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Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.

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.

Background: Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome. Results: Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation. Conclusion: In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. 5KavnCJpVp3k2g6uQCMsTe Video Abstract [ABSTRACT FROM AUTHOR]

Pine Wilt Disease (PWD) is a devastating pine tree disease characterized by rapid onset, high mortality rate, quick spread, and difficulty in control. Plant microbiome plays a significant role in the development of PWD. However, the endophytic microbial communities of Pinus koraiensis infected by pine wood nematode (PWN) Bursaphelenchus xylophilus remain largely unexplored. In this study, we analyzed the structural changes of endophytic communities of P. koraiensis after infection by the PWN using high-throughput sequencing technology. The results showed that the community structure underwent significant changes as the degree of PWN infection intensified. The diversity and abundance of endophytic fungi in P. koraiensis increased, while those of endophytic bacteria in P. koraiensis decreased during the infection process. Meanwhile, the abundance of some dominant microorganisms has also changed, including species such as Graphilbum and Pseudoalteromonas. Functional prediction analysis showed that the functional composition of endophytic fungi in P. koraiensis was significantly different across the development of PWD, while the composition of endophytic bacteria remained essentially similar. The results indicated that PWN infection had a significant impact on the structure, diversity, abundance, and functional gene composition of endophytic microbial communities in P. koraiensis , and most of the main endophytic microbial groups tended to coordinate with each other. This work provides a better understanding of the changes in endophytic community structure and function caused by PWD infection of P. koraiensis , which may benefit the exploration of potential endophytes for PWN biocontrol. [ABSTRACT FROM AUTHOR]

Invasive pathogens threaten the sustainability of forest ecosystems globally. Trees possess intrinsic pathogen defence mechanisms, including major gene resistance (MGR) and quantitative disease resistance (QDR). Plant‐symbiotic fungi can enhance tree defences, generating far‐reaching ecosystem impacts. However, the specific contributions of various fungal guilds to this symbiont‐mediated resistance remain unclear. In this study, we inoculated six Pinus monticola seedling families exhibiting resistance (MGR or QDR) or high susceptibility to the introduced invasive pathogen Cronartium ribicola, the causative agent of white pine blister rust (WPBR), with endophytic and ectomycorrhizal fungi, either alone or in combination (symbiont treatments), in an open‐air greenhouse study. Over a period of 25 months, we monitored the growth, foliar terpene defences, and disease progression in trees before and after C. ribicola infection and in trees inoculated with the symbionts but never inoculated with C. ribicola. We observed enhanced inducible host defences and evidence of defensive priming in response to symbiont treatments. In WPBR‐free control treatments, differences in pine defences coincided with an increased seedling growth rate. For WPBR‐infected seedlings, symbiont treatments reduced disease symptoms in seedlings with QDR and to a lesser extent in susceptible families, but not in those with MGR. Furthermore, disease symptoms correlated with variations in terpene composition. Synthesis and applications: Interactions with fungal symbionts should be considered when breeding native trees for resistance against invasive pathogens. Our study underscores the capacity of endophytic and ectomycorrhizal fungi to enhance tree growth and defence while also reducing disease symptoms. We also show that fungi can induce long‐lasting changes in conifer foliar terpenes, suggesting potential applications in tree protection from invasive pathogens. [ABSTRACT FROM AUTHOR]

• Lessertia frutescens is a medicinal plant that harbours many bacteria endophytes. • Endophytes of Lessertia frutescens have potential plant growth promoting attributes. • Two native Bacillus species are ideal candidates for bio-fertilization. Many endophytic bacteria have plant growth promoting attributes that could improve agricultural yield as well as resistance to various types of stress and disease. Detection of such attributes usually involves in vitro screening and the subsequent testing of the isolates on the plants for specific or combined effects on germination, seedling growth and yield. Despite many studies in this field, there is a knowledge gap on the influence of endophytes on early growth of certain economically important plants such as medicinal plants. In the present study, we evaluated the in vitro capabilities of bacterial endophytes isolated from Lessertia frutescens (L.) Goldblatt & J.C.Manning (syn. Sutherlandia frutescens (L.) W.T.Aiton) for plant growth promotion and their effect on initial seedling growth. Using a culture-dependent approach, plant samples of Lessertia frutes cens were screened for bacterial endophytes. The isolated bacterial endophytes were subsequently evaluated for their plant growth-promoting attributes along with their ability to produce hydrolytic enzymes. Molecular identification of selected endophytic bacteria based on the 16S rRNA genes of strains that tested negative in the hemolysis test was conducted. The two most promising isolates were evaluated for their ability to promote Lessertia frutescens seedling growth in a two-month pot trial study. The obtained results revealed that many of the bacterial endophytes had potential to promote plant growth. Specifically, 86 % of the endophytes possessed nitrogen-fixing, phosphate solubilizing, and IAA-producing abilities, while approximately 71 % were able to exhibit siderophore-producing capabilities. The endophytes exhibited significant production of essential hydrolytic enzymes, including amylase (86 %), gelatinase (86 %), protease (29 %), lipase (43 %), and D-nase (57 %). The two best isolates were identified as relatives of Bacillus spp. (Bacillus licheniformis BaDB06 and Bacillus velezensis strain SM-95). Their plant growth-promoting properties such as their ability to enhance plant height and their ability to be used as bio-agent were further confirmed in the pot trial study as they enhanced the growth of Lessertia frutescens seedlings compared to the control. This study provides insights into the functional roles of endophytic bacteria of Lessertia frutescens in seedling growth and their potential plant growth enhancement, highlighting their potential for sustainable agriculture and ecosystem management. [ABSTRACT FROM AUTHOR]

