Endophytes: Improving Plants Performance

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

Deadline for manuscript submissions: closed (30 March 2023) | Viewed by 21894

Special Issue Editors

Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
Interests: plant–rhizobium symbiosis; systems biology; multipartite genomes; metagenomics; bacterial epigenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Special Issue ‘Endophytes: Improving Plants Performance’ aims to compile the latest information and innovations in the field of plant-microbe interaction research. This includes, but is not limited to, providing fundamental insights into the understanding of the microbial biodiversity of organisms associated with plant systems.

Endophytes represent microorganisms that reside within plant tissues, without typically causing adverse effects to the plants, for a substantial part of their life cycle, and are primarily known for their beneficial role to their host plant. Specific endophytes may have evolved with their host, and could be a source of yet unknown novel molecules, with potential pharmaceutical, agricultural or environmental significance. This Special Issue of Microorganisms will cover the different aspects of microbial endophytes, and their role in plant growth, survival in stress conditions, biological control agents, and in sustainable agricultural production systems.  

The following topics will be considered, among others:

  • Plant-microbe interaction;
  • Biodiversity of endophytic microbiomes in normal, as well as extreme, habitats;
  • Effect of the phyllo- and rhizospheric microbiome in shaping the endophytic microbiome;
  • PGP mechanisms (solubilization, nitrogen fixation, and phytohormone production);
  • Beneficial microbes for nutrient uptake, cycling and soil fertility;
  • Extremophiles (archaea, bacteria, fungi, etc.) in improving crop productivity;
  • Microbe-mediated drought/salinity/heat/cold stress in plants;
  • Metabolic engineering for endophytic strains to improve plant growth promotion;
  • Biofertilizers and biopesticides.

Dr. Camilla Fagorzi
Dr. Alessio Mengoni
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

  • endophytes
  • plant microbiome
  • biofertilizers
  • PGPB
  • plant-microbe interaction
  • plant-bacterium symbiosis

Published Papers (11 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Editorial

Jump to: Research, Review

3 pages, 373 KiB  
Editorial
Endophytes: Improving Plant Performance
by Camilla Fagorzi and Alessio Mengoni
Microorganisms 2022, 10(9), 1777; https://doi.org/10.3390/microorganisms10091777 - 03 Sep 2022
Cited by 4 | Viewed by 1498
Abstract
Endophytes represent microorganisms that reside within plant tissues, without typically causing adverse effects to the plants, for a substantial part of their life cycle, and are primarily known for their beneficial role to their host plant [...] Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

Research

Jump to: Editorial, Review

21 pages, 35493 KiB  
Article
Diversity of Endophytic Microbes in Taxus yunnanensis and Their Potential for Plant Growth Promotion and Taxane Accumulation
by Qiao Liu, Ludan Li, Yujie Chen, Sai Wang, Lina Xue, Weiying Meng, Jihong Jiang and Xiaoying Cao
Microorganisms 2023, 11(7), 1645; https://doi.org/10.3390/microorganisms11071645 - 23 Jun 2023
Cited by 3 | Viewed by 1117
Abstract
Taxus spp. are ancient tree species that have survived from the Quaternary glacier period, and their metabolites, such as taxol, have been used as anticancer drugs globally. Plant–endophytic microbial interaction plays a crucial role in exerting a profound impact on host growth and [...] Read more.
Taxus spp. are ancient tree species that have survived from the Quaternary glacier period, and their metabolites, such as taxol, have been used as anticancer drugs globally. Plant–endophytic microbial interaction plays a crucial role in exerting a profound impact on host growth and secondary metabolite synthesis. In this study, high-throughput sequencing was employed to explore endophytic microbial diversity in the roots, stems, and leaves of the Taxus yunnanensis (T. yunnanensis). The analysis revealed some dominant genera of endophytic bacteria, such as Pseudomonas, Neorhizobium, Acidovorax, and Flavobacterium, with Cladosporium, Phyllosticta, Fusarium, and Codinaeopsis as prominent endophytic fungi genera. We isolated 108 endophytic bacteria and 27 endophytic fungi from roots, stems, and leaves. In vitro assays were utilized to screen for endophytic bacteria with growth-promoting capabilities, including IAA production, cellulase, siderophore production, protease and ACC deaminase activity, inorganic phosphate solubilization, and nitrogen fixation. Three promising strains, Kocuria sp. TRI2-1, Micromonospora sp. TSI4-1, and Sphingomonas sp. MG-2, were selected based on their superior growth-promotion characteristics. These strains exhibited preferable plant growth promotion when applied to Arabidopsis thaliana growth. Fermentation broths of these three strains were also found to significantly promote the accumulation of taxanes in T. yunnanensis stem cells, among which strain TSI4-1 demonstrated outstanding increase potentials, with an effective induction of taxol, baccatin III, and 10-DAB contents. After six days of treatment, the contents of these metabolites were 3.28 times, 2.23 times, and 2.17 times the initial amounts, reaching 8720, 331, and 371 ng/g of dry weight of stem cells, respectively. These findings present new insight into the industrialization of taxol production through Taxus stem cell fermentation, thereby promoting the conservation of wild Taxus resources by maximizing their potential economic benefits. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

