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Roles of Soil and Roots Biotic and Abiotic Conditions in...
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Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Environmental and Ecological Interactions of Fungi".

Deadline for manuscript submissions: closed (15 May 2023) | Viewed by 11385

Special Issue Editors

Dr. Ofir Degani

E-Mail Website
Guest Editor
1. Department of Plant Science, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel
2. Faculty of Sciences, Tel-Hai College, Tel-Hai, Israel
Interests: biological control; chemical control; crop protection; field studies; maize late wilt disease; plant disease; plant host–pathogen interactions; plant microflora
Special Issues, Collections and Topics in MDPI journals
Dr. Leire Molinero-Ruiz

E-Mail Website
Guest Editor
Institute for Sustainable Agriculture, CSIC, Alameda del Obispo s/n, 14004 Cordoba, Spain
Interests: agronomic management and disease development; biological control; disease presymptomatic detection; disease control; diversity of pathogen populations; field crops; genetic resistance; phytopathology; soil-borne pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The natural microorganisms inhabiting the plant rhizosphere (the roots’ surrounding habitat) may include diverse pathogens and various other non-pathogenic species. They live in complex communities in the soil and in the roots, and affect each other and the plants. They are also affected by abiotic sounding and plants’ population structure. Some members of these communities maintain a mutually beneficial relationship with the plants, and may confer protective effects against pathogens. These valuable species can also assist plants, providing better immunity against environmental stresses. Other species are pathogens inhabiting the same ecological niche and either cooperate or compete for the same plant resources. This Special Issue welcomes papers focusing on recent scientific progress and innovation in the intriguing relationships between soil and root microorganisms and their implications for plants’ immunity to biotic and abiotic stresses. Our ability to understand and intervene in this fabric of relationships is essential to increase plant health and crop yields.

Dr. Ofir Degani
Dr. Leire Molinero-Ruiz
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. Journal of Fungi 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 2600 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

  • abiotic stresses
  • biological control
  • crop protection
  • endophytes
  • plant health
  • soil microbiome
  • soil microflora
  • microbial interactions
  • microorganism communities
  • rhizosphere

Published Papers (7 papers)

