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Microorganisms
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Plant Root Interaction with Associated Microbiomes
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Plant Root Interaction with Associated Microbiomes

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 2023) | Viewed by 16846

Special Issue Editors

Dr. Roberto Defez

E-Mail Website
Guest Editor
Institute of Biosciences and BioResources, Via P. Castellino 111, 80131 Naples, Italy
Interests: nitrogen fixation; drought or salt stress; phosphate solubilization; phytohormone delivery from soil bacteria; as rhizobia or endophytic bacteria; when associated with cereals or legumes
Dr. Alessio Mengoni

E-Mail Website
Guest Editor
Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
Interests: rhizospheric and endophytic microbiomes; microbial evolution; bacterial genetics and ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A plethora of microorganisms reside in close association with plants, from the soil surrounding the roots to the leaves to the internal tissue of plants, including seeds. Plant-associated microbiomes have pivotal roles in mediating the interaction between plants and the environment. Being in contact with soil, roots provide one of the most relevant organs impacted by microbes. The root-associated microbiome has been claimed to be as important for plants as the gut microbiome is for animals. Indeed, animal guts and plant roots have absorption roles for nutrient uptake, and, as for the gut microbiome, the root-associated microbiome regulates the host immune response, provides protection against pathogens, additional metabolic capabilities, essential nutrients, and even phytohormone modulation.

In recent years, an ever-increasing interest in plant root interactions with associated microbiomes has been manifested by scholars working in various fields, from basic research on microbial symbioses and molecular signalling to applications in sustainable agriculture, bioremediation, and biodiversity preservation.

This Special Issue addresses the contribution of studies on root-associated microbiomes to emerging research questions raised through the study of plant biotic interactions. The topics include but are not limited to

  • defining a mechanistic interpretation of the role of root microbiomes in a plant’s physiology;
  • the application of root microbiomes in increasing crop productivity and health;
  • the biodiversity and evolution of the root microbiota members.

We look forward to receiving your contributions.

Dr. Roberto Defez
Dr. Alessio Mengoni
Guest Editors

Manuscript Submission Information

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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 microbiota
  • rhizosphere ecology
  • plant-associated microbial communities
  • plant growth-promoting bacteria (PGPB)
  • plant growth-promoting rhizobacteria (PGPR)
  • arbuscular mycorrhizal fungi (AMF)
  • antagonistic fungi
  • antagonistic bacteria
  • root microbiota
  • root exudates
  • phytohormones
  • symbiosis
  • nitrogen fixation
  • synthetic communities
  • bioinoculants

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Published Papers (7 papers)

