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Variovorax species catabolize a wide range of natural and industrial products and have been shown to be integral rhizosphere inhabitants. Here, we report the complete genomes of V. paradoxus 2u118 and V. sp. SPNA7, which were isolated from alfalfa root nodules and possess plant growth-promoting properties.

The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant-fungal interactions today, it is hypothesized these kingdoms have a long-standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free-living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia, interact with P. patens in coculture. We also assess how Mollicute-related or Burkholderia-related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high-throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant-fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens.

Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species' range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.

Introduction: Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. Methods: We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. Results: Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. Discussion: This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera. [ABSTRACT FROM AUTHOR]

Cronartium pini and C. ribicola are rust fungi that cause destructive diseases of pines (Pinus spp.). These rusts spread via alternate hosts, among which Melampyrum spp., Veronica spp. and Impatiens spp. are important for C. pini and Ribes spp. for C. ribicola. Congeneric alternate hosts vary in their susceptibility to Cronartium rusts, but the reasons for this variation are not clear. To clarify whether internal, endophytic fungi could explain these differences, we investigated the temporal and spatial variation in fungal endophyte composition of C. pini-resistant M. pratense, V. chamaedrys and I. glandulifera, C. pini-susceptible M. sylvaticum, V. longifolia and I. balsamina, C. ribicola-resistant R. rubrum and C. ribicola-susceptible R. nigrum. In total, 2695 fungal endophytic isolates were obtained and classified into 37 morphotypes, with 1373 cultures isolated in early summer and 1322 in late summer. Fifty-two isolates were identified to species or genus level. The most common morphotypes were identified as Heterophoma sp. Some variation in the abundance of morphotypes occurred between collection sites, but the same morphotypes dominated across the sites and species. The diversity of morphotypes was higher in early September than in late June in all species and the same morphotypes dominated in both early and late season. The diversity of fungal endophytes was higher in resistant Veronica and Ribes than in susceptible congeneric species, but the results suggest that the diversity or abundance of culturable fungal endophytes does not explain the differences in the congeneric species' susceptibility to rust fungi. [ABSTRACT FROM AUTHOR]

Barley (Hordeum vulgare) is the fourth largest cereal crop in the world, with considerable nutritional value. Recently more studies on the toleration of barley to salt stress have been published, indicating an increased concern for food safety. Salt stress is an increasing threat to agricultural productivity; thus, an attempt was made to explore the growth-promoting capacities of an endophytic fungal strain Aspergillus niger CSR3 in H. vulgare. In the current study, we investigated various physiological and biochemical characteristics of two H. vulgare varieties, namely OM-80 and OM-82, under 300 mM NaCl and 100% seawater treatments with and without the inoculation of CSR3. Our results showed that biopriming of H. vulgare seeds with CSR3 enhanced germination ratio both in control and salt treated conditions. Under salt stress, the growth of H. vulgare plants was significantly reduced; however, CSR3 alleviated the salt stress and significantly increased root/shoot length and weight compared to their respective counterparts both under control and stress conditions. The fungal strain showed an ameliorated response to salt stress by improving the photosynthetic machinery. Results demonstrate that accumulation of reduced glutathione (GSH), catalase (CAT), and flavonoids decreased in inoculated plants as compared to non-inoculated under saline conditions indicating the potential of CSR3 in maintaining cellular homeostasis against salinity stress. Moreover, our finding also revealed that starch accumulation decreased with a gradual increase of salt treatment; however, CSR3 inoculation enhanced starch and decreased sugar level, indicating its potential to convert excess sugar to starch. In conclusion, CSR3 can improve plant performance significantly and can greatly improve sustainable agricultural production in saline marginal lands. [ABSTRACT FROM AUTHOR]

The study of plant–microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota. [ABSTRACT FROM AUTHOR]

Magnaporthiopsis maydis is a maize pathogen that causes severe damage to commercial corn fields in the late growth stages. Late wilt disease (LWD) has spread since its discovery in the 1960s in Egypt and is now reported in about 10 countries. The pathogen has a hidden endophytic lifecycle in resistant corn plants and secondary hosts such as green foxtail, watermelon lupin and cotton. At the same time, it could be an opportunist and hinder the host development under the right conditions. This study uncovered M. maydis interactions with newly identified maize endophytes. To this end, six fungi were isolated from the seeds of three sweet corn cultivars having varying susceptibility to LWD. These isolates were identified using colony morphology and microscopic characterization, universal internal transcribed spacer (ITS) molecular targeting and phylogenetic analysis. Most of them belonged to pathogenic species. Compared to three previously identified bioprotective microorganisms, the new species were tested for their ability to secrete metabolites that repress M. maydis in vitro and to antagonize it in a solid media confront test and a seedlings pathogenicity assay. The opportunistic fungal species Aspergillus flavus (ME1), Aspergillus terreus (PE3) and the reference biocontrol bacteria Bacillus subtilis (R2) achieved the highest M. maydis inhibition degree in the plates tests (74-100% inhibition). The seedlings' pathogenicity assay that predicts the seeds' microflora resistance to M. maydis highlighted the bio-shielding potential of most species (23% or more epicotyl elongation over the infected control). Fusarium sp. (ME2) was the leading species in this measure (43% enhancement), and B. subtilis gave the best protection in terms of seeds' germination (50%) and sprouts' biomass (34%). The results of this study could enhance our understanding of the pathobiome's role in the context of LWD and represent a first step in using the seeds' natural protective microflora to develop novel management strategies. [ABSTRACT FROM AUTHOR]