The research on endophytes is focused on understanding the complex microbiome compositions, their interactions with host plants and their bioactive potential. Our study provided an overview of the diversity, distribution and bioactivities of culturable endophytic fungi associated with fungal endophytes of Dioscorea bulbifera L. The phylogenetic analysis depicted the evolutionary relationship among taxa of endophytic fungal isolates. The isolated fungal endophytes belonged to twenty-five genera and thirty-eight species. Further, diversity indices demonstrated significant diversity of fungal endophytes in the different tissues: stem, leaf, tuber and bulbil. A higher consistency of endophytic fungal isolates in the bulbils was found using Shannon index. Furthermore, Simpson's index revealed that the leaf tissue harboured highly diverse fungal endophytes. Likewise, Margalef's index depicted high taxonomic richness in bulbils. The isolates such as Acrocalymma medicaginis, Curvularia lycoperscii, Talaromyces macrospora, Fusarium laceratum, Paecilomyces formosus and Microascus cirrosus isolated in this study have been reported as endophytes for the first time from any plant. In-vitro antioxidant and antidiabetic activities of the ethyl acetate extracts revealed that Nigrospora oryzae (Z2) effectively inhibited α-glucosidase activity with IC 50 value of 0.6 µg/ml whereas IC 50 value of the acarbose, the positive control was reported to be 0.040 µg/ml. The results of antioxidant activity demonstrated that H15A (Acrocalymma medicaginis) and BD5 (Phomopsis longicolla) could be used as potential sources of antioxidant agents. Moreover, H15A (Acrocalymma medicaginis) was reported to produce 687.1 ± 0.17 µg GAE/mg of TPC and 78.55 ± 0.29 µg QE/mg of TFC quantitatively. These findings suggest that the potential endophytes could be explored using systematic bio-guided investigations to further discover novel natural products. Our study provides an important resource for a deeper understanding of endophyte-plant interactions at molecular and genetic levels. [Display omitted] • First report on the exploration of the culturable fungal endophytes from Dioscorea bulbifera L., an essential ethnomedicinal plant. • The isolated endophytic fungi showed abundant diversity in various tissues of the plant. • Six fungal endophytes obtained in this study have been reported as endophytes for the first time. • Nigrospora oryzae (Z2) exhibited potential α-glucosidase inhibitory activity. • Acrocalymma medicaginis (H15A) could be used as a potential source of antioxidant agents. [ABSTRACT FROM AUTHOR]

Fungal phytopathogens cause severe losses to crops worldwide and significantly reduce the quality and quantity of the produce. A shift towards reducing the usage of chemically synthesized pesticides by various biocontrol methods, strategies and approaches is observed in plant disease management. Symbiotic bacteria that live within the plant i.e. endophytes provide the host plant with many advantages in terms of metabolism and disease resistance. Bacterial antagonists play a significant role in controlling plant pathogens and diseases. In the present study 18 endophytic bacteria isolated from grape leaf were collected from ICAR-NRCG, Pune. In prospect to disease management, various endophytic bacteria were investigated for their antifungal activity against Sclerotium rolfsii, Macrophomina phaseolina, Alternaria spp., Fusarium spp. and Pythium spp. Dual culture antifungal activity indicated that 15 isolates have inhibitory effect against at least one of the tested pathogen. It was also observed that all the isolates have produced significant amount of hydrolytic enzymes i.e. cellulase, chitinase, amylase, protease and lipase, but the first two were the principal enzymes produced by them. These results provide a better understanding of endophytic bacteria in the control of pathogenic fungi and suggest their key role in the domain of biocontrol against diverse plant pathogens. [ABSTRACT FROM AUTHOR]

Vitis vinifera L. is a commercially important horticultural plant with abundant microbial resources. However, the impact of grape-associated microbiota on grape quality and flavor has been largely overlooked. We integrated volatomics and microbiomics to explore temporal variations in berry volatiles and microbial diversity of 'Cabernet Sauvignon' in Ningxia (NX) and Shanxi (SX), and the correlation between microbial communities and volatiles. A total of 38 and 35 free and bound aroma compounds, respectively, were identified in NX berries and SX berries. For free aroma, these 38 compounds were classified into aldehydes (69%), alcohols (22%), acids (4%), aromatics (4%), terpenes (0.6%), esters (0.37%), and norisoprenoids (0.3%). Similarly, the 35 bound aromas were attributed to aromatics (58%), acids (29%), terpenes (4%), esters (3%), alcohols (2.82%), aldehydes (2.78%), and norisoprenoids (0.4%). Additionally, a total of 616 bacterial genera and 254 fungal genera were detected in all samples from both regions. The results demonstrated that vineyard sites significantly shaped the characteristics of berry volatiles and microbial biogeographic patterns. SX berries exhibited more abundant free aroma and higher microbial diversity than NX berries, with three key taxa (Sphingomonas, Massilia, and Bacillus) identified in the bacterial network. Correlation analysis results highlighted that these key taxa might play an important role in berry-free aroma. This study reveals the crucial role of microbes in shaping grape flavor and uncovers the link between microbial diversity and the regional attributes of grapes and wine. [ABSTRACT FROM AUTHOR]

