Endophytic Fungi from Frankincense Tree Improves Host Growth and Produces Extracellular Enzymes and Indole Acetic Acid

Metabolome and Genome Analysis of a Novel Endophytic Fungus Aureobasidium pullulans KB3: Discovery of Polyketones and Polyketone Biosynthesis Pathway

Endophytic fungi associated with plants may contain undiscovered bioactive compounds. Under standard laboratory conditions, most undiscovered compounds are inactive, whereas their production could be stimulated under different cultivation conditions. In this study, six endophytic fungi were isolated from the bark of Koelreuteria paniculata in Quancheng Park, Jinan City, Shandong Province, one of which was identified as a new subspecies of Aureobasidium pullulans, named A. pullulans KB3. Additionally, metabolomic tools were used to screen suitable media for A. pullulans KB3 fermentation, and the results showed that peptone dextrose medium (PDM) was more beneficial to culture A. pullulans KB3 for isolation of novel compounds. Sphaerolone, a polyketone compound, was initially isolated from A. pullulans KB3 via scaled up fermentation utilizing PDM. Additionally, the whole-genome DNA of A. pullulans KB3 was sequenced to facilitate compound isolation and identify the biosynthesis gene clusters (BGCs). This study reports the multi-omics (metabolome and genome) analysis of A. pullulans KB3, laying the foundation for discovering novel compounds of silent BGCs and identifying their biosynthesis pathway.

Endophytic Fungi Residing within Cornus florida L. in Mid-Tennessee: Phylogenetic Diversity, Enzymatic Properties, and Potential Role in Plant Health

Endophytic fungi that reside internally in healthy, asymptomatic plants often benefit their hosts by promoting plant growth and/or providing plant protection against abiotic and biotic stresses. However, only a small fraction of the estimated 1.5 million fungal endophytes have been identified. In this study, a total of 369 isolates of fungal endophytes in 59 distinct taxa were isolated from stem samples of Cornus florida (flowering dogwood). All isolates belonged to species of phyla Ascomycota and Basidiomycota distributed across five orders and 11 genera. Isolates belonging to the same family clustered together in a phylogenetic tree generated from a cluster analysis using MEGA 7 software. Diversity indices of the fungi revealed a rich and diverse community that included several species associated with leaf spots, blight, cankers, and/or dieback diseases. Pathogenicity tests confirmed 16 fungal endophytes as C. florida pathogens, including some well-known destructive pathogens Botryosphaera dothidea, Colletotrichum acutatum, and C. gleosporoides. Isolates of the fungal endophytes possess the capacity to produce extracellular hydrolytic enzymes (cellulase, amylase, pectinase, laccase, chitinase, and protease) that are known to function in tissue penetration, plant colonization, nutrient acquisition, and disease suppression in both plant pathogens and endophytes These results support the interchangeable pathogenic-endophytic roles for some taxa.

Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines

Microbial resource influences the life activities of medicinal plants from several perspectives. Endophytes, rhizosphere microorganisms, and other environmental microorganisms play essential roles in medicinal plant growth and development, plant yield, and clinical efficacy. The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways. They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites. Microorganisms can interact with their host plants to produce long-term, targeted selection results and improve their ability to adapt to the environment. Due to the interdependence and interaction between microorganisms and medicinal plants, Chinese herbal medicines (CHMs) quality is closely related to the associated microorganisms. This review summarizes the relationship between medicinal plants and their associated microorganisms, including their species, distribution, life activities, and metabolites. Microorganisms can aid in quality control, improve the efficacy of medicinal plants, and provide markers for identifying the origin and storage time of CHMs. Therefore, a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.

Insight of endophytic fungi promoting the growth and development of woody plants

Microorganisms play an important role in plant growth and development. In particular, endophytic fungi is one of the important kinds of microorganisms and has a mutually beneficial symbiotic relationship with host plants. Endophytic fungi have many substantial benefits to host plants, especially for woody plants, such as accelerating plant growth, enhancing stress resistance, promoting nutrient absorption, resisting pathogens and etc. However, the effects of endophytic fungi on the growth and development of woody plants have not been systematically summarized. In this review, the functions of endophytic fungi for the growth and development of woody plants have been mainly reviewed, including regulating plant growth (e.g., flowering, root elongation, etc.) by producing nutrients and plant hormones, and improving plant disease, insect resistance and heavy metal resistance by producing secondary metabolites. In addition, the diversity of endophytic fungi could improve the ability of woody plants to adapt to adverse environment. The components produced by endophytic fungi have excellent potential for the growth and development of woody plants. This review has systematically discussed the potential regulation mechanism of endophytic fungi regulating the growth and development of woody plants, it would be of great significance for the development and utilization of endophytic fungi resource from woody plants for the protection of forest resources.

Bioprospecting of endophytic fungi from medicinal plant Anisomeles indica L. for their diverse role in agricultural and industrial sectors

Endophytes are microorganisms that inhabit various plant parts and cause no damage to the host plants. During the last few years, a number of novel endophytic fungi have been isolated and identified from medicinal plants and were found to be utilized as bio-stimulants and bio fertilizers. In lieu of this, the present study aims to isolate and identify endophytic fungi associated with the leaves of Anisomeles indica L. an important medicinal plant of the Terai-Duars region of West Bengal. A total of ten endophytic fungi were isolated from the leaves of A. indica and five were identified using ITS1/ITS4 sequencing based on their ability for plant growth promotion, secondary metabolite production, and extracellular enzyme production. Endophytic fungal isolates were identified as Colletotrichum yulongense Ai1, Colletotrichum cobbittiense Ai2, Colletotrichum alienum Ai2.1, Colletotrichum cobbittiense Ai3, and Fusarium equiseti. Five isolates tested positive for their plant growth promotion potential, while isolates Ai4. Ai1, Ai2, and Ai2.1 showed significant production of secondary metabolites viz. alkaloids, phenolics, flavonoids, saponins, etc. Isolate Ai2 showed maximum total phenolic concentration (25.98 mg g-1), while isolate Ai4 showed maximum total flavonoid concentration (20.10 mg g-1). Significant results were observed for the production of extracellular enzymes such as cellulases, amylases, laccases, lipases, etc. The isolates significantly influenced the seed germination percentage of tomato seedlings and augmented their growth and development under in vitro assay. The present work comprehensively tested these isolates and ascertained their huge application for the commercial utilization of these isolates both in the agricultural and industrial sectors.