Saline soils pose significant challenges to global agricultural productivity, hindering crop growth and efficiency. Despite various mitigation strategies, the issue persists, underscoring the need for innovative and sustainable solutions. One promising approach involves leveraging microorganisms and their plant interactions to reclaim saline soils and bolster crop yields. This review highlights pioneering and recent advancements in utilizing multi-traits Trichoderma and Bacillus species as potent promoters of plant growth and health. It examines the multifaceted impacts of saline stress on plants and microbes, elucidating their physiological and molecular responses. Additionally, it delves into the role of ACC deaminase in mitigating plant ethylene levels by Trichoderma and Bacillus species. Although there are several studies on Trichoderma-Bacillus, much remains to be understood about their synergistic relationships and their potential as auxiliaries in the phytoremediation of saline soils, which is why this work addresses these challenges. [ABSTRACT FROM AUTHOR]

Dendrobium species, which are perennial herbs widely distributed in tropical and subtropical regions, are notable for their therapeutic properties attributed to various bioactive compounds, including dendrobine-type sesquiterpenoid alkaloids (DTSAs). The objective of this review article is to provide a comprehensive overview of recent advances in the biosynthesis of DTSAs, including their extraction from Dendrobium species and endophytes, elucidation of associated genes through genomic and transcriptomic sequencing in both Dendrobium spp. and endophytes, exploration of the biosynthetic pathways of DTSAs, and drawing conclusions and outlining future perspectives in this field. Alkaloids, predominantly nitrogen-containing compounds found in medicinal orchids, include over 140 types discovered across more than 50 species. DTSAs, identified in 37 picrotoxane alkaloids, have a distinctive five-membered nitrogen heterocyclic ring. This review highlights endophytic fungi as alternative sources of DTSAs, emphasizing their potential in pharmaceutical applications when plant-derived compounds are scarce or complex. Genomic and transcriptomic sequencing of Dendrobium spp. and their endophytes has identified key genes involved in DTSAs biosynthesis, elucidating pathways such as the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways. Genes encoding enzymes, such as acetyl-CoA C-acetyltransferase and diphosphomevalonate decarboxylase, are positively associated with dendrobine production. Despite significant advancements, the complexity of terpenoid biosynthesis in different subcellular compartments remains a challenge. Future research should focus on leveraging high-quality genomic data and omics technologies to further understand and manipulate the biosynthetic pathways of DTSAs and enhance their medicinal use. [ABSTRACT FROM AUTHOR]

Introduction: Cistanche salsa (C.A.Mey.) G. Beck is a perennial holoparasitic herb recognized for its medicinal properties, particularly in kidney-tonifying and laxative treatments. Despite its therapeutic potential, little is known about the endophyte communities inhabiting C. salsa and its host plants, and how these microorganisms may impact the production and accumulation of metabolites in C. salsa. Methods: We conducted a dual analysis focusing on metabolomics of wild C. salsa and microbiome characterization of both C. salsa and its host plant, Kalidium foliatum (Pall.) Moq. The metabolomics analysis revealed variations in metabolite composition across different parts of C. salsa. Additionally, the microbiome analysis involved studying endophytic bacteria and fungi, comparing their community structures between parasitic C. salsa and its host plant. Results: Significant variations in metabolite composition were observed through metabolomic profiling, which identified 93 secondary metabolites and 398 primary metabolites across various parts of C. salsa. Emphasis was placed on differences in metabolite composition within the flowers. Microbiome analysis revealed differential community compositions of endophytic bacteria between the parasitic and host plants, whereas differences in endophytic fungi were less pronounced. Certain endophytes, such as Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota, were associated with the production of specific secondary metabolites in C. salsa, including the plant-specific compound salsaside. Discussion: Our findings highlight the intricate relationship between C. salsa and its endophytic microbiota, suggesting a potential role of these microorganisms in modulating the biosynthesis of bioactive compounds. The differential preferences of endophytic bacteria and fungi across various microenvironments within the parasitic plant system underscore the complexity of these interactions. Further elucidation of these dynamics could enhance our understanding of C. salsa's medicinal properties and its ecological adaptations as a holoparasitic herb. [ABSTRACT FROM AUTHOR]

Introduction: Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth. Methods: In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition. Results: Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted. Conclusion: Overall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health. [ABSTRACT FROM AUTHOR]

