Harnessing Bacterial Endophytes for Promotion of Plant Growth and Biotechnological Applications: An Overview

Distinct interactions of ericoid mycorrhizae and plant growth-promoting bacteria: impacts on blueberry growth and heat resilience

Blueberries confront substantial challenges from climate change, such as rising temperatures and extreme heat, necessitating urgent solutions to ensure productivity. We hypothesized that ericoid mycorrhizal fungi (ErM) and plant growth-promoting bacteria (PGPB) would establish symbiotic relationships and increase heat stress tolerance in blueberries. A growth chamber study was designed with low (25/20°C) and high temperature (35/30°C) conditions with micropropagated blueberry plantlets inoculated with ErM, PGPB, and both. Gas exchange and chlorophyll fluorescence properties of the leaves were monitored throughout the growth. At harvest, biochemical assays and biomass analysis were performed to evaluate potential oxidative stress induced by elevated temperatures. ErM application boosted root biomass under 25/20°C conditions but did not impact photosynthetic efficiency. In contrast, PGPB demonstrated a dual role: enhancing photosynthetic capacity and reducing stomatal conductance notably under 35/30°C conditions. Moreover, PGPB showcased conflicting effects, reducing oxidative damage under 25/20°C conditions while intensifying it during 47°C heat shock. A significant highlight lies in the opposing effects of ErM and PGPB on root growth and stomatal conductance, signifying their reciprocal influence on blueberry plant behavior, which may lead to increased water uptake or reduced water use. Understanding these complex interactions holds promise for refining sustainable strategies to overcome climate challenges.

Siderophores and metallophores: Metal complexation weapons to fight environmental pollution

Siderophores are small molecules of organic nature, released by bacteria to chelate iron from the surrounding environment and subsequently incorporate it into the cytoplasm. In addition to iron, these secondary metabolites can complex with a wide variety of metals, which is why they are commonly studied in the environment. Heavy metals can be very toxic when present in large amounts on the planet, affecting public health and all living organisms. The pollution caused by these toxic metals is increasing, and therefore it is urgent to find practical, sustainable, and economical solutions for remediation. One of the strategies is siderophore-assisted bioremediation, an innovative and advantageous alternative for various environmental applications. This research highlights the various uses of siderophores and metallophores in the environment, underscoring their significance to ecosystems. The study delves into the utilization of siderophores and metallophores in both marine and terrestrial settings (e.g. bioremediation, biocontrol of pathogens, and plant growth promotion), such as bioremediation, biocontrol of pathogens, and plant growth promotion, providing context for the different instances outlined in the existing literature and highlighting their relevance in each field. The study delves into the structures and types of siderophores focusing on their singular characteristics for each application and methodologies used. Focusing on recent developments over the last two decades, the opportunities and challenges associated with siderophores and metallophores applications in the environment were mapped to arm researchers in the fight against environmental pollution.

Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds

Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10T was identified as a member of the genus Streptomyces. Strain TML10T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10T and the closest type strain, Streptomyces musisoli CH5-8T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10T = TBRC 15050T = NRRL B-65638T). Strain TML10T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro.

Community-forming traits play role in effective colonization of plant-growth-promoting bacteria and improved plant growth

Community-forming traits (CFts) play an important role in the effective colonization of plant-growth-promoting bacterial communities that influence host plants positively by modulating their adaptive functions. In this study, by considering plant-growth-promoting traits (PGPts) and community-forming traits (CFts), three communities were constructed, viz., SM1 (PGPts), SM2 (CFts), and SM3 (PGPts+CFts). Each category isolates were picked up on the basis of their catabolic diversity of different carbon sources. Results revealed a distinctive pattern in the colonization of the communities possessed with CF traits. It was observed that the community with CFts colonized inside the plant in groups or in large aggregations, whereas the community with only PGPts colonized as separate individual and small colonies inside the plant root and leaf. The effect of SM3 in the microcosm experiment was more significant than the uninoculated control by 22.12%, 27.19%, and 9.11% improvement in germination percentage, chlorophyll content, and plant biomass, respectively. The significant difference shown by the microbial community SM3 clearly demonstrates the integrated effect of CFts and PGPts on effective colonization vis-à-vis positive influence on the host plant. Further detailed characterization of the interaction will take this technology ahead in sustainable agriculture.

Global regulator IrrE on stress tolerance: a review

Stress tolerance is a vital attribute for all living beings to cope with environmental adversities. IrrE (also named PprI) from Deinococcus radiodurans enhances resistance to extreme radiation stress by functioning as a global regulator, mediating the transcription of genes involved in deoxyribonucleic acid (DNA) damage response (DDR). The expression of IrrE augmented the resilience of various species to heat, radiation, oxidation, osmotic stresses and inhibitors, encompassing bacterial, fungal, plant, and mammalian cells. Moreover, IrrE was employed in a global regulator engineering strategy to broaden its applications in stress tolerance. The regulatory impacts of heterologously expressed IrrE have been investigated at the molecular and systems level, including the regulation of genes, proteins, modules, or pathways involved in DNA repair, detoxification proteins, protective molecules, native regulators and other aspects. In this review, we discuss the regulatory role and mechanism of IrrE in the antiradiation response of D. radiodurans. Furthermore, the applications and regulatory effects of heterologous expression of IrrE to enhance abiotic stress tolerance are summarized in particular.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Assessment of Plant Growth-Promoting Parameters of Endophytes Isolated from Calotropis procera and Their Performance Under Irrigated and Non-irrigated Conditions

In the present study, bacterial and fungal endophytes are isolated from Calotropis procera, a drought-resistant plant and studied for their role in plant growth promotion. Among bacterial sp. Enterobacter cloacae subsp. cloacae strain CPR5B and fungus, Penicillium citrinum strain CPL1F, were identified as potent endophytes as both strains were able to produce Indole Acetic Acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and solubilize phosphate. Penicillium citrinum CPL1F also been shown to produce siderophore. The IAA production was observed to be 94.28 μg/mL and 17.1 μg/mL for bacterial and fungal sp., respectively. The phosphate solubilization was observed to be 76.41 μg/mL and 114.57 μg/mL, respectively. The in vitro plant treatment studies with bacterium and fungus under irrigated and non-irrigated conditions showed that both strains had promoted plant growth in both conditions with respect to their control. Both the strains showed significant changes in most of the growth parameters under endophyte-treated irrigated and non-irrigated conditions, suggesting their stress-dependent plant growth promotion. The present findings will contribute to exploring endophytes that enhance plant growth in adverse conditions and act as plant growth-promoting endophytes.

