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Microorganisms
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Rhizosphere Bacteria and Fungi That Promote Plant Growth
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Rhizosphere Bacteria and Fungi That Promote Plant Growth

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

Deadline for manuscript submissions: 28 February 2026 | Viewed by 5568

Special Issue Editor

Prof. Dr. Cesar Arriagada-Escamilla

E-Mail Website
Guest Editor
Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco, Chile
Interests: soil bioremediation, plant growth promotion; soil microbiology; plant-microbe interactions; mycorrhizal fungi; microbial diversity

Special Issue Information

Dear Colleagues,

“Rhizosphere Bacteria and Fungi That Promote Plant Growth” aims to recognize the critical role of microorganisms associated with plant root systems and their physical, chemical and biological interactions in promoting plant growth and health.

The influence zone of plant roots on their associated microorganisms and soil constituents is commonly known as the Rhizosphere. In this soil zone, the plant root system typically obtains nutrients through microbial activity and provides substrate for root-associated microbes through plant photosynthesis. Microorganisms, such as bacteria and fungi, are an important part of the soil system and are key to the breakdown of organic matter and the basis of nutrient cycling.

Before applying soil microbial techniques, it is crucial to understand the fundamentals of rhizosphere microbial ecology, such as the diversity and function of rhizosphere microbes.This Special Issue will focus on various aspects of microbial interactions, plant growth promotion by bacteria and fungi (endophytic or free-living), symbionts (mutualistic relationships) including nitrogen-fixing bacteria (Rhizobium), plant growth-promoting rhizobacteria (PGPR), associative or casual (free-living microorganisms), plant-microbe genetics and genomics, roles of soil microorganisms and their interactions with the plant microbiome interactions, nutrient availability, and mechanisms associated with plant growth promotion.

Prof. Dr. Cesar Arriagada-Escamilla
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

  • rhizosphere
  • fungi
  • bacteria
  • symbionts
  • microbial interactions
  • plant growth promotion

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Published Papers (5 papers)