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Research

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21 pages, 3009 KiB  
Article
Symbiotic Functioning and Photosynthetic Rates Induced by Rhizobia Associated with Jack Bean (Canavalia ensiformis L.) Nodulation in Eswatini
by Zanele D. Ngwenya and Felix D. Dakora
Microorganisms 2023, 11(11), 2786; https://doi.org/10.3390/microorganisms11112786 - 16 Nov 2023
Viewed by 1177
Abstract
Improving the efficiency of the legume–rhizobia symbiosis in African soils for increased grain yield would require the use of highly effective strains capable of nodulating a wide range of legume plants. This study assessed the photosynthetic functioning, N2 fixation, relative symbiotic effectiveness [...] Read more.
Improving the efficiency of the legume–rhizobia symbiosis in African soils for increased grain yield would require the use of highly effective strains capable of nodulating a wide range of legume plants. This study assessed the photosynthetic functioning, N2 fixation, relative symbiotic effectiveness (%RSE) and C assimilation of 22 jack bean (Canavalia ensiformis L.) microsymbionts in Eswatini soils as a first step to identifying superior isolates for inoculant production. The results showed variable nodule number, nodule dry matter, shoot biomass and photosynthetic rates among the strains tested under glasshouse conditions. Both symbiotic parameters and C accumulation differed among the test isolates at the shoot, root and whole-plant levels. Although 7 of the 22 jack bean isolates showed much greater relative symbiotic efficiency than the commercial Bradyrhizobium strain XS21, only one isolate (TUTCEeS2) was statistically superior to the inoculant strain, which indicates its potential for use in inoculant formulation after field testing. Furthermore, the isolates that recorded high %RSE elicited greater amounts of fixed N. Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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16 pages, 2143 KiB  
Article
Arbuscular Mycorrhizal Fungi Associated with Maize (Zea mays L.) in the Formation and Stability of Aggregates in Two Types of Soil
by Juan Florencio Gómez-Leyva, Miguel Angel Segura-Castruita, Laura Verónica Hernández-Cuevas and Mayra Íñiguez-Rivas
Microorganisms 2023, 11(11), 2615; https://doi.org/10.3390/microorganisms11112615 - 24 Oct 2023
Cited by 4 | Viewed by 2141
Abstract
Knowledge of native Arbuscular Mycorrhizal Fungi (AMF) and their relationship with the edaphic characteristics where they live is important to establish the influence of allochthonous AMF, which were inoculated, on the development and stability of soil aggregates. The objectives of this research were [...] Read more.
Knowledge of native Arbuscular Mycorrhizal Fungi (AMF) and their relationship with the edaphic characteristics where they live is important to establish the influence of allochthonous AMF, which were inoculated, on the development and stability of soil aggregates. The objectives of this research were to know the composition of native AMF species from two contrasting soils, and to establish the development and stability of aggregates in those soils with corn plants after inoculating them with allochthonous AMF. The experiment had three factors: Soil (two levels [S1 and S2]), HMA (three levels: without application [A0], with the application of Claroideoglomus claroideum [A1] and with the application of a consortium [A2]) and Fertilization (two levels (without fertilization [f0] and with fertilization [f1])). Twelve treatments were generated, with five replicates (60 experimental units [EU]). The EU consisted of a pot with a corn plant and the distribution was completely random. The results demonstrated that the Typic Ustifluvent presented nine species of native AMF, while the Typic Dystrustert had three; the native AMF in each soil influenced the activity of allochthonous AMF, such as their colonization and sporulation. Likewise, differences were found in the stability of macro-sized aggregates (0.5 to 2.0 mm). Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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14 pages, 1501 KiB  
Article
Investigating the Impact of Tillage and Crop Rotation on the Prevalence of phlD-Carrying Pseudomonas Potentially Involved in Disease Suppression
by Ridhdhi Rathore, Dermot Forristal, John Spink, David Dowling and Kieran J. Germaine
Microorganisms 2023, 11(10), 2459; https://doi.org/10.3390/microorganisms11102459 - 30 Sep 2023
Viewed by 1260
Abstract
Winter oilseed rape (OSR) is becoming an increasingly popular crop in rotations as it provides a cash crop and reduces the incidence of take-all fungal disease (caused by Gaeumannomyces graminis) in subsequent wheat production. The exact mechanism of this inhibition of fungal [...] Read more.
Winter oilseed rape (OSR) is becoming an increasingly popular crop in rotations as it provides a cash crop and reduces the incidence of take-all fungal disease (caused by Gaeumannomyces graminis) in subsequent wheat production. The exact mechanism of this inhibition of fungal pathogens is not fully understood; however, the selective recruitment of bacterial groups with the ability to suppress pathogen growth and reproduction is thought to play a role. Here we examine the effect of tillage practice on the proliferation of microbes that possess the phlD gene involved in the production of the antifungal compound 2,4-diacetylphloroglucinol (2,4-DAPG), in the rhizospheres of both winter oilseed rape and winter wheat grown in rotation over a two-year period. The results showed that conservation strip tillage led to a significantly greater phlD gene copy number, both in the soil and in the roots, of oilseed rape and wheat crops, whereas crop rotation of oilseed rape and wheat did not increase the phlD gene copy number in winter wheat. Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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16 pages, 1841 KiB  
Article
Effects of Male and Female Strains of Salix linearistipularis on Physicochemical Properties and Microbial Community Structure in Saline–Alkali Soil
by Haojun Cui, Yan Li, Wenyi Wang, Lili Chen, Zhouqing Han, Shurong Ma and Weidong Wang
Microorganisms 2023, 11(10), 2455; https://doi.org/10.3390/microorganisms11102455 - 29 Sep 2023
Cited by 3 | Viewed by 1581
Abstract
The woody plant gender difference may lead to alteration in rhizosphere microbial communities and soil physicochemical properties. In this study, we investigated the differences in rhizosphere soil properties and microbial community structures of S. linearistipularis. Rhizosphere microorganisms were analyzed by high-throughput sequencing [...] Read more.