Mapping bark bacteria: initial insights of stemflow-induced changes in bark surface phyla

IMPORTANCE

Compared with the phyllosphere, bacteria inhabiting bark surfaces are inadequately understood. Based on a preliminary pilot study, our work suggests that microbial populations vary across tree bark surfaces and may differ in relation to surrounding land use. Initial results suggest that stemflow, the water that flows along the bark surface, actively moves bacterial communities across a tree. These preliminary findings underscore the need for further study of niche microbial populations to determine whether there are connections between the biodiversity of microbiomes inhabiting corticular surfaces, land use, and hydrology.

Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza

The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.

The phytomicrobiome: solving plant stress tolerance under climate change

With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.

Promising drought and salinity tolerance features of Nigrospora species existing as endophytes in Oryza sativa

In this study, we report the discovery of novel Nigrospora species isolated from the extensively cultivated PUSA 44 rice variety in Punjab, India. Out of the 120 isolates examined, 6.6% and 5% isolates exhibited tolerance to high salinity and drought stress. Isolates 6OSFR2e and 7OSFS3a exhibited the highest indole acetic acid and gibberellic acid production, with 268.32 ± 08.10 and 25.72 ± 0.04 µg/mL. Additionally, isolates 7OSFS3a, 6OSFR2e and 6OSFL4c had highest antioxidant potential with IC50 345.45 ± 11.66, 391.58 ± 10.66, and 474.529 ± 11.08 µg/mL. The isolates 6OSFR2e and 6OSFL4c also exhibited phosphate solubilisation with a PI of 1.06 ± 0.00 and 1.04 ± 0.02. The highest cellulase and laccase production with EI 1.24 ± 0.00 and 1.16 ± 0.00 was observed by isolates 6OSFR2e and 6OSFL4c. Promising results were observed in the case of ammonia production. The isolates belonged to the same phylum, Ascomycota and were identified as Nigrospora zimmermanii (6OSFR2e) and Nigrospora oryzae (7OSFS3a), and Nigrospora sphaerica (6OSFL4c) using morpho-taxonomic and molecular identification. The present study provides a critical insight into the characteristics of these Nigrospora species, which could be used to develop a bio-consortium for the rejuvenation of PUSA-44 cultivation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03679-9.

Contribution of Arbuscular Mycorrhizal and Endophytic Fungi to Drought Tolerance in Araucaria araucana Seedlings

In its natural distribution, Araucaria araucana is a plant species usually exposed to extreme environmental constraints such as wind, volcanism, fires, and low rainfall. This plant is subjected to long periods of drought, accentuated by the current climate emergency, causing plant death, especially in its early growth stages. Understanding the benefits that both arbuscular mycorrhizal fungi (AMF) and endophytic fungi (EF) could provide plants under different water regimes would generate inputs to address the above-mentioned issues. Here, the effect of AMF and EF inoculation (individually and combined) on the morphophysiological variables of A. araucana seedlings subjected to different water regimes was evaluated. Both the AMF and EF inocula were obtained from A. araucana roots growing in natural conditions. The inoculated seedlings were kept for 5 months under standard greenhouse conditions and subsequently subjected to three different irrigation levels for 2 months: 100, 75, and 25% of field capacity (FC). Morphophysiological variables were evaluated over time. Applying AMF and EF + AMF yielded a noticeable survival rate in the most extreme drought conditions (25% FC). Moreover, both the AMF and the EF + AMF treatments promoted an increase in height growth between 6.1 and 16.1%, in the production of aerial biomass between 54.3 and 62.6%, and in root biomass between 42.5 and 65.4%. These treatments also kept the maximum quantum efficiency of PSII (Fv/Fm 0.71 for AMF and 0.64 for EF + AMF) stable, as well as high foliar water content (>60%) and stable CO₂ assimilation under drought stress. In addition, the EF + AMF treatment at 25% FC increased the total chlorophyll content. In conclusion, using indigenous strains of AMF, alone or in combination with EF, is a beneficial strategy to produce A. araucana seedlings with an enhanced ability to tolerate prolonged drought periods, which could be of great relevance for the survival of these native species under the current climate change.

How Deep Can the Endophytic Mycobiome Go? A Case Study on Six Woody Species from the Brazilian Cerrado

Elucidating the complex relationship between plants and endophytic fungi is very important in order to understand the maintenance of biodiversity, equity, stability, and ecosystem functioning. However, knowledge about the diversity of endophytic fungi from species of the native Brazilian Cerrado biome is poorly documented and remains largely unknown. These gaps led us to characterize the diversity of Cerrado endophytic foliar fungi associated with six woody species (Caryocar brasiliense, Dalbergia miscolobium, Leptolobium dasycarpum, Qualea parviflora, Ouratea hexasperma, and Styrax ferrugineus). Additionally, we investigated the influence of host plant identities on the structure of fungal communities. Culture-dependent methods coupled with DNA metabarcoding were employed. Irrespective of the approach, the phylum Ascomycota and the classes Dothideomycetes and Sordariomycetes were dominant. Using the cultivation-dependent method, 114 isolates were recovered from all the host species and classified into more than 20 genera and 50 species. Over 50 of the isolates belonged to the genus Diaporthe, and were distributed into more than 20 species. Metabarcoding revealed the phyla Chytridiomycota, Glomeromycota, Monoblepharomycota, Mortierellomycota, Olpidiomycota, Rozellomycota, and Zoopagomycota. These groups are reported for the first time as components of the endophytic mycobiome of Cerrado plant species. In total, 400 genera were found in all host species. A unique leaf endophytic mycobiome was identified in each host species, which differed not only by the distribution of fungal species, but also by the abundance of shared species. These findings highlight the importance of the Brazilian Cerrado as a reservoir of microbial species, and emphasize how endophytic fungal communities are diversified and adapted.

Potential of Fungal Endophytes Isolated from Pasture Species in Spanish Dehesas to Produce Enzymes under Salt Conditions

Endophytic fungi have been found to produce a wide range of extracellular enzymes, which are increasingly in demand for their industrial applications. Different by-products from the agrifood industry could be used as fungal growth substrates for the massive production of these enzymes, specifically as a way to revalorize them. However, such by-products often present unfavorable conditions for the microorganism’s growth, such as high salt concentrations. Therefore, the objective of the present study was to evaluate the potential of eleven endophytic fungi—which were isolated from plants growing in a harsh environment, specifically, from the Spanish dehesas—for the purposes of the in vitro production of six enzymes (i.e., amylase, lipase, protease, cellulase, pectinase and laccase) under both standard and salt-amended conditions. Under standard conditions, the studied endophytes produced between two and four of the six enzymes evaluated. In most of the producer fungal species, this enzymatic activity was relatively maintained when NaCl was added to the medium. Among the isolates evaluated, Sarocladium terricola (E025), Acremonium implicatum (E178), Microdiplodia hawaiiensis (E198), and an unidentified species (E586) were the most suitable candidates for the massive production of enzymes by using growth substrates with saline properties (such as those found in the many by-products from the agrifood industry). This study should be considered an initial approach by which to further study the identification of these compounds as well as to develop the optimization of their production by directly using those residues.