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16 pages, 1662 KiB  
Article
Identifying Root-Associated Endophytic Fungi and Bacteria in Festuca and Lolium Grasses from a Site in Lithuania
by Violeta Stakelienė, Izolda Pašakinskienė, Saulė Matijošiūtė, Justas Martūnas and Gitana Štukėnienė
Microorganisms 2025, 13(4), 799; https://doi.org/10.3390/microorganisms13040799 - 31 Mar 2025
Viewed by 366
Abstract
This study investigates the diversity and distribution of root endophyte fungi and bacteria across Festuca and Lolium grasses, including open-grassland and forest species. The species examined include perennials such as Festuca arundinacea, F. gigantea, F. pratensis, Lolium perenne, and [...] Read more.
This study investigates the diversity and distribution of root endophyte fungi and bacteria across Festuca and Lolium grasses, including open-grassland and forest species. The species examined include perennials such as Festuca arundinacea, F. gigantea, F. pratensis, Lolium perenne, and L. perenne × F. gigantea hybrids and the annuals L. temulentum and L. multiflorum. A total of 21 fungal species (60 isolates) and 26 bacterial taxa (59 isolates) were recovered in the culture (PDA medium for fungi and LB for bacteria) from the root cuttings of these grasses. Microdochium bolleyi fungi and Bacillus sp. bacteria were the most prevalent endophytes, with each being identified in five of the seven plant species examined. The annuals L. multiflorum and L. temulentum exhibited a higher abundance of endophytes than that in their perennial relatives, suggesting the benefits of microbial associations in supporting their short life cycles. The woodland F. gigantea demonstrated the highest fungal endophyte diversity, with six species identified. In contrast, the open-grassland perennials F. arundinacea, F. pratensis, and L. perenne hosted only one to two species. Two Basidiomycota, Coprinellus disseminatus and Sistotrema brinkmannii, were exclusively obtained from the roots of the forest grass F. gigantea. Notably, the open-grassland perennial F. arundinacea exhibited the highest bacterial diversity, with nine species present. However, it showed the lowest fungal diversity, with only one species detected. Overall, our study reveals distinct patterns of fungal and bacterial endophyte diversity in the roots of Festuca and Lolium grasses, with variations linked to host species, growth type traits, and ecological adaptations. Among the root-derived endophytes isolated, several fungi and bacteria are potential candidates for plant growth promotion and biocontrol. Therefore, the findings of this study provide potential implications for improved grassland management and crop breeding strategies aimed at specific climate and/or soil conditions. Full article
(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi That Promote Plant Growth)
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16 pages, 4957 KiB  
Article
Growth-Promoting Effects of Grass Root-Derived Fungi Cadophora fastigiata, Paraphoma fimeti and Plectosphaerella cucumerina on Spring Barley (Hordeum vulgare) and Italian Ryegrass (Lolium multiflorum)
by Izolda Pašakinskienė, Violeta Stakelienė, Saulė Matijošiūtė, Justas Martūnas, Marius Rimkevičius, Jurga Būdienė, Algis Aučina and Audrius Skridaila
Microorganisms 2025, 13(1), 25; https://doi.org/10.3390/microorganisms13010025 - 26 Dec 2024
Cited by 1 | Viewed by 1129
Abstract
Many endophytic fungi are approved as plant growth stimulants, and several commercial biostimulants have already been introduced in agricultural practice. However, there are still many species of fungi whose plant growth-promoting properties have been understudied or not studied at all. We examined the [...] Read more.
Many endophytic fungi are approved as plant growth stimulants, and several commercial biostimulants have already been introduced in agricultural practice. However, there are still many species of fungi whose plant growth-promoting properties have been understudied or not studied at all. We examined the growth-promoting effect in spring barley (Hordeum vulgare) and Italian ryegrass (Lolium multiflorum) induced by three endophytic fungi previously obtained from the roots of Festuca/Lolium grasses. Surface-sterilized seeds were inoculated with a spore suspension of Cadophora fastigiata (isolate BSG003), Paraphoma fimeti (BSG010), Plectosphaerella cucumerina (BSG006), and their spore mixture. Before harvesting, the inoculated plants were grown in a greenhouse, with the barley being in multi-cavity trays for 30 days and ryegrass being placed in an original cylindric element system for 63 days. All three newly tested fungi had a positive effect on the growth of the barley and ryegrass plants, with the most pronounced impact observed in their root size. The fungal inoculations increased the dry shoot biomass between 11% and 26% in Italian ryegrass, but no such impact was observed in barley. The highest root increment was observed in barley. Herein, P. cucumerina and C. fastigiata inoculations were superior to other treatments, showing an increase in root dry weight of 50% compared to 20%, respectively. All fungal inoculations significantly promoted root growth in Italian ryegrass, resulting in a 20–30% increase in dry weight compared to non-inoculated plants. Moreover, a strong stimulatory effect of the fungi-emitted VOCs on the root development was observed in plate-in-plate arrays. In the presence of C. fastigiata and P. cucumerina cultures, the number of roots and root hairs in barley seedlings doubled compared to control plants. Thus, in our study, we demonstrated the potential of the grass root-derived endophytes C. fastigiata, P. fimeti, and P. cucumerina as growth promoters for spring barley and Italian ryegrass. These studies can be extended to other major crops and grasses by evaluating different fungal isolates. Full article
