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Agriculture
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Occurrence and Functions of Endophytic Fungi in Crop Species
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Occurrence and Functions of Endophytic Fungi in Crop Species

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Protection, Diseases, Pests and Weeds".

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 58983

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Dr. Rosario Nicoletti

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Guest Editor
1. Council for Agricultural Research and Economics, Research Center for Olive, Citrus and Fruit Crops, 81100 Caserta, Italy
2. Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
Interests: endophytes; plant pathogens; entomopathogens; biocontrol; bioactive fungal products; marine fungi
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the past few decades, awareness of the basic role that endophytic fungi play in shaping the fitness of both wild and crop plants has increased significantly. The number of papers on the subject is so large that it is becoming difficult to have a complete overview of the state-of-the-art with reference to specific crops. In the absence of readily available documents providing circumstantial information on the endophytic assemblage of plants, the isolation of a certain fungal species may appear to be occasional or trivial; hence, many important findings are at risk of going unnoticed. This Special Issue aims to present a collection of papers dealing with the occurrence and functions of endophytic fungi in crop species. It may represent a useful tool for stakeholders in this particular research field, with a view to stimulating a more thorough consideration of the opportunities deriving from their discoveries.

Dr. Rosario Nicoletti
Guest Editor

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Keywords

  • endophytic fungi
  • defensive mutualism
  • plant growth promotion
  • biocontrol agents
  • enzymes
  • secondary metabolites
  • bioactive products

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review

2 pages, 161 KiB  
Editorial
Occurrence and Functions of Endophytic Fungi in Crop Species
by Rosario Nicoletti
Agriculture 2021, 11(1), 18; https://doi.org/10.3390/agriculture11010018 - 30 Dec 2020
Cited by 2 | Viewed by 1948
Abstract
After having been initially boosted by the general aim to exploit biodiversity in natural environments, research on endophytic microorganisms has recently started considering their occurrence in crop species [...] Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)

Research

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15 pages, 1154 KiB  
Article
Pathogenic and Non-Pathogenic Fungal Communities in Wheat Grain as Influenced by Recycled Phosphorus Fertilizers: A Case Study
by Magdalena Jastrzębska, Urszula Wachowska and Marta K. Kostrzewska
Agriculture 2020, 10(6), 239; https://doi.org/10.3390/agriculture10060239 - 19 Jun 2020
Cited by 8 | Viewed by 3447
Abstract
Waste-based fertilizers provide an alternative to fertilizers made from non-renewable phosphate rock. Fungal communities colonizing the grain of spring wheat fertilized with preparation from sewage sludge ash and dried animal blood (Rec) and the same fertilizer activated by Bacillus megaterium (Bio) were evaluated [...] Read more.
Waste-based fertilizers provide an alternative to fertilizers made from non-renewable phosphate rock. Fungal communities colonizing the grain of spring wheat fertilized with preparation from sewage sludge ash and dried animal blood (Rec) and the same fertilizer activated by Bacillus megaterium (Bio) were evaluated against those resulting from superphosphate (SP) and no phosphorus (control, C0) treatments. The Illumina MiSeq sequencing system helped to group fungal communities into three clades. Clade 1 (communities from C0, Bio 60 and 80, Rec 80 and SP 40 kg P2O5 ha−1 treatments) was characterized by a high prevalence of Alternaria infectoria, Monographella nivalis and Gibberella tricincta pathogens. Clade 2 (Bio 40 kg, Rec 40 and 60 kg, and SP 60 kg P2O5 ha−1) was characterized by the lowest amount of the identified pathogens. Commercial SP applied at 80 kg P2O5 ha−1 (clade 3) induced the most pronounced changes in the fungal taxa colonizing wheat grain relative to non-fertilized plants. The above was attributed mainly to the lower amount of A. infectoria and higher counts of species of the family Nectriaceae, mostly epiphytic pathogens Fusarium culmorum and Fusarium poae. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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13 pages, 1724 KiB  
Article
The Shifting Mycotoxin Profiles of Endophytic Fusarium Strains: A Case Study
by Gelsomina Manganiello, Roberta Marra, Alessia Staropoli, Nadia Lombardi, Francesco Vinale and Rosario Nicoletti
Agriculture 2019, 9(7), 143; https://doi.org/10.3390/agriculture9070143 - 5 Jul 2019
Cited by 12 | Viewed by 4223
Abstract
Fusarium species are known to establish manifold interactions with wild and crop plants ranging from pathogenicity to endophytism. One of the key factors involved in the regulation of such relationships is represented by the production of secondary metabolites. These include several mycotoxins, which [...] Read more.
Fusarium species are known to establish manifold interactions with wild and crop plants ranging from pathogenicity to endophytism. One of the key factors involved in the regulation of such relationships is represented by the production of secondary metabolites. These include several mycotoxins, which can accumulate in foodstuffs causing severe health problems to humans and animals. In the present study, an endophytic isolate (A1021B), preliminarily ascribed to the Fusarium incarnatum-equiseti species complex (FIESC), was subjected to biochemical and molecular characterization. The metabolomic analysis of axenic cultures of A1021B detected up to 206 compounds, whose production was significantly affected by the medium composition. Among the most representative products, fusaric acid (FA), its derivatives fusarinol and 9,10-dehydro-FA, culmorin and bikaverin were detected. These results were in contrast with previous assessments reporting FIESC members as trichothecene rather than FA producers. However, molecular analysis provided a conclusive indication that A1021B actually belongs to the species Fusarium babinda. These findings highlight the importance of phylogenetic analyses of Fusarium species to avoid misleading identifications, and the opportunity to extend databases with the outcome of metabolomic investigations of strains from natural contexts. The possible contribution of endophytic strains in the differentiation of lineages with an uneven mycotoxin assortment is discussed in view of its ensuing impact on crop productions. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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Review