Isolation, Antimicrobial Effect and Metabolite Analysis of Bacillus amyloliquefaciens ZJLMBA1908 against Citrus Canker Caused by Xanthomonas citri subsp. citri

Citrus canker caused by Xanthomonas citri subsp. citri is a devastating bacterial disease with severe implications for the citrus industry. Microorganisms possessing biocontrol capabilities against X. citri subsp. citri offer a highly promising strategy for healthy citrus management. In the present study, a broad-spectrum antagonist strain ZJLMBA1908 with potent antibacterial activity against X. citri subsp. citri was isolated from symptomatic lemon leaves, and identified as Bacillus amyloliquefaciens. Cell-free supernatant (CFS) of strain ZJLMBA1908 also exhibited remarkable antimicrobial activity, especially suppressing the growth of X. citri subsp. citri and Nigrospora oryzae, with inhibition rates of 27.71% and 63.75%, respectively. The antibacterial crude extract (CE) derived from the CFS displayed effective activity against X. citri subsp. citri. A preventive treatment using the CE significantly reduced the severity and incidence of citrus canker in a highly susceptible citrus host. Additionally, the CE maintained activity in the presence of protease and under a wide range of temperature and pH treatments. Applying high-performance liquid chromatography (HPLC) to separate and purify the CE resulted in the discovery of one highly potent anti-X. citri subsp. citri subfraction, namely CE3, which could completely inhibit the growth of X. citri subsp. citri. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) analysis revealed that CE3 mainly consisted of palmitic acid, surfactin C15, phytosphingosine and dihydrosphingosine. Taken together, the results contribute to the possible biocontrol mechanisms of B. amyloliquefaciens ZJLMBA1908, as well as providing a promising new candidate strain as a biological control agent for controlling citrus canker.

Endophytic bacteria Klebsiella spp. and Bacillus spp. from Alternanthera philoxeroides in Madiwala Lake exhibit additive plant growth-promoting and biocontrol activities

BACKGROUND

The worldwide increase in human population and environmental damage has put immense pressure on the overall global crop production making it inadequate to feed the entire population. Therefore, the need for sustainable and environment-friendly practices to enhance agricultural productivity is a pressing priority. Endophytic bacteria with plant growth-promoting ability and biocontrol activity can strongly enhance plant growth under changing environmental biotic and abiotic conditions. Herein, we isolated halotolerant endophytic bacteria from an aquatic plant, Alternanthera philoxeroides, from the polluted waters of Madiwala Lake in Bangalore and studied their plant growth promotion (PGP) and biocontrol ability for use as bioinoculant.

RESULTS

The isolated bacterial endophytes were screened for salt tolerance ranging from 5 to 15% NaCl concentration. Klebsiella pneumoniae showed halotolerant up to 10% NaCl and Bacillus amyloliquefaciens and Bacillus subtilis showed up to 15%. All three strains demonstrated good PGP abilities such as aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, phosphate solubilization, ammonia production, and nitrogen fixation. In addition, K. pneumoniae also exhibited high indoleacetic acid (IAA) production (195.66 ± 2.51 µg/ml) and potassium solubilization (2.13 ± 0.07 ppm). B. amyloliquefaciens and B. subtilis showed good extracellular enzyme production against cellulase, lipase, protease, and amylase. Both the isolates showed a broad spectrum of antimicrobial activity against the tested organisms. The optimization of IAA production by K. pneumoniae was done by the response surface methodology (RSM) tool. Characterization of IAA produced by the isolate was done by gas chromatography-mass spectrometry (GCMS) analysis. The enhanced plant growth-promoting ability of K. pneumoniae was also demonstrated using various growth parameters in a pot trial experiment using the seeds of Vigna unguiculata.

CONCLUSION

The isolated bacterial endophytes reported in this study can be utilized as PGP promotion and biocontrol agents in agricultural applications, to enhance crop yield under salinity stress. The isolate K. pneumoniae may be used as a biofertilizer in sustainable agriculture and more work can be done to optimize the best formulations for its application as a microbial inoculant for crops.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Fungal endophyte bioinoculants as a green alternative towards sustainable agriculture

Over the past half century, limited use of synthetic fertilizers, pesticides, and conservation of the environment and natural resources have become the interdependent goals of sustainable agriculture. These practices support agriculture sustainability with less environmental and climatic impacts. Therefore, there is an upsurge in the need to introduce compatible booster methods for maximizing net production. The best straightforward strategy is to explore and utilize plant-associated beneficial microorganisms and their products. Bioinoculants are bioformulations consisting of selected microbial strains on a suitable carrier used in the enhancement of crop production. Fungal endophytes used as bioinoculants confer various benefits to the host, such as protection against pathogens by eliciting immune response, mineralization of essential nutrients, and promoting plant growth. Besides, they also produce various bioactive metabolites, phytohormones, and volatile organic compounds. To design various bioformulations, transdisciplinary approaches like genomics, transcriptomics, metabolomics, proteomics, and microbiome modulation strategies like gene editing and metabolic reconstruction have been explored. These studies will refine the existing knowledge on the diversity, phylogeny and beneficial traits of the microbes. This will also help in synthesizing microbial consortia by evaluating the role of structural and functional elements of communities in a controlled manner. The present review summarizes the beneficial aspects associated with fungal endophytes for capitalizing agricultural outputs, enlists various multi-omics techniques for understanding and modulating the mechanism involved in endophytism and the generation of new bioformulations for providing novel solutions for the enhancement of crop production.

Harnessing the action mechanisms of microbial endophytes for enhancing plant performance and stress tolerance: current understanding and future perspectives

Microbial endophytes are microorganisms that reside within plant tissues without causing any harm to their hosts. These microorganisms have been found to confer a range of benefits to plants, including increased growth and stress tolerance. In this review, we summarize the recent advances in our understanding of the mechanisms by which microbial endophytes confer abiotic and biotic stress tolerance to their host plants. Specifically, we focus on the roles of endophytes in enhancing nutrient uptake, modulating plant hormones, producing secondary metabolites, and activating plant defence responses. We also discuss the challenges associated with developing microbial endophyte-based products for commercial use, including product refinement, toxicology analysis, and prototype formulation. Despite these challenges, there is growing interest in the potential applications of microbial endophytes in agriculture and environmental remediation. With further research and development, microbial endophyte-based products have the potential to play a significant role in sustainable agriculture and environmental management.

Myco-synthesized copper oxide nanoparticles using harnessing metabolites of endophytic fungal strain Aspergillus terreus: an insight into antibacterial, anti-Candida, biocompatibility, anticancer, and antioxidant activities

BACKGROUND

The overuse of antibiotics leads to the emergence of antibiotic-resistant microbes which causes high mortality worldwide. Therefore, the synthesis of new active compounds has multifunctional activities are the main challenge. Nanotechnology provides a solution for this issue.

METHOD

The endophytic fungal strain Aspergillus terreus BR.1 was isolated from the healthy root of Allium sativum and identified using internal transcribed spacer (ITS) sequence analysis. The copper oxide nanoparticles (CuO-NPs) were synthesized by harnessing the metabolites of the endophytic fungal strain. The UV-Visble spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), Transmission electron micrscopy (TEM), Energy dispersive X-ray (EDX), X-ray diffraction (XRD), Dynamic light scattering (DLS), and zeta potential (ζ) were used for the characterization of synthesized CuO-NPs. The activity against different pathogenic bacteria and Candida species were investigated by agar well-diffusion method. The biocombatibility and anticancer activity were assessed by MTT assay method. The scavenging of DPPH was used to investigate the antioxidant activity of synthesized CuO-NPs.