The woody plant gender difference may lead to alteration in rhizosphere microbial communities and soil physicochemical properties. In this study, we investigated the differences in rhizosphere soil properties and microbial community structures of S. linearistipularis. Rhizosphere microorganisms were analyzed by high-throughput sequencing technology. The results showed that there were significant differences in rhizosphere soil nutrition between male and female S. linearistipularis plants in saline–alkali soil. The female S. linearistipularis plants significantly reduce soil pH values and significantly increase the soil water content (SWC), available total nitrogen (TN), soil organic matter (SOM), and soil urease activity (S-UE) compared to the male plant. The ACE, Chao, and Shannon index of the female plant was significantly higher than that of the male strain. At the level of Bacteriophyta, the relative abundance of Actinobacteriota in male and female S. linearistipularis was the highest, with 34.26% and 31.03%, respectively. Among the named bacterial genera, the relative abundance of Defluviicoccus of male and female plants was the highest, with 2.67% and 5.27%, respectively. At the level of Eumycophyta, the relative abundance of Ascomycetes in male and female plants was the highest, with 54.93% and 52.10%, respectively. Among the named fungi genera, the relative abundance of male and female plants of Mortierella was the highest, with 6.18% and 9.31%, respectively. In addition, soil pH, SOM, SWC, and S-UE activities were the main driving factors of soil microbial community structures. In the process of restoring saline–alkali land in the Songnen Plain, we may prioritise the planting of female S. linearistipularis, which also provides a theoretical basis for the microorganisms restoration of saline–alkali land in the Songnen plain. Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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20 pages, 1686 KiB  
Article
Changes in the Microbial Composition of the Rhizosphere of Hop Plants Affected by Verticillium Wilt Caused by Verticillium nonalfalfae
by Elena Gallego-Clemente, Víctor Moreno-González, Ana Ibáñez, Carla Calvo-Peña, Seyedehtannaz Ghoreshizadeh, Sebastjan Radišek, Rebeca Cobos and Juan José R. Coque
Microorganisms 2023, 11(7), 1819; https://doi.org/10.3390/microorganisms11071819 - 16 Jul 2023
Cited by 4 | Viewed by 2008
Abstract
Verticillium wilt is a devastating disease affecting many crops, including hops. This study aims to describe fungal and bacterial populations associated with bulk and rhizosphere soils in a hop field cultivated in Slovenia with the Celeia variety, which is highly susceptible to Verticillium [...] Read more.
Verticillium wilt is a devastating disease affecting many crops, including hops. This study aims to describe fungal and bacterial populations associated with bulk and rhizosphere soils in a hop field cultivated in Slovenia with the Celeia variety, which is highly susceptible to Verticillium nonalfalfae. As both healthy and diseased plants coexist in the same field, we focused this study on the detection of putative differences in the microbial communities associated with the two types of plants. Bacterial communities were characterized by sequencing the V4 region of the 16S rRNA gene, whereas sequencing of the ITS2 region was performed for fungal communities. The bacterial community was dominated by phyla Proteobacteria, Acidobacteriota, Bacteroidota, Actinobacteriota, Planctomycetota, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota, which are typically found in crop soils throughout the world. At a fungal level, Fusarium sp. was the dominant taxon in both bulk and rhizosphere soils. Verticillium sp. levels were very low in all samples analyzed and could only be detected by qPCR in the rhizosphere of diseased plants. The rhizosphere of diseased plants underwent important changes with respect to the rhizosphere of healthy plants where significant increases in potentially beneficial fungi such as the basidiomycetes Ceratobasidium sp. and Mycena sp., the zygomycete Mortierella sp., and a member of Glomeralles were observed. However, the rhizosphere of diseased plants experienced a decrease in pathogenic basidiomycetes that can affect the root system, such as Thanatephorus cucumeris (the teleomorph of Rhizoctonia solani) and Calyptella sp. Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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17 pages, 2299 KiB  
Article
A Microbiological Approach to Alleviate Soil Replant Syndrome in Peaches
by Derek R. Newberger, Ioannis S. Minas, Daniel K. Manter and Jorge M. Vivanco
Microorganisms 2023, 11(6), 1448; https://doi.org/10.3390/microorganisms11061448 - 30 May 2023
Cited by 3 | Viewed by 2022
Abstract
Replant syndrome (RS) is a global problem characterized by reduced growth, production life, and yields of tree fruit/nut orchards. RS etiology is unclear, but repeated monoculture plantings are thought to develop a pathogenic soil microbiome. This study aimed to evaluate a biological approach [...] Read more.
Replant syndrome (RS) is a global problem characterized by reduced growth, production life, and yields of tree fruit/nut orchards. RS etiology is unclear, but repeated monoculture plantings are thought to develop a pathogenic soil microbiome. This study aimed to evaluate a biological approach that could reduce RS in peach (Prunus persica) orchards by developing a healthy soil bacteriome. Soil disinfection via autoclave followed by cover cropping and cover crop incorporation was found to distinctly alter the peach soil bacteriome but did not affect the RS etiology of RS-susceptible ‘Lovell’ peach seedlings. In contrast, non-autoclaved soil followed by cover cropping and incorporation altered the soil bacteriome to a lesser degree than autoclaving but induced significant peach growth. Non-autoclaved and autoclaved soil bacteriomes were compared to highlight bacterial taxa promoted by soil disinfection prior to growing peaches. Differential abundance shows a loss of potentially beneficial bacteria due to soil disinfection. The treatment with the highest peach biomass was non-autoclaved soil with a cover crop history of alfalfa, corn, and tomato. Beneficial bacterial species that were cultivated exclusively in the peach rhizosphere of non-autoclaved soils with a cover crop history were Paenibacillus castaneae and Bellilinea caldifistulae. In summary, the non-autoclaved soils show continuous enhancement of beneficial bacteria at each cropping phase, culminating in an enriched rhizosphere which may help alleviate RS in peaches. Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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Review