Achnatherum inebrians is a perennial grass widely distributed in northwest China. Nearly all wild A. inebrians plants are infected by Epichloë endophytes. In this study, bacteria from the phyllosphere were isolated from leaves of both endophyte‐free and endophyte‐infected A. inebrians and sequenced for identification. Pseudomonas, comprising 48.12% of the culturable bacterial communities, was the most dominant bacterial genus. Thirty‐four strains from 12 Pseudomonas species were used to inoculate A. inebrians seeds and plants. Results indicated that Epichloë significantly increased the diversity and richness index of the phyllosphere. Pseudomonas Sp1, Sp3, Sp5 and Sp7 had a significantly positive effect on plant growth and photosynthesis, whereas Sp10, Sp11 and Sp12 had a significantly negative effect. Whole‐genome and pan‐genome analysis suggested that the variability in the effects of Pseudomonas on A. inebrians was related to differences in genome composition and genomic islands. [ABSTRACT FROM AUTHOR]

The South African blueberry industry has grown consistently over the past few years due to an increase in local and international demand. Like many other crops, blueberries are susceptible to grey mould caused by Botrytis cinerea, resulting in significant reductions in yield. In this study, Botrytis isolates were recovered from symptomatic blueberry fruit, flowers, leaves and undifferentiated buds, but were not found as endophytes in healthy tissues. Phylogenetic analysis of the concatenated glyceraldehyde-3-phosphate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60) and DNA-dependent RNA polymerase subunit II (RPB2) genes identified 88 isolates as B. cinerea strains as well as a single B. pelargonii strain. The results presented in this study are the first to contribute towards the characterisation of B. cinerea populations in South African blueberry orchards. [ABSTRACT FROM AUTHOR]

Legumes are notorious for coevolutionary arms races where chemical defenses are employed to ward off herbivores—particularly insect seed predators. Locoweeds are legumes containing the toxic alkaloid swainsonine which can poison livestock, but its role as a deterrent for insects is unknown. Swainsonine is produced by the fungal endophyte Alternaria section Undifilum, and the chemical composition of the toxin has been well characterized. Despite this knowledge, the ecological roles and evolutionary drivers of swainsonine toxins in locoweeds remain uncertain. Here, we quantify swainsonine concentrations and herbivory levels in the hyper-diverse locoweed Astragalus lentiginosus to evaluate its role as an evolved chemical defense. We found that A. lentiginosus shows considerable variation in swainsonine concentrations according to variety, in particular showing presence/absence variation at both population and local geographic scales. Surprisingly, herbivory levels from presumed generalist insects emerging from fruits showed no correlation with swainsonine concentrations. Conversely, seed and fruit herbivory levels linked to specialist Acanthoscelides seed beetles increased with concentrations of swainsonine—suggesting a possible coevolutionary arms race. Our results highlight that variation in endophyte-produced toxin systems may not follow classical expectations for geographic variation and ecological roles of plant chemicals. We discuss the implications of these results on plant-endophytic toxin systems and coevolutionary dynamics more broadly, highlighting a considerable need for more research in these systems. [ABSTRACT FROM AUTHOR]

Objectives: Seeds host microbes that function in plant growth and phytopathogen resistance. The aim of the work was to investigate total bacterial community in malting barley seeds and whether their bacterial seed endophytes have dual functional roles in plant growth-promotion and inhibition of Fusarium graminearum, the causative agent of Fusarium head blight (FHB) in barley. We used culture dependent and culture independent methods. Results: Phylogenetic classification of seed endophytic bacteria based on sequencing data identified B. subtilis, B. licheniformis and B. pumilis as predominant subgroups. Location driven divergence in bacterial endophytic communities was evident based on a clear separation of the samples from Crookston and other location samples. The bio-primed seeds using one hundred and seventy bacterial isolates showed that 3.5% (6/170) of the bacterial isolates conferred greater than 10% increase in both root length (RL) and shoot length (SL), while 19.4% (33/170) and 26.5% (45/170) showed RL and SL specific growth effects, respectively, relative to controls. Among the six bacterial isolates that increased RL and SL, five (#29, #63, #109, #124 and #126) also significantly inhibit the growth of F. graminearum based on in vitro assays. This study identified novel seed bacterial endophytes that could be further exploited for promoting growth during seedling establishment and as biocontrol for combating the devastating scab disease. [ABSTRACT FROM AUTHOR]

Seaweed endophytes are a rich source of microbial diversity and bioactive compounds. This review provides a comprehensive analysis of the microbial diversity associated with seaweeds and their interaction between them. These diverse bacteria and fungi have distinct metabolic pathways, which result in the synthesis of bioactive compounds with potential applications in a variety of health fields. We examine many types of seaweed-associated microorganisms, their bioactive metabolites, and their potential role in cancer treatment using a comprehensive literature review. By incorporating recent findings, we hope to highlight the importance of seaweed endophytes as a prospective source of novel anticancer drugs and promote additional studies in this area. We also investigate the pharmacokinetic and pharmacodynamic profiles of these bioactive compounds because understanding their absorption, distribution, metabolism, excretion (ADMET), and toxicity profiles is critical for developing bioactive compounds with anticancer potential into effective cancer drugs. This knowledge ensures the safety and efficacy of proposed medications prior to clinical trials. This study not only provides promise for novel and more effective treatments for cancer with fewer side effects, but it also emphasizes the necessity of sustainable harvesting procedures and ethical considerations for protecting the delicate marine ecology during bioprospecting activities. [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 review, all known information on endophytic diatom species and their macrophytic hosts is summarized and a history of studies of endophytic diatoms is provided. The mechanism by which endophytic diatoms penetrate into the thallus of macroalgae and the effect that the symbionts have on each other are discussed. The possible patterns of relationships between endophytic diatoms and basiphytes are analyzed based on literature data. [ABSTRACT FROM AUTHOR]

