosphere Microbial Dynamics and Function in Idesia polycarpa through Floral and Fruit Development

by Zhi Li, Qiupeng Yuan, Shasha Wang, Tao Zhang, Yanmei Wang, Qifei Cai, Xiaodong Geng, Yi Yang, Chao Miao, Li Dai, Sohel Rana and Zhen Liu

Microorganisms 2024, 12(10), 2022; https://doi.org/10.3390/microorganisms12102022 - 6 Oct 2024

Viewed by 578

Abstract

Male Idesia polycarpa, which display distinct morphological and physiological traits, exhibit greater adaptability to stressful environments than females. However, the connection between this adaptability and rhizosphere processes remains unclear. Here, we investigate the differences in root bacterial community structures between male and female plants at different developmental stages, identifying bacterial strains associated with plant sex through functional predictions. This study aims to inform the optimal allocation of male and female plants during cultivation and provide a theoretical basis for sex identification and breeding. Samples from seven-year-old male and female plants were collected during the flowering (May) and fruit ripening (October) stages. Rhizosphere nutrient content and bacterial diversity were analyzed using Illumina high-throughput sequencing technology. The results demonstrate that total nitrogen (TN), total carbon (TC), and available potassium (AK) varied between sexes at different times. No significant differences between male and female plants were observed in the Shannon, Simpson, and Chao1 indexes during the flowering period. However, the Chao1 and Shannon indexes were significantly higher at fruit maturity in male rather than female plants. The predominant phyla of rhizosphere bacteria were Pseudomonadota, Acidobacteriota, and Actinomycetes. Interestingly, from flowering to fruit ripening, the dominant phyla in both male and female plants shifted from Actinomycetes to Pseudomonadota. A significant correlation was observed between pH and AK and rhizosphere bacteria (p < 0.05), with metabolism being the main functional difference. This study provides preliminary insights into the functional predictions and analyses of bacteria associated with Idesia polycarpa. The above findings lay the groundwork for further investigation into the sex-specific differences in microbial flora across different developmental stages, elucidating the mechanisms underlying flora changes and offering theoretical support for the high-quality management of Idesia polycarpa. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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9 pages, 443 KiB

Open AccessArticle

The Isolation and Characterization of Novel Caulobacter and Non-Caulobacter Lysogenic Bacteria from Soil and the Discovery of Broad-Host-Range Phages Infecting Multiple Genera

by Tannaz Mohammadi and Bert Ely

Microorganisms 2024, 12(9), 1894; https://doi.org/10.3390/microorganisms12091894 - 14 Sep 2024

Viewed by 1030

Abstract

To explore how microbial interactions within the rhizosphere influence the diversity and functional roles of bacterial communities, we isolated 21 bacterial strains from soil samples collected near Rocky Branch Creek on the University of South Carolina campus. Our findings revealed that a significant proportion of the isolated bacterial strains are lysogenic. Contrary to predictions of a narrow host range, most of the bacteriophages derived from these lysogenic bacteria demonstrated the ability to infect a broad range of bacterial strains. These results suggest that the bacterial community shares a complex phage community, creating an intricate web of interactions. This study enhances our understanding of the relationships between phages and their bacterial hosts in soil ecosystems, with implications for ecological balance and agricultural practices aimed at improving plant health through microbial management strategies. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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17 pages, 8876 KiB

Open AccessArticle

Effects of Deep Tillage on Wheat Regarding Soil Fertility and Rhizosphere Microbial Community

by Junkang Sui, Chenyu Wang, Changqing Ren, Feifan Hou, Yuxuan Zhang, Xueting Shang, Qiqi Zhao, Xuewen Hua, Xunli Liu and Hengjia Zhang

Microorganisms 2024, 12(8), 1638; https://doi.org/10.3390/microorganisms12081638 - 10 Aug 2024

Viewed by 1092

Abstract

Wheat production is intrinsically linked to global food security. However, wheat cultivation is constrained by the progressive degradation of soil conditions resulting from the continuous application of fertilizers. This study aimed to examine the effects of deep tillage on rhizosphere soil microbial communities and their potential role in improving soil quality, given that the specific mechanisms driving these observed benefits remain unclear. Soil fertility in this research was evaluated through the analysis of various soil parameters, including total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium, among others. The high-throughput sequencing technique was utilized to examine the rhizosphere microbial community associated with deep tillage wheat. The findings indicated that deep tillage cultivation of wheat led to reduced fertility levels in the 0–20 cm soil layer in comparison with non-deep tillage cultivation. A sequencing analysis indicated that Acidobacteria and Proteobacteria are the dominant bacterial phyla, with Proteobacteria being significantly more abundant in the deep tillage group. The dominant fungal phyla identified were Ascomycota, Mortierellomycota, and Basidiomycota. Among bacterial genera, Arthrobacter, Bacillus, and Nocardioides were predominant, with Arthrobacter showing a significantly higher presence in the deep tillage group. The predominant fungal genera included Mortierella, Alternaria, Schizothecium, and Cladosporium. Deep tillage cultivation has the potential to enhance soil quality and boost crop productivity through the modulation of soil microbial community structure. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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14 pages, 9863 KiB