Simple Summary: Anise seeds offer nutritional and therapeutic benefits that are valuable to both animal and human health. This study investigated the ability of the endophytic Actinomycetota sp. JW0824 strain to biofortify anise seeds from Egypt, Tunisia, Syria, and Morocco. In this study, significant increases in the dry weight of seeds and oil yields were observed, along with enhancements in the levels of primary and secondary metabolites such as sugars, flavonoids, alkaloids, phenols, vitamins, and essential oils. The number of essential oil metabolic enzymes (PAL and DAHPS) was also consistently increased. The findings suggest that Actinomycetota sp. JW0824 could be used to enhance the yield and quality of anise seeds. Anise (Pimpinella anisum L.) seeds have various nutritional and therapeutic benefits and are thus considered a valuable addition to animal and human health. Hence, in this study, we aimed to induce the nutritive and biological value of anise seeds. To this end, the potential biofortification effect of the endophytic Actinomycetota sp. JW0824 strain, isolated during the fall of 2023 from the medicinal plant Achyranthes aspera, exhibiting natural distribution in the Jazan region of Saudi Arabia, was investigated in four varieties of anise seeds from Egypt, Tunisia, Syria, and Morocco. Results revealed significant increments (p < 0.05) in the seed dry weight percentage (DW%) and oil yields. In line with increased biomass accumulation, the metabolism of the primary and secondary metabolites was increased. There were differential increases in proteins, sugars, flavonoids, alkaloids, phenols, vitamins (e.g., β-carotene, ascorbic acid), and essential oil components (e.g., phenylpropanoids and monoterpenes), along with their precursor phenylalanine. Consistently, the activity of L-phenylalanine aminolyase (PAL) was increased in the Egyptian and Tunisian varieties at 83.88% and 77.19%, respectively, while 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) activity increased in all varieties, with a significant 179.31% rise in the Egyptian variety. These findings highlight the beneficial effects of Actinomycetota sp. JW0824 as a bioinoculant for anise seeds, suggesting its potential application in agricultural practices to improve seed yield and quality. Further field trials are recommended to assess the commercial viability of this endophyte for enhancing anise seed production and potentially benefiting other plant species. [ABSTRACT FROM AUTHOR]

Pastoral agriculture underpins the New Zealand economy. Its success in generating export income is due to a mild and moist temperate climate, productive soils, innovative farmers supported by an effective research and development system, and an energy efficient production system based on year-round grazing. However, pastoral agriculture is entirely reliant on introduced pasture and forage species and their ability to withstand both endemic and introduced pasture pests. Critical to this is the mutualistic relationship between ryegrass and Epichloë fungal endophytes which provide a range of secondary metabolites that deter herbivory by both ruminants and insect pests. The challenge has been to identify and commercialise Epichloë strains which while providing protection against insect pests, ensuring ryegrass persistence, do not cause animal health and welfare issues. The critical role that Epichloë fungal endophytes play in maintaining pasture persistence and as a result the pastoral economy of New Zealand will be reviewed. [ABSTRACT FROM AUTHOR]

In our collections from the Northwest Pacific waters, we found several specimens of the red algae Lukinia dissecta and Callophyllis perestenkoae with darker spots on their thalli, which contained an unusual pennate diatom. A detailed morphological analysis based on light and scanning electron microscopy observations made it possible to describe a new species of endophytic diatom, Pseudogomphonema lukinicum sp. nov. Stonik et Skriptsova. The new species has some morphological features typical of the genus, such as the heteropolarity of the valves, the presence of pseudosepta and small apical chambers at both poles of the valves, and nonporous girdle bands. Pseudogomphonema lukinicum has been described and distinguished from the other species in the genus on the basis of a combination of morphological traits, including relatively small cell dimensions, a slightly asymmetrical valve to the transapical axis, with obtusely rounded headpole and narrower footpole, the large asymmetrical central area, and the presence of apical chambers at both poles. Pseudogomphonema lukinicum is the second representative of Pseudogomphonema known to be living endophytically. The data on the species composition of endophytic diatoms in marine macroalgae, their habitats, and host organisms reported in the literature to date are summarized. [ABSTRACT FROM AUTHOR]

Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production. [ABSTRACT FROM AUTHOR]

In the modern era of human progress and industrialization, various agricultural and industrial activities lead to the accumulation of excessive hazardous substances in the environment. These wastes are continuously being concentrated in agricultural soil or water, thereby affecting and threatening the lives of both flora and fauna. To treat these toxic substances, various physico-chemical practices are performed, which are ultimately associated with the production of other toxic chemicals in the environment. Some of the toxic products formed are recalcitrant and inert which further causes hindrances in the proper removal of contaminants from different pollutant sites. However, various biological approaches are being used nowadays for the remediation of these pollutants from the environment. Microbial bioremediation and phytoremediation represent such environment-friendly approaches that have been employed in the degradation of many of these chemicals. Among the microbes, endophytes are now considered a promising means of the remediation of different pollutants from their natural environments. Therefore, the review focuses on the use of endophytes in the treatment of different kinds of pollutants and highlights the potential of these microbial tools in the removal of heavy metals, plastic, and other contaminants from both terrestrial and aquatic habitats. [ABSTRACT FROM AUTHOR]