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31 pages, 509 KiB  
Review
A Survey of Endophytic Fungi Associated with High-Risk Plants Imported for Ornamental Purposes
by Laura Gioia, Giada d’Errico, Martina Sinno, Marta Ranesi, Sheridan Lois Woo and Francesco Vinale
Agriculture 2020, 10(12), 643; https://doi.org/10.3390/agriculture10120643 - 17 Dec 2020
Cited by 11 | Viewed by 4806
Abstract
An extensive literature search was performed to review current knowledge about endophytic fungi isolated from plants included in the European Food Safety Authority (EFSA) dossier. The selected genera of plants were Acacia, Albizia, Bauhinia, Berberis, Caesalpinia, Cassia, [...] Read more.
An extensive literature search was performed to review current knowledge about endophytic fungi isolated from plants included in the European Food Safety Authority (EFSA) dossier. The selected genera of plants were Acacia, Albizia, Bauhinia, Berberis, Caesalpinia, Cassia, Cornus, Hamamelis, Jasminus, Ligustrum, Lonicera, Nerium, and Robinia. A total of 120 fungal genera have been found in plant tissues originating from several countries. Bauhinia and Cornus showed the highest diversity of endophytes, whereas Hamamelis, Jasminus, Lonicera, and Robinia exhibited the lowest. The most frequently detected fungi were Aspergillus, Colletotrichum, Fusarium, Penicillium, Phyllosticta, and Alternaria. Plants and plant products represent an inoculum source of several mutualistic or pathogenic fungi, including quarantine pathogens. Thus, the movement of living organisms across continents during international trade represents a serious threat to ecosystems and biosecurity measures should be taken at a global level. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
20 pages, 375 KiB  
Review
Endophytic Fungi of Tomato and Their Potential Applications for Crop Improvement
by Martina Sinno, Marta Ranesi, Laura Gioia, Giada d’Errico and Sheridan Lois Woo
Agriculture 2020, 10(12), 587; https://doi.org/10.3390/agriculture10120587 - 27 Nov 2020
Cited by 31 | Viewed by 6815
Abstract
Endophytic fungi (EF) are increasingly gaining attention due to the numerous benefits many species can offer to the plant host, while reducing the application of chemicals in agriculture, thus providing advantages to human health and the environment. The growing demand for safer agrifood [...] Read more.
Endophytic fungi (EF) are increasingly gaining attention due to the numerous benefits many species can offer to the plant host, while reducing the application of chemicals in agriculture, thus providing advantages to human health and the environment. The growing demand for safer agrifood products and the challenge of increasing food production with a lower use of pesticides and fertilizers stimulates investigations on the use and understanding of EF. Other than direct consequences on the plant damaging agents, these microorganisms can also deliver bioactive metabolites with antimicrobial, insecticidal, or plant biostimulant activities. In tomato, EF are artificially introduced as biological control agents or naturally acquired from the surrounding environment. To date, the applications of EF to tomato has been generally limited to a restricted group of beneficial fungi. In this work, considerations are made to the effects and methods of introduction and detection of EF on tomato plants, consolidating in a review the main findings that regard pest and pathogen control, and improvement of plant performance. Moreover, a survey was undertaken of the naturally occurring constitutive endophytes present in this horticultural crop, with the aim to evaluate the potential role in the selection of new beneficial EF useful for tomato crop improvement. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
16 pages, 2562 KiB  
Review
Bioactive Products from Endophytic Fungi of Sages (Salvia spp.)
by Beata Zimowska, Monika Bielecka, Barbara Abramczyk and Rosario Nicoletti
Agriculture 2020, 10(11), 543; https://doi.org/10.3390/agriculture10110543 - 12 Nov 2020
Cited by 21 | Viewed by 4078
Abstract
In the aim of implementing new technologies, sustainable solutions and disruptive innovation to sustain biodiversity and reduce environmental pollution, there is a growing interest by researchers all over the world in bioprospecting endophytic microbial communities as an alternative source of bioactive compounds to [...] Read more.
