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Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant...
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Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (20 January 2025) | Viewed by 16477

Special Issue Editors

Dr. Mohamed Ait-El-Mokhtar

E-Mail Website
Guest Editor
Department of Biology, Hassan II University of Casablanca, Casablanca 20000, Morocco
Interests: plant tolerance; biotic and abiotic stresses; biostimu-lants/biofertilizers; salinity, drought; AMF; PGPR; organic amendments
Special Issues, Collections and Topics in MDPI journals
Dr. Marouane Baslam

E-Mail Website
Guest Editor
Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
Interests: plant–microorganism interactions, -omics; climate change; yield; sustainability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Through thousands of years of evolution, plants and microorganisms have developed fine-tuned associations that result in various protective or destructive mechanisms, leading to plant survival and adaptation to environmental changes. Plants interact with different soil microorganisms, including prokaryotes, fungi, or viruses. Symbiotic microbes can boost or hinder plant nutrient uptake and use efficiency, which affects growth, fitness, yield, and quality even under environmental stresses. Plant-associated microbes activate several physiological, biochemical, and molecular pathways that coordinate carbon and nitrogen metabolism and alter the synthesis and buildup of primary and secondary compounds with osmotic, antioxidant, and hormone-like activity.

This Special Issue of Plants aims to gather recent data and innovations in the research on the mechanisms governing interaction between plants and soil microorganisms, as well as to identify new prospects, directions and challenges in the development of plant and microbial biotechnologies. An integrated understanding of these interactions will empower the design of treatments that specifically promote crop yield and quality under changing climate conditions. We welcome the submission of original research articles, reviews, opinion, and methods, focusing on (but not limited to) the following topics:

  • Microbial application for plant growth promotion and/or protection;
  • Innovative and more effective microbial formulations towards agriculture sustainability;
  • Drivers, roles, processes, and mechanisms in plant-microbe interactions;
  • Molecular, genomic, and metagenomic analysis of plant-associated microbe biodiversity;
  • Physiological, biochemical, and molecular functions of symbiotic microorganisms in plants to mitigate the adverse impact of environmental stresses;
  • Impact of symbiotic microbes application on plant susceptibility to pathogen infection;
  • Impact of microorganisms on nutrient transformations in soil toward promoting plant fitness.

Dr. Mohamed Ait-El-Mokhtar
Dr. Marouane Baslam
Guest Editors

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. Plants is an international peer-reviewed open access semimonthly 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-microbe interactions
  • endosymbiosis
  • biofertilizers/biological fertilizers/biostimulants
  • plant adaptation and stress tolerance
  • biopriming
  • biocontrol agents
  • legume–rhizobial symbioses
  • arbuscular mycorrhiza
  • rhizosphere microbiome
  • endophytic microbiome
  • sustainable agriculture
  • microbial biotechnology
  • pathogen–host interactions
  • plant defense mechanisms
  • plant disease management

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Published Papers (7 papers)