13 pages, 990 KiB  
Article
Utility of Plant Growth-Promoting Rhizobacteria for Sustainable Production of Bermudagrass Forage
by Kayla N. Sullins, S. Leanne Dillard, David W. Held and Elijah P. Carroll
Microorganisms 2023, 11(4), 863; https://doi.org/10.3390/microorganisms11040863 - 28 Mar 2023
Cited by 1 | Viewed by 1578
Abstract
A two-year study was conducted in bermudagrass hay fields in central Alabama to estimate the potential of plant growth-promoting rhizobacteria (PGPR) as a tool for sustainable agriculture in forage management. This study compared the effects of two treatments of PGPR, applied with and [...] Read more.
A two-year study was conducted in bermudagrass hay fields in central Alabama to estimate the potential of plant growth-promoting rhizobacteria (PGPR) as a tool for sustainable agriculture in forage management. This study compared the effects of two treatments of PGPR, applied with and without lowered rates of nitrogen, to a full rate of nitrogen fertilizer in a hay production system. The PGPR treatments included a single-strain treatment of Paenibacillus riograndensis (DH44), and a blend including two Bacillus pumilus strains (AP7 and AP18) and a strain of Bacillus sphaericus (AP282). Data collection included estimates of forage biomass, forage quality, insect populations, soil mesofauna populations, and soil microbial respiration. Applications of PGPR with a half rate of fertilizer yielded similar forage biomass and quality results as that of a full rate of nitrogen. All PGPR treatments increased soil microbial respiration over time. Additionally, treatments containing Paenibacillus riograndensis positively influenced soil mesofauna populations. The results of this study indicated promising potential for PGPR applied with lowered nitrogen rates to reduce chemical inputs while maintaining yield and quality of forage. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

17 pages, 2199 KiB  
Article
Colonization Ability of Bacillus subtilis NCD-2 in Different Crops and Its Effect on Rhizosphere Microorganisms
by Weisong Zhao, Yiyun Ban, Zhenhe Su, Shezeng Li, Xiaomeng Liu, Qinggang Guo and Ping Ma
Microorganisms 2023, 11(3), 776; https://doi.org/10.3390/microorganisms11030776 - 17 Mar 2023
Cited by 2 | Viewed by 1187
Abstract
Bacillus subtilis strain NCD-2 is a promising biocontrol agent for soil-borne plant diseases and shows potential for promoting the growth of some crops. The purposes of this study were to analyze the colonization ability of strain NCD-2 in different crops and reveal the [...] Read more.
Bacillus subtilis strain NCD-2 is a promising biocontrol agent for soil-borne plant diseases and shows potential for promoting the growth of some crops. The purposes of this study were to analyze the colonization ability of strain NCD-2 in different crops and reveal the plant growth promotion mechanism of strain NCD-2 by rhizosphere microbiome analysis. qRT-PCR was used to determine the populations of strain NCD-2, and microbial communities’ structures were analyzed through amplicon sequencing after application of strain NCD-2. Results demonstrated that strain NCD-2 had a good growth promotion effect on tomato, eggplant and pepper, and it was the most abundant in eggplant rhizosphere soil. There were significantly differences in the types of beneficial microorganisms recruited for different crops after application of strain NCD-2. PICRUSt analysis showed that the relative abundances of functional genes for amino acid transport and metabolism, coenzyme transport and metabolism, lipid transport and metabolism, inorganic ion transport and metabolism, and defense mechanisms were enriched in the rhizospheres of pepper and eggplant more than in the rhizospheres of cotton, tomato and maize after application of strain NCD-2. In summary, the colonization ability of strain NCD-2 for five plants was different. There were differences in microbial communities’ structure in rhizosphere of different plants after application of strain NCD-2. Based on the results obtained in this study, it was concluded that the growth promoting ability of strain NCD-2 were correlated with its colonization quantity and the microbial species it recruited. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