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15 pages, 1088 KiB  
Review
Communication between Plants and Rhizosphere Microbiome: Exploring the Root Microbiome for Sustainable Agriculture
by Ben Jesuorsemwen Enagbonma, Ayomide Emmanuel Fadiji, Ayansina Segun Ayangbenro and Olubukola Oluranti Babalola
Microorganisms 2023, 11(8), 2003; https://doi.org/10.3390/microorganisms11082003 - 3 Aug 2023
Cited by 24 | Viewed by 4595
Abstract
Plant roots host numerous microorganisms around and inside their roots, forming a community known as the root microbiome. An increasing bulk of research is underlining the influences root-associated microbial communities can have on plant health and development. However, knowledge on how plant roots [...] Read more.
Plant roots host numerous microorganisms around and inside their roots, forming a community known as the root microbiome. An increasing bulk of research is underlining the influences root-associated microbial communities can have on plant health and development. However, knowledge on how plant roots and their associated microbes interact to bring about crop growth and yield is limited. Here, we presented (i) the communication strategies between plant roots and root-associated microbes and (ii) the applications of plant root-associated microbes in enhancing plant growth and yield. This review has been divided into three main sections: communications between root microbiome and plant root; the mechanism employed by root-associated microbes; and the chemical communication mechanisms between plants and microbes and their application in plant growth and yield. Understanding how plant root and root-associated microbes communicate is vital in designing ecofriendly strategies for targeted disease suppression and improved plant growth that will help in sustainable agriculture. Ensuring that plants become healthy and productive entails keeping plants under surveillance around the roots to recognize disease-causing microbes and similarly exploit the services of beneficial microorganisms in nutrient acquisition, stress mitigation, and growth promotion. Full article
(This article belongs to the Special Issue Plant Root Interaction with Associated Microbiomes)
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