Effects of heavy metals on soil microbial communities have been extensively studied due to their persistence in the environment and imposed threats to living organisms; however, there is a lack of in-depth studies of the impacts of heavy metals on plant endophyte communities. Therefore, the responses of plant endophyte communities to different concentrations of heavy metals were investigated in this study. The endophyte communities of plants existing in severely (W1, Pb, 110.49 mg/kg, Cd, 1.11 mg/kg), moderately (W2, Pb, 55.06 mg/kg, Cd, 0.48 mg/kg), and mildly (W3, Pb, 39.06 mg/kg, Cd, 0.20 mg/kg) contaminated soils were analyzed by 16s rRNA high-throughput Illumina sequencing. Furthermore, networks were constructed to illustrate the relationships between microorganisms and environmental factors. High-quality sequences were clustered at a 97% similarity level. Results revealed that the diversity of the community and relative abundance of Cyanobacteria phylum increased with decreasing levels of pollution. Cyanobacteria and Proteobacteria were found to be the dominant phylum, while Methylobacterium and Sphingomonas were observed as the dominant genus. Tukey's HSD test showed that the relative abundances of Cyanobacteria and Proteobacteria phyla and Methylobacterium and Sphingomonas genera differed significantly (p < 0.01) among the plants of the three sample sites. Environmental factor analysis revealed a significant negative correlation (p < 0.01) of Cyanobacteria and a significant positive correlation (p < 0.01) of Methylobacterium with the heavy metal content in the environment. These findings suggest that Cyanobacteria and Methylobacterium may be phylum and genus indicators, respectively, of heavy metal toxicity. Tax4Fun analysis showed the effect of heavy metal toxicity on the abundance of genes involved in plant metabolism. In addition, culturable endophytic strains were isolated to study their resistance to heavy metal stress and their ability to promote plant growth. The potting tests showed that the JG1 strain was tolerant to heavy metals, and it could significantly promote the growth of the host plant under stress caused by multiple heavy metals. Compared to the control, the JG1-treated plants showed a 23.14% increase in height and a 12.84% increase in biomass. Moreover, AP, AK, and HN contents in JG1-treated plants were 20.87%, 12.55%, and 9.03% higher, respectively, under heavy metal stress. The results of this study provide a scientific basis for the construction of an efficient plant endophyte restoration system. [ABSTRACT FROM AUTHOR]

The objective of the present study was to isolate endophytes from the roots of the halophyte Sesuvium portulacastrum, which is applied for aquatic phytoremediation. From these endophytes, siderophore-producing bacteria were specifically isolated for their potential capacity to promote plant growth. The siderophore production capacity of the isolated bacteria was quantified, and a high-yield siderophore-producing strain was selected for further investigation. A total of 33 endophytic bacteria were successfully isolated and identified using a culturable approach. Of these, 10 siderophore-producing bacteria were identified using the selective agar assay, displaying siderophore unit (SU) values ranging from 11.90% to 80.39%. It is noteworthy that Erwinia sp. QZ-E9 exhibited the highest siderophore production capacity, achieving an SU of 80.39%. A microcosm co-cultivation experiment was conducted with the strain QZ-E9 in iron-deficient conditions (2 μmol/L Fe3⁺). The results demonstrated that strain QZ-E9 significantly enhanced the growth of S. portulacastrum, by increases in both fresh weight (1.41 g) and root length (18.7 cm). Furthermore, fluorescence in situ hybridization (FISH) was utilized to ascertain the colonization pattern of strain QZ-E9 within the plant roots. The analysis demonstrated that strain QZ-E9 exhibited extensive colonization of the epidermal and outer cortical cells of S. portulacastrum roots, as well as the intercellular spaces and vascular tissues. This colonization indicated that Erwinia sp. QZ-E9 plays a crucial role in promoting the growth of S. portulacastrum, presumably through its siderophore-mediated iron acquisition mechanism. [ABSTRACT FROM AUTHOR]

Endophytic fungi are promising producers of phenolic compounds; however, the process of extracting these molecules from the culture medium is a crucial step for obtaining these metabolites. In this context, the best conditions for extracting phenolic compounds produced by Cophinforma mamane CF2-13, isolated from an Amazonian plant, were evaluated. The fungus was cultivated in a liquid medium to obtain its metabolites. The effects of the solvent, time, and temperature were investigated, as well as the use of ultrasound. The total phenolics and the antioxidant activity were assessed to define the best extraction conditions. The optimized extract was chemically characterized and used to analyze its potential in protecting olive oil from lipid oxidation. The best results were found using ethyl acetate at 20 °C for 2 h. These conditions led to 61.61 mg GAEq/g of extract of total phenolics, and an antioxidant capacity of 0.47, 0.45, and 0.29 mmol TEq/g of extract using the DPPH, ABTS, and FRAP methods, respectively. In addition, the optimized extract presented caffeic acid and was able to delay the lipid oxidation of olive oil. The potential of endophytic fungi to produce phenolic compounds is promising for the food industry since natural bioactive compounds have many benefits for human health. [ABSTRACT FROM AUTHOR]