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Research

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13 pages, 2162 KiB  
Article
Mechanism of N-Acetyl-D-alloisoleucine in Controlling Strawberry Black Root Rot
by Jialu Xu, Jianxiu Hao, Mingmin Zhao, Xiaoyu Zhang, Ruixiang Niu, Yiran Li, Zhen Wang, Shuo Zhang, Sumei Zhao, Siran Li and Hongyou Zhou
Plants 2025, 14(5), 829; https://doi.org/10.3390/plants14050829 - 6 Mar 2025
Cited by 2 | Viewed by 752
Abstract
China is the largest strawberry producer in the world. Strawberry black root rot is a novel disease that occurs in Hohhot, Inner Mongolia. In the present study, the inhibitory effects of Bacillus subtilis S-16 and its fermented form on strawberry black root rot [...] Read more.
China is the largest strawberry producer in the world. Strawberry black root rot is a novel disease that occurs in Hohhot, Inner Mongolia. In the present study, the inhibitory effects of Bacillus subtilis S-16 and its fermented form on strawberry black root rot caused by Fusarium asiaticum were tested. The inhibition rates were 56.31% and 65.95%, respectively. Furthermore, the metabolic substances were analysed using LC-MS/MS. A total of 68 substances were identified, including 18 amino acids, 7 of which have been reported to have pro-growth and antibacterial functions. Among these seven amino acids, N-acetyl-D-alloisoleucine (NAD) had the strongest inhibitory effect on F. asiaticum. In addition, NAD caused the mycelia of F. asiaticum to appear shrivelled and deformed under electron microscopy. Furthermore, the effect of NAD on F. asiaticum was tested. The results indicate that NAD had a better prevention effect when used with hymexazol. Finally, the fungal biomass of F. asiaticum in strawberry roots was measured at different times using two treatment methods: treating plant roots with NAD and a spore suspension of F. asiaticum concurrently and with F. asiaticum alone. The colonisation response of F. asiaticum in terms of the target gene EF-1α when treated with F. asiaticum alone at 72 hpi was significantly higher than that when treated with NAD and a spore suspension of F. asiaticum. The relative expression levels of defence-related genes in strawberry roots treated with NAD at 72 hpi were determined. The genes NPR1 and PDF1 were markedly upregulated compared with other genes, suggesting that the expression of genes related to disease resistance was activated by NAD, resulting in disease resistance in strawberries. Our results provide theoretical support for the biological control of strawberry black root rot. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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15 pages, 15476 KiB  
Article
Dynamics of Hydrogen Peroxide Accumulation During Tip Growth of Infection Thread in Nodules and Cell Differentiation in Pea (Pisum sativum L.) Symbiotic Nodules
by Anna V. Tsyganova, Artemii P. Gorshkov, Maxim G. Vorobiev, Igor A. Tikhonovich, Nicholas J. Brewin and Viktor E. Tsyganov
Plants 2024, 13(20), 2923; https://doi.org/10.3390/plants13202923 - 18 Oct 2024
Viewed by 1224
Abstract
Hydrogen peroxide (H2O2) in plants is produced in relatively large amounts and plays a universal role in plant defense and physiological responses, including the regulation of growth and development. In the Rhizobium–legume symbiosis, hydrogen peroxide plays an important [...] Read more.
Hydrogen peroxide (H2O2) in plants is produced in relatively large amounts and plays a universal role in plant defense and physiological responses, including the regulation of growth and development. In the Rhizobium–legume symbiosis, hydrogen peroxide plays an important signaling role throughout the development of this interaction. In the functioning nodule, H2O2 has been shown to be involved in bacterial differentiation into the symbiotic form and in nodule senescence. In this study, the pattern of H2O2 accumulation in pea (Pisum sativum L.) wild-type and mutant nodules blocked at different stages of the infection process was analyzed using a cytochemical reaction with cerium chloride. The observed dynamics of H2O2 deposition in the infection thread walls indicated that the distribution of H2O2 was apparently related to the stiffness of the infection thread wall. The dynamics of H2O2 accumulation was traced, and its patterns in different nodule zones were determined in order to investigate the relationship of H2O2 localization and distribution with the stages of symbiotic nodule development in P. sativum. The patterns of H2O2 localization in different zones of the indeterminate nodule have been partially confirmed by comparative analysis on mutant genotypes. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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13 pages, 6023 KiB  
Article
Assessing the Efficacy of Cyanobacterial Strains as Oryza sativa Growth Biostimulants in Saline Environments
by Meruyert O. Bauenova, Fariza K. Sarsekeyeva, Asemgul K. Sadvakasova, Bekzhan D. Kossalbayev, Ramazan Mammadov, Aziza I. Token, Huma Balouch, Pavel Pashkovskiy, Yoong Kit Leong, Jo-Shu Chang and Suleyman I. Allakhverdiev
Plants 2024, 13(17), 2504; https://doi.org/10.3390/plants13172504 - 6 Sep 2024
Cited by 5 | Viewed by 1487
Abstract
Soil salinity, which affects plant photosynthesis mechanisms, significantly limits plant productivity. Soil microorganisms, including cyanobacteria, can synthesize various exometabolites that contribute to plant growth and development in several ways. These microorganisms can increase plant tolerance to salt stress by secreting various phytoprotectants; therefore, [...] Read more.