An insight into endophytic antimicrobial compounds: an updated analysis

Resistance in micro-organisms against antimicrobial compounds is an emerging phenomenon in the modern era as compared to the traditional world which brings new challenges to discover novel antimicrobial compounds from different available sources, such as, medicinal plants, various micro-organisms, like, bacteria, fungi, algae, actinomycetes, and endophytes. Endophytes reside inside the plants without exerting any harmful impact on the host plant along with providing ample of benefits. In addition, they are capable of producing diverse antimicrobial compounds similar to their host, allowing them to serve as useful micro-organism for a range of therapeutic purposes. In recent years, a large number of studies on the antimicrobial properties of endophytic fungi have been carried out globally. These antimicrobials have been used to treat various bacterial, fungal, and viral infections in humans. In this review, the potential of fungal endophytes to produce diverse antimicrobial compounds along with their various benefits to their host have been focused on. In addition, classification systems of endophytic fungi as well as the need for antimicrobial production with genetic involvement and some of the vital novel antimicrobial compounds of endophytic origin can further be utilized in the pharmaceutical industries for various formulations along with the role of nanoparticles as antimicrobial agents have been highlighted.

Efficacy of endophytic SB10 and glycine betaine duo in alleviating phytotoxic impact of combined heat and salinity in Glycine max L. via regulation of redox homeostasis and physiological and molecular responses

Adverse environmental stresses occurring simultaneously exhibit a lethal effect on crop productivity at the global level. Here, we investigated the individual and synergistic effects of endophytic T. virens SB10 and glycine betaine (GB) on the physiological and biochemical responses of Glycine max L. to alleviate the devastating effects of combined heat and salinity (HS) stress. Screening against HS stress tolerance showed that SB10 has significant tolerance against heat stress and produces hormones such as gibberellins and indole-3-acetic acid upon GB amendment of the growth medium under HS stress. Moreover, the current findings illustrated that the synergistic application of SB10 and GB was effective in alleviating the negative effects of HS stress on plant growth and physiology. The findings revealed that SB10 + GB led to a reduction in proline accumulation and Na⁺ uptake. It also maintained a high K⁺/Na ⁺ ratio by regulating GmHKT1 and GmSOS1 expression and enhanced macronutrient uptake (N, Ca, K) in plants. In turn, plants exhibited a higher growth rate and gaseous exchange attributes coupled with the upregulation of APX, SOD, POD, and GSH antioxidant activities and transcript accumulation of GmSOD1 and GmAPX1 to overcome HS-induced oxidative damage. Furthermore, SB10 + GB downregulated DREB2, DREB1B, and GmNCED3 expression and resulted in the reduced accumulation of endogenous ABA while enhancing endogenous SA accumulation via upregulation of PAL genes. In addition, enhanced accumulation of bioactive gibberellins (GA1, GA3, GA4, and GA7) was detected under HS stress in the SB10 + GB treatment group. Moreover, SB10 + GB also significantly regulated GmHsp90A2 and GmHsfA2 expression in tolerance against HS stress. The combination of SB10 and GB was shown to be an effective and alternative approach for growing G. max at high temperature coupled with saline conditions for sustainable agriculture.

Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips

Endophytic fungi are microorganisms that colonize the interior of plant tissues (e.g. leaves, seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without causing symptoms of disease in host plants. These microorganisms have been isolated from plant species in a wide variety of habitats worldwide, and it is estimated that all terrestrial plants are colonized by one or more species of endophytic fungus. In addition, these microorganisms have been drawing the attention of researchers because of their ability to synthesize a wide range of bioactive molecules with potential for applications in agriculture, medicine and biotechnology. However, several obstacles come up when studying the diversity and chemical potential of endophytic fungi. For example, the usage of an inappropriate surface disinfection method for plant tissue may not eliminate the epiphytic microbiota or may end up interfering with the endophytic mycobiota, which consequently generates erroneous results. Moreover, the composition of the culture medium and the culture conditions can favor the growth of certain species and inhibit others, which generates underestimated results. Other inconsistencies can arise from the fungus misidentification and consequent exploration of its chemical potential. Based on the methodological biases that may occur at all stages of studies dealing with endophytic fungi, the objective of this review is to discuss the main methods employed in these studies as well as highlight the challenges derived from the different approaches. We also report associated tips to help future studies on endophytic fungi as a contribution.

Biochemical Changes in Two Barley Genotypes Inoculated With a Beneficial Fungus Trichoderma harzianum Rifai T-22 Grown in Saline Soil

One of the most important environmental factors impacting crop plant productivity is soil salinity. Fungal endophytes have been characterised as biocontrol agents that help in plant productivity and induce resistance responses to several abiotic stresses, including salinity. In the salt-tolerant cereal crop barley (Hordeum vulgare L.), there is limited information about the metabolites and lipids that change in response to inoculation with fungal endophytes in saline conditions. In this study, gas chromatography coupled to mass spectrometry (GC-MS) and LC-electrospray ionisation (ESI)-quadrupole-quadrupole time of flight (QqTOF)-MS were used to determine the metabolite and lipid changes in two fungal inoculated barley genotypes with differing tolerance levels to saline conditions. The more salt-tolerant cultivar was Vlamingh and less salt tolerant was Gairdner. Trichoderma harzianum strain T-22 was used to treat these plants grown in soil under control and saline (200 mM NaCl) conditions. For both genotypes, fungus-colonised plants exposed to NaCl had greater root and shoot biomass, and better chlorophyll content than non-colonised plants, with colonised-Vlamingh performing better than uninoculated control plants. The metabolome dataset using GC-MS consisted of a total of 93 metabolites of which 74 were identified in roots of both barley genotypes as organic acids, sugars, sugar acids, sugar alcohols, amino acids, amines, and a small number of fatty acids. LC-QqTOF-MS analysis resulted in the detection of 186 lipid molecular species, classified into three major lipid classes-glycerophospholipids, glycerolipids, and sphingolipids, from roots of both genotypes. In Cultivar Vlamingh both metabolites and lipids increased with fungus and salt treatment while in Gairdner they decreased. The results from this study suggest that the metabolic pathways by which the fungus imparts salt tolerance is different for the different genotypes.