In recent decades, there has been a dramatic increase in fundamental microbial disease pervasiveness. The evolution of multi-drug resistant organisms (MDROs) is attributed to the broad usage of commercial antibiotics, which indicates that the previously active antibiotics are now limited in their efficacy. Therefore, this work was designed to examine the antibacterial and antifungal potential of ellagic acid from Xylaria acuta of Millingtonia hortensis L.f. The extraction of the bioactive compound from the extracellular filtrate of the endophytic fungi was performed utilizing the solvent extraction process. The obtained bioactive compound was confirmed as ellagic acid by spectroscopic and chromatographic techniques. The antimicrobial assay was performed using the agar well diffusion method, and the MIC and MBC were performed by the broth microplate dilution technique. The purified compound was characterized as ellagic acid, which showed significant antimicrobial activity against the tested bacterial and fungal pathogens. The MIC of ellagic acid was 62.5 µg/ml against Staphylococcus aureus and Escherichia coli. Further, based on the in silico docking studies, molecular interactions and inhibitory properties of ellagic acid were studied using Autodock Vina. Docking results of ellagic acid predicted the lowest binding free energy against the bacterial target of S. aureus and the fungal target of Cladosporium cladosporioides, to be − 10.3 and − 8.7 kcal/mol, respectively. These results show that ellagic acid is an effective bioactive compound for inhibiting specific bacterial targets and a moderate antifungal agent. Collectively, ellagic acid reported in this study serves as a multi-target bioactive compound and can be used for the development of effective drug with potential health benefits. [ABSTRACT FROM AUTHOR]

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant–microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant–microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security. [ABSTRACT FROM AUTHOR]

Symbiosis plays a critical role in plant biology. Temperate grasses often associate with several symbiotic fungi simultaneously, including Epichloë endophytes and arbuscular mycorrhizal (AM) fungi, in shoots and roots, respectively. These symbionts often modulate plant–herbivore interactions by influencing nutritional traits (i.e. AM fungi‐mediated nutrient uptake) and/or the secondary chemistry (i.e. endophytic alkaloids) of their host plant. Moreover, such grasses also accumulate large amounts of silicon (Si) from the soil, which can be deposited in tissues to act as a physical anti‐herbivore defence. Recent evidence suggests that both endophytes and AM fungi independently facilitate Si uptake. However, the consequences of their interactions with piercing‐sucking insects (i.e. aphids), or whether Si supply, endophytes, and AM fungi interact in this regard, are currently unknown. While Si deposition may be less effective against aphids than other herbivores (i.e. chewing caterpillars), Si supply can also alter plant secondary metabolite defences, which could affect sucking insects. In a factorial greenhouse experiment, we evaluated whether these components, acting alone or in combination, altered (1) foliar primary chemistry, (2) Si and symbiont‐chemical (endophytic alkaloids) defences, as well as (3) performance of the bird cherry‐oat aphid (Rhopalosiphum padi) feeding on tall fescue (Festuca arundinacea). Endophytes decreased all aphid performance parameters, including population growth and reproduction by 40%, but their impact was reversed by the presence of AM fungi, leading to a 52% increase in aphid performance compared with plants solely hosting endophytes. This improvement in performance was associated with reduced loline alkaloid levels and higher shoot nitrogen in AM‐endophytic plants. Endophytes and AM fungi exhibited antagonism, with endophytes reducing AM colonization by 34% and AM presence decreasing endophyte loline alkaloids by 44%. While both fungi jointly increased Si accumulation by 39% under Si‐supplied conditions, Si had no noticeable effects on aphids. Moreover, although Si supply had no identifiable effects on AM colonization, it reduced endophyte peramine alkaloids by 24%. Synthesis. Our findings indicate that symbiotic fungal partnerships and silicon provision may benefit plants but could weaken anti‐herbivore defences when combined. Revealing the complex interactions among diverse fungal symbionts and showcasing their effects on different anti‐herbivore defences (chemical and physical) and herbivore performance for the first time. [ABSTRACT FROM AUTHOR]

Nilgirianthus ciliatus, extensively exploited for its pharmacological properties, is now classified as vulnerable. In vitro micropropagation offers a sustainable approach for ecological conservation and rational utilization of this biodiversity resource. This study aimed to reduce endophytes during in vitro propagation and isolating antimicrobial-resistant endophytes from N. ciliatus by employing various concentrations and exposure times of Plant Preservative Mixture (PPM). Optimal results were observed when nodal explants treated with 0.3% PPM for 8 h, followed by inoculation in Murashige and Skoog (MS) medium supplemented with 3 mg/L 6-benzylaminopurine (BAP) and 0.3% PPM. This protocol achieved 82% shoot regeneration with minimal endophytic contamination, suggesting that the duration of explant exposure to PPM significantly influences endophyte reduction. Two antimicrobial-resistant endophytes were isolated and identified as Bacillus cereus and Acinetobacter pittii through 16S rDNA sequencing. These endophytes exhibited plant growth-promoting characteristics, including amylolytic, proteolytic, lipolytic activities, indole-3-acetic acid production, phosphate solubilization, and stress tolerance. In vivo application of these endophytes as bioinoculants to N. ciliatus not only improved growth parameters but also significantly increased the levels of pharmacologically important compounds, squalene, and stigmasterol, as confirmed by High-performance thin-layer chromatography (HPTLC). This study demonstrates that PPM is a promising alternative for sustainable micropropagation of N. ciliatus. Furthermore, it highlights the potential of antimicrobial-resistant endophytes as bioinoculants to improve growth and medicinal value, offering a sustainable solution for conservation and large-scale cultivation of this species. [ABSTRACT FROM AUTHOR]