Soil salinity, which affects plant photosynthesis mechanisms, significantly limits plant productivity. Soil microorganisms, including cyanobacteria, can synthesize various exometabolites that contribute to plant growth and development in several ways. These microorganisms can increase plant tolerance to salt stress by secreting various phytoprotectants; therefore, it is highly relevant to study soil microorganisms adapted to high salinity and investigate their potential to increase plant resistance to salt stress. This study evaluated the antioxidant activity of four cyanobacterial strains: Spirulina platensis Calu-532, Nostoc sp. J-14, Trichormus variabilis K-31, and Oscillatoria brevis SH-12. Among these, Nostoc sp. J-14 presented the highest antioxidant activity. Their growth-stimulating effects under saline conditions were also assessed under laboratory conditions. These results indicate that Nostoc sp. J-14 and T. variabilis K-31 show significant promise in mitigating the harmful effects of salinity on plant size and weight. Both strains notably enhanced the growth of Oryza sativa plants under saline conditions, suggesting their potential as biostimulants to improve crop productivity in saline environments. This research underscores the importance of understanding the mechanisms by which cyanobacteria increase plant tolerance to salt stress, paving the way for sustainable agricultural practices in saline areas. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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11 pages, 1082 KiB  
Article
Resilience of Canola to Plasmodiophora brassicae (Clubroot) Pathotype 3H under Different Resistance Genes and Initial Inoculum Levels
by Rui Wen, Tao Song, Nazmoon Naher Tonu, Coreen Franke and Gary Peng
Plants 2024, 13(11), 1540; https://doi.org/10.3390/plants13111540 - 2 Jun 2024
Cited by 2 | Viewed by 1492
Abstract
In this study, we explored the resilience of a clubroot resistance (CR) stacking model against a field population of Plasmodiophora brassicae pathotype 3H. This contrasts with our earlier work, where stacking CRaM and Crr1rutb proved only moderately resistant to pathotype X. Canola varieties [...] Read more.
In this study, we explored the resilience of a clubroot resistance (CR) stacking model against a field population of Plasmodiophora brassicae pathotype 3H. This contrasts with our earlier work, where stacking CRaM and Crr1rutb proved only moderately resistant to pathotype X. Canola varieties carrying Rcr1/Crr1rutb and Rcr1 + Crr1rutb were repeatedly exposed to 3H at low (1 × 104/g soil) and high (1 × 107/g soil) initial resting spore concentrations over five planting cycles under controlled environments to mimic intensive canola production. Initially, all resistant varieties showed strong resistance. However, there was a gradual decline in resistance over time for varieties carrying only a single CR gene, particularly with Crr1rutb alone and at the high inoculum level, where the disease severity index (DSI) increased from 9% to 39% over five planting cycles. This suggests the presence of virulent pathotypes at initially low levels in the 3H inoculum. In contrast, the variety with stacked CR genes remained resilient, with DSI staying below 3% throughout, even at the high inoculum level. Furthermore, the use of resistant varieties, carrying either a single or stacked CR genes, reduced the total resting spore numbers in soil over time, while the inoculum level either increased or remained high in soils where susceptible Westar was continuously grown. Our study demonstrates greater resistance resilience for stacking Rcr1 and Crr1rutb against the field population of 3H. Additionally, the results suggest that resistance may persist even longer in fields with lower levels of inoculum, highlighting the value of extended crop rotation (reducing inoculum) alongside strategic CR-gene deployment to maximize resistance resilience. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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19 pages, 1546 KiB  
Article
Effects of Humic Substances and Mycorrhizal Fungi on Drought-Stressed Cactus: Focus on Growth, Physiology, and Biochemistry
by Soufiane Lahbouki, Ana Luísa Fernando, Carolina Rodrigues, Raja Ben-Laouane, Mohamed Ait-El-Mokhtar, Abdelkader Outzourhit and Abdelilah Meddich
Plants 2023, 12(24), 4156; https://doi.org/10.3390/plants12244156 - 14 Dec 2023
Cited by 10 | Viewed by 3595
Abstract
Utilizing water resources rationally has become critical due to the expected increase in water scarcity. Cacti are capable of surviving with minimal water requirements and in poor soils. Despite being highly drought-resistant, cacti still faces limitations in realizing its full potential under drought-stress [...] Read more.
Utilizing water resources rationally has become critical due to the expected increase in water scarcity. Cacti are capable of surviving with minimal water requirements and in poor soils. Despite being highly drought-resistant, cacti still faces limitations in realizing its full potential under drought-stress conditions. To this end, we investigated the interactive effect of humic substances (Hs) and arbuscular mycorrhizal fungi (AMF) on cactus plants under drought stress. In the study, a cactus pot experiment had three irrigation levels (W1: no irrigation, W2: 15% of field capacity, and W3: 30% of field capacity) and two biostimulants (Hs soil amendment and AMF inoculation), applied alone or combined. The findings show that the W1 and W2 regimes affected cactus performance. However, Hs and/or AMF significantly improved growth. Our results revealed that drought increased the generation of reactive oxygen species. However, Hs and/or AMF application improved nutrient uptake and increased anthocyanin content and free amino acids. Furthermore, the soil’s organic matter, phosphorus, nitrogen, and potassium contents were improved by the application of these biostimulants. Altogether, using Hs alone or in combination with AMF can be an effective and sustainable approach to enhance the tolerance of cactus plants to drought conditions, while also improving the soil quality. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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Review

