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A-D. Microbes in plant roots. A. Cloud of bacteria (arrows) around root tip meristem of invasive reed grass (Phragmites australis); stained with aniline blue (0.1% aqueous). B. Root parenchyma cell of P. australis showing replicating protoplasts of bacteria (arrows) in the periplasmic space of the cell (stained with DAB, followed by aniline blue; bar = 15 µ). C. Root hair of grass Cynodon dactylon inoculated with bacterium Pseudomonas sp. showing bacterial protoplasts (arrows) in the periplasmic space of the hair (stained with DAB, followed by aniline blue; bar = 15 µ). D. Root hairs of clover (Trifolium repens) inoculated with endophytic yeast (Rhodotorula sp.) showing yeast being expelled from the root hair tips (black arrows) and yeast protoplasts within root hairs (white arrow)(stained with DAB, followed by aniline blue; bar = 15 µ).
Source publication
Endophytes are microbes (mostly bacteria and fungi) present asymptomatically in plants. Endophytic microbes are often functional in that they may carry nutrients from the soil into plants, modulate plant development, increase stress tolerance of plants, suppress virulence in pathogens, increase disease resistance in plants, and suppress development...
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Citations
... Endophytic bacteria are microorganisms that live within plant tissues without causing harm or disease to the host [120]. Their role in plant microbiomes is well documented [121], with significant applications in plant disease control [122]. ...
Heavy metal (HM) contamination poses a major threat to environmental health, agriculture and human well-being, requiring effective and sustainable remediation strategies. Phytoremediation, an eco-friendly and cost-effective approach, is widely used for the remediation of HM-contaminated soils. Although phytoremediation holds considerable potential in the extraction, stabilisation and degradation of HMs, its effectiveness is often constrained by limited metal bioavailability, plant stress under toxic conditions and slow metal uptake rates. To address these limitations, this review examines the integration of various soil amendments—the application of biochar, compost, plant exudates, microbial agents and chelating agents—to enhance phytoremediation efficiency. This review critically evaluates empirical evidence on the effectiveness, scalability, economic feasibility and environmental impact of these amendments. By synthesising recent studies, this review advances the understanding of amendment-assisted phytoremediation as a viable solution for treating HM-contaminated soils. In addition, this review identifies practical applications, discusses limitations and explores the potential synergies of these amendments to optimise phytoremediation strategies, ultimately contributing to more effective and sustainable environmental cleanup efforts.
... Similar responses were reported for wheat and sorghum by strains of Pseudomonas putida [74,75]. In addition, the literature is full of examples of consortia of mechanisms undertaken by endophytes to enrich/facilitate availability and uptake of nutrients (N, P, K, etc.) for stressed plants through transformation of major and minor elements to soluble forms [61,76,77]; and nitrogen fixation [15,78]. Production of indole acetic acid (IAA) is among the mechanisms of endophytic bacteria that enabled their host plants to improve tolerance in semi-arid habitats, e.g. ...
Drastic consequences of climate change necessitate exploring plant-microbiota of arid desert ecosystems for potential candidates recommended for future microbiota-mediate strategies of stressed agriculture. The prevalent xerophytes (Amaranthaceae, Compositae, Cyperaceae, Gramineae, Plantaginaceae, Scrophulariaceae, and Zygophyllaceae) were tested for culturable associated microbiota. Representative isolates were subjected to PGP functions, API-profiling and 16S rRNA genes sequencing. Xerophytes hosted dense populations of culturable microbiota, ecto-/endo-rhizosphere (> 10 3-10 7 CFUs g −1 root). API microtube analysis confirmed the predominance of representative genera of Gram-positive/ negative bacteria. Isolates expressed multi-functional PGP traits, e.g. nitrogenase activity, indole acetic acid production, P/K-solubilization, ammonia production, salt tolerance, and effective/wide enzymatic activities. Based on 16S rRNA gene sequencing, the dominant phyla were Firmicutes, Gammaproteobacteria and Alphaproteobacteria. Firmicutes represented in ecto-rhizosphere (Bacillus rugosus, B. cereus, and B. altitudinis) and endo-rhizosphere (B. halotolerans, B. safensis subsp. safensis, B. siamensis, B. licheniformis and Brevibacillus parabrevis). Gammaproteobacteria presented in ecto-rhizosphere as Pseudomonas aeruginosa, Ps. hibiscicola, Ps. monteilii, Kosakonia cowanii and Serratia liquefaciens and in