Isolation and characterization of a mesophilic cellulolytic endophyte Preussia africana from Juniperus oxycedrus

The medicinal plant Juniperus oxycedrus is less recognized for the diversity of its fungal endophytes and their potential to produce extracellular enzymes. The present study is the first report on the isolation and identification of a mesophilic endophytic strain JO-A, Preussia africana, from fresh stems of the J. oxycedrus endemic tree in the Ifrane region-Morocco, and the evaluation of its ability to produce cellulases. A one-time multi-parameter one-factor screening was optimized to select factors that enhance cellulase production in P. africana. The maximum production of both CMCase and FPase activities were 1.913 IU.mL^-1 and 0.885 IU.mL^-1, respectively, when the medium was supplemented with 2% w/v glucose. These remarkable titers were tenfold greater than those obtained under the initial non-optimized conditions. This mesophilic P. africana JO-A strain grows and actively produces cellulases at 37 °C demonstrating its great potential for various biotechnology applications. The cellulolytic extract showed the highest enzymatic activities at pH 5.0 and 50 °C with a half-life of 24 h at 50 °C.

Protective Effects of Filtrates and Extracts from Fungal Endophytes on Phytophthora cinnamomi in Lupinus luteus

Fungal endophytes have been found to protect their hosts against multiple fungal pathogens. Frequently, the secondary metabolites produced by the endophyte are responsible for antifungal activity. To develop new bio-products that are more environmentally friendly than synthetic pesticides against Phytophthora cinnamomi, a serious pathogen of many plant species, the antifungal activity of filtrates or extracts from four endophytes was evaluated in different in vitro tests and in plants of Lupinus luteus. In the dual culture assays, the filtrate of one of the endophytes (Drechslera biseptata) completely inhibited the mycelial growth of the pathogen. Moreover, it showed a very low minimal inhibitory concentration (MIC). Epicoccum nigrum, an endophyte that also showed high inhibitory activity and a low MIC against P. cinnamomi in those two experiments, provided a clear growth promotion effect when the extracts were applied to L. luteus seedlings. The extract of Fusarium avenaceum also manifested such a promotion effect and was the most effective in reducing the disease severity caused by the pathogen in lupine plants (73% reduction). Results demonstrated the inhibitory activity of the filtrates or extracts of these endophytes against P. cinnamomi. A better insight into the mechanisms involved may be gained by isolating and identifying the metabolites conferring this inhibitory effect against this oomycete pathogen.

Endophytic community of Chaenomeles speciosa fruits: Screening for biodiversity and antifungal activity

Fruit crops of the genus Chaenomeles Lindl are considered today as a superfood due to accumulation of biologically active compounds with antioxidant ability and known health-promoting properties. Successful introduction of this non-traditional culture in the steppe zone of Ukraine characterised by an unfavourable climate suggests the functioning of effective protective mechanisms in plants, including those that can be provided by the influence of endophytic microorganisms. However, there is little information about the endophytic community of Chaenomeles plants. Herein, the current study was aimed to isolate the endophytic fungi from the Ch. speciosa fruits and evaluate their biological activities against the phytopathogens. The study was carried out based on the collection of the Botanical Garden of Oles Honchar Dnipro National University (Dnipro city, Ukraine). Three media, namely PDA, MPA, and Gause’s medium were used for isolation of endophytic fungi. Colonies of isolates for identification were grown on PDA, Czapek's agar, and Czapek’s yeast autolysate media. Six fungal endophytic isolates derived from both peel and pulp of Ch. speciosa fruits have been morphologically identified using macroscopic and microscopic techniques, and assigned to the genus Penicillium (sections Chrysogena, Penicillium, Viridicata), and genus Talaromyces (section Talaromyces). Species P. expansum, P. viridicatum, and P. hirsutum were identified among the peel isolates, while P. chrysogenum, P. cyclopium, and P. purpurogenum were among the pulp isolates. Antagonistic ability of the endophytic isolates against phytopathogenic fungi was evaluated using the dual culture method. The results showed moderate to high antifungal capacity of the endophytic isolates against the phytopathogenic strains of the Fusarium genus. The growth inhibition of F. culmorum mycelium due to the influence of endophytic isolates was 51.5–81.3%, and the inhibition of the growth of F. oxysporum colonies was in the range of 68.4–86.6% as compared with control. There were no significant differences in the antagonistic ability between endophytic isolates derived from the peel and pulp of the fruit. Taken together, our findings indicated the great potential of the endophytic fungi from Ch. speciosa fruits as a source for the development of biocontrol agents and discovery of new bioactive compounds.

Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches

There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.

Mangrove's rhizospheric engineering with bacterial inoculation improve degradation of diesel contamination

Mangroves (Avicennia marina) growing in intertidal areas are often exposed to diesel spills, adversely damaging the ecosystem. Herein, we showed for the first time that mangrove seedlings' associations with bacteria could reprogram host-growth, physiology, and ability to degrade diesel. We found four bacterial strains [Sphingomonas sp.-LK11, Rhodococcus corynebacterioides-NZ1, Bacillus subtilis-EP1 Bacillus safensis-SH10] exhibiting significant growth during diesel degradation (2% and 5%, v/v) and higher expression of alkane monooxygenase compared to control. This is in synergy with reduced long-chain n-alkanes (C24-C30) during microbe-diesel interactions in the bioreactor. Among individual strains, SH10 exhibited significantly higher potential to improve mangrove seedling's morphology, anatomy and growth during diesel treatment in rhizosphere compared to control. This was also evidenced by reduced activities and gene expression of antioxidant enzymes (catalases, peroxidases, ascorbic peroxidases, superoxide dismutases and polyphenol peroxidases) and lipid peroxidation during microbe-diesel interactions. Interestingly, we noticed significantly higher soil-enzyme activities (phosphatases and glucosidases) and essential metabolites in seedling's rhizosphere after bacteria and diesel treatments. Degradation of longer n-alkane chains in the rhizosphere also revealed a potential pathway that benefits mangroves by bacterial strains during diesel contaminations. Current results support microbes' application to rhizoengineer plant growth, responses, and phytoextraction abilities in environments contaminated with diesel spills. AVAILABILITY OF DATA AND MATERIALS: The datasets generated during the current study are available in the NCBI GenBank ((https://www.ncbi.nlm.nih.gov).

