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Microorganisms
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Microbial Endophytes: Functional Biology and Applications
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Microbial Endophytes: Functional Biology and Applications

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 31158

Special Issue Editors

Prof. Dr. Gustavo Santoyo

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Guest Editor
Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia, Mexico
Interests: PGPR; plant–microbe interactions; biocontrol; plant growth promotion
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. James White

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Guest Editor
Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
Interests: plant microbes; endophytes; rhizophagy cycle
Special Issues, Collections and Topics in MDPI journals
Dr. Ajay Kumar

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Guest Editor
Agriculture Resaerch Organization, Volcani Centre, Rishon 7505101, Israel
Interests: microbial biotechnology; bacterial endophytes; plant microbe interactions
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Virendra Mishra

E-Mail Website
Guest Editor
Institute of Environment and Sustainale Development, Banaras Hindu University, Varanasi 221005, India
Interests: rhizome endophytes; wastewater treatment; rhizospheric remediation

Special Issue Information

Dear Colleagues,

The need for sustainable agricultural and horticultural practices and the changing agro-climatic conditions demand intensive research on endophytic microorganisms. Endophytes have been demonstrated to have significant applications in the management of the challenges associated with an increasing population, polluted lands, and other harsh environmental conditions. Currently, agronomic or horticulture practices are largely dependent on heavy input from chemical fertilizers, pesticides, and fungicides. However, these are known to cause irreparable damage to the environment and to soil, as well as to human beings. Considering these severe challenges associated with agricultural productivity, sustainable horticultural practices, and the management of environmental remediation, the microorganisms reserved within plants as endophytes may represent the perfect solution as they can help to manage these issues naturally. The endophytic microbiome holds much responsibility when it comes to maintaining plant growth under various biotic and abiotic stress conditions due to its remarkable mechanisms for nutrient mobilization, phytohormone modulation, plant protection during pre- or postharvest storage conditions via synthesis of bioactive compounds, antibiotics, production of volatiles, etc. Hence, these natural resources may potentially help to achieve a sustainable agricultural or horticultural production. In this context, the current Special Issue has been launched to describe recent progress on endophytic research and emerging functional applications. Some of the issue’s focal points include but are not limited to the following:

  1. Deciphering endophytic microbial strains in abiotic stress management;
  2. Endophytic microbiome in postharvest disease management: applications and limitations in commercial up-scale production;
  3. Endophytic microbiome diversity and functional attributes;
  4. Multifaceted interactions between endophytes and plants: prospects in sustainable agriculture;
  5. Endophytic microbiome aspect in environmental contamination management.

Prof. Dr. Gustavo Santoyo
Prof. Dr. James White
Dr. Ajay Kumar
Prof. Dr. Virendra Mishra
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. 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

  • endophytic diversity
  • endophytic microbiome
  • abiotic stress management
  • biocontrol mechanism
  • postharvest management

Published Papers (9 papers)

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Editorial

Jump to: Research, Review

3 pages, 197 KiB  
Editorial
Special Issue “Microbial Endophytes: Functional Biology and Applications”: Editorial
by Ajay Kumar, Gustavo Santoyo, James F. White and Virendra Kumar Mishra
Microorganisms 2023, 11(4), 918; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11040918 - 01 Apr 2023
Cited by 1 | Viewed by 897
Abstract
Plants harbour various microbial communities, including bacteria, fungi, actinomycetes, and nematodes, inside or outside their tissues [...] Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)