Here, we report on a Cordyceps species entering into a multi-trophic, multi-kingdom association. Cordyceps cateniannulata , isolated from the stem of wild Coffea arabica in Ethiopia, is shown to function as an endophyte, a mycoparasite and an entomopathogen. A detailed polyphasic taxonomic study, including a multilocus phylogenetic analysis, confirmed its identity. An emended description of C. cateniannulata is provided herein. Previously, this species was known as a pathogen of various insect hosts in both the Old and New World. The endophytic status of C. cateniannulata was confirmed by re-isolating it from inoculated coffee plants. Inoculation studies have further shown that C. cateniannulata is a mycoparasite of Hemileia vastatrix , as well as an entomopathogen of major coffee pests; infecting and killing Hypothenemus hampei and Leucoptera coffeella. This is the first record of C. cateniannulata from Africa, as well as an endophyte and a mycoparasite. The implications for its use as a biocontrol agent are discussed. • An unprecedented case of multi-kingdom host-jumping is reported in Cordyceps. • This is the first record of C. cateniannulata from Africa and as an endophyte. • The fungus was isolated from the stem of wild Coffea arabica in Ethiopia. • Endophytic, mycoparasitic, and entomopathogenic abilities were proven experimentally. • The fungus offers novel biocontrol options for the management of coffee pests and diseases. [ABSTRACT FROM AUTHOR]

Climatic changes and global warming affect the growth, development, and productivity of crops. In this review, we highlight the possible benefits of using innovative breeding techniques like clustered regularly interspaced short palindromic repeats (CRISPRs), exogenous phytohormone-like strigolactones (SLs), nanomaterials (NMs), and beneficial microbial endophytes to address the challenges in sustainable cultivation of horticultural crops. These applications are evaluated by examining how they affect different metabolic, morphological, and biochemical parameters in diverse crops. Endophytes are symbiotic microorganisms and can be used as nematicides for improving crop yield. With an emphasis on quality control, we examined the impacts of applying NMs, a novel family of phytohormones called SLs, and microbial endophytes on horticultural commodities. Furthermore, we reviewed the benefits of CRISPR for the editing of plant genomes, as well as how it affects gene expression and transcription factors to increase crop tolerance and yield. These innovations hold the potential to improve crop yield, quality, and resilience by acting as safe, natural components in biofertilizers and plant protection solutions. Gradually adopting these methods could decrease reliance on agrochemicals, thereby reducing their negative effects on biodiversity, soil fertility, and human health. [ABSTRACT FROM AUTHOR]

Eldana saccharina Walker is a problematic sugarcane stalk borer pest in South Africa. Twenty-eight sugarcane genotypes (Saccharum spp. hybrids) and seven different species of host plants of E. saccharina were surveyed for the presence of endophytic Beauveria bassianasensu lato (s.l.). Collectively, 326 plant samples (roots, stems, or leaves) were collected from five locations in sugarcane-producing areas (KwaZulu-Natal; South Africa). Following plant surface disinfection, 128 fungal colonies morphologically resembling Beauveria spp. were isolated from internal plant tissues. The sequence analysis of the internal transcribed spacer region confirmed that 13 representative isolates were B. bassiana.s.l. Eight B. bassiana isolates were recovered from E. saccharina natural host plants, and 120 from different sugarcane stem parts (top node, top internodes, bottom node, and bottom internode). Endophytic B. bassiana isolates were recovered from 22 of 28 sugarcane genotypes surveyed. The number of B. bassiana isolates obtained from different sugarcane parts differed significantly, with more B. bassiana isolates obtained from the top than the bottom internodes. Furthermore, sugarcane genotypes N31 and N41 yielded B. bassiana from all plant parts sampled, while five sugarcane genotypes harbored no B. bassiana isolates. This study demonstrates for the first time the natural occurrence of endophytic B. bassiana strains in sugarcane plants and E. saccharina host plants in South Africa. [ABSTRACT FROM AUTHOR]