In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture. [ABSTRACT FROM AUTHOR]

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]

Persimmon (Diospyros kaki) is an important fruit crop that is widely cultivated in China, and its production is severely affected by anthracnose. Endophytic bacterial communities play an important role in the establishment of plant diseases, although little is known about these endophytes in persimmon plants. Fangshan persimmon is well known for its excellent quality in Zhejiang Province, China. The present study demonstrated that the Colletotrichum complex was the causal agent of anthracnose in persimmon in Zhejiang. High‐throughput sequencing revealed that bacterial communities in Fangshan persimmon twigs were dominated by the phyla Proteobacteria, Actinobacteriota, Firmicutes and Bacteroidota. Persimmon twigs infected with Colletotrichum showed obvious shifts in the endophytic bacterial communities, and these shifts in slight infections varied from those in severe infections. For slight infections, the genera Pseudomonas and Burkholderia–Caballeronia–Paraburkholderia were significantly more abundant in slightly symptomatic twigs than in healthy twigs, whereas the genera 1174‐901‐12, Methylocella and Streptococcus exhibited the opposite trend. In severe infections, the genera Curtobacterium, Pseudomonas and Kineococcus were significantly more abundant in severely symptomatic twigs than in healthy twigs, whereas the genera 1174‐901‐12, Lactobacillus and Amnibacterium exhibited opposite trends. The genera Pseudomonas and Curtobacterium showed the strongest positive correlation with anthracnose. This is the first report of endophytic bacterial communities associated with persimmon plants and their interaction with anthracnose disease, and these findings are important for developing biocontrol strategies for persimmon anthracnose. [ABSTRACT FROM AUTHOR]

Corylus heterophylla, the majestic hazelnut tree, stands as one of the esteemed quartets of grand nuts reigning across the landscapes of temperate Asia, Europe, and North America. However, its relationship with endophytic fungi remains thinly explored. This study successfully identified a new species designated as Nigrospora coryli through conjoint analysis of morphology and systematics. The genetic regions examined encompassed ITS, TUB2, and TEF1-α. The detailed morphological description, colour photographs of Macro- and microcharacters are presented. [ABSTRACT FROM AUTHOR]

Aims The immense therapeutic value of Valeriana jatamansi is attributed to the presence of bioactive secondary metabolites (valepotriates and sesquiterpenoids). Its over-exploitation in wild habitats resulted in extensive depletion, necessitating alternative approaches to produce its therapeutic metabolites. This study sought to assess the ability of endophytes of V. jatamansi to boost the biosynthesis of secondary metabolites in the leaf-cell suspension (LCS) culture of V. jatamansi. Methods and results A total of 11 fungal endophytes were isolated from the rhizomes of V. jatamansi. Isolated endophytes were found to belong to phylum Ascomycota, Basidiomycota, and Mucoromycota. Supplementation of extracts of endophyte Phaeosphaeriaceae sp. VRzFB, Mucor griseocyanus VRzFD, Penicillium raistrickii VRzFK, and Penicillium sajarovii VRzFL in the LCS culture of V. jatamansi increased the fresh cell biomass by 19.6%–39.1% and dry cell biomass by 23.4%–37.8%. Most of the endophytes' extract could increase the content of valepotriates (26.5%–76.5% valtrate and 40.5%–77.9% acevaltrate) and sesquiterpenoids (19.9%–61.1% hydroxyl valerenic acid) in LCS culture. However, only two endophytes, Irpex lacteus VRzFI and Fusarium oxysporum VRzFF, could increase the sesquiterpenoids acetoxy valerenic acid (36.9%–55.3%). In contrast, some endophytes' extracts caused negative or no significant effect on the cell biomass and targeted metabolites. Increased secondary metabolites were corroborated with increased expression of iridoid biosynthesis genes in LCS culture. Production of H2O2 and lipid peroxidation was also varied with different endophytes indicating the modulation of cellular oxidative stress due to endophyte elicitors. Conclusions The results suggest the distinct effect of different fungal endophytes-extract on LCS culture, and endophytes can serve as biotic elicitors for increasing the secondary metabolite production in plant in vitro systems. [ABSTRACT FROM AUTHOR]