Endophytic fungal communities and their biotechnological implications for agro-environmental sustainability

Endophytic fungal communities have attracted a great attention to chemists, ecologists, and microbiologists as a treasure trove of biological resource. Endophytic fungi play incredible roles in the ecosystem including abiotic and biotic stress tolerance, eco-adaptation, enhancing growth and development, and maintaining the health of their host. In recent times, endophytic fungi have drawn a special focus owing to their indispensable diversity, unique distribution, and unparalleled metabolic pathways. The endophytic fungal communities belong to three phyla, namely Mucoromycota, Basidiomycota, and Ascomycota with seven predominant classes Agaricomycetes, Dothideomycetes, Eurotiomycetes, Mortierellomycotina, Mucoromycotina, Saccharomycetes, and Sordariomycetes. In a review of a huge number of research finding, it was found that endophytic fungal communities of genera Aspergillus, Chaetomium, Fusarium, Gaeumannomyces, Metarhizium, Microsphaeropsis, Paecilomyces, Penicillium, Piriformospora, Talaromyces, Trichoderma, Verticillium, and Xylaria have been sorted out and well characterized for diverse biotechnological applications for future development. Furthermore, these communities are remarkable source of novel bioactive compounds with amazing biological activity for use in agriculture, food, and pharmaceutical industry. Endophytes are endowed with a broad range of structurally unique bioactive natural products, including alkaloids, benzopyranones, chinones, flavonoids, phenolic acids, and quinines. Subsequently, there is still an excellent opportunity to explore novel compounds from endophytic fungi among numerous plants inhabiting different niches. Furthermore, high-throughput sequencing could be a tool to study interaction between plants and endophytic fungi which may provide further opportunities to reveal unknown functions of endophytic fungal communities. The present review deals with the biodiversity of endophytic fungal communities and their biotechnological implications for agro-environmental sustainability.

Functional characterization of culturable fungi from microbiomes of the "conical cobs" Mexican maize (Zea mays L.) landrace

Mexican maize landraces, produced for local consumption, are adapted to different environmental conditions, and their yield is affected by abiotic and biotic factors, including the use of agrochemicals. The search for sustainable alternatives to agrochemicals includes the study of the culturable microbial communities. In this study, the fungal communities associated with 2 Mexican maize landraces reddish and bluish "conical cobs" were found to be comprised of Ascomycota fungi, represented by 89 strains within 6 orders (Pleosporales, Hypocreales, Onygenales, Capnodiales, Helotiales, and Eurotiales) and 16 genera. Cellulases and metallophores production were the primary enzymatic products and plant growth-promoting activities were detected among the isolates. Penicillium, Didymella, and Fusarium strains had the most active enzymatic and plant growth promoting activities, however, Aspergillus sp. HES2-2.2, Talaromyces sp. RS1-7, and Penicillium sp. HFS3-3 showed antagonistic activity against the four phytopathogenic Fusarium strains Fusarium oxysporum, Fusarium sambucinum, Fusarium fujikuroi and Fusarium incarnatum-equiseti and also a high and diverse production of enzymatic and plant growth promoting activities; here we identified fungal strains as candidates to promote maize growth.

Fungal Communities in the Native New Zealand Medicinal Plant Pseudowintera colorata (Horopito) Are Determined by Plant Organ Type and Host Maturity with Key Members Promoting Plant Growth

The plant Pseudowintera colorata is well known for its antimicrobial and medicinal properties and is endemic to New Zealand. Using PCR-Denaturing gradient gel electrophoresis (DGGE), we investigated the factors influencing the composition of endophytic fungal communities in P. colorata from ten distinct sites across New Zealand. Our results showed that plant organs of P. colorata influenced the diversity and richness of endophytic fungi (PERMANOVA, p < 0.05). In addition, plant maturity and its interactions revealed that endophytic fungal communities formed discrete clusters in leaves, stems, and roots of mature and immature P. colorata plants (PERMANOVA; p = 0.002, p = 0.001 and p = 0.039, respectively). For identifying isolates with biocontrol potential, dual culture tests were set up against four different phytopathogenic fungi. Isolates with high activity (zone of inhibition > 10 mm) were sequenced and identified as Trichoderma harzianum, Pezicula neosporulosa, Fusariumtricinctum, Metarhizium sp., and Chaetomium sp. Applying selected endophytic fungi (n = 7) as soil drenchers significantly increased the growth of P. colorata seedlings and produced more internodes. Seedling shoots treated with Trichoderma sp. PRY2BA21 were 2.2 × longer (8.36 cm) than the untreated controls (3.72 cm). Our results elucidate the main plant factors influencing fungal community composition and demonstrate a role for endophytic fungi in P. colorata growth and further demonstrate that medicinal plants are a rich source of endophytes with potential as biocontrol agents.

Biosorption effect of Aspergillus niger and Penicillium chrysosporium for Cd- and Pb-contaminated soil and their physiological effects on Vicia faba L

Phytoremediation is an important solution to soil pollution management. The goal of this study is to determine the biosorption ability of the two selected fungi (Aspergillus niger and Penicillium chrysosporium) under heavy metal stress on faba bean plants. The fungal strains produced phytohormones, siderophore, ACC deaminase, and secondary metabolites. The biosorption capacity of A. niger and P. chrysosporium was 0.09 and 0.06 mg g^-1 and 0.5 and 0.4 mg g^-1 in media containing Cd and Pb, respectively. Fourier transform infrared spectroscopy of the fungal cell wall show primary functional groups like hydroxyl, amide, carboxyl, phosphoryl, sulfhydryl, and nitro. Therefore, A. niger and P. chrysosporium were inoculated to soils, and then the faba bean seeds were sown. After 21 days of sowing, the plants were irrigated with water to severe as control, with 100 mg L^-1 of Cd and 200 mg L^-1 of Pb. The results show that Cd and Pb caused a significant reduction in morphological characteristics, auxin, gibberellins, photosynthetic pigments, minerals content, and antioxidant enzymes as compared to control plants but caused a substantial boost in abscisic acid, ethylene, electrolyte leakage, lipid peroxidation, glutathione, proline, superoxide dismutase, secondary metabolites, and antioxidant capacity. In inoculated plants, metal-induced oxidative stress was modulated by inhibiting the transport of metal and decreased electrolyte leakage and lipid peroxidation. Finally, the inoculation of endophytic fungi contributed actively to the absorption of heavy metals and decreased their content in soil and plants. This could be utilized as an excellent technique in the fields of heavy metal-contaminated sustainable agriculture.

Plant associated fungal endophytes as a source of natural bioactive compounds

Endophytes are a potent source of bioactive compounds that mimic plant-based metabolites. The relationship of host plant and endophyte is significantly associated with alteration in fungal colonisation and the extraction of endophyte-derived bioactive compounds. Screening of fungal endophytes and their relationship with host plants is essential for the isolation of bioactive compounds. Numerous bioactive compounds with antioxidant, antimicrobial, anticancer, and immunomodulatory properties are known to be derived from fungal endophytes. Bioinformatics tools along with the latest techniques such as metabolomics, next-generation sequencing, and metagenomics multilocus sequence typing can potentially fill the gaps in fungal endophyte research. The current review article focuses on bioactive compounds derived from plant-associated fungal endophytes and their pharmacological importance. We conclude with the challenges and opportunities in the research area of fungal endophytes.