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Research

16 pages, 3228 KiB  
Communication
Molecular Real-Time PCR Monitoring of Onion Fusarium Basal Rot Chemical Control
by Elhanan Dimant and Ofir Degani
J. Fungi 2023, 9(8), 809; https://doi.org/10.3390/jof9080809 - 30 Jul 2023
Cited by 4 | Viewed by 1197
Abstract
Fusarium basal rot disease (FBR) is a destructive threat to onion crops around the globe. It causes seedlings’ death, development disruption, and pre- and post-harvest bulb infection and rotting, with a concern for toxin infestation. It is an emerging disease in Israel, with [...] Read more.
Fusarium basal rot disease (FBR) is a destructive threat to onion crops around the globe. It causes seedlings’ death, development disruption, and pre- and post-harvest bulb infection and rotting, with a concern for toxin infestation. It is an emerging disease in Israel, with new reports from farms nationwide. Recently, we reported on a full-season pot experiment to protect two leading commercial cultivars against FBR chemically. Here, we present new real-time qPCR molecular tracking of the pathogens inside the host plant and compare the infection levels to a deep analysis of the impacts of this experiment’s treatments on plant growth and health indexes. The new findings reveal variations within each treatment’s effectiveness regarding sprout development and bulb ripening stages. For instance, in the yellow Orlando cv., high protection was obtained with Azoxystrobin + Tebuconazole (Az-Te) in sprouts against F. oxysporum f. sp. cepae and with Fludioxonil + Sedaxen in mature plants against Fusarium acutatum. Thus, combining these fungicides may protect plants throughout their lifecycle. Also, Prochloraz at low dose was highly efficient in the Orlando cv. Still, to shield red Noam cv. plants from both pathogens, increasing this fungicide concentration towards the season-ending should be preferred. The qPCR tracking showed that all chemical treatments tested could reduce infection from pathogens by 80–90%, even with compounds such as Az-Te that were less effective. This implies that the pesticide was effective but probably phytotoxic to the plants, and thus, lower dosages must be considered. The molecular-based analysis discloses the high infection ability of F. oxysporum f. sp. cepae compared to F. acutatum in both cultivars. It also indicates an antagonism between those species in the Orlando cv. and synergism in the Noam cv. The current work reveals weak and strong points in chemical FBR protection and offers new ways to improve its application. The qPCR-based method enables us to closely monitor the pathogenesis and efficacy of chemical-preventing treatments and optimize crop-protection protocols. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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19 pages, 4763 KiB  
Article
Trichoderma longibrachiatum Inoculation Improves Drought Resistance and Growth of Pinus massoniana Seedlings through Regulating Physiological Responses and Soil Microbial Community
by Cun Yu, Xian Jiang, Hongyun Xu and Guijie Ding
J. Fungi 2023, 9(7), 694; https://doi.org/10.3390/jof9070694 - 21 Jun 2023
Cited by 3 | Viewed by 1262
Abstract
Drought stress poses a serious threat to Pinus massoniana seedling growth in southern China. Trichoderma species, as beneficial microorganisms, have been widely used in agriculture to enhance plant growth and drought tolerance, but the interaction mechanisms remain unclear. To investigate the effect of [...] Read more.
Drought stress poses a serious threat to Pinus massoniana seedling growth in southern China. Trichoderma species, as beneficial microorganisms, have been widely used in agriculture to enhance plant growth and drought tolerance, but the interaction mechanisms remain unclear. To investigate the effect of drought-resistant Trichoderma longibrachiatum inoculation on P. massoniana growth under drought stress, the plant physiological indicators and rhizosphere microbiome diversity were measured to identify Trichoderma-activated mechanisms. Trichoderma longibrachiatum inoculation significantly promoted P. massoniana growth under drought treatment, and enhanced nitrogen, phosphorus, and potassium absorption compared with those of non-inoculated seedlings. Trichoderma longibrachiatum treatment alleviated the damage to cell membranes and needle tissue structure, and significantly increased antioxidant enzyme activities, osmotic substance contents, and photosynthesis in P. massoniana in response to drought stress. Soil nutrient contents, activities of sucrase, phosphatase, and urease as well as the relative abundances of the dominant genera Burkholderia, Rhodanobacter, and Trichoderma were elevated in the rhizosphere soil of P. massoniana inoculated with T. longibrachiatum under drought stress. A network analysis showed that certain crucial dominant taxa driven by T. longibrachiatum inoculation, including Penicillium, Trichoderma, Simplicillium, Saitozyma, Burkholderia, Bradyrhizobium, Sinomonas, and Mycobacterium, had more correlations with other microorganisms in the soil. Trichoderma longibrachiatum enhanced P. massoniana seedling growth under drought stress by regulating physiological responses and soil microbial community. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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13 pages, 4775 KiB  
Article