Research

Jump to: Editorial, Review

10 pages, 542 KiB  
Article
Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds
by Giulia Semenzato, Tania Alonso-Vásquez, Sara Del Duca, Alberto Vassallo, Christopher Riccardi, Marco Zaccaroni, Nadia Mucci, Anna Padula, Giovanni Emiliani, Antonio Palumbo Piccionello, Anna Maria Puglia and Renato Fani
Microorganisms 2022, 10(5), 919; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050919 - 27 Apr 2022
Cited by 14 | Viewed by 2524
Abstract
Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the [...] Read more.
Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes’ adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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14 pages, 1744 KiB  
Article
Isolation and Characterization of Endophytes Bacterial Strains of Momordica charantia L. and Their Possible Approach in Stress Management
by Ritu Singh, Kapil Deo Pandey, Monika Singh, Sandeep Kumar Singh, Abeer Hashem, Al-Bandari Fahad Al-Arjani, Elsayed Fathi Abd_Allah, Prashant Kumar Singh and Ajay Kumar
Microorganisms 2022, 10(2), 290; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020290 - 26 Jan 2022
Cited by 16 | Viewed by 4060
Abstract
In the present study, eight endophytic bacterial strains, namely Bacillus licheniformis R1, Bacillus sp. R2, Agrobacterium tumefaciens R6, uncultured bacterium R11, Bacillus subtilis RS3, Bacillus subtilis RS6, uncultured bacterium RS8 and Lysinibacillus fusiformis RS9, were isolated from the root of Momordica charantia L. [...] Read more.
In the present study, eight endophytic bacterial strains, namely Bacillus licheniformis R1, Bacillus sp. R2, Agrobacterium tumefaciens R6, uncultured bacterium R11, Bacillus subtilis RS3, Bacillus subtilis RS6, uncultured bacterium RS8 and Lysinibacillus fusiformis RS9, were isolated from the root of Momordica charantia L. All the strains, except R6 exhibited positive for IAA production, siderophore production, and phosphate solubilization during plant growth-promoting traits analysis. Strains invariably utilized glucose and sucrose as a carbon source during substrate utilization, while yeast extract, ammonium sulphate, ammonium chloride, glycine, glutamine, and isoleucine as nitrogen sources. In addition, Spectinomycin was found as the most effective during antibiotic sensitivity TEST, followed by Chloramphenicol, Erythromycin, Rifampicin and Kanamycin, while Polymixin B was found least effective, while strains R1, R6, and RS8 were sensitive to all the antibiotics. Strains R1 and RS6 were able to withstand tolerance up to 10% of NaCl. The strains showing resistance against broad-spectrum antibiotics, especially chloramphenicol, can be used in hospital waste management. In addition, strains with a tolerance of 10 % of NaCl can improve plant growth in the saline affected area. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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17 pages, 2804 KiB  
Article
Regulation of Tomato Specialised Metabolism after Establishment of Symbiosis with the Endophytic Fungus Serendipita indica
by Fani Ntana, Sean R. Johnson, Björn Hamberger, Birgit Jensen, Hans J. L. Jørgensen and David B. Collinge
Microorganisms 2022, 10(1), 194; https://doi.org/10.3390/microorganisms10010194 - 16 Jan 2022
Cited by 8 | Viewed by 3337
Abstract
Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its [...] Read more.
Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its products are sometimes overlooked when studying plant-microbe interactions. This limits our understanding of the specific symbiotic associations and potentially future perspectives of their application in agriculture. In this study, we used the interaction between the root endophyte Serendipita indica and tomato (Solanum lycopersicum) plants to explore how specialised metabolism of the host plant is regulated upon a mutualistic symbiotic association. To do so, tomato seedlings were inoculated with S. indica chlamydospores and subjected to RNAseq analysis. Gene expression of the main tomato specialised metabolism pathways was compared between roots and leaves of endophyte-colonised plants and tissues of endophyte-free plants. S. indica colonisation resulted in a strong transcriptional response in the leaves of colonised plants. Furthermore, the presence of the fungus in plant roots appears to induce expression of genes involved in the biosynthesis of lignin-derived compounds, polyacetylenes, and specific terpenes in both roots and leaves, whereas pathways producing glycoalkaloids and flavonoids were expressed in lower or basal levels. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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13 pages, 1414 KiB  
Article
Development of Plant–Fungal Endophyte Associations to Suppress Phoma Stem Canker in Brassica
by Davood Roodi, James P. Millner, Craig R. McGill, Richard D. Johnson, Shen-Yan Hea, Jenny J. Brookes, Travis R. Glare and Stuart D. Card
Microorganisms 2021, 9(11), 2387; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112387 - 19 Nov 2021
Cited by 4 | Viewed by 2039
Abstract
Endophytic microorganisms are found within the tissues of many plants species, with some conferring several benefits to the host plant including resistance to plant diseases. In this study, two putative endophytic fungi that were previously isolated from wild seeds of Brassica, identified [...] Read more.
Endophytic microorganisms are found within the tissues of many plants species, with some conferring several benefits to the host plant including resistance to plant diseases. In this study, two putative endophytic fungi that were previously isolated from wild seeds of Brassica, identified as Beauveria bassiana and Pseudogymnoascus pannorum, were inoculated into cultivars of three Brassica species—Brassica napus, Br. rapa and Br. oleracea. Both fungal endophytes were reisolated from above- and below-ground tissues of inoculated plants at four different plant-growth stages, including cotyledon, one-leaf, two-leaf, and four-leaf stages. None of the plants colonised by these fungi exhibited any obvious disease symptoms, indicating the formation of novel mutualistic associations. These novel plant–endophyte associations formed between Brassica plants and Be. bassiana significantly inhibited phoma stem canker, a devastating disease of Brassica crops worldwide, caused by the fungal pathogen Leptosphaeria maculans. The novel association formed with P. pannorum significantly suppressed the amount of disease caused by L. maculans in one out of two experiments. Although biological control is not a new strategy, endophytic fungi with both antiinsect and antifungal activity are a highly conceivable, sustainable option to manage pests and diseases of economically important crops. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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12 pages, 1726 KiB  