A Lignocellulolytic Colletotrichum sp. OH with Broad-Spectrum Tolerance to Lignocellulosic Pretreatment Compounds and Derivatives and the Efficiency to Produce Hydrogen Peroxide and 5-Hydroxymethylfurfural Tolerant Cellulases

Fungal endophytes are an emerging source of novel traits and biomolecules suitable for lignocellulosic biomass treatment. This work documents the toxicity tolerance of Colletotrichum sp. OH toward various lignocellulosic pretreatment-derived inhibitors. The effects of aldehydes (vanillin, p-hydroxybenzaldehyde, furfural, 5-hydroxymethylfurfural; HMF), acids (gallic, formic, levulinic, and p-hydroxybenzoic acid), phenolics (hydroquinone, p-coumaric acid), and two pretreatment chemicals (hydrogen peroxide and ionic liquid), on the mycelium growth, biomass accumulation, and lignocellulolytic enzyme activities, were tested. The reported Colletotrichum sp. OH was naturally tolerant to high concentrations of single inhibitors like HMF (IC50; 17.5 mM), levulinic acid (IC50; 29.7 mM), hydroquinone (IC50; 10.76 mM), and H2O2 (IC50; 50 mM). The lignocellulolytic enzymes displayed a wide range of single and mixed inhibitor tolerance profiles. The enzymes β-glucosidase and endoglucanase showed H2O2- and HMF-dependent activity enhancements. The enzyme β-glucosidase activity was 34% higher in 75 mM and retained 20% activity in 125 mM H2O2. Further, β-glucosidase activity increased to 24 and 32% in the presence of 17.76 and 8.8 mM HMF. This research suggests that the Colletotrichum sp. OH, or its enzymes, can be used to pretreat plant biomass, hydrolyze it, and remove inhibitory by-products.

Fungal Community Analyses of Endophytic Fungi from Two Oak Species, Quercus mongolica and Quercus serrata, in Korea

Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (Quercus mongolica and Q. serrata) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of Q. serrata were higher than that of Q. mongolica with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that Q. serrata had a significantly higher level of fungal diversity than Q. mongolica. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. Leptosillia, Aureobasidium and Acanthostigma were the most abundant genera detected in Q. serrata with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, Peltaster, Cladosporium and Monochaetia were the most common genera detected in Q. mongolica with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by Raffaelea quercus-mongolicae.

Culture-Based and Culture-Independent Assessments of Endophytic Fungal Diversity in Aquatic Plants in Southwest China

Aquatic ecosystems contain tremendous plant and microbial diversity. However, little is known about endophyte diversity in aquatic plants. In this study, we investigated the diversity of endophytic fungi in aquatic plants in southwest China using both culture-based and culture-independent high-throughput sequencing methods. A total of 1,689 fungal isolates belonging to three phyla and 154 genera were obtained from 15,373 plant tissue segments of 30 aquatic plant species. The most abundant endophytic fungi were those in ascomycete genera Aspergillus, Ceratophoma, Fusarium, Penicillium, Phoma and Plectosporium. No difference in fungal isolation rates was observed among tissues from roots, stems, and leaves. Twenty tissue samples from three most common plant species were further subjected to culture-independent meta-barcode sequencing. The sequence-based analyses revealed a total of 1,074 OTUs belonging to six fungal phyla and 194 genera. Among the three plants, Batrachium bungei harbored the highest number of OTUs. Besides, a total of 66 genera were detected by two methods. Both the culture-dependent and independent methods revealed that aquatic plants in southwest China have abundant endophytic fungal diversity. This study significantly expands our knowledge of the fungal community of aquatic plants.

Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria

Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a “holobiont”. In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.

Comprehensive characterization of stress tolerant bacteria with plant growth-promoting potential isolated from glyphosate-treated environment

The application of plant growth-promoting bacteria in agricultural systems is an efficient and environment-friendly strategy to improve crop yields and maintain soil quality. However, as different soils have diverse and specific ecological characteristics and may represent adverse abiotic conditions, in vivo application requires the careful selection of the desired beneficial microorganisms. In this study we report Ensifer adhaerens SZMC 25856 and Pseudomonas resinovorans SZMC 25875 isolates recovered from glyphosate-treated soil to possess yet undiscovered plant growth-enhancing potential. The strains were found to promote the growth of tomato seedlings significantly, to have the ability of synthesizing indole-3-acetic acid and siderophores, to tolerate pH in the range of 6.59-7.96, salinity up to 12.5 g L-1 NaCl and drought up to 125 g L-1 polyethylene glycol 6000, as well as to survive in the presence of various pesticides including glyphosate, diuron, chlorotoluron, carbendazim and thiabendazole, and heavy metals such as Al, Fe, Mn, Zn, Pb and Cu. The plant growth-promoting traits of the examined E. adhaerens and P. resinovorans isolates and their tolerance to numerous abiotic stress factors make them promising candidates for application in different agricultural environments, including soils polluted with glyphosate.

Endophytic fungus diversity in soybean plants submitted to conditions of elevated atmospheric CO2 and temperature

Global climatic changes can have drastic impacts on plant species, including severe consequences for the agricultural species productivity. Many of these species present important mutualisms with endophytic fungi that positively influence their performance. The present study evaluated whether the increases in CO2 and temperature predicted for the year 2100 may cause changes in foliar carbon (C) and nitrogen (N) concentrations in soybean (Glycine max) and, consequently, the interactions with its endophytic fungi. The effects of elevated CO2 and temperature were evaluated in four treatments in open-top chambers: (i) control, (ii) increased temperature, (iii) increased CO2, and (iv) increased CO2 and temperature. Increased atmospheric CO2 resulted in decreased foliar N concentration, while increased temperature increased it. A total of 16 taxa of endophytic fungi were identified based on sequencing internal transcribed spacer regions of rRNA subunits. Increased atmospheric CO2 and temperature were observed to potentially modify the endophytic mycobiota of soybean plants. The results suggest that the fungi species substitution is a consequence of changes in foliar N concentration and C/N ratio. Predicted climatic changes shall affect the relationships between plant and endophytes, which in turn, will affect the performance and resistance of soybean, one of the most important crops in the world.