Marine ecosystems are important in discovering novel fungi with interesting metabolites that have shown great potential in pharmaceutical and biotechnological industries. Seagrasses, the sole submerged marine angiosperm, host diverse fungal taxa with mostly unknown metabolic capabilities. They are considered to be one of the least studied marine fungal habitats in the world. This review gathers and analyzes data from studies related to seagrasses-associated fungi, including taxonomy and biogeography, and highlights existing research gaps. The significance of the seagrass–fungal associations remains largely unknown, and current understanding of fungal diversity is limited to specific geographical regions such as the Tropical Atlantic, Mediterranean, and Indo-Pacific. Our survey yielded 29 culture-dependent studies on seagrass-associated endophytic and epiphytic fungi, and 13 miscellaneous studies, as well as 11 meta-studies, with no pathogenic true fungi described. There is a significant opportunity to expand existing studies and conduct multidisciplinary research into novel species and their potential applications, especially from understudied geographical locations. Future research should prioritize high-throughput sequencing and mycobiome studies, utilizing both culture-dependent and -independent approaches to effectively identify novel seagrass-associated fungal taxa. [ABSTRACT FROM AUTHOR]

Endophyte bacteria are microorganisms that pass all or part of their life cycle in the tissues of healthy plants without causing any obvious signs of disease. Most siderophore-producing endophytic bacteria could improve the plant growth. Here, the effect of metals, iron (Fe), nickel (Ni), and cobalt (Co), on the growth and siderophore production profiles of 30 endophyte bacterial isolates were investigated. The results of the Minimum Inhibition Concentration (MIC) tests showed that endophytes exhibit varying degrees of tolerance to heavy metals and the metal tolerance decreased in the order Fe3+>Ni2+>Co2+. It was revealed that while 10 isolates could not produce siderophores under any circumstances, 20 isolates produced siderophores at different degrees, and siderophore molecules synthesized and secreted by these 20 isolates had affinities for all three metals (Fe3+, Co2+, and Ni2+). In addition, siderophore production profiles of isolates under each heavy metal stress were investigated by adding these metals to the Chromium Azurol Sulfonate (CAS) medium at optimum concentration. The results suggested that siderophore synthesis could be one of the coping mechanisms of only two isolates with Co2+ and Ni2+ heavy metals. In the final stage of the study, molecular identification of a certain number of isolates selected according to their siderophore production values was carried out by 16S rRNA sequencing. As a result of the sequence analysis, 2 Pseudomonas sp., 4 Bacillus sp., 1 Chryseobacterium sp., 1 Staphylococcus sp., and 1 Peribacillus sp. were revealed. [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]

Endophytic bacteria, which are the subject of this study, serve as natural antifungal agents in the struggle against fungal infections, offering an eco-friendly alternative to chemical fungicides. So, it was aimed to determine the antifungal capacities of endophytic bacteria from Aronia ×prunifolia roots in the study. 25 endophytic bacteria were isolated, and their ability to act as biocontrol agents was evaluated by measuring fungal growth inhibition and chemical properties. Later, bacteria that showed a positive effect were identified through 16S gene sequencing. The results showed that the LB2 bacteria had the greatest ability to inhibit the selected fungi and the biochemical tests showed that the bacteria were Gramnegative, did not form spores, their colonies were well defined, and they could break down starch and gelatin, which was later diagnosed as Pseudomonas brassicacearum according to phylogenetic relationships. This study is the first report on which P. brassicacearum was isolated from A. ×prunifolia roots for the first time. These findings contribute to our understanding of the potential of endophytic bacteria, particularly P. brassicacearum, as natural antifungal agents in plant and human protection, offering a promising and sustainable approach to combat fungal infections while reducing the use of chemical fungicides. [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]

The mangrove ecosystems of the Department of Atlántico (Colombian Caribbean) are seriously threatened by problems of hypersalinization and contamination, especially by heavy metals from the Magdalena River. The mangrove plants have developed various mechanisms to adapt to these stressful conditions, as well as the associated microbial populations that favor their growth. In the present work, the tolerance and detoxification capacity to heavy metals, especially to mercury, of a halotolerant endophytic bacterium isolated from the species Avicennia germinans located in the Balboa Swamp in the Department of Atlántico was characterized. Diverse microorganisms were isolated from superficially sterilized A. germinans leaves. Tolerance to NaCl was evaluated for each of the obtained isolates, and the most resistant was selected to assess its tolerance to Pb2+, Cu2+, Hg2+, Cr3+, Co2+, Ni2+, Zn2+, and Cd2+, many of which have been detected in high concentrations in the area of study. According to the ANI and AAI percentages, the most halotolerant strain was identified as Priestia flexa, named P. flexa 7BS3110, which was able to tolerate up to 12.5% (w/v) NaCl and presented a minimum inhibitory concentrations (MICs) of 0.25 mM for Hg, 10 mM for Pb, and 15 mM for Cr3+. The annotation of the P. flexa 7BS3110 genome revealed the presence of protein sequences associated with exopolysaccharide (EPS) production, thiol biosynthesis, specific proteins for chrome efflux, non-specific proteins for lead efflux, and processes associated with sulfur and iron homeostasis. Scanning electron microscopy (SEM) analysis showed morphological cellular changes and the transmission electron microscopy (TEM) showed an electrodense extracellular layer when exposed to 0.25 mM Hg2+. Due to the high tolerance of P. flexa 7BS3110 to Hg2+ and NaCl, its ability to grow when exposed to both stressors was tested, and it was able to thrive in the presence of 5% (w/v) NaCl and 0.25 mM of Hg2+. In addition, it was able to remove 98% of Hg2+ from the medium when exposed to a concentration of 14 mg/L of this metalloid. P. flexa 7BS3110 has the potential to bioremediate Hg2+ halophilic contaminated ecosystems. [ABSTRACT FROM AUTHOR]

Abstract Background Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome. Results Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation. Conclusion In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. Video Abstract