The wound management field faces significant challenges due to antimicrobial resistance (AMR) and the complexity of chronic wound care. Effective wound treatment requires antimicrobial dressings to prevent bacterial infections. However, the rise of AMR necessitates new antimicrobial agents for wound dressings, particularly for addressing bacterial pathogens like methicillin-resistant Staphylococcus aureus (MRSA). Endophytic fungi, known for producing diverse bioactive compounds, represent a promising source of such new agents. This study tested thirty-two endophytic fungi from thirteen distinct Australian native plants for their antibacterial activity against S. aureus. Ethyl acetate (EtOAc) extracts from fungal culture filtrates exhibited inhibitory effects against both methicillin-sensitive S. aureus ATCC 25923 (MIC = 78.1 µg/mL) and MRSA M180920 (MIC = 78.1 µg/mL). DNA sequence analysis was employed for fungal identification. The most active sample, EL 19 (Chaetomium globosum), was selected for further analysis, revealing that its EtOAc extracts reduced S. aureus ATCC 25923 biofilm formation by 55% and cell viability by 57% to 68% at 1 2 × MIC. Furthermore, cytotoxicity studies using the brine shrimp lethality test demonstrated low cytotoxicity up to 6 × MIC (25% mortality rate) with an LC50 value of 639.1 µg/mL. Finally, the most active sample was incorporated into polycaprolactone (PCL) fiber mats via electrospinning, with resultant inhibition of S. aureus species. This research underscores the potential of endophytic fungi from Australian plants as sources of substances effective against common wound pathogens. Further exploration of the responsible compounds and their mechanisms could facilitate the development of wound dressings effective against MRSA and innovative biofilm-resistant electrospun fibers, contributing to the global efforts to combat AMR. [ABSTRACT FROM AUTHOR]

The most serious problems for cultivated grapes are pathogenic microorganisms, which reduce the yield and quality of fruit. One of the most widespread disease of grapes is "gray mold", caused by the fungus Botrytis cinerea. Some strains of Bacillus, such as Bacillus halotolerans, Bacillus amyloliquefaciens, and Bacillus velezensis, are known to be active against major post-harvest plant rots. In this study, we showed that the endophytic bacteria B. velezensis strain AMR25 isolated from the leaves of wild grapes Vitis amurensis Rupr. exhibited antimicrobial activity against grape pathogens, including B. cinerea. The genome of B. velezensis AMR25 has one circular chromosome with a length of 3,909,646 bp. with 3689 open reading frames. Genomic analysis identified ten gene clusters involved in the nonribosomal synthesis of polyketides (macrolactin, bacillene, and difficidin), lipopeptides (surfactin, fengycin, and bacillizin), and bacteriocins (difficidin). Also, the genome under study contains a number of genes involved in root colonization, biofilm formation, and biosynthesis of phytohormones. Thus, the endophytic bacteria B. velezensis strain AMR25 shows great promise in developing innovative biological products for enhancing plant resistance against various pathogens. [ABSTRACT FROM AUTHOR]

Background: Studies have shown that plant endophytic microbial communities are ubiquitous and closely related to plant growth and health. To clarify the mechanism of the melon varieties with high resistant to wilt, the endophytic microbial compositions and metabolites in roots of melon varieties with high resistant ability to wilt were analyzed. Results: The results showed that the abundances of Firmicutes, Ascomycota, Bacillus, Bradyrhizobium, Amycolatopsis, Actinospica, and Catenulispora all increased in roots of wilt high resistant melon varieties (MT) which compared to wilt susceptible melon varieties (MS). Meanwhile, Ochrobactrum, Bordetella, Roseateles, Staphylococcus, Acidovorax, Amycolatopsis, Catenulispora, Promicromonospora, and Gymnopilus were the unique endophytic microbes in roots of MT. Moreover, in comparison with the MS varieties, the functions of Defense mechanisms, Secondary metabolites biosynthesis, transport and catabolism, Nucleotide transport and metabolism, Signal transduction mechanisms, Coenzyme transport and metabolism, Carbohydrate transport and metabolism and Amino acid transport and metabolism all increased in roots of MT varieties. Additionally, the nucleotide metabolism and biosynthesis of cofactors metabolic pathways were also significantly increased in roots of MT varieties. On the other hand, the untargeted metabolome results showed that Biosynthesis of various plant secondary metabolites, Nucleotide metabolism and Biosynthesis of cofactors metabolic pathways were significantly increased in the expression of MT varieties; and the content of metabolic compounds such as flavonoids, Cinnamic acid compounds, Organic acid compounds, and Nucleotides were increased. In addition, the correlation between microbiome and metabolome indicates a significant correlation between the two. Conclusions: All above results suggested that higher abundant antagonistic microbes and metabolic functions of endophytes in roots of wilt high resistant melon varieties (MT) were the important mechanisms for their high resistance to wilt. [ABSTRACT FROM AUTHOR]

AbstractThis study focused on the biodegradation of acetonitrile (ACN) and subsequent nitrification using a mesophilic microbial consortium isolated from Phragmites australis and Zantedeschia aethiopica plants which were in a nitrile-contaminated habitat. The organisms were identified using 16S rDNA sequencing and were determined to be Bacillus sp., Pseudomonas sp., and Enterobacter sp. organisms. These organisms were used as a consortium in the biodegradation of ACN. The physicochemical conditions including temperature, pH, and ACN concentration were optimized using response surface methodology (RSM). Based on this method, an optimal biodegradation efficiency of 99% was achieved at an optimized temperature of 34.99 °C, pH of 7:03, and an ACN concentration of up to 127.23 mg/L. These optimized parameters were used in the continuous operation over a period of 122 days with increased ACN concentrations of 150–500 mg/L where the biodegradation efficiency exceeded 99% which were accompanied by the production of acetic acid, acetamide, and nitrogenous compounds. Acetic acid and acetamide were completely utilized while total nitrogen (TN) was 1.2 mg/L on the last day of the study. [ABSTRACT FROM AUTHOR]