Isolation and screening of stress-resistant endophytic fungus strains from wild and cultivated soybeans in cold region of China

In this study, we firstly reported the large-scale screening and isolation of endophytic fungi from nine wild and six cultivated soybeans in the cold regions of China. We totally isolated 302 endophytic fungal strains, of which 215 strains are isolated from the wild soybeans and 87 are identified from cultivated soybeans. Among these endophytic fungal strains, in the roots, stems, and leaves, 24.17% were isolated from roots, 28.8% were isolated from stems, and 47.01% were isolated from leaves, respectively. Most endophytic fungal strains isolated from the wild soybean roots were the species of Fusarium genus, and the fungal strains in the stems were the species of ascomycetes and Fusarium fungi, whereas most strains in the leaves were Alternaria fungi. To analyze the taxonomy of the obtained samples, we sequenced and compared their rDNA internal transcribed spacer (ITS) sequences. The data showed that 6 strains are putatively novel strains exhibiting ≤ 97% homology with the known strains. We next measured the secondary metabolites produced by the different strains and we found 11 strains exhibited high-performance synthesis of triterpenoids, phenols, and polysaccharides. Furthermore, we characterized their tolerance to abiotic stresses. The results indicated that 4 strains exhibited high tolerance to cadmium, and some strains exhibited resistance to acid, and alkali. The results of the study could facilitate the further exploration of the diversity of plant endophytic fungi and the potential applications of the fungi to practical agriculture and medicine industries. KEY POINTS: • 302 endophytic fungal strains isolated from wild soybean and cultivated soybean • 11 strains had high contents of triterpenoids, phenols, and polysaccharides • 4 strains exhibited high Cd tolerance, and a few strains with strong tolerance to acid and alkali solution.

A promising growth promoting Meyerozyma caribbica from Solanum xanthocarpum alleviated stress in maize plants

Fungal endophytes are known to secrete a large array of secondary metabolites (phenols, flavonoids, indole acetic acid (IAA) etc.) that facilitate crops under stress conditions. Considering this, a potent plant growth promoting endophyte (SXSp1) from the spines and leaves of Solanum xanthocarpum L. has been isolated. The isolated strain ably secreted high quantities of indole-3-acetic acid, phenols and flavonoids. Also, it exhibited phosphate solubilization, siderophore and had 2,2 diphenyl-1-picrylhydrazyl (DPPH) scavenging activity. The SXSp1 also resisted the salinity stress up to 150 mM. LC/MS analysis of SXSp1 culture filtrate (CF) revealed the presence of p-hydroxyl benzoic acid, diadzein, genistien, myricetin and caffeoyl-d-glucose. Moreover, the inoculation of maize plants with SXSp1 significantly (P=0.05) promoted the chlorophyll and carotenoid contents, root and shoot lengths, plant fresh and dry weights, catalase and peroxidase activities, proline, phenolics, flavonoids and relative water contents (RWCs) under salinity. More interestingly, SXSp1-associated plants showed lower endogenous abscisic acid (ABA) and higher endogenous IAA contents that helped the plants to resist salinity stress up to 100 mM. After sequencing, internal transcribed spacer (ITS) regions (ITS1 and ITS4) and phylogenetic analysis, the SXSp1 was identified as Meyerozyma caribbica.

Škrbić B, Jigjiddorj EA, Vágvölgyi C, Szekeres A. Characterization of the Plant Growth-Promoting Activities of Endophytic Fungi Isolated from Sophora flavescens

Endophytic fungi in symbiotic association with their host plant are well known to improve plant growth and reduce the adverse effects of both biotic and abiotic stresses. Therefore, fungal endophytes are beginning to receive increased attention in an effort to find growth-promoting strains that could be applied to enhance crop yield and quality. In our study, the plant growth-promoting activities of endophytic fungi isolated from various parts of Sophora flavescens (a medicinally important plant in Mongolia and China) have been revealed and investigated. Fungal isolates were identified using molecular taxonomical methods, while their plant growth-promoting abilities were evaluated in plate assays. Altogether, 15 strains were isolated, representing the genera Alternaria, Didymella, Fusarium and Xylogone. Five of the isolates possessed phosphate solubilization activities and twelve secreted siderophores, while all of them were able to produce indoleacetic acid (IAA) in the presence or absence of tryptophan. The endogenous and exogenous accumulation of IAA were also monitored in liquid cultures using the HPLC-MS/MS technique to refine the plate assay results. Furthermore, for the highest IAA producer fungi, the effects of their extracts were also examined in plant bioassays. In these tests, the primary root lengths of the model Arabidopsis thaliana were increased in several cases, while the biomasses were significantly lower than the control IAA treatment. Significant alterations have also been detected in the photosynthetic pigment (chlorophyll-a, -b and carotenoids) content due to the fungal extract treatments, but these changes did not show any specific trends.

Isolation, characterization, and plant growth-promoting activities of endophytic fungi from a wild orchid Vanda cristata

Endophytism is one of the widely explored phenomena related to orchids and fungi. Endophytic fungi assist plants by supplementing nutrient acquisition, and synthesis of plant growth regulators. Vanda cristata is an epiphytic orchid that has a great diversity of endophytic fungi. Endophytic fungi were isolated from roots, stems, and leaves of V.cristata and identified by both morphological and molecular study. Furthermore, the isolated endophytic fungi were subjected to auxin synthesis, phosphate solubilization, ammonia synthesis, and elicitor growth test for understanding their growth-promoting effect in a qualitative and quantitative manner. Altogether, 12 different endophytic fungi were isolated from roots, stems, and leaves of V. cristata of which most species belonged to Ascomycota. Unidentified II fungi were found to be most effective for auxin synthesis and phosphate solubilization while Agaricus bisporous and Mycolepto discus were most effective for ammonia synthesis. We have tested the plant growth-promoting activity of the twelve isolated endophytic fungi on Cymbidium aloifolium protocorms (12 weeks old). All the endophytic fungi showed growth-promoting activity. Plant growth of Cymbidium aloifolium was found higher on the MS medium supplemented with all fungal elicitors. Fungal elicitor CVS4, however, showed the highest plant growth-promoting activity toward C. aloifolium.

Abed RM, Ning Chai Y, N. Al-Rawahi A, Mohanta TK, Al-Rawahi A, Schachtman DP, Al-Harrasi A. Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance

Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.

Diversity and community of culturable endophytic fungi from stems and roots of desert halophytes in northwest China

Halophytes have high species diversity and play important roles in ecosystems. However, endophytic fungi of halophytes in desert ecosystems have been less investigated. In this study, we examined endophytic fungi associated with the stem and root of ten halophytic species colonizing the Gurbantonggut desert. A total of 36 endophytic fungal taxa were obtained, dominated by Alternaria eichhorniae, Monosporascus ibericus, and Pezizomycotina sp.1. The colonization rate and species richness of endophytic fungi varied in the ten plant species, with higher rates in roots than in stems. The endophytic fungal community composition was significantly affected by plant identity and tissue type. Some endophytic fungi showed significant host and tissue preferences. This finding suggests that host identity and tissue type structure endophytic fungal community in a desert ecosystem.