In the aim of implementing new technologies, sustainable solutions and disruptive innovation to sustain biodiversity and reduce environmental pollution, there is a growing interest by researchers all over the world in bioprospecting endophytic microbial communities as an alternative source of bioactive compounds to be used for industrial applications. Medicinal plants represent a considerable source of endophytic fungi of outstanding importance, which highlights the opportunity of identifying and screening endophytes associated with this unique group of plants, widespread in diverse locations and biotopes, in view of assessing their biotechnological potential. As the first contribution of a series of papers dedicated to the Lamiaceae, this article reviews the occurrence and properties of endophytic fungi associated with sages (Salvia spp.). Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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16 pages, 2736 KiB  
Review
Biodiversity, Ecology, and Secondary Metabolites Production of Endophytic Fungi Associated with Amaryllidaceae Crops
by Gianluca Caruso, Nadezhda Golubkina, Alessio Tallarita, Magdi T. Abdelhamid and Agnieszka Sekara
Agriculture 2020, 10(11), 533; https://doi.org/10.3390/agriculture10110533 - 6 Nov 2020
Cited by 13 | Viewed by 4617
Abstract
Amaryllidaceae family comprises many crops of high market potential for the food and pharmaceutical industries. Nowadays, the utilization of plants as a source of bioactive compounds requires the plant/endophytic microbiome interactions, which affect all aspects of crop’s quantity and quality. This review highlights [...] Read more.
Amaryllidaceae family comprises many crops of high market potential for the food and pharmaceutical industries. Nowadays, the utilization of plants as a source of bioactive compounds requires the plant/endophytic microbiome interactions, which affect all aspects of crop’s quantity and quality. This review highlights the taxonomy, ecology, and bioactive chemicals synthesized by endophytic fungi isolated from plants of the Amaryllidaceae family with a focus on the detection of pharmaceutically valuable plant and fungi constituents. The fungal microbiome of Amaryllidaceae is species- and tissue-dependent, although dominating endophytes are ubiquitous and isolated worldwide from taxonomically different hosts. Root sections showed higher colonization as compared to bulbs and leaves through the adaptation of endophytic fungi to particular morphological and physiological conditions of the plant tissues. Fungal endophytes associated with Amaryllidaceae plants are a natural source of ecofriendly bioagents of unique activities, with special regard to those associated with Amarylloidae subfamily. The latter may be exploited as stimuli of alkaloids production in host tissues or can be used as a source of these compounds through in vitro synthesis. Endophytes also showed antagonistic potential against fungal, bacterial, and viral plant diseases and may find an application as alternatives to synthetic pesticides. Although Amaryllidaceae crops are cultivated worldwide and have great economic importance, the knowledge on their endophytic fungal communities and their biochemical potential has been neglected so far. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
22 pages, 1185 KiB  
Review
The Thin Line between Pathogenicity and Endophytism: The Case of Lasiodiplodia theobromae
by Maria Michela Salvatore, Anna Andolfi and Rosario Nicoletti
Agriculture 2020, 10(10), 488; https://doi.org/10.3390/agriculture10100488 - 21 Oct 2020
Cited by 45 | Viewed by 7216
Abstract
Many fungi reported for endophytic occurrence are better known as plant pathogens on different crops, raising questions about their actual relationships with the hosts and other plants in the biocoenosis and about the factors underlying the lifestyle shift. This paper offers an overview [...] Read more.
Many fungi reported for endophytic occurrence are better known as plant pathogens on different crops, raising questions about their actual relationships with the hosts and other plants in the biocoenosis and about the factors underlying the lifestyle shift. This paper offers an overview of the endophytic occurrence of Lasiodiplodia theobromae (Dothideomycetes, Botryosphaeriaceae), a species known to be able to colonize many plants as both an endophyte and a pathogen. Prevalently spread in tropical and subtropical areas, there are concerns that it may propagate to the temperate region following global warming and the increasing trade of plant materials. The state of the art concerning the biochemical properties of endophytic strains of this species is also examined with reference to a range of biotechnological applications. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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23 pages, 3062 KiB  
Review
Linking Endophytic Fungi to Medicinal Plants Therapeutic Activity. A Case Study on Asteraceae
