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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.

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]

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]

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]

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]

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]

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 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]

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]

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]

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]

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.

Abstract Soil salinity is a major environmental stressor impacting global food production. Staple crops like wheat experience significant yield losses in saline environments. Bioprospecting for beneficial microbes associated with stress-resistant plants offers a promising strategy for sustainable agriculture. We isolated two novel endophytic bacteria, Bacillus cereus (ADJ1) and Priestia aryabhattai (ADJ6), from Agave desmettiana Jacobi. Both strains displayed potent plant growth-promoting (PGP) traits, such as producing high amounts of indole-3-acetic acid (9.46, 10.00 µgml−1), ammonia (64.67, 108.97 µmol ml−1), zinc solubilization (Index of 3.33, 4.22, respectively), ACC deaminase production and biofilm formation. ADJ6 additionally showed inorganic phosphate solubilization (PSI of 2.77), atmospheric nitrogen fixation, and hydrogen cyanide production. Wheat seeds primed with these endophytes exhibited enhanced germination, improved growth profiles, and significantly increased yields in field trials. Notably, both ADJ1 and ADJ6 tolerated high salinity (up to 1.03 M) and significantly improved wheat germination and seedling growth under saline stress, acting both independently and synergistically. This study reveals promising stress-tolerance traits within endophytic bacteria from A. desmettiana. Exploiting such under-explored plant microbiomes offers a sustainable approach to developing salt-tolerant crops, mitigating the impact of climate change-induced salinization on global food security.

Abstract Background Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. Results Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. Conclusion Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.

Abstract There is an urgent need for new bioactive molecules with unique mechanisms of action and chemistry to address the issue of incorrect use of chemical fertilizers and pesticides, which hurts both the environment and the health of humans. In light of this, research was done for this work to isolate, identify, and evaluate the germination-promoting potential of various plant species’ fungal endophytes. Zea mays L. (maize) seed germination was examined using spore suspension of 75 different endophytic strains that were identified. Three promising strains were identified through screening to possess the ability mentioned above. These strains Alternaria alternate, Aspergilus flavus, and Aspergillus terreus were isolated from the stem of Tecoma stans, Delonix regia, and Ricinus communis, respectively. The ability of the three endophytic fungal strains to produce siderophore and indole acetic acid (IAA) was also examined. Compared to both Aspergillus flavus as well as Aspergillus terreus, Alternaria alternata recorded the greatest rates of IAA, according to the data that was gathered. On CAS agar versus blue media, all three strains failed to produce siderophores. Moreover, the antioxidant and antifungal potentials of extracts from these fungi were tested against different plant pathogens. The obtained results indicated the antioxidant and antifungal activities of the three fungal strains. GC-Mass studies were carried out to determine the principal components in extracts of all three strains of fungi. The three strains’ fungus extracts included both well-known and previously unidentified bioactive compounds. These results may aid in the development of novel plant growth promoters by suggesting three different fungal strains as sources of compounds that may improve seed germination. According to the study that has been given, as unexplored sources of bioactive compounds, fungal endophytes have great potential.

Abstract Efforts to characterize microbial life across diverse environments have progressed tremendously, yet the microbiome of Earth's largest biomass reservoir—the wood of living trees—has been largely unexplored. Current understanding of the tree microbiome is largely confined to roots and leaves, with little attention given to the endophytic microbiome of wood, even though emergent studies have indicated this zone as a niche for unique taxa, of consequence for ecosystem health and global biogeochemical cycles. The lack of investigation derives partly from the physical recalcitrance of wood, which presents challenges during sampling, homogenization, and the extraction of nucleic acids. In response to these issues, we present an optimized method for processing wood for use in microbial analyses, from sampling through to downstream analyses. Using methane‐cycling taxa as model endophytes, we assess losses in recovery during our method, and determine a limit‐of‐detection of approximately 500 cells per 100 mg of (dry) wood. For all six species evaluated—which represented several diverse taxa of hardwoods and softwoods—PCR inhibition proved minimal, and we expect this method to be applicable for a majority of tree species. The methods presented herein can facilitate future investigation into the wood microbiome and global microbial ecology of methane cycling.