Bacterial and Fungal Endophytes: Tiny Giants with Immense Beneficial Potential for Plant Growth and Sustainable Agricultural Productivity

The conventional means of achieving enhanced agricultural productivity are not ecologically balanced and sustainable. The excessive use of synthetic agrochemicals, declining soil nutrients, and water-use issues, amongst others, are threats to the ecosystem. Additionally, environmental degradation and an increasing global population that will reach 9 billion by 2030 are further considerations. These issues mean a decline in the volume of food resources available to feed the world. Therefore, sustainably increasing agricultural productivity is a necessity for restoring soil fertility, feeding the populace, and improving the ecosystem. A way to achieve this is by using eco-friendly microbial inoculants. Endophytes inhabit the tissues of plants asymptomatically without causing adverse effects. Bacterial and fungal endophytes benefit plants by promoting growth, suppressing pathogens, and improving the stress tolerance and immunity of plants. Despite this vital role played by endophytes in their interactions with host plants, there is still a paucity of relevant review data. More importantly, the prospective use of endophytes as an alternative to synthetic agrochemicals to ensure agro-ecological crop productivity has not been well reviewed in the literature. Therefore, this review sought to highlight the potential use of endophytic microbial resources to achieve enhancements in agro-food system crops in a sustainable manner.

Rhizobacteria AK1 remediates the toxic effects of salinity stress via regulation of endogenous phytohormones and gene expression in soybean

Salinity stress adversely affects the growth and productivity of different crops. In the present study, we isolated the rhizospheric bacteria Arthrobacter woluwensis AK1 from Pohang beach, South Korea and determined its plant growth-promoting potential under NaCl salt stress (0, 100, and 200 mM). AK1 has phosphate-solubilizing activity and produce siderophores, organic acids, and phytohormones such as gibberellic acid (GA) and indole-3-acetic acid (IAA) that significantly alleviate sodium chloride (NaCl) stress and increase all plant growth attributes. Furthermore, inoculation of AK1 significantly decreased endogenous abscisic acid (ABA) content, extensively regulated the antioxidant activities and mitigated NaCl stress. Similarly, inductively coupled plasma mass spectrometry results showed that soybean plants inoculated with AK1 significantly decreased the amount of sodium (Na+) uptake during NaCl stress after 6 and 12 days. Four genes, auxin resistant 1 (GmLAX1), potassium channel AKT2 (GmAKT2), soybean salt tolerance 1 (GmST1), and salt tolerance-associated gene on chromosome 3 (GmSALT3) were up-regulated, while two genes chloride channel gene (GmNHX1) and Na+/H+ antiporter (GmCLC1) were down-regulated in soybean AK1treated plants. In conclusion, AK1 can mitigate salinity stress, increase plant growth and could be utilized as an eco-friendly bio-fertilizer under salinity stress.

Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

Isolation and Characterization of Plant Growth-Promoting Endophytic Fungi from the Roots of Dendrobium moniliforme

The present study aims to identify the diverse endophytic fungi residing in the roots of Dendrobium moniliforme and their role in plant growth and development. Nine endophytic fungi were isolated from the root sections and characterized by molecular technique. Quantification of the indole acetic acid (IAA) compound by these endophytes was done. Further, Chemical profiling of R11 and R13 fungi was done by Gas Chromatography-Mass Spectroscopy (GC-MS). Asymbiotic seed derived protocorms of Rhynchostylis retusa was used for the plant growth assay to investigate the growth promoting activities of the fungal elicitor prepared from the isolated fungi from D. moniliforme. Among the isolated fungi, the relative dominant fungus was Fusarium sp. The R13 and R6 fungi were identified only at the genus level which concludes the fungi are of new species or strain. The indole acetic acid production was relatively higher in R10. Bioactive compound diversity was observed in the organic extract of R11 and R6. The presence of phenolic compound and essential oil suggest their contribution for the antimicrobial and antioxidant properties to their host plant, D. moniliforme. The plant growth assay result concluded, the fungal elicitor prepared from R10, Colletotrichum alatae was the best among all other for the plant growth activities.

Endogenous phytohormones of frankincense producing Boswellia sacra tree populations

Boswellia sacra, an endemic tree to Oman, is exposed to man-made incisions for commercial level frankincense production, whereas unsustainable harvesting may lead to population decline. In this case, assessment of endogenous phytohormones (gibberellic acid (GA), indole-acetic acid (IAA), salicylic acid (SA) and kinetin) can help to understand population health and growth dynamics. Hence, it was aimed to devise a robust method using Near-Infrared spectroscopy (NIRS) coupled with multivariate methods for phytohormone analysis of thirteen different populations of B. sacra. NIRS data was recorded in absorption mode (10000-4000 cm-1) to build partial least squares regression model (calibration set 70%). Model was externally cross validated (30%) as a test set to check their prediction ability before the application to quantify the unknown amount of phytohormones in thirteen different populations of B. sacra. The results showed that phytohormonal contents varied significantly, showing a trend of SA>GA/IAA>kinetin across different populations. SA and GA contents were significantly higher in Pop13 (Hasik), followed by Pop2 (Dowkah)-an extreme end of B. sacra tree cover in Dhofar region. A similar trend in the concentration of phytohormones was found when the samples from 13 populations were subjected to advance liquid chromatography mass spectrophotometer and gas chromatograph with selected ion monitor analysis. The current analysis provides alternative tool to assess plant health, which could be important to in situ propagation of tree population as well as monitoring tree population growth dynamics.

Illumina-MiSeq analysis of fungi in acid lime roots reveals dominance of Fusarium and variation in fungal taxa

A study was conducted to analyze fungal diversity in the roots of acid lime (Citrus aurantifolia) collected from Oman, a semi-arid country located in the South Eastern part of the Arabian Peninsula. MiSeq analysis showed the Ascomycota and Sordariomycetes were the most abundant phylum and class in acid lime roots, respectively. Glomeromycota, Basidiomycota and Microsporidia were the other fungal phyla, while Glomeromycetes and some other classes belonging to Ascomycota and Basidiomycota were detected at lower frequencies. The genus Fusarium was the most abundant in all samples, making up 46 to 95% of the total reads. Some fungal genera of Arbuscular mycorrhizae and nematophagous fungi were detected in some of the acid lime roots. Analysis of the level of fungal diversity showed that no significant differences exist among groups of root samples (from different locations) in their Chao richness and Shannon diversity levels (P < 0.05). Principle component analysis of fungal communities significantly separated samples according to their locations. This is the first study to evaluate fungal diversity in acid lime roots using high throughput sequencing analysis. The study reveals the presence of various fungal taxa in the roots, dominated by Fusarium species and including some mycorrhizae and nematophagous fungi.