endo-rhizosphere as Pantoea vagans, P. conspicua and Stenotrophomonas maltophilia. Alphaproteobacteria, Azospiril-lum zeae, Azospirillum oryzae and Agrobacterium salinitolerans, were present in ecto-rhizosphere. Conformity among API profiling and 16S rRNA gene sequencing on the genus level (> 58%) indicated the reliability of API profiling as pre-identification scheme. It is concluded that the present study provides additional information regarding microbiota associated with xerophytes. Beside their taxonomic diversity, they are of potential/ functional impact that recommend their use as candidates of synthetic communities (SynCom) for the modification of economic crops introduced to arid deserts. Graphical Abstract Keywords Semi/arid deserts · Xerophytes · PGPR/plant microbiota · Climate change/stress agriculture · Ecto-/endo-rhizosphere · API profiling/16S rRNA gene sequencing
... Therefore, some species of Vaccinium, such as V. corymbosum, V. oldhamii, and V. myrtillus, have been documented to harbor a diverse array of root-associated fungi, particularly ericoid mycorrhizas. These fungal associations play an important role in nitrogen sequestration and mobilization, plant growth, stress tolerance and protections against pathogens (Yang et al., 2002;Baba et al., 2016;White et al., 2019). Likewise, endogenous bacteria residing within the plant contribute to nutrient acquisition and play essential roles in promoting plant growth (Dudeja et al., 2021;Rosenblueth & Martínez-Romero, 2006). ...
The Vaccinium genus consists of a variety of berries with high nutritious components consumed worldwide leading to the development of micropropagation protocols to supply the demand. Mortiño, the Andean Blueberry (Vaccinium floribundum Kunth) is a wild berry that grows in high-altitude grasslands with nutritious and commercial potential in Ecuador. In this study, the use of PPMTM (Plant Preservative Mixture™) was effective controlling contamination for the in vitro establishment of Vaccinium floribundum Kunth in contrast to a conventional method using EtOH and Clorox. Stems were defoliated and cut into 1 cm segments, then immersed in liquid MS (Murashige & Skoog) supplemented with 5% v/v PPMTM without pH adjustment for 5 hours under constant shaking. After immersion, segments were transferred to flasks containing WPM (Woody Plant Media) medium supplemented with an additional 2 mlL-1 PPMTM. Persistent microbial contaminants in the in vitro explants were isolated and identified through molecular methods and gene sequences analyzed using the GenBank database resulted in the identification of three bacterial species: Methylobacterium sp., Methylobacterium radiotolerans, and Bacillus pumilus. In addition, three fungal species were also discovered: Xylaria sp., Xylaria feejeensis, and Diaporthe lutecens. Additionally, a multiplication assay was made with the aseptic stems from the sterilization protocol to evaluate four different growth regulators: 2ip, kinetin, zeatin and meta-topolin. kinetin showed very low responses with a mean of 1.2 shoots per stem. The highest number of shoots per stem (9 shoots) was obtained with 5 mg L-1 2ip. The use of zeatin and meta-topolin facilitated shoot proliferation with the following concentrations: 3 mg L-1 zeatin + 0.5 mg L-1 NAA (1-Naphthaleneacetic Acid) and 3 mg L-1 Meta-topolin + 0.5 mg L-1 NAA. These findings demonstrate the successful establishment of an in vitro disinfection and multiplication protocol for V. floribundum.
... These genes can be classified into various categories, including those involved in quorum sensing, antibiotic biosynthesis, and the secretion of lytic enzymes that degrade pathogen cell walls (Ali et al., 2022;Lugtenberg and Kamilova, 2009) While virulence genes are typically associated with pathogenic bacteria, their presence in non-pathogenic microbes is not uncommon. These genes can provide competitive advantages in the microbial community and may reduce the pathogenic potential of these microbes under certain environmental conditions (Negi et al., 2023;White et al., 2019). ...
Background
As industrial chicory is significant for food, fodder, and medicinal purposes, its cultivation is increasingly crucial for producers. To enhance productivity, resistance, and the nutritional and functional values of this plant, we aimed to investigate its interactions with the microbial environment. We performed the first comprehensive taxonomic and functional characterization of the rhizosphere microbiota associated with industrial chicory, investigating how environmental factors influence its composition.
Methods
Six different land plots were simultaneously cultivated with the same chicory genotype in northern France. Using soil analyses and metagenomic approaches, we characterized the diversity of bacterial and fungal communities in the soil microbiome associated with chicory plants and discussed their functional traits.