RESULTS

Data showed the successful formation of crystalline nature and spherical shape CuO-NPs with sizes in the ranges of 15-55 nm. The EDX reveals that the as-formed sample contains ions of C, O, Cl, and Cu with weight percentages of 18.7, 23.82, 11.31, and 46.17%, respectively. The DLS and ζ-potential showed high homogeneity and high stability of synthesized CuO-NPs with a polydispersity index (PDI) of 0.362 and ζ-value of - 26.6 mV. The synthesized CuO-NPs exhibited promising antibacterial and anti-Candida activity (concentration-dependent) with minimum inhibitory concentration (MIC) values in the ranges of 25-50 µg mL^-1. Moreover, the fungal mediated-CuO-NPs targeted cancer cells of MCF7 and PC3 at low IC₅₀ concentrations of 159.2 ± 4.5 and 116.2 ± 3.6 µg mL^-1, respectively as compared to normal cells (Vero and Wi38 with IC₅₀ value of 220.6 ± 3.7 and 229.5 ± 2.1 µg mL^-1, respectively). The biosynthesized CuO-NPs showed antioxidant activity as detected by the DPPH method with scavenging percentages of 80.5 ± 1.2% at a concentration of 1000 µg mL^-1 and decreased to 20.4 ± 4.2% at 1.9 µg mL^-1 as compared to ascorbic acid (control) with scavenging activity of 97.3 ± 0.2 and 37.5 ± 1.3% at the same concentrations, respectively.

CONCLUSION

The fungal mediated-CuO-NPs exhibited promising activity and can be integrated into various biomedical and theraputic applications.

Analysis of Endophytic Bacterial Diversity in Rice Seeds with Regional Characteristics in Yunnan Province, China, Based on High-Throughput Sequencing Technology

Examining the endophytic bacteria in rice seeds from Yunnan Province displaying regional characteristics is vital for exploring strain resources, improving rice production, and conducting subsequent research. This study investigated nine characteristic rice varieties from Yunnan Province using high-throughput sequencing technology based on the Illumina Novaseq platform to reveal their dominant bacterial communities and discussed their endophytic bacterial community differences. A total of 829 shared OTUs, and 233 unique OTUs were identified in the nine samples, while the bacteria included Proteobacteria, Actinobacteriota, and Firmicutes, of which Proteobacteria was the most dominant. Pantoea and Methylorubrum were the most abundant at the genus level, with Curtobacterium, Brevundimonas, and Luteibacter representing the specific genera in the rice seed samples. This study revealed the endophytic structure and diversity in the seeds of nine rice varieties displaying regional characteristics and provided a foundation for further research into rice containing endophytic bacteria.

Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil

Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.

Coffee-Associated Endophytes: Plant Growth Promotion and Crop Protection

Endophytic microbes are a ubiquitous group of plant-associated communities that colonize the intercellular or intracellular host tissues while providing numerous beneficial effects to the plants. All the plant species are thought to be associated with endophytes, majorly constituted with bacteria and fungi. During the last two decades, there has been a considerable movement toward the study of endophytes associated with coffee plants. In this review, the main consideration is given to address the coffee-associated endophytic bacteria and fungi, particularly their action on plant growth promotion and the biocontrol of pests. In addition, we sought to identify and analyze the gaps in the available research. Additionally, the potential of endophytes to improve the quality of coffee seeds is briefly discussed. Even though there are limited studies on the subject, the potentiality of coffee endophytes in plant growth promotion through enhancing nitrogen fixation, availability of minerals, nutrient absorption, secretion of phytohormones, and other bioactive metabolites has been well recognized. Further, the antagonistic effect against various coffee pathogenic bacteria, fungi, nematodes, and also insect pests leads to the protection of the crop. Furthermore, it is recognized that endophytes enhance the sensory characteristics of coffee as a new field of study.

A Comparative Study of the Synthesis and Characterization of Biogenic Selenium Nanoparticles by Two Contrasting Endophytic Selenobacteria

The present study examined the biosynthesis and characterization of selenium nanoparticles (SeNPs) using two contrasting endophytic selenobacteria, one Gram-positive (Bacillus sp. E5 identified as Bacillus paranthracis) and one Gram-negative (Enterobacter sp. EC5.2 identified as Enterobacter ludwigi), for further use as biofortifying agents and/or for other biotechnological purposes. We demonstrated that, upon regulating culture conditions and selenite exposure time, both strains were suitable "cell factories" for producing SeNPs (B-SeNPs from B. paranthracis and E-SeNPs from E. ludwigii) with different properties. Briefly, dynamic light scattering (DLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) studies revealed that intracellular E-SeNPs (56.23 ± 4.85 nm) were smaller in diameter than B-SeNPs (83.44 ± 2.90 nm) and that both formulations were located in the surrounding medium or bound to the cell wall. AFM images indicated the absence of relevant variations in bacterial volume and shape and revealed the existence of layers of peptidoglycan surrounding the bacterial cell wall under the conditions of biosynthesis, particularly in the case of B. paranthracis. Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), energy-dispersive X-ray (EDS), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) showed that SeNPs were surrounded by the proteins, lipids, and polysaccharides of bacterial cells and that the numbers of the functional groups present in B-SeNPs were higher than in E-SeNPs. Thus, considering that these findings support the suitability of these two endophytic stains as potential biocatalysts to produce high-quality Se-based nanoparticles, our future efforts must be focused on the evaluation of their bioactivity, as well as on the determination of how the different features of each SeNP modulate their biological action and their stability.

Secondary metabolites from endophytic fungi: Production, methods of analysis, and diverse pharmaceutical potential

The synthesis of secondary metabolites is a constantly functioning metabolic pathway in all living systems. Secondary metabolites can be broken down into numerous classes, including alkaloids, coumarins, flavonoids, lignans, saponins, terpenes, quinones, xanthones, and others. However, animals lack the routes of synthesis of these compounds, while plants, fungi, and bacteria all synthesize them. The primary function of bioactive metabolites (BM) synthesized from endophytic fungi (EF) is to make the host plants resistant to pathogens. EF is a group of fungal communities that colonize host tissues' intracellular or intercellular spaces. EF serves as a storehouse of the above-mentioned bioactive metabolites, providing beneficial effects to their hosts. BM of EF could be promising candidates for anti-cancer, anti-malarial, anti-tuberculosis, antiviral, anti-inflammatory, etc. because EF is regarded as an unexploited and untapped source of novel BM for effective drug candidates. Due to the emergence of drug resistance, there is an urgent need to search for new bioactive compounds that combat resistance. This article summarizes the production of BM from EF, high throughput methods for analysis, and their pharmaceutical application. The emphasis is on the diversity of metabolic products from EF, yield, method of purification/characterization, and various functions/activities of EF. Discussed information led to the development of new drugs and food additives that were more effective in the treatment of disease. This review shed light on the pharmacological potential of the fungal bioactive metabolites and emphasizes to exploit them in the future for therapeutic purposes.