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30 pages, 1200 KiB  
Review
Signals and Machinery for Mycorrhizae and Cereal and Oilseed Interactions towards Improved Tolerance to Environmental Stresses
by Aiman Slimani, Mohamed Ait-El-Mokhtar, Raja Ben-Laouane, Abderrahim Boutasknit, Mohamed Anli, El Faiza Abouraicha, Khalid Oufdou, Abdelilah Meddich and Marouane Baslam
Plants 2024, 13(6), 826; https://doi.org/10.3390/plants13060826 - 13 Mar 2024
Cited by 4 | Viewed by 2279
Abstract
In the quest for sustainable agricultural practices, there arises an urgent need for alternative solutions to mineral fertilizers and pesticides, aiming to diminish the environmental footprint of farming. Arbuscular mycorrhizal fungi (AMF) emerge as a promising avenue, bestowing plants with heightened nutrient absorption [...] Read more.
In the quest for sustainable agricultural practices, there arises an urgent need for alternative solutions to mineral fertilizers and pesticides, aiming to diminish the environmental footprint of farming. Arbuscular mycorrhizal fungi (AMF) emerge as a promising avenue, bestowing plants with heightened nutrient absorption capabilities while alleviating plant stress. Cereal and oilseed crops benefit from this association in a number of ways, including improved growth fitness, nutrient uptake, and tolerance to environmental stresses. Understanding the molecular mechanisms shaping the impact of AMF on these crops offers encouraging prospects for a more efficient use of these beneficial microorganisms to mitigate climate change-related stressors on plant functioning and productivity. An increased number of studies highlighted the boosting effect of AMF on grain and oil crops’ tolerance to (a)biotic stresses while limited ones investigated the molecular aspects orchestrating the different involved mechanisms. This review gives an extensive overview of the different strategies initiated by mycorrhizal cereal and oilseed plants to manage the deleterious effects of environmental stress. We also discuss the molecular drivers and mechanistic concepts to unveil the molecular machinery triggered by AMF to alleviate the tolerance of these crops to stressors. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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23 pages, 3686 KiB  
Review
Beneficial Microorganisms as Bioprotectants against Foliar Diseases of Cereals: A Review
by Ilham Dehbi, Oussama Achemrk, Rachid Ezzouggari, Moussa El Jarroudi, Fouad Mokrini, Ikram Legrifi, Zineb Belabess, Salah-Eddine Laasli, Hamid Mazouz and Rachid Lahlali
Plants 2023, 12(24), 4162; https://doi.org/10.3390/plants12244162 - 14 Dec 2023
Cited by 6 | Viewed by 3920
Abstract
Cereal production plays a major role in both animal and human diets throughout the world. However, cereal crops are vulnerable to attacks by fungal pathogens on the foliage, disrupting their biological cycle and photosynthesis, which can reduce yields by 15–20% or even 60%. [...] Read more.
Cereal production plays a major role in both animal and human diets throughout the world. However, cereal crops are vulnerable to attacks by fungal pathogens on the foliage, disrupting their biological cycle and photosynthesis, which can reduce yields by 15–20% or even 60%. Consumers are concerned about the excessive use of synthetic pesticides given their harmful effects on human health and the environment. As a result, the search for alternative solutions to protect crops has attracted the interest of scientists around the world. Among these solutions, biological control using beneficial microorganisms has taken on considerable importance, and several biological control agents (BCAs) have been studied, including species belonging to the genera Bacillus, Pseudomonas, Streptomyces, Trichoderma, Cladosporium, and Epicoccum, most of which include plants of growth-promoting rhizobacteria (PGPRs). Bacillus has proved to be a broad-spectrum agent against these leaf cereal diseases. Interaction between plant and beneficial agents occurs as direct mycoparasitism or hyperparasitism by a mixed pathway via the secretion of lytic enzymes, growth enzymes, and antibiotics, or by an indirect interaction involving competition for nutrients or space and the induction of host resistance (systemic acquired resistance (SAR) or induced systemic resistance (ISR) pathway). We mainly demonstrate the role of BCAs in the defense against fungal diseases of cereal leaves. To enhance a solution-based crop protection approach, it is also important to understand the mechanism of action of BCAs/molecules/plants. Research in the field of preventing cereal diseases is still ongoing. Full article
(This article belongs to the Special Issue Plant-Associated Microorganisms: Exploring Their Beneficial and Harmful Impacts on Plant Production in Response to a Changing Climate)
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