18 pages, 2579 KiB  
Article
The Endophytic Fungi Diversity, Community Structure, and Ecological Function Prediction of Sophora alopecuroides in Ningxia, China
by Ruotong Wang, Qingchen Zhang, Mingxiu Ju, Siyuan Yan, Qiangqiang Zhang and Peiwen Gu
Microorganisms 2022, 10(11), 2099; https://doi.org/10.3390/microorganisms10112099 - 22 Oct 2022
Cited by 7 | Viewed by 1385
Abstract
Sophora alopecuroides L. has great medicinal and ecological value in northwestern China. The host and its microbiota are mutually symbiotic, collectively forming a holobiont, conferring beneficial effects to the plant. However, the analysis of diversity, mycobiota composition, and the ecological function of endophytic [...] Read more.
Sophora alopecuroides L. has great medicinal and ecological value in northwestern China. The host and its microbiota are mutually symbiotic, collectively forming a holobiont, conferring beneficial effects to the plant. However, the analysis of diversity, mycobiota composition, and the ecological function of endophytic fungi in the holobiont of S. alopecuroides is relatively lacking. In this article, the fungal community profiling of roots, stems, leaves, and seeds of S. alopecuroides (at the fruit maturity stage) from Huamachi and Baofeng in Ningxia, China were investigated based on the ITS1 region, using high-throughput sequencing technology. As a result, a total of 751 operational taxonomic units (OTUs) were obtained and further classified into 9 phyla, 27 classes, 66 orders, 141 families, 245 genera, and 340 species. The roots had the highest fungal richness and diversity, while the stems had the highest evenness and pedigree diversity. There also was a significant difference in the richness of the endophytic fungal community between root and seed (p < 0.05). The organ was the main factor affecting the community structure of endophytic fungi in S. alopecuroides. The genera of unclassified Ascomycota, Tricholoma, Apiotrichum, Alternaria, and Aspergillus made up the vast majority of relative abundance, which were common in all four organs as well. The dominant and endemic genera and biomarkers of endophytic fungi in four organs of S. alopecuroides were different and exhibited organ specificity or tissue preference. The endophytic fungi of S. alopecuroides were mainly divided into 15 ecological function groups, among which saprotroph was absolutely dominant, followed by mixotrophic and pathotroph, and the symbiotroph was the least. With this study, we revealed the diversity and community structure and predicted the ecological function of the endophytic fungi of S. alopecuroides, which provided a theoretical reference for the further development and utilization of the endophytic fungi resources of S. alopecuroides. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

23 pages, 5010 KiB  
Article
Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds
by Giulia Semenzato, Teresa Faddetta, Sara Falsini, Sara Del Duca, Antonia Esposito, Anna Padula, Claudia Greco, Nadia Mucci, Marco Zaccaroni, Anna Maria Puglia, Alessio Papini and Renato Fani
Microorganisms 2022, 10(10), 2086; https://doi.org/10.3390/microorganisms10102086 - 21 Oct 2022
Cited by 3 | Viewed by 1623
Abstract
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic [...] Read more.
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