A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index

Recent advances in genome sequencing have led to an increase in the number of sequenced genomes. However, the presence of repetitive sequences complicates the assembly of plant genomes. The LTR assembly index (LAI) has recently been widely used to assess the quality of genome assembly, as a higher LAI is associated with a higher quality of assembly. Here, we assessed the quality of assembled genomes of 1664 plant and algal genomes using LAI and reported the results as data repository called PlantLAI (https://bioinformatics.um6p.ma/PlantLAI). A number of 55 117 586 pseudomolecules/scaffolds with a total length of 988.11 gigabase-pairs were examined using the LAI workflow. A total of 46 583 551 accurate LTR-RTs were discovered, including 2 263 188 Copia, 2 933 052 Gypsy, and 1 387 311 unknown superfamilies. Consequently, only 1136 plant genomes are suitable for LAI calculation, with values ranging from 0 to 31.59. Based on the quality classification system, 476 diploid genomes were classified as draft, 472 as reference, and 135 as gold genomes. We also provide a free webtool to calculate the LAI of newly assembled genomes and the ability to save the result in the repository. The data repository is designed to fill in the gaps in the reported LAI of existing genomes, while the webtool is designed to help researchers calculate the LAI of their newly sequenced genomes.

Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria

This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.

Complete genome of Sphingomonas paucimobilis ZJSH1, an endophytic bacterium from Dendrobium officinale with stress resistance and growth promotion potential

Sphingomonas paucimobilis ZJSH1 is an endophytic bacterium isolated from the roots of Dendrobium officinale with the ability to promote plant growth. It was found that the genome of strain ZJSH1 had gene fragment rearrangement compared with the genomes of the other four strains of S. paucimobilis, and the genome was integrated with phage genes. Functional analysis showed that the strain contained colonization-related genes, chemotaxis and invasion. A variety of genes encoding active materials, such as hormones (IAA, SA, ABA and zeaxanthin), phosphate cycle, antioxidant enzymes, and polysaccharides were identified which provide the strain with growth promotion and stress-resistant characteristics. Experiments proved that S. paucimobilis ZJSH1 grew well in media containing 80 g/L sodium chloride, 240 g/L polyethylene glycol and 800 μmol/L Cd²⁺, indicating its potential for resistance to stresses of salt, drought and cadmium, respectively. S. paucimobilis ZJSH1 is the only endophytic bacterium of this species that has been reported to promote plant growth. The analysis of its genome is conducive to understanding its growth-promoting mechanism and laying a foundation for the development and utilization of this species in the field of agriculture.

Plant-Growth Promoting Microbes Change the Photosynthetic Response to Light Quality in Spinach

In this study, the combined effect of plant growth under different light quality and the application of plant-growth-promoting microbes (PGPM) was considered on spinach (Spinacia oleracea L.) to assess the influence of these factors on the photosynthetic performance. To pursue this goal, spinach plants were grown in a growth chamber at two different light quality regimes, full-spectrum white light (W) and red-blue light (RB), with (I) or without (NI) PGPM-based inoculants. Photosynthesis-light response curves (LRC) and photosynthesis-CO₂ response curves (CRC) were performed for the four growth conditions (W-NI, RB-NI, W-I, and RB-I). At each step of LRC and CRC, net photosynthesis (P_N), stomatal conductance (g_s), C_i/C_a ratio, water use efficiency (WUE_i), and fluorescence indexes were calculated. Moreover, parameters derived from the fitting of LRC, such as light-saturated net photosynthesis (P_Nmax), apparent light efficiency (Q_pp), and dark respiration (R_d), as well as the Rubisco large subunit amount, were also determined. In not-inoculated plants, the growth under RB- regime improved P_N compared to W-light because it increased stomatal conductance and favored the Rubisco synthesis. Furthermore, the RB regime also stimulates the processes of light conversion into chemical energy through chloroplasts, as indicated by the higher values of Q_pp and P_Nmax in RB compared to W plants. On the contrary, in inoculated plants, the P_N enhancement was significantly higher in W (30%) than in RB plants (17%), which showed the highest Rubisco content among all treatments. Our results indicate that the plant-growth-promoting microbes alter the photosynthetic response to light quality. This issue must be considered when PGPMs are used to improve plant growth performance in a controlled environment using artificial lighting.

Additive Effect of the Composition of Endophytic Bacteria Bacillus subtilis on Systemic Resistance of Wheat against Greenbug Aphid Schizaphis graminum Due to Lipopeptides

The use of biocontrol agents based on endophytic bacteria against phloem-feeding insects is limited by a lack of knowledge and understanding of the mechanism of action of the endophyte community that makes up the plant microbiome. In this work, the mechanisms of the additive action of endophytic strains B. subtilis 26D and B. subtilis 11VM on the resistance of bread spring wheat against greenbug aphid Schizaphis graminum, was studied. It was shown that B. subtilis 26D secreted lipopeptide surfactin and phytohormones cytokinins, and B. subtilis 11VM produced iturin and auxins into the cultivation medium. Both strains and their lipopeptide-rich fractions showed direct aphicidal activity against greenbug aphid. For the first time, it was shown that B. subtilis 26D and B. subtilis 11VM in the same manner, as well as their lipopeptide-rich fractions, activated the expression of salicylate- and ethylene-dependent PR genes, and influenced plant redox metabolism, which led to an increase in plant endurance against aphids. The composition of endophytic strains B. subtilis 26D + B. subtilis 11VM had an additive effect on plant resistance to aphids due to an increase in the number of endophytic bacterial cells, and, as well as due to the synergistic effect of their mixture of lipopeptides - surfactin + iturin, both on the aphid mortality and on the expression of PR1 and PR3 genes. All these factors can be the reason for the observed increase in the growth of plants affected by aphids under the influence of B. subtilis 26D and B. subtilis 11VM, individually and in composition. The study demonstrates the possibility of creating in the future an artificial composition to enhance plant microbiome with endophytic bacteria, which combines growth-promoting and plant immunity stimulating properties against phloem-feeding insects. This direction is one of the most promising approaches to green pesticide discovery in the future.

Bacteria Associated with the Roots of Common Bean (Phaseolus vulgaris L.) at Different Development Stages: Diversity and Plant Growth Promotion

Current agricultural methodologies are vulnerable to erratic climate and are dependent on cost-intensive fertilization to ensure high yields. Sustainable practices should be pursued to ensure food security. Phaseolus vulgaris L. is one of the most produced legumes worldwide and may be an alternative to reduce the environmental impact of meat production as a reliable source of high-quality protein. Plant growth-promoting rhizobacteria (PGPR) are emerging as a sustainable option to increase agricultural production. To understand the dynamics between plants and microorganisms, the culturable microbiota of bean roots was isolated and identified at distinct stages of plant development (early and late vegetative growth, flowering, and pod) and root compartments (rhizoplane, endosphere, and nodules). Diversity and abundance of bacteria associated with root compartments differed throughout the plant life cycle. Bacterial plant growth promotion (PGP) and protection abilities (indole-3-acetic acid production, siderophore synthesis, and antifungal activity) were assessed and associated with plant phenology, demonstrating that among the bacteria associated with plant roots, several strains had an active role in the response to plant biological needs at each stage. Several strains stood out for their ability to display one or more PGP traits, being excellent candidates for efficient stage-specific biostimulants for application in precision agriculture.