A Natural Moisture Gradient Affects Soil Fungal Communities on the South Shore of Hulun Lake, Inner Mongolia, China
by Xin Chen, Yujue Wang, Yao Wang, Yushu Zhang, Yuting Shen, Xiaojia He and Chunwang Xiao
J. Fungi 2023, 9(5), 549; https://doi.org/10.3390/jof9050549 - 10 May 2023
Cited by 3 | Viewed by 1254
Abstract
Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we [...] Read more.
Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we set up a natural moisture gradient that was subdivided into high (HW), medium (MW), and low (LW) water contents. Vegetation was investigated by quadrat method, and aboveground biomass was collected by the mowing method. Soil physicochemical properties were obtained by internal experiments. The composition of the soil fungal community was determined using high-throughput sequencing technology. The results showed significant differences in soil texture, nutrients, and fungal species diversity under the moisture gradients. Although there was significant clustering of fungal communities in different treatments, the fungal community composition was not significantly different. According to the phylogenetic tree, the Ascomycota and Basidiomycota were the most important branches. The fungal species diversity was smaller when SWC was higher, and in this environment (HW), the fungal-dominant species were significantly related to SWC and soil nutrients. At this time, soil clay formed a protective barrier for the survival of the dominant classes Sordariomycetes and Dothideomycetes and increased their relative abundance. In summary, the fungal community responded significantly to SWC on the southern shore of the Hulun Lake ecosystem in Inner Mongolia, China, and the fungal community composition of the HW group was stable and easier to survive. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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14 pages, 2512 KiB  
Article
Soil Structure and Ectomycorrhizal Root Colonization of Pecan Orchards in Northern Mexico
by Hilda Karina Sáenz-Hidalgo, Juan Luis Jacobo-Cuellar, Erick Zúñiga-Rodríguez, Graciela Dolores Avila-Quezada, Víctor Olalde-Portugal, Abeer Hashem and Elsayed Fathi Abd_Allah
J. Fungi 2023, 9(4), 440; https://doi.org/10.3390/jof9040440 - 04 Apr 2023
Viewed by 1431
Abstract
Pecan trees form a symbiotic relationship with ectomycorrhizal fungi (ECM), which actively provide nutrition to the roots and protect them from phytopathogens. Although these trees originated in the southern United States and northern Mexico, information on their root colonization by ECM is insufficient [...] Read more.
Pecan trees form a symbiotic relationship with ectomycorrhizal fungi (ECM), which actively provide nutrition to the roots and protect them from phytopathogens. Although these trees originated in the southern United States and northern Mexico, information on their root colonization by ECM is insufficient in terms of a representative number of samples, both in these regions and worldwide. Therefore, the objectives of this study were to determine the percentage of ectomycorrhizal colonization (ECM) of pecan trees of different ages in conventional and organic agronomic orchards and to identify ectomycorrhizal sporocarps, both morphologically and molecularly. The rhizospheric soil properties and the ECM percentages were analyzed for 14 Western variety pecan tree orchards between 3 and 48 years of age and grouped according to the agronomic management method. DNA extraction, internal transcribed spacer amplification, and sequencing were conducted on the fungal macroforms. The ECM colonization percentage fluctuated between 31.44 and 59.89%. Soils with low phosphorus content showed higher ECM colonization. The ECM concentrations were relatively homogeneous in relation to the ages of the trees, and organic matter content did not affect the percentage of ECM colonization. The highest ECM percentages occurred with the sandy clay crumb texture soil, with an average of 55% ECM, followed by sandy clay loam soils with 49.5%. The Pisolithus arenarius and Pisolithus tinctorius fungi were molecularly identified from sporocarps associated with pecan trees. This is the first study that reports Pisolithus arenarius as being associated with this tree. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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15 pages, 2291 KiB  
Article
Soil Microbial Community Responses to Different Management Strategies in Almond Crop
by Miguel Camacho-Sanchez, Juan F. Herencia, Francisco T. Arroyo and Nieves Capote
J. Fungi 2023, 9(1), 95; https://doi.org/10.3390/jof9010095 - 10 Jan 2023
Cited by 3 | Viewed by 2177
Abstract
A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were [...] Read more.