Abstract Nilgirianthus ciliatus, extensively exploited for its pharmacological properties, is now classified as vulnerable. In vitro micropropagation offers a sustainable approach for ecological conservation and rational utilization of this biodiversity resource. This study aimed to reduce endophytes during in vitro propagation and isolating antimicrobial-resistant endophytes from N. ciliatus by employing various concentrations and exposure times of Plant Preservative Mixture (PPM). Optimal results were observed when nodal explants treated with 0.3% PPM for 8 h, followed by inoculation in Murashige and Skoog (MS) medium supplemented with 3 mg/L 6-benzylaminopurine (BAP) and 0.3% PPM. This protocol achieved 82% shoot regeneration with minimal endophytic contamination, suggesting that the duration of explant exposure to PPM significantly influences endophyte reduction. Two antimicrobial-resistant endophytes were isolated and identified as Bacillus cereus and Acinetobacter pittii through 16S rDNA sequencing. These endophytes exhibited plant growth-promoting characteristics, including amylolytic, proteolytic, lipolytic activities, indole-3-acetic acid production, phosphate solubilization, and stress tolerance. In vivo application of these endophytes as bioinoculants to N. ciliatus not only improved growth parameters but also significantly increased the levels of pharmacologically important compounds, squalene, and stigmasterol, as confirmed by High-performance thin-layer chromatography (HPTLC). This study demonstrates that PPM is a promising alternative for sustainable micropropagation of N. ciliatus. Furthermore, it highlights the potential of antimicrobial-resistant endophytes as bioinoculants to improve growth and medicinal value, offering a sustainable solution for conservation and large-scale cultivation of this species.

Dendrobium ovatum is a tropical epiphytic orchid endemic to the Western Ghats of India and has been listed as a threatened species in recent research due to its declining populations and changes in flowering and fruit set patterns. This study aims to investigate the mycoflora associated with the roots, stems and leaves of D. ovatum. Both surface‐associated and endophytic fungal associates were isolated and identified using morphological and molecular methods. The study resulted in the isolation of 139 cultures, which were divided into 24 morphotypes, 99% of which belonged to Ascomycota. The most dominant members, Trichoderma harzianum and Colletotrichum gloeosporioides, were consistently observed across all the study sites. Tissue‐specific fungal diversity analysis revealed that each organ was dominated by a distinct fungal group, forming characteristic communities specific to each tissue. The roots of D. ovatum exhibited the highest species richness and diversity, compared to the stem and leaves. This research also represents the first documentation of fungal associates of the threatened orchid D. ovatum.

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]

Bleeding from a wound as a result of physical injury is a life-threatening condition. In pursuing new drug structures, the effect of crude fungal extracts fungal isolated from Jatropha multifida on wound healing and coagulation of mouse whole blood was investigated. Jatropha multifida leaves were sterilized, cut into small segments, and then incubated in Potato Dextrose Agar for seven days. Four isolates were purified and their morphologies were characterized. Identification of isolates was confirmed by a molecular protocol. Two crude extracts from Phlebiopsis gigantea (OK021602) and Phyllosticta sp (OK021603), which exhibited higher phytochemicals composition, were selected and evaluated using wound excision and coagulation of mouse whole blood, by administering 30 µg/mL, 50 µg/mL and 70 µg/mL crude extracts respectively. The percentage of wound healing in mice was higher (p<0.05) for the crude extracts of Phlebiopsis gigantea (OK021602) as compared to that of Phyllosticta sp (OK021603). The highest percentages of wound contraction were 99% at 70 µg/mL, and 53% at 70 µg/mL for Phlebiopsis gigantea (OK021602) and Phyllosticta sp (OK021603), respectively as compared to the control group which had 42% wound contraction at day 15 post-treatment. The results of the present study clearly indicate that Jatropha multifida leaves harbor endophytic fungi that produce pharmacologically important bioactive secondary metabolites with wound and hemostatic effects; therefore, further exploration is inevitable, particularly for the purification and identification of specific chemical structures of bioactive compounds. [ABSTRACT FROM AUTHOR]

Dendrobium ovatum is an epiphytic orchid endemic to the Western Ghats of India. Due to its valuable medicinal and therapeutic properties, the plant has become extensively sought after, leading to its classification as 'threatened' in the latest research findings. The present study aims to identify the surface-associated and endophytic bacterial associates of Dendrobium ovatum, which may be of great significance from a conservation standpoint. The investigation resulted in isolating and identifying 21 bacterial isolates representing six genera from the absorption roots, stem, and leaves. Bacillus was the most dominant genus, with seven representative species from root and stem segments. Enterobacter formed the second most dominant genus, with four representatives from leaf and stem. Bacillus cereus was found to be the most prevalent species, with a relative frequency of 28.57%. Root segments were found to be the most diverse tissue compared to stem and leaves. The study concluded that each tissue represents a unique ecological niche harbouring specific bacterial associate. The study also illuminates the intricacies of the orchids' microbial community structure and forms the first documentation of bacterial associates of the threatened endemic orchid D. ovatum. Key policy insights: First report focussing on the bacterial associates of the threatened orchid, D. ovatum. Twenty-one bacterial isolates were identified, representing six genera. Each tissue of the orchid represents a distinct ecological niche. Reports the PGP traits of the isolates. Points to the importance of the conservation of holobionts. [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.

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.