Alleviate the Drought Stress on Triticum aestivum L. Using the Algal Extracts of Sargassum latifolium and Corallina elongate Versus the Commercial Algal Products

Herein, two seaweed extracts (Sargassum latifolium and Corallina elongate), and two commercial seaweed products (Canada power and Oligo-X) with a concentration of 5% were used to alleviate the drought stress on wheat plants. The extract of C. elongate had the highest capacity to ameliorate the deleterious effects of water scarcity followed by S. latifolium and the commercial products. The drought stress reduced wheat shoots length and the contents of pigments (chlorophyll and carotenoids), carbohydrates, and proteins. While the highest increment in the total carbohydrates and protein contents of the wheat shoot after two stages, 37-and 67-days-old, were noted in drought-stressed plants treated with C. elongate extract with values of (34.6% and 22.8%) and (51.9% and 39.5%), respectively, compared to unstressed plants. Decreasing the activity of antioxidant enzymes, peroxidase, superoxidase dismutase, and polyphenol oxidase in drought-stressed plants treated with algal extracts indicated amelioration of the response actions. Analysis of phytohormones in wheat plants exhibited increasing GA3 and IAA contents with percentages of (20.3-13.8%) and (72.7-25%), respectively. Interestingly, all morphological and metabolic characteristics of yield were improved due to the algal treatments compared with untreated drought-stressed plants. Overall, the algal extracts, especially those from seaweed of C. elongate, could represent a sustainable candidate to overcome the damage effects of water deficiency in the wheat plant.

The Diversity of Fungal Endophytes from Wild Grape Vitis amurensis Rupr

Grapevine endophytic fungi have great potential for application in agriculture and represent an important source of various compounds with valuable biological activities. Wild grapevine is known to host a great number of rare and unidentified endophytes and may represent a rich repository of potential vineyard biocontrol agents. This investigation aimed to study the fungal endophytic community of wild grape Vitis amurensis Rupr. using a cultivation-dependent (fungi sowing) and a cultivation-independent (next-generation sequencing, NGS) approach. A comprehensive analysis of the endophytic fungal community in different organs of V. amurensis and under different environmental conditions has been performed. According to the NGS analysis, 12 taxa of class level were presented in different grapevine organs (stem, leaf, berry, seed). Among the 12 taxa, sequences of two fungal classes were the most represented: Dothideomycetes-60% and Tremellomycetes-33%. The top five taxa included Vishniacozyma, Aureobasidiaceae, Cladosporium, Septoria and Papiliotrema. The highest number of fungal isolates and sequences were detected in the grape leaves. The present data also revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic fungi in the wild Amur grape. The number of fungi recovered from grape tissues in autumn was two times higher than in summer. Thus, this study is the first to describe and analyze the biodiversity of the endophytic fungal community in wild grapevine V. amurensis.

An Insight into the Endophytic Bacterial Community of Tomato after Spray Application of Propiconazole and Bacillus subtilis Strain NBRI-W9

Propiconazole (PCZ) is a commonly sprayed fungicide against fungal pathogens. Being systemic in action, it reaches subcellular layers and impacts the endophytes. Although PCZ is a fungicide, it is hypothesized to exert an inhibitory effect on the bacterial endophytes. Therefore, this study aims to get an insight into the perturbations caused by the systemically acting antifungal agents PCZ and Bacillus subtilis (W9) and the consequences thereof. The current study compared the 16S rRNA microbial diversity, abundance, and functions of the endophytic bacterial community of tomato in response to PCZ, W9, and PCZ+W9 application. The implications of these treatments on the development of bacterial speck disease by Pseudomonas syringae were also studied. The culturable endophyte population fluctuated after (bio)fungicide application and stabilized by 72 h. At 72 h, the endophyte population was ~3.6 × 103 CFUg-1 in control and ~3.6 × 104 in W9, ~3.0 × 102 in PCZ, and ~5.3 × 103 in PCZ+W9 treatment. A bacterial community analysis showed a higher relative abundance of Bacillales, Burkholderiales, Rhizobiales, Pseudomonadales, and Actinomycetales in the W9 treatment compared with that in the PCZ treatment and control. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis showed enhanced metabolic pathways related to secretion, stress, chemotaxis, and mineral nutrition in the W9 treatment. Disease severity was greater in PCZ than that in the W9 treatment. Disease severity on tomato plants showed strong negative correlations with Sphingomonas (r = -0.860) and Janthinobacterium (r = -0.810), indicating that the natural biocontrol communities are agents of plant resistance to diseases. Outcomes show that systemic chemicals are a potential threat to the nontarget endophytes and that plants became susceptible to disease on endophyte decline; this issue could be overcome by the application of microbial inoculums. IMPORTANCE Endophytes are plant inhabitants acting as its extended genome. The present study highlights the importance of maintaining plant endophytes for sustainable disease resistance in plants. The impact of chemical fungicides and biofungicides was shown on tomato endophytes, in addition to their implications on plant susceptibility to bacterial speck disease. The observations point toward the deleterious effects of systemic pesticide application on endophyte niches that disrupt their diversity and functions compromising plant immunity.

Enhanced legume growth and adaptation to degraded estuarine soils using Pseudomonas sp. nodule endophytes

The joint estuary of Tinto and Odiel rivers (SW Spain) is one of the most degraded and polluted areas in the world and its recovery is mandatory. Legumes and their associated bacteria are recommended sustainable tools to fight against soils degradation and loss of fertility due to their known positive impacts on soils. The aim of this work was to isolate and characterize plant growth promoting nodule endophytes (PGPNE) from inside nodules of Medicago spp. naturally growing in the estuary of the Tinto and Odiel Rivers and evaluate their ability to promote legume adaptation in degraded soils. The best rhizobia and non-rhizobia among 33 endophytes were selected based on their plant growth promoting properties and bacterial enzymatic activities. These strains, identified as Pseudomonas sp. N4, Pseudomonas sp. N8, Ensifer sp. N10 and Ensifer sp. N12, were used for in vitro studies using Medicago sativa plants. The effects of individual or combined inoculation on seed germination, plant growth and nodulation were studied, both on plates and pots containing nutrient-poor soils and moderately contaminated with metals/loids from the estuary. In general, inoculation with combinations of rhizobia and Pseudomonas increased plant biomass (up to 1.5-fold) and nodules number (up to 2-fold) compared to single inoculation with rhizobia, ameliorating the physiological state of the plants and helping to regulate plant stress mechanisms. The greatest benefits were observed in plants inoculated with the consortium containing the four strains. In addition, combined inoculation with Ensifer and Pseudomonas increased As and metals accumulation in plant roots, without significant differences in shoot metal accumulation. These results suggest that PGPNE are useful biotools to promote legume growth and phytostabilization potential in nutrient-poor and/or metals contaminated estuarine soils.