Results
We observed significant taxonomic variability, influenced by soil composition and cultivation history across each plot. The presence of chicory plants distinctly shaped the microbial community. Specifically, chicory was found to recruit Streptomyces species that produce plant hormones and Penicillium species that facilitate phosphate solubilization and promote plant growth. Moreover, the plant demonstrated an ability to repel pathogens and adapt to local microbial communities by selectively favoring beneficial microorganisms according to local stresses and nutritional needs.
Discussion
Our study represents a comprehensive taxonomic and functional analysis of the Cichorium intybus rhizosphere microbiome, underscoring the pivotal role of soil composition and land-use history. The specific microbial recruitment by chicory was also addressed.
... These microorganisms show great potential as biocontrol agents (BCAs) of plant disease, as they establish complex interplay with the host plant [17], and antagonize the plant pathogens through the induction of resistance mechanisms [18]. Endophytes represent an environmentally friendly alternative to chemicals [19,20], and their use is considered one of the most promising methods for a more sustainable control of plant diseases [21], and crop-management practices [22]. Endophytes are able to modulate host immunity [21] and offer different strategies and modes of action for controlling vascular wilt diseases, in which the pathogen occupies the same ecological niche of phytopathogens [12][13][14][15][16][17][18][19][20][21][22][23]. ...
... Endophytes represent an environmentally friendly alternative to chemicals [19,20], and their use is considered one of the most promising methods for a more sustainable control of plant diseases [21], and crop-management practices [22]. Endophytes are able to modulate host immunity [21] and offer different strategies and modes of action for controlling vascular wilt diseases, in which the pathogen occupies the same ecological niche of phytopathogens [12][13][14][15][16][17][18][19][20][21][22][23]. Several endophytic bacteria can occupy the same niche/habitat as the phytopathogen Xf in the lumen of xylem vessels [24]. ...
... They are facultative-aerobic, Gram-negative rods, able to grow on methanol and methylamine, and to use a variety of C 2 , C 3 , and C 4 compounds as carbon source. The genus Methylobacterium contains species that are ubiquitous on the surface and the interior of plants [10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29]. Members of the genus can form beneficial associations with different plant species and have been reported as both plant growth promoting bacteria and potential BCAs [30]. ...
Background
Olive quick decline syndrome (OQDS), caused by Xylella fastidiosa subsp. pauca (Xfp), is a destructive vascular disease affecting olive trees, particularly in Apulia, Southeastern Italy. Control measures rely on containment and replanting with resistant cultivars. Endophytic bacteria, including Methylobacterium spp., have shown potential in mitigating vascular diseases. These facultative methylotrophic bacteria inhabit xylem vessels and compete with pathogens like Xfp by producing siderophores that limit iron availability.
Results
Analysis of endophytic bacterial populations in olive trees identified Methylobacterium spp. in both healthy and Xfp-infected plants, with variable isolation frequencies. Molecular identification based on 16S rDNA and mxaF gene sequences classified isolates as M. radiotolerans (70%) and M. mesophilicum (30%). Phylogenetic analysis showed limited genetic variation, clustering isolates with reference strains. In vitro experiments revealed that culture supernatants from Methylobacterium spp., grown in siderophore-inducing media, affected Xfp growth in a concentration-dependent manner. At low concentrations (up to 2%), supernatants stimulated Xfp growth, while higher concentrations (20% and 50%) inhibited growth. Selected strains of M. radiotolerans and M. mesophilicum were confirmed as siderophore producers through CAS blue agar tests and targeted LC–MS/MS analysis. LC–MS/MS identified ferrioxamine E and ferrichrome in all Methylobacterium strains, with the highest levels in M. organophilum and M. aminovorans. Deferoxamine was absent, whereas Xfp exhibited elevated production of ferrioxamine E, deferoxamine, and ferrichrome.
Conclusions
This study underscores the biocontrol potential of Methylobacterium spp. against Xfp, suggesting an ability to compete with the pathogen through siderophore-mediated mechanisms. The dual effect of Methylobacterium supernatants—stimulatory at low concentrations and inhibitory at higher levels—highlights the complexity of plant–microbe–pathogen interactions. The production of ferrioxamine E and ferrichrome suggests a possible role in modulating iron availability in vivo, potentially reducing Xfp's growth and virulence. These findings provide a basis for developing Methylobacterium spp. as sustainable biocontrol agents to manage Xfp in olive production systems.