(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi That Promote Plant Growth)
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21 pages, 1995 KiB  
Article
Alginate–Bentonite Encapsulation of Extremophillic Bacterial Consortia Enhances Chenopodium quinoa Tolerance to Metal Stress
by Roxana Alvarado, Cesar Arriagada-Escamilla, Javier Ortiz, Reinaldo Campos-Vargas and Pablo Cornejo
Microorganisms 2024, 12(10), 2066; https://doi.org/10.3390/microorganisms12102066 - 15 Oct 2024
Cited by 1 | Viewed by 1674 | Correction
Abstract
This study explores the encapsulation in alginate/bentonite beads of two metal(loid)-resistant bacterial consortia (consortium A: Pseudomonas sp. and Bacillus sp.; consortium B: Pseudomonas sp. and Bacillus sp.) from the Atacama Desert (northern Chile) and Antarctica, and their influence on physiological traits of Chenopodium [...] Read more.
This study explores the encapsulation in alginate/bentonite beads of two metal(loid)-resistant bacterial consortia (consortium A: Pseudomonas sp. and Bacillus sp.; consortium B: Pseudomonas sp. and Bacillus sp.) from the Atacama Desert (northern Chile) and Antarctica, and their influence on physiological traits of Chenopodium quinoa growing in metal(loid)-contaminated soils. The metal(loid) sorption capacity of the consortia was determined. Bacteria were encapsulated using ionic gelation and were inoculated in soil of C. quinoa. The morphological variables, photosynthetic pigments, and lipid peroxidation in plants were evaluated. Consortium A showed a significantly higher biosorption capacity than consortium B, especially for As and Cu. The highest viability of consortia was achieved with matrices A1 (3% alginate and 2% bentonite) and A3 (3% alginate, 2% bentonite and 2.5% LB medium) at a drying temperature of 25 °C and storage at 4 °C. After 12 months, the highest viability was detected using matrix A1 with a concentration of 106 CFU g−1. Further, a greenhouse experiment using these consortia in C. quinoa plants showed that, 90 days after inoculation, the morphological traits of both consortia improved. Chemical analysis of metal(loid) contents in the leaves indicated that consortium B reduced the absorption of Cu to 32.1 mg kg−1 and that of Mn to 171.9 mg kg−1. Encapsulation resulted in a significant increase in bacterial survival. This highlights the benefits of using encapsulated microbial consortia from extreme environments, stimulating the growth of C. quinoa, especially in soils with metal(loid) levels that can be a serious constraint for plant growth. Full article
(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi That Promote Plant Growth)
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21 pages, 2195 KiB  
Article
Does Bidens pilosa L. Affect Carbon and Nitrogen Contents, Enzymatic Activities, and Bacterial Communities in Soil Treated with Different Forms of Nitrogen Deposition?
by Yingsheng Liu, Yizhuo Du, Yue Li, Chuang Li, Shanshan Zhong, Zhelun Xu, Congyan Wang and Daolin Du
Microorganisms 2024, 12(8), 1624; https://doi.org/10.3390/microorganisms12081624 - 9 Aug 2024
Cited by 2 | Viewed by 1064
Abstract
The deposition of nitrogen in soil may be influenced by the presence of different nitrogen components, which may affect the accessibility of soil nitrogen and invasive plant–soil microbe interactions. This, in turn, may alter the success of invasive plants. This study aimed to [...] Read more.
The deposition of nitrogen in soil may be influenced by the presence of different nitrogen components, which may affect the accessibility of soil nitrogen and invasive plant–soil microbe interactions. This, in turn, may alter the success of invasive plants. This study aimed to clarify the influences of the invasive plant Bidens pilosa L. on the physicochemical properties, carbon and nitrogen contents, enzymatic activities, and bacterial communities in soil in comparison to the native plant Pterocypsela laciniata (Houtt.) Shih treated with simulated nitrogen deposition at 5 g nitrogen m−2 yr−1 in four forms (nitrate, ammonium, urea, and mixed nitrogen). Monocultural B. pilosa resulted in a notable increase in soil pH but a substantial decrease in the moisture, electrical conductivity, ammonium content, and the activities of polyphenol oxidase, β-xylosidase, FDA hydrolase, and sucrase in soil in comparison to the control. Co-cultivating B. pilosa and P. laciniata resulted in a notable increase in total soil organic carbon content in comparison to the control. Monocultural B. pilosa resulted in a notable decrease in soil bacterial alpha diversity in comparison to monocultural P. laciniata. Soil FDA hydrolase activity and soil bacterial alpha diversity, especially the indices of Shannon’s diversity, Simpson’s dominance, and Pielou’s evenness, exhibited a notable decline under co-cultivated B. pilosa and P. laciniata treated with nitrate in comparison to those treated with ammonium, urea, and mixed nitrogen. Full article
(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi That Promote Plant Growth)
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1 pages, 161 KiB  
Correction
Correction: Alvarado et al. Alginate–Bentonite Encapsulation of Extremophillic Bacterial Consortia Enhances Chenopodium quinoa Tolerance to Metal Stress. Microorganisms 2024, 12, 2066
by Roxana Alvarado, Cesar Arriagada-Escamilla, Javier Ortiz, Reinaldo Campos-Vargas and Pablo Cornejo
Microorganisms 2024, 12(11), 2356; https://doi.org/10.3390/microorganisms12112356 - 19 Nov 2024
Viewed by 534
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi That Promote Plant Growth)
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