15 pages, 2033 KiB  
Article
Plant Growth-Promoting Bacterial Consortia as a Strategy to Alleviate Drought Stress in Spinacia oleracea
by Claudia Petrillo, Ermenegilda Vitale, Patrizia Ambrosino, Carmen Arena and Rachele Isticato
Microorganisms 2022, 10(9), 1798; https://doi.org/10.3390/microorganisms10091798 - 06 Sep 2022
Cited by 7 | Viewed by 2221
Abstract
Drought stress is one of the most severe abiotic stresses affecting soil fertility and plant health, and due to climate change, it is destined to increase even further, becoming a serious threat to crop production. An efficient, eco-friendly alternative is the use of [...] Read more.
Drought stress is one of the most severe abiotic stresses affecting soil fertility and plant health, and due to climate change, it is destined to increase even further, becoming a serious threat to crop production. An efficient, eco-friendly alternative is the use of plant growth-promoting bacteria (PGPB), which can promote plant fitness through direct and indirect approaches, protecting plants from biotic and abiotic stresses. The present study aims to identify bacterial consortia to promote Spinacia oleracea L. cv Matador’s seed germination and protect its seedlings from drought stress. Eight PGPB strains belonging to the Bacillus, Azotobacter, and Pseudomonas genera, previously characterized in physiological conditions, were analyzed under water-shortage conditions, and a germination bioassay was carried out by biopriming S. oleracea seeds with either individual strains or consortia. The consortia of B. amyloliquefaciens RHF6, B. amyloliquefaciens LMG9814, and B. sp. AGS84 displayed the capacity to positively affect seed germination and seedlings’ radical development in both standard and drought conditions, ameliorating the plants’ growth rate compared to the untreated ones. These results sustain using PGPB consortia as a valid ameliorating water stress strategy in the agro-industrial field. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

13 pages, 2310 KiB  
Article
Effect of Site and Phenological Status on the Potato Bacterial Rhizomicrobiota
by Lisa Cangioli, Marco Mancini, Ada Baldi, Camilla Fagorzi, Simone Orlandini, Francesca Vaccaro and Alessio Mengoni
Microorganisms 2022, 10(9), 1743; https://doi.org/10.3390/microorganisms10091743 - 29 Aug 2022
Cited by 2 | Viewed by 1529
Abstract
The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, [...] Read more.
The potato is the fourth major food crop in the world. Its cultivation can encounter problems, resulting in poor growth and reduced yield. Plant microbiota has shown an ability to increase growth and resistance. However, in the development of effective microbiota manipulation strategies, it is essential to know the effect of environmental variables on microbiota composition and function. Here, we aimed to identify the differential impact of the site of cultivation and plant growth stage on potato rhizosphere microbiota. We performed a 16S rRNA gene amplicon sequencing analysis of rhizospheric soil collected from potato plants grown at four sites in central Italy during two phenological stages. Rhizomicrobiota was mainly composed of members of phyla Acidobacteriota, Actinobacteriota, Chloroflexi, and Proteobacteria and was affected by both the site of cultivation and the plant stages. However, cultivation sites overcome the effect of plant phenological stages. The PiCRUST analysis suggested a high abundance of functions related to the biosynthesis of the siderophore enterobactin. The presence of site-specific taxa and functional profiling of the microbiota could be further exploited in long-term studies to evaluate the possibility of developing biomarkers for traceability of the products and to exploit plant growth-promoting abilities in the native potato microbiota. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

20 pages, 1917 KiB  
Article
Characterization of the Cultivable Endophytic Bacterial Community of Seeds and Sprouts of Cannabis sativa L. and Perspectives for the Application as Biostimulants
by Morena Gabriele, Francesco Vitali, Elisa Chelucci and Carolina Chiellini
Microorganisms 2022, 10(9), 1742; https://doi.org/10.3390/microorganisms10091742 - 29 Aug 2022
Cited by 4 | Viewed by 3883
Abstract
Endophytes are beneficial microorganisms exerting growth-promoting activities in plants; they are most often located within the plant intercellular spaces and can be found in all plant tissues, including roots, leaves, stems, flowers, and seeds. In this work, we investigated the cultivable bacterial community [...] Read more.
Endophytes are beneficial microorganisms exerting growth-promoting activities in plants; they are most often located within the plant intercellular spaces and can be found in all plant tissues, including roots, leaves, stems, flowers, and seeds. In this work, we investigated the cultivable bacterial community of the seeds and the two-week sprouts of the Cannabis sativa L. cultivar “Futura 75”. Endophytes were genotypically and phenotypically characterized and were exposed to different concentrations of seed extracts to verify their susceptibility. A bacterial strain among all the isolates was selected for germination tests of C. sativa in different experimental conditions. The results revealed the dominance of Firmicutes (Staphylococcus sp.) among the isolated strains. Two strains were different from the others for indole-3-acetic acid (IAA) production and for their resistance patterns towards abiotic and biotic stresses. The Sphingomonas sp. strain Can_S11 (Alphaproteobacteria) showed a potential ability to increase the nutraceutical features of its sprouts, particularly an increase in the polyphenol content and antioxidant activity. None of the isolated strains were susceptible to the seed extracts, which were previously tested as antimicrobial and antibiofilm agents against human pathogenic bacteria. The results open new perspectives for the study of the endophytes of C. sativa as possible biostimulants. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