Graphical Abstract
... Interactions between microorganisms and roots improve plant mineral nutrition and strengthen defenses against pathogens. Understanding these interactions is crucial for developing sustainable agricultural practices that use microorganisms as allies in promoting plant growth and soil health (Gomes et al., 2016;Cardoso & Andreote, 2016;Jacob, 2017;Sender et al., 2016;Thomashow et al., 2019;White et al., 2019). ...
Rhizophagy is a biological process in which microorganisms are temporarily internalized by plant roots, facilitating the absorption of essential nutrients. This study aims to explore the mechanisms of rhizophagy and its potential to promote more sustainable agriculture. The methodology was based on a systematic review of scientific literature, examining articles addressing plant-microorganism interactions and their impacts on plant nutrition. The results show that rhizophagy significantly enhances the uptake of nutrients such as nitrogen, phosphorus, and other essential minerals, while reducing dependence on chemical fertilizers. This interaction promotes more efficient use of natural resources and contributes to sustainable agricultural practices. Moreover, integrating rhizophagy into agricultural systems can increase plants’ resilience to environmental stresses such as drought and salinity while improving soil fertility and supporting microbial biodiversity. These benefits are relevant for addressing challenges related to food security and environmental conservation. In summary, rhizophagy offers a promising pathway toward more ecological and efficient agricultural practices, aligning with global sustainable development goals. Future studies are recommended to explore practical applications of this phenomenon in different cropping systems, aiming at innovation and sustainability in agricultural production.
... These relationships are dynamic and are shaped according to the plant tissue, the genetic profile of the host, and the prevailing environmental conditions. Numerous literature reports are concerned with the recording of the endophytic communities (such as bacterial endophytes) from many plant species and the examination of their plant beneficial functions due to the advantageous location from where they thrive and act [63][64][65]. ...
The endophytic strain Amfr20 was isolated from roots of the olive tree var. Amfissa. Based on core-genome phylogenomic analyses, it was classified as Bacillus velezensis. The isolate showed positive results in numerous plant growth promoting traits, as well as in abiotic stress tolerance and in colonization related traits in vitro. Furthermore, the strain exhibited antifungal activity in vitro through diffusible and volatile compounds. Whole genome analysis revealed that the strain possesses large and various arsenals of secondary metabolite biosynthetic gene clusters involved in the bioagent’s functional properties, including plant growth promotion, colonization, and plant defense elicitation, as well as having the genomic potential for abiotic stress mediation. Based on TLC-bioautography, the ethyl acetate extracts of secreted agar-diffusible compounds from Amfr20 through single and dual cultures were found to be bioactive independently of the fungal pathogen’s interaction. The bacterial endophyte also proved efficient in suppressing the severity of anthracnose olive rot and gray mold post-harvest diseases on olive fruits and table grape berries, respectively. Lastly, Amfr20 beneficially affected Arabidopsis thaliana growth under normal and saline conditions, while boosting the plant development of Solanum lycopersicum through seed biopriming and root irrigation methods. The results of this multilevel study indicate that the novel endophyte Amfr20 Bacillus velezensis is a promising bioagent that should be exploited in the future as an ecological biopesticide and/or biostimulant.
... However, it is clear that chemical fertilizers can reduce soil fertility and microorganisms [ 2 ]. Therefore, to produce sustainably lychee, endophytic microorganisms are thought to be the best solution [3][4][5]. Previously, we have established data on the endophytic microbiome of numerous crops, including coffee, black pepper, sugarcane, rice, banana, cashew, and citrus [6][7][8][9][10][11][12][13]; however, the endophytic microbial data of lychee are still unknown. Hence, the aim of this work was to establish data on the endophytic bacteriome of lychee ( Litchi chinensis S.) grown in this province using the metagenomic 16S rRNA gene sequencing for subsequent experiments towards sustainable lychee cultivation by applying endophytic bacteria. ...
This work reported the diversity profiling and predicted metabolic function of the endophytic bacteriome of lychee (Litchi chinensis S.) cultivated in Dak Lak Province of Vietnam for the first time. Roots of lychee were collected from three different fields in Krong Ana District in Dak Lak. 16S rRNA primers were used to sequence the metagenomic library. Kraken 2 was used to analyze the taxonomic distribution, while the MetaCyc database was used to predict the metabolic function. We identified 10 phyla, 14 classes, 27 orders, 30 families, and 27 genera of the endophytic bacteria from the sample. Actinomycetota was the most predominant phylum (84.49%), and biosynthesis was the bacteriome's primary function (75.42%). Data provided insight into the taxonomic distribution and metabolic function of lychee endophytic bacteria and might be helpful for the next steps concerning sustainable lychee cultivation using endophytic bacteria.