Article
Interactive Effects of Epichloë Endophyte, Dormancy-Breaking Treatments and Geographic Origin on Seed Germination of Achnatherum inebrians
by Yaqi Chen, Kaiqi Su, Chunjie Li and James F. White
Microorganisms 2021, 9(11), 2183; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9112183 - 20 Oct 2021
Cited by 8 | Viewed by 1579
Abstract
Background: the cool-season grass Achnatherum inebrians (drunken horse grass) is an important species in the northwest grasslands of China. This grass engages in a symbiotic relationship with Epichloë endophytes, which affect host plants by increasing growth, repelling herbivores, and increasing tolerance to stressful [...] Read more.
Background: the cool-season grass Achnatherum inebrians (drunken horse grass) is an important species in the northwest grasslands of China. This grass engages in a symbiotic relationship with Epichloë endophytes, which affect host plants by increasing growth, repelling herbivores, and increasing tolerance to stressful environments. Methods: in this work, we evaluated the interaction effects of the endophyte on various dormancy-breaking treatments on A. inebrians seeds from six different locations. We used both endophyte-infected plants and noninfected plants and applied four dormancy-breaking methods to test germination. Results: our results showed that the germination rate of endophytic Achnatherum inebrians seeds from the Xiahe site (with highest altitude) was significantly higher than that from other sites when water soaking was applied (p < 0.05). Endophytic seeds had a greater germination rate, and soluble sugar, indole acetic acid (IAA), and gibberellin (GA) contents, under any condition. There was a significant interaction among the method, endophyte status, and origin regarding germination (p < 0.001); particularly, the effects of warm water soaking and endophyte infection on the germination of seeds from the Xiahe site was significant (p < 0.05). Conclusions: the infection of Epichloë endophyte is able to increase the content of soluble sugar, IAA, and GA, and stimulate the seed germination of A. inebrians. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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17 pages, 2225 KiB  
Article
Can Bacterial Endophytes Be Used as a Promising Bio-Inoculant for the Mitigation of Salinity Stress in Crop Plants?—A Global Meta-Analysis of the Last Decade (2011–2020)
by Muhammad Aammar Tufail, Ana Bejarano, Awais Shakoor, Asif Naeem, Muhammad Saleem Arif, Afzal Ahmed Dar, Taimoor Hassan Farooq, Ilaria Pertot and Gerardo Puopolo
Microorganisms 2021, 9(9), 1861; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091861 - 02 Sep 2021
Cited by 21 | Viewed by 4368
Abstract
Soil salinity is a major problem affecting crop production worldwide. Lately, there have been great research efforts in increasing the salt tolerance of plants through the inoculation of plant growth-promoting endophytic bacteria. However, their ability to promote plant growth under no-stress and salinity-stress [...] Read more.
Soil salinity is a major problem affecting crop production worldwide. Lately, there have been great research efforts in increasing the salt tolerance of plants through the inoculation of plant growth-promoting endophytic bacteria. However, their ability to promote plant growth under no-stress and salinity-stress conditions remains largely uncertain. Here, we carried out a global meta-analysis to quantify the plant growth-promoting effects (improvement of morphological attributes, photosynthetic capacity, antioxidative ability, and ion homeostasis) of endophytic bacteria in plants under no-stress and salinity-stress conditions. In addition, we elucidated the underlying mechanisms of growth promotion in salt-sensitive (SS) and salt-tolerant (ST) plants derived from the interaction with endophytic bacteria under no-stress and salinity-stress conditions. Specifically, this work encompassed 42 peer-reviewed articles, a total of 77 experiments, and 24 different bacterial genera. On average, endophytic bacterial inoculation increased morphological parameters. Moreover, the effect of endophytic bacteria on the total dry biomass, number of leaves, root length, shoot length, and germination rate was generally greater under salinity-stress conditions than no-stress conditions. On a physiological level, the relative better performance of the bacterial inoculants under the salinity-stress condition was associated with the increase in total chlorophyll and chlorophyll-b, as well as with the decrease of 1-aminocylopropane-1-carboxylate concentration. Moreover, under the salinity-stress condition, bacterial inoculation conferred a significantly higher increase in root K+ concentration and decrease in leaf Na+ concentration than under the no-stress condition. In SS plants, bacterial inoculation induced a higher increase in chlorophyll-b and superoxide dismutase activity, as well as a higher decrease in abscisic acid content, than in ST plants. Under salinity-stress, endophytic bacterial inoculation increased root K+ concentration in both SS and ST plants but decreased root Na+ concentration only in ST plants. Overall, this meta-analysis suggests that endophytic bacterial inoculation is beneficial under both no salinity-stress and salinity-stress conditions, but the magnitude of benefit is definitely higher under salinity-stress conditions and varies with the salt tolerance level of plants. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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Review