by Gianluca Caruso, Magdi T. Abdelhamid, Andrzej Kalisz and Agnieszka Sekara
Agriculture 2020, 10(7), 286; https://doi.org/10.3390/agriculture10070286 - 10 Jul 2020
Cited by 51 | Viewed by 8910
Abstract
Endophytes are isolated from every plant species investigated to date, so the metabolome coevolution has been affecting the plants’ (microbiota) ethnobotanic, especially therapeutic, usage. Asteraceae fulfill the rationale for plant selection to isolate endophytes since most of the species of this family have [...] Read more.
Endophytes are isolated from every plant species investigated to date, so the metabolome coevolution has been affecting the plants’ (microbiota) ethnobotanic, especially therapeutic, usage. Asteraceae fulfill the rationale for plant selection to isolate endophytes since most of the species of this family have a long tradition of healing usage, confirmed by modern pharmacognosy. The present review compiles recent references on the endophyte−Asteraceae spp. interactions, targeting the secondary metabolites profile as created by both members of this biological system. Endophyte fungi associated with Asteraceae have been collected globally, however, dominant taxa that produce bioactive compounds were specific for the plant populations of different geographic origins. Endophytic fungi richness within the host plant and the biological activity were positively associated. Moreover, the pharmacological action was linked to the plant part, so differential forms of biological interactions in roots, stem, leaves, inflorescences were developed between endophytic fungi and host plants. The comparative analysis of the Asteraceae host and/or fungal endophyte therapeutic activity showed similarities that need a future explanation on the metabolome level. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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16 pages, 814 KiB  
Review
Endophytism of Lecanicillium and Akanthomyces
by Rosario Nicoletti and Andrea Becchimanzi
Agriculture 2020, 10(6), 205; https://doi.org/10.3390/agriculture10060205 - 6 Jun 2020
Cited by 36 | Viewed by 5287
Abstract
The rise of the holobiont concept confers a prominent importance to the endophytic associates of plants, particularly to species known to be able to exert a mutualistic role as defensive or growth-promoting agents. The finding that many entomopathogenic fungi are harbored within plant [...] Read more.
The rise of the holobiont concept confers a prominent importance to the endophytic associates of plants, particularly to species known to be able to exert a mutualistic role as defensive or growth-promoting agents. The finding that many entomopathogenic fungi are harbored within plant tissues and possess bioactive properties going beyond a merely anti-insectan effect has recently prompted a widespread investigational activity concerning their occurrence and functions in crops, in the aim of an applicative exploitation conforming to the paradigm of sustainable agriculture. The related aspects particularly referring to species of Lecanicillium and Akanthomyces (Sordariomycetes, Cordycipitaceae) are revised in this paper, also in light of recent and ongoing taxonomic reassessments. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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13 pages, 319 KiB  
Review
Endophytic Fungi of Citrus Plants
by Rosario Nicoletti
Agriculture 2019, 9(12), 247; https://doi.org/10.3390/agriculture9120247 - 21 Nov 2019
Cited by 20 | Viewed by 6469
Abstract
Besides a diffuse research activity on drug discovery and biodiversity carried out in natural contexts, more recently, investigations concerning endophytic fungi have started considering their occurrence in crops based on the major role that these microorganisms have been recognized to play in plant [...] Read more.
Besides a diffuse research activity on drug discovery and biodiversity carried out in natural contexts, more recently, investigations concerning endophytic fungi have started considering their occurrence in crops based on the major role that these microorganisms have been recognized to play in plant protection and growth promotion. Fruit growing is particularly involved in this new wave, by reason that the pluriannual crop cycle likely implies a higher impact of these symbiotic interactions. Aspects concerning occurrence and effects of endophytic fungi associated with citrus species are revised in the present paper. Full article
(This article belongs to the Special Issue Occurrence and Functions of Endophytic Fungi in Crop Species)
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