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Microorganisms
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Insights into Plant–Soil–Microbe Interactions
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Insights into Plant–Soil–Microbe Interactions

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

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 5527

Special Issue Editor

Prof. Dr. Wajid Zaman

E-Mail Website
Guest Editor
Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
Interests: sustainable catalysis; green chemistry; renewable energy; biochar; nanotechnology; biocatalysis; CO2 conversion; biomass valorization; circular economy; machine learning; medicinal plants; climate change mitigation; salinity stress; antioxidants; CRISPR/Cas genome editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Understanding the intricate interactions between plants, soil, and microbes is essential for advancing agricultural productivity, ecosystem sustainability, and environmental health. The dynamic relationships within the plant–soil–microbe nexus influence nutrient cycling, plant health, soil structure, and ecosystem resilience. Microbial diversity and function in different soil types are crucial for nutrient cycling and the decomposition of organic matter. Key areas of study include plant–microorganism relationships such as mycorrhizal and rhizobial symbioses, mechanisms of plant growth promotion by beneficial microbes, and plant immune responses to microbial pathogens and mutualists.

Soil health and microbial ecology focus on how soil physicochemical properties impact microbial communities and how microbiome engineering can improve soil health. Microbial soil health and fertility indicators are particularly important for assessing soil quality. Biotechnological applications involve developing and applying microbial inoculants in agriculture, biocontrol agents for sustainable pest and disease management, and microbial remediation of contaminated soils.

The impacts of climate change and environmental stress on soil microbes are also critical areas of research. Studies on microbial responses to climate change factors, the role of microbes in enhancing plant tolerance to abiotic stresses such as drought and salinity, and how microbial activity influences soil carbon sequestration and greenhouse gas emissions are vital for understanding ecosystem resilience.

Integrating these insights can lead to innovative approaches in agriculture, environmental management, and biotechnology, ultimately contributing to sustainable practices and enhanced ecosystem services.

Prof. Dr. Wajid Zaman
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–microbe interactions
  • soil microbiomes
  • microbial diversity
  • soil health
  • nutrient cycling
  • mycorrhizae
  • Rhizobia
  • biocontrol
  • microbial inoculants
  • climate change effects
  • abiotic stress tolerance
  • carbon sequestration
  • ecosystem sustainability
  • soil biodiversity
  • rhizosphere dynamics
  • microbial community structure
  • soil organic matter
  • microbial symbiosis
  • soil fertility
  • environmental microbiology
  • sustainable agriculture
  • soil enzymes
  • soil carbon dynamics
  • microbial ecology
  • phytobiomes
  • microbial metabolites

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Published Papers (5 papers)