16 pages, 6846 KiB  
Article
Endophytic Bacteria and Essential Oil from Origanum vulgare ssp. vulgare Share Some VOCs with an Antibacterial Activity
by Giulia Polito, Giulia Semenzato, Sara Del Duca, Lara Mitia Castronovo, Alberto Vassallo, Sofia Chioccioli, Duccio Borsetti, Vittoria Calabretta, Anna Maria Puglia, Renato Fani and Antonio Palumbo Piccionello
Microorganisms 2022, 10(7), 1424; https://doi.org/10.3390/microorganisms10071424 - 14 Jul 2022
Cited by 11 | Viewed by 2178
Abstract
Medicinal aromatic plants’ essential oils (EOs) are mixtures of volatile compounds showing antimicrobial activity, which could be exploited to face the emerging problem of multi-drug resistance. Their chemical composition can depend on the interactions between the plant and its endophytic microbiota, which is [...] Read more.
Medicinal aromatic plants’ essential oils (EOs) are mixtures of volatile compounds showing antimicrobial activity, which could be exploited to face the emerging problem of multi-drug resistance. Their chemical composition can depend on the interactions between the plant and its endophytic microbiota, which is known to synthesize volatile organic compounds (VOCs). However, it is still not clear whether those volatile metabolites can contribute to the composition of the aroma profile of plants’ EOs. The aims of this study were to characterize medicinal plant O. vulgare ssp. vulgare bacterial endophyte VOCs, evaluating their ability to antagonize the growth of opportunistic human pathogens belonging to the Burkholderia cepacia complex (Bcc) and compare them with O. vulgare EO composition. Many of the tested endophytic strains showed (i) a bactericidal and/or bacteriostatic activity against most of Bcc strains and (ii) the production of VOCs with widely recognized antimicrobial properties, such as dimethyl disulfide, dimethyl trisulfide, and monoterpenes. Moreover, these monoterpenes were also detected in the EOs extracted from the same O. vulgare plants from which endophytes were isolated. Obtained results suggest that endophytes could also play a role in the antibacterial properties of O. vulgare ssp. vulgare and, potentially, in determining its aromatic composition. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

Review

Jump to: Editorial, Research

29 pages, 2772 KiB  
Review
Endophytes in Agriculture: Potential to Improve Yields and Tolerances of Agricultural Crops
by Declan Watts, Enzo A. Palombo, Alex Jaimes Castillo and Bita Zaferanloo
Microorganisms 2023, 11(5), 1276; https://doi.org/10.3390/microorganisms11051276 - 12 May 2023
Cited by 10 | Viewed by 2484
Abstract
Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting [...] Read more.
Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting in improved crop yields. Evidence shows that endophytes can provide improved tolerances to salinity, moisture, and drought conditions, highlighting the capacity to farm them in marginal land with the use of endophyte-based strategies. Furthermore, endophytes offer a sustainable alternative to traditional agricultural practices, reducing the need for synthetic fertilizers and pesticides, and in turn reducing the risks associated with chemical treatments. In this review, we summarise the current knowledge on endophytes in agriculture, highlighting their potential as a sustainable solution for improving crop productivity and general plant health. This review outlines key nutrient, environmental, and biotic stressors, providing examples of endophytes mitigating the effects of stress. We also discuss the challenges associated with the use of endophytes in agriculture and the need for further research to fully realise their potential. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
Show Figures

Figure 1

Back to TopTop