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24 pages, 1415 KiB  
Review
Metabolic Potential of Epichloë Endophytes for Host Grass Fungal Disease Resistance
by Krishni Fernando, Priyanka Reddy, German C. Spangenberg, Simone J. Rochfort and Kathryn M. Guthridge
Microorganisms 2022, 10(1), 64; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010064 - 29 Dec 2021
Cited by 6 | Viewed by 2077
Abstract
Asexual species of the genus Epichloë (Clavicipitaceae, Ascomycota) form endosymbiotic associations with Pooidae grasses. This association is important both ecologically and to the pasture and turf industries, as the endophytic fungi confer a multitude of benefits to their host plant that improve competitive [...] Read more.
Asexual species of the genus Epichloë (Clavicipitaceae, Ascomycota) form endosymbiotic associations with Pooidae grasses. This association is important both ecologically and to the pasture and turf industries, as the endophytic fungi confer a multitude of benefits to their host plant that improve competitive ability and performance such as growth promotion, abiotic stress tolerance, pest deterrence and increased host disease resistance. Biotic stress tolerance conferred by the production of bioprotective metabolites has a critical role in an industry context. While the known antimammalian and insecticidal toxins are well characterized due to their impact on livestock welfare, antimicrobial metabolites are less studied. Both pasture and turf grasses are challenged by many phytopathogenic diseases that result in significant economic losses and impact livestock health. Further investigations of Epichloë endophytes as natural biocontrol agents can be conducted on strains that are safe for animals. With the additional benefits of possessing host disease resistance, these strains would increase their commercial importance. Field reports have indicated that pasture grasses associated with Epichloë endophytes are superior in resisting fungal pathogens. However, only a few antifungal compounds have been identified and chemically characterized, and these from sexual (pathogenic) Epichloë species, rather than those utilized to enhance performance in turf and pasture industries. This review provides insight into the various strategies reported in identifying antifungal activity from Epichloë endophytes and, where described, the associated antifungal metabolites responsible for the activity. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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20 pages, 1643 KiB  
Review
The Potential Application of Endophytes in Management of Stress from Drought and Salinity in Crop Plants
by Hariom Verma, Dharmendra Kumar, Vinod Kumar, Madhuree Kumari, Sandeep Kumar Singh, Vijay Kumar Sharma, Samir Droby, Gustavo Santoyo, James F. White and Ajay Kumar
Microorganisms 2021, 9(8), 1729; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081729 - 13 Aug 2021
Cited by 63 | Viewed by 7620
Abstract
Endophytic microorganisms present inside the host plant play an essential role in host fitness, nutrient supply and stress tolerance. Endophytes are often used in sustainable agriculture as biofertilizers, biopesticides and as inoculants to mitigate abiotic stresses including salinity, drought, cold and pH variation [...] Read more.
Endophytic microorganisms present inside the host plant play an essential role in host fitness, nutrient supply and stress tolerance. Endophytes are often used in sustainable agriculture as biofertilizers, biopesticides and as inoculants to mitigate abiotic stresses including salinity, drought, cold and pH variation in the soil. In changing climatic conditions, abiotic stresses create global challenges to achieve optimum crop yields in agricultural production. Plants experience stress conditions that involve endogenous boosting of their immune system or the overexpression of their defensive redox regulatory systems with increased reactive oxygen species (ROS). However, rising stress factors overwhelm the natural redox protection systems of plants, which leads to massive internal oxidative damage and death. Endophytes are an integral internal partner of hosts and have been shown to mitigate abiotic stresses via modulating local or systemic mechanisms and producing antioxidants to counteract ROS in plants. Advancements in omics and other technologies have been made, but potential application of endophytes remains largely unrealized. In this review article, we will discuss the diversity, population and interaction of endophytes with crop plants as well as potential applications in abiotic stress management. Full article
(This article belongs to the Special Issue Microbial Endophytes: Functional Biology and Applications)
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