A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed and compared. Several biochemical and biological parameters were measured (soil pH, electrical conductivity, total nitrogen, organic material, total phosphorous, total DNA, and fungal and bacterial DNA copies). Massive parallel sequencing of regions from fungal ITS rRNA and bacterial 16 S genes was carried out to characterize their diversity in the soil. We report a larger abundance of bacteria and fungi in soils under OM, with a more balanced fungi:bacteria ratio, compared to bacteria-skewed proportions under CM and NM. The fungal phylum Ascomycota corresponded to around the 75% relative abundance in the soil, whereas for bacteria, the phyla Proteobacteria, Acidobacteriota and Bacteroidota integrated around 50% of their diversity. Alpha diversity was similar across practices, but beta diversity was highly clustered by soil management. Linear discriminant analysis effect size (LEfSE) identified bacterial and fungal taxa associated with each type of soil management. Analyses of fungal functional guilds revealed 3–4 times larger abundance of pathogenic fungi under CM compared to OM and NM treatments. Among them, the genus Cylindrocarpon was more abundant under CM, and Fusarium under OM. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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16 pages, 4505 KiB  
Article
Variation in Community Structure of the Root-Associated Fungi of Cinnamomum camphora Forest
by Deqiang Chen, Jiaoyan Zeng, Xiaohui Wan, Yonglong Wang, Siren Lan, Shuangquan Zou and Xin Qian
J. Fungi 2022, 8(11), 1210; https://doi.org/10.3390/jof8111210 - 15 Nov 2022
Cited by 2 | Viewed by 1730
Abstract
Plant-associated microbial communities play essential roles in the vegetative cycle, growth, and development of plants. Cinnamomum camphora is an evergreen tree species of the Lauraceae family with high ornamental, medicinal, and economic values. The present study analyzed the composition, diversity, and functions of [...] Read more.
Plant-associated microbial communities play essential roles in the vegetative cycle, growth, and development of plants. Cinnamomum camphora is an evergreen tree species of the Lauraceae family with high ornamental, medicinal, and economic values. The present study analyzed the composition, diversity, and functions of the fungal communities in the bulk soil, rhizosphere, and root endosphere of C. camphora at different slope positions by high-throughput sequencing. The results showed that the alpha diversity of the fungal communities in the bulk soil and rhizosphere of the downhill plots was relatively higher than those uphill. A further analysis revealed that Mucoromycota, the dominant fungus at the phylum level, was positively correlated with soil bulk density, total soil porosity, mass water content, alkaline-hydrolyzable nitrogen, maximum field capacity, and least field capacity. Meanwhile, the prevalent fungus at the class level, Mortierellomycetes, was positively correlated with total phosphorus and available and total potassium, but negatively with alkaline-hydrolyzable nitrogen. Finally, the assignment of the functional guilds to the fungal operational taxonomic units (OTUs) revealed that the OTUs highly enriched in the downhill samples compared with the uphill samples, which were saprotrophs. Thus, this study is the first to report differences in the fungal community among the different soil/root samples and between C. camphora forests grown at different slope positions. We also identified the factors favoring the root-associated beneficial fungi in these forests, providing theoretical guidance for managing C. camphora forests. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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18 pages, 1842 KiB  
Article
Effect of Previous Crops and Soil Physicochemical Properties on the Population of Verticillium dahliae in the Iberian Peninsula
by Antonio Santos-Rufo, Mario Pérez-Rodriguez, Juan Heis Serrano, Luis Fernando Roca Castillo and Francisco Javier López-Escudero
J. Fungi 2022, 8(10), 988; https://doi.org/10.3390/jof8100988 - 21 Sep 2022
Cited by 2 | Viewed by 1678
Abstract
The soil infestation of Verticillium dahliae has significant Verticillium wilt of olive (VWO) with epidemiological consequences which could limit the expansion of the crop. In this context, there is a misunderstood history of the crops and soil property interactions associated with inoculum density [...] Read more.
The soil infestation of Verticillium dahliae has significant Verticillium wilt of olive (VWO) with epidemiological consequences which could limit the expansion of the crop. In this context, there is a misunderstood history of the crops and soil property interactions associated with inoculum density (ID) increases in the soil. In this study, the effect of the combination of both factors was assessed on the ID of V. dahliae in the olive-growing areas of the Iberian Peninsula. Afterwards, the relationship of the ID to the mentioned factors was explored. The detection percentage and ID were higher in Spain than Portugal, even though the fields with a very favourable VWO history had a higher ID than that of the fields with a barely favourable history, regardless of the origin. The soil physicochemical parameters were able to detect the degree to which the ID was increased by the previous cropping history. By using a decision tree classifier, the percentage of clay was the best indicator for the V. dahliae ID regardless of the history of the crops. However, active limestone and the cation exchange capacity were only suitable ID indicators when <2 or 4 host crops of the pathogen were established in the field for five years, respectively. The V. dahliae ID was accurately predicted in this study for the orchard choices in the establishment of the olive. Full article
(This article belongs to the Special Issue Roles of Soil and Roots Biotic and Abiotic Conditions in Fungal-Plant Interactions and Plant Performance, 2nd Edition)
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