Plants in various republics of the world face many dangers, including diseases that threaten crop productivity. The development and increase of novel species of infectious pathogens have made plant growth threatened. Fusarium wilt is one of the fiercest diseases affecting vegetables, which causes a great loss in the quality and quantity of pepper plants all over the world. In this study, stimulation of physiological immune responses in pepper plant using ecofriendly inducers (Aspergillus alabamensis, Aspergillus oryzae, and Aspergillus tubingensis) against Fusarium wilt had been studied. Endophytic fungi were assayed for their capability to synthesize hydrocyanic acid, phosphate solubilization, siderophores, and indole acetic acid synthesis, and the antifungal potential of ecofriendly inducers against F. oxysporum was also examined. A notable antifungal potential antifusarial with a supreme activity of A. tubingensis was found. More ultrastructure by TEM of Fusarium showed that sharp changes occurred in the cell wall, mycelium, and conidia as a result of treatment with A. tubingensis, A. oryzae, and A. alabamensis. The results demonstrated the high severity of F. oxysporum on pepper seedlings. Infected seedlings showed a high reduction in all vegetative parameters, photosynthesis, entire protein, and total carbohydrate. In the current study, the potential of endophytic fungi through foliar and soil application was applied to the Fusarium-infected pepper plants under pot conditions. Disease index, vegetative growth, photosynthetic pigments, osmolyte content, stress markers, and antioxidant isozymes were assessed. The achieved result indicates that tested endophytes through two modes (foliar and soil) lowered PDI and produced high protection, with the most protection influence represented by A. tubingensis (through the soil) by 83.33%. It was concluded that use of A. tubingensis, A. alabamensis, and A. oryzae could be commercially used as eco-friendly agents for the defense of pepper seedlings against Fusarium wilt disease. [ABSTRACT FROM AUTHOR]

Endophyte-host interactions lead to the production of various bioactive compounds. Thus, endophytes from a medicinal plant such as Momordica charantia, can be promising candidates for producing pharmacological compounds. Our study therefore aims to evaluate these endophytes as sustainable sources of potential low-cost lung cancer drugs. We determined the endophytes associated with M. charantia (fruit and leaf) and assessed anti-inflammatory, antioxidant and antiproliferative potential against NCI-H23 lung cancer cells. LC-Q-TOF-MS of the endophyte extracts was conducted to determine the metabolite profile. Leaf endophyte F. circinatum showed anti-inflammatory (114.29 %), antioxidant (IC 50 =27.39 µg/ml) and antiproliferative activity (IC 50 =98.62 µl/ml) with decreased Beclin1 expression (autophagy regulator) in NCI-H23 cells. It produced five anticancer compounds namely linamarin, xestoaminol C, phytosphingosine, cucurbitacin E and margarolic acid. Fruit endophyte E. fergusonii also showed significant antiproliferative potential (IC 50 =170.8 µl/ml) with upregulated apoptosis regulator Bcl2 expression. It produced compounds such as eplerenone, kuguacin C and H. With the production of triterpenoids momordicine I, cucurbitacin E and kuguaglycoside A, leaf endophyte A. faecalis showed antioxidant potential (IC 50 =29.65 µg/ml) but limited antiproliferative activity. This is the first report of endophytes-mediated biosynthesis of host-specific compounds in M. charantia including momordicine I, cucurbitacin E and kuguacins, which are known to have anti-cancer properties. Thus, these medicinal plant endophytes can be low-cost sustainable candidates with anti-cancerous potential, especially against lung cancer. [Display omitted] • Culturable endophytes density in Momordica charantia fruit was higher than leaf. • Promising antiproliferative and antioxidant activity by M. charantia endophytes. • Fusarium circinatum and Escherichia fergusonii promoted apoptosis in NCI-H23 cells. • M. charantia endophytes produced momordicine I, cucurbitacin E, kuguacin C and H. • Phytochemical biosynthesis varied with endophyte type and plant part interaction. [ABSTRACT FROM AUTHOR]