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Research

19 pages, 3147 KiB  
Article
Deciphering the Effects of Phosphate Fertiliser on Rhizospheric Bacterial Community Structure and Potato Common Scab
by Shanshan Chen, Jingjing Cao, Pan Zhao, Zhiqin Wang, Xiu Wang, Genhong Liu and Naiqin Zhong
Microorganisms 2024, 12(11), 2322; https://doi.org/10.3390/microorganisms12112322 - 15 Nov 2024
Viewed by 611
Abstract
The prolonged practice of continuous potato cropping, coupled with inadequate field management, disrupts the soil bacterial community equilibrium. Such disturbances compromise the resilience of the soil ecosystem, predisposing it to an increased incidence of potato diseases. However, the effects of the phosphorus fertiliser [...] Read more.
The prolonged practice of continuous potato cropping, coupled with inadequate field management, disrupts the soil bacterial community equilibrium. Such disturbances compromise the resilience of the soil ecosystem, predisposing it to an increased incidence of potato diseases. However, the effects of the phosphorus fertiliser application rate on the rhizosphere soil bacterial community composition of potatoes and the occurrence of potato common scab (CS) have not been adequately studied. Here, diseased field soils from Dingxi and Huidong Counties were collected for potting tests, and field tests were conducted in Huidong County for validation. An examination of the relationship between the bacterial community composition in the potato rhizosphere soil and potato CS under different phosphate fertiliser treatments was conducted using 16S rRNA high-throughput sequencing. The results show that a lower phosphorus fertiliser application rate was more conducive to maintaining soil bacterial community diversity under different phosphorus fertiliser treatments in different habitats. In addition, the relative abundance of the txtA gene increased significantly (p < 0.05) with the increase in the phosphate fertiliser application rate. Field trials conducted in Huidong revealed that treatments F1, F2, and F3 had respective CS incidence rates of 28.33%, 46.67%, and 59.44%, while their corresponding disease severity indices were 7.67, 17.33, and 29.44. Further analysis revealed that the relative abundance of antagonistic genera of pathogenic S. scabies decreased significantly (p < 0.05) with increases in the phosphorus fertiliser application rate. In summary, the correlation between potato CS and changes in the bacterial community of rhizosphere soil was used to determine the optimal phosphorus application rate during potato production, which can provide a scientific basis for the management of phosphorus fertiliser in potato farmland. Full article
(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)
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24 pages, 3192 KiB  
Article
Cenchrus spinifex Invasion Alters Soil Nitrogen Dynamics and Competition
by Meng Meng, Baihui Ren, Jianxin Yu, Daiyan Li, Haoyan Li, Jiahuan Li, Jiyun Yang, Long Bai and Yulong Feng
Microorganisms 2024, 12(11), 2120; https://doi.org/10.3390/microorganisms12112120 - 23 Oct 2024
Viewed by 903
Abstract
Invasive plants often alter biological soil conditions to increase their own competitiveness. Through indoor simulated nitrogen deposition culture experiments, we investigated the differences in growth indicators and nutrient content levels between the invasive plant Cenchrus spinifex Cav. and the native symbiotic plant Agropyron [...] Read more.
Invasive plants often alter biological soil conditions to increase their own competitiveness. Through indoor simulated nitrogen deposition culture experiments, we investigated the differences in growth indicators and nutrient content levels between the invasive plant Cenchrus spinifex Cav. and the native symbiotic plant Agropyron cristatum (L.) Gaertn. under diverse nitrogen application modes and planting-competition ratios. Furthermore, we examined the alterations in key microbial communities involved in soil nitrogen cycling of C. spinifex. The results indicated that the invasion of C. spinifex could inhibit the growth of native plants, and in fact altered the accumulation and transformation processes related to soil nitrogen, resulting in reduced rates of soil nitrogen transformation. The overarching aim of this research was to construct a theoretical foundation for the scientific comprehension of the invasion mechanisms of C. spinifex, in order to better prevent the further spread of this invasive plant and mitigate its pernicious impact on the current environment. Full article
(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)
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20 pages, 4758 KiB  
Article
Soil Microorganism Interactions under Biological Fumigations Compared with Chemical Fumigation
by Hui Li, Huali Man, Jia Han, Xixia Jia, Li Wang, Hongyu Yang and Guiying Shi
Microorganisms 2024, 12(10), 2044; https://doi.org/10.3390/microorganisms12102044 - 10 Oct 2024
Viewed by 955
Abstract
Background: Biological fumigation, a potential alternative to chemical fumigation, shows a wide range of prospective applications. In this study, we carried out biological fumigation experiments to evaluate its effect on alleviating consecutive cropping problems (CRPs) when compared with chemical fumigation. Methods: We designed [...] Read more.