Open AccessArticle

Relationships between Wheat Development, Soil Properties, and Rhizosphere Mycobiota

by Hang Jiang, Liguo Ma, Peixin Gao, Yueli Zhang, Bo Zhang, Guoping Ma, Kai Qi and Junshan Qi

Microorganisms 2024, 12(8), 1516; https://doi.org/10.3390/microorganisms12081516 - 24 Jul 2024

Viewed by 1089

Abstract

Wheat is a vital global food crop, yet it faces challenges in saline–alkali soils where Fusarium crown rot significantly impacts growth. Variations in wheat growth across regions are often attributed to uneven terrain. To explore these disparities, we examined well-growing and poorly growing wheat samples and their rhizosphere soils. Measurements included wheat height, root length, fresh weight, and Fusarium crown rot severity. Well-growing wheat exhibited greater height, root length, and fresh weight, with a lower Fusarium crown rot disease index compared to poorly growing wheat. Analysis of rhizosphere soil revealed higher alkalinity; lower nutrient levels; and elevated Na, K, and Ca levels in poorly growing wheat compared to well-growing wheat. High-throughput sequencing identified a higher proportion of unique operational taxonomic units (OTUs) in poorly growing wheat, suggesting selection for distinct fungal species under stress. FUNGuild analysis indicated a higher prevalence of pathogenic microbial communities in poorly growing wheat rhizosphere soil. This study underscores how uneven terrains in saline–alkali soils affect pH, nutrient dynamics, mineral content, wheat health, and rhizosphere fungal community structure. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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21 pages, 4561 KiB

Open AccessArticle

The Effects of Exogenous Benzoic Acid on the Physicochemical Properties, Enzyme Activities and Microbial Community Structures of Perilla frutescens Inter-Root Soil

by Tongtong Xue, Yuxin Fang, Hui Li, Mengsha Li and Chongwei Li

Microorganisms 2024, 12(6), 1190; https://doi.org/10.3390/microorganisms12061190 - 13 Jun 2024

Cited by 1 | Viewed by 1147

Abstract

This study analyzed the effects of benzoic acid (BA) on the physicochemical properties and microbial community structure of perilla rhizosphere soil. The analysis was based on high-throughput sequencing technology and physiological and biochemical detection. The results showed that with the increase in BA concentration, soil pH significantly decreased, while the contents of total nitrogen (TN), alkaline nitrogen (AN), available phosphorus (AP), and available potassium (AK) significantly increased. The activities of soil conversion enzymes urease and phosphatase significantly increased, but the activities of catalase and peroxidase significantly decreased. This indicates that BA can increase soil enzyme activity and improve nutrient conversion; the addition of BA significantly altered the composition and diversity of soil bacterial and fungal communities. The relative abundance of beneficial bacteria such as Gemmatimonas, Pseudolabrys, and Bradyrhizobium decreased significantly, while the relative abundance of harmful fungi such as Pseudogymnoascus, Pseudoeurotium, and Talaromyces increased significantly. Correlation analysis shows that AP, AN, and TN are the main physicochemical factors affecting the structure of soil microbial communities. This study elucidates the effects of BA on the physicochemical properties and microbial community structure of perilla soil, and preliminarily reveals the mechanism of its allelopathic effect on the growth of perilla. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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15 pages, 3304 KiB

Open AccessArticle

Rhizospheric Bacteria of Cover Legumes from Acidic Soils Are Capable of Solubilizing Different Inorganic Phosphates

by Winston F. Ríos-Ruiz, Roy D. Casique-Huamanguli, Renzo A. Valdez-Nuñez, Jose C. Rojas-García, Anderson R. Calixto-García, Franz Ríos-Reátegui, Danny F. Pompa-Vásquez and Euler Padilla-Santa-Cruz

Microorganisms 2024, 12(6), 1101; https://doi.org/10.3390/microorganisms12061101 - 29 May 2024

Cited by 2 | Viewed by 778

Abstract

Due to its adsorption with aluminum and iron hydroxides, phosphorus viability is low in acidic soils; thus, the aim of this study was to isolate and identify bacteria from the rhizosphere of four legumes growing in acidic soils of the Cumbaza Sub-basin, San Martín, Peru, as well as to characterize their ability to solubilize aluminum phosphate and iron phosphate. The isolation process was conducted on TSA medium and the isolates were classified based on their origin and morphocolonial characteristics, with the bacillary shape being the most frequent, followed by cocci. To assess the solubilization of aluminum and iron phosphates, the liquid medium GELP was employed. Sixteen strains were selected, among which three stood out for their effectiveness in solubilizing AlPO₄ (Sfcv-098-02, 22.65 mg L⁻¹; Sfc-093-04, 26.50 mg L⁻¹; and Sfcv-041-01-2, 55.98 mg L⁻¹) and one for its ability to solubilize FePO₄ (Sfcr-043-02, 32.61 mg L⁻¹). These four strains were molecularly characterized, being identified as Enterobacter sp., Pseudomonas sp., and Staphylococcus sp. Additionally, a decrease in pH was observed in the reactions, with values ranging from 5.23 to 3.29, which enhanced the phosphate of solubilization. This suggests that the selected bacteria could be used to improve phosphorus availability in agricultural soils. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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