Endophytes and their potential in biotic stress management and crop production

Biotic stress is caused by harmful microbes that prevent plants from growing normally and also having numerous negative effects on agriculture crops globally. Many biotic factors such as bacteria, fungi, virus, weeds, insects, and nematodes are the major constrains of stress that tends to increase the reactive oxygen species that affect the physiological and molecular functioning of plants and also led to the decrease in crop productivity. Bacterial and fungal endophytes are the solution to overcome the tasks faced with conventional farming, and these are environment friendly microbial commodities that colonize in plant tissues without causing any damage. Endophytes play an important role in host fitness, uptake of nutrients, synthesis of phytohormone and diminish the injury triggered by pathogens via antibiosis, production of lytic enzymes, secondary metabolites, and hormone activation. They are also reported to help plants in coping with biotic stress, improving crops and soil health, respectively. Therefore, usage of endophytes as biofertilizers and biocontrol agent have developed an eco-friendly substitute to destructive chemicals for plant development and also in mitigation of biotic stress. Thus, this review highlighted the potential role of endophytes as biofertilizers, biocontrol agent, and in mitigation of biotic stress for maintenance of plant development and soil health for sustainable agriculture.

Antimicrobial, Antiviral, and In-Vitro Cytotoxicity and Mosquitocidal Activities of Portulaca oleracea-Based Green Synthesis of Selenium Nanoparticles

The aqueous extract of Portulaca oleracea was used as a biocatalyst for the reduction of Na₂SeO₃ to form Se-NPs that appeared red in color and showed maximum surface plasmon resonance at a wavelength of 266 nm, indicating the successful Phyto-fabrication of Se-NPs. A FT-IR chart clarified the role of plant metabolites such as proteins, carbohydrates, and amino acids in capping and stabilizing Se-NPs. TEM, SAED, and XRD analyses indicated the formation of spherical, well-arranged, and crystalline Se-NPs with sizes in the range of 2-22 nm. SEM-EDX mapping showed the maximum peaks of Se at 1.4, 11.3, and 12.4 KeV, with weight and atomic percentages of 36.49 and 30.39%, respectively. A zeta potential of -43.8 mV also indicated the high stability of the synthesized Se-NPs. The Phyto-synthesized Se-NPs showed varied biological activities in a dose-dependent manner, including promising activity against pathogenic bacteria and Candida species with varied MIC values in the range of 12.5-50 µg·mL^-1. Moreover, the Se-NPs showed antiviral activity toward HAV and Cox-B4, with percentages of 70.26 and 62.58%, respectively. Interestingly, Se-NPs showed a target orientation to cancer cell lines (HepG2) with low IC₅₀ concentration at 70.79 ± 2.2 µg·mL^-1 compared to normal cell lines (WI-38) with IC₅₀ at165.5 ± 5.4 µg·mL^-1. Moreover, the as-formed Se-NPs showed high activity against various instar larvae I, II, III, and IV of Culex pipiens, with the highest mortality percentages of 89 ± 3.1, 73 ± 1.2, 68 ± 1.4, and 59 ± 1.0%, respectively, at 50 mg L^-1. Thus, P. oleracea-based Se-NPs would be strong potential antimicrobial, anti-viral, anti-cancer, and anti-insect agents in the pharmaceutical and biomedical industries.

Bacterial bioinoculants adapted for sustainable plant health and soil fertility enhancement in Namibia

The increase in dryland agriculture elicits the need to develop sustainable practices that improve crop yield and protect soil fertility. The use of biofertilisers adapted to nutrient deficient soils and arid climates would help achieve this. In this review, the use of plant growth-promoting bacteria is explored as a possible solution to the current state of dryland agriculture and climate change threats to agriculture. Plant microbe interactions form the basis of this review as evidence has shown that these interactions often exist to improve the health of plants. This is achieved by the production of important biochemicals and enzymes like indole acetic acid and amino cyclopropane-1-carboxylate deaminase while also actively protecting plants from pathogens including fungal pathogens. Research, therefore, has shown that these plant-growth promoting bacteria may be exploited and developed into biofertilisers. These biofertilisers are both economically and environmentally sustainable while improving soil quality and crop yield. The literature presented in this review is in context of the Namibian climate and soil profiles.

A Plant Growth Promoting of Rhizobacteria and Endophytic Bacteria in Vegetable Rhizosphere and Root Samples

Rhizobacteria and endophytic bacteria are popular for its abilities in influencing plant growth and development. The strategy employed these bacteria as biofertilizer for planting is believed to bring several benefits such as low cost, eco-friendly, and feasible. One of the remarkable products for plant growth promoting provided by rhizobacteria and endophytic bacteria were the advantageous enzymes such as 1-aminocyclopropane-1-carboxylate deaminase, phosphatase, and cellulase. These biocatalysts then involve in several direct or indirect pathways of nutrient, growth factor, and/or defense factor synthesizes. From five different essential leafy vegetables in Thailand, this study aimed to investigate the plant growth promoting potentials of endophytic bacteria and rhizobacteria isolated from root tissue and rhizosphere, respectively, via IAA quantitative and enzyme activity assays. The selected bacterial strains were further identified using 16S rRNA gene sequencing and observed their interaction with plant root using scanning electron microscope method. Our study, thus far, has isolated two bacterial strains of Bacillus subtilis MSE5 and Bacillus cereus AVR1, respectively, with multifunctional traits of potential on the plant growth. Importantly, these two strains of MSE5 and AVR1 had shown the capacity to advance root colonization. Therefore, MSE5 and AVR1 are recommended for further studies in developing eco-friendly biofertilizer. In addition, some novel cellulose-degrading bacterial strains with significant potential on hydrolysis capacity were also isolated that might be valuable for industrial applications.

Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica

There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.

Biocontrol of early blight disease of eggplant using endophytic Aspergillus terreus: improving plant immunological, physiological and antifungal activities

BACKGROUND

The eggplant suffers from many biotic stresses that cause severe damage to crop production. One of the most destructive eggplant pathogens is Alternaria solani, which causes early blight disease. A pot experiment was conducted to evaluate the role of fungal endophytes in protecting eggplant against early blight as well as in improving its growth performance.

RESULTS

Endophytic Aspergillus terreus was isolated from Ocimum basilicum leaves and identified morphologically and genetically. In vitro, crude extract of endophytic A. terreus exhibited promising antifungal activity against A. solani where minimum inhibitory concentration (MIC) was 1.25 mg/ml. Severity of the disease and rate of protection from the disease were recorded. Vegetative growth indices, physiological resistance signs (photosynthetic pigments, carbohydrates, proteins, phenols, proline, malondialdehyde (MDA), antioxidant enzymes), and isozymes were estimated. Alternaria solani caused a highly disease severity (87.5%) and a noticeable decreasing in growth characteristics and photosynthetic pigments except for carotenoids. Also, infection with A. solani caused significant decreases in the contents of carbohydrate and protein by 29.94% and 10.52%, respectively. Infection with A. solani caused enhancement in phenolics (77.21%), free proline (30.56%), malondialdehyde (30.26%), superoxide dismutase (SOD) (125.47%), catalase (CAT) (125.93%), peroxidase (POD) (25.07%) and polyphenol oxidase (PPO) (125.37%) compared to healthy plants. In contrast, the use of A. terreus on infected plants succeeded in recovering eggplants from the disease, as the disease severity was recorded (caused protection by 66.67%). Application of A. terreus either on healthy or infected eggplants showed several responses in number and density of peroxidase (POD) and polyphenol oxidase (PPO) isozymes.