Background: Biological fumigation, a potential alternative to chemical fumigation, shows a wide range of prospective applications. In this study, we carried out biological fumigation experiments to evaluate its effect on alleviating consecutive cropping problems (CRPs) when compared with chemical fumigation. Methods: We designed five treatments, namely, CR (no treatment), LN (chemical fumigation with lime nitrogen), Ta (fumigation with marigold), Ra (fumigation with radish), and Br (fumigation with mustard), for soils for replanting eggplant and measured the crop’s growth status, soil bacterial and fungal communities, and soil physicochemical properties. Results: The results showed that the Br and Ra treatments formed similar microbial communities, while the Ta treatment formed unique microbial communities. The genera Olpidiomycota and Rozellomycota could be used as indicator species for the transformation process of soil microbial communities after the Br and Ta treatments, respectively. When compared with the CR and LN treatments, the soil’s physicochemical properties were optimized under the Br treatment, and the soil organic matter content increased by 64.26% and 79.22%, respectively. Moreover, under the Br treatment, the soil’s biological properties enhanced the bacterial and fungal alpha diversity, and the saprotrophic fungi increased with the depletion of pathotrophic fungi, while some specific probiotic microorganisms (such as Olpidiomycota, Microascales, Bacillus, etc.) were significantly enriched. In contrast, under the Ta treatment, soil nutrient levels decreased and the soil’s biological indices deteriorated, whereas the bacterial diversity decreased and the pathogenic fungi increased. Conclusions: Among these three biological fumigation methods, the Br pre-treatment was the best way to alleviate the crop’s CRPs and may be a good substitute for chemical fumigation in some situations. However, the Ta treatment also had some risks, such as the loss of land quality and reduced productivity. Full article
(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)
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20 pages, 703 KiB  
Article
Increasing Ages of Inga punctata Tree Soils Facilitate Greater Fungal Community Abundance and Successional Development, and Efficiency of Microbial Organic Carbon Utilization
by William D. Eaton and Debra A. Hamilton
Microorganisms 2024, 12(10), 1996; https://doi.org/10.3390/microorganisms12101996 - 30 Sep 2024
Viewed by 1015
Abstract
Leguminous Inga trees are thought to enhance soil carbon (C) accumulation following reforestation, through mostly unknown mechanisms. This study amplified soil DNA using the ITS1F and ITS4 primers for PCR and Illumina MiSeq methods to identify fungal taxa, and traditional C analysis methods [...] Read more.
Leguminous Inga trees are thought to enhance soil carbon (C) accumulation following reforestation, through mostly unknown mechanisms. This study amplified soil DNA using the ITS1F and ITS4 primers for PCR and Illumina MiSeq methods to identify fungal taxa, and traditional C analysis methods to evaluate how planted 4-, 8-, and 11-year-old Inga punctata trees affected soil fungal community compositions and C utilization patterns compared to old-growth I. punctata trees and an adjacent unplanted pasture within the same reforestation zone in Monteverde, Costa Rica. Along the tree age gradient, the planted I. punctata trees enhanced the tree soil C capture capacity, as indicated by increased levels of soil biomass C, Respiration, and efficiency of organic C use (with lower qCO2 values), and development of increasingly more abundant, stable, and successionally developed fungal communities, including those associated with the decomposition of complex organic C compounds. The level and strength of differences coincided with differences in the time of separation between the pasture and tree age or between the different tree ages. Fungal taxa were also identified as potential indicators of the early and late stages of soil recovery. Thus, planting I. punctata should be part of future reforestation strategies used in this region of the Monteverde Cloud Forest in Costa Rica. Full article
(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)
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18 pages, 5402 KiB  
Article
Enhancing Growth in Vigna radiata through the Inhibition of Charcoal Rot Disease: A Strategic Approach Using Plant Growth-Promoting Rhizobacteria
by Imran Khan, Sahar Ghulam Mohyuddin, Sohail, Shah Zaman, Muhammad Qadir, Juxian Guo and Guihua Li
Microorganisms 2024, 12(9), 1852; https://doi.org/10.3390/microorganisms12091852 - 6 Sep 2024
Viewed by 1231
Abstract
Macrophomina phaseolina is a vital seed and soil-borne phytopathogen responsible for substantial crop yield losses. Although various methods exist for managing soil-borne pathogens, such as agronomic practices, chemical treatments, and varietal tolerance, biological control utilizing plant growth-promoting rhizobacteria (PGPR) or their secondary metabolites [...] Read more.
Macrophomina phaseolina is a vital seed and soil-borne phytopathogen responsible for substantial crop yield losses. Although various methods exist for managing soil-borne pathogens, such as agronomic practices, chemical treatments, and varietal tolerance, biological control utilizing plant growth-promoting rhizobacteria (PGPR) or their secondary metabolites presents promising avenues. In this study, a screening of 150 isolates from the rhizosphere of Vigna radiata L. was conducted to identify strains capable of promoting host growth and controlling charcoal rot disease. Among the tested isolates, only 15 strains demonstrated the ability to produce plant growth-related metabolites, including indole acetic acid, hydrogen cyanide, ammonia, and lytic enzymes, and solubilize inorganic phosphate. Subsequently, these potent strains were evaluated for their antifungal activity against Macrophomina phaseolina in vitro. Three strains, namely MRP-7 (58% growth inhibition), MRP-12 (55% growth inhibition), and MRP-8 (44% growth inhibition), exhibited the highest percent growth inhibition (PGI.). Furthermore, a pot experiment demonstrated that the selected strains acted as effective growth promoters and ROS (reactive oxygen species) scavengers, and served as potential biocontrol agents, significantly reducing the incidence of charcoal rot disease and improving various agronomic attributes of the host plant. These findings highlight the potential of these strains to be utilized as biofertilizers and biocontrol agents for sustainable agricultural practices. Full article
(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)
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