Abstract Multi resistant fungi are on the rise, and our arsenal compounds are limited to few choices in the market such as polyenes, pyrimidine analogs, azoles, allylamines, and echinocandins. Although each of these drugs featured a unique mechanism, antifungal resistant strains did emerge and continued to arise against them worldwide. Moreover, the genetic variation between fungi and their host humans is small, which leads to significant challenges in new antifungal drug discovery. Endophytes are still an underexplored source of bioactive secondary metabolites. Many studies were conducted to isolate and screen endophytic pure compounds with efficacy against resistant yeasts and fungi; especially, Candida albicans, C. auris, Cryptococcus neoformans and Aspergillus fumigatus, which encouraged writing this review to critically analyze the chemical nature, potency, and fungal source of the isolated endophytic compounds as well as their novelty features and SAR when possible. Herein, we report a comprehensive list of around 320 assayed antifungal compounds against Candida albicans, C. auris, Cryptococcus neoformans and Aspergillus fumigatus in the period 1980–2024, the majority of which were isolated from fungi of orders Eurotiales and Hypocreales associated with terrestrial plants, probably due to the ease of laboratory cultivation of these strains. 46% of the reviewed compounds were active against C. albicans, 23% against C. neoformans, 29% against A. fumigatus and only 2% against C. auris. Coculturing was proved to be an effective technique to induce cryptic metabolites absent in other axenic cultures or host extract cultures, with Irperide as the most promising compounds MIC value 1 μg/mL. C. auris was susceptible to only persephacin and rubiginosin C. The latter showed potent inhibition against this recalcitrant strain in a non-fungicide way, which unveils the potential of fungal biofilm inhibition. Further development of culturing techniques and activation of silent metabolic pathways would be favorable to inspire the search for novel bioactive antifungals. Graphic abstract

Beneficial endophytic bacteria can suppress the development of insect pests through direct antagonism, with the help of metabolites, or indirectly by the induction of systemic resistance through the regulation of hormonal signaling pathways. Lipopeptides are bacterial metabolites that exhibit direct antagonistic activity against many organisms, including insects. Also, lipopeptides are able to trigger induced systemic resistance (ISR) in plants against harmful organisms, but the physiological mechanisms of their action are just beginning to be studied. In this work, we studied ten strains of bacteria isolated from the tissues of wheat and potatoes. Sequencing of the 16S rRNA gene showed that all isolates belong to the genus Bacillus and to two species, B. subtilis and B. velezensis. The genes for lipopeptide synthetase – surfactin synthetase (Bs_srf ), iturin synthetase (Bs_ituA, Bs_ituB) and fengycin synthetase (Bs_fenD) – were identified in all bacterial isolates using PCR. All strains had high aphicidal activity against the Greenbug aphid (Schizaphis graminum Rond.) due to the synthesis of lipopeptides, which was proven using lipopeptiderich fractions (LRFs) isolated from the strains. Endophytic lipopeptide-synthesizing strains of Bacillus spp. indirectly affected the viability of aphids, the endurance of plants against aphids and triggered ISR in plants, which manifested itself in the regulation of oxidative metabolism and the accumulation of transcripts of the Pr1, Pr2, Pr3, Pr6 and Pr9 genes due to the synthesis of lipopeptides, which was proven using LRF isolated from three strains: B. subtilis 26D, B. subtilis 11VM, and B. thuringiensis B-6066. We have for the first time demonstrated the aphicidal effect of fengycin and the ability of the fengycin-synthesizing strains and isolates, B. subtilis Ttl2, Bacillus sp. Stl7 and B. thuringiensis B-6066, to regulate components of the pro-/antioxidant system of aphid-infested plants. In addition, this work is the first to demonstrate an elicitor role of fengycin in triggering a systemic resistance to S. graminum in wheat plants. We have discovered new promising strains and isolates of endophytes of the genus Bacillus, which may be included in the composition of new biocontrol agents against aphids. One of the criteria for searching for new bacteria active against phloem-feeding insects can be the presence of lipopeptide synthetase genes in the bacterial genome.

Abstract Endophytes of Panax have the potential to produce their host plant secondary metabolites, ginsenosides. Panax sokpayensis, an endemic traditional medicinal plant of the Sikkim Himalayas was explored for the isolation of endophytic fungi. In the present study, we have isolated 35 endophytic fungal cultures from the rhizome of P. sokpayensis and screened for ginsenosides production by HPLC by comparing the peak retention time with that of standard ginsenosides. The HPLC analysis revealed that out of 35 isolates, the mycelial extracts of four fungal endophytes (PSRF52, PSRF53, PSRF49 and PSRF58) exhibited peaks with a similar retention time of the standard ginsenoside, Compound K (CK). LC–ESI–MS/MS analysis led to the confirmation of ginsenoside CK production by the four fungal endophytes which showed a compound with m/z 639.6278, similar to that of standard ginsenoside CK with yield in potato dextrose broth flask fermentation ranging from 0.0019 to 0.0386 mg/g of mycelial mass in dry weight basis. The four prospective fungal endophyte isolates were identified as Thermothielavioides terrestris PSRF52, Aspergillus sp. PSRF49, Rutstroemiaceae sp. strain PSRF53, and Phaeosphaeriaceae sp. strain PSRF58 based on ITS sequencing. The present finding highlights the need for further study on growth optimization and other culture parameters to exploit the endophytes as an alternative source for ginsenoside CK production.

Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products. [ABSTRACT FROM AUTHOR]

Background: Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. Results: Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. Conclusion: Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs. [ABSTRACT FROM AUTHOR]