CONCLUSION

It is necessary for us to address the remarkable improvement in the photosynthetic pigments, protein, carbohydrates, and enzymatic activity compared to infected control, which opens the way for more studies on the use of biocides as safe alternatives against fungal diseases.

Overview of biofertilizers in crop production and stress management for sustainable agriculture

With the increase in world population, the demography of humans is estimated to be exceeded and it has become a major challenge to provide an adequate amount of food, feed, and agricultural products majorly in developing countries. The use of chemical fertilizers causes the plant to grow efficiently and rapidly to meet the food demand. The drawbacks of using a higher quantity of chemical or synthetic fertilizers are environmental pollution, persistent changes in the soil ecology, physiochemical composition, decreasing agricultural productivity and cause several health hazards. Climatic factors are responsible for enhancing abiotic stress on crops, resulting in reduced agricultural productivity. There are various types of abiotic and biotic stress factors like soil salinity, drought, wind, improper temperature, heavy metals, waterlogging, and different weeds and phytopathogens like bacteria, viruses, fungi, and nematodes which attack plants, reducing crop productivity and quality. There is a shift toward the use of biofertilizers due to all these facts, which provide nutrition through natural processes like zinc, potassium and phosphorus solubilization, nitrogen fixation, production of hormones, siderophore, various hydrolytic enzymes and protect the plant from different plant pathogens and stress conditions. They provide the nutrition in adequate amount that is sufficient for healthy crop development to fulfill the demand of the increasing population worldwide, eco-friendly and economically convenient. This review will focus on biofertilizers and their mechanisms of action, role in crop productivity and in biotic/abiotic stress tolerance.

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.

Temporal Dynamics of Endogenous Bacterial Composition in Rice Seeds During Maturation and Storage, and Spatial Dynamics of the Bacteria During Seedling Growth

Seed endophytes are of interest because they are believed to affect seed quality, and ultimately, plant growth and fitness. A comprehensive understanding of the assembly of the seed microbiome during seed development and maturation, the fate of microbes during storage, and the migration of microbes during seedling growth are still lacking. In this study, to understand the assembly and fate of endogenous bacteria in rice seeds from the ripening stage to the storage and seedling stages, we employed culture-dependent and metagenomic analyses. Bacterial communities in rice seeds were composed of a few dominant taxa that were introduced at the milky and dough stages, and they persisted during seed maturation. The culturable bacterial population gradually increased during the ripening stage, whereas there was a gradual decrease during storage. Bacteria that persisted during storage proliferated after imbibition and were distributed and established in the shoots and roots of rice seedlings. The storage temperature influenced the abundance of bacteria, which consequently changed the bacterial composition in the shoots and roots of seedlings. Pantoea, Pseudomonas, and Allorhizobium were consistently abundant from seed development to the germination stage. Some endogenous bacterial strains significantly promoted the growth of Arabidopsis and rice plants. Overall, our results indicate that rice seeds are colonized by a few bacterial taxa during seed development, and their relative abundance fluctuates during storage and contributes significantly to the establishment of endophytes in the stems and roots of rice plants. The selected bacterial isolates can be used to improve the growth and health of rice plants. To the best of our knowledge, this is the first study to reveal the dynamics of bacterial populations during storage of rice seeds at different temperatures. The temporal dynamics of the bacterial community during seed storage provide clues for the manipulation of endogenous bacteria in rice plants.

Light enhanced the antimicrobial, anticancer, and catalytic activities of selenium nanoparticles fabricated by endophytic fungal strain, Penicillium crustosum EP-1

Selenium nanoparticles (Se-NPs) has recently received great attention over owing to their superior optical properties and wide biological and biomedical applications. Herein, crystallographic and dispersed spherical Se-NPs were green synthesized using endophytic fungal strain, Penicillium crustosum EP-1. The antimicrobial, anticancer, and catalytic activities of biosynthesized Se-NPs were investigated under dark and light (using Halogen tungsten lamp, 100 Watt, λ > 420 nm, and light intensity of 2.87 W m⁻²) conditions. The effect of Se-NPs was dose dependent and higher activities against Gram-positive and Gram-negative bacteria as well different Candida spp. were attained in the presence of light than obtained under dark conditions. Moreover, the viabilities of two cancer cells (T47D and HepG2) were highly decreased from 95.8 ± 2.9% and 93.4 ± 3.2% in dark than those of 84.8 ± 2.9% and 46.4 ± 3.3% under light-irradiation conditions, respectively. Significant decreases in IC₅₀ values of Se-NPs against T47D and HepG2 were obtained at 109.1 ± 3.8 and 70.4 ± 2.5 µg mL⁻¹, respectively in dark conditions than 19.7 ± 7.2 and 4.8 ± 4.2 µg mL⁻¹, respectively after exposure to light-irradiation. The photoluminescence activity of Se-NPs revealed methylene blue degradation efficiency of 89.1 ± 2.1% after 210 min under UV-irradiation compared to 59.7 ± 0.2% and 68.1 ± 1.03% in dark and light conditions, respectively. Moreover, superior stability and efficient MB degradation efficiency were successfully achieved for at least five cycles.

Biosynthetic Mechanisms of Secondary Metabolites Promoted by the Interaction Between Endophytes and Plant Hosts

Endophytes is a kind of microorganism resource with great potential medicinal value. The interactions between endophytes and host not only promote the growth and development of each other but also drive the biosynthesis of many new medicinal active substances. In this review, we summarized recent reports related to the interactions between endophytes and hosts, mainly regarding the research progress of endophytes affecting the growth and development of host plants, physiological stress and the synthesis of new compounds. Then, we also discussed the positive effects of multiomics analysis on the interactions between endophytes and their hosts, as well as the application and development prospects of metabolites synthesized by symbiotic interactions. This review may provide a reference for the further development and utilization of endophytes and the study of their interactions with their hosts.

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.)

Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.