... Modulation of seedling development by endophytes such as fungal and bacterial entomopathogens is likely as a result of the continuous symbiosis of these microbes in colonizing seed tissues and thus, reliably participating in the development process such as the widespread capacity of fungal and bacterial entomopathogens to produce plant signal molecules (such as nitric oxide) growth regulators (such as auxins and ethylene) which could be the reflection of co-evolutionary association of microbes and plants [27]. An increase in the germination of seeds after treatment with fungal entomopathogens can also be caused by the fungus ability in producing phyto-hormones that stimulate seed germination [26]. ...
The use of bio-control measures as alternative to chemical pesticides is increasingly encouraged on the basis of food safety as chemical pesticides are dangerous to human health. However, limited attention is paid to the impact of these bio-control measures on the germination performance of treated seeds. In this study, the germination performance of stored cowpea seeds treated with isolates of entomopathogens (Beauveria bassiana, Metarhizium anisopliae, Verticillium lecanii and Bacillus thuringensis) usually used as bio-pesticides was investigated. The pure isolates were subjected to liquid fermentation technology using sucrose water. The isolates obtained through liquid fermentation were also inoculated into talc powder as solid medium. The germination viability of the cowpea seeds treated with the liquid and solid mediums of the isolates and stored for ten (10) weeks was determined using the standard germination test adopting the seed germination vigour (SGV) and the seed germination ability (SGA) as parameters. The study revealed that the cowpea seed treatment with the isolates in their liquid and solid mediums showed no significant impact on SGV and SGA when compared with control at the end of 1st and 5th week storage post-treatment. However a significant effect was seen at the end of 10th week storage post-treatment with the liquid medium of Verticillium lecanii showing better germination performance (SGV=58.33±1.67 and SGA=71.67±3.33) among other liquid isolates when compared with the control (SGV=68.33±1.67 and SGA=80.00±2.89), and the solid medium of Bacillus thuringensis revealing better germination performance (SGV=58.33±3.33 and SGA=71.67±1.67) among other solid isolates when compared with the control (SGV=68.33±1.67 and SGA=80.00±2.89). This study concludes that isolates of Beauveria bassiana, Metarhizium anisopliae, Verticillium lecanii and Bacillus thuringensis do not reduce germination performance of cowpea seeds when used as bio-control against cowpea storage pest. However, at longer storage post-treatment of cowpea seeds with the isolates, the germination performance may be reduced.
... In this study, we examined and analyzed the isolation and identification of endophytic fungi from a halophytic plant in two locations (inland and coastal). These isolates could help their host plant withstand salinity, heat, and drought and defend against various phytopathogens (Singh et al. 2021;Verma et al. 2021;White et al. 2019). In a previous study, the endophytic bacteria were extracted from surface sterilized leaves of L. axillare, identified, and analyzed for growth promotor (Alhaddad, Bitaar, and Abu-Dieyeh 2024). ...
Halophytes, plants that thrive in high‐salinity environments, host unique microbial communities, including fungal endophytes, which contribute to plant growth and pathogen resistance. This study aimed to isolate, identify, and evaluate the antagonistic potential of fungal endophytes from the halophytic plant Limonium axillare, collected from both inland and coastal habitats. Fungal endophytes were isolated, identified via molecular techniques, and tested for antagonistic activity against phytopathogenic fungi using dual‐culture assays. The results showed a diverse range of fungal endophytes, with Aspergillus and Cladosporium being the dominant genera. A total of 152 endophytic fungi were isolated from both locations, with 95 isolates coming from coastal plants and 57 from inland species. The isolates exhibited varying degrees of antagonistic activity against phytopathogens, highlighting their potential role in plant protection. Further research is needed to clarify these interactions' mechanisms and investigate their practical applications in agriculture. An endophytic isolate of Aspergillus terreus strain ((AL10) lim10qu) (ON210104.1) exhibited potent in vitro antifungal activity against Fusarium oxysporum, a pathogenic fungus affecting tomato plants. Greenhouse experiments demonstrated that the fungus significantly increased both the length of tomato seedlings and the overall plant biomass. Both laboratory‐based (in vitro) and field‐based (in vivo) evaluations of the strain ((AL10) lim10qu) (A. terreus) against F. oxysporum suggest the promising role of endophytes as effective biological control agents. Analysis using Gas Chromatography–Mass Spectrometry of the fungal extract detected around 100 compounds (secondary metabolites). In addition to gradually reducing the need for chemical fungicides, bio‐products can also contribute to sustainable agriculture.