Recently, there has been a worldwide call to explore nature-friendly compounds, which could enhance plant growth and substitute for chemically synthesized products. Endophytes are a group of microorganisms that lives in the plants and algae symbiotically. In this research, endophytes were isolated from leaves of the halophyte, Limonium axillare. A total of 280 bacterial isolates were obtained from the leaves of L. axillare. Strains displaying similarities in terms of morphology and biochemical reactions were categorized into 48 groups. One representative from each group was identified and subjected to enzymatic and plant growth-promoting tests. Forty-eight isolates were identified using a sequence similarity-based method based on the 16S rDNA gene. The identified strains were categorized into two genera: Bacillus and Staphylococcus. Our investigation uncovered 44 isolates from the Bacillus genus, representing 10 different species, including Bacillus sp., B. pseudomycoides, B. cereus, B. paramycoides, B. velezensis, B. subtilis, B. thuringiensis, B. wiedmannii, B. anthracis, and B. bacterium. Furthermore, we observed that only 4 isolates belonged to the Staphylococcus genus, encompassing 3 distinct species: S. bacterium, S. succinus, and S. saprophyticus. The isolated bacteria were screened for extracellular enzymes, plant growth promoting traits, antifungal activity, and salinity tolerance. From the previous screening, diverse responses were obtained. Most of the isolates were secreted at least one of the hydrolysis enzymes (protease, lipase and amylase). (93.8%) of the strains showed phosphate solubilization activity. (33.3%) produce (IAA). Siderophore production potential was present in 91.7% of isolates, while ACC deaminase and HCN production activities were identified in 52.1 and 41.7% of strains, respectively. Additionally, DNase activity was evident in 27.1%, and ammonia production was observed in 31.3% of the isolates. The isolates Bacillus velezensis (AL4QUA) strain showed positive effect in the greenhouse experiment in terms of plant growth promoter agent and biocontrol agent against Fusarium oxysporum pathogen of tomato seedling. Thus, endophytes have the potential to reduce chemical inputs in conventional agricultural practices, increase nutrient uptake and improve plant stress resilience. [ABSTRACT FROM AUTHOR]

Abstract Background Studies have shown that plant endophytic microbial communities are ubiquitous and closely related to plant growth and health. To clarify the mechanism of the melon varieties with high resistant to wilt, the endophytic microbial compositions and metabolites in roots of melon varieties with high resistant ability to wilt were analyzed. Results The results showed that the abundances of Firmicutes, Ascomycota, Bacillus, Bradyrhizobium, Amycolatopsis, Actinospica, and Catenulispora all increased in roots of wilt high resistant melon varieties (MT) which compared to wilt susceptible melon varieties (MS). Meanwhile, Ochrobactrum, Bordetella, Roseateles, Staphylococcus, Acidovorax, Amycolatopsis, Catenulispora, Promicromonospora, and Gymnopilus were the unique endophytic microbes in roots of MT. Moreover, in comparison with the MS varieties, the functions of Defense mechanisms, Secondary metabolites biosynthesis, transport and catabolism, Nucleotide transport and metabolism, Signal transduction mechanisms, Coenzyme transport and metabolism, Carbohydrate transport and metabolism and Amino acid transport and metabolism all increased in roots of MT varieties. Additionally, the nucleotide metabolism and biosynthesis of cofactors metabolic pathways were also significantly increased in roots of MT varieties. On the other hand, the untargeted metabolome results showed that Biosynthesis of various plant secondary metabolites, Nucleotide metabolism and Biosynthesis of cofactors metabolic pathways were significantly increased in the expression of MT varieties; and the content of metabolic compounds such as flavonoids, Cinnamic acid compounds, Organic acid compounds, and Nucleotides were increased. In addition, the correlation between microbiome and metabolome indicates a significant correlation between the two. Conclusions All above results suggested that higher abundant antagonistic microbes and metabolic functions of endophytes in roots of wilt high resistant melon varieties (MT) were the important mechanisms for their high resistance to wilt. Graphical Abstract

Endophytes are potential partners for improving the resource use efficiency of bioenergy feedstock systems such as short rotation coppice Populus species. Endophytes isolated from members of the Salicaceae family have broad host compatibility and can improve water use efficiency (WUE) through decreases in stomatal conductance. However, the literature is inconsistent with regard to the environmental conditions and temporal patterns of these benefits. This study investigated how endophyte-mediated changes in Populus trichocarpa ‘Nisqually-1’ stomatal conductance and WUE shift with time and scale in response to water deficit stress. Leaf gas exchange and aboveground productivity were used to evaluate the carbon and water balance of greenhouse-grown plants in response to endophyte inoculation and water deficit. Differences in stomatal conductance between control and inoculated plants were more pronounced (39.7% decrease, Welch two-sample t [14.34 adjusted degrees of freedom] = –2.358, P = 0.033) under water deficit conditions in the late morning during a period of higher light intensity. The decrease in stomatal conductance accompanied a substantial increase in intrinsic WUE (iWUE) for water deficit inoculated plants. However, increases in iWUE did not result in improvements in aboveground productivity or shoot biomass WUE for water deficit inoculated plants. This decoupling between iWUE and aboveground productivity may be an indicator of assimilate allocation to microbial metabolism as an additional carbon sink or a shift in carbon allocation toward belowground biomass. Future work should take a whole plant approach that accounts for diurnal patterns in incident irradiance to evaluate the impact of endophyte inoculation on host WUE and stress tolerance.