The influence of endophytes on rice fitness under environmental stresses

KEY MESSAGE

Endophytes are crucial for the promotion of rice growth and stress tolerance and can be used to increase rice crop yield. Endophytes can thus be exploited in biotechnology and genetic engineering as eco-friendly and cost-effective means for the development of high-yielding and stress-tolerant rice plants. Rice (Oryza sativa) crop is continuously subjected to biotic and abiotic stresses, compromising growth and consequently yield. The situation is exacerbated by climate change impacting on ecosystems and biodiversity. Genetic engineering has been used to develop stress-tolerant rice, alongside physical and chemical methods to mitigate the effect of these stresses. However, the success of these strategies has been hindered by short-lived field success and public concern on adverse effects associated. The limited success in the field of stress-tolerant cultivars developed through breeding or transgenic approaches is due to the complex nature of stress tolerance as well as to the resistance breakdown caused by accelerated evolution of pathogens. It is therefore necessary to develop novel and acceptable strategies to enhance rice stress tolerance and durable resistance and consequently improve yield. In the last decade, plant growth promoting (PGP) microbes, especially endophytes, have drawn the attention of agricultural scientists worldwide, due to their ability to mitigate environmental stresses in crops, without causing adverse effects. Increasing evidence indicates that endophytes effectively confer fitness benefits also to rice under biotic and abiotic stress conditions. Endophyte-produced metabolites can control the expression of stress-responsive genes and improve the physiological performance and growth of rice plants. This review highlights the current evidence available for PGP microbe-promoted tolerance of rice to abiotic stresses such as salinity and drought and to biotic ones, with special emphasis on endophytes. Associated molecular mechanisms are illustrated, and prospects for sustainable rice production also in the light of the impending climate change, discussed.

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence.

The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management

Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture.

Potential of biosynthesized zinc oxide nanoparticles to control Fusarium wilt disease in eggplant (Solanum melongena) and promote plant growth

In this study, a novel, non-toxic, eco-friendly zinc oxide nanoparticles (ZnO-NPs) was used instead of the synthetic fungicides widely used to control the destructive phytopathogenic fungus Fusarium oxysporum, the causative agent of wilt disease in Solanum melongena L. Herein, the biosynthesized ZnO-NPs was carried out by Penicillium expansum ATCC 7861. In vitro, mycosynthesized ZnO-NPs exhibited antifungal activity against Fusarium oxysporum. In vivo, ZnO-NPs suppressed Fusarium wilt disease in cultivated Solanum melongena L. by decreasing the disease severity with 75% of plant protection. Moreover, ZnO-NPs stimulated the recovery of eggplant as an indicated by improving of morphological and metabolic indicators including plant height(152.5%), root length(106.6%), plant fresh biomass (146%), chlorophyll a (102.8%), chlorophyll b (67.86%), total soluble carbohydrates (48.5%), total soluble protein (81.8%), phenol (10.5%), antioxidant activity and isozymes compared with infected control. Therefore, this study suggests using mycosynthesized ZnO-NPs as an alternative to synthetic fungicides not only to eradicate the Fusarium wilt disease in cultivated eggplant (Solanum melongena) but also to promote the growth parameters and metabolic aspects.

Pseudomonas stutzeri and Kushneria marisflavi Alleviate Salinity Stress-Associated Damages in Barley, Lettuce, and Sunflower

Soil salinity is one of the most important abiotic factors limiting plant productivity. The aim of this study was to determine the effect of selected halotolerant plant growth-promoting endophytes (PGPEs, Pseudomonas stutzeri ISE12 and Kushneria marisflavi CSE9) on the growth parameters of barley (Hordeum vulgare), lettuce (Lactuca sativa), and sunflower (Helianthus annuus) cultivated under salt stress conditions. A negative effect of two higher tested salinities (150 and 300 mM NaCl) was observed on the growth parameters of all investigated plants, including germination percentage and index (decreasing compared to the non-saline control variant in the ranges 5.3-91.7 and 13.6-90.9%, respectively), number of leaves (2.2-39.2%), fresh weight (24.2-81.6%); however, differences in salt stress tolerance among the investigated crops were observed (H. annuus > H. vulgare > L. sativa). Our data showed that the most crucial traits affected by endophyte inoculation under salt stress were chlorophyll concentration, leaf development, water storage, root development, and biomass accumulation. Thus, the influence of endophytes was species specific. K. marisflavi CSE9 promoted the growth of all tested plant species and could be considered a universal PGPEs for many plant genotypes cultivated under saline conditions (e.g., increasing of fresh weight compared to the non-inoculated control variant of barley, lettuce, and sunflower in the ranges 11.4-246.8, 118.9-201.2, and 16.4-77.7%, respectively). P. stutzeri ISE12 stimulated growth and mitigated salinity stress only in the case of barley. Bioaugmentation of crops with halotolerant bacterial strains can alleviate salt stress and promote plant growth; however, the selection of compatible strains and the verification of universal plant stress indicators are the key factors.

Synthesis and characterization of new functionalized chitosan and its antimicrobial and in-vitro release behavior from topical gel

Recently, chitosan and its derivatives have been gaining more attention due to their high integration into various biomedical applications. Herein, a new chitosan derivative was prepared by linking the chitosan (Cs) with a novel heterocyclic compound, Benzoimidazolyl-thiadiazole (BzimTD) to form Cs-BzimTD. The synthesis of the new chitosan derivative was confirmed by Fourier-Transform Infrared (FT-IR) spectroscopy, proton nuclear magnetic resonance (¹H NMR), thermogravimetric (TGA-DTG) analysis, elemental analysis, and UV-Visible spectrophotometer. Data showed the high efficacy of functionalized Cs-BzimTD to inhibit the growth of pathogenic microbes, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans, with inhibition zones of 15.3 ± 0.6 - 9.2 ± 0.3 mm. Also, Cs-BzimTD was applied in a topical gel formulation by using two different polymers, Carbopol 940 (CP) and Carboxymethyl Cellulose (CMC) to form three gel formulations: Cs-BzimTD-CP, Cs-BzimTD-CMC, and Cs-BzimTD-CP-CMC. The new gels were checked for physical appearance, viscosity, Cs-BzimTD release, pH, spread-ability, and drug content. The results showed that all formulations were clear, transparent, and homogeneous with non-irritant pH values for skin (6.4 - 6.8). The spread-ability was found in the range of 7.1 - 9.4 g.cm/s. The Cs-BzimTD-CP formula showed the maximal Cs-BzimTD content percentage (86.5%) and the Cs-BzimTD release varied from 89.9 to 81.6% after 8 h depending on the gel formulation, with a maximum release achieved for Cs-BzimTD-CMC.

Root Cultures, a Boon for the Production of Valuable Compounds: A Comparative Review

Medicinal plants are an inevitable source of pharmaceutical drugs and most of the world population depends on these plants for health benefits. The increasing global demand for bioactive compounds from medicinal plants has posed a great threat to their existence due to overexploitation. Adventitious root and hairy root culture systems are an alternative approach to the conventional method for mass production of valuable compounds from medicinal plants owing to their rapid growth, biosynthetic and genetic stability. The main purpose of this review is to investigate the recent scientific research published worldwide on the application of adventitious and hairy root cultures to produce valuable compounds from medicinal plants. Furthermore, a comparison of adventitious root vs. hairy root cultures to produce valuable compounds has also been discussed. Various aspects such as medium composition, carbon source, pH, amount of macronutrients, optimization strategy, scale-up cultures, and use of biotic abiotic and nano-elicitors at various concentrations are the topic of discussion in this review. Several studies on adventitious and hairy root cultures of Polygonum multiflorum¸ Withania somnifera¸ Echinacea purpurea and Ajuga bracteosa have been discussed in detail which highlights the importance of elicitation strategies and bioreactor system, presenting commercial applications.