Drought is one of the environmental stresses that threaten food availability. It results in decreased crop yields and developments and diminishes overall plant health. Chemical solutions for alleviating drought stress may be harmful to the environment. Using an alternative, microorganisms help counter the effects of drought stress. Endophytes have a mutualistic relationship with the host as they provide protection and get nutrients. Fungal endophytes assist plants in countering the damaging results of drought stress by producing phytohormones and growth-promoting compounds that promote root and shoot growth and enhance crop productivity. Inoculating maize plants with endophytic fungi like Fusarium oxysporum and Penicillium sp. have a higher chance of surviving drought stress. These organisms can increase root length, allowing moisture to reach deeper into the soil. This review explores endophytic fungi's roles in alleviating drought stress's consequences on plants. More investigations should be carried out on the favourable effects of fungal endophytes in the mitigation of drought stress through pot and field inoculation.

Rafflesia is an endangered endophytic holoparasitic plant that lives the majority of its life inside the tissues of its sole plant host, Tetrastigma. Rafflesia floral buds emerge to produce the world's largest single flower. Like other plants, holoparasites harbor a diverse microbiome, the role(s) of which has remained largely unstudied. We characterized the bacterial microbiome of seeds of Rafflesia speciosa and cuttings of its host. We found evidence that R. speciosa seed has similar bacterial profiles to its infected host, which suggests that seeds sequester certain host bacteria, as well as acquire unique bacterial taxa from biotic associates of the fruit. We did not find evidence of mycorrhizal taxa in the microbiome. This is the first study of the microbial endophytes associated with any Rafflesia species and its host, a tripartite holobiont, and provides insights on its cryptic microbial partners. We discuss how this may aid horticultural propagation of Rafflesia. [ABSTRACT FROM AUTHOR]

The management and treatment of cancer and related disorders is still a challenging goal for the scientists. The current global scenario of cancer mortality is demanding to discover and develop new, safe, cost effective and potent anticancer medications. The anticancer drugs vinblastine and vincristine are solely produced by medicinal herb Catharanthus roseus. These drugs are second most widely consumed anticancer drugs after Taxol in the world; however, the plant is well recognised to produce very modest levels of these important compounds (0.0002–0.0005 %). To address this issue, the review delves into the promising alternative of using endophytic fungi which reside within the healthy plant tissues and have ability to produce host-specific bioactive compounds including vinblastine and vincristine. An endophytic fungus Talaromyces radicus is reported to produce vincristine up to 670 µg/L while Curvularia verruculosa is able to secret vinblastine at a concentration of 182 µg/L in liquid cultures respectively. Some other fungal species reported to produce either vincristine or vinblastine includes Fusarium, Alternaria, Chaetomium, Nigrospora and Eutypella. The review begins by discussing the therapeutic importance of vinblastine and vincristine, highlighting their mechanisms of action and their critical roles in chemotherapy regimens for various types of cancer. Next, the review also provides an in-depth analysis of various endophytic fungi producing vinblastine and vincristine detailing their identification, characterization, biosynthetic ability and strain improvement processes. It aims to contribute to the ongoing efforts to develop more effective and sustainable strategies for producing these critical anticancer agents, ultimately enhancing cancer treatment options and outcomes. [Display omitted] • Vinblastine and vincristine are among the major anticancer compounds used worldwide for treatment of various cancers. • Natural production of these anticancer drugs is limited because of the very low yield in Catharanthus plant. • The endophytic fungi isolated from Catharanthus roseus are reported to produce vinblastine and vincristine in sufficient quantities. • The challenge in fungal production of these drugs is related with optimization and sustainable yield at commercial level. [ABSTRACT FROM AUTHOR]

In this study, we used 16S rRNA gene sequence analysis to describe the diversity of cultivable endophytic bacteria associated with fennel (Foeniculum vulgare Mill.) and determined their plant-beneficial traits. The bacterial isolates from the roots of fennel belonged to four phyla: Firmicutes (BRN1 and BRN3), Proteobacteria (BRN5, BRN6, and BRN7), Gammaproteobacteria (BRN2), and Actinobacteria (BRN4). The bacterial isolates from the shoot of fennel represented the phyla Proteobacteria (BSN1, BSN2, BSN3, BSN5, BSN6, BSN7, and BSN8), Firmicutes (BSN4, BRN1, and BRN3), and Actinobacteria (BRN4). The bacterial species Bacillus megaterium, Bacillus aryabhattai, and Brevibacterium frigoritolerans were found both in the roots and shoots of fennel. The bacterial isolates were found to produce siderophores, HCN, and indole-3-acetic acid (IAA), as well as hydrolytic enzymes such as chitinase, protease, glucanase, and lipase. Seven bacterial isolates showed antagonistic activity against Fusarium culmorum, Fusarium solani, and Rhizoctonia. solani. Our findings show that medicinal plants with antibacterial activity may serve as a source for the selection of microorganisms that exhibit antagonistic activity against plant fungal infections and may be considered as a viable option for the management of fungal diseases. They can also serve as an active part of biopreparation, improving plant growth.